From 0d90689e9f5911222a25d2f821cc2419c4391443 Mon Sep 17 00:00:00 2001
From: Geoff Ower <gdower@illinois.edu>
Date: Fri, 28 Oct 2022 16:38:04 -0500
Subject: [PATCH 001/160] Add basic metadata.yaml

---
 lib/export/coldp.rb | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/lib/export/coldp.rb b/lib/export/coldp.rb
index 766a24dbeb..769f1dda46 100644
--- a/lib/export/coldp.rb
+++ b/lib/export/coldp.rb
@@ -1,4 +1,5 @@
 require 'zip'
+require 'yaml'
 
 module Export
 
@@ -28,6 +29,7 @@ def self.otus(otu_id)
 
     def self.export(otu_id, prefer_unlabelled_otus: true)
       otus = otus(otu_id)
+      Current.project_id = Otu.find(otu_id).project_id
 
       # source_id: [csv_array]
       ref_csv = {}
@@ -35,6 +37,19 @@ def self.export(otu_id, prefer_unlabelled_otus: true)
       # TODO: This will likely have to change, it is renamed on serving the file.
       zip_file_path = "/tmp/_#{SecureRandom.hex(8)}_coldp.zip"
 
+      metadata_path = Zaru::sanitize!("/tmp/#{::Project.find(Current.project_id).name}_#{DateTime.now}_metadata.yaml").gsub(' ', '_').downcase
+      version = Taxonworks::VERSION
+      if Settings.sandbox_mode?
+        version = Settings.sandbox_commit_sha
+      end
+      metadata = {"title" =>::Project.find(Current.project_id).name,
+                  "version" => version,
+                  "issued" => DateTime.now.strftime('%Y-%m-%d'),
+      }
+      metadata_file = Tempfile.new(metadata_path)
+      metadata_file.write(metadata.to_yaml)
+      metadata_file.close
+
       Zip::File.open(zip_file_path, Zip::File::CREATE) do |zipfile|
         (FILETYPES - ['Name']).each do |ft|
           m = "Export::Coldp::Files::#{ft}".safe_constantize
@@ -57,6 +72,7 @@ def self.export(otu_id, prefer_unlabelled_otus: true)
         end
 
         zipfile.get_output_stream('References.csv') { |f| f.write d }
+        zipfile.add("metadata.yaml", metadata_file.path)
       end
 
       zip_file_path

From f754e1427af102e4fc0ed11a0efb7f9577baa336 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 8 Nov 2022 15:53:05 -0300
Subject: [PATCH 002/160] Add component

---
 .../tasks/collection_objects/filter/app.vue   |  8 ++-
 .../components/DeleteCollectionObjects.vue    | 55 +++++++++++++++++++
 2 files changed, 61 insertions(+), 2 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue

diff --git a/app/javascript/vue/tasks/collection_objects/filter/app.vue b/app/javascript/vue/tasks/collection_objects/filter/app.vue
index e4efe2b761..fded4c6ec2 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/app.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/app.vue
@@ -44,7 +44,8 @@
         @urlRequest="urlRequest = $event"
         @result="loadList"
         @pagination="pagination = getPagination($event)"
-        @reset="resetTask"/>
+        @reset="resetTask"
+      />
       <div class="full_width overflow-x-auto">
         <div
           v-if="recordsFound"
@@ -75,6 +76,7 @@
               :url="urlRequest"
               class="margin-small-left"
             />
+            <DeleteCollectionObjects :ids="ids" />
             <RadialFilter
               :disabled="!ids.length"
               object-type="CollectingEvent"
@@ -127,6 +129,7 @@ import SelectAll from './components/selectAll.vue'
 import MatchButton from './components/matchButton.vue'
 import JsonRequestUrl from 'tasks/people/filter/components/JsonRequestUrl.vue'
 import RadialFilter from 'components/radials/filter/radial.vue'
+import DeleteCollectionObjects from './components/DeleteCollectionObjects.vue'
 
 export default {
   name: 'FilterCollectionObjects',
@@ -142,7 +145,8 @@ export default {
     SelectAll,
     MatchButton,
     JsonRequestUrl,
-    RadialFilter
+    RadialFilter,
+    DeleteCollectionObjects
   },
 
   computed: {
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
new file mode 100644
index 0000000000..792cfedb90
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -0,0 +1,55 @@
+<template>
+  <ConfirmationModal ref="confirmationModal" />
+  <VBtn
+    color="primary"
+    medium
+    @click="openModal"
+  >
+    Delete collection objects
+  </VBtn>
+</template>
+
+<script setup>
+import { ref } from 'vue'
+import { CollectionObject } from 'routes/endpoints'
+import VBtn from 'components/ui/VBtn/index.vue'
+import ConfirmationModal from 'components/ConfirmationModal.vue'
+
+const CONFIRM_WORD = 'delete'
+const MAX = 25
+
+const props = defineProps({
+  ids: {
+    type: Array,
+    default: () => []
+  }
+})
+
+const emit = defineEmits(['delete'])
+const confirmationModal = ref(null)
+
+function deleteCOs () {
+  const ids = [...props.ids]
+  const requests = ids.map(id => CollectionObject.destroy(id))
+
+  Promise.all(requests).then(_ => {
+    emit('delete', { ids })
+  })
+}
+
+async function openModal () {
+  const ok = await confirmationModal.value.show({
+    title: 'Delete collection objects',
+    message: `This will delete ${props.ids.length} collection objects. Are you sure you want to proceed?`,
+    confirmationWord: 'DESTROY',
+    okButton: 'Delete',
+    cancelButton: 'Cancel',
+    typeButton: 'delete'
+  })
+
+  if (ok) {
+    deleteCOs()
+  }
+}
+
+</script>

From 27c125514e6ab437feabd5854b33946ab535b780 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 8 Nov 2022 18:55:28 -0300
Subject: [PATCH 003/160] Fix #3189

---
 CHANGELOG.md                                  |  7 +++++++
 .../tasks/collection_objects/browse/App.vue   | 21 +++++++++++++++++--
 .../browse/components/CONavegation.vue        | 10 ++++-----
 .../collection_objects/browse/utils/loadCO.js |  5 +++++
 4 files changed, 35 insertions(+), 8 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/browse/utils/loadCO.js

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b5715a4aec..c03cc03e91 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,13 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
+### Added
+- Autocomplete on Browse collection object [#3189]
+
+[#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
+
+## [0.29.6] - 2022-11-08
+
 ### Added
 - Print unit-tray headers from TaxonNames via Filter nomenclature [#3160]
 - New radial "Filter" navigators facilitating cross-linking to filters [#2297]
diff --git a/app/javascript/vue/tasks/collection_objects/browse/App.vue b/app/javascript/vue/tasks/collection_objects/browse/App.vue
index a8f3f36f0a..20910f1ccb 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/App.vue
@@ -1,6 +1,17 @@
 <template>
   <div id="vue-browse-collection-object">
-    <h1>Browse collection object</h1>
+    <div class="flex flex-separate middle">
+      <h1>Browse collection object</h1>
+      <VAutocomplete
+        class="autocomplete"
+        url="/collection_objects/autocomplete"
+        placeholder="Search a collection object"
+        param="term"
+        label="label_html"
+        clear-after
+        @get-item="loadCO($event.id)"
+      />
+    </div>
     <COHeader />
     <TableGrid
       :columns="1"
@@ -31,13 +42,15 @@ import { computed } from 'vue'
 import { useStore } from 'vuex'
 import { URLParamsToJSON } from 'helpers/url/parse'
 import { ActionNames } from './store/actions/actions'
+import { GetterNames } from './store/getters/getters'
+import VAutocomplete from 'components/ui/Autocomplete.vue'
 import COHeader from './components/COHeader.vue'
 import TableGrid from 'components/layout/Table/TableGrid.vue'
 import PanelCE from './components/PanelCE/PanelCE.vue'
 import PanelCO from './components/Panel/PanelCO.vue'
 import ColumnThree from './components/ColumnThree.vue'
 import PanelDerived from './components/Panel/PanelDerived.vue'
-import { GetterNames } from './store/getters/getters'
+import loadCO from './utils/loadCO.js'
 
 const store = useStore()
 const collectingEvent = computed(() => store.getters[GetterNames.GetCollectingEvent])
@@ -72,5 +85,9 @@ if (coId) {
       padding: 2em;
     }
   }
+
+  .autocomplete {
+    width: 600px;
+  }
 }
 </style>
diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue b/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue
index f05b14f99c..5474ba8ed2 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue
@@ -35,7 +35,7 @@
                   type="button"
                   class="button normal-input button-default"
                   :disabled="!navigate.previous_by[key]"
-                  @click="openCO(navigate.previous_by[key])"
+                  @click="loadCO(navigate.previous_by[key])"
                 >
                   {{ key.replaceAll('_', ' ') }}
                 </button>
@@ -45,7 +45,7 @@
                   class="button normal-input button-default"
                   type="button"
                   :disabled="!navigate.next_by[key]"
-                  @click="openCO(navigate.next_by[key])"
+                  @click="loadCO(navigate.next_by[key])"
                 >
                   {{ key.replaceAll('_', ' ') }}
                 </button>
@@ -63,8 +63,8 @@
 import { useStore } from 'vuex'
 import { computed, ref } from 'vue'
 import { GetterNames } from '../store/getters/getters'
-import { RouteNames } from 'routes/routes'
 import ModalComponent from 'components/ui/Modal'
+import loadCO from '../utils/loadCO.js'
 
 const store = useStore()
 const navigate = computed(() => store.getters[GetterNames.GetNavigation])
@@ -72,7 +72,5 @@ const collectionObject = computed(() => store.getters[GetterNames.GetCollectionO
 
 const isVisible = ref(false)
 
-function openCO (id) {
-  window.open(`${RouteNames.BrowseCollectionObject}?collection_object_id=${id}`, '_self')
-}
+
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/browse/utils/loadCO.js b/app/javascript/vue/tasks/collection_objects/browse/utils/loadCO.js
new file mode 100644
index 0000000000..c13274f3ba
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/browse/utils/loadCO.js
@@ -0,0 +1,5 @@
+import { RouteNames } from 'routes/routes'
+
+export default (id) => {
+  window.open(`${RouteNames.BrowseCollectionObject}?collection_object_id=${id}`, '_self')
+}

From 7eea7ef7f2374f6673c58f960f046223aca04ece Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 9 Nov 2022 09:37:00 -0300
Subject: [PATCH 004/160] Fix link

---
 CHANGELOG.md                                  |  3 ++
 .../vue/tasks/nomenclature/by_source/app.vue  | 31 ++++++++++---------
 .../components/Table/TableCitationRow.vue     |  2 +-
 .../components/BiologicalAssociations.vue     |  2 +-
 4 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c03cc03e91..e40ae24b4a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,9 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Added
 - Autocomplete on Browse collection object [#3189]
 
+### Fixed
+- Citation link in Biological association panel on Browse OTU
+
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
 
 ## [0.29.6] - 2022-11-08
diff --git a/app/javascript/vue/tasks/nomenclature/by_source/app.vue b/app/javascript/vue/tasks/nomenclature/by_source/app.vue
index 3d3ffc5a36..9d25c30097 100644
--- a/app/javascript/vue/tasks/nomenclature/by_source/app.vue
+++ b/app/javascript/vue/tasks/nomenclature/by_source/app.vue
@@ -4,7 +4,7 @@
       <h1>Citations by source</h1>
       <ul class="context-menu">
         <li>
-          <SourcePicker/>
+          <SourcePicker />
         </li>
         <li>
           <a href="/tasks/sources/hub">Back to source hub</a>
@@ -31,52 +31,53 @@
     </div>
   </div>
 </template>
-<script>
-export default {
-  name: 'CitationsBySource',
-}
-</script>
+
 <script setup>
 
 import HeaderBar from './components/HeaderBar.vue'
 import CitationSummary from './components/CitationSummary.vue'
 import OtusMatchProxy from './components/OtusMatchProxy'
 import SourcePicker from './components/SourcePicker.vue'
-import { 
+import {
   TAXON_NAME,
   TAXON_NAME_RELATIONSHIP,
   TAXON_NAME_CLASSIFICATION,
   BIOLOGICAL_ASSOCIATION,
   ASSERTED_DISTRIBUTION,
-  OTU 
+  OTU
 } from 'constants/index.js'
 
 const CITATION_BLOCKS = {
-  [TAXON_NAME]: { 
+  [TAXON_NAME]: {
     title: 'Taxon names',
     summarizeParam: 'taxon_name_ids'
   },
-  [TAXON_NAME_CLASSIFICATION]: { 
+  [TAXON_NAME_CLASSIFICATION]: {
     title: 'Nomenclature status',
     summarizeParam: 'taxon_name_classification_ids'
   },
-  [TAXON_NAME_RELATIONSHIP]: { 
+  [TAXON_NAME_RELATIONSHIP]: {
     title: 'Taxon name relationships',
     summarizeParam: 'taxon_name_relationship_ids'
   },
-  [BIOLOGICAL_ASSOCIATION]: { 
+  [BIOLOGICAL_ASSOCIATION]: {
     title: 'Biological associations',
     summarizeParam: 'biological_association_ids'
   },
-  [ASSERTED_DISTRIBUTION]: { 
+  [ASSERTED_DISTRIBUTION]: {
     title: 'Asserted distributions',
     summarizeParam: 'asserted_distribution_ids'
   },
-  [OTU]: { 
+  [OTU]: {
     title: 'OTUs',
     summarizeParam: 'otu_ids'
-  },
+  }
 }
 
 </script>
 
+<script>
+export default {
+  name: 'CitationsBySource'
+}
+</script>
diff --git a/app/javascript/vue/tasks/nomenclature/by_source/components/Table/TableCitationRow.vue b/app/javascript/vue/tasks/nomenclature/by_source/components/Table/TableCitationRow.vue
index 290cd1e87a..ba5e3a28eb 100644
--- a/app/javascript/vue/tasks/nomenclature/by_source/components/Table/TableCitationRow.vue
+++ b/app/javascript/vue/tasks/nomenclature/by_source/components/Table/TableCitationRow.vue
@@ -17,7 +17,7 @@
       >
     </td>
     <td class="full_width">
-      <a 
+      <a
         :href="citation.citation_object.object_url"
         v-html="citation.citation_object.object_tag"
       />
diff --git a/app/javascript/vue/tasks/otu/browse/components/BiologicalAssociations.vue b/app/javascript/vue/tasks/otu/browse/components/BiologicalAssociations.vue
index 701419d14a..0fcd0c8a36 100644
--- a/app/javascript/vue/tasks/otu/browse/components/BiologicalAssociations.vue
+++ b/app/javascript/vue/tasks/otu/browse/components/BiologicalAssociations.vue
@@ -30,7 +30,7 @@
           <td v-html="biologicalAssociation.object.family_name"/>
           <td v-html="biologicalAssociation.object.object_tag"/>
           <td>
-            <a v-for="citation in biologicalAssociation.citations" :key="citation.id" :href="`/tasks/nomenclature/by_source?source_id=${citation.source.id}`" :title="`${citation.source.cached}`">
+            <a v-for="citation in biologicalAssociation.citations" :key="citation.id" :href="`/tasks/nomenclature/by_source?source_id=${citation.source_id}`" :title="`${citation.source.cached}`">
               <span v-html="authorString(citation)"/>&nbsp;
             </a>
           </td>

From 36679044b9a25b331ebf0915fa594f6a8abeaf61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 9 Nov 2022 12:00:53 -0300
Subject: [PATCH 005/160] Fix #3182

---
 CHANGELOG.md                                  |  1 +
 .../new_taxon_name/components/listEntrys.vue  | 28 +++++++++++--------
 .../new_taxon_name/components/type.vue        |  4 +--
 3 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e40ae24b4a..be6d5c3c60 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Fixed
 - Citation link in Biological association panel on Browse OTU
+- Type relationship text/rendering is inverted in New taxon name [#3182]
 
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
 
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/listEntrys.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/listEntrys.vue
index 69e62dd3ea..95fa4b16b1 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/listEntrys.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/listEntrys.vue
@@ -10,14 +10,17 @@
         class="list-complete-item flex-separate middle">
         <span class="list-item">
           <template v-for="show in display">
-            <a
-              v-if="isLink(show)"
-              target="_blank"
-              :href="composeLink(item, show)"
-              v-html="item[show.label]"/>
+            <span v-if="isLink(show)">
+              <a
+                target="_blank"
+                :href="composeLink(item, show)"
+                v-html="item[show.label]"
+              />
+            </span>
             <span
               v-else
-              v-html="item[show]"/>
+              v-html="item[show]"
+            />
           </template>
         </span>
         <div class="list-controls">
@@ -59,10 +62,10 @@ export default {
     RadialAnnotator
   },
   props: {
-    list: { 
+    list: {
       type: Array,
-      default: () => { return [] }
-    }, 
+      default: () => []
+    },
     display: {
       type: Array
     },
@@ -133,12 +136,13 @@ export default {
 .pages:disabled {
   background-color: #F5F5F5;
 }
+
 .list-item {
-  a {
-    padding-left: 4px;
-    padding-right: 4px;
+  span {
+    margin-right: 4px;
   }
 }
+
 .table-entrys-list {
   padding: 0px;
   position: relative;
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/type.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/type.vue
index 6721718b25..6f741dc649 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/type.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/type.vue
@@ -14,7 +14,7 @@
           v-if="editType"
           class="horizontal-left-content">
           <span>
-            <span v-html="GetRelationshipsCreated[0].object_status_tag"/>
+            <span v-html="GetRelationshipsCreated[0].object_tag"/>
             <a
               v-html="GetRelationshipsCreated[0].subject_object_tag"
               :href="`/tasks/nomenclature/browse?taxon_name_id=${GetRelationshipsCreated[0].subject_taxon_name_id}`"/>
@@ -89,7 +89,7 @@
       </div>
       <list-entrys
         :list="GetRelationshipsCreated"
-        :display="['subject_status_tag', { link: '/tasks/nomenclature/browse?taxon_name_id=', label: 'subject_object_tag', param: 'subject_taxon_name_id'}]"
+        :display="[{ link: '/tasks/nomenclature/browse?taxon_name_id=', label: 'subject_object_tag', param: 'subject_taxon_name_id'}, 'subject_status_tag', 'object_object_tag']"
         edit
         @delete="removeType"
         @edit="setEdit"

From 0790c6e41ea9b2b5d8a3b4820e5716b4a16bcda6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 9 Nov 2022 14:03:53 -0300
Subject: [PATCH 006/160] Add scaffold

---
 app/javascript/packs/application.js           |  1 +
 .../simple_new_specimen/App.vue               | 10 ++++++
 .../simple_new_specimen/components/FormCE.vue | 27 ++++++++++++++++
 .../simple_new_specimen/components/FormCO.vue | 13 ++++++++
 .../components/GeographicArea.vue             | 22 +++++++++++++
 .../composition/useStore.js                   | 31 +++++++++++++++++++
 .../simple_new_specimen/index.js              | 14 +++++++++
 .../accessions/quick/simple/new.html.erb      |  6 ++--
 8 files changed, 122 insertions(+), 2 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js

diff --git a/app/javascript/packs/application.js b/app/javascript/packs/application.js
index 0794d310c5..bfb5153121 100644
--- a/app/javascript/packs/application.js
+++ b/app/javascript/packs/application.js
@@ -79,3 +79,4 @@ require('../vue/tasks/extracts/filter/main.js')
 require('../vue/tasks/people/filter/main.js')
 require('../vue/tasks/collection_objects/stepwise/determinations/main.js')
 require('../vue/tasks/content/publisher/main.js')
+require('../vue/tasks/collection_objects/simple_new_specimen/index')
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
new file mode 100644
index 0000000000..aa25eb352f
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -0,0 +1,10 @@
+<template>
+  <div>
+    <h1>Simplete new specimen</h1>
+    <FormCE />
+  </div>
+</template>
+
+<script setup>
+import FormCE from './components/FormCE.vue'
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
new file mode 100644
index 0000000000..bfe1777981
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
@@ -0,0 +1,27 @@
+<template>
+  <BlockLayout>
+    <template #header>
+      <h3>Collecting event</h3>
+    </template>
+    <template #body>
+      <div class="field label-above">
+        <label>Verbatim label</label>
+        <textarea />
+      </div>
+      <div class="field label-above">
+        <label>Verbatim label</label>
+        <input
+          type="text"
+        >
+      </div>
+      <div class="field label-above">
+        <label>Verbatim label</label>
+        <textarea />
+      </div>
+    </template>
+  </BlockLayout>
+</template>
+
+<script setup>
+import BlockLayout from 'components/layout/BlockLayout.vue'
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
new file mode 100644
index 0000000000..b80f4b1023
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
@@ -0,0 +1,13 @@
+<template>
+  <BlockLayout>
+    <template #header>
+      <h3>Collection object</h3>
+    </template>
+    <template #body>
+    </template>
+  </BlockLayout>
+</template>
+
+<script setup>
+import BlockLayout from 'components/layout/BlockLayout.vue'
+</script>
\ No newline at end of file
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
new file mode 100644
index 0000000000..7c7df15b4d
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
@@ -0,0 +1,22 @@
+<template>
+  <div>
+    <SmartSelector
+      ref="smartSelector"
+      model="geographic_areas"
+      target="CollectingEvent"
+      label="name"
+      klass="CollectingEvent"
+      @selected="selectGeographicArea"
+    />
+    <SmartSelectorItem
+      :item="geographicArea"
+      label="object_tag"
+      @unset="state.geographicArea = undefined"
+    />
+  </div>
+</template>
+
+<script setup>
+import SmartSelector from 'components/ui/SmartSelector.vue'
+import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js
new file mode 100644
index 0000000000..4228bd95a2
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js
@@ -0,0 +1,31 @@
+import { reactive } from 'vue'
+import { CollectionObject } from 'routes/endpoints'
+
+const state = reactive({
+  collectingEvent: {},
+  collectionObject: {},
+  identifier: {}
+})
+
+export default () => {
+  const getters = {
+    getCollectingEvent: () => state.collectingEvent
+  }
+
+  const actions = {
+    createCollectionObject: () => {
+      CollectionObject.create({
+        collection_object: {
+          ...state.collectionObject,
+          collecting_event_id: state.collectingEvent.id
+        }
+      })
+    }
+  }
+
+  return {
+    getters,
+    actions,
+    state
+  }
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
new file mode 100644
index 0000000000..b80fbe23e8
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
@@ -0,0 +1,14 @@
+import { createApp } from 'vue'
+import App from './App.vue'
+
+function initApp (element) {
+  const app = createApp(App)
+
+  app.mount(element)
+}
+
+document.addEventListener('turbolinks:load', () => {
+  const el = document.querySelector('#vue-simple-new-specimen')
+
+  if (el) { initApp(el) }
+})
diff --git a/app/views/tasks/accessions/quick/simple/new.html.erb b/app/views/tasks/accessions/quick/simple/new.html.erb
index 87225e0ee1..25a4126763 100644
--- a/app/views/tasks/accessions/quick/simple/new.html.erb
+++ b/app/views/tasks/accessions/quick/simple/new.html.erb
@@ -1,3 +1,5 @@
+<div id="vue-simple-new-specimen"></div>
+
 <h2> Task: Simple new specimen </h2>
 
 <%= form_for(@specimen, as: :specimen, url: create_simple_specimen_task_path, html: {class: :dropzone, id: 'simple-specimen-task'}) do |f| -%>
@@ -67,7 +69,7 @@
 
 
           <hr>
-          <div class="flex-wrap-row" data-help="These fields are used to create a related collecting event."> <!---- collecting event block ---->
+          <div class="flex-wrap-row" data-help="These fields are used to create a related collecting event."> 
             <div class="flex-wrap-column">
               <div id="collecting_event_fields" <%= 'hidden' if @specimen.collecting_event_id -%> >
                 <%= f.fields_for(:collecting_event, CollectingEvent.new, include_id: false) do |c| -%>
@@ -110,7 +112,7 @@
               <%= link_to("return", "#", id: 'collecting_event_form_toggle', data: { turbolinks: false }, class: ['button-undo'], hidden: (@specimen.collecting_event_id ? false : true)) -%>
             </div>
           </div>
-        </div> <!---- end column 1 ---->
+        </div> 
 
 
     <div class="flex-wrap-column small_space">

From 1c83f03b0bb6159aa09899d6f9d3341c4cf3f01c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Wed, 9 Nov 2022 17:27:34 -0300
Subject: [PATCH 007/160] Fix #3033: Selenium and capybara versions unlocked

---
 Gemfile                                 |  4 ++--
 Gemfile.lock                            | 14 +++++++-------
 spec/features/tasks/otus/filter_spec.rb |  4 ++--
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/Gemfile b/Gemfile
index 42cdb86778..5fa3bc80f3 100644
--- a/Gemfile
+++ b/Gemfile
@@ -145,7 +145,7 @@ group :test, :development do
   gem 'byebug', '~> 11.1', {}.merge(ENV['RM_INFO'] ? {require: false} : {})
   gem 'factory_bot_rails', '~> 6.2'
   gem 'webdrivers', '~> 5.0', require: false
-  gem 'selenium-webdriver', '~> 4.2.0'
+  gem 'selenium-webdriver', '~> 4.6', '>= 4.6.1'
   gem 'prawn', '~> 2.4.0'
   gem 'puma', '~> 5.5'
 end
@@ -178,7 +178,7 @@ group :test do
   gem 'rspec', '~> 3.6'
   gem 'codecov', '~> 0.6.0'
   gem 'simplecov', :require => false
-  gem 'capybara', '3.37.1' # TODO: Fix features/tasks/otus/filter_spec to remove strict version locking
+  gem 'capybara', '~> 3.18'
   gem 'timecop', '~> 0.9.1'
   gem 'webmock', '~> 3.8' # , '>= 3.6.2'
   gem 'vcr', '~> 6.0'
diff --git a/Gemfile.lock b/Gemfile.lock
index 80fdf86524..65db1aae41 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -157,7 +157,7 @@ GEM
     brakeman (5.3.1)
     builder (3.2.4)
     byebug (11.1.3)
-    capybara (3.37.1)
+    capybara (3.38.0)
       addressable
       matrix
       mini_mime (>= 0.1.3)
@@ -217,7 +217,7 @@ GEM
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
-    excon (0.93.1)
+    excon (0.94.0)
     execjs (2.8.1)
     factory_bot (6.2.1)
       activesupport (>= 5.0.0)
@@ -427,7 +427,7 @@ GEM
     rdoc (6.3.3)
     redcarpet (3.5.1)
     redis (4.8.0)
-    regexp_parser (1.8.2)
+    regexp_parser (2.6.0)
     request_store (1.5.1)
       rack (>= 1.4)
     require_all (3.0.0)
@@ -529,7 +529,7 @@ GEM
       rdoc (>= 5.0)
     seedbank (0.5.0)
       rake (>= 10.0)
-    selenium-webdriver (4.2.1)
+    selenium-webdriver (4.6.1)
       childprocess (>= 0.5, < 5.0)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
@@ -633,7 +633,7 @@ GEM
     xpath (3.2.0)
       nokogiri (~> 1.8)
     zaru (0.3.0)
-    zeitwerk (2.6.5)
+    zeitwerk (2.6.6)
     zip_tricks (5.6.0)
 
 PLATFORMS
@@ -655,7 +655,7 @@ DEPENDENCIES
   brakeman (~> 5.1, >= 4.6.1)
   bundler (~> 2.0)
   byebug (~> 11.1)
-  capybara (= 3.37.1)
+  capybara (~> 3.18)
   chartkick (~> 4.0)
   chronic (~> 0.10.2)
   chunky_png (~> 1.4.0)
@@ -740,7 +740,7 @@ DEPENDENCIES
   sassc-rails (~> 2.1.0)
   sdoc (~> 2.2.0)
   seedbank (~> 0.5.0)
-  selenium-webdriver (~> 4.2.0)
+  selenium-webdriver (~> 4.6, >= 4.6.1)
   serrano!
   shakapacker (~> 6.3)
   shortener (~> 0.8.0)
diff --git a/spec/features/tasks/otus/filter_spec.rb b/spec/features/tasks/otus/filter_spec.rb
index dc0ae05aed..6bbdd23b31 100644
--- a/spec/features/tasks/otus/filter_spec.rb
+++ b/spec/features/tasks/otus/filter_spec.rb
@@ -45,7 +45,7 @@
           find('#label_toggle_slide_area').click
           # TODO: Helper method to calculate x-y and perform interaction
           [[256, 128], [270, 128], [270, 143], [256, 143], [256, 128]]
-            .inject(find('#drawable_map_canvas')) { |e, (x, y)| sleep 1; e.hover.click(x: x, y: y) }
+            .inject(find('#drawable_map_canvas')) { |e, (x, y)| sleep 1; e.hover.click(x: x-256, y: y-128) }
           click_button('Set area')
           expect(page).to have_css('#area_count', text: '4')
         end
@@ -55,7 +55,7 @@
           find('#label_toggle_slide_area').click
           # TODO: Helper method to calculate x-y and perform interaction
           [[256, 113], [270, 113], [270, 143], [256, 143], [256, 113]]
-            .inject(find('#drawable_map_canvas')) { |e, (x, y)| sleep 1; e.hover.click(x: x, y: y) }
+            .inject(find('#drawable_map_canvas')) { |e, (x, y)| sleep 1; e.hover.click(x: x-256, y: y-128) }
           click_button('Set area')
           expect(page).to have_css('#area_count', text: '9')
         end

From 9c3f9512776421de08858c2604b291a2109e9ce7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Fri, 11 Nov 2022 16:17:01 -0300
Subject: [PATCH 008/160] Add stores and adapters. Add Pinia for state
 management

---
 app/javascript/vue/adapters/index.js          |  3 +
 .../vue/adapters/makeCollectingEvent.js       | 47 +++++++++++
 .../vue/adapters/makeCollectionObject.js      |  2 +-
 .../payload/makeCollectingEventPayload.js     | 15 ++++
 .../payload/makeCollectionObjectPayload.js    | 46 +++++++++++
 .../simple_new_specimen/App.vue               |  2 +
 .../simple_new_specimen/components/FormCO.vue |  6 +-
 .../FormCO/FormCOPreparationType.vue          | 30 +++++++
 .../composition/useStore.js                   | 31 -------
 .../simple_new_specimen/index.js              |  3 +
 .../store/useCollectingEventStore.js          | 20 +++++
 .../store/useCollectionObjectStore.js         | 28 +++++++
 .../store/useIdentifierStore.js               | 32 ++++++++
 .../store/useTaxonDeterminationStore.js       | 33 ++++++++
 package-lock.json                             | 80 +++++++++++++++++--
 package.json                                  |  1 +
 16 files changed, 340 insertions(+), 39 deletions(-)
 create mode 100644 app/javascript/vue/adapters/makeCollectingEvent.js
 create mode 100644 app/javascript/vue/adapters/payload/makeCollectingEventPayload.js
 create mode 100644 app/javascript/vue/adapters/payload/makeCollectionObjectPayload.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue
 delete mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js

diff --git a/app/javascript/vue/adapters/index.js b/app/javascript/vue/adapters/index.js
index 4b6a60a839..e72e06a9b2 100644
--- a/app/javascript/vue/adapters/index.js
+++ b/app/javascript/vue/adapters/index.js
@@ -1,2 +1,5 @@
 export * from './makeCollectionObject'
+export * from './makeCollectingEvent'
 export * from './makeIdentifier'
+export * from './payload/makeCollectingEventPayload'
+export * from './payload/makeCollectionObjectPayload'
diff --git a/app/javascript/vue/adapters/makeCollectingEvent.js b/app/javascript/vue/adapters/makeCollectingEvent.js
new file mode 100644
index 0000000000..65eea25e34
--- /dev/null
+++ b/app/javascript/vue/adapters/makeCollectingEvent.js
@@ -0,0 +1,47 @@
+export function makeCollectingEvent (ceData = {}) {
+  return {
+    id: ceData.id,
+    globalId: ceData.global_id,
+    printLabel: ceData.print_label,
+    printLabelNumberToPrint: ceData.print_label_number_to_print,
+    documentLabel: ceData.document_label,
+    verbatimLabel: ceData.verbatim_label,
+    verbatimLocality: ceData.verbatim_locality,
+    verbatimDate: ceData.verbatim_date,
+    verbatimLongitude: ceData.verbatim_longitude,
+    verbatimLatitude: ceData.verbatim_latitude,
+    verbatimGeolocationUncertainty: ceData.verbatim_geolocation_uncertainty,
+    verbatimTripIdentifier: ceData.verbatim_trip_identifier,
+    verbatimCollectors: ceData.verbatim_collectors,
+    verbatimMethod: ceData.verbatim_method,
+    verbatimHabitat: ceData.verbatim_habitat,
+    verbatimDatum: ceData.verbatim_datum,
+    verbatimElevation: ceData.verbatim_elevation,
+    geographicAreaId: ceData.geographic_area_id,
+    minimumElevation: ceData.minimum_elevation,
+    maximumElevation: ceData.maximum_elevation,
+    elevationPrecision: ceData.elevation_precision,
+    timeStartHour: ceData.time_start_hour,
+    timeStartMinute: ceData.time_start_minute,
+    timeStartSecond: ceData.time_start_second,
+    timeEndHour: ceData.time_end_hour,
+    timeEndMinute: ceData.time_end_minute,
+    timeEndSecond: ceData.time_end_second,
+    startDateDay: ceData.start_date_day,
+    startDateMonth: ceData.start_date_month,
+    startDateYear: ceData.start_date_year,
+    endDateDay: ceData.end_date_day,
+    endDateMonth: ceData.end_date_month,
+    endDateYear: ceData.end_date_year,
+    group: ceData.group,
+    member: ceData.member,
+    formation: ceData.formation,
+    lithology: ceData.lithology,
+    maxMa: ceData.max_ma,
+    minMa: ceData.min_ma,
+    fieldNotes: ceData.field_notes,
+    metaPrioritizeGeographicArea: ceData.meta_prioritize_geographic_area,
+    rolesAttributes: ceData.role_attributes || [],
+    identifiersAttributes: ceData.identifiers_attributes || []
+  }
+}
diff --git a/app/javascript/vue/adapters/makeCollectionObject.js b/app/javascript/vue/adapters/makeCollectionObject.js
index 26939b520d..65e17efeca 100644
--- a/app/javascript/vue/adapters/makeCollectionObject.js
+++ b/app/javascript/vue/adapters/makeCollectionObject.js
@@ -1,4 +1,4 @@
-export function makeCollectionObject (coData) {
+export function makeCollectionObject (coData = {}) {
   return {
     id: coData.id,
     bufferedCollectingEvent: coData.buffered_collecting_event,
diff --git a/app/javascript/vue/adapters/payload/makeCollectingEventPayload.js b/app/javascript/vue/adapters/payload/makeCollectingEventPayload.js
new file mode 100644
index 0000000000..2f1529c0bf
--- /dev/null
+++ b/app/javascript/vue/adapters/payload/makeCollectingEventPayload.js
@@ -0,0 +1,15 @@
+export function makeCollectionObjectPayload (coData) {
+  return {
+    id: coData.id,
+    buffered_collecting_event: coData.bufferedCollectingEvent,
+    buffered_determinations: coData.bufferedDeterminations,
+    buffered_other_labels: coData.bufferedLabels,
+    accesioned_at: coData.accesionedAt,
+    deaccessioned_at: coData.deaccessionedAt,
+    deaccession_reason: coData.deaccessionReason,
+    repository_id: coData.repositoryId,
+    current_repository_id: coData.currentRepositoryId,
+    total: coData.total,
+    preparation_type_id: coData.preparationTypeId
+  }
+}
diff --git a/app/javascript/vue/adapters/payload/makeCollectionObjectPayload.js b/app/javascript/vue/adapters/payload/makeCollectionObjectPayload.js
new file mode 100644
index 0000000000..0c9907040b
--- /dev/null
+++ b/app/javascript/vue/adapters/payload/makeCollectionObjectPayload.js
@@ -0,0 +1,46 @@
+export function makeCollectingEventPayload (ceData) {
+  return {
+    id: ceData.id,
+    print_label: ceData.printLabel,
+    print_label_number_to_print: ceData.printLabelNumberToPrint,
+    document_label: ceData.documentLabel,
+    verbatim_label: ceData.verbatimLabel,
+    verbatim_locality: ceData.verbatimLocality,
+    verbatim_date: ceData.verbatimDate,
+    verbatim_longitude: ceData.verbatimLongitude,
+    verbatim_latitude: ceData.verbatimLatitude,
+    verbatim_geolocation_uncertainty: ceData.verbatimGeolocationUncertainty,
+    verbatim_trip_identifier: ceData.verbatimTripIdentifier,
+    verbatim_collectors: ceData.verbatimCollectors,
+    verbatim_method: ceData.verbatimMethod,
+    verbatim_habitat: ceData.verbatimHabitat,
+    verbatim_datum: ceData.verbatimDatum,
+    verbatim_elevation: ceData.verbatimElevation,
+    geographic_area_id: ceData.geographicAreaId,
+    minimum_elevation: ceData.minimumElevation,
+    maximum_elevation: ceData.maximumElevation,
+    elevation_precision: ceData.elevationPrecision,
+    time_start_hour: ceData.timeStartHour,
+    time_start_minute: ceData.timeStartMinute,
+    time_start_second: ceData.timeStartSecond,
+    time_end_hour: ceData.timeEndHour,
+    time_end_minute: ceData.timeEndMinute,
+    time_end_second: ceData.timeEndSecond,
+    start_date_day: ceData.startDateDay,
+    start_date_month: ceData.startDateMonth,
+    start_date_year: ceData.startDateYear,
+    end_date_day: ceData.endDateDay,
+    end_date_month: ceData.endDateMonth,
+    end_date_year: ceData.endDateYear,
+    group: ceData.group,
+    member: ceData.member,
+    formation: ceData.formation,
+    lithology: ceData.lithology,
+    max_ma: ceData.maxMa,
+    min_ma: ceData.minMa,
+    field_notes: ceData.fieldNotes,
+    meta_prioritize_geographic_area: ceData.metaPrioritizeGeographicArea,
+    role_attributes: ceData.rolesAttributes,
+    identifiers_attributes: ceData.identifiersAttributes
+  }
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index aa25eb352f..32ed4e20ac 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -1,10 +1,12 @@
 <template>
   <div>
     <h1>Simplete new specimen</h1>
+    <FormCO />
     <FormCE />
   </div>
 </template>
 
 <script setup>
 import FormCE from './components/FormCE.vue'
+import FormCO from './components/FormCO.vue'
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
index b80f4b1023..f220570efe 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
@@ -4,10 +4,14 @@
       <h3>Collection object</h3>
     </template>
     <template #body>
+      <div>
+        <FormCOPreparationType />
+      </div>
     </template>
   </BlockLayout>
 </template>
 
 <script setup>
 import BlockLayout from 'components/layout/BlockLayout.vue'
-</script>
\ No newline at end of file
+import FormCOPreparationType from './FormCO/FormCOPreparationType.vue'
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue
new file mode 100644
index 0000000000..eec0f40b45
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue
@@ -0,0 +1,30 @@
+<template>
+  <div class="field label-above">
+    <label>Preparation type</label>
+    <select v-model="store.collectionObject.preparationTypeId">
+      <option :value="undefined">
+        None
+      </option>
+      <option
+        v-for="(item, key) in preparationTypes"
+        :key="key"
+        :value="item.id"
+      >
+        {{ item.name }}
+      </option>
+    </select>
+  </div>
+</template>
+
+<script setup>
+import { ref } from 'vue'
+import { PreparationType } from 'routes/endpoints'
+import { useCollectionObjectStore } from '../../store/useCollectionObjectStore.js'
+
+const store = useCollectionObjectStore()
+const preparationTypes = ref([])
+
+PreparationType.where({}).then(({ body }) => {
+  preparationTypes.value = body
+})
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js
deleted file mode 100644
index 4228bd95a2..0000000000
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/composition/useStore.js
+++ /dev/null
@@ -1,31 +0,0 @@
-import { reactive } from 'vue'
-import { CollectionObject } from 'routes/endpoints'
-
-const state = reactive({
-  collectingEvent: {},
-  collectionObject: {},
-  identifier: {}
-})
-
-export default () => {
-  const getters = {
-    getCollectingEvent: () => state.collectingEvent
-  }
-
-  const actions = {
-    createCollectionObject: () => {
-      CollectionObject.create({
-        collection_object: {
-          ...state.collectionObject,
-          collecting_event_id: state.collectingEvent.id
-        }
-      })
-    }
-  }
-
-  return {
-    getters,
-    actions,
-    state
-  }
-}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
index b80fbe23e8..5c0f7d3aa6 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
@@ -1,9 +1,12 @@
 import { createApp } from 'vue'
+import { createPinia } from 'pinia'
 import App from './App.vue'
 
 function initApp (element) {
   const app = createApp(App)
+  const pinia = createPinia()
 
+  app.use(pinia)
   app.mount(element)
 }
 
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js
new file mode 100644
index 0000000000..a0dda5af3b
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js
@@ -0,0 +1,20 @@
+import { CollectingEvent } from 'routes/endpoints'
+import { defineStore } from 'pinia'
+import makeCollectingEvent from 'factory/CollectingEvent'
+
+export const useCollectingEventStore = defineStore('collectingEvent', {
+  state: () => ({
+    collectingEvent: makeCollectingEvent()
+  }),
+
+  actions: {
+    createCollectingEvent () {
+      CollectingEvent.create({
+        collection_object: {
+          ...this.collectionObject,
+          collecting_event_id: this.collectingEvent.id
+        }
+      })
+    }
+  }
+})
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js
new file mode 100644
index 0000000000..f4cbbade22
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js
@@ -0,0 +1,28 @@
+import { CollectionObject } from 'routes/endpoints'
+import { defineStore } from 'pinia'
+import { makeCollectionObject, makeCollectionObjectPayload } from 'adapters/index.js'
+
+export const useCollectionObjectStore = defineStore('collectionObject', {
+  state: () => ({
+    collectionObject: makeCollectionObject({})
+  }),
+
+  actions: {
+    async saveCollectionObject (params) {
+      const payload = {
+        collection_object: {
+          ...makeCollectionObjectPayload(this.collectionObject),
+          ...params
+        }
+      }
+
+      const response = payload.id
+        ? await CollectionObject.update(payload.id, payload)
+        : await CollectionObject.create(payload)
+
+      this.collectionObject = makeCollectionObject(response.body)
+
+      return response
+    }
+  }
+})
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js
new file mode 100644
index 0000000000..cb16ab156b
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js
@@ -0,0 +1,32 @@
+import { Identifier } from 'routes/endpoints'
+import { defineStore } from 'pinia'
+
+export const useCollectingEventStore = defineStore('collectingEvent', {
+  state: () => ({
+    identifier: {
+      id: undefined,
+      namespace_id: undefined,
+      type: undefined,
+      identifier: undefined,
+      identifier_object_type: undefined,
+      identifier_object_id: undefined
+    }
+  }),
+
+  actions: {
+    async saveIdentifier (params) {
+      const payload = {
+        identifier: {
+          ...this.identifier,
+          ...params
+        }
+      }
+
+      const response = payload.id
+        ? await Identifier.update(payload.id, payload)
+        : await Identifier.create(payload)
+
+      this.identifier = response.body
+    }
+  }
+})
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js
new file mode 100644
index 0000000000..c5ded71f52
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js
@@ -0,0 +1,33 @@
+import { TaxonDetermination } from 'routes/endpoints'
+import { defineStore } from 'pinia'
+
+export const useTaxonDeterminationStore = defineStore('taxonDetermination', {
+  state: () => ({
+    taxonDetermination: {
+      id: undefined,
+      biological_collection_object_id: undefined,
+      otu_id: undefined,
+      year_made: undefined,
+      month_made: undefined,
+      day_made: undefined,
+      roles_attributes: []
+    }
+  }),
+
+  actions: {
+    async saveTaxonDetermination (params) {
+      const payload = {
+        taxon_determination: {
+          ...this.taxonDetermination,
+          ...params
+        }
+      }
+
+      const response = payload.id
+        ? await TaxonDetermination.update(payload.id, payload)
+        : await TaxonDetermination.create(payload)
+
+      this.taxonDetermination = response.body
+    }
+  }
+})
diff --git a/package-lock.json b/package-lock.json
index c888fd7f77..ce507e7ea2 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -23,6 +23,7 @@
         "leaflet.pattern": "^0.1.0",
         "parse-dms": "0.0.5",
         "pdfjs-dist": "3.0.279",
+        "pinia": "^2.0.23",
         "qs": "^6.11.0",
         "shakapacker": "6.5.4",
         "v-hotkey": "^0.9.0",
@@ -2742,9 +2743,9 @@
       }
     },
     "node_modules/@vue/devtools-api": {
-      "version": "6.4.1",
-      "resolved": "https://registry.npmjs.org/@vue/devtools-api/-/devtools-api-6.4.1.tgz",
-      "integrity": "sha512-tY5m7kwu0R+9GWHSncsE40rCX9ou4HhjhlbgdEMci8j08BE7pLlOpHRcyv6eEP0VYrW1JV0zFh6AoWsoHrVyFw=="
+      "version": "6.4.5",
+      "resolved": "https://registry.npmjs.org/@vue/devtools-api/-/devtools-api-6.4.5.tgz",
+      "integrity": "sha512-JD5fcdIuFxU4fQyXUu3w2KpAJHzTVdN+p4iOX2lMWSHMOoQdMAcpFLZzm9Z/2nmsoZ1a96QEhZ26e50xLBsgOQ=="
     },
     "node_modules/@vue/reactivity": {
       "version": "3.2.41",
@@ -8058,6 +8059,56 @@
         "node": ">=0.10.0"
       }
     },
+    "node_modules/pinia": {
+      "version": "2.0.23",
+      "resolved": "https://registry.npmjs.org/pinia/-/pinia-2.0.23.tgz",
+      "integrity": "sha512-N15hFf4o5STrxpNrib1IEb1GOArvPYf1zPvQVRGOO1G1d74Ak0J0lVyalX/SmrzdT4Q0nlEFjbURsmBmIGUR5Q==",
+      "dependencies": {
+        "@vue/devtools-api": "^6.4.4",
+        "vue-demi": "*"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/posva"
+      },
+      "peerDependencies": {
+        "@vue/composition-api": "^1.4.0",
+        "typescript": ">=4.4.4",
+        "vue": "^2.6.14 || ^3.2.0"
+      },
+      "peerDependenciesMeta": {
+        "@vue/composition-api": {
+          "optional": true
+        },
+        "typescript": {
+          "optional": true
+        }
+      }
+    },
+    "node_modules/pinia/node_modules/vue-demi": {
+      "version": "0.13.11",
+      "resolved": "https://registry.npmjs.org/vue-demi/-/vue-demi-0.13.11.tgz",
+      "integrity": "sha512-IR8HoEEGM65YY3ZJYAjMlKygDQn25D5ajNFNoKh9RSDMQtlzCxtfQjdQgv9jjK+m3377SsJXY8ysq8kLCZL25A==",
+      "hasInstallScript": true,
+      "bin": {
+        "vue-demi-fix": "bin/vue-demi-fix.js",
+        "vue-demi-switch": "bin/vue-demi-switch.js"
+      },
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/antfu"
+      },
+      "peerDependencies": {
+        "@vue/composition-api": "^1.0.0-rc.1",
+        "vue": "^3.0.0-0 || ^2.6.0"
+      },
+      "peerDependenciesMeta": {
+        "@vue/composition-api": {
+          "optional": true
+        }
+      }
+    },
     "node_modules/pkg-dir": {
       "version": "4.2.0",
       "resolved": "https://registry.npmjs.org/pkg-dir/-/pkg-dir-4.2.0.tgz",
@@ -13476,9 +13527,9 @@
       }
     },
     "@vue/devtools-api": {
-      "version": "6.4.1",
-      "resolved": "https://registry.npmjs.org/@vue/devtools-api/-/devtools-api-6.4.1.tgz",
-      "integrity": "sha512-tY5m7kwu0R+9GWHSncsE40rCX9ou4HhjhlbgdEMci8j08BE7pLlOpHRcyv6eEP0VYrW1JV0zFh6AoWsoHrVyFw=="
+      "version": "6.4.5",
+      "resolved": "https://registry.npmjs.org/@vue/devtools-api/-/devtools-api-6.4.5.tgz",
+      "integrity": "sha512-JD5fcdIuFxU4fQyXUu3w2KpAJHzTVdN+p4iOX2lMWSHMOoQdMAcpFLZzm9Z/2nmsoZ1a96QEhZ26e50xLBsgOQ=="
     },
     "@vue/reactivity": {
       "version": "3.2.41",
@@ -17323,6 +17374,23 @@
       "integrity": "sha512-udgsAY+fTnvv7kI7aaxbqwWNb0AHiB0qBO89PZKPkoTmGOgdbrHDKD+0B2X4uTfJ/FT1R09r9gTsjUjNJotuog==",
       "dev": true
     },
+    "pinia": {
+      "version": "2.0.23",
+      "resolved": "https://registry.npmjs.org/pinia/-/pinia-2.0.23.tgz",
+      "integrity": "sha512-N15hFf4o5STrxpNrib1IEb1GOArvPYf1zPvQVRGOO1G1d74Ak0J0lVyalX/SmrzdT4Q0nlEFjbURsmBmIGUR5Q==",
+      "requires": {
+        "@vue/devtools-api": "^6.4.4",
+        "vue-demi": "*"
+      },
+      "dependencies": {
+        "vue-demi": {
+          "version": "0.13.11",
+          "resolved": "https://registry.npmjs.org/vue-demi/-/vue-demi-0.13.11.tgz",
+          "integrity": "sha512-IR8HoEEGM65YY3ZJYAjMlKygDQn25D5ajNFNoKh9RSDMQtlzCxtfQjdQgv9jjK+m3377SsJXY8ysq8kLCZL25A==",
+          "requires": {}
+        }
+      }
+    },
     "pkg-dir": {
       "version": "4.2.0",
       "resolved": "https://registry.npmjs.org/pkg-dir/-/pkg-dir-4.2.0.tgz",
diff --git a/package.json b/package.json
index 744db7245e..0aa362a9b9 100644
--- a/package.json
+++ b/package.json
@@ -17,6 +17,7 @@
     "leaflet.pattern": "^0.1.0",
     "parse-dms": "0.0.5",
     "pdfjs-dist": "3.0.279",
+    "pinia": "^2.0.23",
     "qs": "^6.11.0",
     "shakapacker": "6.5.4",
     "v-hotkey": "^0.9.0",

From 4207273df4f46b88859e4126b446a86833d63bb4 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Sun, 13 Nov 2022 09:21:45 -0600
Subject: [PATCH 009/160] Add Task collection object chronology

---
 CHANGELOG.md                                  |  1 +
 .../chronology_controller.rb                  |  8 +++++++
 .../chronology/index.html.erb                 | 24 +++++++++++++++++++
 .../projects/activity/user_activity.html.erb  |  5 ++--
 config/interface/hub/user_tasks.yml           |  8 +++++++
 config/routes/tasks.rb                        |  4 ++++
 6 files changed, 47 insertions(+), 3 deletions(-)
 create mode 100644 app/controllers/tasks/collection_objects/chronology_controller.rb
 create mode 100644 app/views/tasks/collection_objects/chronology/index.html.erb

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be6d5c3c60..8ae02b4644 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Added
 - Autocomplete on Browse collection object [#3189]
+- Task - Collection object chronology, a plot of object by year collected
 
 ### Fixed
 - Citation link in Biological association panel on Browse OTU
diff --git a/app/controllers/tasks/collection_objects/chronology_controller.rb b/app/controllers/tasks/collection_objects/chronology_controller.rb
new file mode 100644
index 0000000000..d8b40bc5d5
--- /dev/null
+++ b/app/controllers/tasks/collection_objects/chronology_controller.rb
@@ -0,0 +1,8 @@
+class Tasks::CollectionObjects::ChronologyController < ApplicationController
+  include TaskControllerConfiguration
+
+  # GET
+  def index
+  end
+
+end
\ No newline at end of file
diff --git a/app/views/tasks/collection_objects/chronology/index.html.erb b/app/views/tasks/collection_objects/chronology/index.html.erb
new file mode 100644
index 0000000000..b046fa12a6
--- /dev/null
+++ b/app/views/tasks/collection_objects/chronology/index.html.erb
@@ -0,0 +1,24 @@
+<%= content_for :head do -%>
+  <%= javascript_include_tag "https://cdnjs.cloudflare.com/ajax/libs/Chart.js/3.7.1/chart.js",
+    "https://cdn.jsdelivr.net/npm/chartjs-adapter-date-fns/dist/chartjs-adapter-date-fns.bundle.min.js"  %>
+<% end %>
+
+<%= tag.h1 'Task - Collection object chronology', id: :top -%>
+
+<div class="flexbox">
+  <div class="item item1">
+    <h2> Collection objects per start year collected </h2>
+    <%= column_chart CollectionObject.joins(:collecting_event)
+    .where(project_id: sessions_current_project_id)
+    .where('collecting_events.start_date_year is not null')
+    .group('collecting_events.start_date_year')
+    .count, 
+      discrete: true, ytitle: 'Count', xtitle: 'Year collected', height: '400px', download: true
+    %>
+
+    <%= tag.em CollectionObject.joins(:collecting_event)
+    .where(project_id: sessions_current_project_id)
+    .where('collecting_events.start_date_year is null')
+    .group('collecting_events.start_date_year').count.first.last.to_s + ' Collection object records without collecting event date start year.' %>
+  </div>
+</div>
\ No newline at end of file
diff --git a/app/views/tasks/projects/activity/user_activity.html.erb b/app/views/tasks/projects/activity/user_activity.html.erb
index 89a0fc438d..c906aa7b58 100644
--- a/app/views/tasks/projects/activity/user_activity.html.erb
+++ b/app/views/tasks/projects/activity/user_activity.html.erb
@@ -55,7 +55,7 @@
 
 <div class="flexbox">
   <div class="item item1">
-    <h2> Users per project ---</h2>
+    <h2> Users per project </h2>
     <%= column_chart Project.joins(:users).group(:id).count.to_a.sort_by(&:second).reverse!, xtitle: 'Project', ytitle: 'Number of users', discrete: true %>
   </div>
 </div>
@@ -66,5 +66,4 @@
     <h2> User activity over time </h2>
     <%= column_chart User.group_by_day(:last_seen_at, format: "%a").count, xtitle: 'Day', ytitle: 'Number of users' %>
   </div>
-</div>
-
+</div>
\ No newline at end of file
diff --git a/config/interface/hub/user_tasks.yml b/config/interface/hub/user_tasks.yml
index ab81abe9cc..99850cbba1 100644
--- a/config/interface/hub/user_tasks.yml
+++ b/config/interface/hub/user_tasks.yml
@@ -738,3 +738,11 @@ paper_catalog_generator_task:
     - export
   status: prototype
   description: 'Experimenting with rendering nomenclature as a paper catalog'
+collection_object_chronology_task:
+  hub: true
+  name: 'Collection object chronology'
+  related:
+  categories:
+  - collection_object
+  status: prototype
+  description: 'All collection objects by year collected.'
\ No newline at end of file
diff --git a/config/routes/tasks.rb b/config/routes/tasks.rb
index 2c3290f916..7dfd6a2e69 100644
--- a/config/routes/tasks.rb
+++ b/config/routes/tasks.rb
@@ -225,6 +225,10 @@
   end
 
   scope :collection_objects do
+      scope :chronology, controller: 'tasks/collection_objects/chronology' do
+        get '/', action: :index, as: 'collection_object_chronology_task'
+      end
+
     scope :stepwise do
       scope :determinations, controller: 'tasks/collection_objects/stepwise/determinations' do
         get '/', action: :index, as: 'stepwise_determinations_task'

From ab1d317dc675400e995fa26bb3c3756c55095517 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 14 Nov 2022 16:10:25 -0600
Subject: [PATCH 010/160] Remove media observations if they have no more
 depictions after update

---
 CHANGELOG.md                  |  1 +
 app/models/depiction.rb       | 13 +++++++++++--
 spec/models/depiction_spec.rb |  8 ++++++++
 3 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8ae02b4644..d8ef452fba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Task - Collection object chronology, a plot of object by year collected
 
 ### Fixed
+- Media observations removed if they have no more depictions via updates
 - Citation link in Biological association panel on Browse OTU
 - Type relationship text/rendering is inverted in New taxon name [#3182]
 
diff --git a/app/models/depiction.rb b/app/models/depiction.rb
index 336eee4177..b670a9cf78 100644
--- a/app/models/depiction.rb
+++ b/app/models/depiction.rb
@@ -62,7 +62,8 @@ class Depiction < ApplicationRecord
   validates_presence_of :depiction_object
   validates_uniqueness_of :sled_image_id, scope: [:project_id, :sled_image_x_position, :sled_image_y_position], allow_nil: true, if: Proc.new {|n| !n.sled_image_id.nil?}
 
-  after_destroy :remove_media_observations, if: Proc.new {|o| o.depiction_object.class.name == 'Observation::Media' }
+  before_update :remove_media_observation2, if: Proc.new {|o| o.depiction_object.type == 'Observation::Media' && o.depiction_object_id_changed? }
+  after_destroy :remove_media_observation, if: Proc.new {|o| o.depiction_object.type == 'Observation::Media' }
 
   def from_sled?
     !sled_image_id.nil?
@@ -90,9 +91,17 @@ def sled_extraction_path(size = :thumb)
 
   private
 
-  def remove_media_observations
+  def remove_media_observation2
+    o = Observation::Media.find(depiction_object_id_was)
+    if o.depictions.size == 1 # it will be zero
+      o.destroy!
+    end
+  end
+
+  def remove_media_observation
     if depiction_object.depictions.size == 0
       depiction_object.destroy!
     end
   end
+
 end
diff --git a/spec/models/depiction_spec.rb b/spec/models/depiction_spec.rb
index eadf656db7..ffd3ca21c3 100644
--- a/spec/models/depiction_spec.rb
+++ b/spec/models/depiction_spec.rb
@@ -15,6 +15,14 @@
     expect(Observation.find(o.id)).to be_truthy
   end
 
+  specify 'updating depiction destroys related Observation::Media 1 if there are no others' do
+    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test')) 
+    d = FactoryBot.create(:valid_depiction, depiction_object: o)
+    d.update!(depiction_object: FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test2') ) )
+
+    expect {Observation.find(o.id)}.to raise_error ActiveRecord::RecordNotFound
+  end
+
   specify 'destroying depiction destroys related Observation::Media 1' do
     o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test')) 
     d = FactoryBot.create(:valid_depiction, depiction_object: o)

From 7c28c39ec8ab4ea47a7499593ed46ff8b3ba9863 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 14 Nov 2022 17:05:40 -0600
Subject: [PATCH 011/160] Fix observation media destruction test

---
 app/models/depiction.rb       | 10 ++++++----
 spec/models/depiction_spec.rb |  1 +
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/app/models/depiction.rb b/app/models/depiction.rb
index b670a9cf78..75c83fd7eb 100644
--- a/app/models/depiction.rb
+++ b/app/models/depiction.rb
@@ -62,7 +62,7 @@ class Depiction < ApplicationRecord
   validates_presence_of :depiction_object
   validates_uniqueness_of :sled_image_id, scope: [:project_id, :sled_image_x_position, :sled_image_y_position], allow_nil: true, if: Proc.new {|n| !n.sled_image_id.nil?}
 
-  before_update :remove_media_observation2, if: Proc.new {|o| o.depiction_object.type == 'Observation::Media' && o.depiction_object_id_changed? }
+  after_update :remove_media_observation2, if: Proc.new {|o| o.depiction_object.type == 'Observation::Media' }
   after_destroy :remove_media_observation, if: Proc.new {|o| o.depiction_object.type == 'Observation::Media' }
 
   def from_sled?
@@ -92,9 +92,11 @@ def sled_extraction_path(size = :thumb)
   private
 
   def remove_media_observation2
-    o = Observation::Media.find(depiction_object_id_was)
-    if o.depictions.size == 1 # it will be zero
-      o.destroy!
+    if v = previous_changes['depiction_object_id']
+      o = Observation::Media.find(v[0])
+      if o.depictions.size == 0
+        o.destroy!
+      end
     end
   end
 
diff --git a/spec/models/depiction_spec.rb b/spec/models/depiction_spec.rb
index ffd3ca21c3..d0c1c7b9c2 100644
--- a/spec/models/depiction_spec.rb
+++ b/spec/models/depiction_spec.rb
@@ -21,6 +21,7 @@
     d.update!(depiction_object: FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test2') ) )
 
     expect {Observation.find(o.id)}.to raise_error ActiveRecord::RecordNotFound
+    expect(Depiction.find(d.id).id).to be_truthy
   end
 
   specify 'destroying depiction destroys related Observation::Media 1' do

From 7353338eca7fde5054d29aca248f1a2eba5c7d5c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Mon, 14 Nov 2022 20:30:35 -0300
Subject: [PATCH 012/160] Refactor cell component

---
 CHANGELOG.md                                  |   3 +
 app/javascript/vue/constants/modelTypes.js    |   8 +-
 .../image/components/CellObservation.vue      | 348 ++++++++----------
 .../image/components/MatrixTable.vue          |  20 +-
 .../image/store/actions/actionNames.js        |   3 +-
 .../image/store/actions/actions.js            |   4 +-
 .../image/store/actions/moveDepiction.js      |  44 +++
 .../image/store/mutations/addDepiction.js     |   9 +-
 8 files changed, 223 insertions(+), 216 deletions(-)
 create mode 100644 app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d8ef452fba..36de7a9814 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,9 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Citation link in Biological association panel on Browse OTU
 - Type relationship text/rendering is inverted in New taxon name [#3182]
 
+### Changed
+- Refactored observation cell component for Image matrix
+
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
 
 ## [0.29.6] - 2022-11-08
diff --git a/app/javascript/vue/constants/modelTypes.js b/app/javascript/vue/constants/modelTypes.js
index 351e3bfd09..ea1a1be4ec 100644
--- a/app/javascript/vue/constants/modelTypes.js
+++ b/app/javascript/vue/constants/modelTypes.js
@@ -1,21 +1,23 @@
 export const ASSERTED_DISTRIBUTION = 'AssertedDistribution'
+export const BIOCURATION_CLASS = 'BiocurationClass'
+export const BIOCURATION_GROUP = 'BiocurationGroup'
 export const BIOLOGICAL_ASSOCIATION = 'BiologicalAssociation'
 export const COLLECTING_EVENT = 'CollectingEvent'
 export const COLLECTION_OBJECT = 'CollectionObject'
 export const COMBINATION = 'Combination'
 export const CONTAINER = 'Container'
 export const CONTROLLED_VOCABULARY_TERM = 'ControlledVocabularyTerm'
+export const DEPICTION = 'Depiction'
 export const DESCRIPTOR = 'Descriptor'
 export const EXTRACT = 'Extract'
 export const IMAGE = 'Image'
 export const LOT = 'Lot'
+export const OBSERVATION = 'Observation'
 export const OTU = 'Otu'
 export const RANGED_LOT = 'RangedLot'
 export const SPECIMEN = 'Specimen'
 export const TAG = 'Tag'
 export const TAXON_NAME = 'TaxonName'
-export const TYPE_MATERIAL = 'TypeMaterial'
 export const TAXON_NAME_CLASSIFICATION = 'TaxonNameClassification'
 export const TAXON_NAME_RELATIONSHIP = 'TaxonNameRelationship'
-export const BIOCURATION_GROUP = 'BiocurationGroup'
-export const BIOCURATION_CLASS = 'BiocurationClass'
+export const TYPE_MATERIAL = 'TypeMaterial'
diff --git a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
index 10af3fac7c..936bffa03a 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
+++ b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
@@ -7,7 +7,7 @@
     <dropzone-component
       v-show="show"
       class="dropzone-card"
-      ref="dropzone"
+      ref="dropzoneElement"
       url="/observations"
       use-custom-dropzone-options
       @vdropzone-sending="sending"
@@ -67,7 +67,7 @@
   </div>
 </template>
 
-<script>
+<script setup>
 
 import DropzoneComponent from 'components/dropzone'
 import DraggableComponent from 'vuedraggable'
@@ -76,215 +76,179 @@ import ImageViewer from 'components/ui/ImageViewer/ImageViewer.vue'
 import SpinnerComponent from 'components/spinner'
 import VIcon from 'components/ui/VIcon/index.vue'
 import ButtonCitation from './ButtonCitation.vue'
+import { useStore } from 'vuex'
+import { ref, computed } from 'vue'
 import { Observation, Depiction } from 'routes/endpoints'
 import { GetterNames } from '../store/getters/getters'
 import { MutationNames } from '../store/mutations/mutations'
+import { ActionNames } from '../store/actions/actions'
+import { OBSERVATION_MEDIA } from 'constants/index'
+
+const CSRF_TOKEN = document.querySelector('meta[name="csrf-token"]').getAttribute('content')
+
+const dropzoneObservation = {
+  paramName: 'observation[images_attributes][][image_file]',
+  url: '/observations',
+  autoProcessQueue: true,
+  parallelUploads: 1,
+  headers: {
+    'X-CSRF-Token': CSRF_TOKEN
+  },
+  acceptedFiles: 'image/*,.heic'
+}
+const dropzoneDepiction = {
+  paramName: 'depiction[image_attributes][image_file]',
+  url: '/depictions',
+  autoProcessQueue: true,
+  headers: {
+    'X-CSRF-Token': CSRF_TOKEN
+  },
+  acceptedFiles: 'image/*,.heic'
+}
 
-export default {
-  components: {
-    DropzoneComponent,
-    DraggableComponent,
-    SpinnerComponent,
-    ImageViewer,
-    VIcon,
-    RadialAnnotator,
-    ButtonCitation
+const props = defineProps({
+  columnIndex: {
+    type: Number,
+    required: true
   },
 
-  props: {
-    depictions: {
-      type: Array,
-      required: true
-    },
-
-    rowObject: {
-      type: Object,
-      required: true
-    },
-
-    column: {
-      type: Object,
-      required: true
-    },
-
-    show: {
-      type: Boolean,
-      default: true
-    }
+  depictions: {
+    type: Array,
+    required: true
   },
 
-  emits: [
-    'removeDepiction',
-    'addDepiction'
-  ],
-
-  computed: {
-    observationMoved: {
-      get () {
-        return this.$store.getters[GetterNames.GetObservationMoved]
-      },
-      set (value) {
-        this.$store.commit(MutationNames.SetObservationMoved, value)
-      }
-    },
-
-    depictionMoved: {
-      get () {
-        return this.$store.getters[GetterNames.GetDepictionMoved]
-      },
-      set (value) {
-        this.$store.commit(MutationNames.SetDepictionMoved, value)
-      }
-    },
-
-    existObservations () {
-      return this.depictions.length > 0
-    },
-
-    rowObjectId () {
-      return this.rowObject.observation_object_id || this.rowObject.id
-    },
-
-    rowObjectBaseCassParam () {
-      return this.rowObject.observation_object_type || this.rowObject.base_class
-    },
-
-    observationId () {
-      return this.depictions.length && this.depictions[0].depiction_object_id
-    }
+  rowObject: {
+    type: Object,
+    required: true
   },
 
-  data () {
-    return {
-      isLoading: false,
-      dropzoneObservation: {
-        paramName: 'observation[images_attributes][][image_file]',
-        url: '/observations',
-        autoProcessQueue: true,
-        parallelUploads: 1,
-        headers: {
-          'X-CSRF-Token': document.querySelector('meta[name="csrf-token"]').getAttribute('content')
-        },
-        acceptedFiles: 'image/*,.heic'
-      },
-      dropzoneDepiction: {
-        paramName: 'depiction[image_attributes][image_file]',
-        url: '/depictions',
-        autoProcessQueue: true,
-        headers: {
-          'X-CSRF-Token': document.querySelector('meta[name="csrf-token"]').getAttribute('content')
-        },
-        acceptedFiles: 'image/*,.heic'
-      }
-    }
+  rowIndex: {
+    type: Number,
+    required: true
   },
 
-  methods: {
-    movedDepiction (event) {
-      if (this.depictions.length === 1) {
-        const observation = {
-          descriptor_id: this.column.id,
-          type: 'Observation::Media',
-          observation_object_type: this.rowObjectBaseCassParam,
-          observation_object_id: this.rowObjectId
-        }
-
-        Observation.create({ observation, extend: ['depictions'] }).then(({ body }) => {
-          this.updateDepiction(body.id)
-        })
-      } else {
-        this.updateDepiction()
-      }
-    },
-
-    openInputFile () {
-      this.$refs.dropzone.$el.click()
-    },
-
-    updateDepiction (observationId) {
-      const depiction = {
-        id: this.depictionMoved.id,
-        depiction_object_id: observationId || this.observationId,
-        depiction_object_type: 'Observation'
-      }
-      const observation = {
-        id: this.observationMoved,
-        depictions_attributes: [depiction]
-      }
-
-      this.$store.commit(MutationNames.SetIsSaving, true)
-
-      const request = observation.id
-        ? Observation
-          .update(observation.id, { observation, extend: ['depictions'] })
-          .then(({ body }) => {
-            const existDepiction = body.depictions.find(d => d.depiction_object_id === this.observationMoved)
-
-            if (!existDepiction) {
-              Observation.destroy(body.id)
-            }
-
-            this.$emit('addDepiction', {
-              ...this.depictionMoved,
-              ...depiction
-            })
-          })
-        : Depiction.update(depiction.id, { depiction }).then(({ body }) => {
-          this.$emit('addDepiction', body)
-        })
+  descriptorId: {
+    type: Number,
+    required: true
+  },
+
+  show: {
+    type: Boolean,
+    default: true
+  }
+})
+
+const emit = defineEmits([
+  'removeDepiction',
+  'addDepiction'
+])
+
+const store = useStore()
+const dropzoneElement = ref(null)
+
+const observationMoved = computed({
+  get: () => store.getters[GetterNames.GetObservationMoved],
+  set: value => store.commit(MutationNames.SetObservationMoved, value)
+})
+
+const depictionMoved = computed({
+  get: () => store.getters[GetterNames.GetDepictionMoved],
+  set: value => store.commit(MutationNames.SetDepictionMoved, value)
+})
+
+const existObservations = computed(() => props.depictions.length > 0)
+const rowObjectId = computed(() => props.rowObject.observation_object_id || props.rowObject.id)
+const rowObjectType = computed(() => props.rowObject.observation_object_type || props.rowObject.base_class)
+const observationId = computed(() => props.depictions.length && props.depictions[0].depiction_object_id)
+
+const isLoading = ref(false)
+
+function movedDepiction (_) {
+  if (props.depictions.length === 1) {
+    const observation = {
+      descriptor_id: props.descriptorId,
+      type: OBSERVATION_MEDIA,
+      observation_object_type: rowObjectType.value,
+      observation_object_id: rowObjectId.value
+    }
+
+    store.commit(MutationNames.SetIsSaving, true)
 
-      request.finally(() => {
-        this.depictionMoved = undefined
-        this.observationMoved = undefined
-        this.$store.commit(MutationNames.SetIsSaving, false)
+    Observation.create({ observation, extend: ['depictions'] })
+      .then(({ body }) => {
+        store.dispatch(ActionNames.MoveDepiction, {
+          columnIndex: props.columnIndex,
+          rowIndex: props.rowIndex,
+          observationId: body.id
+        })
       })
-    },
+      .catch(() => store.commit(MutationNames.SetIsSaving, false))
+  } else {
+    store.dispatch(ActionNames.MoveDepiction, {
+      columnIndex: props.columnIndex,
+      rowIndex: props.rowIndex,
+      observationId: observationId.value
+    })
+  }
+}
 
-    setObservationDragged (event) {
-      this.depictionMoved = this.depictions[event.oldIndex]
-      this.observationMoved = this.observationId
-    },
+function openInputFile () {
+  dropzoneElement.value.$el.click()
+}
 
-    removeDepiction (depiction) {
-      if (window.confirm('You\'re trying to delete this record. Are you sure want to proceed?')) {
-        this.$store.commit(MutationNames.SetIsSaving, true)
-        Depiction.destroy(depiction.id).then(() => {
-          const index = this.depictions.findIndex(item => item.id === depiction.id)
+function setObservationDragged (event) {
+  depictionMoved.value = props.depictions[event.oldIndex]
+  observationMoved.value = observationId.value
+}
 
-          this.$emit('removeDepiction', index)
-          this.$store.commit(MutationNames.SetIsSaving, false)
-        })
-      }
-    },
-
-    success (file, response) {
-      if (!this.existObservations) {
-        this.$refs.dropzone.setOption('url', this.dropzoneDepiction.url)
-        this.$refs.dropzone.setOption('paramName', this.dropzoneDepiction.paramName)
-      }
-
-      this.$emit('addDepiction', response.base_class === 'Depiction' ? response : response.depictions[0])
-
-      this.$refs.dropzone.removeFile(file)
-      this.isLoading = false
-    },
-
-    sending (file, xhr, formData) {
-      if (this.existObservations) {
-        formData.append('depiction[depiction_object_id]', this.observationId)
-        formData.append('depiction[depiction_object_type]', 'Observation')
-      } else {
-        formData.append('observation[descriptor_id]', this.column.id)
-        formData.append('observation[type]', 'Observation::Media')
-        formData.append('observation[observation_object_id]', this.rowObjectId)
-        formData.append('observation[observation_object_type]', this.rowObjectBaseCassParam)
-        formData.append('extend[]', 'depictions')
-      }
-
-      this.isLoading = true
-    }
+function removeDepiction (depiction) {
+  if (window.confirm('You\'re trying to delete this record. Are you sure want to proceed?')) {
+    store.commit(MutationNames.SetIsSaving, true)
+
+    Depiction.destroy(depiction.id).then(() => {
+      const index = props.depictions.findIndex(item => item.id === depiction.id)
+
+      emit('removeDepiction', index)
+      store.commit(MutationNames.SetIsSaving, false)
+    })
   }
 }
+
+function success (file, response) {
+  if (!existObservations.value) {
+    dropzoneElement.value.setOption('url', dropzoneDepiction.url)
+    dropzoneElement.value.setOption('paramName', dropzoneDepiction.paramName)
+  }
+
+  addDepiction(response.base_class === 'Depiction' ? response : response.depictions[0])
+
+  dropzoneElement.value.removeFile(file)
+  isLoading.value = false
+}
+
+function sending (file, xhr, formData) {
+  if (existObservations.value) {
+    formData.append('depiction[depiction_object_id]', observationId.value)
+    formData.append('depiction[depiction_object_type]', 'Observation')
+  } else {
+    formData.append('observation[descriptor_id]', props.descriptorId)
+    formData.append('observation[type]', OBSERVATION_MEDIA)
+    formData.append('observation[observation_object_id]', rowObjectId.value)
+    formData.append('observation[observation_object_type]', rowObjectType.value)
+    formData.append('extend[]', 'depictions')
+  }
+
+  isLoading.value = true
+}
+
+function addDepiction (depiction) {
+  store.commit(MutationNames.AddDepiction, {
+    columnIndex: props.columnIndex,
+    rowIndex: props.rowIndex,
+    depiction
+  })
+}
+
 </script>
 
 <style scoped>
diff --git a/app/javascript/vue/tasks/observation_matrices/image/components/MatrixTable.vue b/app/javascript/vue/tasks/observation_matrices/image/components/MatrixTable.vue
index 96dc2802fb..b12445593c 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/components/MatrixTable.vue
+++ b/app/javascript/vue/tasks/observation_matrices/image/components/MatrixTable.vue
@@ -20,7 +20,8 @@
       <div class="header-cell">
         <label
           class="header-label cursor-pointer ellipsis"
-          title="OTU depictions">
+          title="OTU depictions"
+        >
           <input
             type="checkbox"
             value="otu"
@@ -79,7 +80,7 @@
         class="observation-cell padding-small edit-cell"
         :show="!filterCell('otu', rowIndex)"
         :depictions="row.objectDepictions || []"
-        @removeDepiction="removeOtuDepiction({ rowIndex, index: $event })"
+        @remove-depiction="removeOtuDepiction({ rowIndex, index: $event })"
       />
       <template
         v-for="(depictions, columnIndex) in row.depictions"
@@ -87,12 +88,13 @@
       >
         <cell-observation
           class="observation-cell padding-small edit-cell full_width"
-          :column="imageColums[columnIndex]"
+          :descriptor-id="imageColums[columnIndex].id"
           :show="!filterCell(columnIndex, rowIndex)"
           :row-object="row.object"
           :depictions="depictions"
-          @addDepiction="addDepiction({ rowIndex, columnIndex, depiction: $event })"
-          @removeDepiction="removeDepiction({ rowIndex, columnIndex, index: $event })"
+          :column-index="columnIndex"
+          :row-index="rowIndex"
+          @remove-depiction="removeDepiction({ rowIndex, columnIndex, index: $event })"
         />
       </template>
     </template>
@@ -167,14 +169,6 @@ export default {
       return this.collapseColumns.includes(cIndex) || this.collapseRows.includes(index)
     },
 
-    addDepiction ({ rowIndex, columnIndex, depiction }) {
-      this.$store.commit(MutationNames.AddDepiction, {
-        rowIndex,
-        columnIndex,
-        depiction
-      })
-    },
-
     removeDepiction ({ rowIndex, columnIndex, index }) {
       this.$store.commit(MutationNames.RemoveDepiction, {
         rowIndex,
diff --git a/app/javascript/vue/tasks/observation_matrices/image/store/actions/actionNames.js b/app/javascript/vue/tasks/observation_matrices/image/store/actions/actionNames.js
index 15e865ff8b..2479235e34 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/store/actions/actionNames.js
+++ b/app/javascript/vue/tasks/observation_matrices/image/store/actions/actionNames.js
@@ -2,7 +2,8 @@ const ActionNames = {
   CreateNewColumn: 'createNewColumn',
   CreateObservation: 'createObservation',
   LoadObservationMatrix: 'loadObservationMatrix',
-  LoadOtuDepictions: 'loadOtuDepictions'
+  LoadOtuDepictions: 'loadOtuDepictions',
+  MoveDepiction: 'moveDepiction'
 }
 
 export default ActionNames
diff --git a/app/javascript/vue/tasks/observation_matrices/image/store/actions/actions.js b/app/javascript/vue/tasks/observation_matrices/image/store/actions/actions.js
index 7f6bfa728c..cc7611406c 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/store/actions/actions.js
+++ b/app/javascript/vue/tasks/observation_matrices/image/store/actions/actions.js
@@ -3,12 +3,14 @@ import createNewColumn from './createNewColumn'
 import createObservation from './createObservation'
 import loadObservationMatrix from './loadObservationMatrix'
 import loadOtuDepictions from './loadOtuDepictions'
+import moveDepiction from './moveDepiction'
 
 const ActionFunctions = {
   [ActionNames.CreateNewColumn]: createNewColumn,
   [ActionNames.CreateObservation]: createObservation,
   [ActionNames.LoadObservationMatrix]: loadObservationMatrix,
-  [ActionNames.LoadOtuDepictions]: loadOtuDepictions
+  [ActionNames.LoadOtuDepictions]: loadOtuDepictions,
+  [ActionNames.MoveDepiction]: moveDepiction
 }
 
 export {
diff --git a/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js b/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
new file mode 100644
index 0000000000..bd20d644d7
--- /dev/null
+++ b/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
@@ -0,0 +1,44 @@
+import { MutationNames } from '../mutations/mutations'
+import { Observation, Depiction } from 'routes/endpoints'
+import { OBSERVATION } from 'constants/index'
+
+export default async ({ state, commit }, { observationId, columnIndex, rowIndex }) => {
+  const {
+    depictionMoved,
+    observationMoved
+  } = state
+
+  const depiction = {
+    id: depictionMoved.id,
+    depiction_object_id: observationId,
+    depiction_object_type: OBSERVATION
+  }
+
+  const observation = {
+    id: observationMoved.id,
+    depictions_attributes: [depiction]
+  }
+
+  commit(MutationNames.SetIsSaving, true)
+
+  const { body } = observation.id
+    ? await Observation.update(observation.id, { observation })
+    : await Depiction.update(depiction.id, { depiction })
+
+  const payload = body.base_class === OBSERVATION
+    ? {
+        ...depictionMoved.value,
+        ...depiction
+      }
+    : body
+
+  commit(MutationNames.AddDepiction, {
+    rowIndex,
+    columnIndex,
+    depiction: payload
+  })
+
+  state.depictionMoved = undefined
+  state.observationMoved = undefined
+  commit(MutationNames.SetIsSaving, false)
+}
diff --git a/app/javascript/vue/tasks/observation_matrices/image/store/mutations/addDepiction.js b/app/javascript/vue/tasks/observation_matrices/image/store/mutations/addDepiction.js
index 2e06377db5..32af0c0cbf 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/store/mutations/addDepiction.js
+++ b/app/javascript/vue/tasks/observation_matrices/image/store/mutations/addDepiction.js
@@ -1,10 +1,7 @@
+import { addToArray } from 'helpers/arrays'
+
 export default (state, { rowIndex, columnIndex, depiction }) => {
   const depictions = state.observationRows[rowIndex].depictions[columnIndex]
-  const index = depictions.findIndex(d => d.id === depiction.id)
 
-  if (index > -1) {
-    depictions[index] = depiction
-  } else {
-    depictions.push(depiction)
-  }
+  addToArray(depictions, depiction)
 }

From b11f7437f3385fb5cc3eeb67146ad6e903f4a3b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Mon, 14 Nov 2022 22:05:09 -0300
Subject: [PATCH 013/160] Update cell observation

---
 .../image/components/CellObservation.vue      |  2 +-
 .../image/store/actions/moveDepiction.js      | 28 +++++--------------
 2 files changed, 8 insertions(+), 22 deletions(-)

diff --git a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
index 936bffa03a..3eb73e99a9 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
+++ b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
@@ -164,7 +164,7 @@ const observationId = computed(() => props.depictions.length && props.depictions
 const isLoading = ref(false)
 
 function movedDepiction (_) {
-  if (props.depictions.length === 1) {
+  if (props.depictions.length === 1 && props.depictions[0].depiction_object_id === observationId.value) {
     const observation = {
       descriptor_id: props.descriptorId,
       type: OBSERVATION_MEDIA,
diff --git a/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js b/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
index bd20d644d7..c0b430e6b7 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
+++ b/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
@@ -1,12 +1,9 @@
 import { MutationNames } from '../mutations/mutations'
-import { Observation, Depiction } from 'routes/endpoints'
+import { Depiction } from 'routes/endpoints'
 import { OBSERVATION } from 'constants/index'
 
 export default async ({ state, commit }, { observationId, columnIndex, rowIndex }) => {
-  const {
-    depictionMoved,
-    observationMoved
-  } = state
+  const { depictionMoved } = state
 
   const depiction = {
     id: depictionMoved.id,
@@ -14,31 +11,20 @@ export default async ({ state, commit }, { observationId, columnIndex, rowIndex
     depiction_object_type: OBSERVATION
   }
 
-  const observation = {
-    id: observationMoved.id,
-    depictions_attributes: [depiction]
-  }
-
   commit(MutationNames.SetIsSaving, true)
 
-  const { body } = observation.id
-    ? await Observation.update(observation.id, { observation })
-    : await Depiction.update(depiction.id, { depiction })
-
-  const payload = body.base_class === OBSERVATION
-    ? {
-        ...depictionMoved.value,
-        ...depiction
-      }
-    : body
+  const { body } = await Depiction.update(depiction.id, { depiction })
 
   commit(MutationNames.AddDepiction, {
     rowIndex,
     columnIndex,
-    depiction: payload
+    depiction: body
   })
 
   state.depictionMoved = undefined
   state.observationMoved = undefined
+
   commit(MutationNames.SetIsSaving, false)
+
+  console.log('Depiction moved')
 }

From 41504b69f3bf71ddf2bd0ccd6489f92c7e11bc65 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 15 Nov 2022 10:37:42 -0600
Subject: [PATCH 014/160] Tune depiction destroy checks

---
 app/models/depiction.rb       | 4 ++--
 spec/models/depiction_spec.rb | 7 ++++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/app/models/depiction.rb b/app/models/depiction.rb
index 75c83fd7eb..5baeeab9bd 100644
--- a/app/models/depiction.rb
+++ b/app/models/depiction.rb
@@ -62,8 +62,8 @@ class Depiction < ApplicationRecord
   validates_presence_of :depiction_object
   validates_uniqueness_of :sled_image_id, scope: [:project_id, :sled_image_x_position, :sled_image_y_position], allow_nil: true, if: Proc.new {|n| !n.sled_image_id.nil?}
 
-  after_update :remove_media_observation2, if: Proc.new {|o| o.depiction_object.type == 'Observation::Media' }
-  after_destroy :remove_media_observation, if: Proc.new {|o| o.depiction_object.type == 'Observation::Media' }
+  after_update :remove_media_observation2, if: Proc.new {|d| d.depiction_object_type == 'Observation' && d.depiction_object.type == 'Observation::Media' }
+  after_destroy :remove_media_observation, if: Proc.new {|d| d.depiction_object_type == 'Observation' && d.depiction_object.type == 'Observation::Media' }
 
   def from_sled?
     !sled_image_id.nil?
diff --git a/spec/models/depiction_spec.rb b/spec/models/depiction_spec.rb
index d0c1c7b9c2..18642efc73 100644
--- a/spec/models/depiction_spec.rb
+++ b/spec/models/depiction_spec.rb
@@ -6,7 +6,7 @@
   let(:specimen) { FactoryBot.create(:valid_specimen) }
 
   specify 'destroying depiction does not destroy related Observation::Media 2 when not last' do
-    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test')) 
+    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test'))
     d = FactoryBot.create(:valid_depiction, depiction_object: o)
 
     FactoryBot.create(:valid_depiction, depiction_object: o)
@@ -16,8 +16,9 @@
   end
 
   specify 'updating depiction destroys related Observation::Media 1 if there are no others' do
-    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test')) 
+    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test'))
     d = FactoryBot.create(:valid_depiction, depiction_object: o)
+
     d.update!(depiction_object: FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test2') ) )
 
     expect {Observation.find(o.id)}.to raise_error ActiveRecord::RecordNotFound
@@ -25,7 +26,7 @@
   end
 
   specify 'destroying depiction destroys related Observation::Media 1' do
-    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test')) 
+    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test'))
     d = FactoryBot.create(:valid_depiction, depiction_object: o)
     d.destroy!
     expect {Observation.find(o.id)}.to raise_error ActiveRecord::RecordNotFound

From 65a340980f0aa047af4cef7ec0966a2057499f57 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Tue, 15 Nov 2022 14:20:19 -0300
Subject: [PATCH 015/160] CHANGELOG amendment [skip ci]

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 36de7a9814..389a209db5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -35,6 +35,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Updated Browse collection object interface [#2297]
 - Reload New source task by pressing New and loading source
 - Updated Ruby gems
+- Updated node packages
 
 ### Fixed
 - Browse nomenclature crashing when taxon name descendants have no cached author year

From 47464b3993898528cd530c5a6ee02006c3657943 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Tue, 15 Nov 2022 14:22:54 -0300
Subject: [PATCH 016/160] CHANGELOG amendment [skip ci]

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 389a209db5..4848efeb00 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3018,7 +3018,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
 
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.5...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.6...development
+[0.29.6]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.5...v0.29.6
 [0.29.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.4...v0.29.5
 [0.29.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.3...v0.29.4
 [0.29.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.2...v0.29.3

From babfe25eaf20a50252a0bebc9c504cdc13ef1cb7 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 15 Nov 2022 11:47:03 -0600
Subject: [PATCH 017/160] Fix tab in castor demo file

---
 .../taxon_names/taxon_names_castor_batch_load.tab               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/batch_load_templates/taxon_names/taxon_names_castor_batch_load.tab b/public/batch_load_templates/taxon_names/taxon_names_castor_batch_load.tab
index 192e4ff145..43cd76047d 100644
--- a/public/batch_load_templates/taxon_names/taxon_names_castor_batch_load.tab
+++ b/public/batch_load_templates/taxon_names/taxon_names_castor_batch_load.tab
@@ -6,6 +6,6 @@ id	taxon_name	parent_id	rank	related_name_id	related_name_nomen_class	name_nomen
 5	eus123	3	species			TaxonNameClassification::Iczn::Unavailable::NotLatin			
 6	fus	4	species						
 7	gus	3	species	5	TaxonNameRelationship::Iczn::Invalidating::Synonym		(Smith, 1920)	https://my.uri/123	Cus nr. gus 22x
-8	hus	4	species	6	TaxonNameRelationship::Iczn::Invalidating::Synonym	(Jones)			
+8	hus	4	species	6	TaxonNameRelationship::Iczn::Invalidating::Synonym		(Jones)			
 9	ius	3	species	5	TaxonNameRelationship::Iczn::Invalidating::Synonym				
 10	jus	3	species	6	TaxonNameRelationship::Iczn::Invalidating::Synonym				my_otu_name_22

From a5254cdcdf3a61119da1e43b89740c9201f96229 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 15 Nov 2022 16:03:12 -0300
Subject: [PATCH 018/160] Fix depiction update object id

---
 .../observation_matrices/image/components/CellObservation.vue   | 2 +-
 app/models/depiction.rb                                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
index 3eb73e99a9..79b6a09632 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
+++ b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
@@ -164,7 +164,7 @@ const observationId = computed(() => props.depictions.length && props.depictions
 const isLoading = ref(false)
 
 function movedDepiction (_) {
-  if (props.depictions.length === 1 && props.depictions[0].depiction_object_id === observationId.value) {
+  if (props.depictions.length === 1 && (depictionMoved.value.depiction_object_id === observationId.value || depictionMoved.value.depiction_object_type !== 'Observation')) {
     const observation = {
       descriptor_id: props.descriptorId,
       type: OBSERVATION_MEDIA,
diff --git a/app/models/depiction.rb b/app/models/depiction.rb
index 5baeeab9bd..39eb77d4d3 100644
--- a/app/models/depiction.rb
+++ b/app/models/depiction.rb
@@ -62,7 +62,7 @@ class Depiction < ApplicationRecord
   validates_presence_of :depiction_object
   validates_uniqueness_of :sled_image_id, scope: [:project_id, :sled_image_x_position, :sled_image_y_position], allow_nil: true, if: Proc.new {|n| !n.sled_image_id.nil?}
 
-  after_update :remove_media_observation2, if: Proc.new {|d| d.depiction_object_type == 'Observation' && d.depiction_object.type == 'Observation::Media' }
+  after_update :remove_media_observation2, if: Proc.new {|d| d.depiction_object_type == 'Observation' && d.depiction_object.type == 'Observation::Media' && d.depiction_object_type_previously_was == 'Observation' }
   after_destroy :remove_media_observation, if: Proc.new {|d| d.depiction_object_type == 'Observation' && d.depiction_object.type == 'Observation::Media' }
 
   def from_sled?

From ad4d829368a0f7623cbd617d2a89d46b7b4f3b93 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 15 Nov 2022 13:37:21 -0600
Subject: [PATCH 019/160] Edge handling for depiction/observation updating

---
 app/models/depiction.rb       |  6 +++---
 spec/models/depiction_spec.rb | 13 +++++++++++++
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/app/models/depiction.rb b/app/models/depiction.rb
index 5baeeab9bd..dce29dfe5e 100644
--- a/app/models/depiction.rb
+++ b/app/models/depiction.rb
@@ -62,7 +62,7 @@ class Depiction < ApplicationRecord
   validates_presence_of :depiction_object
   validates_uniqueness_of :sled_image_id, scope: [:project_id, :sled_image_x_position, :sled_image_y_position], allow_nil: true, if: Proc.new {|n| !n.sled_image_id.nil?}
 
-  after_update :remove_media_observation2, if: Proc.new {|d| d.depiction_object_type == 'Observation' && d.depiction_object.type == 'Observation::Media' }
+  after_update :remove_media_observation2, if: Proc.new {|d| d.depiction_object_type_previously_was == 'Observation' && d.depiction_object.type_was == 'Observation::Media' }
   after_destroy :remove_media_observation, if: Proc.new {|d| d.depiction_object_type == 'Observation' && d.depiction_object.type == 'Observation::Media' }
 
   def from_sled?
@@ -92,8 +92,8 @@ def sled_extraction_path(size = :thumb)
   private
 
   def remove_media_observation2
-    if v = previous_changes['depiction_object_id']
-      o = Observation::Media.find(v[0])
+    if v = depiction_object_id_previously_was
+      o = Observation::Media.find(v)
       if o.depictions.size == 0
         o.destroy!
       end
diff --git a/spec/models/depiction_spec.rb b/spec/models/depiction_spec.rb
index 18642efc73..beb6ed2b8b 100644
--- a/spec/models/depiction_spec.rb
+++ b/spec/models/depiction_spec.rb
@@ -25,6 +25,19 @@
     expect(Depiction.find(d.id).id).to be_truthy
   end
 
+  specify 'updating from OTU to Observation' do
+    o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test'))
+    d1 = FactoryBot.create(:valid_depiction, depiction_object: o)
+
+    otu = Otu.create!(name: 'Foo') 
+    d2 = FactoryBot.create(:valid_depiction, depiction_object: otu)
+
+    d2.update!(depiction_object: o)
+
+    expect(d2.depiction_object).to eq(o)
+    expect(otu.reload).to be_truthy
+  end
+
   specify 'destroying depiction destroys related Observation::Media 1' do
     o = FactoryBot.create(:valid_observation, type: 'Observation::Media', descriptor: Descriptor::Media.create!(name: 'test'))
     d = FactoryBot.create(:valid_depiction, depiction_object: o)

From c3a27f947607054187eff405493e98925211b505 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 15 Nov 2022 14:05:39 -0600
Subject: [PATCH 020/160] Skip ImageMagic processing errors

---
 lib/tasks/maintenance/images.rake | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/tasks/maintenance/images.rake b/lib/tasks/maintenance/images.rake
index d4ecbc400d..1757ad27d8 100644
--- a/lib/tasks/maintenance/images.rake
+++ b/lib/tasks/maintenance/images.rake
@@ -5,6 +5,7 @@ namespace :tw do
 
     namespace :images do
 
+      # rake tw:maintenance:images:recalculate_sqed_boundaries project_id=20 id_start=1 id_end=999999
       desc 'Re-calculate the boundaries for Sqed depictions'
       task recalculate_sqed_boundaries: [:environment, :project_id, :id_start, :id_end] do |t|
         project_id = ENV['project_id']
@@ -29,12 +30,15 @@ namespace :tw do
             begin
               print Rainbow("Writing\n").bold
               group.each do |o|
-                o.preprocess
                 print " id: #{o.id}\n"
+                o.preprocess
                 i += 1
               end
               print Rainbow("...saved.\n").bold
 
+            rescue Magick::ImageMagickError => e
+              puts Rainbow("Error: #{e}. ImageMagick processing error. Current batch of 3 records not written, skipping.").red.bold
+              next
             rescue RuntimeError => e
               puts Rainbow("Error: #{e}. Current batch of 3 records not written, skipping.").red.bold
               next

From c45829dc7c90b951ef3f7655d116370439142a84 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 15 Nov 2022 17:22:16 -0300
Subject: [PATCH 021/160] Fix draggable depictions

---
 .../image/components/CellObservation.vue      | 16 +++++++++----
 .../image/store/actions/moveDepiction.js      | 24 +++++++++----------
 2 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
index 79b6a09632..37ab69afee 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
+++ b/app/javascript/vue/tasks/observation_matrices/image/components/CellObservation.vue
@@ -159,12 +159,18 @@ const depictionMoved = computed({
 const existObservations = computed(() => props.depictions.length > 0)
 const rowObjectId = computed(() => props.rowObject.observation_object_id || props.rowObject.id)
 const rowObjectType = computed(() => props.rowObject.observation_object_type || props.rowObject.base_class)
-const observationId = computed(() => props.depictions.length && props.depictions[0].depiction_object_id)
+const observationId = computed(() => {
+  const depictions = props.depictions
+
+  return depictionMoved.value
+    ? depictions.find(d => d.depiction_object_id !== depictionMoved.value.depiction_object_id)?.depiction_object_id
+    : depictions[0].depiction_object_id
+})
 
 const isLoading = ref(false)
 
 function movedDepiction (_) {
-  if (props.depictions.length === 1 && (depictionMoved.value.depiction_object_id === observationId.value || depictionMoved.value.depiction_object_type !== 'Observation')) {
+  if (props.depictions.length === 1) {
     const observation = {
       descriptor_id: props.descriptorId,
       type: OBSERVATION_MEDIA,
@@ -174,7 +180,7 @@ function movedDepiction (_) {
 
     store.commit(MutationNames.SetIsSaving, true)
 
-    Observation.create({ observation, extend: ['depictions'] })
+    Observation.create({ observation })
       .then(({ body }) => {
         store.dispatch(ActionNames.MoveDepiction, {
           columnIndex: props.columnIndex,
@@ -182,7 +188,9 @@ function movedDepiction (_) {
           observationId: body.id
         })
       })
-      .catch(() => store.commit(MutationNames.SetIsSaving, false))
+      .catch(() =>
+        store.commit(MutationNames.SetIsSaving, false)
+      )
   } else {
     store.dispatch(ActionNames.MoveDepiction, {
       columnIndex: props.columnIndex,
diff --git a/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js b/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
index c0b430e6b7..f732fc0bb5 100644
--- a/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
+++ b/app/javascript/vue/tasks/observation_matrices/image/store/actions/moveDepiction.js
@@ -13,18 +13,16 @@ export default async ({ state, commit }, { observationId, columnIndex, rowIndex
 
   commit(MutationNames.SetIsSaving, true)
 
-  const { body } = await Depiction.update(depiction.id, { depiction })
-
-  commit(MutationNames.AddDepiction, {
-    rowIndex,
-    columnIndex,
-    depiction: body
+  Depiction.update(depiction.id, { depiction }).then(({ body }) => {
+    commit(MutationNames.AddDepiction, {
+      rowIndex,
+      columnIndex,
+      depiction: body
+    })
+  }).finally(_ => {
+    state.depictionMoved = undefined
+    state.observationMoved = undefined
+
+    commit(MutationNames.SetIsSaving, false)
   })
-
-  state.depictionMoved = undefined
-  state.observationMoved = undefined
-
-  commit(MutationNames.SetIsSaving, false)
-
-  console.log('Depiction moved')
 }

From 2b3e9fa4048d6b9701071f5574df865b5fe87503 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Tue, 15 Nov 2022 18:07:27 -0300
Subject: [PATCH 022/160] Fix #3188: Enable HEIC enconding

---
 .github/workflows/build.yml | 2 +-
 Dockerfile.base             | 2 +-
 exe/install-imagemagick7.sh | 1 +
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 3877664529..76c9458df8 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -66,7 +66,7 @@ jobs:
       uses: actions/cache@v3
       with:
         path: vendor/bundle
-        key: ${{ runner.os }}-gems-rev6-${{ hashFiles('**/Gemfile.lock') }}
+        key: ${{ runner.os }}-gems-rev6-${{ hashFiles('**/Gemfile.lock', 'exe/install-imagemagick7.sh') }}
 
     - name: Set up Node 16 LTS
       uses: actions/setup-node@v3
diff --git a/Dockerfile.base b/Dockerfile.base
index 856c8c0256..d2595b8a8d 100644
--- a/Dockerfile.base
+++ b/Dockerfile.base
@@ -45,4 +45,4 @@ COPY --from=imagemagick /etc/ImageMagick-6 /usr/local/etc/ImageMagick-7
 
 # Set up ImageMagick
 RUN sed -i 's/name="disk" value="1GiB"/name="disk" value="8GiB"/' /usr/local/etc/ImageMagick-7/policy.xml && \
-      identify -list resource | grep Disk | grep 8GiB && identify --version | grep heic # Confirm HEIC support and that 8GB disk setting is active
+      identify -list resource | grep Disk | grep 8GiB && magick -list format | grep "HEIC      rw+" # Confirm HEIC support and that 8GB disk setting is active
diff --git a/exe/install-imagemagick7.sh b/exe/install-imagemagick7.sh
index bd0f654401..07bdaa3396 100755
--- a/exe/install-imagemagick7.sh
+++ b/exe/install-imagemagick7.sh
@@ -2,6 +2,7 @@
 set -e
 set -x
 apt-get update
+apt-get install -y libx265-dev
 apt-get build-dep -y libmagickcore-dev
 
 cd /usr/src/

From 9b203b63337a41f587a892205ff1ef5bb2092703 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Tue, 15 Nov 2022 18:12:13 -0300
Subject: [PATCH 023/160] CHANGELOG update [skip ci]

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4848efeb00..1a0714cb4e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,10 +14,13 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Media observations removed if they have no more depictions via updates
 - Citation link in Biological association panel on Browse OTU
 - Type relationship text/rendering is inverted in New taxon name [#3182]
+- Sqed processing failing to encode HEIC images [#3188]
 
 ### Changed
 - Refactored observation cell component for Image matrix
 
+[#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
+[#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
 
 ## [0.29.6] - 2022-11-08

From 26c3f0a3a66210ea90541e3456fde715a314211d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 15 Nov 2022 18:32:43 -0300
Subject: [PATCH 024/160] Add edit parameter

---
 .../radials/object/components/observation_matrices/main.vue   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/components/radials/object/components/observation_matrices/main.vue b/app/javascript/vue/components/radials/object/components/observation_matrices/main.vue
index a82f33cf38..33d1aba320 100644
--- a/app/javascript/vue/components/radials/object/components/observation_matrices/main.vue
+++ b/app/javascript/vue/components/radials/object/components/observation_matrices/main.vue
@@ -195,11 +195,11 @@ export default {
 
     openImageMatrix (observationMatrixId) {
       if (this.alreadyInCurrentMatrix.length) {
-        window.open(`/tasks/matrix_image/matrix_image/index?observation_matrix_id=${this.selectedMatrix.id}&row_filter=${this.getRowId(observationMatrixId)}`, '_blank')
+        window.open(`/tasks/matrix_image/matrix_image/index?observation_matrix_id=${this.selectedMatrix.id}&row_filter=${this.getRowId(observationMatrixId)}&edit=true`, '_blank')
         this.$emit('close')
       } else {
         this.createRow().then(() => {
-          window.open(`/tasks/matrix_image/matrix_image/index?observation_matrix_id=${this.selectedMatrix.id}&row_filter=${this.getRowId(observationMatrixId)}`, '_blank')
+          window.open(`/tasks/matrix_image/matrix_image/index?observation_matrix_id=${this.selectedMatrix.id}&row_filter=${this.getRowId(observationMatrixId)}&edit=true`, '_blank')
           this.$emit('close')
         })
       }

From 298193737364e61ea07d14143ca0d788c5d90486 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 15 Nov 2022 16:52:24 -0600
Subject: [PATCH 025/160] SqedDepiction filter, stubbing TODO map for filter
 update

---
 .../collection_objects_controller.rb          |   2 +-
 .../breakdown/sqed_depiction_controller.rb    |  29 ++++-
 .../sqed_depiction/todo_map.html.erb          |   2 +-
 .../sqed_depiction/todo_map.json.jbuilder     |   4 +
 lib/queries/collection_object/filter.rb       |   1 -
 lib/queries/sqed_depiction/filter.rb          | 108 ++++++++++++++++++
 6 files changed, 142 insertions(+), 4 deletions(-)
 create mode 100644 app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
 create mode 100644 lib/queries/sqed_depiction/filter.rb

diff --git a/app/controllers/collection_objects_controller.rb b/app/controllers/collection_objects_controller.rb
index a29d75d6c4..51edbfac85 100644
--- a/app/controllers/collection_objects_controller.rb
+++ b/app/controllers/collection_objects_controller.rb
@@ -21,7 +21,7 @@ def index
         render '/shared/data/all/index'
       end
       format.json {
-        # see app/controllers/collection_objects/filter_params.rb
+        # see app/controllers/collection_objects50/filter_params.rb
         @collection_objects = filtered_collection_objects.order('collection_objects.id').page(params[:page]).per(params[:per] || 50)
       }
     end
diff --git a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
index 27c55ad8f2..dad6641c19 100644
--- a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
+++ b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
@@ -2,11 +2,18 @@ class Tasks::Accessions::Breakdown::SqedDepictionController < ApplicationControl
   include TaskControllerConfiguration
 
   before_action :set_sqed_depiction, except: [:todo_map]
+  after_action -> { set_pagination_headers(:sqed_depictions) }, only: [:todo_map], if: :json_request?
 
   # /tasks/accessions/breakdown/sqed_depiction/todo_map
   def todo_map
     SqedDepiction.clear_stale_progress
-    @sqed_depictions = SqedDepiction.where(project_id: sessions_current_project_id).order(:id).page(params[:page]).per(100)
+    @sqed_depictions = 
+      ::Queries::SqedDepiction::Filter.new(filter_params).all.where(project_id: sessions_current_project_id)
+      .order(:id).page(params[:page]).per(50)
+    respond_to do |format|
+      format.html {}
+      format.json {}
+    end
   end
 
   # GET /tasks/accession/breakdown/depiction/:id # id is a collection_object_id !!
@@ -62,4 +69,24 @@ def set_sqed_depiction
     # @sqed_depiction.preprocess
   end
 
+  private
+
+  def filter_params
+    a = params.permit(
+      ::Queries::SqedDepiction::Filter::COLLECTION_OBJECT_FILTER_PARAMS,
+      :recent,
+      :user_date_end,
+      :user_date_start,
+      :user_id,
+      :user_target,
+    )
+
+    # TODO: check user_id: []
+
+    a[:user_id] = params[:user_id] if params[:user_id] && is_project_member_by_id(params[:user_id], sessions_current_project_id) # double check vs. setting project_id from API
+    a
+  end
+
+
+
 end
diff --git a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb
index 36fff1174c..b42fb6a107 100644
--- a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb
+++ b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb
@@ -2,7 +2,7 @@
 
 <p> Overview: 
 <%= sqed_done_tag(sessions_current_project_id) -%> done. <%= sqed_not_done_tag(sessions_current_project_id) -%> remaining. <br>
-<%= page_entries_info @sqed_depictions %>.  <%= SqedDepiction.where(project_id: sessions_current_project_id).where.not(in_progress: nil).count(:all) -%> in progress.</p>
+<%= page_entries_info @sqed_depictions %>. <%= SqedDepiction.where(project_id: sessions_current_project_id).where.not(in_progress: nil).count(:all) -%> in progress.</p>
 
 <fieldset title="Navigate">
   <legend> Navigate </legend>
diff --git a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
new file mode 100644
index 0000000000..d08f125e8d
--- /dev/null
+++ b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
@@ -0,0 +1,4 @@
+json.svg_map sqed_waxy_layout(@sqed_depictions)
+json.svg_legend sqed_waxy_legend_tag
+json.navigation {}
+json.metadata { }
diff --git a/lib/queries/collection_object/filter.rb b/lib/queries/collection_object/filter.rb
index deaf1eaef8..ffe89295f7 100644
--- a/lib/queries/collection_object/filter.rb
+++ b/lib/queries/collection_object/filter.rb
@@ -12,7 +12,6 @@ class Filter < Queries::Query
 
       include Queries::Concerns::Tags
       include Queries::Concerns::Users
-      include Queries::Concerns::Identifiers
       include Queries::Concerns::Notes
       include Queries::Concerns::DataAttributes
 
diff --git a/lib/queries/sqed_depiction/filter.rb b/lib/queries/sqed_depiction/filter.rb
new file mode 100644
index 0000000000..2ab975bae0
--- /dev/null
+++ b/lib/queries/sqed_depiction/filter.rb
@@ -0,0 +1,108 @@
+module Queries
+  module SqedDepiction
+    class Filter < Queries::Query
+      include Queries::Helpers
+      include Queries::Concerns::Users
+
+      COLLECTION_OBJECT_FILTER_PARAMS = %w{
+       collecting_event
+       taxon_determinations
+       with_buffered_determinations
+       with_buffered_collecting_event
+       with_buffered_other_labels
+      }  
+
+      attr_accessor :collection_object_filter_params
+
+      attr_accessor :recent
+
+      def initialize(params)
+        @recent = params[:recent]
+        @collection_object_filter_params = params.permit(COLLECTION_OBJECT_FILTER_PARAMS).to_h.select{|k,v| COLLECTION_OBJECT_FILTER_PARAMS.include?(k) ? k : nil}
+      
+        set_identifier(params)
+        set_user_dates(params)
+      end
+
+      # @return [Arel::Table]
+      def table
+        ::SqedDepiction.arel_table
+      end
+
+      def base_query
+        ::SqedDepiction.select('sqed_depiction.*')
+      end
+
+      def collection_object_query_facet
+        q = ::Queries::CollectionObject::Filter.new(collection_object_filter_params).all
+        ::SqedDepiction.joins(:collection_object).where(collection_objects: q)  
+      end
+
+      # @return [ActiveRecord::Relation]
+      def and_clauses
+        clauses = base_and_clauses
+
+        return nil if clauses.empty?
+
+        a = clauses.shift
+        clauses.each do |b|
+          a = a.and(b)
+        end
+        a
+      end
+
+      # @return [Array]
+      def base_and_clauses
+        clauses = []
+        clauses += [ ]
+        clauses.compact!
+        clauses
+      end
+
+      def base_merge_clauses
+        clauses = []
+
+        clauses += [
+          created_updated_facet,  # See Queries::Concerns::Users
+          identifiers_facet,
+          collection_object_query_facet,
+        ]
+
+        clauses.compact!
+        clauses
+      end
+
+      # @return [ActiveRecord::Relation]
+      def merge_clauses
+        clauses = base_merge_clauses
+        return nil if clauses.empty?
+        a = clauses.shift
+        clauses.each do |b|
+          a = a.merge(b)
+        end
+        a
+      end
+
+      # @return [ActiveRecord::Relation]
+      def all
+        a = and_clauses
+        b = merge_clauses
+        # q = nil
+        if a && b
+          q = b.where(a)
+        elsif a
+          q = ::SqedDepiction.where(a)
+        elsif b
+          q = b
+        else
+          q = ::SqedDepiction.all
+        end
+
+        # TODO: needs to go, orders mess with chaining.
+        q = q.order(updated_at: :desc) if recent
+        q
+      end
+    end
+
+  end
+end

From 1115d163604235258ea0d1b887be9c2b8cea045b Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 15 Nov 2022 17:18:40 -0600
Subject: [PATCH 026/160] Add navigation params to response

---
 .../breakdown/sqed_depiction_controller.rb    |  6 +++---
 .../sqed_depiction/todo_map.json.jbuilder     | 20 +++++++++++++++++--
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
index dad6641c19..28011d6434 100644
--- a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
+++ b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
@@ -7,9 +7,9 @@ class Tasks::Accessions::Breakdown::SqedDepictionController < ApplicationControl
   # /tasks/accessions/breakdown/sqed_depiction/todo_map
   def todo_map
     SqedDepiction.clear_stale_progress
-    @sqed_depictions = 
-      ::Queries::SqedDepiction::Filter.new(filter_params).all.where(project_id: sessions_current_project_id)
-      .order(:id).page(params[:page]).per(50)
+    @base_query = ::Queries::SqedDepiction::Filter.new(filter_params).all.where(project_id: sessions_current_project_id)
+      .order(:id)
+    @sqed_depictions = @base_query.page(params[:page]).per(50)
     respond_to do |format|
       format.html {}
       format.json {}
diff --git a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
index d08f125e8d..52394445f6 100644
--- a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
+++ b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
@@ -1,4 +1,20 @@
 json.svg_map sqed_waxy_layout(@sqed_depictions)
 json.svg_legend sqed_waxy_legend_tag
-json.navigation {}
-json.metadata { }
+json.navigation do
+  json.global do
+    json.first_with_data SqedDepiction.where(project_id: sessions_current_project_id).with_collection_object_data.first&.id
+    json.last_with_data SqedDepiction.with_collection_object_data.where(project_id: sessions_current_project_id).last&.id
+    json.last_without_data SqedDepiction.where(project_id: sessions_current_project_id).without_collection_object_data.last&.id
+    json.first_without_data SqedDepiction.where(project_id: sessions_current_project_id).without_collection_object_data.first&.id
+    json.last_by_user SqedDepiction.joins(:collection_object).where(project_id: sessions_current_project_id, updated_by_id: sessions_current_user_id).with_collection_object_data.order('collection_objects.updated_at').first&.id
+  end
+  json.filtered do
+    json.first_with_data @base_query.with_collection_object_data.first&.id
+    json.last_with_data @base_query.with_collection_object_data.last&.id
+    json.last_without_data @base_query.without_collection_object_data.last&.id
+    json.first_without_data @base_query.without_collection_object_data.first&.id
+    json.last_by_user @base_query.joins(:collection_object).where(updated_by_id: sessions_current_user_id).with_collection_object_data.order('collection_objects.updated_at').first&.id
+  end
+end
+
+

From c45466fb2520ba08850034c4164abf12e8516d8b Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 15 Nov 2022 19:43:55 -0600
Subject: [PATCH 027/160] Fix hours ago radial graph

---
 app/views/administration/_users_past_day.html.erb | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/app/views/administration/_users_past_day.html.erb b/app/views/administration/_users_past_day.html.erb
index ba4a2b6266..0669299989 100644
--- a/app/views/administration/_users_past_day.html.erb
+++ b/app/views/administration/_users_past_day.html.erb
@@ -1,7 +1,7 @@
 <div class="panel content">
   <h2> Activity of past 24 hours</h2>
 
-  <% d = User.where('last_seen_at > ?', 1.day.ago).group_by_hour_of_day(:last_seen_at, format: "%H").count.sort.collect{|a,b| b} %><br>
+<% d = User.where('last_seen_at > ?', 1.day.ago).order(:last_seen_at).pluck(:last_seen_at).collect{|t| ((Time.now - t) / 3600).to_i  }.inject(Hash.new(0)){|hsh, v| hsh[v] += 1; hsh} %><br>
 
   <div style="height: 280px; width: 420px;">
     <canvas id="myChart"></canvas>
@@ -14,10 +14,10 @@
     type: 'polarArea',
 
     data:  {
-      labels: [<%= (1..24).collect{|t| ('"' + t.to_s + '"').html_safe}.join(', ').html_safe %>],
+      labels: [<%= (0..23).collect{|t| ('"' + t.to_s + '"').html_safe}.join(', ').html_safe %>],
       datasets: [{
         label: 'Users in past 24 hours',
-        data: <%= d %> ,
+        data: <%=  (0..23).collect{|h| d[h] || 0} %> ,
         backgroundColor: [
           'rgb(250, 250, 110)',
           'rgb(228, 245, 112)',
@@ -46,6 +46,14 @@
       }]
     },
     options: {
+      scales: {
+        r: {
+         ticks: {
+           stepSize: 2.0
+          }
+        }
+      },
+
       responsibe: true,
       maintainAspectRatio: false,
       plugins: {

From ba06564b5686bc09fd840b62c9255cf3bb29f139 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 16 Nov 2022 12:51:48 -0300
Subject: [PATCH 028/160] Update packages

---
 package-lock.json | 529 +++++++++++++++++++++++-----------------------
 package.json      |  26 +--
 2 files changed, 279 insertions(+), 276 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index c888fd7f77..8399ecc621 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8,14 +8,14 @@
       "name": "app",
       "version": "0.1.0",
       "dependencies": {
-        "@geoman-io/leaflet-geoman-free": "^2.13.0",
+        "@geoman-io/leaflet-geoman-free": "^2.13.1",
         "@ibm/plex": "^6.1.1",
         "@sfgrp/sled": "^1.0.3",
         "@sfgrp/svg-radial-menu": "^1.0.7",
         "axios": "^1.1.3",
-        "chart.js": "^3.9.1",
+        "chart.js": "^4.0.1",
         "d3": "^7.6.1",
-        "dompurify": "^2.4.0",
+        "dompurify": "^2.4.1",
         "easymde": "^2.18.0",
         "exif-js": "^2.3.0",
         "json2csv": "^5.0.7",
@@ -26,7 +26,7 @@
         "qs": "^6.11.0",
         "shakapacker": "6.5.4",
         "v-hotkey": "^0.9.0",
-        "vue": "^3.2.41",
+        "vue": "^3.2.45",
         "vue-handy-scroll": "^3.0.1",
         "vue-hotkeys": "0.0.1",
         "vue-tippy": "^6.0.0-alpha.58",
@@ -36,39 +36,39 @@
       },
       "devDependencies": {
         "@babel/core": "^7.19.3",
-        "@babel/plugin-transform-runtime": "^7.19.1",
+        "@babel/plugin-transform-runtime": "^7.19.6",
         "@babel/preset-env": "^7.19.3",
         "@babel/runtime": "^7.19.0",
-        "@vue/compiler-sfc": "^3.2.41",
+        "@vue/compiler-sfc": "^3.2.45",
         "babel-loader": "^8.2.5",
         "compression-webpack-plugin": "^10.0.0",
-        "css-loader": "^6.7.1",
+        "css-loader": "^6.7.2",
         "css-minimizer-webpack-plugin": "^4.2.2",
         "eslint": "^8.27.0",
         "eslint-config-standard": "^17.0.0",
         "eslint-plugin-import": "^2.26.0",
-        "eslint-plugin-n": "^15.5.0",
+        "eslint-plugin-n": "^15.5.1",
         "eslint-plugin-node": "^11.1.0",
         "eslint-plugin-promise": "^6.1.1",
         "eslint-plugin-standard": "^4.1.0",
         "eslint-plugin-vue": "^9.7.0",
         "mini-css-extract-plugin": "^2.6.1",
-        "postcss": "^8.4.18",
+        "postcss": "^8.4.19",
         "postcss-flexbugs-fixes": "^5.0.2",
         "postcss-import": "^15.0.0",
         "postcss-loader": "^7.0.1",
-        "postcss-preset-env": "^7.8.2",
+        "postcss-preset-env": "^7.8.3",
         "raw-loader": "^4.0.2",
         "resolve-url-loader": "^5.0.0",
-        "sass": "^1.56.0",
-        "sass-loader": "^13.1.0",
+        "sass": "^1.56.1",
+        "sass-loader": "^13.2.0",
         "style-loader": "^3.3.1",
         "stylus": "^0.59.0",
         "stylus-loader": "^7.1.0",
         "terser-webpack-plugin": "^5.3.6",
         "url": "^0.11.0",
         "vue-loader": "^17.0.1",
-        "webpack": "^5.74.0",
+        "webpack": "^5.75.0",
         "webpack-assets-manifest": "^5.1.0",
         "webpack-cli": "^4.10.0",
         "webpack-dev-server": "^4.11.1",
@@ -1319,9 +1319,9 @@
       }
     },
     "node_modules/@babel/plugin-transform-runtime": {
-      "version": "7.19.1",
-      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-runtime/-/plugin-transform-runtime-7.19.1.tgz",
-      "integrity": "sha512-2nJjTUFIzBMP/f/miLxEK9vxwW/KUXsdvN4sR//TmuDhe6yU2h57WmIOE12Gng3MDP/xpjUV/ToZRdcf8Yj4fA==",
+      "version": "7.19.6",
+      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-runtime/-/plugin-transform-runtime-7.19.6.tgz",
+      "integrity": "sha512-PRH37lz4JU156lYFW1p8OxE5i7d6Sl/zV58ooyr+q1J1lnQPyg5tIiXlIwNVhJaY4W3TmOtdc8jqdXQcB1v5Yw==",
       "dependencies": {
         "@babel/helper-module-imports": "^7.18.6",
         "@babel/helper-plugin-utils": "^7.19.0",
@@ -1925,9 +1925,9 @@
       }
     },
     "node_modules/@geoman-io/leaflet-geoman-free": {
-      "version": "2.13.0",
-      "resolved": "https://registry.npmjs.org/@geoman-io/leaflet-geoman-free/-/leaflet-geoman-free-2.13.0.tgz",
-      "integrity": "sha512-8uVVcRSAgZLQPfaEIAGitZEoG1v++tmPJlJYVCbGx7FbJYP9jmErsamECO0dz4eMkWLusIaEDgADY9WzAapcEQ==",
+      "version": "2.13.1",
+      "resolved": "https://registry.npmjs.org/@geoman-io/leaflet-geoman-free/-/leaflet-geoman-free-2.13.1.tgz",
+      "integrity": "sha512-csTmg0JJegXRfwGpNXQ9wy1Y1wha8AcrxhvaVFGm3xrhpPG8l3wouMZvO91PN8ZthG3xpZtfDnUQF+7Pm4mwXQ==",
       "dependencies": {
         "@turf/boolean-contains": "^6.5.0",
         "@turf/kinks": "^6.5.0",
@@ -2696,36 +2696,36 @@
       "dev": true
     },
     "node_modules/@vue/compiler-core": {
-      "version": "3.2.41",
-      "resolved": "https://registry.npmjs.org/@vue/compiler-core/-/compiler-core-3.2.41.tgz",
-      "integrity": "sha512-oA4mH6SA78DT+96/nsi4p9DX97PHcNROxs51lYk7gb9Z4BPKQ3Mh+BLn6CQZBw857Iuhu28BfMSRHAlPvD4vlw==",
+      "version": "3.2.45",
+      "resolved": "https://registry.npmjs.org/@vue/compiler-core/-/compiler-core-3.2.45.tgz",
+      "integrity": "sha512-rcMj7H+PYe5wBV3iYeUgbCglC+pbpN8hBLTJvRiK2eKQiWqu+fG9F+8sW99JdL4LQi7Re178UOxn09puSXvn4A==",
       "dependencies": {
         "@babel/parser": "^7.16.4",
-        "@vue/shared": "3.2.41",
+        "@vue/shared": "3.2.45",
         "estree-walker": "^2.0.2",
         "source-map": "^0.6.1"
       }
     },
     "node_modules/@vue/compiler-dom": {
-      "version": "3.2.41",
-      "resolved": "https://registry.npmjs.org/@vue/compiler-dom/-/compiler-dom-3.2.41.tgz",
-      "integrity": "sha512-xe5TbbIsonjENxJsYRbDJvthzqxLNk+tb3d/c47zgREDa/PCp6/Y4gC/skM4H6PIuX5DAxm7fFJdbjjUH2QTMw==",
+      "version": "3.2.45",
+      "resolved": "https://registry.npmjs.org/@vue/compiler-dom/-/compiler-dom-3.2.45.tgz",
+      "integrity": "sha512-tyYeUEuKqqZO137WrZkpwfPCdiiIeXYCcJ8L4gWz9vqaxzIQRccTSwSWZ/Axx5YR2z+LvpUbmPNXxuBU45lyRw==",
       "dependencies": {
-        "@vue/compiler-core": "3.2.41",
-        "@vue/shared": "3.2.41"
+        "@vue/compiler-core": "3.2.45",
+        "@vue/shared": "3.2.45"
       }
     },
     "node_modules/@vue/compiler-sfc": {
-      "version": "3.2.41",
-      "resolved": "https://registry.npmjs.org/@vue/compiler-sfc/-/compiler-sfc-3.2.41.tgz",
-      "integrity": "sha512-+1P2m5kxOeaxVmJNXnBskAn3BenbTmbxBxWOtBq3mQTCokIreuMULFantBUclP0+KnzNCMOvcnKinqQZmiOF8w==",
+      "version": "3.2.45",
+      "resolved": "https://registry.npmjs.org/@vue/compiler-sfc/-/compiler-sfc-3.2.45.tgz",
+      "integrity": "sha512-1jXDuWah1ggsnSAOGsec8cFjT/K6TMZ0sPL3o3d84Ft2AYZi2jWJgRMjw4iaK0rBfA89L5gw427H4n1RZQBu6Q==",
       "dependencies": {
         "@babel/parser": "^7.16.4",
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-        "@vue/compiler-dom": "3.2.41",
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-          "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.7.tgz",
-          "integrity": "sha512-QlYTucUYOews+WeEujDoEGziz4K6c47V/Bd+LjSSYcA94p+DmINdf7ncaUinThfvZyu13lN9OY1XDxt8C0Tw0g==",
+          "version": "7.3.8",
+          "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz",
+          "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==",
           "dev": true,
           "requires": {
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@@ -14604,9 +14607,9 @@
       "dev": true
     },
     "cssdb": {
-      "version": "7.0.1",
-      "resolved": "https://registry.npmjs.org/cssdb/-/cssdb-7.0.1.tgz",
-      "integrity": "sha512-pT3nzyGM78poCKLAEy2zWIVX2hikq6dIrjuZzLV98MumBg+xMTNYfHx7paUlfiRTgg91O/vR889CIf+qiv79Rw==",
+      "version": "7.1.0",
+      "resolved": "https://registry.npmjs.org/cssdb/-/cssdb-7.1.0.tgz",
+      "integrity": "sha512-Sd99PrFgx28ez4GHu8yoQIufc/70h9oYowDf4EjeIKi8mac9whxRjhM3IaMr6EllP6KKKWtJrMfN6C7T9tIWvQ==",
       "dev": true
     },
     "cssesc": {
@@ -15083,9 +15086,9 @@
       }
     },
     "dompurify": {
-      "version": "2.4.0",
-      "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-2.4.0.tgz",
-      "integrity": "sha512-Be9tbQMZds4a3C6xTmz68NlMfeONA//4dOavl/1rNw50E+/QO0KVpbcU0PcaW0nsQxurXls9ZocqFxk8R2mWEA=="
+      "version": "2.4.1",
+      "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-2.4.1.tgz",
+      "integrity": "sha512-ewwFzHzrrneRjxzmK6oVz/rZn9VWspGFRDb4/rRtIsM1n36t9AKma/ye8syCpcw+XJ25kOK/hOG7t1j2I2yBqA=="
     },
     "domutils": {
       "version": "2.8.0",
@@ -15472,25 +15475,25 @@
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     },
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-      "version": "15.5.0",
-      "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.5.0.tgz",
-      "integrity": "sha512-VCqQiZDpdm1Q9grnvy+XsENZoXDgTLqPHRQwgl9qFNNgTKR4YEnQOMN0pFB/9TbmrQ88jdeTnqTcNwRvjqMOtg==",
+      "version": "15.5.1",
+      "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.5.1.tgz",
+      "integrity": "sha512-kAd+xhZm7brHoFLzKLB7/FGRFJNg/srmv67mqb7tto22rpr4wv/LV6RuXzAfv3jbab7+k1wi42PsIhGviywaaw==",
       "dev": true,
       "requires": {
         "builtins": "^5.0.1",
         "eslint-plugin-es": "^4.1.0",
         "eslint-utils": "^3.0.0",
         "ignore": "^5.1.1",
-        "is-core-module": "^2.10.0",
+        "is-core-module": "^2.11.0",
         "minimatch": "^3.1.2",
         "resolve": "^1.22.1",
-        "semver": "^7.3.7"
+        "semver": "^7.3.8"
       },
       "dependencies": {
         "semver": {
-          "version": "7.3.7",
-          "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.7.tgz",
-          "integrity": "sha512-QlYTucUYOews+WeEujDoEGziz4K6c47V/Bd+LjSSYcA94p+DmINdf7ncaUinThfvZyu13lN9OY1XDxt8C0Tw0g==",
+          "version": "7.3.8",
+          "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz",
+          "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==",
           "dev": true,
           "requires": {
             "lru-cache": "^6.0.0"
@@ -16364,9 +16367,9 @@
       "dev": true
     },
     "is-core-module": {
-      "version": "2.10.0",
-      "resolved": "https://registry.npmjs.org/is-core-module/-/is-core-module-2.10.0.tgz",
-      "integrity": "sha512-Erxj2n/LDAZ7H8WNJXd9tw38GYM3dv8rk8Zcs+jJuxYTW7sozH+SS8NtrSjVL1/vpLvWi1hxy96IzjJ3EHTJJg==",
+      "version": "2.11.0",
+      "resolved": "https://registry.npmjs.org/is-core-module/-/is-core-module-2.11.0.tgz",
+      "integrity": "sha512-RRjxlvLDkD1YJwDbroBHMb+cukurkDWNyHx7D3oNB5x9rb5ogcksMC5wHCadcXoo67gVr/+3GFySh3134zi6rw==",
       "requires": {
         "has": "^1.0.3"
       }
@@ -16732,9 +16735,9 @@
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     },
     "loader-utils": {
-      "version": "2.0.2",
-      "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.2.tgz",
-      "integrity": "sha512-TM57VeHptv569d/GKh6TAYdzKblwDNiumOdkFnejjD0XwTH87K90w3O7AiJRqdQoXygvi1VQTJTLGhJl7WqA7A==",
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.4.tgz",
+      "integrity": "sha512-xXqpXoINfFhgua9xiqD8fPFHgkoq1mmmpE92WlDbm9rNRd/EbRb+Gqf908T2DMfuHjjJlksiK2RbHVOdD/MqSw==",
       "requires": {
         "big.js": "^5.2.2",
         "emojis-list": "^3.0.0",
@@ -17375,9 +17378,9 @@
       }
     },
     "postcss": {
-      "version": "8.4.18",
-      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.18.tgz",
-      "integrity": "sha512-Wi8mWhncLJm11GATDaQKobXSNEYGUHeQLiQqDFG1qQ5UTDPTEvKw0Xt5NsTpktGTwLps3ByrWsBrG0rB8YQ9oA==",
+      "version": "8.4.19",
+      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.19.tgz",
+      "integrity": "sha512-h+pbPsyhlYj6N2ozBmHhHrs9DzGmbaarbLvWipMRO7RLS+v4onj26MPFXA5OBYFxyqYhUJK456SwDcY9H2/zsA==",
       "requires": {
         "nanoid": "^3.3.4",
         "picocolors": "^1.0.0",
@@ -17471,9 +17474,9 @@
       }
     },
     "postcss-custom-properties": {
-      "version": "12.1.9",
-      "resolved": "https://registry.npmjs.org/postcss-custom-properties/-/postcss-custom-properties-12.1.9.tgz",
-      "integrity": "sha512-/E7PRvK8DAVljBbeWrcEQJPG72jaImxF3vvCNFwv9cC8CzigVoNIpeyfnJzphnN3Fd8/auBf5wvkw6W9MfmTyg==",
+      "version": "12.1.10",
+      "resolved": "https://registry.npmjs.org/postcss-custom-properties/-/postcss-custom-properties-12.1.10.tgz",
+      "integrity": "sha512-U3BHdgrYhCrwTVcByFHs9EOBoqcKq4Lf3kXwbTi4hhq0qWhl/pDWq2THbv/ICX/Fl9KqeHBb8OVrTf2OaYF07A==",
       "dev": true,
       "requires": {
         "postcss-value-parser": "^4.2.0"
@@ -17887,12 +17890,12 @@
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     },
     "postcss-preset-env": {
-      "version": "7.8.2",
-      "resolved": "https://registry.npmjs.org/postcss-preset-env/-/postcss-preset-env-7.8.2.tgz",
-      "integrity": "sha512-rSMUEaOCnovKnwc5LvBDHUDzpGP+nrUeWZGWt9M72fBvckCi45JmnJigUr4QG4zZeOHmOCNCZnd2LKDvP++ZuQ==",
+      "version": "7.8.3",
+      "resolved": "https://registry.npmjs.org/postcss-preset-env/-/postcss-preset-env-7.8.3.tgz",
+      "integrity": "sha512-T1LgRm5uEVFSEF83vHZJV2z19lHg4yJuZ6gXZZkqVsqv63nlr6zabMH3l4Pc01FQCyfWVrh2GaUeCVy9Po+Aag==",
       "dev": true,
       "requires": {
-        "@csstools/postcss-cascade-layers": "^1.1.0",
+        "@csstools/postcss-cascade-layers": "^1.1.1",
         "@csstools/postcss-color-function": "^1.1.1",
         "@csstools/postcss-font-format-keywords": "^1.0.1",
         "@csstools/postcss-hwb-function": "^1.0.2",
@@ -17906,19 +17909,19 @@
         "@csstools/postcss-text-decoration-shorthand": "^1.0.0",
         "@csstools/postcss-trigonometric-functions": "^1.0.2",
         "@csstools/postcss-unset-value": "^1.0.2",
-        "autoprefixer": "^10.4.11",
-        "browserslist": "^4.21.3",
+        "autoprefixer": "^10.4.13",
+        "browserslist": "^4.21.4",
         "css-blank-pseudo": "^3.0.3",
         "css-has-pseudo": "^3.0.4",
         "css-prefers-color-scheme": "^6.0.3",
-        "cssdb": "^7.0.1",
+        "cssdb": "^7.1.0",
         "postcss-attribute-case-insensitive": "^5.0.2",
         "postcss-clamp": "^4.1.0",
         "postcss-color-functional-notation": "^4.2.4",
         "postcss-color-hex-alpha": "^8.0.4",
         "postcss-color-rebeccapurple": "^7.1.1",
         "postcss-custom-media": "^8.0.2",
-        "postcss-custom-properties": "^12.1.9",
+        "postcss-custom-properties": "^12.1.10",
         "postcss-custom-selectors": "^6.0.3",
         "postcss-dir-pseudo-class": "^6.0.5",
         "postcss-double-position-gradients": "^3.1.2",
@@ -18385,9 +18388,9 @@
       "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
     },
     "sass": {
-      "version": "1.56.0",
-      "resolved": "https://registry.npmjs.org/sass/-/sass-1.56.0.tgz",
-      "integrity": "sha512-WFJ9XrpkcnqZcYuLRJh5qiV6ibQOR4AezleeEjTjMsCocYW59dEG19U3fwTTXxzi2Ed3yjPBp727hbbj53pHFw==",
+      "version": "1.56.1",
+      "resolved": "https://registry.npmjs.org/sass/-/sass-1.56.1.tgz",
+      "integrity": "sha512-VpEyKpyBPCxE7qGDtOcdJ6fFbcpOM+Emu7uZLxVrkX8KVU/Dp5UF7WLvzqRuUhB6mqqQt1xffLoG+AndxTZrCQ==",
       "dev": true,
       "requires": {
         "chokidar": ">=3.0.0 <4.0.0",
@@ -18396,9 +18399,9 @@
       }
     },
     "sass-loader": {
-      "version": "13.1.0",
-      "resolved": "https://registry.npmjs.org/sass-loader/-/sass-loader-13.1.0.tgz",
-      "integrity": "sha512-tZS1RJQ2n2+QNyf3CCAo1H562WjL/5AM6Gi8YcPVVoNxQX8d19mx8E+8fRrMWsyc93ZL6Q8vZDSM0FHVTJaVnQ==",
+      "version": "13.2.0",
+      "resolved": "https://registry.npmjs.org/sass-loader/-/sass-loader-13.2.0.tgz",
+      "integrity": "sha512-JWEp48djQA4nbZxmgC02/Wh0eroSUutulROUusYJO9P9zltRbNN80JCBHqRGzjd4cmZCa/r88xgfkjGD0TXsHg==",
       "dev": true,
       "requires": {
         "klona": "^2.0.4",
@@ -19119,15 +19122,15 @@
       "integrity": "sha512-BNGbWLfd0eUPabhkXUVm0j8uuvREyTh5ovRa/dyow/BqAbZJyC+5fU+IzQOzmAKzYqYRAISoRhdQr3eIZ/PXqg=="
     },
     "vue": {
-      "version": "3.2.41",
-      "resolved": "https://registry.npmjs.org/vue/-/vue-3.2.41.tgz",
-      "integrity": "sha512-uuuvnrDXEeZ9VUPljgHkqB5IaVO8SxhPpqF2eWOukVrBnRBx2THPSGQBnVRt0GrIG1gvCmFXMGbd7FqcT1ixNQ==",
+      "version": "3.2.45",
+      "resolved": "https://registry.npmjs.org/vue/-/vue-3.2.45.tgz",
+      "integrity": "sha512-9Nx/Mg2b2xWlXykmCwiTUCWHbWIj53bnkizBxKai1g61f2Xit700A1ljowpTIM11e3uipOeiPcSqnmBg6gyiaA==",
       "requires": {
-        "@vue/compiler-dom": "3.2.41",
-        "@vue/compiler-sfc": "3.2.41",
-        "@vue/runtime-dom": "3.2.41",
-        "@vue/server-renderer": "3.2.41",
-        "@vue/shared": "3.2.41"
+        "@vue/compiler-dom": "3.2.45",
+        "@vue/compiler-sfc": "3.2.45",
+        "@vue/runtime-dom": "3.2.45",
+        "@vue/server-renderer": "3.2.45",
+        "@vue/shared": "3.2.45"
       }
     },
     "vue-eslint-parser": {
@@ -19286,9 +19289,9 @@
       "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ=="
     },
     "webpack": {
-      "version": "5.74.0",
-      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.74.0.tgz",
-      "integrity": "sha512-A2InDwnhhGN4LYctJj6M1JEaGL7Luj6LOmyBHjcI8529cm5p6VXiTIW2sn6ffvEAKmveLzvu4jrihwXtPojlAA==",
+      "version": "5.75.0",
+      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.75.0.tgz",
+      "integrity": "sha512-piaIaoVJlqMsPtX/+3KTTO6jfvrSYgauFVdt8cr9LTHKmcq/AMd4mhzsiP7ZF/PGRNPGA8336jldh9l2Kt2ogQ==",
       "requires": {
         "@types/eslint-scope": "^3.7.3",
         "@types/estree": "^0.0.51",
diff --git a/package.json b/package.json
index 744db7245e..d371c2c026 100644
--- a/package.json
+++ b/package.json
@@ -2,14 +2,14 @@
   "name": "app",
   "private": true,
   "dependencies": {
-    "@geoman-io/leaflet-geoman-free": "^2.13.0",
+    "@geoman-io/leaflet-geoman-free": "^2.13.1",
     "@ibm/plex": "^6.1.1",
     "@sfgrp/sled": "^1.0.3",
     "@sfgrp/svg-radial-menu": "^1.0.7",
     "axios": "^1.1.3",
-    "chart.js": "^3.9.1",
+    "chart.js": "^4.0.1",
     "d3": "^7.6.1",
-    "dompurify": "^2.4.0",
+    "dompurify": "^2.4.1",
     "easymde": "^2.18.0",
     "exif-js": "^2.3.0",
     "json2csv": "^5.0.7",
@@ -20,7 +20,7 @@
     "qs": "^6.11.0",
     "shakapacker": "6.5.4",
     "v-hotkey": "^0.9.0",
-    "vue": "^3.2.41",
+    "vue": "^3.2.45",
     "vue-handy-scroll": "^3.0.1",
     "vue-hotkeys": "0.0.1",
     "vue-tippy": "^6.0.0-alpha.58",
@@ -39,39 +39,39 @@
   ],
   "devDependencies": {
     "@babel/core": "^7.19.3",
-    "@babel/plugin-transform-runtime": "^7.19.1",
+    "@babel/plugin-transform-runtime": "^7.19.6",
     "@babel/preset-env": "^7.19.3",
     "@babel/runtime": "^7.19.0",
-    "@vue/compiler-sfc": "^3.2.41",
+    "@vue/compiler-sfc": "^3.2.45",
     "babel-loader": "^8.2.5",
     "compression-webpack-plugin": "^10.0.0",
-    "css-loader": "^6.7.1",
+    "css-loader": "^6.7.2",
     "css-minimizer-webpack-plugin": "^4.2.2",
     "eslint": "^8.27.0",
     "eslint-config-standard": "^17.0.0",
     "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-n": "^15.5.0",
+    "eslint-plugin-n": "^15.5.1",
     "eslint-plugin-node": "^11.1.0",
     "eslint-plugin-promise": "^6.1.1",
     "eslint-plugin-standard": "^4.1.0",
     "eslint-plugin-vue": "^9.7.0",
     "mini-css-extract-plugin": "^2.6.1",
-    "postcss": "^8.4.18",
+    "postcss": "^8.4.19",
     "postcss-flexbugs-fixes": "^5.0.2",
     "postcss-import": "^15.0.0",
     "postcss-loader": "^7.0.1",
-    "postcss-preset-env": "^7.8.2",
+    "postcss-preset-env": "^7.8.3",
     "raw-loader": "^4.0.2",
     "resolve-url-loader": "^5.0.0",
-    "sass": "^1.56.0",
-    "sass-loader": "^13.1.0",
+    "sass": "^1.56.1",
+    "sass-loader": "^13.2.0",
     "style-loader": "^3.3.1",
     "stylus": "^0.59.0",
     "stylus-loader": "^7.1.0",
     "terser-webpack-plugin": "^5.3.6",
     "url": "^0.11.0",
     "vue-loader": "^17.0.1",
-    "webpack": "^5.74.0",
+    "webpack": "^5.75.0",
     "webpack-assets-manifest": "^5.1.0",
     "webpack-cli": "^4.10.0",
     "webpack-dev-server": "^4.11.1",

From 88a2d9b7511a81588434859f8660d9445745de88 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 16 Nov 2022 14:27:57 -0600
Subject: [PATCH 029/160] Fix "castor" batch load OTU setting

---
 CHANGELOG.md                                            | 1 +
 app/views/taxon_names/batch_load/castor/_form.html.erb  | 4 ++--
 lib/batch_load/import/taxon_names/castor_interpreter.rb | 8 +++++++-
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1a0714cb4e..cd838a9602 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Task - Collection object chronology, a plot of object by year collected
 
 ### Fixed
+- 'Also create OTU' on batch taxon name upload causing raise
 - Media observations removed if they have no more depictions via updates
 - Citation link in Biological association panel on Browse OTU
 - Type relationship text/rendering is inverted in New taxon name [#3182]
diff --git a/app/views/taxon_names/batch_load/castor/_form.html.erb b/app/views/taxon_names/batch_load/castor/_form.html.erb
index 3f2c1355db..e5771509ef 100644
--- a/app/views/taxon_names/batch_load/castor/_form.html.erb
+++ b/app/views/taxon_names/batch_load/castor/_form.html.erb
@@ -17,8 +17,8 @@
 
     <div class="field">
       <%= label_tag :also_create_otu, 'Also create OTU:' -%>
-      <%= tag.strong(@result.also_create_otu&.to_i == 1 ? 'yes' : 'no') %>
-      <%= hidden_field_tag(:also_create_otu, @result.also_create_otu&.to_i == 1 ? '1' : '0' )  -%>
+      <%= tag.strong(@result.also_create_otu ? 'yes' : 'no') %>
+      <%= hidden_field_tag(:also_create_otu, @result.also_create_otu ? '1' : '0' )  -%>
     </div>
 
   <% else %>
diff --git a/lib/batch_load/import/taxon_names/castor_interpreter.rb b/lib/batch_load/import/taxon_names/castor_interpreter.rb
index c1fda37dae..a433c0541c 100644
--- a/lib/batch_load/import/taxon_names/castor_interpreter.rb
+++ b/lib/batch_load/import/taxon_names/castor_interpreter.rb
@@ -10,6 +10,7 @@ class Import::TaxonNames::CastorInterpreter < BatchLoad::Import
     # The code (Rank Class) that new names will use
     attr_accessor :nomenclature_code
 
+    # @return Boolean
     # Whether to create an OTU as well
     attr_accessor :also_create_otu
 
@@ -27,6 +28,11 @@ def initialize(nomenclature_code: nil, parent_taxon_name_id: nil, also_create_ot
       super(**args)
     end
 
+    def also_create_otu
+      return true if [1, '1', true].include?(@also_create_otu)
+      false
+    end
+
     # @return [String]
     def parent_taxon_name
       Project.find(@project_id).root_taxon_name
@@ -155,7 +161,7 @@ def build_taxon_names
           else
             # Note we are not technically using the param like TaxonName.new(), so we can't just set the attribute
             # So we hack in the OTUs 'manually".  This also lets us see them in the result
-            if also_create_otu == '1'
+            if also_create_otu 
               parse_result.objects[:otu].push( Otu.new(taxon_name: p) )
             end
           end

From ae0b90aee8596d475bd64296ffc129995b83f342 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 16 Nov 2022 15:14:03 -0600
Subject: [PATCH 030/160] Add loan/deccession banners to collection object
 labels. Close #3192

---
 CHANGELOG.md                                  |  2 ++
 app/helpers/collection_objects_helper.rb      | 19 +++++++++++++++++--
 .../autocomplete.json.jbuilder                |  2 +-
 3 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be6d5c3c60..49f5f1f937 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,12 +7,14 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- Collection object Autocomplete has loan and deaccession banners [#3192]
 - Autocomplete on Browse collection object [#3189]
 
 ### Fixed
 - Citation link in Biological association panel on Browse OTU
 - Type relationship text/rendering is inverted in New taxon name [#3182]
 
+[#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
 
 ## [0.29.6] - 2022-11-08
diff --git a/app/helpers/collection_objects_helper.rb b/app/helpers/collection_objects_helper.rb
index 342da9e149..db26342fb0 100644
--- a/app/helpers/collection_objects_helper.rb
+++ b/app/helpers/collection_objects_helper.rb
@@ -5,6 +5,7 @@ module CollectionObjectsHelper
   def collection_object_tag(collection_object)
     return nil if collection_object.nil?
     a = [
+      collection_object_loan_tag(collection_object),
       collection_object_deaccession_tag(collection_object),
       collection_object_identifier_tag(collection_object),
       taxon_determination_tag(collection_object.taxon_determinations.order(:position).first)
@@ -41,8 +42,11 @@ def label_for_collection_object(collection_object)
 
   def collection_object_autocomplete_tag(collection_object)
     return nil if collection_object.nil?
-    [collection_object_identifier_tag(collection_object),
-     collection_object_taxon_determination_tag(collection_object)
+    [
+      collection_object_loan_tag(collection_object),
+      collection_object_deaccession_tag(collection_object),
+      collection_object_identifier_tag(collection_object),
+      collection_object_taxon_determination_tag(collection_object)
     ].join(' ').html_safe
   end
 
@@ -77,6 +81,17 @@ def collection_object_deaccession_tag(collection_object)
     ]).html_safe
   end
 
+  def collection_object_loan_tag(collection_object)
+    return nil if collection_object.nil? || !collection_object.on_loan?
+    msg = ['On Loan until', collection_object.loan_return_date].compact.join(' ')
+    content_tag(:span, msg, class: [
+      :feedback,
+      'feedback-thin',
+      'feedback-warning'
+    ]).html_safe
+  end
+
+
   # @return [Array [Identifier, String (type)], nil]
   #    also checks virtual container for identifier by proxy
   def collection_object_visualized_identifier(collection_object)
diff --git a/app/views/collection_objects/autocomplete.json.jbuilder b/app/views/collection_objects/autocomplete.json.jbuilder
index 8a6a55daac..f3946a050d 100644
--- a/app/views/collection_objects/autocomplete.json.jbuilder
+++ b/app/views/collection_objects/autocomplete.json.jbuilder
@@ -1,7 +1,7 @@
 json.array! @collection_objects do |s|
   v = collection_object_autocomplete_tag(s)
   json.id s.id
-  json.label  label_for_collection_object(s)
+  json.label label_for_collection_object(s)
   json.gid s.to_global_id.to_s
   json.label_html v
 

From 4f2cae02c5fb79fe7061ca705d97f9c39f65fe82 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 16 Nov 2022 16:40:32 -0600
Subject: [PATCH 031/160] Add loan/deaccession banner to collection object tag.
 Fix #3192.

---
 CHANGELOG.md                                  |  2 ++
 app/helpers/collection_objects_helper.rb      | 19 +++++++++++++++++--
 .../autocomplete.json.jbuilder                |  2 +-
 3 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd838a9602..a3be85402d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- Collection object Autocomplete has loan and deaccession banners [#3192]
 - Autocomplete on Browse collection object [#3189]
 - Task - Collection object chronology, a plot of object by year collected
 
@@ -20,6 +21,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Changed
 - Refactored observation cell component for Image matrix
 
+[#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
 [#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
diff --git a/app/helpers/collection_objects_helper.rb b/app/helpers/collection_objects_helper.rb
index 342da9e149..db26342fb0 100644
--- a/app/helpers/collection_objects_helper.rb
+++ b/app/helpers/collection_objects_helper.rb
@@ -5,6 +5,7 @@ module CollectionObjectsHelper
   def collection_object_tag(collection_object)
     return nil if collection_object.nil?
     a = [
+      collection_object_loan_tag(collection_object),
       collection_object_deaccession_tag(collection_object),
       collection_object_identifier_tag(collection_object),
       taxon_determination_tag(collection_object.taxon_determinations.order(:position).first)
@@ -41,8 +42,11 @@ def label_for_collection_object(collection_object)
 
   def collection_object_autocomplete_tag(collection_object)
     return nil if collection_object.nil?
-    [collection_object_identifier_tag(collection_object),
-     collection_object_taxon_determination_tag(collection_object)
+    [
+      collection_object_loan_tag(collection_object),
+      collection_object_deaccession_tag(collection_object),
+      collection_object_identifier_tag(collection_object),
+      collection_object_taxon_determination_tag(collection_object)
     ].join(' ').html_safe
   end
 
@@ -77,6 +81,17 @@ def collection_object_deaccession_tag(collection_object)
     ]).html_safe
   end
 
+  def collection_object_loan_tag(collection_object)
+    return nil if collection_object.nil? || !collection_object.on_loan?
+    msg = ['On Loan until', collection_object.loan_return_date].compact.join(' ')
+    content_tag(:span, msg, class: [
+      :feedback,
+      'feedback-thin',
+      'feedback-warning'
+    ]).html_safe
+  end
+
+
   # @return [Array [Identifier, String (type)], nil]
   #    also checks virtual container for identifier by proxy
   def collection_object_visualized_identifier(collection_object)
diff --git a/app/views/collection_objects/autocomplete.json.jbuilder b/app/views/collection_objects/autocomplete.json.jbuilder
index 8a6a55daac..f3946a050d 100644
--- a/app/views/collection_objects/autocomplete.json.jbuilder
+++ b/app/views/collection_objects/autocomplete.json.jbuilder
@@ -1,7 +1,7 @@
 json.array! @collection_objects do |s|
   v = collection_object_autocomplete_tag(s)
   json.id s.id
-  json.label  label_for_collection_object(s)
+  json.label label_for_collection_object(s)
   json.gid s.to_global_id.to_s
   json.label_html v
 

From e41d0deb633038edfa6c4174364d40b568f58f55 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 17 Nov 2022 11:28:55 -0300
Subject: [PATCH 032/160] Add mass delete button #3174

---
 .../tasks/collection_objects/filter/app.vue    |  5 ++++-
 .../components/DeleteCollectionObjects.vue     | 18 +++++++++++++-----
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/filter/app.vue b/app/javascript/vue/tasks/collection_objects/filter/app.vue
index fded4c6ec2..68f8f84294 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/app.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/app.vue
@@ -76,7 +76,10 @@
               :url="urlRequest"
               class="margin-small-left"
             />
-            <DeleteCollectionObjects :ids="ids" />
+            <DeleteCollectionObjects
+              :ids="ids"
+              @delete="list.data = list.data.filter(r => !$event.includes(r[0]))"
+            />
             <RadialFilter
               :disabled="!ids.length"
               object-type="CollectingEvent"
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index 792cfedb90..7fb5ade86e 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -15,8 +15,9 @@ import { CollectionObject } from 'routes/endpoints'
 import VBtn from 'components/ui/VBtn/index.vue'
 import ConfirmationModal from 'components/ConfirmationModal.vue'
 
-const CONFIRM_WORD = 'delete'
+const CONFIRM_WORD = 'DELETE'
 const MAX = 25
+const MIN_CONFIRM = 5
 
 const props = defineProps({
   ids: {
@@ -30,18 +31,25 @@ const confirmationModal = ref(null)
 
 function deleteCOs () {
   const ids = [...props.ids]
-  const requests = ids.map(id => CollectionObject.destroy(id))
+  const destroyedIds = []
+  const requests = ids.map(id => CollectionObject.destroy(id).then(_ => destroyedIds.push(id)))
 
-  Promise.all(requests).then(_ => {
-    emit('delete', { ids })
+  Promise.allSettled(requests).then(_ => {
+    emit('delete', destroyedIds)
   })
 }
 
 async function openModal () {
+  if (props.ids.length > MAX) {
+    TW.workbench.alert.create(`Select a maximum of ${MAX} objects to delete.`, 'error')
+
+    return
+  }
+
   const ok = await confirmationModal.value.show({
     title: 'Delete collection objects',
     message: `This will delete ${props.ids.length} collection objects. Are you sure you want to proceed?`,
-    confirmationWord: 'DESTROY',
+    confirmationWord: props.ids.length >= MIN_CONFIRM ? CONFIRM_WORD : '',
     okButton: 'Delete',
     cancelButton: 'Cancel',
     typeButton: 'delete'

From c9e354c30e643664df050e2e150218cb7a176951 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 17 Nov 2022 11:50:43 -0300
Subject: [PATCH 033/160] Change select all button for input checkbox

---
 .../tasks/collection_objects/filter/app.vue   |  12 +-
 .../components/DeleteCollectionObjects.vue    |  18 +--
 .../filter/components/list.vue                | 128 +++++++++---------
 3 files changed, 80 insertions(+), 78 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/filter/app.vue b/app/javascript/vue/tasks/collection_objects/filter/app.vue
index 68f8f84294..b897df71d5 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/app.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/app.vue
@@ -52,10 +52,11 @@
           class="horizontal-left-content flex-separate separate-bottom"
         >
           <div class="horizontal-left-content">
-            <select-all
-              v-model="ids"
-              :ids="coIds"
+            <tag-all
+              :ids="ids"
+              type="CollectionObject"
             />
+
             <span class="separate-left separate-right">|</span>
             <csv-button
               :url="urlRequest"
@@ -77,6 +78,7 @@
               class="margin-small-left"
             />
             <DeleteCollectionObjects
+              class="margin-small-left"
               :ids="ids"
               @delete="list.data = list.data.filter(r => !$event.includes(r[0]))"
             />
@@ -128,7 +130,7 @@ import PaginationCount from 'components/pagination/PaginationCount'
 import GetPagination from 'helpers/getPagination'
 import DwcDownload from './components/dwcDownload.vue'
 import DwcReindex from './components/dwcReindex.vue'
-import SelectAll from './components/selectAll.vue'
+import TagAll from './components/tagAll'
 import MatchButton from './components/matchButton.vue'
 import JsonRequestUrl from 'tasks/people/filter/components/JsonRequestUrl.vue'
 import RadialFilter from 'components/radials/filter/radial.vue'
@@ -145,7 +147,7 @@ export default {
     PaginationCount,
     DwcDownload,
     DwcReindex,
-    SelectAll,
+    TagAll,
     MatchButton,
     JsonRequestUrl,
     RadialFilter,
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index 7fb5ade86e..65ff80ca26 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -1,12 +1,14 @@
 <template>
-  <ConfirmationModal ref="confirmationModal" />
-  <VBtn
-    color="primary"
-    medium
-    @click="openModal"
-  >
-    Delete collection objects
-  </VBtn>
+  <div>
+    <ConfirmationModal ref="confirmationModal" />
+    <VBtn
+      color="primary"
+      medium
+      @click="openModal"
+    >
+      Delete collection objects
+    </VBtn>
+  </div>
 </template>
 
 <script setup>
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/list.vue b/app/javascript/vue/tasks/collection_objects/filter/components/list.vue
index 62ad949a4f..6cc07ae611 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/list.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/list.vue
@@ -1,5 +1,5 @@
 <template>
-  <HandyScroll>
+  <HandyScroll ref="root">
     <div>
       <table
         ref="tableBar"
@@ -8,17 +8,21 @@
         <thead>
           <tr>
             <th>
-              <tag-all
-                :ids="ids"
-                type="CollectionObject"
-                class="separate-right"/>
+              <input
+                type="checkbox"
+                v-model="selectIds"
+              >
             </th>
             <th>Collection object</th>
             <template
-              v-for="(item, index) in list.column_headers">
+              v-for="(item, index) in list.column_headers"
+              :key="item"
+            >
               <th
                 v-if="index > 2"
-                @click="sortTable(index)">{{item}}
+                @click="sortTable(index)"
+              >
+                {{ item }}
               </th>
             </template>
           </tr>
@@ -28,23 +32,29 @@
             class="contextMenuCells"
             :class="{ even: indexR % 2 }"
             v-for="(row, indexR) in list.data"
-            :key="row[0]">
+            :key="row[0]"
+          >
             <td>
               <input
                 v-model="ids"
                 :value="row[0]"
-                type="checkbox">
+                type="checkbox"
+              >
             </td>
             <td>
               <a
                 :href="`/tasks/collection_objects/browse?collection_object_id=${row[0]}`"
-                target="_blank">
+                target="_blank"
+              >
                 Show
               </a>
             </td>
-            <template v-for="(item, index) in row">
+            <template
+              v-for="(item, index) in row"
+              :key="index"
+            >
               <td v-if="index > 2">
-                <span>{{item}}</span>
+                <span>{{ item }}</span>
               </td>
             </template>
           </tr>
@@ -54,71 +64,59 @@
   </HandyScroll>
 </template>
 
-<script>
-
+<script setup>
+import { computed, watch, ref } from 'vue'
 import { sortArray } from 'helpers/arrays.js'
 import { vResizeColumn } from 'directives/resizeColumn.js'
-import TagAll from './tagAll'
 import HandyScroll from 'vue-handy-scroll'
 
-export default {
-  components: {
-    TagAll,
-    HandyScroll
-  },
-
-  directives: {
-    ResizeColumn: vResizeColumn
+const props = defineProps({
+  list: {
+    type: Object,
+    default: undefined
   },
+  modelValue: {
+    type: Array,
+    default: () => []
+  }
+})
 
-  props: {
-    list: {
-      type: Object,
-      default: undefined
-    },
-    modelValue: {
-      type: Array,
-      default: () => []
-    }
-  },
+const emit = defineEmits([
+  'onSort',
+  'update:modelValue'
+])
 
-  emits: [
-    'onSort',
-    'update:modelValue'
-  ],
+const root = ref(null)
 
-  computed: {
-    ids: {
-      get () {
-        return this.modelValue
-      },
-      set (value) {
-        this.$emit('update:modelValue', value)
-      }
-    }
+const ids = computed({
+  get () {
+    return props.modelValue
   },
+  set (value) {
+    emit('update:modelValue', value)
+  }
+})
 
-  data () {
-    return {
-      ascending: false
-    }
-  },
+const selectIds = computed({
+  get: () => props.list?.data?.length === ids.value.length,
+  set: value => {
+    ids.value = value
+      ? props.list.data.map(r => r[0])
+      : []
+  }
+})
 
-  watch: {
-    list: {
-      handler () {
-        HandyScroll.EventBus.emit('update', { sourceElement: this.$el })  
-      },
-      immediate: true
-    }
-  },
+const ascending = ref(false)
 
-  methods: {
-    sortTable (sortProperty) {
-      this.$emit('onSort', sortArray(this.list.data, sortProperty, this.ascending))
-      this.ascending = !this.ascending
-    }
-  }
+watch(
+  () => props.list,
+  () => {
+    HandyScroll.EventBus.emit('update', { sourceElement: root.value })
+  })
+
+const sortTable = (sortProperty) => {
+  emit('onSort', sortArray(props.list.data, sortProperty, ascending.value))
+  ascending.value = !ascending.value
 }
 </script>
 

From b2b0002818dfab04de3d58ee8e297c91e1e3f549 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 17 Nov 2022 16:17:07 -0300
Subject: [PATCH 034/160] Add character state filter

---
 .../MatrixColumnCoder/MatrixColumnCoder.vue   | 11 ++--
 .../Option/OptionCharacterStateDispaly.vue    | 55 +++++++++++++++++++
 .../Option/OptionCharacterStateFilter.vue     |  4 +-
 .../QualitativeDescriptor.vue                 |  5 ++
 .../store/getters/getRowObjects.js            |  8 +--
 .../store/getters/getters.js                  |  5 +-
 .../options/GetDisplayCharacterStates.js      |  1 +
 .../options/GetFilterCharacterStates.js       |  1 -
 .../options/GetScoredCharacterStates.js       |  1 +
 .../store/mutations/mutations.js              |  7 ++-
 .../options/setDisplayCharacterStates.js      |  2 +-
 .../setDisplayScoredCharacterStates.js        |  3 +
 .../matrix_column_coder/store/store.js        |  3 +-
 13 files changed, 90 insertions(+), 16 deletions(-)
 create mode 100644 app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateDispaly.vue
 create mode 100644 app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetDisplayCharacterStates.js
 delete mode 100644 app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetFilterCharacterStates.js
 create mode 100644 app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetScoredCharacterStates.js
 create mode 100644 app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayScoredCharacterStates.js

diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/MatrixColumnCoder.vue b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/MatrixColumnCoder.vue
index 91167869c1..be62682369 100755
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/MatrixColumnCoder.vue
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/MatrixColumnCoder.vue
@@ -24,10 +24,10 @@
           class="horizontal-right-content middle"
         >
           <OptionUnsecoredRows class="margin-medium-right" />
-          <OptionCharacterStateFilter
-            v-if="descriptor.type === componentName.Qualitative"
-            class="margin-small-right"
-          />
+          <template v-if="descriptor.type === componentName.Qualitative">
+            <OptionCharacterStatDisplay class="margin-small-right" />
+            <OptionCharacterStateFilter class="margin-small-right" />
+          </template>
           <RowObjectList class="margin-small-right" />
           <CodeColumn
             class="margin-small-right"
@@ -64,6 +64,7 @@ import { GetterNames } from '../store/getters/getters'
 import componentName from '../helpers/ComponentNames'
 import OptionUnsecoredRows from './Option/OptionUnsecoredRows.vue'
 import OptionCharacterStateFilter from './Option/OptionCharacterStateFilter.vue'
+import OptionCharacterStatDisplay from './Option/OptionCharacterStateDispaly.vue'
 import ContinuousDescriptor from './ContinuousDescriptor/ContinuousDescriptor.vue'
 import FreeTextDescriptor from './SingleObservationDescriptor/FreeText/FreeText.vue'
 import PresenceDescriptor from './SingleObservationDescriptor/PresenceDescriptor/PresenceDescriptor.vue'
@@ -78,6 +79,7 @@ import RowObjectList from './RowObjects/RowObjects.vue'
 import CodeColumn from './CodeColumn/CodeColumn.vue'
 import ObservationRowDestroy from './ObservationRow/ObservationRowDestroy.vue'
 
+
 export default {
   name: 'MatrixColumnCoder',
 
@@ -94,6 +96,7 @@ export default {
     RadialNavigator,
     OptionUnsecoredRows,
     OptionCharacterStateFilter,
+    OptionCharacterStatDisplay,
     Spinner,
     CodeColumn,
     ObservationRowDestroy
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateDispaly.vue b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateDispaly.vue
new file mode 100644
index 0000000000..c68832878d
--- /dev/null
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateDispaly.vue
@@ -0,0 +1,55 @@
+<template>
+  <div>
+    <VModal
+      v-if="showModal"
+      @close="showModal = false"
+    >
+      <template #header>
+        <h3>Show character states</h3>
+      </template>
+      <template #body>
+        <ul class="no_bullets">
+          <li
+            v-for="characterState in descriptor.characterStates"
+            :key="characterState.id"
+          >
+            <label>
+              <input
+                v-model="filterCharacterStates"
+                :value="characterState.id"
+                type="checkbox"
+              >
+              {{ characterState.name }}
+            </label>
+          </li>
+        </ul>
+      </template>
+    </VModal>
+    <VBtn
+      color="primary"
+      medium
+      @click="showModal = true"
+    >
+      Show character states
+    </VBtn>
+  </div>
+</template>
+
+<script setup>
+import { useStore } from 'vuex'
+import { computed, ref } from 'vue'
+import { GetterNames } from '../../store/getters/getters'
+import { MutationNames } from '../../store/mutations/mutations'
+import VModal from 'components/ui/Modal.vue'
+import VBtn from 'components/ui/VBtn/index.vue'
+
+const store = useStore()
+const showModal = ref(false)
+const filterCharacterStates = computed({
+  get: () => store.getters[GetterNames.GetDisplayCharacterStates],
+  set: value => store.commit(MutationNames.SetDisplayCharacterStates, value)
+})
+
+const descriptor = computed(() => store.getters[GetterNames.GetDescriptor])
+
+</script>
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateFilter.vue b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateFilter.vue
index 4e6962bec1..cf2a9200f3 100644
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateFilter.vue
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/Option/OptionCharacterStateFilter.vue
@@ -46,8 +46,8 @@ import VBtn from 'components/ui/VBtn/index.vue'
 const store = useStore()
 const showModal = ref(false)
 const filterCharacterStates = computed({
-  get: () => store.getters[GetterNames.GetDisplayCharacterStates],
-  set: value => store.commit(MutationNames.SetDisplayCharacterStates, value)
+  get: () => store.getters[GetterNames.GetDisplayScoredCharacterStates],
+  set: value => store.commit(MutationNames.SetDisplayScoredCharacterStates, value)
 })
 
 const descriptor = computed(() => store.getters[GetterNames.GetDescriptor])
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/QualitativeDescriptor/QualitativeDescriptor.vue b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/QualitativeDescriptor/QualitativeDescriptor.vue
index 39366b2e01..c610ce5790 100755
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/QualitativeDescriptor/QualitativeDescriptor.vue
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/MatrixColumnCoder/QualitativeDescriptor/QualitativeDescriptor.vue
@@ -10,6 +10,7 @@
           class="horizontal-left-content middle qualitative-descriptor__descriptor-li"
           v-for="characterState in descriptor.characterStates"
           :key="characterState.id"
+          v-show="!showCharacterStates.length || showCharacterStates.includes(characterState.id)"
         >
           <label class="margin-small-right middle">
             <input
@@ -73,6 +74,10 @@ export default {
         o.rowObjectId === this.rowObject.id &&
         o.rowObjectType === this.rowObject.type
       )
+    },
+
+    showCharacterStates () {
+      return this.$store.getters[GetterNames.GetDisplayCharacterStates]
     }
   },
 
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getRowObjects.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getRowObjects.js
index c391a187cc..d3a67847cb 100644
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getRowObjects.js
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getRowObjects.js
@@ -7,14 +7,14 @@ export default state => {
 
   const {
     showOnlyUnscoredRows,
-    characterStates
+    showScoredCharacterStates
   } = state.options
 
-  const rowObjectIdsWithObservations = characterStates.length
-    ? getRowObjectIdsByCharacterStateCreated(observations, characterStates)
+  const rowObjectIdsWithObservations = showScoredCharacterStates.length
+    ? getRowObjectIdsByCharacterStateCreated(observations, showScoredCharacterStates)
     : getRowObjectIdsByObservationCreated(observations)
 
-  if (characterStates.length) {
+  if (showScoredCharacterStates.length) {
     return rowObjects.filter(item => rowObjectIdsWithObservations.includes(item.id))
   }
 
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getters.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getters.js
index fe64cdbd30..b109f34b8b 100644
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getters.js
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/getters.js
@@ -2,7 +2,8 @@ import doesRowObjectNeedCountdown from './doesRowObjectNeedCountdown.js'
 import getCharacterStateChecked from './getCharacterStateChecked.js'
 import getDescriptor from './getDescriptor.js'
 import getDisplayUnscoredRows from './options/GetDisplayUnscoredRows.js'
-import getDisplayCharacterStates from './options/GetFilterCharacterStates.js'
+import getDisplayCharacterStates from './options/GetDisplayCharacterStates.js'
+import getDisplayScoredCharacterStates from './options/GetScoredCharacterStates.js'
 import getFreeTextValueFor from './getFreeTextValueFor.js'
 import getNextColumn from './getNextColumn.js'
 import getObservationMatrix from './getObservationMatrix.js'
@@ -22,6 +23,7 @@ const GetterNames = {
   GetDescriptor: 'getDescriptor',
   GetDisplayUnscoredRows: 'getDisplayUnscoredRows',
   GetDisplayCharacterStates: 'getDisplayCharacterStates',
+  GetDisplayScoredCharacterStates: 'getDisplayScoredCharacterStates',
   GetFreeTextValueFor: 'getFreeTextValueFor',
   GetNextColumn: 'getNextColumn',
   GetObservationColumnId: 'getObservationColumnId',
@@ -41,6 +43,7 @@ const GetterFunctions = {
   [GetterNames.GetDescriptor]: getDescriptor,
   [GetterNames.GetDisplayUnscoredRows]: getDisplayUnscoredRows,
   [GetterNames.GetDisplayCharacterStates]: getDisplayCharacterStates,
+  [GetterNames.GetDisplayScoredCharacterStates]: getDisplayScoredCharacterStates,
   [GetterNames.GetFreeTextValueFor]: getFreeTextValueFor,
   [GetterNames.GetNextColumn]: getNextColumn,
   [GetterNames.GetObservationColumnId]: getObservationColumnId,
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetDisplayCharacterStates.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetDisplayCharacterStates.js
new file mode 100644
index 0000000000..3130afea8d
--- /dev/null
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetDisplayCharacterStates.js
@@ -0,0 +1 @@
+export default state => state.options.showCharacterStates
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetFilterCharacterStates.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetFilterCharacterStates.js
deleted file mode 100644
index 341cbd9f11..0000000000
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetFilterCharacterStates.js
+++ /dev/null
@@ -1 +0,0 @@
-export default state => state.options.characterStates
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetScoredCharacterStates.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetScoredCharacterStates.js
new file mode 100644
index 0000000000..5ca994bb1f
--- /dev/null
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/getters/options/GetScoredCharacterStates.js
@@ -0,0 +1 @@
+export default state => state.options.showScoredCharacterStates
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/mutations.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/mutations.js
index ae3eec4489..55d180ae23 100644
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/mutations.js
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/mutations.js
@@ -28,6 +28,7 @@ import setPresence from './setPresence'
 import setYearFor from './setYearFor'
 import setDisplayOnlyUnscored from './options/setDisplayOnlyUnscored'
 import setDisplayCharacterStates from './options/setDisplayCharacterStates'
+import setDisplayScoredCharacterStates from './options/setDisplayScoredCharacterStates'
 
 const MutationNames = {
   AddObservation: 'addObservation',
@@ -59,7 +60,8 @@ const MutationNames = {
   SetPresence: 'setPresence',
   SetYearFor: 'setYearFor',
   SetDisplayOnlyUnscored: 'setDisplayOnlyUnscored',
-  SetDisplayCharacterStates: 'setDisplayCharacterStates'
+  SetDisplayCharacterStates: 'setDisplayCharacterStates',
+  SetDisplayScoredCharacterStates: 'setDisplayScoredCharacterStates'
 }
 
 const MutationFunctions = {
@@ -92,7 +94,8 @@ const MutationFunctions = {
   [MutationNames.SetPresence]: setPresence,
   [MutationNames.SetYearFor]: setYearFor,
   [MutationNames.SetDisplayOnlyUnscored]: setDisplayOnlyUnscored,
-  [MutationNames.SetDisplayCharacterStates]: setDisplayCharacterStates
+  [MutationNames.SetDisplayCharacterStates]: setDisplayCharacterStates,
+  [MutationNames.SetDisplayScoredCharacterStates]: setDisplayScoredCharacterStates
 }
 
 export {
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayCharacterStates.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayCharacterStates.js
index a26ddee936..9199f80e6a 100644
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayCharacterStates.js
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayCharacterStates.js
@@ -1,3 +1,3 @@
 export default (state, value) => {
-  state.options.characterStates = value
+  state.options.showCharacterStates = value
 }
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayScoredCharacterStates.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayScoredCharacterStates.js
new file mode 100644
index 0000000000..8b24634d21
--- /dev/null
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/mutations/options/setDisplayScoredCharacterStates.js
@@ -0,0 +1,3 @@
+export default (state, value) => {
+  state.options.showScoredCharacterStates = value
+}
diff --git a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/store.js b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/store.js
index b15772bffc..fcda140775 100644
--- a/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/store.js
+++ b/app/javascript/vue/tasks/observation_matrices/matrix_column_coder/store/store.js
@@ -16,7 +16,8 @@ const makeInitialState = () => ({
   previousColumn: {},
   options: {
     showOnlyUnscoredRows: false,
-    characterStates: []
+    showCharacterStates: [],
+    showScoredCharacterStates: []
   }
 })
 

From 52bb9c0e68ea511d92eee6afb6baf0f2aa6814e0 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Thu, 17 Nov 2022 15:40:53 -0600
Subject: [PATCH 035/160] nexml bug fix

---
 app/helpers/observation_matrices/export/nexml_helper.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/helpers/observation_matrices/export/nexml_helper.rb b/app/helpers/observation_matrices/export/nexml_helper.rb
index eab1f4e4ca..4d1299069b 100644
--- a/app/helpers/observation_matrices/export/nexml_helper.rb
+++ b/app/helpers/observation_matrices/export/nexml_helper.rb
@@ -24,7 +24,7 @@ def nexml_descriptors(options = {})
                       xml.meta(
                         'xsi:type' => 'ResourceMeta',
                         'rel' => 'foaf:depiction',
-                        'href' => image_short_url(d.image), # see app/helpers/images_helper.rb
+                        'href' => short_url(d.image.image_file.url(:original)), # see app/helpers/images_helper.rb
                         'label' => c.target_name(:description, nil) + ' ' + cs.target_name(:description, nil)
                       )
                     end
@@ -222,7 +222,7 @@ def nexml_otus(options = {})
                   'xsi:type' => 'ResourceMeta',
                   'rel' => 'foaf:depiction',
                   'about' => "row_#{r.id}",
-                  'href' => image_short_url( im.image_hash[depiction[:image_id]][:original_url] ),
+                  'href' => short_url( im.image_hash[depiction[:image_id]][:original_url]),
                   'label' => lbl
                   #'object' => object[1][:object].otu_name,
                   #'label' => descriptors[index][:name], ###

From 12fdf9626df0eb7cd9bd7e3d439e8965f18a0315 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Thu, 17 Nov 2022 16:06:32 -0600
Subject: [PATCH 036/160] fixes #3184

---
 CHANGELOG.md                          |  1 +
 app/models/taxon_name_relationship.rb | 10 +++++-----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a3be85402d..b468eaecd2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,6 +44,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Updated node packages
 
 ### Fixed
+- Incorrect soft validation message on TaxonName relationship [#3184]
 - Browse nomenclature crashing when taxon name descendants have no cached author year
 - Soft validation crashing when cached nomenclature date is absent
 - Role picker is missing after create a source from BibTeX [#3180]
diff --git a/app/models/taxon_name_relationship.rb b/app/models/taxon_name_relationship.rb
index 278ba98c7d..f24ea4c8e0 100644
--- a/app/models/taxon_name_relationship.rb
+++ b/app/models/taxon_name_relationship.rb
@@ -1,4 +1,4 @@
-require_dependency Rails.root.to_s + '/app/models/taxon_name_classification.rb'  
+require_dependency Rails.root.to_s + '/app/models/taxon_name_classification.rb'
 
 # A NOMEN https://github.com/SpeciesFileGroup/nomen relationship between two Protonyms.
 #
@@ -388,7 +388,7 @@ def validate_subject_and_object_ranks
   end
 
   ##### Protonym historically could be listed as a synonym to different taxa
-  #def validate_uniqueness_of_synonym_subject 
+  #def validate_uniqueness_of_synonym_subject
   #  if !self.type.nil? && /Synonym/.match(self.type_name) && !TaxonNameRelationship.where(subject_taxon_name_id: self.subject_taxon_name_id).with_type_contains('Synonym').not_self(self).empty?
   #    errors.add(:subject_taxon_name_id, 'Only one synonym relationship is allowed')
   #  end
@@ -422,7 +422,7 @@ def set_cached_names_for_taxon_names
       TaxonName.transaction do
         if is_invalidating?
           t = subject_taxon_name
-          
+
           if type_name =~/Misspelling/
             t.update_column(:cached_misspelling, t.get_cached_misspelling)
             t.update_columns(
@@ -581,7 +581,7 @@ def sv_coordinated_taxa
     o = object_taxon_name
     s_new = s.lowest_rank_coordinated_taxon
     if s != s_new
-      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s.cached_html}",
+      soft_validations.add(:subject_taxon_name_id, "Relationship should move from #{s.rank_class.rank_name} #{s.cached_html} to #{s_new.rank_class.rank_name} #{s_new.cached_html}",
                            success_message: "Relationship moved to  #{s_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
     end
   end
@@ -591,7 +591,7 @@ def sv_coordinated_taxa_object
     o = object_taxon_name
     o_new = o.lowest_rank_coordinated_taxon
     if o != o_new && type_name != 'TaxonNameRelationship::Iczn::Validating::UncertainPlacement'
-      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o.cached_html}",
+      soft_validations.add(:object_taxon_name_id, "Relationship should move from #{o.rank_class.rank_name} #{o.cached_html} to #{o_new.rank_class.rank_name} #{o_new.cached_html}",
                            success_message: "Relationship moved to  #{o_new.rank_class.rank_name}", failure_message:  'Failed to update relationship')
     end
   end

From 38059a9a000580946bb0b37e67b106a61a862fea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Fri, 18 Nov 2022 13:22:47 -0300
Subject: [PATCH 037/160] Add sqed filter interface

---
 app/javascript/packs/application.js           |   1 +
 .../vue/routes/endpoints/CollectionObject.js  |   4 +-
 .../tasks/accessions/breakdown/filter/App.vue | 100 ++++++++++++++
 .../filter/components/MenuPreferences.vue     |  41 ++++++
 .../breakdown/filter/components/filter.vue    | 124 ++++++++++++++++++
 .../breakdown/filter/components/list.vue      |  24 ++++
 .../helpers/checkMatchIdentifiersParams.js    |   4 +
 .../tasks/accessions/breakdown/filter/main.js |  16 +++
 .../sqed_depiction/todo_map.html.erb          |  28 +---
 9 files changed, 314 insertions(+), 28 deletions(-)
 create mode 100644 app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
 create mode 100644 app/javascript/vue/tasks/accessions/breakdown/filter/components/MenuPreferences.vue
 create mode 100644 app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue
 create mode 100644 app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue
 create mode 100644 app/javascript/vue/tasks/accessions/breakdown/filter/helpers/checkMatchIdentifiersParams.js
 create mode 100644 app/javascript/vue/tasks/accessions/breakdown/filter/main.js

diff --git a/app/javascript/packs/application.js b/app/javascript/packs/application.js
index 0794d310c5..53beae61c6 100644
--- a/app/javascript/packs/application.js
+++ b/app/javascript/packs/application.js
@@ -79,3 +79,4 @@ require('../vue/tasks/extracts/filter/main.js')
 require('../vue/tasks/people/filter/main.js')
 require('../vue/tasks/collection_objects/stepwise/determinations/main.js')
 require('../vue/tasks/content/publisher/main.js')
+require('../vue/tasks/accessions/breakdown/filter/main')
diff --git a/app/javascript/vue/routes/endpoints/CollectionObject.js b/app/javascript/vue/routes/endpoints/CollectionObject.js
index f480084841..0907d18e29 100644
--- a/app/javascript/vue/routes/endpoints/CollectionObject.js
+++ b/app/javascript/vue/routes/endpoints/CollectionObject.js
@@ -66,5 +66,7 @@ export const CollectionObject = {
 
   stepwiseDeterminations: (params) => AjaxCall('get', '/tasks/collection_objects/stepwise/determinations/data.json', { params }),
 
-  timeline: (id) => AjaxCall('get', `/${controller}/${id}/timeline`)
+  timeline: (id) => AjaxCall('get', `/${controller}/${id}/timeline`),
+
+  sqedFilter: (params) => AjaxCall('get', '/tasks/accessions/breakdown/sqed_depiction/todo_map.json', { params })
 }
diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
new file mode 100644
index 0000000000..bdbe916d82
--- /dev/null
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
@@ -0,0 +1,100 @@
+<template>
+  <div>
+    <spinner-component
+      v-if="isLoading"
+      full-screen
+      legend="Searching..."
+      :logo-size="{ width: '100px', height: '100px'}"
+    />
+    <div class="flex-separate middle">
+      <h1>Collection object image breakdown (sqed) TODO list</h1>
+      <menu-preferences v-model="preferences" />
+    </div>
+
+    <JsonRequestUrl
+      v-show="preferences.activeJSONRequest"
+      class="panel content separate-bottom"
+      :url="urlRequest"
+    />
+
+    <div class="horizontal-left-content align-start">
+      <filter-component
+        class="margin-medium-right"
+        v-show="preferences.activeFilter"
+        @parameters="makeFilterRequest"
+        @reset="resetFilter"
+      />
+      <div class="full_width overflow-x-auto">
+        <div
+          class="flex-separate margin-medium-bottom"
+          v-if="pagination"
+        >
+          <pagination-component
+            :pagination="pagination"
+            @next-page="loadPage"
+          />
+          <pagination-count
+            v-model="per"
+            :pagination="pagination"
+          />
+        </div>
+
+        <list-component
+          v-if="Object.keys(sqedResult).length"
+          :list="list"
+        />
+      </div>
+    </div>
+  </div>
+</template>
+
+<script setup>
+import FilterComponent from './components/filter.vue'
+import ListComponent from './components/list'
+import PaginationComponent from 'components/pagination'
+import PaginationCount from 'components/pagination/PaginationCount'
+import MenuPreferences from './components/MenuPreferences.vue'
+import SpinnerComponent from 'components/spinner.vue'
+import useFilter from 'tasks/extracts/filter/composables/useFilter.js'
+import JsonRequestUrl from 'tasks/people/filter/components/JsonRequestUrl.vue'
+import { CollectionObject } from 'routes/endpoints'
+import { computed, reactive } from 'vue'
+import { URLParamsToJSON } from 'helpers/url/parse'
+
+const preferences = reactive({
+  activeFilter: true,
+  activeJSONRequest: false
+})
+
+const {
+  isLoading,
+  list,
+  pagination,
+  per,
+  urlRequest,
+  loadPage,
+  makeFilterRequest,
+  resetFilter
+} = useFilter({ filter: CollectionObject.sqedFilter })
+
+const sqedResult = computed(() => Array.isArray(list.value) ? {} : list.value)
+
+const urlParams = URLParamsToJSON(location.href)
+
+if (Object.keys(urlParams).length) {
+  makeFilterRequest(urlParams)
+}
+
+</script>
+
+<script>
+export default {
+  name: 'BreakdownSqed'
+}
+</script>
+
+<style scoped>
+  .no-found-message {
+    height: 70vh;
+  }
+</style>
diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/components/MenuPreferences.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/components/MenuPreferences.vue
new file mode 100644
index 0000000000..f12366aa9a
--- /dev/null
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/components/MenuPreferences.vue
@@ -0,0 +1,41 @@
+<template>
+  <ul class="context-menu">
+    <li>
+      <label>
+        <input
+          type="checkbox"
+          v-model="preferences.activeFilter">
+        Show filter
+      </label>
+    </li>
+    <li>
+      <label>
+        <input
+          type="checkbox"
+          v-model="preferences.activeJSONRequest">
+        Show JSON Request
+      </label>
+    </li>
+  </ul>
+</template>
+
+<script setup>
+import { computed } from 'vue'
+
+const props = defineProps({
+  modelValue: {
+    type: Object,
+    required: true
+  }
+})
+
+const emit = defineEmits([
+  'update:modelValue'
+])
+
+const preferences = computed({
+  get: () => props.modelValue,
+  set: value => emit('update:modelValue', value)
+})
+
+</script>
diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue
new file mode 100644
index 0000000000..cbda0ad606
--- /dev/null
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue
@@ -0,0 +1,124 @@
+<template>
+  <div
+    class="panel vue-filter-container"
+    v-hotkey="shortcuts"
+  >
+    <div class="flex-separate content middle action-line">
+      <span>Filter</span>
+      <button
+        type="button"
+        data-icon="w_reset"
+        class="button circle-button button-default center-icon no-margin"
+        @click="resetFilter"
+      />
+    </div>
+
+    <div class="content">
+      <button
+        class="button button-default normal-input full_width margin-medium-bottom"
+        type="button"
+        @click="handleSearch"
+      >
+        Search
+      </button>
+
+      <user-component
+        class="margin-large-bottom"
+        v-model="params.user"
+      />
+
+      <WithComponent
+        class="margin-large-bottom"
+        v-for="(_, key) in params.with"
+        :key="key"
+        :title="withTitles[key] || key"
+        :param="key"
+        v-model="params.with[key]"
+      />
+    </div>
+  </div>
+</template>
+
+<script setup>
+
+import UserComponent from 'tasks/collection_objects/filter/components/filters/user'
+import platformKey from 'helpers/getPlatformKey.js'
+import WithComponent from 'tasks/sources/filter/components/filters/with'
+import { removeEmptyProperties } from 'helpers/objects'
+import { computed, ref } from 'vue'
+
+const withTitles = {
+  with_buffered_determinations: 'Buffered determinations',
+  with_buffered_collecting_event: 'Buffered collecting event',
+  with_buffered_other_labels: 'Buffered other labels'
+}
+
+const emit = defineEmits([
+  'parameters',
+  'reset'
+])
+
+const shortcuts = computed(() => {
+  const keys = {}
+
+  keys[`${platformKey()}+r`] = resetFilter
+  keys[`${platformKey()}+f`] = handleSearch
+
+  return keys
+})
+
+const parseParams = computed(() =>
+  removeEmptyProperties({
+    ...params.value.base,
+    ...params.value.with,
+    ...filterEmptyParams(params.value.user)
+  })
+)
+
+const resetFilter = () => {
+  emit('reset')
+  params.value = initParams()
+}
+
+const initParams = () => ({
+  base: {
+  },
+  with: {
+    identifiers: undefined,
+    collecting_event: undefined,
+    taxon_determinations: undefined,
+    with_buffered_determinations: undefined,
+    with_buffered_collecting_event: undefined,
+    with_buffered_other_labels: undefined
+  },
+  user: {
+    user_id: undefined,
+    user_target: undefined,
+    user_date_start: undefined,
+    user_date_end: undefined
+  }
+})
+
+const params = ref(initParams())
+
+const handleSearch = () => {
+  emit('parameters', parseParams.value)
+}
+
+const filterEmptyParams = object => {
+  const keys = Object.keys(object)
+
+  keys.forEach(key => {
+    if (object[key] === '') {
+      delete object[key]
+    }
+  })
+  return object
+}
+
+</script>
+<style scoped>
+:deep(.btn-delete) {
+  background-color: #5D9ECE;
+}
+</style>
diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue
new file mode 100644
index 0000000000..3d0d3579b5
--- /dev/null
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue
@@ -0,0 +1,24 @@
+<template>
+  <div class="panel content">
+    <div>
+      <span class="feedback feedback-success feedback-thin">First with data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.first_with_data}`">{{ list.navigation.filtered.first_with_data }}</a></span>&nbsp;
+      <span class="feedback feedback-warning feedback-thin">First without data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.first_without_data}`">{{ list.navigation.filtered.first_without_data }}</a></span>&nbsp;
+      <span class="feedback feedback-success feedback-thin">Last with data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.last_with_data}`">{{ list.navigation.filtered.last_with_data }}</a></span>&nbsp;
+      <span class="feedback feedback-warning feedback-thin">Last without data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.last_without_data}`">{{ list.navigation.filtered.last_without_data }}</a></span>&nbsp;
+    </div>
+    <div class="full_width horizontal-left-content flex-start">
+      <h3 v-html="list.svg_legend" />
+      <div v-html="list.svg_map" />
+    </div>
+  </div>
+</template>
+
+<script setup>
+
+defineProps({
+  list: {
+    type: Object,
+    default: undefined
+  }
+})
+</script>
diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/helpers/checkMatchIdentifiersParams.js b/app/javascript/vue/tasks/accessions/breakdown/filter/helpers/checkMatchIdentifiersParams.js
new file mode 100644
index 0000000000..4e7d99f4f2
--- /dev/null
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/helpers/checkMatchIdentifiersParams.js
@@ -0,0 +1,4 @@
+export default params =>
+  params.match_identifiers
+    ? params
+    : {}
diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/main.js b/app/javascript/vue/tasks/accessions/breakdown/filter/main.js
new file mode 100644
index 0000000000..9f0fbb4142
--- /dev/null
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/main.js
@@ -0,0 +1,16 @@
+import { createApp } from 'vue'
+import App from './App.vue'
+import hotkey from 'plugins/v-hotkey'
+
+function initApp (element) {
+  const app = createApp(App)
+
+  app.directive('hotkey', hotkey)
+  app.mount(element)
+}
+
+document.addEventListener('turbolinks:load', () => {
+  const el = document.querySelector('#vue-breakdown-sqed')
+
+  if (el) { initApp(el) }
+})
diff --git a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb
index b42fb6a107..55af4d1c90 100644
--- a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb
+++ b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.html.erb
@@ -1,27 +1 @@
-<h1> Collection object image breakdown (sqed) TODO list </h1>
-
-<p> Overview: 
-<%= sqed_done_tag(sessions_current_project_id) -%> done. <%= sqed_not_done_tag(sessions_current_project_id) -%> remaining. <br>
-<%= page_entries_info @sqed_depictions %>. <%= SqedDepiction.where(project_id: sessions_current_project_id).where.not(in_progress: nil).count(:all) -%> in progress.</p>
-
-<fieldset title="Navigate">
-  <legend> Navigate </legend>
-  <%= paginate @sqed_depictions %><br>
-  <%= sqed_first_with_data_tag -%>&nbsp;
-  <%= sqed_first_without_data_tag -%>&nbsp;
-  <%= sqed_last_with_data_tag -%>&nbsp;
-  <%= sqed_last_without_data_tag -%>&nbsp;
-  <%= sqed_last_by_user_tag -%>&nbsp;
-</fieldset><br>
-
-<div class="flexbox" data-turbolinks="false" id="todo_map">
-  <div class="item item1">
-    <%= sqed_waxy_legend_tag -%>
-  </div>
-
-  <div class="item item2">
-    <h3> Stage images </h3>
-    <p><i> Purple borders indicate record is in progress </i></p>
-    <%= sqed_waxy_layout(@sqed_depictions) -%>
-  </div>
-</div>
+<div id="vue-breakdown-sqed"></div>

From 900cfe4a305c8ef2ff59d56497f0113eb850db29 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Fri, 18 Nov 2022 16:18:34 -0300
Subject: [PATCH 038/160] Request when task is open

---
 app/javascript/vue/tasks/accessions/breakdown/filter/App.vue | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
index bdbe916d82..431ce618ae 100644
--- a/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
@@ -78,12 +78,9 @@ const {
 } = useFilter({ filter: CollectionObject.sqedFilter })
 
 const sqedResult = computed(() => Array.isArray(list.value) ? {} : list.value)
-
 const urlParams = URLParamsToJSON(location.href)
 
-if (Object.keys(urlParams).length) {
-  makeFilterRequest(urlParams)
-}
+makeFilterRequest(urlParams)
 
 </script>
 

From 0fb45407b1d2a15c9a0a06af7394428364767318 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Fri, 18 Nov 2022 16:58:06 -0300
Subject: [PATCH 039/160] Add label footer

---
 app/helpers/labels_helper.rb                   |  4 +++-
 app/javascript/vue/assets/styles/labels.scss   | 18 ++++++++++++++----
 .../labels/print_labels/stylesheets/ce.scss    | 17 +++++++++++++----
 3 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/app/helpers/labels_helper.rb b/app/helpers/labels_helper.rb
index fdd9b5f8e8..b16696bc35 100644
--- a/app/helpers/labels_helper.rb
+++ b/app/helpers/labels_helper.rb
@@ -75,7 +75,9 @@ def label_unit_tray_header1_tag(label)
       "\n" +
       tag.span(
         [o.taxonomy['order'], o.taxonomy['family']].compact.join(': '), class: 'unit_tray_header1_bottom'
-      ), class: 'unit_tray_header1')
+      ) +
+      tag.div('', class: 'unit_tray_header1_footer'),
+      class: 'unit_tray_header1')
   end
 
   # Object is a Container
diff --git a/app/javascript/vue/assets/styles/labels.scss b/app/javascript/vue/assets/styles/labels.scss
index 949ea170e7..a0a54a92e2 100644
--- a/app/javascript/vue/assets/styles/labels.scss
+++ b/app/javascript/vue/assets/styles/labels.scss
@@ -5,8 +5,7 @@
 }
 
 .unit_tray_header1 {
-  padding-left: 2pt;
-  padding-right: 2pt;
+
   font-family: Arial, sans-serif;
   height: 38mm; 
   width: 74mm;
@@ -26,7 +25,18 @@
   .unit_tray_header1_top {
     display: flex;
     flex-direction: row;
-    justify-content: space-between
+    justify-content: space-between;
+    height: 100%;
+    padding-left: 2pt;
+    padding-right: 2pt;
+  };
+  .unit_tray_header1_bottom {
+    padding-left: 2pt;
+    padding-right: 2pt;
   };
-  .unit_tray_header1_bottom {};
+
+  .unit_tray_header1_footer {
+    border-top: 2px solid black;
+    height: 10mm;
+  }
 }
\ No newline at end of file
diff --git a/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss b/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
index b09a982db9..cc1d641897 100644
--- a/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
+++ b/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
@@ -131,8 +131,6 @@ div.ce_label_pg {
 }
 
 .unit_tray_header1 {
-  padding-left: 2pt;
-  padding-right: 2pt;
   font-family: Arial, sans-serif;
   height: 38mm; 
   width: 74mm;
@@ -152,7 +150,18 @@ div.ce_label_pg {
   .unit_tray_header1_top {
     display: flex;
     flex-direction: row;
-    justify-content: space-between
+    justify-content: space-between;
+    padding-left: 2pt;
+    padding-right: 2pt;
+    height: 100%;
   };
-  .unit_tray_header1_bottom {};
+  .unit_tray_header1_bottom {
+    padding-left: 2pt;
+    padding-right: 2pt;
+  };
+
+  .unit_tray_header1_footer {
+    border-top: 2px solid black;
+    height: 10mm;
+  }
 }
\ No newline at end of file

From 88340da572929ad33f6be260242ae2673e42297c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Fri, 18 Nov 2022 17:13:27 -0300
Subject: [PATCH 040/160] Change footer size

---
 app/javascript/vue/assets/styles/labels.scss                    | 2 +-
 .../vue/tasks/labels/print_labels/stylesheets/ce.scss           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/assets/styles/labels.scss b/app/javascript/vue/assets/styles/labels.scss
index a0a54a92e2..78faafb832 100644
--- a/app/javascript/vue/assets/styles/labels.scss
+++ b/app/javascript/vue/assets/styles/labels.scss
@@ -37,6 +37,6 @@
 
   .unit_tray_header1_footer {
     border-top: 2px solid black;
-    height: 10mm;
+    height: 6.35mm;
   }
 }
\ No newline at end of file
diff --git a/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss b/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
index cc1d641897..b3f3351d88 100644
--- a/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
+++ b/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
@@ -162,6 +162,6 @@ div.ce_label_pg {
 
   .unit_tray_header1_footer {
     border-top: 2px solid black;
-    height: 10mm;
+    height: 6.35mm;
   }
 }
\ No newline at end of file

From 5f964254a9ac3bed28aed4cff34ce75de1345d36 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Fri, 18 Nov 2022 17:12:15 -0600
Subject: [PATCH 041/160] fixes #3181

---
 CHANGELOG.md                |  1 +
 app/models/source/bibtex.rb | 80 ++++++++++++++++++++-----------------
 2 files changed, 45 insertions(+), 36 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b468eaecd2..218ea94b0a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -58,6 +58,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [0.29.5] - 2022-10-10
 
 ### Changed
+- Source cached_value calculation [#3181]
 - Changed author labels on Filter source [#3134]
 - Minor changes to plots on administration activity dashboard 
 - Parallelize some indexing rake tasks
diff --git a/app/models/source/bibtex.rb b/app/models/source/bibtex.rb
index 339cbbdf86..8e14dde05b 100644
--- a/app/models/source/bibtex.rb
+++ b/app/models/source/bibtex.rb
@@ -870,24 +870,30 @@ def authority_name(reload = true)
     end
   end
 
-  protected
-
-  def validate_year_suffix
-    a = get_author
-    unless year_suffix.blank? || year.blank? || a.blank?
-      if new_record?
-        s = Source.where(author: a, year: year, year_suffix: year_suffix).first
-      else
-        s = Source.where(author: a, year: year, year_suffix: year_suffix).not_self(self).first
-      end
-      errors.add(:year_suffix, " '#{year_suffix}' is already used for #{a} #{year}") unless s.nil?
+  # TODO: Replace with taxonworks.csl.  Move unsupported fields to
+  # wrappers in vue rendering.
+  # set cached values and copies active record relations into bibtex values
+  # @return [Ignored]
+  def set_cached
+    if errors.empty?
+      attributes_to_update = {}
+      attributes_to_update[:author] = get_bibtex_names('author') if authors.reload.size > 0
+      attributes_to_update[:editor] = get_bibtex_names('editor') if editors.reload.size > 0
+      attributes_to_update.merge!(
+        cached: get_cached,
+        cached_nomenclature_date: nomenclature_date,
+        cached_author_string: authority_name(false)
+      )
+      update_columns(attributes_to_update)
     end
   end
 
-  def italics_are_paired
-    l = title.scan('<i>')&.count
-    r = title.scan('</i>')&.count
-    errors.add(:title, 'italic markup is not paired') unless l == r
+  def get_cached
+    if errors.empty?
+      c = cached_string('html') # preserves our convention of <i>
+      return c
+    end
+    nil
   end
 
   # @param [String] type either `author` or `editor`
@@ -915,30 +921,24 @@ def create_authors
     end
   end
 
-  # TODO: Replace with taxonworks.csl.  Move unsupported fields to
-  # wrappers in vue rendering.
-  # set cached values and copies active record relations into bibtex values
-  # @return [Ignored]
-  def set_cached
-    if errors.empty?
-      attributes_to_update = {}
-      attributes_to_update[:author] = get_bibtex_names('author') if authors.reload.size > 0
-      attributes_to_update[:editor] = get_bibtex_names('editor') if editors.reload.size > 0
-      attributes_to_update.merge!(
-        cached: get_cached,
-        cached_nomenclature_date: nomenclature_date,
-        cached_author_string: authority_name(false)
-      )
-      update_columns(attributes_to_update)
+  protected
+
+  def validate_year_suffix
+    a = get_author
+    unless year_suffix.blank? || year.blank? || a.blank?
+      if new_record?
+        s = Source.where(author: a, year: year, year_suffix: year_suffix).first
+      else
+        s = Source.where(author: a, year: year, year_suffix: year_suffix).not_self(self).first
+      end
+      errors.add(:year_suffix, " '#{year_suffix}' is already used for #{a} #{year}") unless s.nil?
     end
   end
 
-  def get_cached
-    if errors.empty?
-      c = cached_string('html') # preserves our convention of <i>
-      return c
-    end
-    nil
+  def italics_are_paired
+    l = title.scan('<i>')&.count
+    r = title.scan('</i>')&.count
+    errors.add(:title, 'italic markup is not paired') unless l == r
   end
 
   #region hard validations
@@ -983,3 +983,11 @@ def sv_cached_names # this cannot be moved to soft_validation_extensions
   end
 end
 
+def aaa
+  ids = []
+  Source.joins(:project_sources).where('project_sources.project_id = 13').first(100).each do |s|
+    s.soft_validate
+    ids.append(s.id) if s.soft_validations.messages.include?('Cached values should be updated')
+  end
+  ids
+end

From 28576e79f947bb5ab1166f8c12c282dcbfd1580a Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Fri, 18 Nov 2022 18:15:40 -0600
Subject: [PATCH 042/160] fixes #3161

---
 app/models/protonym.rb       | 10 +++++++++-
 spec/models/protonym_spec.rb | 26 ++++++++++++++++++--------
 2 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/app/models/protonym.rb b/app/models/protonym.rb
index bab73c6385..9308ad0c9a 100644
--- a/app/models/protonym.rb
+++ b/app/models/protonym.rb
@@ -27,6 +27,7 @@ class Protonym < TaxonName
   validates_presence_of :rank_class, message: 'is a required field'
 
   validate :validate_rank_class_class,
+    :validate_same_nomenclatural_code,
     :validate_parent_rank_is_higher,
     :validate_child_rank_is_equal_or_lower,
     :check_new_rank_class,
@@ -203,7 +204,7 @@ def synonymize_with(protonym)
         TaxonNameRelationship::Icnp::Unaccepting::Synonym.create!(subject_taxon_name: self, object_taxon_name: protonym)
       when :icvnc
         TaxonNameRelationship::Icnp::Unaccepting::SupressedSynony.create!(subject_taxon_name: self, object_taxon_name: protonym)
-      else 
+      else
         return false
       end
     rescue ActiveRecord::RecordInvalid
@@ -958,9 +959,16 @@ def validate_parent_rank_is_higher
     end
   end
 
+  def validate_same_nomenclatural_code
+    if parent&.nomenclatural_code && nomenclatural_code != parent.nomenclatural_code
+      errors.add(:rank_class, "The parent nomenclatural code (#{parent.nomenclatural_code.to_s.upcase}) is not matching to the nomenclatural code (#{nomenclatural_code.to_s.upcase}) of this taxon")
+    end
+  end
+
   # This is a *very* expensive soft validation, it should be fragemented into individual parts likely
   # It should also not be necessary by default our code should be good enough to handle these
   # issues in the long run.
+  # DD: rules for cached tend to evolve, what was good in the past, may not be true today
   def sv_cached_names # this cannot be moved to soft_validation_extensions
   is_cached = true
   is_cached = false if cached_author_year != get_author_and_year
diff --git a/spec/models/protonym_spec.rb b/spec/models/protonym_spec.rb
index 9cf6312ce9..293260afc5 100644
--- a/spec/models/protonym_spec.rb
+++ b/spec/models/protonym_spec.rb
@@ -2,7 +2,7 @@
 
 describe Protonym, type: :model, group: [:nomenclature, :protonym] do
 
-  # TODO: cleanup don't leave dirty .... 
+  # TODO: cleanup don't leave dirty ....
   before(:all) do
     TaxonNameRelationship.delete_all
     TaxonNameClassification.delete_all
@@ -22,7 +22,7 @@
 
   let(:protonym) { Protonym.new }
   let(:root) { Protonym.where(name: 'Root').first  }
- 
+
   context 'validation' do
 
     specify '#verbatim_author without digits' do
@@ -92,6 +92,16 @@
         t.valid?
         expect(t.errors.include?(:project_id)).to be_truthy
       end
+
+      specify 'parent in different code' do
+        genus = FactoryBot.create(:iczn_genus)
+        genus.valid?
+        expect(genus.errors.include?(:rank_class)).to be_falsey
+        genus.rank_class = Ranks.lookup(:icn, 'genus')
+        genus.valid?
+        expect(genus.errors.include?(:rank_class)).to be_truthy
+      end
+
     end
 
     specify 'name' do
@@ -99,7 +109,7 @@
         expect(protonym.errors.include?(:name)).to be_truthy
     end
 
-    context 'latinization requires' do 
+    context 'latinization requires' do
       let(:error_message) {  'Name must be latinized, no digits or spaces allowed' }
       specify 'no digits are present at end' do
         protonym.name = 'aus1'
@@ -118,7 +128,7 @@
         protonym.valid?
         expect(protonym.errors.messages[:name]).to include(error_message)
       end
-        
+
       specify 'no spaces are present' do
         protonym.name = 'ab us'
         protonym.valid?
@@ -126,7 +136,7 @@
       end
     end
   end
-  
+
   context 'usage' do
     before(:each) do
       @f = FactoryBot.create(:relationship_family, name: 'Aidae', parent: @order)
@@ -151,7 +161,7 @@
         subject_taxon_name: @o,
         object_taxon_name: @s,
         type: 'TaxonNameRelationship::OriginalCombination::OriginalGenus')
-      
+
       # Recast as the subclass
       # first_original_genus_relation = temp_relation.becomes(temp_relation.type_class)
       expect(@s.original_combination_relationships.count).to eq(1)
@@ -283,7 +293,7 @@
     let(:p) {Protonym.new(parent: @order , name: 'Aus', rank_class: Ranks.lookup(:iczn, 'genus')) }
 
     specify '#also_create_otu with new creates an otu after_create' do
-      expect(Otu.count).to eq(0) 
+      expect(Otu.count).to eq(0)
       p.also_create_otu = true
       p.save!
       expect(Otu.first.taxon_name_id).to eq(p.id)
@@ -344,7 +354,7 @@
     end
 
     context 'verbatim references' do
-      let(:v) { FactoryBot.create(:valid_source_verbatim) } 
+      let(:v) { FactoryBot.create(:valid_source_verbatim) }
       specify 'are not allowed via nested attributes' do
         expect(g1.update(origin_citation_attributes: { source_id: v.id })).to be_falsey
       end

From d8842893a58910211ea14a3e90618ce8dc1c9029 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Sat, 19 Nov 2022 09:10:52 -0300
Subject: [PATCH 043/160] Fix watcher

---
 .../Classification/ClassificationMain.vue           |  2 +-
 .../new_taxon_name/components/manageSynonym.vue     | 13 ++++++++-----
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
index 4e5950eee8..864b848249 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
@@ -34,6 +34,6 @@ watch([taxonRank, parent], () => {
     taxon.value.rank_string,
     parent.value.rank_string
   )
-}, { immediate: true })
+})
 
 </script>
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue
index 706f357d7a..e4d1062d72 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue
@@ -61,11 +61,14 @@
                     :add-params="{ type: 'Protonym', 'nomenclature_group[]': 'Genus' }"
                     :placeholder="validTaxon.name"/>
                 </td>
-                <td class="horizontal-left-content">
-                  <span
-                    class="circle-button btn-edit"
-                    @click="loadTaxon(child.id)"/>
-                  <radial-annotator :global-id="child.global_id"/>
+                <td>
+                  <div class="horizontal-left-content">
+                    <span
+                      class="circle-button btn-edit"
+                      @click="loadTaxon(child.id)"
+                    />
+                    <radial-annotator :global-id="child.global_id" />
+                  </div>
                 </td>
                 <td>
                   <input

From 084d0b00f3acb3148d5b3e8b1775a649c217f798 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Sat, 19 Nov 2022 09:18:26 -0300
Subject: [PATCH 044/160] Fix watcher

---
 .../Classification/ClassificationMain.vue      | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
index 864b848249..bdc1ad61e1 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
@@ -28,12 +28,16 @@ const objectLists = ref({
   all: []
 })
 
-watch([taxonRank, parent], () => {
-  objectLists.value = createStatusLists(
-    statusList.value[nomenclaturalCode.value] || {},
-    taxon.value.rank_string,
-    parent.value.rank_string
-  )
-})
+watch([taxonRank, parent],
+  () => {
+    if (taxon.value && parent.value) {
+      objectLists.value = createStatusLists(
+        statusList.value[nomenclaturalCode.value] || {},
+        taxon.value.rank_string,
+        parent.value.rank_string
+      )
+    }
+  },
+  { immediate: true })
 
 </script>

From ad44323c5cc1dac2b0ff8421e214196fd605ec1a Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 21 Nov 2022 15:53:02 -0600
Subject: [PATCH 045/160] Local identifier facet params

---
 .../breakdown/sqed_depiction_controller.rb    |  4 +++-
 app/models/concerns/shared/identifiers.rb     | 13 ++++++-------
 lib/queries/concerns/identifiers.rb           | 19 +++++++++++++++++++
 lib/queries/sqed_depiction/filter.rb          |  7 ++++---
 4 files changed, 32 insertions(+), 11 deletions(-)

diff --git a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
index 28011d6434..c8a1efa8b8 100644
--- a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
+++ b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
@@ -7,7 +7,8 @@ class Tasks::Accessions::Breakdown::SqedDepictionController < ApplicationControl
   # /tasks/accessions/breakdown/sqed_depiction/todo_map
   def todo_map
     SqedDepiction.clear_stale_progress
-    @base_query = ::Queries::SqedDepiction::Filter.new(filter_params).all.where(project_id: sessions_current_project_id)
+    @base_query = ::Queries::SqedDepiction::Filter.new(filter_params).all
+      .where(project_id: sessions_current_project_id)
       .order(:id)
     @sqed_depictions = @base_query.page(params[:page]).per(50)
     respond_to do |format|
@@ -74,6 +75,7 @@ def set_sqed_depiction
   def filter_params
     a = params.permit(
       ::Queries::SqedDepiction::Filter::COLLECTION_OBJECT_FILTER_PARAMS,
+      :local_identifiers,
       :recent,
       :user_date_end,
       :user_date_start,
diff --git a/app/models/concerns/shared/identifiers.rb b/app/models/concerns/shared/identifiers.rb
index 24ea397c09..969339b32e 100644
--- a/app/models/concerns/shared/identifiers.rb
+++ b/app/models/concerns/shared/identifiers.rb
@@ -5,14 +5,14 @@ module Shared::Identifiers
   extend ActiveSupport::Concern
   included do
     Identifier.related_foreign_keys.push self.name.foreign_key
-    
+
     # Validation happens on the parent side!
     has_many :identifiers, as: :identifier_object, validate: true, dependent: :destroy # TODO: add for validation, inverse_of: :identifier_object
     accepts_nested_attributes_for :identifiers, reject_if: :reject_identifiers, allow_destroy: true
-    
+
     scope :with_identifier_type, ->(identifier_type) { joins(:identifiers).where('identifiers.type = ?', identifier_type).references(:identifiers) }
     scope :with_identifier_namespace, ->(namespace_id) { joins(:identifiers).where('identifiers.namespace_id = ?', namespace_id).references(:identifiers) }
-    
+
     # !! This only is able to match numeric identifiers, other results are excluded !!
     def self.with_identifiers_sorted(sort_order = 'ASC')
       raise "illegal sort_order" if !['ASC', 'DESC'].include?(sort_order)
@@ -21,12 +21,11 @@ def self.with_identifiers_sorted(sort_order = 'ASC')
         .order(cached_numeric_identifier: sort_order)
         .references(:identifiers)
     end
-    
-    
+
     scope :with_identifier_type_and_namespace, ->(identifier_type = nil, namespace_id = nil, sorted = nil) {
       with_identifier_type_and_namespace_method(identifier_type, namespace_id, sorted)
     }
-    
+
     # Used to memoize identifier for navigating purposes
     attr_accessor :navigating_identifier
   end
@@ -96,7 +95,7 @@ def identified?
   def next_by_identifier
     # TODO: Memoize i so it can be shared with previous etc.
     # LIke attr_accessor @navigating_identifier
-    if @navigating_identifier ||= identifiers.where("type ILIKE 'Identifier::Local%'").order(:position).first
+    if @navigating_identifier ||= identifiers.where("identifiers.type ILIKE 'Identifier::Local%'").order(:position).first
       self.class
         .where(project_id: project_id)
         .where.not(id: id)
diff --git a/lib/queries/concerns/identifiers.rb b/lib/queries/concerns/identifiers.rb
index 0d010e09e1..7380039015 100644
--- a/lib/queries/concerns/identifiers.rb
+++ b/lib/queries/concerns/identifiers.rb
@@ -39,6 +39,12 @@ module Queries::Concerns::Identifiers
     #   nil - not applied
     attr_accessor :identifiers
 
+    # @return [True, False, nil]
+    #   true - has an local identifier
+    #   false - does not have an local identifier
+    #   nil - not applied
+    attr_accessor :local_identifiers
+
     attr_accessor :match_identifiers
 
     attr_accessor :match_identifiers_delimiter
@@ -73,6 +79,7 @@ def set_identifier(params)
     @identifier_end = params[:identifier_end]
     @identifier = params[:identifier]
     @identifiers = boolean_param(params, :identifiers)
+    @local_identifiers = boolean_param(params, :local_identifiers)
 
     @identifier_exact = boolean_param(params, :identifier_exact)
     @identifier_type = params[:identifier_type] || []
@@ -141,6 +148,18 @@ def identifiers_facet
     end
   end
 
+  def local_identifiers_facet
+    return nil if local_identifiers.nil?
+    if local_identifiers
+      query_base.joins(:identifiers).where("identifiers.type ILIKE 'Identifier::Local%'").distinct
+    else
+      query_base.left_outer_joins(:identifiers)
+        .where(identifiers: {id: nil})
+        .where.not("identifiers.type ILIKE 'Identifier::Local%'")
+        .distinct
+    end
+  end
+
   def identifier_facet
     return nil if identifier.blank?
 
diff --git a/lib/queries/sqed_depiction/filter.rb b/lib/queries/sqed_depiction/filter.rb
index 2ab975bae0..ed10729b58 100644
--- a/lib/queries/sqed_depiction/filter.rb
+++ b/lib/queries/sqed_depiction/filter.rb
@@ -30,7 +30,7 @@ def table
       end
 
       def base_query
-        ::SqedDepiction.select('sqed_depiction.*')
+        ::SqedDepiction.select('sqed_depictions.*')
       end
 
       def collection_object_query_facet
@@ -64,6 +64,7 @@ def base_merge_clauses
 
         clauses += [
           created_updated_facet,  # See Queries::Concerns::Users
+          local_identifiers_facet,
           identifiers_facet,
           collection_object_query_facet,
         ]
@@ -89,9 +90,9 @@ def all
         b = merge_clauses
         # q = nil
         if a && b
-          q = b.where(a)
+          q = b.where(a).distinct
         elsif a
-          q = ::SqedDepiction.where(a)
+          q = ::SqedDepiction.where(a).distinct
         elsif b
           q = b
         else

From a257184559ad93dccaf862817cd3643a4a7e5b8a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Mon, 21 Nov 2022 19:09:38 -0300
Subject: [PATCH 046/160] add local_identifiers param to CO and sqed filters

---
 .../vue/tasks/accessions/breakdown/filter/components/filter.vue | 2 +-
 .../vue/tasks/collection_objects/filter/components/filter.vue   | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue
index cbda0ad606..3e59794a1c 100644
--- a/app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/components/filter.vue
@@ -84,7 +84,7 @@ const initParams = () => ({
   base: {
   },
   with: {
-    identifiers: undefined,
+    local_identifiers: undefined,
     collecting_event: undefined,
     taxon_determinations: undefined,
     with_buffered_determinations: undefined,
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue b/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue
index 13371d10f6..bf4ac2d98b 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue
@@ -299,6 +299,7 @@ export default {
           geographic_area: undefined,
           georeferences: undefined,
           identifiers: undefined,
+          local_identifiers: undefined,
           taxon_determinations: undefined,
           type_material: undefined,
           current_repository: undefined,

From fd2cfb95812c245e8707009a46879763702df4c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Mon, 21 Nov 2022 19:17:53 -0300
Subject: [PATCH 047/160] add local_identifiers param to CO and sqed filters

---
 .../vue/tasks/collecting_events/filter/components/Filter.vue   | 3 ++-
 .../vue/tasks/collection_objects/filter/components/filter.vue  | 1 -
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue b/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue
index 259ffc54c0..5aab2ff8d9 100644
--- a/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue
+++ b/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue
@@ -219,7 +219,8 @@ export default {
           data_attributes: undefined,
           geographic_area: undefined,
           georeferences: undefined,
-          identifiers: undefined
+          identifiers: undefined,
+          local_identifiers: undefined
         },
         identifier: {
           identifier: undefined,
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue b/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue
index bf4ac2d98b..596906f65c 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/filter.vue
@@ -298,7 +298,6 @@ export default {
           depictions: undefined,
           geographic_area: undefined,
           georeferences: undefined,
-          identifiers: undefined,
           local_identifiers: undefined,
           taxon_determinations: undefined,
           type_material: undefined,

From 993a01d5cabd07af7352746ff339254cb9022800 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 21 Nov 2022 16:50:48 -0600
Subject: [PATCH 048/160] Stub figure, fig-caption scss.

---
 app/assets/stylesheets/base/figures.scss | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 app/assets/stylesheets/base/figures.scss

diff --git a/app/assets/stylesheets/base/figures.scss b/app/assets/stylesheets/base/figures.scss
new file mode 100644
index 0000000000..0376dee3e6
--- /dev/null
+++ b/app/assets/stylesheets/base/figures.scss
@@ -0,0 +1,5 @@
+figure {
+  background-color: green;
+}
+
+fig-caption { font-size: 10px; }

From 7f5ab4ba1a3a810b022b17f98a1156d19d30a7a6 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 21 Nov 2022 22:23:06 -0600
Subject: [PATCH 049/160] Update todo legend and identifiers params

---
 app/assets/stylesheets/base/figures.scss      |  3 ++-
 app/controllers/project_members_controller.rb |  2 +-
 .../breakdown/buffered_data_controller.rb     |  3 ---
 .../breakdown/sqed_depiction_controller.rb    |  1 -
 app/helpers/sqed_depictions_helper.rb         | 23 +++++++++----------
 app/models/identifier.rb                      | 15 +++++++-----
 lib/queries/collection_object/filter.rb       |  1 +
 lib/queries/concerns/identifiers.rb           | 13 +++++++----
 lib/queries/sqed_depiction/filter.rb          | 13 +++++------
 lib/queries/taxon_name/filter.rb              |  8 +++----
 10 files changed, 42 insertions(+), 40 deletions(-)

diff --git a/app/assets/stylesheets/base/figures.scss b/app/assets/stylesheets/base/figures.scss
index 0376dee3e6..7cfa702a2b 100644
--- a/app/assets/stylesheets/base/figures.scss
+++ b/app/assets/stylesheets/base/figures.scss
@@ -1,5 +1,6 @@
 figure {
+  // fix me :)
   background-color: green;
 }
 
-fig-caption { font-size: 10px; }
+fig-caption {  }
diff --git a/app/controllers/project_members_controller.rb b/app/controllers/project_members_controller.rb
index dad2cfcf51..c50c0918e1 100644
--- a/app/controllers/project_members_controller.rb
+++ b/app/controllers/project_members_controller.rb
@@ -10,7 +10,7 @@ class ProjectMembersController < ApplicationController
 
   # GET /project_members.json
   def index
-    @project_members = ProjectMember.joins(:user).where(project_id: sessions_current_project_id).order('users.name ASC')
+    @project_members = ProjectMember.joins(:user).where(project_id: sessions_current_project_id).order('users.name ASC').includes(:user)
   end
 
   # GET /project_members/new
diff --git a/app/controllers/tasks/accessions/breakdown/buffered_data_controller.rb b/app/controllers/tasks/accessions/breakdown/buffered_data_controller.rb
index 4e6e4268b0..939c3dac67 100644
--- a/app/controllers/tasks/accessions/breakdown/buffered_data_controller.rb
+++ b/app/controllers/tasks/accessions/breakdown/buffered_data_controller.rb
@@ -1,11 +1,8 @@
-
 class Tasks::Accessions::Breakdown::BufferedDataController < ApplicationController
   include TaskControllerConfiguration
 
   before_action :set_collection_object, only: [:index, :update]
 
-  # before_filter
-
   # GET /tasks/accession/breakdown/buffered_data/:id
   def index
     @collection_object.collecting_event = CollectingEvent.new if @collection_object.collecting_event.nil?
diff --git a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
index c8a1efa8b8..2c7d5a578c 100644
--- a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
+++ b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
@@ -75,7 +75,6 @@ def set_sqed_depiction
   def filter_params
     a = params.permit(
       ::Queries::SqedDepiction::Filter::COLLECTION_OBJECT_FILTER_PARAMS,
-      :local_identifiers,
       :recent,
       :user_date_end,
       :user_date_start,
diff --git a/app/helpers/sqed_depictions_helper.rb b/app/helpers/sqed_depictions_helper.rb
index 5a4e86f093..3dbeee5ee9 100644
--- a/app/helpers/sqed_depictions_helper.rb
+++ b/app/helpers/sqed_depictions_helper.rb
@@ -22,7 +22,7 @@ def sqed_depiction_collecting_event_label_thumb_preview(sqed_depiction)
         depiction_id: sqed_depiction.depiction.id,
       )
 
-     return image_tag(result.image_path_for_large_image(section), id: 'little1', class: 'little_image clickable')
+      return image_tag(result.image_path_for_large_image(section), id: 'little1', class: 'little_image clickable')
     rescue
       return content_tag(:div, link_to('Error parsing.', depiction_path(sqed_depiction.depiction)), class: :warning)
     end
@@ -123,7 +123,7 @@ def sqed_last_by_user_tag
       .with_collection_object_data
       .order('collection_objects.updated_at')
       .first
-      content_tag(:span, ('Last update by you: ' + sqed_card_link(o)).html_safe, class: [:feedback, 'feedback-success', 'feedback-thin'])
+    content_tag(:span, ('Last update by you: ' + sqed_card_link(o)).html_safe, class: [:feedback, 'feedback-success', 'feedback-thin'])
     else
       nil
     end
@@ -161,7 +161,7 @@ def sqed_waxy_layout(sqed_depictions)
   def sqed_waxy_metadata(sqed_depiction)
     o = sqed_depiction.depiction_object
     [
-      (o.identifiers.visible(sessions_current_project_id).any? ? 1 : 0),
+      (o.identifiers.local.any? ? 1 : 0),
       (o.buffered_collecting_event.blank? ? 0 : 1),
       (o.buffered_determinations.blank? ? 0 : 1),
       (o.buffered_other_labels.blank? ? 0 : 1),
@@ -173,8 +173,8 @@ def sqed_waxy_metadata(sqed_depiction)
   def sqed_waxy_legend_section_tag(position, label)
     layout = Waxy::Geometry::Layout.new(
       Waxy::Geometry::Orientation::LAYOUT_POINTY,
-      Waxy::Geometry::Point.new(15,15), # size
-      Waxy::Geometry::Point.new(15,15), # start
+      Waxy::Geometry::Point.new(10,10), # size
+      Waxy::Geometry::Point.new(10,10), # start
     )
 
     a = Waxy::Meta.new
@@ -185,16 +185,16 @@ def sqed_waxy_legend_section_tag(position, label)
     c = Waxy::Render::Svg::Canvas.new(35, 35)
     c.body << Waxy::Render::Svg.rectangle(layout, meta)
 
-    content_tag(:figure) do
+    tag.figure do
       c.to_svg.html_safe +
-        content_tag(:figcaption, label)
+        tag.fig_caption(label)
     end
   end
 
   def sqed_waxy_legend_tag
     l = ''
     {
-      0 => 'Identifier(s)',
+      0 => 'Local identifier(s)',
       1 => 'Buffered collecting event',
       2 => 'Buffered determination',
       3 => 'Buffered other labels',
@@ -203,10 +203,9 @@ def sqed_waxy_legend_tag
     }.each do |i,label|
       l << sqed_waxy_legend_section_tag(i, label)
     end
-    content_tag(:div) do
-      content_tag(:h3, 'Legend') +
-        content_tag(:p, content_tag(:em, 'Triangle indicates data presence')) +
-        content_tag(:div, l.html_safe)
+    tag.div do
+      tag.h3('Legend') +
+        l.html_safe
     end
   end
 
diff --git a/app/models/identifier.rb b/app/models/identifier.rb
index c3218e99c3..a03036b786 100644
--- a/app/models/identifier.rb
+++ b/app/models/identifier.rb
@@ -42,8 +42,8 @@
 #
 # @!attribute cached_numeric_identifier
 #   @return [Float, nil]
-#     If `identifier` contains a numeric string, then record this as a float.  
-#     !! This should never be exposed, it's used for internal next/previous options only. 
+#     If `identifier` contains a numeric string, then record this as a float.
+#     !! This should never be exposed, it's used for internal next/previous options only.
 #  See `build_cached_numeric_identifier`.
 #     This does account for identifiers like:
 #       123,123
@@ -54,7 +54,7 @@
 #       123,123a
 #       123a
 #       123.123a
-#        
+#
 class Identifier < ApplicationRecord
   acts_as_list scope: [:project_id, :identifier_object_type, :identifier_object_id ], add_new_at: :top
 
@@ -90,6 +90,9 @@ class Identifier < ApplicationRecord
 
   scope :visible, -> (project_id) { where("identifiers.project_id = ? OR identifiers.type ILIKE 'Identifier::Global%'", project_id) }
 
+  scope :local, -> {where("identifiers.type ILIKE 'Identifier::Local%'") }
+  scope :global, -> {where("identifiers.type ILIKE 'Identifier::Global%'") }
+
   # @return [String, Identifer]
   def self.prototype_identifier(project_id, created_by_id)
     identifiers = Identifier.where(project_id: project_id, created_by_id: created_by_id).limit(1)
@@ -110,15 +113,15 @@ def is_global?
   end
 
   protected
- 
-  # See subclasses 
+
+  # See subclasses
   def build_cached
     nil
   end
 
   def build_cached_numeric_identifier
     return nil if is_global?
-    if a = identifier.match(/\A[\d\.\,]+\z/)  
+    if a = identifier.match(/\A[\d\.\,]+\z/)
       b = a.to_s.gsub(',', '')
       b.to_f
     else
diff --git a/lib/queries/collection_object/filter.rb b/lib/queries/collection_object/filter.rb
index ffe89295f7..f5902edf90 100644
--- a/lib/queries/collection_object/filter.rb
+++ b/lib/queries/collection_object/filter.rb
@@ -629,6 +629,7 @@ def base_merge_clauses
           identifier_facet,
           identifier_namespace_facet,
           identifiers_facet,
+          local_identifiers_facet,
           match_identifiers_facet,
 
           keyword_id_facet,       # See Queries::Concerns::Tags
diff --git a/lib/queries/concerns/identifiers.rb b/lib/queries/concerns/identifiers.rb
index 7380039015..a7e36dca02 100644
--- a/lib/queries/concerns/identifiers.rb
+++ b/lib/queries/concerns/identifiers.rb
@@ -112,7 +112,7 @@ def between
     )
   end
 
-  def identifiers_to_match 
+  def identifiers_to_match
     ids = match_identifiers.strip.split(match_identifiers_delimiter).flatten.map(&:strip).uniq
     if match_identifiers_type == 'internal'
       ids = ids.select{|i| i =~ /^\d+$/}
@@ -148,15 +148,18 @@ def identifiers_facet
     end
   end
 
+  # TODOL presently very slow
   def local_identifiers_facet
     return nil if local_identifiers.nil?
     if local_identifiers
       query_base.joins(:identifiers).where("identifiers.type ILIKE 'Identifier::Local%'").distinct
     else
-      query_base.left_outer_joins(:identifiers)
-        .where(identifiers: {id: nil})
-        .where.not("identifiers.type ILIKE 'Identifier::Local%'")
-        .distinct
+
+      i = ::Identifier.arel_table[:identifier_object_id].eq(table[:id]).and(
+        ::Identifier.arel_table[:identifier_object_type].eq( table.name.classify.to_s )
+      )
+
+      query_base.where.not(::Identifier::Local.where(i).arel.exists)
     end
   end
 
diff --git a/lib/queries/sqed_depiction/filter.rb b/lib/queries/sqed_depiction/filter.rb
index ed10729b58..60da9612b1 100644
--- a/lib/queries/sqed_depiction/filter.rb
+++ b/lib/queries/sqed_depiction/filter.rb
@@ -10,7 +10,9 @@ class Filter < Queries::Query
        with_buffered_determinations
        with_buffered_collecting_event
        with_buffered_other_labels
-      }  
+       identifiers
+       local_identifiers
+      }
 
       attr_accessor :collection_object_filter_params
 
@@ -19,8 +21,7 @@ class Filter < Queries::Query
       def initialize(params)
         @recent = params[:recent]
         @collection_object_filter_params = params.permit(COLLECTION_OBJECT_FILTER_PARAMS).to_h.select{|k,v| COLLECTION_OBJECT_FILTER_PARAMS.include?(k) ? k : nil}
-      
-        set_identifier(params)
+
         set_user_dates(params)
       end
 
@@ -29,13 +30,13 @@ def table
         ::SqedDepiction.arel_table
       end
 
-      def base_query
+      def query_base
         ::SqedDepiction.select('sqed_depictions.*')
       end
 
       def collection_object_query_facet
         q = ::Queries::CollectionObject::Filter.new(collection_object_filter_params).all
-        ::SqedDepiction.joins(:collection_object).where(collection_objects: q)  
+        ::SqedDepiction.joins(:collection_object).where(collection_objects: q)
       end
 
       # @return [ActiveRecord::Relation]
@@ -64,8 +65,6 @@ def base_merge_clauses
 
         clauses += [
           created_updated_facet,  # See Queries::Concerns::Users
-          local_identifiers_facet,
-          identifiers_facet,
           collection_object_query_facet,
         ]
 
diff --git a/lib/queries/taxon_name/filter.rb b/lib/queries/taxon_name/filter.rb
index a31e7161f6..187390957a 100644
--- a/lib/queries/taxon_name/filter.rb
+++ b/lib/queries/taxon_name/filter.rb
@@ -195,7 +195,7 @@ def initialize(params)
 
         @taxon_name_author_ids = params[:taxon_name_author_ids].blank? ? [] : params[:taxon_name_author_ids]
         @taxon_name_author_ids_or = boolean_param(params, :taxon_name_author_ids_or)
-     
+
         set_identifier(params)
         set_notes_params(params)
         set_data_attributes_params(params)
@@ -516,18 +516,18 @@ def merge_clauses
           citations_facet,
           combination_taxon_name_id_facet,
           created_updated_facet,
-          data_attribute_predicate_facet, 
+          data_attribute_predicate_facet,
           data_attribute_value_facet,
           data_attributes_facet,
           descendant_facet,
           keyword_id_facet,
           leaves_facet,
-         
+
           identifier_between_facet,
           identifier_facet,
           identifier_namespace_facet,
           match_identifiers_facet,
-          
+
           matching_taxon_name_author_ids,
           not_specified_facet,
           note_text_facet,        # See Queries::Concerns::Notes

From c28691f997cc974c12e0db4a13600c742c0c35e9 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 21 Nov 2022 23:00:13 -0600
Subject: [PATCH 050/160] Remove TODO button links (speed/redundancy)

---
 .../sqed_depiction/todo_map.json.jbuilder     | 32 +++++++++----------
 lib/queries/concerns/identifiers.rb           |  3 --
 2 files changed, 16 insertions(+), 19 deletions(-)

diff --git a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
index 52394445f6..15ded03659 100644
--- a/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
+++ b/app/views/tasks/accessions/breakdown/sqed_depiction/todo_map.json.jbuilder
@@ -1,20 +1,20 @@
 json.svg_map sqed_waxy_layout(@sqed_depictions)
 json.svg_legend sqed_waxy_legend_tag
-json.navigation do
-  json.global do
-    json.first_with_data SqedDepiction.where(project_id: sessions_current_project_id).with_collection_object_data.first&.id
-    json.last_with_data SqedDepiction.with_collection_object_data.where(project_id: sessions_current_project_id).last&.id
-    json.last_without_data SqedDepiction.where(project_id: sessions_current_project_id).without_collection_object_data.last&.id
-    json.first_without_data SqedDepiction.where(project_id: sessions_current_project_id).without_collection_object_data.first&.id
-    json.last_by_user SqedDepiction.joins(:collection_object).where(project_id: sessions_current_project_id, updated_by_id: sessions_current_user_id).with_collection_object_data.order('collection_objects.updated_at').first&.id
-  end
-  json.filtered do
-    json.first_with_data @base_query.with_collection_object_data.first&.id
-    json.last_with_data @base_query.with_collection_object_data.last&.id
-    json.last_without_data @base_query.without_collection_object_data.last&.id
-    json.first_without_data @base_query.without_collection_object_data.first&.id
-    json.last_by_user @base_query.joins(:collection_object).where(updated_by_id: sessions_current_user_id).with_collection_object_data.order('collection_objects.updated_at').first&.id
-  end
-end
+# json.navigation do
+#   json.global do
+#     json.first_with_data SqedDepiction.where(project_id: sessions_current_project_id).with_collection_object_data.first&.id
+#     json.last_with_data SqedDepiction.with_collection_object_data.where(project_id: sessions_current_project_id).last&.id
+#     json.last_without_data SqedDepiction.where(project_id: sessions_current_project_id).without_collection_object_data.last&.id
+#     json.first_without_data SqedDepiction.where(project_id: sessions_current_project_id).without_collection_object_data.first&.id
+#     json.last_by_user SqedDepiction.joins(:collection_object).where(project_id: sessions_current_project_id, updated_by_id: sessions_current_user_id).with_collection_object_data.order('collection_objects.updated_at').first&.id
+#   end
+#   json.filtered do
+#     json.first_with_data @base_query.with_collection_object_data.first&.id
+#     json.last_with_data @base_query.with_collection_object_data.last&.id
+#     json.last_without_data @base_query.without_collection_object_data.last&.id
+#     json.first_without_data @base_query.without_collection_object_data.first&.id
+#     json.last_by_user @base_query.joins(:collection_object).where(updated_by_id: sessions_current_user_id).with_collection_object_data.order('collection_objects.updated_at').first&.id
+#   end
+# end
 
 
diff --git a/lib/queries/concerns/identifiers.rb b/lib/queries/concerns/identifiers.rb
index a7e36dca02..7ad67bbaf7 100644
--- a/lib/queries/concerns/identifiers.rb
+++ b/lib/queries/concerns/identifiers.rb
@@ -148,17 +148,14 @@ def identifiers_facet
     end
   end
 
-  # TODOL presently very slow
   def local_identifiers_facet
     return nil if local_identifiers.nil?
     if local_identifiers
       query_base.joins(:identifiers).where("identifiers.type ILIKE 'Identifier::Local%'").distinct
     else
-
       i = ::Identifier.arel_table[:identifier_object_id].eq(table[:id]).and(
         ::Identifier.arel_table[:identifier_object_type].eq( table.name.classify.to_s )
       )
-
       query_base.where.not(::Identifier::Local.where(i).arel.exists)
     end
   end

From 5d6404665ee74fce154e059fa55aa17ed3b75d35 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 22 Nov 2022 10:26:56 -0300
Subject: [PATCH 051/160] Update style

---
 app/assets/stylesheets/base/figures.scss      |  6 ----
 app/helpers/sqed_depictions_helper.rb         |  2 +-
 .../breakdown/filter/components/list.vue      | 31 ++++++++++++++-----
 3 files changed, 24 insertions(+), 15 deletions(-)
 delete mode 100644 app/assets/stylesheets/base/figures.scss

diff --git a/app/assets/stylesheets/base/figures.scss b/app/assets/stylesheets/base/figures.scss
deleted file mode 100644
index 7cfa702a2b..0000000000
--- a/app/assets/stylesheets/base/figures.scss
+++ /dev/null
@@ -1,6 +0,0 @@
-figure {
-  // fix me :)
-  background-color: green;
-}
-
-fig-caption {  }
diff --git a/app/helpers/sqed_depictions_helper.rb b/app/helpers/sqed_depictions_helper.rb
index 3dbeee5ee9..0fc48f5bb8 100644
--- a/app/helpers/sqed_depictions_helper.rb
+++ b/app/helpers/sqed_depictions_helper.rb
@@ -187,7 +187,7 @@ def sqed_waxy_legend_section_tag(position, label)
 
     tag.figure do
       c.to_svg.html_safe +
-        tag.fig_caption(label)
+        tag.figcaption(label)
     end
   end
 
diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue
index 3d0d3579b5..8c5f310e2d 100644
--- a/app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/components/list.vue
@@ -1,13 +1,10 @@
 <template>
   <div class="panel content">
-    <div>
-      <span class="feedback feedback-success feedback-thin">First with data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.first_with_data}`">{{ list.navigation.filtered.first_with_data }}</a></span>&nbsp;
-      <span class="feedback feedback-warning feedback-thin">First without data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.first_without_data}`">{{ list.navigation.filtered.first_without_data }}</a></span>&nbsp;
-      <span class="feedback feedback-success feedback-thin">Last with data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.last_with_data}`">{{ list.navigation.filtered.last_with_data }}</a></span>&nbsp;
-      <span class="feedback feedback-warning feedback-thin">Last without data: <a :href="`/tasks/accessions/breakdown/sqed_depiction/${list.navigation.filtered.last_without_data}`">{{ list.navigation.filtered.last_without_data }}</a></span>&nbsp;
-    </div>
-    <div class="full_width horizontal-left-content flex-start">
-      <h3 v-html="list.svg_legend" />
+    <div class="full_width horizontal-left-content align-start">
+      <div
+        class="waxy-legend margin-large-right"
+        v-html="list.svg_legend"
+      />
       <div v-html="list.svg_map" />
     </div>
   </div>
@@ -22,3 +19,21 @@ defineProps({
   }
 })
 </script>
+
+<style lang="scss">
+.waxy-legend {
+  figure {
+    display: flex;
+    flex-direction: row;
+    align-items: center;
+    margin: 0;
+    margin-top: .5em;
+  }
+
+  #image-fill {
+    height: 20px;
+    width: 20px;
+    margin-right: 6px;
+  }
+}
+</style>

From df93a0c91f538c586b0fa26f3d11b14da0e736c8 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 22 Nov 2022 09:32:36 -0600
Subject: [PATCH 052/160] Param fixes,

---
 .../tasks/accessions/breakdown/sqed_depiction_controller.rb   | 2 +-
 lib/queries/collection_object/filter.rb                       | 2 +-
 lib/queries/concerns/identifiers.rb                           | 3 ++-
 lib/queries/query.rb                                          | 4 ++--
 lib/queries/sqed_depiction/filter.rb                          | 2 +-
 5 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
index 2c7d5a578c..684cb3391b 100644
--- a/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
+++ b/app/controllers/tasks/accessions/breakdown/sqed_depiction_controller.rb
@@ -10,7 +10,7 @@ def todo_map
     @base_query = ::Queries::SqedDepiction::Filter.new(filter_params).all
       .where(project_id: sessions_current_project_id)
       .order(:id)
-    @sqed_depictions = @base_query.page(params[:page]).per(50)
+    @sqed_depictions = @base_query.page(params[:page]).per(params[:per] || 50)
     respond_to do |format|
       format.html {}
       format.json {}
diff --git a/lib/queries/collection_object/filter.rb b/lib/queries/collection_object/filter.rb
index f5902edf90..d1a565a1ba 100644
--- a/lib/queries/collection_object/filter.rb
+++ b/lib/queries/collection_object/filter.rb
@@ -623,7 +623,7 @@ def base_merge_clauses
           dwc_indexed_facet,
           geographic_area_facet,
           georeferences_facet,
-         
+
           # See Queries::Concerns::Identifiers
           identifier_between_facet,
           identifier_facet,
diff --git a/lib/queries/concerns/identifiers.rb b/lib/queries/concerns/identifiers.rb
index 7ad67bbaf7..8f8f1bc8c8 100644
--- a/lib/queries/concerns/identifiers.rb
+++ b/lib/queries/concerns/identifiers.rb
@@ -1,7 +1,7 @@
 # Helpers for queries that reference Identifier
 #
 # For filter queries:
-# !! requires a `query_base` method
+# !! Note that query_base here is *not* the same as base_query
 # !! requires `set_identifiers` be called in initialize()
 #
 # See spec/lib/queries/collection_object/filter_spec.rb for existing spec tests
@@ -257,6 +257,7 @@ def autocomplete_identifier_matching_cached_fragments_anywhere
 
   private
 
+  # !! This is not the same as base_query !!
   def query_base
     table.name.classify.safe_constantize
   end
diff --git a/lib/queries/query.rb b/lib/queries/query.rb
index bf5b3f71fc..1a8047d0fd 100644
--- a/lib/queries/query.rb
+++ b/lib/queries/query.rb
@@ -384,12 +384,12 @@ def common_name_wild_pieces
 
     def autocomplete_common_name_exact
       return nil if no_terms?
-      query_base.joins(:common_names).where(common_name_name.to_sql).limit(1)
+      base_query.joins(:common_names).where(common_name_name.to_sql).limit(1)
     end
 
     def autocomplete_common_name_like
       return nil if no_terms?
-      query_base.joins(:common_names).where(common_name_wild_pieces.to_sql).limit(5)
+      base_query.joins(:common_names).where(common_name_wild_pieces.to_sql).limit(5)
     end
 
   end
diff --git a/lib/queries/sqed_depiction/filter.rb b/lib/queries/sqed_depiction/filter.rb
index 60da9612b1..938aec2113 100644
--- a/lib/queries/sqed_depiction/filter.rb
+++ b/lib/queries/sqed_depiction/filter.rb
@@ -30,7 +30,7 @@ def table
         ::SqedDepiction.arel_table
       end
 
-      def query_base
+      def base_query
         ::SqedDepiction.select('sqed_depictions.*')
       end
 

From 529e6cc9cab387dfcf60f5ada4f1f7f710ee068d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 22 Nov 2022 12:44:25 -0300
Subject: [PATCH 053/160] Update per param

---
 app/javascript/vue/tasks/accessions/breakdown/filter/App.vue | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
index 431ce618ae..0aa87a6e81 100644
--- a/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
@@ -80,6 +80,8 @@ const {
 const sqedResult = computed(() => Array.isArray(list.value) ? {} : list.value)
 const urlParams = URLParamsToJSON(location.href)
 
+per.value = 50
+
 makeFilterRequest(urlParams)
 
 </script>

From 35d8fdfdf539e2047202eb34cc4956fdc6d804c0 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 22 Nov 2022 12:47:04 -0600
Subject: [PATCH 054/160] Rename TODO list Filter staged images.

---
 .../vue/tasks/accessions/breakdown/filter/App.vue           | 2 +-
 config/interface/hub/user_tasks.yml                         | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
index 0aa87a6e81..9774472bea 100644
--- a/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
+++ b/app/javascript/vue/tasks/accessions/breakdown/filter/App.vue
@@ -7,7 +7,7 @@
       :logo-size="{ width: '100px', height: '100px'}"
     />
     <div class="flex-separate middle">
-      <h1>Collection object image breakdown (sqed) TODO list</h1>
+      <h1>Filter staged images</h1>
       <menu-preferences v-model="preferences" />
     </div>
 
diff --git a/config/interface/hub/user_tasks.yml b/config/interface/hub/user_tasks.yml
index 99850cbba1..aee8b6b525 100644
--- a/config/interface/hub/user_tasks.yml
+++ b/config/interface/hub/user_tasks.yml
@@ -193,9 +193,10 @@ author_list_task:
   status: stable
 sqed_depiction_breakdown_todo_map_task:
   hub: true
-  name: 'Collection object image breakdown TODO list'
-  description: 'Lists all collection objects currently being processed through depictions.  Indicates those that have transcribed provisional ("buffered") collecting event data.'
+  name: 'Filter staged images'
+  description: 'Filter staged images currently being processed. Visualize current data extracted from an image. Was "TODO list".'
   categories:
+    - filters
     - collecting_event
     - collection_object
     - image
@@ -695,6 +696,7 @@ filter_people_task:
   name: 'Filter people'
   related:
   categories:
+    - filters
   status: prototype
   description: 'Filter people.'
 stepwise_determinations_task:

From 3c95278dcd171ff4cfab54cbe0a47b66afb7dbc6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Tue, 22 Nov 2022 17:22:30 -0300
Subject: [PATCH 055/160] bundle update

---
 CHANGELOG.md |  1 +
 Gemfile.lock | 22 +++++++++++-----------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 218ea94b0a..414cb980b0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Changed
 - Refactored observation cell component for Image matrix
+- Updated Ruby gems
 
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
diff --git a/Gemfile.lock b/Gemfile.lock
index 65db1aae41..a703df64d8 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -154,7 +154,7 @@ GEM
     bindex (0.8.1)
     binding_of_caller (1.0.0)
       debug_inspector (>= 0.0.1)
-    brakeman (5.3.1)
+    brakeman (5.4.0)
     builder (3.2.4)
     byebug (11.1.3)
     capybara (3.38.0)
@@ -210,7 +210,7 @@ GEM
       unf (>= 0.0.5, < 1.0.0)
     dropzonejs-rails (0.8.5)
       rails (> 3.1)
-    dwc_agent (3.0.1.5)
+    dwc_agent (3.0.2.0)
       namae (~> 1)
       namecase (~> 2)
     erubi (1.11.0)
@@ -226,7 +226,7 @@ GEM
       railties (>= 5.0.0)
     faker (2.23.0)
       i18n (>= 1.8.11, < 2)
-    faraday (2.6.0)
+    faraday (2.7.1)
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-excon (2.1.0)
@@ -234,7 +234,7 @@ GEM
       faraday (~> 2.0)
     faraday-follow_redirects (0.3.0)
       faraday (>= 1, < 3)
-    faraday-net_http (3.0.1)
+    faraday-net_http (3.0.2)
     ffi (1.15.5)
     ffi-geos (2.3.1)
       ffi (>= 1.0.0)
@@ -273,7 +273,7 @@ GEM
     jbuilder (2.11.5)
       actionview (>= 5.0.0)
       activesupport (>= 5.0.0)
-    jquery-rails (4.5.0)
+    jquery-rails (4.5.1)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
@@ -361,7 +361,7 @@ GEM
       hashery (~> 2.0)
       ruby-rc4
       ttfunk
-    pg (1.4.4)
+    pg (1.4.5)
     polyglot (0.3.5)
     postgresql_cursor (0.6.6)
       activerecord (>= 3.1.0)
@@ -427,7 +427,7 @@ GEM
     rdoc (6.3.3)
     redcarpet (3.5.1)
     redis (4.8.0)
-    regexp_parser (2.6.0)
+    regexp_parser (2.6.1)
     request_store (1.5.1)
       rack (>= 1.4)
     require_all (3.0.0)
@@ -484,7 +484,7 @@ GEM
       rspec-support (~> 3.10)
     rspec-support (3.12.0)
     rtesseract (3.1.2)
-    rubocop (1.38.0)
+    rubocop (1.39.0)
       json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.1.2.1)
@@ -499,10 +499,10 @@ GEM
     rubocop-faker (1.1.0)
       faker (>= 2.12.0)
       rubocop (>= 0.82.0)
-    rubocop-performance (1.15.0)
+    rubocop-performance (1.15.1)
       rubocop (>= 1.7.0, < 2.0)
       rubocop-ast (>= 0.4.0)
-    rubocop-rails (2.17.2)
+    rubocop-rails (2.17.3)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
@@ -581,7 +581,7 @@ GEM
     timecop (0.9.5)
     timeliness (0.4.4)
     timeout (0.3.0)
-    tins (1.31.1)
+    tins (1.32.1)
       sync
     treetop (1.6.11)
       polyglot (~> 0.3)

From 96556312f8e3c5b611ffb80ee550957051e55745 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 22 Nov 2022 19:22:06 -0300
Subject: [PATCH 056/160] Add components, change layout

---
 .../vue/components/ui/SmartSelector.vue       |  7 +-
 app/javascript/vue/constants/modelTypes.js    |  1 +
 .../simple_new_specimen/App.vue               | 45 +++++++++--
 .../simple_new_specimen/components/FormCE.vue | 50 ++++++------
 .../simple_new_specimen/components/FormCO.vue | 17 ----
 .../FormCO/FormCOPreparationType.vue          | 30 -------
 .../components/FormCatalogNumber.vue          | 79 +++++++++++++++++++
 .../components/FormDepictions.vue             | 34 ++++++++
 .../components/FormDetermination.vue          | 35 ++++++++
 .../components/FormPreparationType.vue        | 55 +++++++++++++
 .../components/GeographicArea.vue             | 12 ++-
 .../store/useCollectingEventStore.js          | 20 -----
 .../store/useCollectionObjectStore.js         | 28 -------
 .../store/useIdentifierStore.js               | 32 --------
 .../simple_new_specimen/store/useStore.js     | 73 +++++++++++++++++
 .../store/useTaxonDeterminationStore.js       | 33 --------
 16 files changed, 357 insertions(+), 194 deletions(-)
 delete mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
 delete mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
 delete mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js
 delete mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js
 delete mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
 delete mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js

diff --git a/app/javascript/vue/components/ui/SmartSelector.vue b/app/javascript/vue/components/ui/SmartSelector.vue
index 1594fc8a49..1560dfa17f 100644
--- a/app/javascript/vue/components/ui/SmartSelector.vue
+++ b/app/javascript/vue/components/ui/SmartSelector.vue
@@ -5,13 +5,16 @@
         class="full_width capitalize"
         v-model="view"
         ref="tabselector"
-        :options="options"/>
+        :options="options"
+      />
       <default-pin
         v-if="pinSection"
         class="margin-small-left"
         :section="pinSection"
         :type="pinType"
-        @getId="getObject"/>
+        @get-id="getObject"
+      />
+      <slot name="tabs-right" />
     </div>
     <slot name="header"/>
     <template v-if="!addTabs.includes(view)">
diff --git a/app/javascript/vue/constants/modelTypes.js b/app/javascript/vue/constants/modelTypes.js
index 351e3bfd09..1745e0287e 100644
--- a/app/javascript/vue/constants/modelTypes.js
+++ b/app/javascript/vue/constants/modelTypes.js
@@ -15,6 +15,7 @@ export const SPECIMEN = 'Specimen'
 export const TAG = 'Tag'
 export const TAXON_NAME = 'TaxonName'
 export const TYPE_MATERIAL = 'TypeMaterial'
+export const TAXON_DETERMINATION = 'TaxonDetermination'
 export const TAXON_NAME_CLASSIFICATION = 'TaxonNameClassification'
 export const TAXON_NAME_RELATIONSHIP = 'TaxonNameRelationship'
 export const BIOCURATION_GROUP = 'BiocurationGroup'
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index 32ed4e20ac..da9c6c0343 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -1,12 +1,45 @@
 <template>
-  <div>
-    <h1>Simplete new specimen</h1>
-    <FormCO />
-    <FormCE />
-  </div>
+  <h1>Simple new specimen</h1>
+  <BlockLayout>
+    <template #header>
+      <h3>Form</h3>
+    </template>
+    <template #body>
+      <div
+        class="margin-medium-bottom"
+        id="collection-object-form"
+      >
+        <FormCatalogNumber />
+        <FormPreparationType />
+        <FormDetermination />
+        <FormDepictions />
+      </div>
+      <FormCE />
+    </template>
+  </BlockLayout>
 </template>
 
 <script setup>
 import FormCE from './components/FormCE.vue'
-import FormCO from './components/FormCO.vue'
+import FormPreparationType from './components/FormPreparationType.vue'
+import FormCatalogNumber from './components/FormCatalogNumber.vue'
+import FormDepictions from './components/FormDepictions.vue'
+import FormDetermination from './components/FormDetermination.vue'
+import BlockLayout from 'components/layout/BlockLayout.vue'
 </script>
+
+<style lang="scss">
+#vue-simple-new-specimen {
+  flex-direction: column-reverse;
+  margin: 0 auto;
+  margin-top: 1em;
+  max-width: 1240px;
+
+  #collection-object-form {
+    display: grid;
+    grid-template-columns: repeat(2, minmax(250px, 1fr) );
+    gap: 1em;
+    grid-auto-flow: dense;
+  }
+}
+</style>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
index bfe1777981..5670b67dd5 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
@@ -1,27 +1,33 @@
 <template>
-  <BlockLayout>
-    <template #header>
-      <h3>Collecting event</h3>
-    </template>
-    <template #body>
-      <div class="field label-above">
-        <label>Verbatim label</label>
-        <textarea />
-      </div>
-      <div class="field label-above">
-        <label>Verbatim label</label>
-        <input
-          type="text"
-        >
-      </div>
-      <div class="field label-above">
-        <label>Verbatim label</label>
-        <textarea />
-      </div>
-    </template>
-  </BlockLayout>
+  <div class="panel content">
+    <div class="flex-separate middle">
+      <h2>Collecting event</h2>
+      <VLock v-model="store.settings.lock.collectingEvent"/>
+    </div>
+    <div class="field label-above">
+      <label>Verbatim label</label>
+      <textarea
+        class="full_width"
+        rows="5"
+        v-model="store.collectingEvent.verbatim_label"
+      />
+    </div>
+    <div class="field label-above">
+      <label>Verbatim locality</label>
+      <input
+        class="full_width"
+        v-model="store.collectingEvent.verbatim_locality"
+        type="text"
+      >
+    </div>
+    <GeographicArea />
+  </div>
 </template>
 
 <script setup>
-import BlockLayout from 'components/layout/BlockLayout.vue'
+import { useStore } from '../store/useStore'
+import GeographicArea from './GeographicArea.vue'
+import VLock from 'components/ui/VLock/index.vue'
+
+const store = useStore()
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
deleted file mode 100644
index f220570efe..0000000000
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO.vue
+++ /dev/null
@@ -1,17 +0,0 @@
-<template>
-  <BlockLayout>
-    <template #header>
-      <h3>Collection object</h3>
-    </template>
-    <template #body>
-      <div>
-        <FormCOPreparationType />
-      </div>
-    </template>
-  </BlockLayout>
-</template>
-
-<script setup>
-import BlockLayout from 'components/layout/BlockLayout.vue'
-import FormCOPreparationType from './FormCO/FormCOPreparationType.vue'
-</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue
deleted file mode 100644
index eec0f40b45..0000000000
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCO/FormCOPreparationType.vue
+++ /dev/null
@@ -1,30 +0,0 @@
-<template>
-  <div class="field label-above">
-    <label>Preparation type</label>
-    <select v-model="store.collectionObject.preparationTypeId">
-      <option :value="undefined">
-        None
-      </option>
-      <option
-        v-for="(item, key) in preparationTypes"
-        :key="key"
-        :value="item.id"
-      >
-        {{ item.name }}
-      </option>
-    </select>
-  </div>
-</template>
-
-<script setup>
-import { ref } from 'vue'
-import { PreparationType } from 'routes/endpoints'
-import { useCollectionObjectStore } from '../../store/useCollectionObjectStore.js'
-
-const store = useCollectionObjectStore()
-const preparationTypes = ref([])
-
-PreparationType.where({}).then(({ body }) => {
-  preparationTypes.value = body
-})
-</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
new file mode 100644
index 0000000000..1a6ea64901
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -0,0 +1,79 @@
+<template>
+  <div class="panel content">
+    <h2>Catalog number</h2>
+    <fieldset>
+      <legend>Namespace</legend>
+      <SmartSelector
+        model="namespaces"
+        :klass="COLLECTION_OBJECT"
+        @get-item="setNamespace"
+      >
+        <template #tabs-right>
+          <VLock
+            class="margin-small-left"
+            v-model="store.settings.lock.identifier"
+          />
+        </template>
+      </SmartSelector>
+    </fieldset>
+
+    <div class="separate-top">
+      <label>Identifier</label>
+      <div class="horizontal-left-content field">
+        <input
+          id="identifier-field"
+          :class="{ 'validate-identifier': store.createdIdentifiers.length }"
+          type="text"
+          @input="checkIdentifier"
+          v-model="store.identifier.identifier"
+        >
+        <label>
+          <input
+            v-model="store.settings.increment"
+            type="checkbox"
+          >
+          Increment
+        </label>
+      </div>
+      <span
+        v-if="!store.identifier.namespace_id"
+        style="color: red"
+      >
+        Namespace is needed.
+      </span>
+      <template v-if="store.createdIdentifiers.length">
+        <span
+          style="color: red"
+        >Identifier already exists, and it won't be saved:</span>
+        <a
+          :href="store.createdIdentifiers[0].identifier_object.object_url"
+          v-html="store.createdIdentifiers[0].identifier_object.object_tag"
+        />
+      </template>
+    </div>
+  </div>
+</template>
+
+<script setup>
+import { useStore } from '../store/useStore'
+import { COLLECTION_OBJECT } from 'constants/index'
+import SmartSelector from 'components/ui/SmartSelector.vue'
+import VLock from 'components/ui/VLock/index.vue'
+
+const store = useStore()
+const DELAY = 1000
+let timeoutRequest
+
+function checkIdentifier () {
+  clearTimeout(timeoutRequest)
+
+  timeoutRequest = setTimeout(() => {
+    store.getIdentifiers()
+  }, DELAY)
+}
+
+function setNamespace ({ id }) {
+  store.identifier.namespace_id = id
+}
+
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue
new file mode 100644
index 0000000000..e1977dc27e
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue
@@ -0,0 +1,34 @@
+<template>
+  <div class="panel content">
+    <VDropzone
+      @vdropzone-sending="sending"
+      @vdropzone-file-added="addedfile"
+      @vdropzone-success="success"
+      @vdropzone-error="error"
+      ref="dropzoneComponent"
+      url="/depictions"
+      use-custom-dropzone-options
+      :dropzone-options="dropzoneOptions"
+    />
+  </div>
+</template>
+
+<script setup>
+import { ref } from 'vue'
+import VDropzone from 'components/dropzone.vue'
+
+const dropzoneOptions = {
+  paramName: 'depiction[image_attributes][image_file]',
+  url: '/depictions',
+  autoProcessQueue: false,
+  addRemoveLinks: true,
+  headers: {
+    'X-CSRF-Token': document.querySelector('meta[name="csrf-token"]').getAttribute('content')
+  },
+  dictDefaultMessage: 'Drop image or click to browse',
+  acceptedFiles: 'image/*,.heic'
+}
+
+const dropzoneComponent = ref(null)
+
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
new file mode 100644
index 0000000000..36e04a4130
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
@@ -0,0 +1,35 @@
+<template>
+  <div class="panel content">
+    <h2>Determination</h2>
+    <fieldset>
+      <legend>OTU</legend>
+      <SmartSelector
+        model="otus"
+        :target="TAXON_DETERMINATION"
+        :klass="TAXON_DETERMINATION"
+        @get-item="setOtu"
+      >
+        <template #tabs-right>
+          <VLock
+            class="margin-small-left"
+            v-model="store.settings.lock.determination"
+          />
+        </template>
+      </SmartSelector>
+    </fieldset>
+  </div>
+</template>
+
+<script setup>
+import { TAXON_DETERMINATION } from 'constants/index'
+import { useStore } from '../store/useStore'
+import SmartSelector from 'components/ui/SmartSelector.vue'
+import VLock from 'components/ui/VLock/index.vue'
+
+const store = useStore()
+
+function setOtu (value) {
+  store.otu = value
+}
+
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
new file mode 100644
index 0000000000..00ee81cc3c
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
@@ -0,0 +1,55 @@
+<template>
+  <div class="panel content">
+    <div class="flex-separate middle">
+      <h2>Preparation</h2>
+      <VLock v-model="store.settings.lock.preparationType" />
+    </div>
+    <div class="horizontal-left-content align-start">
+      <ul
+        v-for="(itemsGroup, index) in chunkList"
+        :key="index"
+        class="no_bullets full_width"
+      >
+        <li
+          v-for="preparationType in itemsGroup"
+          :key="preparationType.id"
+        >
+          <label>
+            <input
+              type="radio"
+              :value="preparationType.id"
+              v-model="store.collectionObject.preparation_type_id"
+              name="collection-object-type"
+            >
+            {{ preparationType.name }}
+          </label>
+        </li>
+      </ul>
+    </div>
+  </div>
+</template>
+
+<script setup>
+import { computed, ref } from 'vue'
+import { PreparationType } from 'routes/endpoints'
+import { useStore } from '../store/useStore.js'
+import VLock from 'components/ui/VLock/index.vue'
+
+const store = useStore()
+const preparationTypes = ref([])
+
+PreparationType.where({}).then(({ body }) => {
+  preparationTypes.value = [
+    ...body,
+    {
+      id: null,
+      name: 'None'
+    }
+  ]
+})
+
+const chunkList = computed(() =>
+  preparationTypes.value.chunk(Math.ceil(preparationTypes.value.length / 3))
+)
+
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
index 7c7df15b4d..5dc8e41969 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
@@ -1,22 +1,26 @@
 <template>
-  <div>
+  <fieldset>
+    <legend>Geographic area</legend>
     <SmartSelector
       ref="smartSelector"
       model="geographic_areas"
       target="CollectingEvent"
       label="name"
       klass="CollectingEvent"
-      @selected="selectGeographicArea"
+      @selected="store.geographicArea = $event"
     />
     <SmartSelectorItem
-      :item="geographicArea"
+      :item="store.geographicArea"
       label="object_tag"
       @unset="state.geographicArea = undefined"
     />
-  </div>
+  </fieldset>
 </template>
 
 <script setup>
 import SmartSelector from 'components/ui/SmartSelector.vue'
 import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
+import { useStore } from '../store/useStore'
+
+const store = useStore()
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js
deleted file mode 100644
index a0dda5af3b..0000000000
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectingEventStore.js
+++ /dev/null
@@ -1,20 +0,0 @@
-import { CollectingEvent } from 'routes/endpoints'
-import { defineStore } from 'pinia'
-import makeCollectingEvent from 'factory/CollectingEvent'
-
-export const useCollectingEventStore = defineStore('collectingEvent', {
-  state: () => ({
-    collectingEvent: makeCollectingEvent()
-  }),
-
-  actions: {
-    createCollectingEvent () {
-      CollectingEvent.create({
-        collection_object: {
-          ...this.collectionObject,
-          collecting_event_id: this.collectingEvent.id
-        }
-      })
-    }
-  }
-})
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js
deleted file mode 100644
index f4cbbade22..0000000000
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useCollectionObjectStore.js
+++ /dev/null
@@ -1,28 +0,0 @@
-import { CollectionObject } from 'routes/endpoints'
-import { defineStore } from 'pinia'
-import { makeCollectionObject, makeCollectionObjectPayload } from 'adapters/index.js'
-
-export const useCollectionObjectStore = defineStore('collectionObject', {
-  state: () => ({
-    collectionObject: makeCollectionObject({})
-  }),
-
-  actions: {
-    async saveCollectionObject (params) {
-      const payload = {
-        collection_object: {
-          ...makeCollectionObjectPayload(this.collectionObject),
-          ...params
-        }
-      }
-
-      const response = payload.id
-        ? await CollectionObject.update(payload.id, payload)
-        : await CollectionObject.create(payload)
-
-      this.collectionObject = makeCollectionObject(response.body)
-
-      return response
-    }
-  }
-})
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js
deleted file mode 100644
index cb16ab156b..0000000000
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useIdentifierStore.js
+++ /dev/null
@@ -1,32 +0,0 @@
-import { Identifier } from 'routes/endpoints'
-import { defineStore } from 'pinia'
-
-export const useCollectingEventStore = defineStore('collectingEvent', {
-  state: () => ({
-    identifier: {
-      id: undefined,
-      namespace_id: undefined,
-      type: undefined,
-      identifier: undefined,
-      identifier_object_type: undefined,
-      identifier_object_id: undefined
-    }
-  }),
-
-  actions: {
-    async saveIdentifier (params) {
-      const payload = {
-        identifier: {
-          ...this.identifier,
-          ...params
-        }
-      }
-
-      const response = payload.id
-        ? await Identifier.update(payload.id, payload)
-        : await Identifier.create(payload)
-
-      this.identifier = response.body
-    }
-  }
-})
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
new file mode 100644
index 0000000000..df805b8705
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
@@ -0,0 +1,73 @@
+import { defineStore } from 'pinia'
+import {
+  CollectionObject,
+  CollectingEvent,
+  Identifier
+} from 'routes/endpoints'
+import { IDENTIFIER_LOCAL_CATALOG_NUMBER, COLLECTION_OBJECT } from 'constants/index'
+
+const makeInitialState = () => ({
+  settings: {
+    lock: {
+      collectingEvent: false,
+      determination: false,
+      identifier: false,
+      namespace: false,
+      preparationType: false
+    },
+    increment: false
+  },
+  createdIdentifiers: [],
+  collectionObject: {
+    preparation_type_id: undefined
+  },
+  collectingEvent: {
+    verbatim_label: undefined,
+    verbatim_locality: undefined,
+    geographic_area_id: undefined
+  },
+  geographicArea: undefined,
+  identifier: {
+    identifier: undefined,
+    identifier_object_id: undefined,
+    identifier_object_type: COLLECTION_OBJECT,
+    namespace_id: undefined,
+    type: IDENTIFIER_LOCAL_CATALOG_NUMBER
+  },
+  otu: undefined
+})
+
+export const useStore = defineStore('main', {
+  state: makeInitialState,
+
+  actions: {
+    async createNewSpecimen () {
+      const payload = {
+        collection_object: {
+          ...this.collectionObject
+        }
+      }
+
+      const response = payload.id
+        ? await CollectionObject.update(payload.id, payload)
+        : await CollectionObject.create(payload)
+
+      return response
+    },
+
+    getIdentifiers () {
+      if (!this.identifier.identifier) {
+        this.createdIdentifiers = []
+        return
+      }
+
+      Identifier.where({
+        type: IDENTIFIER_LOCAL_CATALOG_NUMBER,
+        namespace_id: this.identifier.namespace_id,
+        identifier: this.identifier.identifier
+      }).then(({ body }) => {
+        this.createdIdentifiers = body
+      })
+    }
+  }
+})
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js
deleted file mode 100644
index c5ded71f52..0000000000
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useTaxonDeterminationStore.js
+++ /dev/null
@@ -1,33 +0,0 @@
-import { TaxonDetermination } from 'routes/endpoints'
-import { defineStore } from 'pinia'
-
-export const useTaxonDeterminationStore = defineStore('taxonDetermination', {
-  state: () => ({
-    taxonDetermination: {
-      id: undefined,
-      biological_collection_object_id: undefined,
-      otu_id: undefined,
-      year_made: undefined,
-      month_made: undefined,
-      day_made: undefined,
-      roles_attributes: []
-    }
-  }),
-
-  actions: {
-    async saveTaxonDetermination (params) {
-      const payload = {
-        taxon_determination: {
-          ...this.taxonDetermination,
-          ...params
-        }
-      }
-
-      const response = payload.id
-        ? await TaxonDetermination.update(payload.id, payload)
-        : await TaxonDetermination.create(payload)
-
-      this.taxonDetermination = response.body
-    }
-  }
-})

From ab4eff9d2e293feeeafa626717915bc2243df3c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 22 Nov 2022 19:40:47 -0300
Subject: [PATCH 057/160] Fix #3205

---
 CHANGELOG.md                                  |  1 +
 .../ClassificationListCommon.vue              |  3 +-
 .../Classification/ClassificationMain.vue     |  8 +++
 .../new_taxon_name/components/commonList.vue  | 56 ++++++++++---------
 .../components/statusPicker.vue               |  1 +
 5 files changed, 41 insertions(+), 28 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 414cb980b0..19e4ea65cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Citation link in Biological association panel on Browse OTU
 - Type relationship text/rendering is inverted in New taxon name [#3182]
 - Sqed processing failing to encode HEIC images [#3188]
+- Common list component doesn't filter created status on New taxon name task [#3205]
 
 ### Changed
 - Refactored observation cell component for Image matrix
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationListCommon.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationListCommon.vue
index 02615c3488..655462a9ee 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationListCommon.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationListCommon.vue
@@ -4,7 +4,8 @@
     :object-lists="lists.common"
     display="name"
     @add-entry="emit('select', $event)"
-    :list-created="created"/>
+    :list-created="created"
+  />
 </template>
 
 <script setup>
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
index bdc1ad61e1..04061f7cf4 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/Classification/ClassificationMain.vue
@@ -1,6 +1,7 @@
 <template>
   <classification-list
     :lists="objectLists"
+    :created="created"
     @select="emit('select', $event)"
   />
 </template>
@@ -12,6 +13,13 @@ import { ref, computed, watch } from 'vue'
 import { useStore } from 'vuex'
 import ClassificationList from './ClassificationList.vue'
 
+defineProps({
+  created: {
+    type: Array,
+    default: () => []
+  }
+})
+
 const emit = defineEmits(['select'])
 
 const store = useStore()
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/commonList.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/commonList.vue
index a1d26f4ac8..6a576203ee 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/commonList.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/commonList.vue
@@ -4,13 +4,16 @@
       <template v-for="item in objectLists">
         <li
           class="status-item"
-          v-if="!filter || !filterAlreadyPicked(listCreated, item.base_class)">
+          :key="item.id"
+          v-if="!filter || !filterAlreadyPicked(listCreated, item.type)"
+        >
           <label>
             <input
               type="radio"
               name="status-item"
-              @click="$emit('addEntry', item)"
-              :value="item.base_class">
+              :value="item.base_class"
+              @click="emit('addEntry', item)"
+            >
             <span>{{ item[display] }}</span>
           </label>
         </li>
@@ -18,33 +21,32 @@
     </ul>
   </div>
 </template>
-<script>
-export default {
-  props: {
-    objectLists: {
-      type: Array,
-      default: () => []
-    },
-
-    listCreated: {
-      type: Array,
-      required: true
-    },
+<script setup>
+defineProps({
+  objectLists: {
+    type: Array,
+    default: () => []
+  },
 
-    display: {
-      type: String,
-      required: true
-    },
+  listCreated: {
+    type: Array,
+    required: true
+  },
 
-    filter: {
-      type: Boolean,
-      default: false
-    }
+  display: {
+    type: String,
+    required: true
   },
-  methods: {
-    filterAlreadyPicked (list, type) {
-      return list.find(item => item.base_class === type)
-    }
+
+  filter: {
+    type: Boolean,
+    default: false
   }
+})
+
+const emit = defineEmits('addEntry')
+
+function filterAlreadyPicked (list, type) {
+  return list.find(item => item.type === type)
 }
 </script>
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/statusPicker.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/statusPicker.vue
index 49425d9d1c..c71a78013d 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/statusPicker.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/statusPicker.vue
@@ -19,6 +19,7 @@
       </div>
       <classification-main
         @select="saveClassification"
+        :created="getStatusCreated"
       />
       <ul
         v-if="!getStatusCreated.length && taxon.cached_is_valid"

From ea43001ef803d2532ee1c46f4443353adfab0460 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Tue, 22 Nov 2022 20:08:27 -0300
Subject: [PATCH 058/160] Lock GitHub Actions to Ubuntu 20.04

---
 .github/workflows/base-image.yml | 2 +-
 .github/workflows/build.yml      | 2 +-
 .github/workflows/deliver.yml    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/base-image.yml b/.github/workflows/base-image.yml
index ad60b63a5c..87af194a24 100644
--- a/.github/workflows/base-image.yml
+++ b/.github/workflows/base-image.yml
@@ -8,7 +8,7 @@ on:
 jobs:
   base-image:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
 
     - name: Git checkout
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 76c9458df8..26ce543ee6 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -30,7 +30,7 @@ jobs:
       RAILS_ENV: test
       CROSSREF_EMAIL: ${{ secrets.CROSSREF_EMAIL }}
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         worker: [0, 1, 2, 3]
diff --git a/.github/workflows/deliver.yml b/.github/workflows/deliver.yml
index 9f070291dd..9480525853 100644
--- a/.github/workflows/deliver.yml
+++ b/.github/workflows/deliver.yml
@@ -26,7 +26,7 @@ jobs:
       REF_SHA: ${{ github.event.pull_request.head.sha || github.sha }}
       CACHE_PATH: ".github/.docker-cache"
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
     - name: Get startup date
       id: datetime

From f341007a3ea3615af426e576071ee4e96f55955b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 23 Nov 2022 11:26:07 -0300
Subject: [PATCH 059/160] Add actions

---
 .../simple_new_specimen/App.vue                 |  9 +++++++++
 .../components/FormCatalogNumber.vue            | 10 ++++++++--
 .../components/FormDetermination.vue            | 12 +++++++-----
 .../simple_new_specimen/store/useStore.js       | 17 +++++++++++++++--
 4 files changed, 39 insertions(+), 9 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index da9c6c0343..289f2eac4e 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -41,5 +41,14 @@ import BlockLayout from 'components/layout/BlockLayout.vue'
     gap: 1em;
     grid-auto-flow: dense;
   }
+
+  hr {
+    height: 1px;
+    color: #f5f5f5;
+    background: #f5f5f5;
+    font-size: 0;
+    margin: 15px;
+    border: 0;
+  }
 }
 </style>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
index 1a6ea64901..c06ea49df8 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -6,7 +6,7 @@
       <SmartSelector
         model="namespaces"
         :klass="COLLECTION_OBJECT"
-        @get-item="setNamespace"
+        v-model="store.namespace"
       >
         <template #tabs-right>
           <VLock
@@ -15,6 +15,11 @@
           />
         </template>
       </SmartSelector>
+      <SmartSelectorItem
+        :item="store.namespace"
+        label="name"
+        @unset="store.namespace = undefined"
+      />
     </fieldset>
 
     <div class="separate-top">
@@ -36,7 +41,7 @@
         </label>
       </div>
       <span
-        v-if="!store.identifier.namespace_id"
+        v-if="!store.namespace && store.identifier.identifier"
         style="color: red"
       >
         Namespace is needed.
@@ -58,6 +63,7 @@
 import { useStore } from '../store/useStore'
 import { COLLECTION_OBJECT } from 'constants/index'
 import SmartSelector from 'components/ui/SmartSelector.vue'
+import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
 import VLock from 'components/ui/VLock/index.vue'
 
 const store = useStore()
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
index 36e04a4130..8209d14c63 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
@@ -7,7 +7,7 @@
         model="otus"
         :target="TAXON_DETERMINATION"
         :klass="TAXON_DETERMINATION"
-        @get-item="setOtu"
+        v-model="store.otu"
       >
         <template #tabs-right>
           <VLock
@@ -16,6 +16,11 @@
           />
         </template>
       </SmartSelector>
+      <hr>
+      <SmartSelectorItem
+        :item="store.otu"
+        @unset="store.otu = undefined"
+      />
     </fieldset>
   </div>
 </template>
@@ -24,12 +29,9 @@
 import { TAXON_DETERMINATION } from 'constants/index'
 import { useStore } from '../store/useStore'
 import SmartSelector from 'components/ui/SmartSelector.vue'
+import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
 import VLock from 'components/ui/VLock/index.vue'
 
 const store = useStore()
 
-function setOtu (value) {
-  store.otu = value
-}
-
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
index df805b8705..91699f486e 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
@@ -2,6 +2,7 @@ import { defineStore } from 'pinia'
 import {
   CollectionObject,
   CollectingEvent,
+  TaxonDetermination,
   Identifier
 } from 'routes/endpoints'
 import { IDENTIFIER_LOCAL_CATALOG_NUMBER, COLLECTION_OBJECT } from 'constants/index'
@@ -32,8 +33,8 @@ const makeInitialState = () => ({
     identifier_object_id: undefined,
     identifier_object_type: COLLECTION_OBJECT,
     namespace_id: undefined,
-    type: IDENTIFIER_LOCAL_CATALOG_NUMBER
   },
+  namespace: undefined,
   otu: undefined
 })
 
@@ -63,11 +64,23 @@ export const useStore = defineStore('main', {
 
       Identifier.where({
         type: IDENTIFIER_LOCAL_CATALOG_NUMBER,
-        namespace_id: this.identifier.namespace_id,
+        namespace_id: this.namespace.id,
         identifier: this.identifier.identifier
       }).then(({ body }) => {
         this.createdIdentifiers = body
       })
+    },
+
+    createIdentifier (coId) {
+      const payload = {
+        identifier: this.identifier,
+        namespace_id: this.namespace.id,
+        type: IDENTIFIER_LOCAL_CATALOG_NUMBER,
+        identifier_object_id: coId,
+        identifier_object_type: COLLECTION_OBJECT
+      }
+
+      Identifier.create({ identifier: payload })
     }
   }
 })

From 15c57831e1203218933eecff1ee8d3c2b82a4ed7 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 23 Nov 2022 09:28:13 -0600
Subject: [PATCH 060/160] Shorten label

---
 .../tasks/collection_objects/filter/components/matchButton.vue  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/matchButton.vue b/app/javascript/vue/tasks/collection_objects/filter/components/matchButton.vue
index e9f39e8a74..a7e490eccd 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/matchButton.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/matchButton.vue
@@ -5,7 +5,7 @@
     :disabled="!urlParams"
     @click="openTask"
   >
-    Send this filter to Match collection object
+    Send result to Match collection object
   </v-btn>
 </template>
 <script setup>

From b47fc216d623e801f0b940b4e3f15bda0f09fb3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 23 Nov 2022 12:48:00 -0300
Subject: [PATCH 061/160] Fix mass delete button

---
 .../tasks/collection_objects/filter/app.vue   |   9 +-
 .../components/DeleteCollectionObjects.vue    |  18 ++-
 .../filter/components/tagAll.vue              | 115 +++++++++---------
 3 files changed, 84 insertions(+), 58 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/filter/app.vue b/app/javascript/vue/tasks/collection_objects/filter/app.vue
index b897df71d5..f35eba22ad 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/app.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/app.vue
@@ -80,7 +80,8 @@
             <DeleteCollectionObjects
               class="margin-small-left"
               :ids="ids"
-              @delete="list.data = list.data.filter(r => !$event.includes(r[0]))"
+              :disabled="!ids.length"
+              @delete="removeCOFromList"
             />
             <RadialFilter
               :disabled="!ids.length"
@@ -226,6 +227,12 @@ export default {
     loadPage (event) {
       this.$refs.filterComponent.loadPage(event.page)
     },
+
+    removeCOFromList (ids) {
+      this.list.data = this.list.data.filter(r => !ids.includes(r[0]))
+      this.ids = this.ids.filter(id => !ids.includes(id))
+    },
+
     getPagination: GetPagination
   }
 }
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index 65ff80ca26..69d12331c7 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -4,6 +4,7 @@
     <VBtn
       color="primary"
       medium
+      :disabled="disabled"
       @click="openModal"
     >
       Delete collection objects
@@ -25,6 +26,11 @@ const props = defineProps({
   ids: {
     type: Array,
     default: () => []
+  },
+
+  disabled: {
+    type: Boolean,
+    default: false
   }
 })
 
@@ -32,11 +38,21 @@ const emit = defineEmits(['delete'])
 const confirmationModal = ref(null)
 
 function deleteCOs () {
+  let failedCount = 0
   const ids = [...props.ids]
   const destroyedIds = []
-  const requests = ids.map(id => CollectionObject.destroy(id).then(_ => destroyedIds.push(id)))
+  const requests = ids.map(id =>
+    CollectionObject.destroy(id)
+      .then(_ => destroyedIds.push(id))
+      .catch(_ => failedCount++)
+  )
 
   Promise.allSettled(requests).then(_ => {
+    const message = failedCount
+      ? `Deleted: ${destroyedIds.length} object(s). Failed to delete: ${failedCount}`
+      : `Deleted: ${destroyedIds.length} object(s).`
+
+    TW.workbench.alert.create(message, 'notice')
     emit('delete', destroyedIds)
   })
 }
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/tagAll.vue b/app/javascript/vue/tasks/collection_objects/filter/components/tagAll.vue
index c7e4e7e3fd..79ca99e838 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/tagAll.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/tagAll.vue
@@ -1,72 +1,75 @@
 <template>
   <div>
-    <spinner-component 
+    <VSpinner
       v-if="showSpinner"
-      :full-screen="true"
-      legend="Creating tags..."/>
-    <button
-      class="button normal-input button-submit"
-      type="button"
-      @click="tagAll"
-      :disabled="!keywordId || !ids.length">
-      Tag
-    </button>
+      full-screen
+      legend="Creating tags..."
+    />
+    <VBtn
+      circle
+      color="create"
+      @click="createTags"
+      :disabled="!keywordId || !ids.length"
+    >
+      <VIcon
+        x-small
+        name="label"
+      />
+    </VBtn>
   </div>
 </template>
 
-<script>
-
+<script setup>
+import { ref, onUnmounted } from 'vue'
 import { Tag } from 'routes/endpoints'
-import SpinnerComponent from 'components/spinner'
+import { CONTROLLED_VOCABULARY_TERM } from 'constants/index'
+import VSpinner from 'components/spinner'
+import VBtn from 'components/ui/VBtn/index.vue'
+import VIcon from 'components/ui/VIcon/index.vue'
 
-export default {
-  components: {
-    SpinnerComponent
+const props = defineProps({
+  ids: {
+    type: Array,
+    default: () => []
   },
 
-  props: {
-    ids: {
-      type: Array,
-      default: () => []
-    },
-    type: {
-      type: String,
-      required: true
-    }
-  },
+  type: {
+    type: String,
+    required: true
+  }
+})
 
-  data () {
-    return {
-      keywordId: this.getDefault(),
-      showSpinner: false
-    }
-  },
+const keywordId = ref(getDefault())
+const showSpinner = ref(false)
 
-  created () {
-    document.addEventListener('pinboard:insert', (event) => {
-      if (event.detail.type === 'ControlledVocabularyTerm') {
-        this.keywordId = this.getDefault()
-      }
-    })
-  },
+function getDefault () {
+  const defaultTag = document.querySelector('[data-pinboard-section="Keywords"] [data-insert="true"]')
 
-  methods: {
-    getDefault () {
-      const defaultTag = document.querySelector('[data-pinboard-section="Keywords"] [data-insert="true"]')
-      return defaultTag ? defaultTag.getAttribute('data-pinboard-object-id') : undefined
-    },
+  return defaultTag && defaultTag.getAttribute('data-pinboard-object-id')
+}
 
-    tagAll () {
-      this.showSpinner = true
-      Tag.createBatch({
-        object_type: this.type,
-        keyword_id: this.keywordId,
-        object_ids: this.ids
-      }).then(() => {
-        this.showSpinner = false
-        TW.workbench.alert.create('Tags was successfully created', 'notice')
-      })
-    }
+function createTags () {
+  showSpinner.value = true
+
+  Tag.createBatch({
+    object_type: props.type,
+    keyword_id: keywordId.value,
+    object_ids: props.ids
+  }).then(() => {
+    showSpinner.value = false
+    TW.workbench.alert.create('Tags was successfully created', 'notice')
+  })
+}
+
+function handleEvent (event) {
+  if (event.detail.type === CONTROLLED_VOCABULARY_TERM) {
+    keywordId.value = getDefault()
   }
 }
-</script>
\ No newline at end of file
+
+document.addEventListener('pinboard:insert', handleEvent)
+
+onUnmounted(() => {
+  document.removeEventListener('pinboard:insert', handleEvent)
+})
+</script>

From da1abcffe0e64f262c6c3ec18c1033d7f3c91a1a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 23 Nov 2022 20:05:31 -0300
Subject: [PATCH 062/160] Add actions and storage changes

---
 .../simple_new_specimen/App.vue               |  14 ++
 .../simple_new_specimen/components/FormCE.vue |  14 +-
 .../components/FormCatalogNumber.vue          |  11 +-
 .../components/FormDepictions.vue             |  40 +++++-
 .../components/FormDetermination.vue          |   4 +-
 .../components/FormPreparationType.vue        |   4 +-
 .../components/GeographicArea.vue             |   7 +-
 .../store/actions/actionNames.js              |   9 ++
 .../store/actions/actions.js                  |  23 ++++
 .../store/actions/createCollectingEvent.js    |  14 ++
 .../store/actions/createCollectionObject.js   |  13 ++
 .../store/actions/createIdentifier.js         |  17 +++
 .../store/actions/createNewSpecimen.js        |  28 ++++
 .../store/actions/createTaxonDetermination.js |  10 ++
 .../store/actions/getIdentifiers.js           |  17 +++
 .../store/actions/resetStore.js               |  28 ++++
 .../simple_new_specimen/store/useStore.js     |  73 ++--------
 .../accessions/quick/simple/new.html.erb      | 129 ------------------
 18 files changed, 245 insertions(+), 210 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectingEvent.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectionObject.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getIdentifiers.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/resetStore.js

diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index 289f2eac4e..319868bc8f 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -4,6 +4,15 @@
     <template #header>
       <h3>Form</h3>
     </template>
+    <template #options>
+      <VBtn
+        color="create"
+        medium
+        @click="store.createNewSpecimen()"
+      >
+        Create
+      </VBtn>
+    </template>
     <template #body>
       <div
         class="margin-medium-bottom"
@@ -26,6 +35,11 @@ import FormCatalogNumber from './components/FormCatalogNumber.vue'
 import FormDepictions from './components/FormDepictions.vue'
 import FormDetermination from './components/FormDetermination.vue'
 import BlockLayout from 'components/layout/BlockLayout.vue'
+import VBtn from 'components/ui/VBtn/index.vue'
+
+import { useStore } from './store/useStore'
+
+const store = useStore()
 </script>
 
 <style lang="scss">
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
index 5670b67dd5..9871316964 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
@@ -2,7 +2,7 @@
   <div class="panel content">
     <div class="flex-separate middle">
       <h2>Collecting event</h2>
-      <VLock v-model="store.settings.lock.collectingEvent"/>
+      <VLock v-model="store.settings.lock.collectingEvent" />
     </div>
     <div class="field label-above">
       <label>Verbatim label</label>
@@ -25,9 +25,21 @@
 </template>
 
 <script setup>
+import { watch } from 'vue'
 import { useStore } from '../store/useStore'
 import GeographicArea from './GeographicArea.vue'
 import VLock from 'components/ui/VLock/index.vue'
 
 const store = useStore()
+
+watch(
+  [
+    () => store.geographicArea,
+    store.collectingEvent
+  ],
+  () => {
+    store.createdCE = undefined
+  },
+  { deep: true }
+)
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
index c06ea49df8..4a82711d1b 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -11,10 +11,11 @@
         <template #tabs-right>
           <VLock
             class="margin-small-left"
-            v-model="store.settings.lock.identifier"
+            v-model="store.settings.lock.namespace"
           />
         </template>
       </SmartSelector>
+      <hr v-if="store.namespace">
       <SmartSelectorItem
         :item="store.namespace"
         label="name"
@@ -30,7 +31,7 @@
           :class="{ 'validate-identifier': store.createdIdentifiers.length }"
           type="text"
           @input="checkIdentifier"
-          v-model="store.identifier.identifier"
+          v-model="store.identifier"
         >
         <label>
           <input
@@ -41,7 +42,7 @@
         </label>
       </div>
       <span
-        v-if="!store.namespace && store.identifier.identifier"
+        v-if="!store.namespace && store.identifier"
         style="color: red"
       >
         Namespace is needed.
@@ -78,8 +79,4 @@ function checkIdentifier () {
   }, DELAY)
 }
 
-function setNamespace ({ id }) {
-  store.identifier.namespace_id = id
-}
-
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue
index e1977dc27e..2b523e7d54 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDepictions.vue
@@ -2,20 +2,28 @@
   <div class="panel content">
     <VDropzone
       @vdropzone-sending="sending"
-      @vdropzone-file-added="addedfile"
       @vdropzone-success="success"
-      @vdropzone-error="error"
+      @vdropzone-queue-complete="isUploading = false"
       ref="dropzoneComponent"
       url="/depictions"
       use-custom-dropzone-options
       :dropzone-options="dropzoneOptions"
     />
+    <VSpinner
+      v-if="isUploading"
+      full-screen
+      legend="Uploading images..."
+    />
   </div>
 </template>
 
 <script setup>
 import { ref } from 'vue'
+import { useStore } from '../store/useStore'
+import { COLLECTION_OBJECT } from 'constants/index'
+import { ActionNames } from '../store/actions/actions'
 import VDropzone from 'components/dropzone.vue'
+import VSpinner from 'components/spinner.vue'
 
 const dropzoneOptions = {
   paramName: 'depiction[image_attributes][image_file]',
@@ -29,6 +37,34 @@ const dropzoneOptions = {
   acceptedFiles: 'image/*,.heic'
 }
 
+const store = useStore()
 const dropzoneComponent = ref(null)
+const isUploading = ref(false)
+
+const unsubscribe = store.$onAction(
+  ({
+    name,
+    after
+  }) => {
+    if (name !== ActionNames.CreateNewSpecimen) {
+      return
+    }
+
+    after(_ => {
+      if (dropzoneComponent.value.dropzone.getQueuedFiles().length) {
+        isUploading.value = true
+        dropzoneComponent.value.processQueue()
+      }
+    })
+  })
+
+const success = (file) => {
+  dropzoneComponent.value.removeFile(file)
+}
+
+const sending = (file, xhr, formData) => {
+  formData.append('depiction[depiction_object_id]', store.createdCO.id)
+  formData.append('depiction[depiction_object_type]', COLLECTION_OBJECT)
+}
 
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
index 8209d14c63..36af532d4e 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
@@ -12,11 +12,11 @@
         <template #tabs-right>
           <VLock
             class="margin-small-left"
-            v-model="store.settings.lock.determination"
+            v-model="store.settings.lock.otu"
           />
         </template>
       </SmartSelector>
-      <hr>
+      <hr v-if="store.otu">
       <SmartSelectorItem
         :item="store.otu"
         @unset="store.otu = undefined"
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
index 00ee81cc3c..2fbc302904 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
@@ -2,7 +2,7 @@
   <div class="panel content">
     <div class="flex-separate middle">
       <h2>Preparation</h2>
-      <VLock v-model="store.settings.lock.preparationType" />
+      <VLock v-model="store.settings.lock.preparationTypeId" />
     </div>
     <div class="horizontal-left-content align-start">
       <ul
@@ -18,7 +18,7 @@
             <input
               type="radio"
               :value="preparationType.id"
-              v-model="store.collectionObject.preparation_type_id"
+              v-model="store.preparationTypeId"
               name="collection-object-type"
             >
             {{ preparationType.name }}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
index 5dc8e41969..bfb9d32d64 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
@@ -2,17 +2,18 @@
   <fieldset>
     <legend>Geographic area</legend>
     <SmartSelector
+      v-model="store.geographicArea"
       ref="smartSelector"
       model="geographic_areas"
       target="CollectingEvent"
       label="name"
       klass="CollectingEvent"
-      @selected="store.geographicArea = $event"
     />
+    <hr v-if="store.geographicArea">
     <SmartSelectorItem
       :item="store.geographicArea"
-      label="object_tag"
-      @unset="state.geographicArea = undefined"
+      label="name"
+      @unset="store.geographicArea = undefined"
     />
   </fieldset>
 </template>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js
new file mode 100644
index 0000000000..cbf3f28027
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js
@@ -0,0 +1,9 @@
+export default {
+  CreateCollectingEvent: 'createCollectingEvent',
+  CreateCollectionObject: 'createCollectionObject',
+  CreateIdentifier: 'createIdentifier',
+  CreateNewSpecimen: 'createNewSpecimen',
+  CreateTaxonDetermination: 'createTaxonDetermination',
+  GetIdentifiers: 'getIdentifiers',
+  ResetStore: 'resetStore'
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js
new file mode 100644
index 0000000000..7b2d6aeeff
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js
@@ -0,0 +1,23 @@
+import ActionNames from './actionNames.js'
+import createCollectionObject from './createCollectionObject.js'
+import createCollectingEvent from './createCollectingEvent.js'
+import createIdentifier from './createIdentifier.js'
+import createNewSpecimen from './createNewSpecimen.js'
+import createTaxonDetermination from './createTaxonDetermination.js'
+import getIdentifiers from './getIdentifiers.js'
+import resetStore from './resetStore.js'
+
+const ActionFunctions = {
+  [ActionNames.CreateCollectionObject]: createCollectionObject,
+  [ActionNames.CreateCollectingEvent]: createCollectingEvent,
+  [ActionNames.CreateIdentifier]: createIdentifier,
+  [ActionNames.CreateNewSpecimen]: createNewSpecimen,
+  [ActionNames.CreateTaxonDetermination]: createTaxonDetermination,
+  [ActionNames.GetIdentifiers]: getIdentifiers,
+  [ActionNames.ResetStore]: resetStore
+}
+
+export {
+  ActionNames,
+  ActionFunctions
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectingEvent.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectingEvent.js
new file mode 100644
index 0000000000..4cf17d0791
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectingEvent.js
@@ -0,0 +1,14 @@
+import { CollectingEvent } from 'routes/endpoints'
+
+export default function () {
+  const payload = {
+    ...this.collectingEvent,
+    geographic_area_id: this.geographicArea?.id
+  }
+
+  return CollectingEvent
+    .create({ collecting_event: payload })
+    .then(({ body }) => {
+      this.createdCE = body
+    })
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectionObject.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectionObject.js
new file mode 100644
index 0000000000..f7c85e08ca
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createCollectionObject.js
@@ -0,0 +1,13 @@
+import { CollectionObject } from 'routes/endpoints'
+
+export default function () {
+  const payload = {
+    collection_object: {
+      preparation_type_id: this.preparationTypeId,
+      collecting_event_id: this.createdCE?.id,
+      total: 1
+    }
+  }
+
+  return CollectionObject.create(payload)
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js
new file mode 100644
index 0000000000..ece7ed26d6
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js
@@ -0,0 +1,17 @@
+import { Identifier } from 'routes/endpoints'
+import {
+  IDENTIFIER_LOCAL_CATALOG_NUMBER,
+  COLLECTION_OBJECT
+} from 'constants/index'
+
+export default function () {
+  const payload = {
+    identifier: this.identifier,
+    namespace_id: this.namespace.id,
+    type: IDENTIFIER_LOCAL_CATALOG_NUMBER,
+    identifier_object_id: this.createdCO.id,
+    identifier_object_type: COLLECTION_OBJECT
+  }
+
+  Identifier.create({ identifier: payload })
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
new file mode 100644
index 0000000000..696fe5c5e1
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
@@ -0,0 +1,28 @@
+export default async function () {
+  if (
+    !this.createdCE &&
+    (
+      this.collectingEvent.verbatim_label ||
+      this.collectingEvent.verbatim_locality ||
+      this.geographicArea
+    )
+  ) {
+    await this.createCollectingEvent()
+  }
+
+  this.createdCO = (await this.createCollectionObject()).body
+
+  if (
+    this.identifier &&
+    this.namespace &&
+    !this.createdIdentifiers.length
+  ) {
+    this.createIdentifier()
+  }
+
+  if (this.otu) {
+    this.createTaxonDetermination()
+  }
+
+  this.resetStore()
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js
new file mode 100644
index 0000000000..2ba198a046
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js
@@ -0,0 +1,10 @@
+import { TaxonDetermination } from 'routes/endpoints'
+
+export default function () {
+  const payload = {
+    otu_id: this.otu.id,
+    biological_collection_object_id: this.createdCO.id
+  }
+
+  TaxonDetermination.create({ taxon_determination: payload })
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getIdentifiers.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getIdentifiers.js
new file mode 100644
index 0000000000..36827df845
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getIdentifiers.js
@@ -0,0 +1,17 @@
+import { Identifier } from 'routes/endpoints'
+import { IDENTIFIER_LOCAL_CATALOG_NUMBER } from 'constants/index'
+
+export default function () {
+  if (!this.identifier || !this.namespace) {
+    this.createdIdentifiers = []
+    return
+  }
+
+  Identifier.where({
+    type: IDENTIFIER_LOCAL_CATALOG_NUMBER,
+    namespace_id: this.namespace.id,
+    identifier: this.identifier
+  }).then(({ body }) => {
+    this.createdIdentifiers = body
+  })
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/resetStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/resetStore.js
new file mode 100644
index 0000000000..06eba8fa0c
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/resetStore.js
@@ -0,0 +1,28 @@
+import incrementIdentifier from 'tasks/digitize/helpers/incrementIdentifier'
+
+export default function () {
+  const { collectingEvent, ...rest } = this.settings.lock
+
+  for (const key in rest) {
+    const isLocked = this.settings.lock[key]
+
+    if (!isLocked) {
+      this.$patch({ [key]: undefined })
+    }
+  }
+
+  if (!collectingEvent) {
+    this.$patch({
+      collectingEvent: {
+        verbatim_label: undefined,
+        verbatim_locality: undefined
+      },
+      geographicArea: undefined,
+      createdCE: undefined
+    })
+  }
+
+  this.identifier = this.settings.increment
+    ? incrementIdentifier(this.identifier)
+    : undefined
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
index 91699f486e..efd89ebf21 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
@@ -1,86 +1,31 @@
 import { defineStore } from 'pinia'
-import {
-  CollectionObject,
-  CollectingEvent,
-  TaxonDetermination,
-  Identifier
-} from 'routes/endpoints'
-import { IDENTIFIER_LOCAL_CATALOG_NUMBER, COLLECTION_OBJECT } from 'constants/index'
+import { ActionFunctions } from './actions/actions'
 
 const makeInitialState = () => ({
   settings: {
     lock: {
       collectingEvent: false,
-      determination: false,
-      identifier: false,
+      otu: false,
       namespace: false,
-      preparationType: false
+      preparationTypeId: false
     },
     increment: false
   },
   createdIdentifiers: [],
-  collectionObject: {
-    preparation_type_id: undefined
-  },
+  createdCO: undefined,
+  createdCE: undefined,
+  preparationTypeId: undefined,
   collectingEvent: {
     verbatim_label: undefined,
-    verbatim_locality: undefined,
-    geographic_area_id: undefined
+    verbatim_locality: undefined
   },
   geographicArea: undefined,
-  identifier: {
-    identifier: undefined,
-    identifier_object_id: undefined,
-    identifier_object_type: COLLECTION_OBJECT,
-    namespace_id: undefined,
-  },
+  identifier: undefined,
   namespace: undefined,
   otu: undefined
 })
 
 export const useStore = defineStore('main', {
   state: makeInitialState,
-
-  actions: {
-    async createNewSpecimen () {
-      const payload = {
-        collection_object: {
-          ...this.collectionObject
-        }
-      }
-
-      const response = payload.id
-        ? await CollectionObject.update(payload.id, payload)
-        : await CollectionObject.create(payload)
-
-      return response
-    },
-
-    getIdentifiers () {
-      if (!this.identifier.identifier) {
-        this.createdIdentifiers = []
-        return
-      }
-
-      Identifier.where({
-        type: IDENTIFIER_LOCAL_CATALOG_NUMBER,
-        namespace_id: this.namespace.id,
-        identifier: this.identifier.identifier
-      }).then(({ body }) => {
-        this.createdIdentifiers = body
-      })
-    },
-
-    createIdentifier (coId) {
-      const payload = {
-        identifier: this.identifier,
-        namespace_id: this.namespace.id,
-        type: IDENTIFIER_LOCAL_CATALOG_NUMBER,
-        identifier_object_id: coId,
-        identifier_object_type: COLLECTION_OBJECT
-      }
-
-      Identifier.create({ identifier: payload })
-    }
-  }
+  actions: ActionFunctions
 })
diff --git a/app/views/tasks/accessions/quick/simple/new.html.erb b/app/views/tasks/accessions/quick/simple/new.html.erb
index 25a4126763..099fad7493 100644
--- a/app/views/tasks/accessions/quick/simple/new.html.erb
+++ b/app/views/tasks/accessions/quick/simple/new.html.erb
@@ -1,134 +1,5 @@
 <div id="vue-simple-new-specimen"></div>
 
-<h2> Task: Simple new specimen </h2>
-
-<%= form_for(@specimen, as: :specimen, url: create_simple_specimen_task_path, html: {class: :dropzone, id: 'simple-specimen-task'}) do |f| -%>
-  <div class="flex-wrap-row get_fields">
-        <div class="panel no-shadow small_space">
-          <%= f.fields_for(:identifiers, @specimen.identifiers) do |i| -%>
-              <%= i.hidden_field :type -%>
-
-              <div class="side_by_side_fields">
-                <div class="field input-checkbox-field">
-                  <%= i.label :namespace_id, 'Catalog number' %>
-                  <%= render '/workbench/elements/forms/ajax_select',
-                             controller:        '/namespaces',
-                             object:            "specimen[identifiers_attributes][#{i.index}]",
-                             method:            'namespace_id',
-                             tag_id:            "namespace_id_for_identifier_#{i.index}",
-                             display:           (i.object.namespace ? i.object.namespace.short_name : nil),
-                             size:              20,
-                             fields_for_object: i
-                  %>
-
-                  <% if @specimen.identifiers.size == 1 %>
-                      <%= lock_tag(@locks, :identifier, :namespace_id) -%>
-                  <% end %>
-                  </div>
-                   <div class="field input-checkbox-field">
-
-                  <%= i.text_field :identifier %>
-
-                  <% if @specimen.identifiers.size == 1 %>
-                      <%= lock_tag(@locks, :identifier, :increment, 'increment') -%>
-                  <% end %>
-                  </div>
-                  <%= destroy_related_link(i) -%>
-                </div>
-          <% end %>
-
-          <%= f.fields_for(:taxon_determinations, @specimen.taxon_determinations) do |o| -%>
-              <div class="field">
-                <label>OTU</label>
-                <div class="field input-checkbox-field">
-                  <%= render '/otus/otu_picker', otu: o.object.otu, f: o -%>
-                  <%= lock_tag(@locks, :taxon_determination, :otu_id) -%>
-                </div>
-              </div>
-          <% end %>
-
-          <%= f.fields_for(:depictions, @specimen.depictions) do |d| -%>
-              <%= d.fields_for :image_attributes, Image.new do |i| %>
-                  <div class="field">
-                    <%= i.label :image_file, 'Specimen images' %>
-                    <div class="field dz-message vue-dropzone dz-file-preview dz-clickable" id="dropzone_previews" data-help="Images can be attached to the specimen by dropping them anywhere on this form.">
-                      <div class="dz-default dz-message">
-                        <span>Click to browse, or drop an image</span>
-                      </div>
-                    </div>
-                  </div>
-              <% end %>
-         <% end %>
-
-        <div class="field input-checkbox-field">
-          <%= f.label :preparation_type %>
-          <br>
-          <%= f.select :preparation_type_id, options_from_collection_for_select(PreparationType.all, :id, :name, f.object.preparation_type_id),  include_blank: true  -%>
-          <%= lock_tag(@locks, :specimen, :preparation_type_id) -%>
-        </div>
-
-
-          <hr>
-          <div class="flex-wrap-row" data-help="These fields are used to create a related collecting event."> 
-            <div class="flex-wrap-column">
-              <div id="collecting_event_fields" <%= 'hidden' if @specimen.collecting_event_id -%> >
-                <%= f.fields_for(:collecting_event, CollectingEvent.new, include_id: false) do |c| -%>
-                    <div class="field">
-                      <%= c.label :verbatim_label %>
-                      <%= c.text_area :verbatim_label, cols: 40, rows: 6 %>
-                    </div>
-
-                    <div class="field">
-                      <%= c.label :verbatim_locality %>
-                      <%= c.text_field :verbatim_locality, size: 40, id: 'verbatim_locality' %>
-                    </div>
-
-                    <div class="field">
-                      <%= c.label :geographic_area_id, 'Geographic area' %>
-
-                      <%= render '/workbench/elements/forms/ajax_select',
-                                 controller:        '/geographic_areas',
-                                 object:            'specimen[collecting_event_attributes]',
-                                 method:            'geographic_area_id',
-                                 tag_id:            'geographic_area_id_for_collecting_event',
-                                 fields_for_object: c,
-                                 size:              30,
-                                 display:           geographic_area_tag(c.object.geographic_area)
-                      %>
-                    </div>
-                <% end %>
-              </div>
-
-              <div id="selected_collecting_event">
-                <% if @specimen.collecting_event_id -%>
-                    <%= render('/collecting_events/card', object: @specimen.collecting_event) -%>
-                    <%= f.hidden_field(:collecting_event_id, id: 'selected_collecting_event_id') -%>
-                <% end %>
-              </div>
-            </div>
-
-            <div class="flex-wrap-column tiny_space">
-              <%= lock_tag(@locks, :collecting_event, :collecting_event_id) -%>
-              <%= link_to("return", "#", id: 'collecting_event_form_toggle', data: { turbolinks: false }, class: ['button-undo'], hidden: (@specimen.collecting_event_id ? false : true)) -%>
-            </div>
-          </div>
-        </div> 
-
-
-    <div class="flex-wrap-column small_space">
-      <%= submit_tag 'Create', id: :simple_create %>
-    </div>
-
-    <div class="flex-wrap-column small_space">
-      <div class="actions">
-        <div id="collecting_event_filter" class="panel"></div>
-      </div>
-    </div>
-
-  </div>
-
-<% end %>
-
 <h3> Recently created</h3>
 <div>
   <%= render('/tasks/accessions/report/dwc/table', collection_objects: @recent) -%>

From 43f6926ce2994be90e72af67545fef61d1657ff4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 23 Nov 2022 20:50:12 -0300
Subject: [PATCH 063/160] Add recent list, update actions

---
 .../simple_new_specimen/App.vue               | 64 ++++++++-------
 .../components/RecentTable.vue                | 79 +++++++++++++++++++
 .../store/actions/actionNames.js              |  1 +
 .../store/actions/actions.js                  |  2 +
 .../store/actions/createNewSpecimen.js        | 13 +--
 .../store/actions/getRecent.js                |  7 ++
 .../simple_new_specimen/store/useStore.js     |  3 +-
 .../accessions/quick/simple/new.html.erb      |  5 --
 8 files changed, 134 insertions(+), 40 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/RecentTable.vue
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getRecent.js

diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index 319868bc8f..d0e12a221a 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -1,31 +1,34 @@
 <template>
-  <h1>Simple new specimen</h1>
-  <BlockLayout>
-    <template #header>
-      <h3>Form</h3>
-    </template>
-    <template #options>
-      <VBtn
-        color="create"
-        medium
-        @click="store.createNewSpecimen()"
-      >
-        Create
-      </VBtn>
-    </template>
-    <template #body>
-      <div
-        class="margin-medium-bottom"
-        id="collection-object-form"
-      >
-        <FormCatalogNumber />
-        <FormPreparationType />
-        <FormDetermination />
-        <FormDepictions />
-      </div>
-      <FormCE />
-    </template>
-  </BlockLayout>
+  <div id="vue-simple-new-specimen-container">
+    <h1>Simple new specimen</h1>
+    <BlockLayout>
+      <template #header>
+        <h3>Form</h3>
+      </template>
+      <template #options>
+        <VBtn
+          color="create"
+          medium
+          @click="store.createNewSpecimen()"
+        >
+          Create
+        </VBtn>
+      </template>
+      <template #body>
+        <div
+          class="margin-medium-bottom"
+          id="collection-object-form"
+        >
+          <FormCatalogNumber />
+          <FormPreparationType />
+          <FormDetermination />
+          <FormDepictions />
+        </div>
+        <FormCE />
+      </template>
+    </BlockLayout>
+  </div>
+  <RecentTable />
 </template>
 
 <script setup>
@@ -36,14 +39,17 @@ import FormDepictions from './components/FormDepictions.vue'
 import FormDetermination from './components/FormDetermination.vue'
 import BlockLayout from 'components/layout/BlockLayout.vue'
 import VBtn from 'components/ui/VBtn/index.vue'
-
+import RecentTable from './components/RecentTable.vue'
 import { useStore } from './store/useStore'
+import { ActionNames } from './store/actions/actions'
 
 const store = useStore()
+
+store[ActionNames.GetRecent]()
 </script>
 
 <style lang="scss">
-#vue-simple-new-specimen {
+#vue-simple-new-specimen-container {
   flex-direction: column-reverse;
   margin: 0 auto;
   margin-top: 1em;
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/RecentTable.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/RecentTable.vue
new file mode 100644
index 0000000000..b9793f1fa7
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/RecentTable.vue
@@ -0,0 +1,79 @@
+<template>
+  <div>
+    <h2>Recently created</h2>
+    <VSpinner v-if="isLoading" />
+    <table class="full_width">
+      <thead>
+        <tr>
+          <th>Catalog number</th>
+          <th>Total</th>
+          <th>Family</th>
+          <th>Genus</th>
+          <th>Scientific name</th>
+          <th>Identifier</th>
+          <th>Level 1</th>
+          <th>Level 2</th>
+          <th>Level 3</th>
+          <th>Verbatim locality</th>
+          <th>Container</th>
+          <th>Updated by</th>
+          <th>Updated at</th>
+          <th />
+        </tr>
+      </thead>
+      <tbody>
+        <tr
+          v-for="(item, index) in store.recentList"
+          :key="item.id"
+          class="contextMenuCells"
+          :class="{ 'even': (index % 2 == 0) }"
+        >
+          <td>{{ item.dwc_attributes.catalogNumber }}</td>
+          <td>{{ item.dwc_attributes.individualCount }}</td>
+          <td>{{ item.dwc_attributes.family }}</td>
+          <td>{{ item.dwc_attributes.genus }}</td>
+          <td>{{ item.dwc_attributes.scientificName }}</td>
+          <td
+            v-if="item.identifier_from_container"
+            v-html="item.object_tag"
+          />
+          <td v-else>
+            {{ item.dwc_attributes.catalogNumber }}
+          </td>
+          <td>{{ item.dwc_attributes.country }}</td>
+          <td>{{ item.dwc_attributes.stateProvince }}</td>
+          <td>{{ item.dwc_attributes.county }}</td>
+          <td>{{ item.dwc_attributes.verbatimLocality }}</td>
+          <td v-html="item.container" />
+          <td>{{ item.updater }}</td>
+          <td>{{ item.updated_at }}</td>
+          <td>
+            <div class="horizontal-right-content">
+              <TagButtom
+                class="circle-button"
+                :global-id="item.global_id"
+              />
+              <RadialObject :global-id="item.global_id" />
+              <RadialAnnotator :global-id="item.global_id" />
+              <RadialNavigation :global-id="item.global_id" />
+            </div>
+          </td>
+        </tr>
+      </tbody>
+    </table>
+  </div>
+</template>
+
+<script setup>
+import { ref } from 'vue'
+import { useStore } from '../store/useStore'
+import RadialNavigation from 'components/radials/navigation/radial.vue'
+import RadialAnnotator from 'components/radials/annotator/annotator.vue'
+import RadialObject from 'components/radials/object/radial.vue'
+import TagButtom from 'components/defaultTag.vue'
+import VSpinner from 'components/spinner'
+
+const store = useStore()
+const isLoading = ref(false)
+
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js
index cbf3f28027..b535a5c92c 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actionNames.js
@@ -5,5 +5,6 @@ export default {
   CreateNewSpecimen: 'createNewSpecimen',
   CreateTaxonDetermination: 'createTaxonDetermination',
   GetIdentifiers: 'getIdentifiers',
+  GetRecent: 'getRecent',
   ResetStore: 'resetStore'
 }
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js
index 7b2d6aeeff..e4b9e4f7e9 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/actions.js
@@ -5,6 +5,7 @@ import createIdentifier from './createIdentifier.js'
 import createNewSpecimen from './createNewSpecimen.js'
 import createTaxonDetermination from './createTaxonDetermination.js'
 import getIdentifiers from './getIdentifiers.js'
+import getRecent from './getRecent.js'
 import resetStore from './resetStore.js'
 
 const ActionFunctions = {
@@ -14,6 +15,7 @@ const ActionFunctions = {
   [ActionNames.CreateNewSpecimen]: createNewSpecimen,
   [ActionNames.CreateTaxonDetermination]: createTaxonDetermination,
   [ActionNames.GetIdentifiers]: getIdentifiers,
+  [ActionNames.GetRecent]: getRecent,
   [ActionNames.ResetStore]: resetStore
 }
 
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
index 696fe5c5e1..f6c2a688f2 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
@@ -1,3 +1,5 @@
+import ActionNames from './actionNames.js'
+
 export default async function () {
   if (
     !this.createdCE &&
@@ -7,22 +9,23 @@ export default async function () {
       this.geographicArea
     )
   ) {
-    await this.createCollectingEvent()
+    await this[ActionNames.CreateCollectingEvent]()
   }
 
-  this.createdCO = (await this.createCollectionObject()).body
+  this.createdCO = (await this[ActionNames.CreateCollectionObject]()).body
 
   if (
     this.identifier &&
     this.namespace &&
     !this.createdIdentifiers.length
   ) {
-    this.createIdentifier()
+    this[ActionNames.CreateIdentifier]()
   }
 
   if (this.otu) {
-    this.createTaxonDetermination()
+    this[ActionNames.CreateTaxonDetermination]()
   }
 
-  this.resetStore()
+  this[ActionNames.GetRecent]()
+  this[ActionNames.ResetStore]()
 }
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getRecent.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getRecent.js
new file mode 100644
index 0000000000..b401073250
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/getRecent.js
@@ -0,0 +1,7 @@
+import { CollectionObject } from 'routes/endpoints'
+
+export default function () {
+  CollectionObject.reportDwc({ per: 10 }).then(({ body }) => {
+    this.recentList = body
+  })
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
index efd89ebf21..0d7777af78 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
@@ -22,7 +22,8 @@ const makeInitialState = () => ({
   geographicArea: undefined,
   identifier: undefined,
   namespace: undefined,
-  otu: undefined
+  otu: undefined,
+  recentList: []
 })
 
 export const useStore = defineStore('main', {
diff --git a/app/views/tasks/accessions/quick/simple/new.html.erb b/app/views/tasks/accessions/quick/simple/new.html.erb
index 099fad7493..3b98f6fdd9 100644
--- a/app/views/tasks/accessions/quick/simple/new.html.erb
+++ b/app/views/tasks/accessions/quick/simple/new.html.erb
@@ -1,6 +1 @@
 <div id="vue-simple-new-specimen"></div>
-
-<h3> Recently created</h3>
-<div>
-  <%= render('/tasks/accessions/report/dwc/table', collection_objects: @recent) -%>
-</div>

From f94ecbd3a49a6489098809b10b194b9aa74780ab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 24 Nov 2022 00:07:26 -0300
Subject: [PATCH 064/160] Refactor layout

---
 .../vue/components/ui/VLock/index.vue         |  8 +--
 .../simple_new_specimen/App.vue               | 56 ++++++++++++----
 .../simple_new_specimen/components/FormCE.vue |  5 +-
 .../components/FormCatalogNumber.vue          | 64 +++++++++++--------
 .../components/FormDetermination.vue          | 46 ++++++-------
 .../components/FormPreparationType.vue        | 46 ++++++-------
 .../components/GeographicArea.vue             | 37 ++++++-----
 .../components/SelectedItem.vue               | 40 ++++++++++++
 .../store/actions/createIdentifier.js         |  2 +-
 .../store/actions/createNewSpecimen.js        | 12 ++--
 .../store/actions/createTaxonDetermination.js |  2 +-
 11 files changed, 196 insertions(+), 122 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/SelectedItem.vue

diff --git a/app/javascript/vue/components/ui/VLock/index.vue b/app/javascript/vue/components/ui/VLock/index.vue
index 0cb9ac9136..84e045bf89 100644
--- a/app/javascript/vue/components/ui/VLock/index.vue
+++ b/app/javascript/vue/components/ui/VLock/index.vue
@@ -43,7 +43,7 @@ $primary: #FFDA44;
 $lightGrey: #99A3BA;
 
 .switch-lock {
-  height: 26px;
+  height: 28px;
   display: block;
   position: relative;
   cursor: pointer;
@@ -51,8 +51,8 @@ $lightGrey: #99A3BA;
     display: none;
     & + span {
       padding-left: 50px;
-      min-height: 26px;
-      line-height: 26px;
+      min-height: 28px;
+      line-height: 28px;
       display: block;
       color: $lightGrey;
       position: relative;
@@ -89,7 +89,7 @@ $lightGrey: #99A3BA;
         background: $lightGrey;
         position: absolute;
         left: 11px;
-        bottom: 7px;
+        bottom: 8px;
         border-radius: 2px;
         display: block;
         z-index: 1;
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index d0e12a221a..1b48f27a82 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -3,28 +3,32 @@
     <h1>Simple new specimen</h1>
     <BlockLayout>
       <template #header>
-        <h3>Form</h3>
-      </template>
-      <template #options>
-        <VBtn
-          color="create"
-          medium
-          @click="store.createNewSpecimen()"
-        >
-          Create
-        </VBtn>
+        <h3>Information</h3>
       </template>
       <template #body>
         <div
           class="margin-medium-bottom"
           id="collection-object-form"
+          ref="root"
         >
-          <FormCatalogNumber />
-          <FormPreparationType />
-          <FormDetermination />
+          <div>
+            <FormCatalogNumber class="margin-medium-bottom" />
+            <FormPreparationType class="margin-medium-bottom" />
+            <FormDetermination class="margin-medium-bottom" />
+            <FormCE />
+          </div>
           <FormDepictions />
+          <div>
+            <VBtn
+              color="create"
+              medium
+              @click="store.createNewSpecimen()"
+              @keydown.tab.prevent="setFristAutofocusElement"
+            >
+              Create
+            </VBtn>
+          </div>
         </div>
-        <FormCE />
       </template>
     </BlockLayout>
   </div>
@@ -40,12 +44,36 @@ import FormDetermination from './components/FormDetermination.vue'
 import BlockLayout from 'components/layout/BlockLayout.vue'
 import VBtn from 'components/ui/VBtn/index.vue'
 import RecentTable from './components/RecentTable.vue'
+import { ref } from 'vue'
 import { useStore } from './store/useStore'
 import { ActionNames } from './store/actions/actions'
 
 const store = useStore()
+const root = ref(null)
 
 store[ActionNames.GetRecent]()
+
+const setFristAutofocusElement = () => {
+  const element = root.value.querySelector('#collection-object-form input[type="text"]:not([disabled])')
+
+  if (element) {
+    element.focus()
+  }
+}
+
+const unsubscribe = store.$onAction(
+  ({
+    name,
+    after
+  }) => {
+    if (name !== ActionNames.CreateNewSpecimen) {
+      return
+    }
+
+    after(_ => {
+      setFristAutofocusElement()
+    })
+  })
 </script>
 
 <style lang="scss">
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
index 9871316964..2bf2dcf293 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
@@ -1,7 +1,8 @@
 <template>
-  <div class="panel content">
+  <div>
+    <hr>
     <div class="flex-separate middle">
-      <h2>Collecting event</h2>
+      <h3>Collecting event</h3>
       <VLock v-model="store.settings.lock.collectingEvent" />
     </div>
     <div class="field label-above">
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
index 4a82711d1b..e0957cc0d6 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -1,37 +1,40 @@
 <template>
-  <div class="panel content">
-    <h2>Catalog number</h2>
-    <fieldset>
-      <legend>Namespace</legend>
-      <SmartSelector
-        model="namespaces"
-        :klass="COLLECTION_OBJECT"
-        v-model="store.namespace"
-      >
-        <template #tabs-right>
-          <VLock
-            class="margin-small-left"
-            v-model="store.settings.lock.namespace"
-          />
-        </template>
-      </SmartSelector>
-      <hr v-if="store.namespace">
-      <SmartSelectorItem
+  <div>
+    <label>Namespace</label>
+    <div class="horizontal-left-content middle field">
+      <SelectedItem
+        v-if="store.namespace"
+        class="full_width"
+        label="label"
         :item="store.namespace"
-        label="name"
         @unset="store.namespace = undefined"
       />
-    </fieldset>
+      <Autocomplete
+        v-else
+        ref="autocompleteComponent"
+        class="full_width"
+        url="/namespaces/autocomplete"
+        param="term"
+        label="label_html"
+        clear-after
+        autofocus
+        placeholder="Search a namespace..."
+        @get-item="store.namespace = $event"
+      />
+      <VLock
+        class="margin-small-left"
+        v-model="store.settings.lock.namespace"
+      />
+    </div>
 
-    <div class="separate-top">
+    <div class="">
       <label>Identifier</label>
-      <div class="horizontal-left-content field">
+      <div class="horizontal-left-content">
         <input
-          id="identifier-field"
-          :class="{ 'validate-identifier': store.createdIdentifiers.length }"
           type="text"
-          @input="checkIdentifier"
+          class="half_width"
           v-model="store.identifier"
+          @input="checkIdentifier"
         >
         <label>
           <input
@@ -61,12 +64,13 @@
 </template>
 
 <script setup>
+import { onMounted, ref } from 'vue'
 import { useStore } from '../store/useStore'
-import { COLLECTION_OBJECT } from 'constants/index'
-import SmartSelector from 'components/ui/SmartSelector.vue'
-import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
+import SelectedItem from './SelectedItem.vue'
+import Autocomplete from 'components/ui/Autocomplete.vue'
 import VLock from 'components/ui/VLock/index.vue'
 
+const autocompleteComponent = ref(null)
 const store = useStore()
 const DELAY = 1000
 let timeoutRequest
@@ -79,4 +83,8 @@ function checkIdentifier () {
   }, DELAY)
 }
 
+onMounted(() => {
+  setTimeout(() => autocompleteComponent.value.setFocus(), 250)
+})
+
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
index 36af532d4e..06e201282c 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
@@ -1,35 +1,35 @@
 <template>
-  <div class="panel content">
-    <h2>Determination</h2>
-    <fieldset>
-      <legend>OTU</legend>
-      <SmartSelector
-        model="otus"
-        :target="TAXON_DETERMINATION"
-        :klass="TAXON_DETERMINATION"
-        v-model="store.otu"
-      >
-        <template #tabs-right>
-          <VLock
-            class="margin-small-left"
-            v-model="store.settings.lock.otu"
-          />
-        </template>
-      </SmartSelector>
-      <hr v-if="store.otu">
-      <SmartSelectorItem
+  <div>
+    <label>OTU</label>
+    <div class="horizontal-left-content middle field">
+      <SelectedItem
+        v-if="store.otu"
+        class="full_width"
         :item="store.otu"
         @unset="store.otu = undefined"
       />
-    </fieldset>
+      <Autocomplete
+        v-else
+        class="full_width"
+        url="/otus/autocomplete"
+        placeholder="Search an OTU"
+        label="label_html"
+        display="label"
+        param="term"
+        @get-item="store.otu = $event"
+      />
+      <VLock
+        class="margin-small-left"
+        v-model="store.settings.lock.otu"
+      />
+    </div>
   </div>
 </template>
 
 <script setup>
-import { TAXON_DETERMINATION } from 'constants/index'
 import { useStore } from '../store/useStore'
-import SmartSelector from 'components/ui/SmartSelector.vue'
-import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
+import Autocomplete from 'components/ui/Autocomplete.vue'
+import SelectedItem from './SelectedItem.vue'
 import VLock from 'components/ui/VLock/index.vue'
 
 const store = useStore()
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
index 2fbc302904..24606fd0b2 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
@@ -1,36 +1,34 @@
 <template>
-  <div class="panel content">
+  <div>
     <div class="flex-separate middle">
-      <h2>Preparation</h2>
-      <VLock v-model="store.settings.lock.preparationTypeId" />
+      <span>Preparation type</span>
     </div>
     <div class="horizontal-left-content align-start">
-      <ul
-        v-for="(itemsGroup, index) in chunkList"
-        :key="index"
-        class="no_bullets full_width"
+      <select
+        class="half_width"
+        v-model="store.preparationTypeId"
       >
-        <li
-          v-for="preparationType in itemsGroup"
-          :key="preparationType.id"
+        <option :value="undefined">
+          None
+        </option>
+        <option
+          v-for="(item) in preparationTypes"
+          :key="item.id"
+          :value="item.id"
         >
-          <label>
-            <input
-              type="radio"
-              :value="preparationType.id"
-              v-model="store.preparationTypeId"
-              name="collection-object-type"
-            >
-            {{ preparationType.name }}
-          </label>
-        </li>
-      </ul>
+          {{ item.name }}
+        </option>
+      </select>
+      <VLock
+        class="margin-small-left"
+        v-model="store.settings.lock.preparationTypeId"
+      />
     </div>
   </div>
 </template>
 
 <script setup>
-import { computed, ref } from 'vue'
+import { ref } from 'vue'
 import { PreparationType } from 'routes/endpoints'
 import { useStore } from '../store/useStore.js'
 import VLock from 'components/ui/VLock/index.vue'
@@ -48,8 +46,4 @@ PreparationType.where({}).then(({ body }) => {
   ]
 })
 
-const chunkList = computed(() =>
-  preparationTypes.value.chunk(Math.ceil(preparationTypes.value.length / 3))
-)
-
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
index bfb9d32d64..ff00620a0e 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
@@ -1,26 +1,25 @@
 <template>
-  <fieldset>
-    <legend>Geographic area</legend>
-    <SmartSelector
-      v-model="store.geographicArea"
-      ref="smartSelector"
-      model="geographic_areas"
-      target="CollectingEvent"
-      label="name"
-      klass="CollectingEvent"
-    />
-    <hr v-if="store.geographicArea">
-    <SmartSelectorItem
-      :item="store.geographicArea"
-      label="name"
-      @unset="store.geographicArea = undefined"
-    />
-  </fieldset>
+  <label>Geographic area</label>
+  <SelectedItem
+    v-if="store.geographicArea"
+    :item="store.geographicArea"
+    @unset="store.geographicArea = undefined"
+  />
+  <Autocomplete
+    v-else
+    url="/geographic_areas/autocomplete"
+    param="term"
+    label="label_html"
+    autofocus
+    placeholder="Search a geographic area"
+    clear-after
+    @get-item="store.geographicArea = $event"
+  />
 </template>
 
 <script setup>
-import SmartSelector from 'components/ui/SmartSelector.vue'
-import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
+import Autocomplete from 'components/ui/Autocomplete.vue'
+import SelectedItem from './SelectedItem.vue'
 import { useStore } from '../store/useStore'
 
 const store = useStore()
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/SelectedItem.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/SelectedItem.vue
new file mode 100644
index 0000000000..9cf34cdc35
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/SelectedItem.vue
@@ -0,0 +1,40 @@
+<template>
+  <div class="flex-separate middle">
+    <input
+      class="full_width"
+      type="text"
+      :value="item[label]"
+      disabled
+    >
+    <VBtn
+      class="margin-small-left"
+      color="primary"
+      circle
+      @click="emit('unset')"
+    >
+      <VIcon
+        x-small
+        name="trash"
+      />
+    </VBtn>
+  </div>
+</template>
+
+<script setup>
+import VBtn from 'components/ui/VBtn/index.vue'
+import VIcon from 'components/ui/VIcon/index.vue'
+
+defineProps({
+  item: {
+    type: Object,
+    required: true
+  },
+
+  label: {
+    type: String,
+    default: 'label'
+  }
+})
+
+const emit = defineEmits(['unset'])
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js
index ece7ed26d6..873e4fc0df 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createIdentifier.js
@@ -13,5 +13,5 @@ export default function () {
     identifier_object_type: COLLECTION_OBJECT
   }
 
-  Identifier.create({ identifier: payload })
+  return Identifier.create({ identifier: payload })
 }
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
index f6c2a688f2..77cc67d934 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
@@ -1,6 +1,8 @@
 import ActionNames from './actionNames.js'
 
 export default async function () {
+  const promises = []
+
   if (
     !this.createdCE &&
     (
@@ -19,13 +21,15 @@ export default async function () {
     this.namespace &&
     !this.createdIdentifiers.length
   ) {
-    this[ActionNames.CreateIdentifier]()
+    promises.push(this[ActionNames.CreateIdentifier]())
   }
 
   if (this.otu) {
-    this[ActionNames.CreateTaxonDetermination]()
+    promises.push(this[ActionNames.CreateTaxonDetermination]())
   }
 
-  this[ActionNames.GetRecent]()
-  this[ActionNames.ResetStore]()
+  Promise.allSettled(promises).then(_ => {
+    this[ActionNames.GetRecent]()
+    this[ActionNames.ResetStore]()
+  })
 }
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js
index 2ba198a046..df32a5876f 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createTaxonDetermination.js
@@ -6,5 +6,5 @@ export default function () {
     biological_collection_object_id: this.createdCO.id
   }
 
-  TaxonDetermination.create({ taxon_determination: payload })
+  return TaxonDetermination.create({ taxon_determination: payload })
 }

From fe0a37551084683a75090e6fcf874a1fc803d6c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Mon, 28 Nov 2022 11:55:55 -0300
Subject: [PATCH 065/160] Fix axios request

---
 .../tasks/dwca_import/store/actions/loadDataSetRecords.js | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js b/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js
index cdc80fd823..05205c7ba8 100644
--- a/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js
+++ b/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js
@@ -19,7 +19,13 @@ export default ({ state, commit, getters }, page) => {
     state.temporary.downloadingPages.push(pagePosition)
 
     GetDatasetRecords(state.dataset.id, {
-      params: Object.assign({}, { page: loadPage }, state.paramsFilter), paramsSerializer: (params) => Qs.stringify(params, { arrayFormat: 'brackets' })
+      params: {
+        page: loadPage,
+        ...state.paramsFilter,
+        paramsSerializer: {
+          serialize: (params) => Qs.stringify(params, { arrayFormat: 'brackets' })
+        }
+      }
     }).then(response => {
       commit(MutationNames.SetPagination, GetPagination(response))
       state.dataset.progress = response.body.progress

From fca3a72d3f49fcc2803f81fa6033527c7d0662ee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Mon, 28 Nov 2022 11:56:15 -0300
Subject: [PATCH 066/160] Update packages

---
 package-lock.json | 786 +++++++++++++++++++++++++---------------------
 package.json      |  18 +-
 2 files changed, 437 insertions(+), 367 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 8399ecc621..43a77b6ba7 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -12,17 +12,17 @@
         "@ibm/plex": "^6.1.1",
         "@sfgrp/sled": "^1.0.3",
         "@sfgrp/svg-radial-menu": "^1.0.7",
-        "axios": "^1.1.3",
+        "axios": "^1.2.0",
         "chart.js": "^4.0.1",
         "d3": "^7.6.1",
         "dompurify": "^2.4.1",
         "easymde": "^2.18.0",
         "exif-js": "^2.3.0",
         "json2csv": "^5.0.7",
-        "leaflet": "^1.9.2",
+        "leaflet": "^1.9.3",
         "leaflet.pattern": "^0.1.0",
         "parse-dms": "0.0.5",
-        "pdfjs-dist": "3.0.279",
+        "pdfjs-dist": "3.1.81",
         "qs": "^6.11.0",
         "shakapacker": "6.5.4",
         "v-hotkey": "^0.9.0",
@@ -35,24 +35,24 @@
         "vuex": "^4.1.0"
       },
       "devDependencies": {
-        "@babel/core": "^7.19.3",
+        "@babel/core": "^7.20.5",
         "@babel/plugin-transform-runtime": "^7.19.6",
-        "@babel/preset-env": "^7.19.3",
-        "@babel/runtime": "^7.19.0",
+        "@babel/preset-env": "^7.20.2",
+        "@babel/runtime": "^7.20.6",
         "@vue/compiler-sfc": "^3.2.45",
         "babel-loader": "^8.2.5",
         "compression-webpack-plugin": "^10.0.0",
         "css-loader": "^6.7.2",
         "css-minimizer-webpack-plugin": "^4.2.2",
-        "eslint": "^8.27.0",
+        "eslint": "^8.28.0",
         "eslint-config-standard": "^17.0.0",
         "eslint-plugin-import": "^2.26.0",
         "eslint-plugin-n": "^15.5.1",
         "eslint-plugin-node": "^11.1.0",
         "eslint-plugin-promise": "^6.1.1",
         "eslint-plugin-standard": "^4.1.0",
-        "eslint-plugin-vue": "^9.7.0",
-        "mini-css-extract-plugin": "^2.6.1",
+        "eslint-plugin-vue": "^9.8.0",
+        "mini-css-extract-plugin": "^2.7.0",
         "postcss": "^8.4.19",
         "postcss-flexbugs-fixes": "^5.0.2",
         "postcss-import": "^15.0.0",
@@ -106,28 +106,28 @@
       }
     },
     "node_modules/@babel/compat-data": {
-      "version": "7.19.3",
-      "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.19.3.tgz",
-      "integrity": "sha512-prBHMK4JYYK+wDjJF1q99KK4JLL+egWS4nmNqdlMUgCExMZ+iZW0hGhyC3VEbsPjvaN0TBhW//VIFwBrk8sEiw==",
+      "version": "7.20.5",
+      "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.20.5.tgz",
+      "integrity": "sha512-KZXo2t10+/jxmkhNXc7pZTqRvSOIvVv/+lJwHS+B2rErwOyjuVRh60yVpb7liQ1U5t7lLJ1bz+t8tSypUZdm0g==",
       "engines": {
         "node": ">=6.9.0"
       }
     },
     "node_modules/@babel/core": {
-      "version": "7.19.3",
-      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.19.3.tgz",
-      "integrity": "sha512-WneDJxdsjEvyKtXKsaBGbDeiyOjR5vYq4HcShxnIbG0qixpoHjI3MqeZM9NDvsojNCEBItQE4juOo/bU6e72gQ==",
+      "version": "7.20.5",
+      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.20.5.tgz",
+      "integrity": "sha512-UdOWmk4pNWTm/4DlPUl/Pt4Gz4rcEMb7CY0Y3eJl5Yz1vI8ZJGmHWaVE55LoxRjdpx0z259GE9U5STA9atUinQ==",
       "dependencies": {
         "@ampproject/remapping": "^2.1.0",
         "@babel/code-frame": "^7.18.6",
-        "@babel/generator": "^7.19.3",
-        "@babel/helper-compilation-targets": "^7.19.3",
-        "@babel/helper-module-transforms": "^7.19.0",
-        "@babel/helpers": "^7.19.0",
-        "@babel/parser": "^7.19.3",
+        "@babel/generator": "^7.20.5",
+        "@babel/helper-compilation-targets": "^7.20.0",
+        "@babel/helper-module-transforms": "^7.20.2",
+        "@babel/helpers": "^7.20.5",
+        "@babel/parser": "^7.20.5",
         "@babel/template": "^7.18.10",
-        "@babel/traverse": "^7.19.3",
-        "@babel/types": "^7.19.3",
+        "@babel/traverse": "^7.20.5",
+        "@babel/types": "^7.20.5",
         "convert-source-map": "^1.7.0",
         "debug": "^4.1.0",
         "gensync": "^1.0.0-beta.2",
@@ -143,11 +143,11 @@
       }
     },
     "node_modules/@babel/generator": {
-      "version": "7.19.3",
-      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.19.3.tgz",
-      "integrity": "sha512-fqVZnmp1ncvZU757UzDheKZpfPgatqY59XtW2/j/18H7u76akb8xqvjw82f+i2UKd/ksYsSick/BCLQUUtJ/qQ==",
+      "version": "7.20.5",
+      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.20.5.tgz",
+      "integrity": "sha512-jl7JY2Ykn9S0yj4DQP82sYvPU+T3g0HFcWTqDLqiuA9tGRNIj9VfbtXGAYTTkyNEnQk1jkMGOdYka8aG/lulCA==",
       "dependencies": {
-        "@babel/types": "^7.19.3",
+        "@babel/types": "^7.20.5",
         "@jridgewell/gen-mapping": "^0.3.2",
         "jsesc": "^2.5.1"
       },
@@ -192,11 +192,11 @@
       }
     },
     "node_modules/@babel/helper-compilation-targets": {
-      "version": "7.19.3",
-      "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.19.3.tgz",
-      "integrity": "sha512-65ESqLGyGmLvgR0mst5AdW1FkNlj9rQsCKduzEoEPhBCDFGXvz2jW6bXFG6i0/MrV2s7hhXjjb2yAzcPuQlLwg==",
+      "version": "7.20.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.20.0.tgz",
+      "integrity": "sha512-0jp//vDGp9e8hZzBc6N/KwA5ZK3Wsm/pfm4CrY7vzegkVxc65SgSn6wYOnwHe9Js9HRQ1YTCKLGPzDtaS3RoLQ==",
       "dependencies": {
-        "@babel/compat-data": "^7.19.3",
+        "@babel/compat-data": "^7.20.0",
         "@babel/helper-validator-option": "^7.18.6",
         "browserslist": "^4.21.3",
         "semver": "^6.3.0"
@@ -324,18 +324,18 @@
       }
     },
     "node_modules/@babel/helper-module-transforms": {
-      "version": "7.19.0",
-      "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.19.0.tgz",
-      "integrity": "sha512-3HBZ377Fe14RbLIA+ac3sY4PTgpxHVkFrESaWhoI5PuyXPBBX8+C34qblV9G89ZtycGJCmCI/Ut+VUDK4bltNQ==",
+      "version": "7.20.2",
+      "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.20.2.tgz",
+      "integrity": "sha512-zvBKyJXRbmK07XhMuujYoJ48B5yvvmM6+wcpv6Ivj4Yg6qO7NOZOSnvZN9CRl1zz1Z4cKf8YejmCMh8clOoOeA==",
       "dependencies": {
         "@babel/helper-environment-visitor": "^7.18.9",
         "@babel/helper-module-imports": "^7.18.6",
-        "@babel/helper-simple-access": "^7.18.6",
+        "@babel/helper-simple-access": "^7.20.2",
         "@babel/helper-split-export-declaration": "^7.18.6",
-        "@babel/helper-validator-identifier": "^7.18.6",
+        "@babel/helper-validator-identifier": "^7.19.1",
         "@babel/template": "^7.18.10",
-        "@babel/traverse": "^7.19.0",
-        "@babel/types": "^7.19.0"
+        "@babel/traverse": "^7.20.1",
+        "@babel/types": "^7.20.2"
       },
       "engines": {
         "node": ">=6.9.0"
@@ -353,9 +353,9 @@
       }
     },
     "node_modules/@babel/helper-plugin-utils": {
-      "version": "7.19.0",
-      "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.19.0.tgz",
-      "integrity": "sha512-40Ryx7I8mT+0gaNxm8JGTZFUITNqdLAgdg0hXzeVZxVD6nFsdhQvip6v8dqkRHzsz1VFpFAaOCHNn0vKBL7Czw==",
+      "version": "7.20.2",
+      "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.20.2.tgz",
+      "integrity": "sha512-8RvlJG2mj4huQ4pZ+rU9lqKi9ZKiRmuvGuM2HlWmkmgOhbs6zEAw6IEiJ5cQqGbDzGZOhwuOQNtZMi/ENLjZoQ==",
       "engines": {
         "node": ">=6.9.0"
       }
@@ -393,11 +393,11 @@
       }
     },
     "node_modules/@babel/helper-simple-access": {
-      "version": "7.18.6",
-      "resolved": "https://registry.npmjs.org/@babel/helper-simple-access/-/helper-simple-access-7.18.6.tgz",
-      "integrity": "sha512-iNpIgTgyAvDQpDj76POqg+YEt8fPxx3yaNBg3S30dxNKm2SWfYhD0TGrK/Eu9wHpUW63VQU894TsTg+GLbUa1g==",
+      "version": "7.20.2",
+      "resolved": "https://registry.npmjs.org/@babel/helper-simple-access/-/helper-simple-access-7.20.2.tgz",
+      "integrity": "sha512-+0woI/WPq59IrqDYbVGfshjT5Dmk/nnbdpcF8SnMhhXObpTq2KNBdLFRFrkVdbDOyUmHBCxzm5FHV1rACIkIbA==",
       "dependencies": {
-        "@babel/types": "^7.18.6"
+        "@babel/types": "^7.20.2"
       },
       "engines": {
         "node": ">=6.9.0"
@@ -426,9 +426,9 @@
       }
     },
     "node_modules/@babel/helper-string-parser": {
-      "version": "7.18.10",
-      "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.18.10.tgz",
-      "integrity": "sha512-XtIfWmeNY3i4t7t4D2t02q50HvqHybPqW2ki1kosnvWCwuCMeo81Jf0gwr85jy/neUdg5XDdeFE/80DXiO+njw==",
+      "version": "7.19.4",
+      "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.19.4.tgz",
+      "integrity": "sha512-nHtDoQcuqFmwYNYPz3Rah5ph2p8PFeFCsZk9A/48dPc/rGocJ5J3hAAZ7pb76VWX3fZKu+uEr/FhH5jLx7umrw==",
       "engines": {
         "node": ">=6.9.0"
       }
@@ -464,13 +464,13 @@
       }
     },
     "node_modules/@babel/helpers": {
-      "version": "7.19.0",
-      "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.19.0.tgz",
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+      "version": "3.1.81",
+      "resolved": "https://registry.npmjs.org/pdfjs-dist/-/pdfjs-dist-3.1.81.tgz",
+      "integrity": "sha512-hZHVVbjU2Ac1VYyPFrg9fBcyS7EEdB8YFy5upk6LmnsXl10WxAavdiViGWi2C/xK0GZObEpSSJU1VnoF9t8n9w==",
       "requires": {
-        "canvas": "^2.10.1",
+        "canvas": "^2.10.2",
         "web-streams-polyfill": "^3.2.1"
       }
     },
@@ -18206,9 +18265,9 @@
       }
     },
     "regenerator-runtime": {
-      "version": "0.13.9",
-      "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.13.9.tgz",
-      "integrity": "sha512-p3VT+cOEgxFsRRA9X4lkI1E+k2/CtnKtU4gcxyaCUreilL/vqI6CdZ3wxVUx3UOUg+gnUOQQcRI7BmSI656MYA=="
+      "version": "0.13.11",
+      "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.13.11.tgz",
+      "integrity": "sha512-kY1AZVr2Ra+t+piVaJ4gxaFaReZVH40AKNo7UCX6W+dEwBo/2oZJzqfuN1qLq1oL45o56cPaTXELwrTh8Fpggg=="
     },
     "regenerator-transform": {
       "version": "0.15.0",
@@ -18566,7 +18625,8 @@
     "set-blocking": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/set-blocking/-/set-blocking-2.0.0.tgz",
-      "integrity": "sha512-KiKBS8AnWGEyLzofFfmvKwpdPzqiy16LvQfK3yv/fVH7Bj13/wl3JSR1J+rfgRE9q7xUJK4qvgS8raSOeLUehw=="
+      "integrity": "sha512-KiKBS8AnWGEyLzofFfmvKwpdPzqiy16LvQfK3yv/fVH7Bj13/wl3JSR1J+rfgRE9q7xUJK4qvgS8raSOeLUehw==",
+      "optional": true
     },
     "setprototypeof": {
       "version": "1.2.0",
@@ -18622,12 +18682,14 @@
     "simple-concat": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/simple-concat/-/simple-concat-1.0.1.tgz",
-      "integrity": "sha512-cSFtAPtRhljv69IK0hTVZQ+OfE9nePi/rtJmw5UjHeVyVroEqJXP1sFztKUy1qU+xvz3u/sfYJLa947b7nAN2Q=="
+      "integrity": "sha512-cSFtAPtRhljv69IK0hTVZQ+OfE9nePi/rtJmw5UjHeVyVroEqJXP1sFztKUy1qU+xvz3u/sfYJLa947b7nAN2Q==",
+      "optional": true
     },
     "simple-get": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.1.tgz",
       "integrity": "sha512-CQ5LTKGfCpvE1K0n2us+kuMPbk/q0EKl82s4aheV9oXjFEz6W/Y7oQFVJuU6QG77hRT4Ghb5RURteF5vnWjupA==",
+      "optional": true,
       "requires": {
         "decompress-response": "^4.2.0",
         "once": "^1.3.1",
@@ -18726,6 +18788,7 @@
       "version": "4.2.3",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
       "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==",
+      "optional": true,
       "requires": {
         "emoji-regex": "^8.0.0",
         "is-fullwidth-code-point": "^3.0.0",
@@ -18758,6 +18821,7 @@
       "version": "6.0.1",
       "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
       "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==",
+      "devOptional": true,
       "requires": {
         "ansi-regex": "^5.0.1"
       }
@@ -18865,6 +18929,7 @@
       "version": "6.1.12",
       "resolved": "https://registry.npmjs.org/tar/-/tar-6.1.12.tgz",
       "integrity": "sha512-jU4TdemS31uABHd+Lt5WEYJuzn+TJTCBLljvIAHZOz6M9Os5pJ4dD+vRFLxPa/n3T0iEFzpi+0x1UfuDZYbRMw==",
+      "optional": true,
       "requires": {
         "chownr": "^2.0.0",
         "fs-minipass": "^2.0.0",
@@ -18956,7 +19021,8 @@
     "tr46": {
       "version": "0.0.3",
       "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz",
-      "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw=="
+      "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw==",
+      "optional": true
     },
     "tsconfig-paths": {
       "version": "3.14.1",
@@ -19286,7 +19352,8 @@
     "webidl-conversions": {
       "version": "3.0.1",
       "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
-      "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ=="
+      "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ==",
+      "optional": true
     },
     "webpack": {
       "version": "5.75.0",
@@ -19588,6 +19655,7 @@
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
       "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
+      "optional": true,
       "requires": {
         "tr46": "~0.0.3",
         "webidl-conversions": "^3.0.0"
@@ -19618,6 +19686,7 @@
       "version": "1.1.5",
       "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz",
       "integrity": "sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg==",
+      "optional": true,
       "requires": {
         "string-width": "^1.0.2 || 2 || 3 || 4"
       }
@@ -19676,7 +19745,8 @@
     "yallist": {
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
-      "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A=="
+      "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
+      "devOptional": true
     },
     "yaml": {
       "version": "1.10.2",
diff --git a/package.json b/package.json
index d371c2c026..0020352adf 100644
--- a/package.json
+++ b/package.json
@@ -6,17 +6,17 @@
     "@ibm/plex": "^6.1.1",
     "@sfgrp/sled": "^1.0.3",
     "@sfgrp/svg-radial-menu": "^1.0.7",
-    "axios": "^1.1.3",
+    "axios": "^1.2.0",
     "chart.js": "^4.0.1",
     "d3": "^7.6.1",
     "dompurify": "^2.4.1",
     "easymde": "^2.18.0",
     "exif-js": "^2.3.0",
     "json2csv": "^5.0.7",
-    "leaflet": "^1.9.2",
+    "leaflet": "^1.9.3",
     "leaflet.pattern": "^0.1.0",
     "parse-dms": "0.0.5",
-    "pdfjs-dist": "3.0.279",
+    "pdfjs-dist": "3.1.81",
     "qs": "^6.11.0",
     "shakapacker": "6.5.4",
     "v-hotkey": "^0.9.0",
@@ -38,24 +38,24 @@
     "defaults"
   ],
   "devDependencies": {
-    "@babel/core": "^7.19.3",
+    "@babel/core": "^7.20.5",
     "@babel/plugin-transform-runtime": "^7.19.6",
-    "@babel/preset-env": "^7.19.3",
-    "@babel/runtime": "^7.19.0",
+    "@babel/preset-env": "^7.20.2",
+    "@babel/runtime": "^7.20.6",
     "@vue/compiler-sfc": "^3.2.45",
     "babel-loader": "^8.2.5",
     "compression-webpack-plugin": "^10.0.0",
     "css-loader": "^6.7.2",
     "css-minimizer-webpack-plugin": "^4.2.2",
-    "eslint": "^8.27.0",
+    "eslint": "^8.28.0",
     "eslint-config-standard": "^17.0.0",
     "eslint-plugin-import": "^2.26.0",
     "eslint-plugin-n": "^15.5.1",
     "eslint-plugin-node": "^11.1.0",
     "eslint-plugin-promise": "^6.1.1",
     "eslint-plugin-standard": "^4.1.0",
-    "eslint-plugin-vue": "^9.7.0",
-    "mini-css-extract-plugin": "^2.6.1",
+    "eslint-plugin-vue": "^9.8.0",
+    "mini-css-extract-plugin": "^2.7.0",
     "postcss": "^8.4.19",
     "postcss-flexbugs-fixes": "^5.0.2",
     "postcss-import": "^15.0.0",

From a68c4def23785b25fca1d6ed257ca74991207304 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 28 Nov 2022 09:25:52 -0600
Subject: [PATCH 067/160] minor "CASTOR" related cleanups

---
 app/controllers/taxon_names_controller.rb     |  4 +--
 app/models/taxon_name_classification.rb       |  3 +-
 app/models/taxon_name_relationship.rb         |  7 +++--
 lib/batch_load/import.rb                      | 16 ++++++-----
 .../import/taxon_names/castor_interpreter.rb  | 28 +++++++++----------
 5 files changed, 31 insertions(+), 27 deletions(-)

diff --git a/app/controllers/taxon_names_controller.rb b/app/controllers/taxon_names_controller.rb
index 2569b2c4f8..64034ff662 100644
--- a/app/controllers/taxon_names_controller.rb
+++ b/app/controllers/taxon_names_controller.rb
@@ -186,7 +186,7 @@ def create_simple_batch_load
   def preview_castor_batch_load
     if params[:file]
       @result = BatchLoad::Import::TaxonNames::CastorInterpreter.new(**batch_params)
-      digest_cookie(params[:file].tempfile, :Castor_taxon_names_md5)
+      digest_cookie(params[:file].tempfile, :nomen_taxon_names_md5)
       render 'taxon_names/batch_load/castor/preview'
     else
       flash[:notice] = 'No file provided!'
@@ -195,7 +195,7 @@ def preview_castor_batch_load
   end
 
   def create_castor_batch_load
-    if params[:file] && digested_cookie_exists?(params[:file].tempfile, :Castor_taxon_names_md5)
+    if params[:file] && digested_cookie_exists?(params[:file].tempfile, :nomen_taxon_names_md5)
       @result = BatchLoad::Import::TaxonNames::CastorInterpreter.new(**batch_params)
       if @result.create
         flash[:notice] = "Successfully proccessed file, #{@result.total_records_created} items were created."
diff --git a/app/models/taxon_name_classification.rb b/app/models/taxon_name_classification.rb
index 447735a9cb..44c022f57e 100644
--- a/app/models/taxon_name_classification.rb
+++ b/app/models/taxon_name_classification.rb
@@ -28,7 +28,7 @@ class TaxonNameClassification < ApplicationRecord
   before_validation :validate_uniqueness_of_latinized
   validates_presence_of :taxon_name
   validates_presence_of :type
-  validates_uniqueness_of :taxon_name_id, scope: :type
+  validates_uniqueness_of :taxon_name_id, scope: [:type, :project_id]
 
   validate :nomenclature_code_matches
 
@@ -321,6 +321,7 @@ def nomenclature_code_matches
     end
   end
 
+  # TODO: unnecessary! Type handling will raise here
   def validate_taxon_name_classification
     errors.add(:type, 'Status not found') if !self.type.nil? and !TAXON_NAME_CLASSIFICATION_NAMES.include?(self.type.to_s)
   end
diff --git a/app/models/taxon_name_relationship.rb b/app/models/taxon_name_relationship.rb
index f24ea4c8e0..6be09bbc68 100644
--- a/app/models/taxon_name_relationship.rb
+++ b/app/models/taxon_name_relationship.rb
@@ -58,12 +58,14 @@ class TaxonNameRelationship < ApplicationRecord
   after_save :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
   after_destroy :set_cached_names_for_taxon_names, unless: -> {self.no_cached}
 
+  # TODO: remove, it's required by STI
   validates_presence_of :type, message: 'Relationship type should be specified'
+  
   validates_presence_of :subject_taxon_name, message: 'Missing taxon name on the left side'
   validates_presence_of :object_taxon_name, message: 'Missing taxon name on the right side'
 
-  validates_uniqueness_of :object_taxon_name_id, scope: :type, if: :is_combination?
-  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id], unless: :is_combination?
+  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :project_id], if: :is_combination?
+  validates_uniqueness_of :object_taxon_name_id, scope: [:type, :subject_taxon_name_id, :project_id], unless: :is_combination?
 
   validate :validate_type, :validate_subject_and_object_are_not_identical
 
@@ -321,6 +323,7 @@ def subject_and_object_in_same_project
   end
 
   def validate_type
+    # TODO: Remove, handled by STI
     if type && !TAXON_NAME_RELATIONSHIP_NAMES.include?(type.to_s)
       errors.add(:type, "'#{type}' is not a valid taxon name relationship")
     elsif self.type_class && object_taxon_name.class.to_s == 'Protonym' && !self.type_class.valid_object_ranks.include?(object_taxon_name.rank_string)
diff --git a/lib/batch_load/import.rb b/lib/batch_load/import.rb
index 07c17a7d27..8b68582b40 100644
--- a/lib/batch_load/import.rb
+++ b/lib/batch_load/import.rb
@@ -103,12 +103,13 @@ def csv
         @csv ||= CSV.parse(
           @file.tempfile.read.force_encoding('utf-8'), # force encoding is likely a very bad idea, but instructinos say "utf-8"
           headers: true,
-          header_converters: [:downcase,
-                              lambda { |h| h.strip },
-                              lambda { |h| user_map(h) }],
-        col_sep: "\t",
-        encoding: 'UTF-8',
-        skip_blanks: true)
+          header_converters: [
+            :downcase,
+            lambda { |h| h.strip },
+            lambda { |h| user_map(h) }],
+          col_sep: "\t",
+          encoding: 'UTF-8',
+          skip_blanks: true)
 
         #  rescue Encoding::UndefinedConversionError => e
 
@@ -189,6 +190,7 @@ def create
               end
             end
           end
+          
         else
           sorted_processed_rows.each_value do |rp|
             rp.objects.each_value do |objs|
@@ -238,7 +240,7 @@ def total_records_created
     # return [Hash] processed rows, sorted by line number
     #  ?! key order might not persist ?!
     def sorted_processed_rows
-      @processed_rows.sort.to_h
+      processed_rows.sort.to_h
     end
 
     # return [Array] all objects (parsed records) that are .valid?
diff --git a/lib/batch_load/import/taxon_names/castor_interpreter.rb b/lib/batch_load/import/taxon_names/castor_interpreter.rb
index a433c0541c..d3187f4534 100644
--- a/lib/batch_load/import/taxon_names/castor_interpreter.rb
+++ b/lib/batch_load/import/taxon_names/castor_interpreter.rb
@@ -62,18 +62,14 @@ def build_taxon_names
         @processed_rows[i] = parse_result
 
         begin
-          next if row['rank'] == 'complex'
-          next if row['rank'] == 'species group'
-          next if row['rank'] == 'series'
-          next if row['rank'] == 'variety'
-          next if row['taxon_name'] == 'unidentified'
+          next if ['complex', 'species group', 'series', 'variety', 'unidentified'].include?(row['rank'])
 
           protonym_attributes = {
             name: row['taxon_name'],
             year_of_publication: year_of_publication(row['author_year']),
             rank_class: Ranks.lookup(@nomenclature_code.to_sym, row['rank']),
-            by: @user,
-            project: @project,
+            by: user,
+            project: project,
             verbatim_author: verbatim_author(row['author_year']),
             taxon_name_authors_attributes: taxon_name_authors_attributes(verbatim_author(row['author_year']))
           }
@@ -85,8 +81,8 @@ def build_taxon_names
               year_of_publication: year_of_publication(row['author_year']),
               rank_class: Ranks.lookup(@nomenclature_code.to_sym, row['original_rank']),
               parent: parent_taxon_name,
-              by: @user,
-              project: @project,
+              by: user,
+              project: project,
               verbatim_author: verbatim_author(row['author_year']),
               taxon_name_authors_attributes: taxon_name_authors_attributes(verbatim_author(row['author_year']))
             }
@@ -119,17 +115,18 @@ def build_taxon_names
 
           # TaxonNameRelationship
           related_name_id = row['related_name_id']
-
-          if !taxon_names[related_name_id].nil?
+          
+          if !taxon_names[related_name_id].blank?
             related_name_nomen_class = nil
 
             begin
-              related_name_nomen_class = row['related_name_nomen_class'].constantize
+              related_name_nomen_class = row['related_name_nomen_class'].safe_constantize
 
               if related_name_nomen_class.ancestors.include?(TaxonNameRelationship)
-                p.name = row['taxon_name'].split(' ')[-1]
-                p.verbatim_name = row['taxon_name']
-                taxon_name_relationship = related_name_nomen_class.new(subject_taxon_name: p, object_taxon_name: taxon_names[related_name_id])
+                
+                taxon_name_relationship = related_name_nomen_class.new(
+                  subject_taxon_name: p, object_taxon_name: taxon_names[related_name_id]
+                )
                 parse_result.objects[:taxon_name_relationship].push taxon_name_relationship
               end
             rescue NameError
@@ -138,6 +135,7 @@ def build_taxon_names
 
           # TaxonNameClassification
 
+          # TODO: add to index, not here
           if name_nomen_classification = row['name_nomen_classification']
             if c = name_nomen_classification.safe_constantize
               # if EXCEPTED_FORM_TAXON_NAME_CLASSIFICATIONS.include?(name_nomen_classification)

From c424476f9c5096bd7082d92d17fa5eed3c41167a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Mon, 28 Nov 2022 15:19:48 -0300
Subject: [PATCH 068/160] Fix serialize parameters

---
 .../tasks/dwca_import/store/actions/loadDataSetRecords.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js b/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js
index 05205c7ba8..9450f7b438 100644
--- a/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js
+++ b/app/javascript/vue/tasks/dwca_import/store/actions/loadDataSetRecords.js
@@ -21,10 +21,10 @@ export default ({ state, commit, getters }, page) => {
     GetDatasetRecords(state.dataset.id, {
       params: {
         page: loadPage,
-        ...state.paramsFilter,
-        paramsSerializer: {
-          serialize: (params) => Qs.stringify(params, { arrayFormat: 'brackets' })
-        }
+        ...state.paramsFilter
+      },
+      paramsSerializer: {
+        serialize: (params) => Qs.stringify(params, { arrayFormat: 'brackets' })
       }
     }).then(response => {
       commit(MutationNames.SetPagination, GetPagination(response))

From e7350616776fc41183e3f739a9d9fd59f10066c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 29 Nov 2022 14:29:34 -0300
Subject: [PATCH 069/160] Change button

---
 .../tasks/collection_objects/filter/app.vue   | 22 +++++++++----------
 .../components/DeleteCollectionObjects.vue    |  9 ++++++--
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/filter/app.vue b/app/javascript/vue/tasks/collection_objects/filter/app.vue
index f35eba22ad..892b87c42d 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/app.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/app.vue
@@ -53,9 +53,20 @@
         >
           <div class="horizontal-left-content">
             <tag-all
+              class="circle-button"
               :ids="ids"
               type="CollectionObject"
             />
+            <DeleteCollectionObjects
+              :ids="ids"
+              :disabled="!ids.length"
+              @delete="removeCOFromList"
+            />
+            <RadialFilter
+              :disabled="!ids.length"
+              object-type="CollectingEvent"
+              :parameters="{ collection_object_id: ids }"
+            />
 
             <span class="separate-left separate-right">|</span>
             <csv-button
@@ -77,17 +88,6 @@
               :url="urlRequest"
               class="margin-small-left"
             />
-            <DeleteCollectionObjects
-              class="margin-small-left"
-              :ids="ids"
-              :disabled="!ids.length"
-              @delete="removeCOFromList"
-            />
-            <RadialFilter
-              :disabled="!ids.length"
-              object-type="CollectingEvent"
-              :parameters="{ collection_object_id: ids }"
-            />
           </div>
         </div>
         <div
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index 69d12331c7..89ea8bf002 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -2,12 +2,16 @@
   <div>
     <ConfirmationModal ref="confirmationModal" />
     <VBtn
+      class="circle-button"
       color="primary"
-      medium
+      circle
       :disabled="disabled"
       @click="openModal"
     >
-      Delete collection objects
+      <VIcon
+        name="trash"
+        x-small
+      />
     </VBtn>
   </div>
 </template>
@@ -16,6 +20,7 @@
 import { ref } from 'vue'
 import { CollectionObject } from 'routes/endpoints'
 import VBtn from 'components/ui/VBtn/index.vue'
+import VIcon from 'components/ui/VIcon/index.vue'
 import ConfirmationModal from 'components/ConfirmationModal.vue'
 
 const CONFIRM_WORD = 'DELETE'

From 446d2aefb5f642230f75c6591a7da8a836d76528 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 29 Nov 2022 14:43:00 -0500
Subject: [PATCH 070/160] Add /<model>/metadata/related_summary.

---
 app/controllers/metadata_controller.rb        | 11 ++++--
 .../components/DeleteCollectionObjects.vue    |  4 +-
 app/models/concerns/shared/is_data.rb         | 39 +++++++++++++++++++
 config/routes/base.rb                         | 13 ++++---
 4 files changed, 57 insertions(+), 10 deletions(-)

diff --git a/app/controllers/metadata_controller.rb b/app/controllers/metadata_controller.rb
index 74790af500..0e69fd5375 100644
--- a/app/controllers/metadata_controller.rb
+++ b/app/controllers/metadata_controller.rb
@@ -9,7 +9,7 @@ def index
   end
 
   # :klass is a base class name, like "Otu"
-  def object_radial 
+  def object_radial
     get_klass
     @data = OBJECT_RADIALS[@klass]
     render '/workbench/navigation/object_radial'
@@ -17,7 +17,12 @@ def object_radial
 
   def object_navigation
     @object = GlobalID::Locator.locate(params.require(:global_id))
-    render json: {status: 200} 
+    render json: {status: 200}
+  end
+
+  def related_summary
+    @klass = params.require(:klass).safe_constantize
+    render json: @klass.related_summary(params.require(:id))
   end
 
   protected
@@ -26,7 +31,7 @@ def get_klass
     render json: {status: 400} if (params[:type] && params[:global_id]) || (params[:type].blank? && params[:global_id].blank?)
 
     if params[:type]
-      @klass = params[:type] 
+      @klass = params[:type]
       @object = nil
     else
       @object = GlobalID::Locator.locate(params.require(:global_id))
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index 69d12331c7..15f6df8683 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -49,7 +49,7 @@ function deleteCOs () {
 
   Promise.allSettled(requests).then(_ => {
     const message = failedCount
-      ? `Deleted: ${destroyedIds.length} object(s). Failed to delete: ${failedCount}`
+      ? `Deleted: ${destroyedIds.length} object(s). Failed to delete: ${failedCount}.`
       : `Deleted: ${destroyedIds.length} object(s).`
 
     TW.workbench.alert.create(message, 'notice')
@@ -66,7 +66,7 @@ async function openModal () {
 
   const ok = await confirmationModal.value.show({
     title: 'Delete collection objects',
-    message: `This will delete ${props.ids.length} collection objects. Are you sure you want to proceed?`,
+    message: `This will delete ${props.ids.length} collection objects and their associated determinations and annotations (e.g. Notes). Are you sure you want to proceed?`,
     confirmationWord: props.ids.length >= MIN_CONFIRM ? CONFIRM_WORD : '',
     okButton: 'Delete',
     cancelButton: 'Cancel',
diff --git a/app/models/concerns/shared/is_data.rb b/app/models/concerns/shared/is_data.rb
index 0bdf58a4a3..ffeb98b66c 100644
--- a/app/models/concerns/shared/is_data.rb
+++ b/app/models/concerns/shared/is_data.rb
@@ -89,6 +89,45 @@ def identical(attr)
       scope
     end
 
+    # @return Hash
+    #  { restrict: {}, destroy: {} }
+    #
+    #  Summarizes the count of records that will be destroyed if these ids are destroyed, or records that
+    #  will prevent destruction.
+    def related_summary(ids)
+      h = { restrict: {}, destroy: {} }
+      objects = self.where(id: ids)
+
+      base = self.table_name.to_sym
+
+      [ self.reflect_on_all_associations(:has_many),
+        self.reflect_on_all_associations(:has_one)
+      ].each do |rt|
+
+        rt.each do |r|
+          d = r.options.dig(:dependent)
+          next if d.nil?
+
+          c = nil
+          if r.type
+            c =  r.klass.where(r.type.to_sym =>  self.name, r.type.gsub('_type', '_id').to_sym => objects.map(&:id)).count
+          else
+            c = r.klass.where(r.foreign_key.to_sym => objects.map(&:id)).count
+          end
+
+          if c > 0
+            case d
+            when :destroy
+              h[:destroy][r.name] = c
+            when :restrict_with_error
+              h[:restrict][r.name] = c
+            end
+          end
+        end
+      end
+      h
+    end
+
   end  # END CLASS METHODS
 
   # Returns whether it is permissible to try to destroy
diff --git a/config/routes/base.rb b/config/routes/base.rb
index c7e15c93e7..0d358dbc25 100644
--- a/config/routes/base.rb
+++ b/config/routes/base.rb
@@ -17,15 +17,18 @@
   get 'tasks', defaults: {format: :json}
 end
 
-scope :metadata, controller: 'metadata', only: [:index] do
+scope :metadata, controller: 'metadata' do
+  get :related_summary
+  post :related_summary
   get 'object_radial/', action: :object_radial, defaults: {format: :json}
   get 'object_navigation/:global_id', action: :object_navigation, defaults: {format: :json}
   get '(/:klass)', action: :index, defaults: {format: :json}
 end
 
-scope :annotations, controller: :annotations do
-  get ':global_id/metadata', action: :metadata, defaults: {format: :json}
-  get :types, defaults: {format: :json}
+scope :annotations, controller: :annotations, defaults: {format: :json} do
+  get ':global_id/metadata', action: :metadata
+  get :types
+
 end
 
 scope :graph, controller: :graph do
@@ -37,7 +40,7 @@
   collection do
     get 'list'
     get 'search'
-    get 'autocomplete' 
+    get 'autocomplete'
   end
 
   member do

From 23fa5593d6b01c8e0021b7fb2719d30eaef3dbb4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 29 Nov 2022 17:25:15 -0300
Subject: [PATCH 071/160] Add metadata information

---
 .../vue/routes/endpoints/Metadata.js          |  5 ++++
 app/javascript/vue/routes/endpoints/index.js  |  1 +
 .../components/DeleteCollectionObjects.vue    | 23 +++++++++++++++++--
 3 files changed, 27 insertions(+), 2 deletions(-)
 create mode 100644 app/javascript/vue/routes/endpoints/Metadata.js

diff --git a/app/javascript/vue/routes/endpoints/Metadata.js b/app/javascript/vue/routes/endpoints/Metadata.js
new file mode 100644
index 0000000000..7e8c6b316c
--- /dev/null
+++ b/app/javascript/vue/routes/endpoints/Metadata.js
@@ -0,0 +1,5 @@
+import AjaxCall from 'helpers/ajaxCall'
+
+export const Metadata = {
+  relatedSummary: params => AjaxCall('post', '/metadata/related_summary', params)
+}
diff --git a/app/javascript/vue/routes/endpoints/index.js b/app/javascript/vue/routes/endpoints/index.js
index 1c20bd5550..b7678f585f 100644
--- a/app/javascript/vue/routes/endpoints/index.js
+++ b/app/javascript/vue/routes/endpoints/index.js
@@ -33,6 +33,7 @@ export { Label } from './Label'
 export { Language } from './Language'
 export { Loan } from './Loan'
 export { LoanItem } from './LoanItem'
+export { Metadata } from './Metadata'
 export { Namespace } from './Namespace'
 export { Observation } from './Observation'
 export { ObservationMatrix } from './ObservationMatrix'
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index cc7198780c..5eecc192f9 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -18,7 +18,9 @@
 
 <script setup>
 import { ref } from 'vue'
-import { CollectionObject } from 'routes/endpoints'
+import { CollectionObject, Metadata } from 'routes/endpoints'
+import { COLLECTION_OBJECT } from 'constants/index'
+import { humanize } from 'helpers/strings'
 import VBtn from 'components/ui/VBtn/index.vue'
 import VIcon from 'components/ui/VIcon/index.vue'
 import ConfirmationModal from 'components/ConfirmationModal.vue'
@@ -41,6 +43,7 @@ const props = defineProps({
 
 const emit = defineEmits(['delete'])
 const confirmationModal = ref(null)
+const metadata = ref({})
 
 function deleteCOs () {
   let failedCount = 0
@@ -69,9 +72,25 @@ async function openModal () {
     return
   }
 
+  metadata.value = (await Metadata.relatedSummary({
+    id: props.ids,
+    klass: COLLECTION_OBJECT
+  })).body
+
   const ok = await confirmationModal.value.show({
     title: 'Delete collection objects',
-    message: `This will delete ${props.ids.length} collection objects and their associated determinations and annotations (e.g. Notes). Are you sure you want to proceed?`,
+    message: `
+      This will delete ${props.ids.length} collection objects and their associated determinations and annotations (e.g. Notes).
+      <br>
+      <h3>Related records that will be destroyed:</h3>
+      <ul>
+        ${Object.entries(metadata.value.destroy).map(([type, count]) => `<li>${humanize(type)}: ${count}</li>`).join('')}
+      </ul>
+      <h3>Records preventing the destruction of one or more objects exist:</h3>
+      <ul>
+        ${Object.entries(metadata.value.restrict).map(([type, count]) => `<li>${humanize(type)}: ${count}</li>`).join('')}
+      </ul>      
+      Are you sure you want to proceed?`,
     confirmationWord: props.ids.length >= MIN_CONFIRM ? CONFIRM_WORD : '',
     okButton: 'Delete',
     cancelButton: 'Cancel',

From f9413e22185da7f926e05dd2e6be3d30a96219ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Tue, 29 Nov 2022 18:45:23 -0300
Subject: [PATCH 072/160] Remove title on empty list

---
 .../components/DeleteCollectionObjects.vue    | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index 5eecc192f9..97539ec442 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -65,6 +65,14 @@ function deleteCOs () {
   })
 }
 
+function makeList (title, obj) {
+  const entries = Object.entries(obj)
+
+  return entries.length
+    ? `<h3>${title}</h3>` + entries.map(([type, count]) => `<li>${humanize(type)}: ${count}</li>`).join('')
+    : ''
+}
+
 async function openModal () {
   if (props.ids.length > MAX) {
     TW.workbench.alert.create(`Select a maximum of ${MAX} objects to delete.`, 'error')
@@ -82,14 +90,9 @@ async function openModal () {
     message: `
       This will delete ${props.ids.length} collection objects and their associated determinations and annotations (e.g. Notes).
       <br>
-      <h3>Related records that will be destroyed:</h3>
-      <ul>
-        ${Object.entries(metadata.value.destroy).map(([type, count]) => `<li>${humanize(type)}: ${count}</li>`).join('')}
-      </ul>
-      <h3>Records preventing the destruction of one or more objects exist:</h3>
-      <ul>
-        ${Object.entries(metadata.value.restrict).map(([type, count]) => `<li>${humanize(type)}: ${count}</li>`).join('')}
-      </ul>      
+      ${makeList('Related records that will be destroyed:', metadata.value.destroy)}
+      ${makeList('Records preventing the destruction of one or more objects exist:', metadata.value.restrict)}
+      <br>
       Are you sure you want to proceed?`,
     confirmationWord: props.ids.length >= MIN_CONFIRM ? CONFIRM_WORD : '',
     okButton: 'Delete',

From 85d5c28f470a52a5bdf6033dc277052cffcdc2b5 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 29 Nov 2022 16:49:34 -0500
Subject: [PATCH 073/160] Status message.

---
 .../filter/components/DeleteCollectionObjects.vue               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
index 97539ec442..1e4972d5fb 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/DeleteCollectionObjects.vue
@@ -88,7 +88,7 @@ async function openModal () {
   const ok = await confirmationModal.value.show({
     title: 'Delete collection objects',
     message: `
-      This will delete ${props.ids.length} collection objects and their associated determinations and annotations (e.g. Notes).
+      This will delete ${props.ids.length} collection objects and their associate records (see below).
       <br>
       ${makeList('Related records that will be destroyed:', metadata.value.destroy)}
       ${makeList('Records preventing the destruction of one or more objects exist:', metadata.value.restrict)}

From 2910d8cc143d202fb3471e26029865231659984f Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 29 Nov 2022 17:20:13 -0500
Subject: [PATCH 074/160] CHANGELOG.md [skip-ci]

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 19e4ea65cc..70d2674842 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,9 +7,11 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- Delete selected collection objects (and their related data) from filter [#3174]
 - Collection object Autocomplete has loan and deaccession banners [#3192]
 - Autocomplete on Browse collection object [#3189]
 - Task - Collection object chronology, a plot of object by year collected
+- Endpoint to return related data preventing or included in destroy, e.g. `/metadata/related_summary?klass=CollectionObject&id[]=16701&id[]...`
 
 ### Fixed
 - 'Also create OTU' on batch taxon name upload causing raise
@@ -23,6 +25,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Refactored observation cell component for Image matrix
 - Updated Ruby gems
 
+[#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
 [#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188

From 11d31ede503595e676b32f786012db9bfb29a509 Mon Sep 17 00:00:00 2001
From: Geoff Ower <gdower@illinois.edu>
Date: Tue, 29 Nov 2022 16:29:35 -0600
Subject: [PATCH 075/160] Closes #3207

---
 lib/export/coldp/files/name.rb  | 20 ++++++++++++++------
 lib/export/coldp/files/taxon.rb | 19 +++++++++++++------
 2 files changed, 27 insertions(+), 12 deletions(-)

diff --git a/lib/export/coldp/files/name.rb b/lib/export/coldp/files/name.rb
index d85cee44db..8d160be3bf 100644
--- a/lib/export/coldp/files/name.rb
+++ b/lib/export/coldp/files/name.rb
@@ -17,8 +17,12 @@ def self.code_field(taxon_name)
     end
   end
 
-  def self.remarks_field(taxon_name)
-    Utilities::Strings.nil_squish_strip(taxon_name.notes.collect{|n| n.text}.join('; ')) # remarks - !! check for tabs
+  def self.remarks(name, name_remarks_vocab_id)
+    if !name.data_attributes.find_by(controlled_vocabulary_term_id: name_remarks_vocab_id).nil?
+      name.data_attributes.find_by(controlled_vocabulary_term_id: name_remarks_vocab_id).value
+    else
+      nil
+    end
   end
 
   # @return String
@@ -54,7 +58,7 @@ def self.nom_status_field(taxon_name)
   # Invalid Protonyms are rendered only as their original Combination
   # @param t [Protonym]
   #    only place that var./frm can be handled.
-  def self.add_original_combination(t, csv, origin_citation)
+  def self.add_original_combination(t, csv, origin_citation, name_remarks_vocab_id)
     e = t.original_combination_elements
 
     infraspecific_element = t.original_combination_infraspecific_element(e)
@@ -129,7 +133,7 @@ def self.add_original_combination(t, csv, origin_citation)
       code_field(t),                                             # code
       nil,                                                       # status https://api.catalogue.life/vocab/nomStatus
       nil,                                                       # link (probably TW public or API)
-      remarks_field(t),                                          # remarks
+      remarks(t, name_remarks_vocab_id),                         # remarks
     ]
   end
 
@@ -163,6 +167,10 @@ def self.generate(otu, reference_csv = nil)
         remarks
       }
 
+      Current.project_id = otu.project_id
+      name_remarks_vocab_id = Predicate.find_by(uri: 'https://github.com/catalogueoflife/coldp#Name.remarks',
+                                                project_id: Current.project_id)&.id
+
       otu.taxon_name.self_and_descendants.that_is_valid
         .pluck(:id, :cached)
         .each do |name|
@@ -238,14 +246,14 @@ def self.generate(otu, reference_csv = nil)
               code_field(t),                            # code
               nom_status_field(t),                      # nomStatus
               nil,                                      # link (probably TW public or API)
-              remarks_field(t),                         # remarks
+              remarks(t, name_remarks_vocab_id),        # remarks
             ]
           end
 
           # Here we truly want no higher
           if !t.cached_original_combination.blank? && (is_genus_species && !t.is_combination? && (!t.is_valid? || t.has_alternate_original?))
             name_total += 1
-            add_original_combination(t, csv, origin_citation)
+            add_original_combination(t, csv, origin_citation, name_remarks_vocab_id)
           end
 
           Export::Coldp::Files::Reference.add_reference_rows([origin_citation.source].compact, reference_csv) if reference_csv && origin_citation
diff --git a/lib/export/coldp/files/taxon.rb b/lib/export/coldp/files/taxon.rb
index 12cea016ac..8bc156f2ef 100644
--- a/lib/export/coldp/files/taxon.rb
+++ b/lib/export/coldp/files/taxon.rb
@@ -84,11 +84,9 @@ def self.according_to_date(otu)
   def self.link(otu)
     # API or public interface
   end
-
-  # TODO: flag/exclude ! is_public
-  def self.remarks(otu)
-    if otu.notes.load.any?
-      otu.notes.pluck(:text).join('|')
+  def self.remarks(otu, taxon_remarks_vocab_id)
+    if !otu.data_attributes.find_by(controlled_vocabulary_term_id: taxon_remarks_vocab_id).nil?
+      otu.data_attributes.find_by(controlled_vocabulary_term_id: taxon_remarks_vocab_id).value
     else
       nil
     end
@@ -130,6 +128,15 @@ def self.generate(otus, root_otu_id = nil, reference_csv = nil, prefer_unlabelle
         remarks
       }
 
+      if root_otu_id.nil?
+        Current.project_id = otus[0].project_id
+      else
+        Current.project_id = Otu.find(root_otu_id).project_id
+      end
+
+      taxon_remarks_vocab_id = Predicate.find_by(uri: 'https://github.com/catalogueoflife/coldp#Taxon.remarks',
+                                                 project_id: Current.project_id)&.id
+
       otus.each do |o|
         # !! When a name is a synonmy (combination), but that combination has no OTU
         # !! then the parent of the name in the taxon table is nil
@@ -179,7 +186,7 @@ def self.generate(otus, root_otu_id = nil, reference_csv = nil, prefer_unlabelle
           predicate_value(o, :temporal_range_end),   # temporalRangeEnd
           predicate_value(o, :lifezone),             # lifezone
           link(o),                                   # link
-          remarks(o)                                 # remarks
+          remarks(o, taxon_remarks_vocab_id)         # remarks
         ]
 
         Export::Coldp::Files::Reference.add_reference_rows(sources, reference_csv) if reference_csv

From 93cb330129163e9e8d21d998b7652a7e3cb6866f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 30 Nov 2022 12:23:20 -0300
Subject: [PATCH 076/160] Update webpack bins

---
 CHANGELOG.md             | 1 +
 bin/webpacker            | 2 +-
 bin/webpacker-dev-server | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 70d2674842..d106616063 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Changed
 - Refactored observation cell component for Image matrix
 - Updated Ruby gems
+- Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
 
 [#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
diff --git a/bin/webpacker b/bin/webpacker
index 4c942e3867..6bb60087f3 100755
--- a/bin/webpacker
+++ b/bin/webpacker
@@ -9,7 +9,7 @@ ENV["RAILS_ENV"] ||= "development"
 ENV["NODE_ENV"]  ||= ENV["RAILS_ENV"]
 ENV["BUNDLE_GEMFILE"] ||= File.expand_path("../../Gemfile", Pathname.new(__FILE__).realpath)
 
-ENV["WEBPACKER_NODE_MODULES_BIN_PATH"] = `npm bin`.chomp
+ENV["WEBPACKER_NODE_MODULES_BIN_PATH"] = `npm root`.chomp + '/.bin'
 
 APP_ROOT = File.expand_path("..", __dir__)
 Dir.chdir(APP_ROOT) do
diff --git a/bin/webpacker-dev-server b/bin/webpacker-dev-server
index 7294e8a3ca..d3723901e1 100755
--- a/bin/webpacker-dev-server
+++ b/bin/webpacker-dev-server
@@ -7,7 +7,7 @@ require "pathname"
 ENV["BUNDLE_GEMFILE"] ||= File.expand_path("../../Gemfile",
   Pathname.new(__FILE__).realpath)
 
-ENV["WEBPACKER_NODE_MODULES_BIN_PATH"] = `npm bin`.chomp
+ENV["WEBPACKER_NODE_MODULES_BIN_PATH"] = `npm root`.chomp + '/.bin'
 
 require "bundler/setup"
 

From d676ff141b2c63a30f0b34b2798809f0825fcf54 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 30 Nov 2022 11:02:12 -0600
Subject: [PATCH 077/160] Remove CAST for identifiers

---
 lib/queries/concerns/identifiers.rb | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/lib/queries/concerns/identifiers.rb b/lib/queries/concerns/identifiers.rb
index 8f8f1bc8c8..022954d964 100644
--- a/lib/queries/concerns/identifiers.rb
+++ b/lib/queries/concerns/identifiers.rb
@@ -94,17 +94,13 @@ def identifier_table
     ::Identifier.arel_table
   end
 
-  def cast
-    Arel::Nodes::NamedFunction.new('CAST', [substring])
-  end
-
-  def substring
-    Arel::Nodes::NamedFunction.new('SUBSTRING', [ identifier_table[:identifier], Arel::Nodes::SqlLiteral.new("'([\\d]{1,9})$'") ]).as('integer')
-  end
+  # def substring
+  #   Arel::Nodes::NamedFunction.new('SUBSTRING', [ identifier_table[:identifier], Arel::Nodes::SqlLiteral.new("'([\\d]{1,9})$'") ]).as('integer')
+  # end
 
   def between
     Arel::Nodes::Between.new(
-      cast,
+      identifier_table[:cached_numeric_identifier],
       Arel::Nodes::And.new(
         [ Arel::Nodes::SqlLiteral.new(identifier_start),
           Arel::Nodes::SqlLiteral.new(identifier_end) ]

From 5f490476999eb43acb67d9f050cacde810ab4e7a Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 30 Nov 2022 11:57:47 -0600
Subject: [PATCH 078/160] CHANGELOG.md. Close #3173, #3171. [skip-ci]

---
 CHANGELOG.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d106616063..6d5f9f9421 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- With/out local identifier facet for collection objects and stagd images [#3173]
+- Filter by housekeeping and staged-image data attributes [#3171]
 - Delete selected collection objects (and their related data) from filter [#3174]
 - Collection object Autocomplete has loan and deaccession banners [#3192]
 - Autocomplete on Browse collection object [#3189]
@@ -22,10 +24,13 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Common list component doesn't filter created status on New taxon name task [#3205]
 
 ### Changed
+- "TODO list" now a faceted search [#3171]
 - Refactored observation cell component for Image matrix
 - Updated Ruby gems
 - Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
 
+[#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173
+[#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171
 [#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182

From 8c502d736e9b880e90691ac1db369846e836ace0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Wed, 30 Nov 2022 15:22:43 -0300
Subject: [PATCH 079/160] Clear on unlock

---
 .../simple_new_specimen/components/FormCE.vue | 15 +++++++++++++
 .../components/FormCatalogNumber.vue          | 11 +++++++++-
 .../components/FormDetermination.vue          | 22 ++++++++++++-------
 3 files changed, 39 insertions(+), 9 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
index 2bf2dcf293..bd42ec0033 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
@@ -43,4 +43,19 @@ watch(
   },
   { deep: true }
 )
+
+watch(
+  () => store.settings.lock.collectingEvent,
+  newVal => {
+    if (!newVal) {
+      store.$patch({
+        collectingEvent: {
+          verbatim_locality: undefined,
+          verbatim_label: undefined
+        },
+        geographicArea: undefined
+      })
+    }
+  }
+)
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
index e0957cc0d6..0f061f71f8 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -64,7 +64,7 @@
 </template>
 
 <script setup>
-import { onMounted, ref } from 'vue'
+import { onMounted, ref, watch } from 'vue'
 import { useStore } from '../store/useStore'
 import SelectedItem from './SelectedItem.vue'
 import Autocomplete from 'components/ui/Autocomplete.vue'
@@ -87,4 +87,13 @@ onMounted(() => {
   setTimeout(() => autocompleteComponent.value.setFocus(), 250)
 })
 
+watch(
+  () => store.settings.lock.namespace,
+  newVal => {
+    if (!newVal) {
+      store.namespace = undefined
+    }
+  }
+)
+
 </script>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
index 06e201282c..5976c32421 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
@@ -8,15 +8,11 @@
         :item="store.otu"
         @unset="store.otu = undefined"
       />
-      <Autocomplete
+      <OtuPicker
         v-else
         class="full_width"
-        url="/otus/autocomplete"
-        placeholder="Search an OTU"
-        label="label_html"
-        display="label"
-        param="term"
-        @get-item="store.otu = $event"
+        clear-after
+        @get-item="store.otu = { ...$event, label: $event.name || $event.label }"
       />
       <VLock
         class="margin-small-left"
@@ -28,10 +24,20 @@
 
 <script setup>
 import { useStore } from '../store/useStore'
-import Autocomplete from 'components/ui/Autocomplete.vue'
+import { watch } from 'vue'
+import OtuPicker from 'components/otu/otu_picker/otu_picker.vue'
 import SelectedItem from './SelectedItem.vue'
 import VLock from 'components/ui/VLock/index.vue'
 
 const store = useStore()
 
+watch(
+  () => store.settings.lock.otu,
+  newVal => {
+    if (!newVal) {
+      store.otu = undefined
+    }
+  }
+)
+
 </script>

From 508f40a3c0e60474329485c236414b2b5f4ffed8 Mon Sep 17 00:00:00 2001
From: Geoff Ower <gdower@illinois.edu>
Date: Wed, 30 Nov 2022 14:14:59 -0600
Subject: [PATCH 080/160] 554 coldp update specifications

---
 lib/export/coldp/files/name.rb            |  8 ++--
 lib/export/coldp/files/synonym.rb         | 27 +++++++++++-
 lib/export/coldp/files/taxon.rb           | 53 ++++++++++++++++-------
 lib/export/coldp/files/vernacular_name.rb | 11 +----
 4 files changed, 69 insertions(+), 30 deletions(-)

diff --git a/lib/export/coldp/files/name.rb b/lib/export/coldp/files/name.rb
index d85cee44db..d0fe75c951 100644
--- a/lib/export/coldp/files/name.rb
+++ b/lib/export/coldp/files/name.rb
@@ -26,7 +26,7 @@ def self.authorship_field(taxon_name, original)
     original ? taxon_name.original_author_year : taxon_name.cached_author_year
   end
 
-  # https://api.catalogue.life/vocab/nomStatus
+  # https://api.checklistbank.org/vocab/nomStatus
   # @return [String, nil]
   # @params taxon_name [TaxonName]
   #   any TaxonName
@@ -122,12 +122,12 @@ def self.add_original_combination(t, csv, origin_citation)
       subgenus,                                                  # subgenus (no parens)
       species,                                                   # species
       infraspecific_element ? infraspecific_element.last : nil,  # infraspecificEpithet
-      origin_citation&.source_id,                                # publishedInID    |
+      origin_citation&.source_id,                                # referenceID    |
       origin_citation&.pages,                                    # publishedInPage  | !! All origin citations get added to reference_csv via the main loop, not here
       t.year_of_publication,                                     # publishedInYear  |
       true,                                                      # original
       code_field(t),                                             # code
-      nil,                                                       # status https://api.catalogue.life/vocab/nomStatus
+      nil,                                                       # status https://api.checklistbank.org/vocab/nomStatus
       nil,                                                       # link (probably TW public or API)
       remarks_field(t),                                          # remarks
     ]
@@ -153,7 +153,7 @@ def self.generate(otu, reference_csv = nil)
         infragenericEpithet
         specificEpithet
         infraspecificEpithet
-        publishedInID
+        referenceID
         publishedInPage
         publishedInYear
         original
diff --git a/lib/export/coldp/files/synonym.rb b/lib/export/coldp/files/synonym.rb
index 21f8db47e0..371224afd1 100644
--- a/lib/export/coldp/files/synonym.rb
+++ b/lib/export/coldp/files/synonym.rb
@@ -7,7 +7,7 @@
 module Export::Coldp::Files::Synonym
 
   # @return String
-  # Last 3 of https://api.catalogue.life/vocab/taxonomicstatus
+  # Last 3 of https://api.checklistbank.org/vocab/taxonomicstatus
   def self.status(o, t)
     #'accepted'
     #'provisionally accepted'
@@ -60,10 +60,33 @@ def self.generate(otus, reference_csv = nil)
           #   .where(cached_valid_taxon_name_id: o[2]) # == .historical_taxon_names
           #   .where("( ((taxon_names.id != taxon_names.cached_valid_taxon_name_id) OR ((taxon_names.cached_original_combination != taxon_names.cached))) AND NOT (taxon_names.type = 'Combination' AND taxon_names.cached = ?))", o[1]) # see name.rb
 
-          c.pluck(:id, :cached, :cached_original_combination, :type)
+          c.pluck(:id, :cached, :cached_original_combination, :type, :rank_class, :cached_secondary_homonym)
             .each do |t|
               reified_id = ::Export::Coldp.reified_id(t[0], t[1], t[2])
 
+              # skips including parent binomial as a synonym of autonym trinomial
+              unless t[5].nil?
+                if !t[1].nil? and t[1].include? t[5] and (t[4].match(/::Subspecies$/) or t[4].match(/::Form$/) or t[4].match(/::Variety$/))
+                  next
+                end
+
+                if !t[2].nil? and t[2].include? t[5] and o[1].include? t[5] and t[4].match(/::Species$/)
+                  next
+                end
+              end
+
+              matches = t[1].match(/([A-Z][a-z]+) \(.+\) ([a-z]+)/)
+              if matches&.size == 3
+                if t[5] == "#{matches[1]} #{matches[2]}" and t[2] != t[5]
+                  next
+                end
+              end
+
+              # skips combinations including parent binomial as a synonym of autonym trinomial
+              if t[3] == 'Combination' and o[1].include? t[1]
+                next
+              end
+
               csv << [
                 o[0],           # taxonID attached to the current valid concept
                 reified_id,     # nameID
diff --git a/lib/export/coldp/files/taxon.rb b/lib/export/coldp/files/taxon.rb
index 12cea016ac..68d7e804f6 100644
--- a/lib/export/coldp/files/taxon.rb
+++ b/lib/export/coldp/files/taxon.rb
@@ -11,10 +11,10 @@
 module Export::Coldp::Files::Taxon
 
   IRI_MAP = {
-    extinct: 'https://api.catalogue.life/datapackage#Taxon.extinct',                         # 1,0
-    temporal_range_end: 'https://api.catalogue.life/datapackage#Taxon.temporal_range_end',   # from https://api.catalogue.life/vocab/geotime
-    temporal_range_start: 'https://api.catalogue.life/datapackage#Taxon.temporal_range_end', # from https://api.catalogue.life/vocab/geotime
-    lifezone: 'https://api.catalogue.life/datapackage#Taxon.lifezone',                       # from https://api.catalogue.life/vocab/lifezone
+    extinct: 'https://api.checklistbank.org/datapackage#Taxon.extinct',                         # 1,0
+    temporal_range_end: 'https://api.checklistbank.org/datapackage#Taxon.temporal_range_end',   # from https://api.checklistbank.org/vocab/geotime
+    temporal_range_start: 'https://api.checklistbank.org/datapackage#Taxon.temporal_range_end', # from https://api.checklistbank.org/vocab/geotime
+    lifezone: 'https://api.checklistbank.org/datapackage#Taxon.lifezone',                       # from https://api.checklistbank.org/vocab/lifezone
   }
 
   SKIPPED_RANKS = %w{
@@ -43,6 +43,15 @@ def self.provisional(otu)
     nil
   end
 
+
+  # Name phrase is for appended phrases like senso stricto and senso lato
+  def self.name_phrase(otu, vocab_id)
+    da = DataAttribute.find_by(type: 'InternalAttribute',
+                               controlled_vocabulary_term_id: vocab_id,
+                               attribute_subject_id: otu.id)
+    da&.value
+  end
+
   # The scrutinizer concept is unused at present
   # We're looking for the canonical implementation of it
   # before we implement/extrapolate from data here.
@@ -110,12 +119,16 @@ def self.generate(otus, root_otu_id = nil, reference_csv = nil, prefer_unlabelle
     #   `taxon_name_id: nil`  - uniquify via Ruby hash keys
     observed_taxon_name_ids = { }
 
+    # TODO: optional Taxon.alternativeID field allows inclusion of external identifiers: https://github.com/CatalogueOfLife/coldp#alternativeid-1 https://github.com/CatalogueOfLife/coldp#identifiers
+    #   e.g., gbif:2704179,col:6W3C4,BOLD:AAJ2287,wikidata:Q157571
+
     CSV.generate(col_sep: "\t") do |csv|
 
       csv << %w{
         ID
         parentID
         nameID
+        namePhrase
         provisional
         accordingToID
         scrutinizer
@@ -125,11 +138,20 @@ def self.generate(otus, root_otu_id = nil, reference_csv = nil, prefer_unlabelle
         extinct
         temporalRangeStart
         temporalRangeEnd
-        lifezone
+        environment
         link
         remarks
       }
 
+      if root_otu_id.nil?
+        Current.project_id = otus[0].project_id
+      else
+        Current.project_id = Otu.find(root_otu_id).project_id
+      end
+
+      name_phrase_vocab_id =  Predicate.find_by(uri: 'https://github.com/catalogueoflife/coldp#namephrase',
+                                                project_id: Current.project_id)&.id
+
       otus.each do |o|
         # !! When a name is a synonmy (combination), but that combination has no OTU
         # !! then the parent of the name in the taxon table is nil
@@ -165,19 +187,20 @@ def self.generate(otus, root_otu_id = nil, reference_csv = nil, prefer_unlabelle
         parent_id = (root_otu_id == o.id ? nil : parent_id )
 
         csv << [
-          o.id,                                      # ID (Taxon)
-          parent_id,                                 # parentID (Taxon)
-          o.taxon_name.id,                           # nameID (Name)
-          provisional(o),                            # provisional
-          according_to_id(o),                        # accordingToID
-          scrutinizer(o),                            # scrutinizer
-          scrutinizer_id(o),                         # scrutinizerID
-          scrutinizer_date(o),                       # scrutizinerDate
-          reference_id(sources),                     # referenceID
+          o.id,                                              # ID (Taxon)
+          parent_id,                                         # parentID (Taxon)
+          o.taxon_name.id,                                   # nameID (Name)
+          name_phrase(o, name_phrase_vocab_id),              # namePhrase
+          provisional(o),                                    # provisional
+          according_to_id(o),                                # accordingToID
+          scrutinizer(o),                                    # scrutinizer
+          scrutinizer_id(o),                                 # scrutinizerID
+          scrutinizer_date(o),                               # scrutizinerDate
+          reference_id(sources),                             # referenceID
           predicate_value(o, :extinct),              # extinct
           predicate_value(o, :temporal_range_start), # temporalRangeStart
           predicate_value(o, :temporal_range_end),   # temporalRangeEnd
-          predicate_value(o, :lifezone),             # lifezone
+          predicate_value(o, :lifezone),             # environment (formerly named lifezone)
           link(o),                                   # link
           remarks(o)                                 # remarks
         ]
diff --git a/lib/export/coldp/files/vernacular_name.rb b/lib/export/coldp/files/vernacular_name.rb
index 10f32a0dd1..5d01e77a13 100644
--- a/lib/export/coldp/files/vernacular_name.rb
+++ b/lib/export/coldp/files/vernacular_name.rb
@@ -4,13 +4,12 @@
 # language
 # country
 # area
-# lifestage
 # sex
 # reference_id
 #
 module Export::Coldp::Files::VernacularName
 
-  # @return [String, nil] 
+  # @return [String, nil]
   #   the 'English' translation(s) if available
   def self.transliteration(common_name)
     n = common_name.alternate_values.where(type: 'AlternateValue::Translation', alternate_value_object_attribute: :name).load
@@ -25,11 +24,6 @@ def self.area(common_name)
     common_name.geographic_area&.self_and_ancestors&.collect{|a| a.name}&.join('; ')
   end
 
-  # TODO: Map to biocuration attribute via URI
-  def self.life_stage(common_name)
-    nil
-  end
-
   # TODO: Map to biocuration attribute via URI
   def self.sex(common_name)
     nil
@@ -48,8 +42,7 @@ def self.reference_id(common_name)
   def self.generate(otus, reference_csv = nil )
     CSV.generate(col_sep: "\t") do |csv|
 
-      # TODO: Biocuration attributes on these two 
-      # lifestage
+      # TODO: Biocuration attributes on these two
       # sex
 
       csv << %w{

From 93d2e9f6c3e9c4116cf92788a470092c22a9365f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 1 Dec 2022 16:46:33 -0300
Subject: [PATCH 081/160] Fix #3212

---
 CHANGELOG.md                                                | 2 ++
 .../tasks/nomenclature/filter/components/filters/status.vue | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6d5f9f9421..c2d7f62cba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Autocomplete on Browse collection object [#3189]
 - Task - Collection object chronology, a plot of object by year collected
 - Endpoint to return related data preventing or included in destroy, e.g. `/metadata/related_summary?klass=CollectionObject&id[]=16701&id[]...`
+- Gender and form classifications to filter nomenclature
 
 ### Fixed
 - 'Also create OTU' on batch taxon name upload causing raise
@@ -36,6 +37,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
 [#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
+[#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
 
 ## [0.29.6] - 2022-11-08
 
diff --git a/app/javascript/vue/tasks/nomenclature/filter/components/filters/status.vue b/app/javascript/vue/tasks/nomenclature/filter/components/filters/status.vue
index 978cf8a4c9..865479e36c 100644
--- a/app/javascript/vue/tasks/nomenclature/filter/components/filters/status.vue
+++ b/app/javascript/vue/tasks/nomenclature/filter/components/filters/status.vue
@@ -162,12 +162,12 @@ export default {
 
       nomenclatureCodes.forEach(key => {
         if (statusList[key]) {
-          newList.all = Object.assign(newList.all, statusList[key].all)
-          newList.tree = Object.assign(newList.tree, statusList[key].tree)
+          newList.all = { ...newList.all, ...statusList[key].all, ...statusList?.latinized?.all }
+          newList.tree = { ...newList.tree, ...statusList[key].tree, ...statusList?.latinized?.tree }
           for (const keyType in statusList[key].common) {
             statusList[key].common[keyType].name = `${statusList[key].common[keyType].name} (${key})`
           }
-          newList.common = Object.assign(newList.common, statusList[key].common)
+          newList.common = { ...newList.common, ...statusList[key].common, ...statusList?.latinized?.common }
         }
       })
       this.getTreeList(newList.tree, newList.all)

From d6d2295e078183a1aae2ded3f823beae1e754cae Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 1 Dec 2022 14:58:04 -0600
Subject: [PATCH 082/160] serial param for Source filter. #3211

---
 app/controllers/sources_controller.rb |  2 ++
 lib/queries/source/filter.rb          | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)

diff --git a/app/controllers/sources_controller.rb b/app/controllers/sources_controller.rb
index ab323cab7b..ef0cff8f4c 100644
--- a/app/controllers/sources_controller.rb
+++ b/app/controllers/sources_controller.rb
@@ -275,6 +275,7 @@ def filter_params
       :recent,
       :roles,
       :source_type,
+      :serial,
       :tags,
       :title,
       :user_date_end,
@@ -323,6 +324,7 @@ def api_params
       :query_term,
       :recent,
       :roles,
+      :serial,
       :source_type,
       :tags,
       :title,
diff --git a/lib/queries/source/filter.rb b/lib/queries/source/filter.rb
index 1bbdcfa1a8..a85b8230f5 100644
--- a/lib/queries/source/filter.rb
+++ b/lib/queries/source/filter.rb
@@ -107,6 +107,12 @@ class Filter < Queries::Query
       #   ignored if ancestor_id is not provided; if true then also include sources linked to OTUs that are in the scope of ancestor_id
       attr_accessor :citations_on_otus
 
+      # @return [Boolean, nil]
+      attr_accessor :serial
+      # true - with serial_id
+      # false - without_serial_id
+      # nil - both
+
       # @param [Hash] params
       def initialize(params)
         @query_string = params[:query_term]&.delete("\u0000") # TODO, we need to sanitize params in general.
@@ -136,6 +142,8 @@ def initialize(params)
         @year_start = params[:year_start]
         @recent = (params[:recent]&.to_s&.downcase == 'true' ? true : false) if !params[:recent].nil?
 
+        @serial = boolean_param(params,:serial)
+
         @citations_on_otus = (params[:citations_on_otus]&.to_s&.downcase == 'true' ? true : false) if !params[:citations_on_otus].nil?
         @ancestor_id = params[:ancestor_id]
 
@@ -326,6 +334,16 @@ def document_facet
         end
       end
 
+      def serial_facet
+        return nil if serial.nil?
+
+        if serial
+          table[:serial_id].not_eq(nil)
+        else
+          table[:serial_id].eq(nil)
+        end
+      end
+
       # TODO: move to citation concern
       def citation_object_type_facet
         return nil if citation_object_type.empty?
@@ -386,6 +404,7 @@ def and_clauses
 
         clauses += [
           cached,
+          serial_facet,
           source_ids_facet,
           serial_ids_facet,
           attribute_exact_facet(:author),

From a8ad324e55f3c2fb96eb2d2cd33f56f7a7ffe84b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 1 Dec 2022 18:09:34 -0300
Subject: [PATCH 083/160] Fix #3211

---
 CHANGELOG.md                                                  | 1 +
 app/javascript/vue/tasks/sources/filter/components/filter.vue | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c2d7f62cba..3fc6ee3cfc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Task - Collection object chronology, a plot of object by year collected
 - Endpoint to return related data preventing or included in destroy, e.g. `/metadata/related_summary?klass=CollectionObject&id[]=16701&id[]...`
 - Gender and form classifications to filter nomenclature
+- Serial facet to Filter sources [#3211]
 
 ### Fixed
 - 'Also create OTU' on batch taxon name upload causing raise
diff --git a/app/javascript/vue/tasks/sources/filter/components/filter.vue b/app/javascript/vue/tasks/sources/filter/components/filter.vue
index 9a4bf6b0c5..15102504f3 100644
--- a/app/javascript/vue/tasks/sources/filter/components/filter.vue
+++ b/app/javascript/vue/tasks/sources/filter/components/filter.vue
@@ -194,7 +194,8 @@ const initParams = () => ({
     nomenclature: undefined,
     with_doi: undefined,
     tags: undefined,
-    notes: undefined
+    notes: undefined,
+    serial: undefined
   },
   identifier: {
     namespace_id: undefined,

From a9ef6ffad13177135537190790e923ad9ff207c2 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 1 Dec 2022 15:15:09 -0600
Subject: [PATCH 084/160] Use boolean_param in source filter

---
 lib/queries/source/filter.rb | 38 ++++++++++++++++--------------------
 1 file changed, 17 insertions(+), 21 deletions(-)

diff --git a/lib/queries/source/filter.rb b/lib/queries/source/filter.rb
index a85b8230f5..401403a357 100644
--- a/lib/queries/source/filter.rb
+++ b/lib/queries/source/filter.rb
@@ -117,35 +117,31 @@ class Filter < Queries::Query
       def initialize(params)
         @query_string = params[:query_term]&.delete("\u0000") # TODO, we need to sanitize params in general.
 
+        @ancestor_id = params[:ancestor_id]
         @author = params[:author]
         @author_ids = params[:author_ids] || []
-
-        @author_ids_or = (params[:author_ids_or]&.to_s&.downcase == 'true' ? true : false) if !params[:author_ids_or].nil?
-
-        @ids = params[:ids] || []
-        @topic_ids = params[:topic_ids] || []
-        @serial_ids = params[:serial_ids] || []
+        @author_ids_or =  boolean_param(params,:author_ids_or)
         @citation_object_type = params[:citation_object_type] || []
-        @citations = (params[:citations]&.to_s&.downcase == 'true' ? true : false) if !params[:citations].nil?
-        @documents = (params[:documents]&.to_s&.downcase == 'true' ? true : false) if !params[:documents].nil?
-        @exact_author = (params[:exact_author]&.to_s&.downcase == 'true' ? true : false) if !params[:exact_author].nil?
-        @exact_title = (params[:exact_title]&.to_s&.downcase == 'true' ? true : false) if !params[:exact_title].nil?
-        @in_project = (params[:in_project]&.to_s&.downcase == 'true' ? true : false) if !params[:in_project].nil?
-        @nomenclature = (params[:nomenclature]&.to_s&.downcase == 'true' ? true : false) if !params[:nomenclature].nil?
-        @notes = (params[:notes]&.to_s&.downcase == 'true' ? true : false) if !params[:notes].nil?
+        @citations =  boolean_param(params,:citations)
+        @citations_on_otus = boolean_param(params,:citations_on_otus)
+        @documents = boolean_param(params,:documents)
+        @exact_author = boolean_param(params,:exact_author)
+        @exact_title = boolean_param(params,:exact_title)
+        @ids = params[:ids] || []
+        @in_project = boolean_param(params,:in_project) 
+        @nomenclature = boolean_param(params,:nomenclature)
+        @notes = boolean_param(params,:notes)
         @project_id = params[:project_id] # TODO: also in Queries::Query
-        @roles = (params[:roles]&.to_s&.downcase == 'true' ? true : false) if !params[:roles].nil?
+        @recent =  boolean_param(params,:recent)
+        @roles = boolean_param(params,:roles)
+        @serial = boolean_param(params,:serial)
+        @serial_ids = params[:serial_ids] || []
         @source_type = params[:source_type]
         @title = params[:title]
-        @with_doi = (params[:with_doi]&.to_s&.downcase == 'true' ? true : false) if !params[:with_doi].nil?
+        @topic_ids = params[:topic_ids] || []
+        @with_doi = boolean_param(params,:with_doi)
         @year_end = params[:year_end]
         @year_start = params[:year_start]
-        @recent = (params[:recent]&.to_s&.downcase == 'true' ? true : false) if !params[:recent].nil?
-
-        @serial = boolean_param(params,:serial)
-
-        @citations_on_otus = (params[:citations_on_otus]&.to_s&.downcase == 'true' ? true : false) if !params[:citations_on_otus].nil?
-        @ancestor_id = params[:ancestor_id]
 
         build_terms
         set_identifier(params)

From cb641458557f0caf094aad4942e455c85ef4eed9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 1 Dec 2022 18:35:20 -0300
Subject: [PATCH 085/160] Check if all fields are locked

---
 .../collection_objects/simple_new_specimen/App.vue |  3 ++-
 .../components/FormCatalogNumber.vue               |  9 +++++++--
 .../simple_new_specimen/store/getters/getters.js   | 14 ++++++++++++++
 .../store/getters/isAllLocked.js                   |  5 +++++
 .../simple_new_specimen/store/useStore.js          |  2 ++
 5 files changed, 30 insertions(+), 3 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/getters.js
 create mode 100644 app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/isAllLocked.js

diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index 1b48f27a82..4728136dbc 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -47,6 +47,7 @@ import RecentTable from './components/RecentTable.vue'
 import { ref } from 'vue'
 import { useStore } from './store/useStore'
 import { ActionNames } from './store/actions/actions'
+import { GetterNames } from './store/getters/getters'
 
 const store = useStore()
 const root = ref(null)
@@ -56,7 +57,7 @@ store[ActionNames.GetRecent]()
 const setFristAutofocusElement = () => {
   const element = root.value.querySelector('#collection-object-form input[type="text"]:not([disabled])')
 
-  if (element) {
+  if (!store[GetterNames.IsAllLocked] && element) {
     element.focus()
   }
 }
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
index 0f061f71f8..6a6e52d998 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -7,7 +7,7 @@
         class="full_width"
         label="label"
         :item="store.namespace"
-        @unset="store.namespace = undefined"
+        @unset="unsetNamespace"
       />
       <Autocomplete
         v-else
@@ -83,6 +83,11 @@ function checkIdentifier () {
   }, DELAY)
 }
 
+function unsetNamespace () {
+  store.namespace = undefined
+  store.identifier = undefined
+}
+
 onMounted(() => {
   setTimeout(() => autocompleteComponent.value.setFocus(), 250)
 })
@@ -91,7 +96,7 @@ watch(
   () => store.settings.lock.namespace,
   newVal => {
     if (!newVal) {
-      store.namespace = undefined
+      unsetNamespace()
     }
   }
 )
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/getters.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/getters.js
new file mode 100644
index 0000000000..021b5b3ca2
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/getters.js
@@ -0,0 +1,14 @@
+import isAllLocked from './isAllLocked'
+
+const GetterNames = {
+  IsAllLocked: 'isAllLocked'
+}
+
+const GetterFunctions = {
+  [GetterNames.IsAllLocked]: isAllLocked
+}
+
+export {
+  GetterNames,
+  GetterFunctions
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/isAllLocked.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/isAllLocked.js
new file mode 100644
index 0000000000..307891336f
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/getters/isAllLocked.js
@@ -0,0 +1,5 @@
+export default state => {
+  const lockValues = Object.values(state.settings.lock)
+
+  return lockValues.every(Boolean)
+}
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
index 0d7777af78..6a8dbe1dab 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/useStore.js
@@ -1,4 +1,5 @@
 import { defineStore } from 'pinia'
+import { GetterFunctions } from './getters/getters'
 import { ActionFunctions } from './actions/actions'
 
 const makeInitialState = () => ({
@@ -28,5 +29,6 @@ const makeInitialState = () => ({
 
 export const useStore = defineStore('main', {
   state: makeInitialState,
+  getters: GetterFunctions,
   actions: ActionFunctions
 })

From 046a53e7219142c663ea1c37498bfb29f7af3220 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Thu, 1 Dec 2022 19:15:19 -0300
Subject: [PATCH 086/160] Add locked data attribute

---
 .../tasks/collection_objects/simple_new_specimen/App.vue    | 6 +++++-
 .../simple_new_specimen/components/FormCE.vue               | 2 ++
 .../simple_new_specimen/components/FormCatalogNumber.vue    | 1 +
 .../simple_new_specimen/components/FormPreparationType.vue  | 1 +
 4 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index 4728136dbc..5a2ec4a1c6 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -55,7 +55,11 @@ const root = ref(null)
 store[ActionNames.GetRecent]()
 
 const setFristAutofocusElement = () => {
-  const element = root.value.querySelector('#collection-object-form input[type="text"]:not([disabled])')
+  const element = root.value.querySelector(`
+    input[type="text"]:not([disabled], [data-locked="true"]), 
+    textarea[type="text"]:not([disabled], [data-locked="true"]), 
+    select:not([disabled], [data-locked="true"])`
+  )
 
   if (!store[GetterNames.IsAllLocked] && element) {
     element.focus()
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
index bd42ec0033..020e8b3e58 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCE.vue
@@ -10,6 +10,7 @@
       <textarea
         class="full_width"
         rows="5"
+        :data-locked="store.settings.lock.collectingEvent"
         v-model="store.collectingEvent.verbatim_label"
       />
     </div>
@@ -17,6 +18,7 @@
       <label>Verbatim locality</label>
       <input
         class="full_width"
+        :data-locked="store.settings.lock.collectingEvent"
         v-model="store.collectingEvent.verbatim_locality"
         type="text"
       >
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
index 6a6e52d998..07ebcc91ab 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -34,6 +34,7 @@
           type="text"
           class="half_width"
           v-model="store.identifier"
+          :data-locked="store.settings.lock.namespace"
           @input="checkIdentifier"
         >
         <label>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
index 24606fd0b2..7afdf099df 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormPreparationType.vue
@@ -7,6 +7,7 @@
       <select
         class="half_width"
         v-model="store.preparationTypeId"
+        :data-locked="store.settings.lock.preparationTypeId"
       >
         <option :value="undefined">
           None

From 577d514d86e0ba108b2ebfb4f3397a1d8d0db8f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Fri, 2 Dec 2022 11:27:06 -0300
Subject: [PATCH 087/160] Add hotkey lib, cleaup

---
 .../javascripts/vendor/lib/dropzone/config.js |  66 -----------
 .../views/tasks/accessions/quick/simple.js    | 107 ------------------
 .../components/otu/otu_picker/otu_picker.vue  |  23 ++--
 .../vue/components/ui/Autocomplete.vue        |   6 +
 .../simple_new_specimen/App.vue               |  33 +++++-
 .../components/FormCatalogNumber.vue          |   3 +
 .../components/FormDetermination.vue          |   3 +
 .../components/GeographicArea.vue             |   3 +
 .../simple_new_specimen/index.js              |   2 +
 package-lock.json                             | 105 +++++++++++++++++
 package.json                                  |   1 +
 11 files changed, 170 insertions(+), 182 deletions(-)
 delete mode 100644 app/assets/javascripts/views/tasks/accessions/quick/simple.js

diff --git a/app/assets/javascripts/vendor/lib/dropzone/config.js b/app/assets/javascripts/vendor/lib/dropzone/config.js
index a404304852..f5df65a94b 100644
--- a/app/assets/javascripts/vendor/lib/dropzone/config.js
+++ b/app/assets/javascripts/vendor/lib/dropzone/config.js
@@ -33,73 +33,7 @@ _init_dropzone_for_depictions = function init_dropzone_for_depictions() {
   }
 };
 
-var _init_dropzone_for_task_simple_specimen;
-
-// https://github.com/enyo/dropzone/wiki/Combine-normal-form-with-Dropzone
-_init_dropzone_for_task_simple_specimen = function init_dropzone_for_task_simple_specimen() {
-
-  if ( $("#simple-specimen-task").length ) {
-    Dropzone.options.simpleSpecimenTask = {
-      autoProcessQueue: false,
-      uploadMultiple: true,
-      paramName: "specimen[image_array]",
-      maxFiles: 100,
-      maxFilesize: 150,
-      timeout: 0,
-      previewsContainer: '#dropzone_previews',
-
-      // The setting up of the dropzone
-      init: function() {
-        var myDropzone = this;
-
-        // First change the button to actually tell Dropzone to process the queue.
-        this.element.querySelector("#simple_create").addEventListener("click", function(e) {
-          // Make sure that the form isn't actually being sent.
-          e.preventDefault();
-          e.stopPropagation();
-
-          if (myDropzone.getQueuedFiles().length > 0) {
-            myDropzone.processQueue();
-          } else {
-            return $('#simple-specimen-task').submit();
-          }
-        });
-
-        this.on("addedfile", function(file) { $('.dz-default').remove(); });
-
-        // Listen to the sendingmultiple event. In this case, it's the sendingmultiple event instead
-        // of the sending event because uploadMultiple is set to true.
-        this.on("sendingmultiple", function() {
-          // Gets triggered when the form is actually being sent.
-          // Hide the success button or the complete form.
-        });
-        this.on("successmultiple", function(files, response) {
-          // Gets triggered when the files have successfully been sent.
-          // Redirect user or notify of success.
-          // alert(response.otu_id);
-
-          // work with the json response to reset the form, which is then 
-          // used in the GET request to reset the window
-
-          TW.tasks.accessions.quick.simple.new_from_dropzone(response);
-          // serialize and re-render the page
-          return window.location.href = '/tasks/accessions/simple/new?' + $( "div.flexbox input" ).serialize();
-        });
-        this.on("errormultiple", function(files, response) {
-          alert('error');
-          // Gets triggered when there was an error sending the files.
-          // Maybe show form again, and notify user of error
-        });
-        this.on("success", function(fields, response) {
-          // return window.location.href = '/tasks/accessions/simple/new';
-        });
-      }
-    };
-  }
-};
-
 $(document).on('turbolinks:load', function(event) {
-  _init_dropzone_for_task_simple_specimen();
   _init_dropzone_for_images();
   _init_dropzone_for_depictions();
 });
diff --git a/app/assets/javascripts/views/tasks/accessions/quick/simple.js b/app/assets/javascripts/views/tasks/accessions/quick/simple.js
deleted file mode 100644
index b51169d48c..0000000000
--- a/app/assets/javascripts/views/tasks/accessions/quick/simple.js
+++ /dev/null
@@ -1,107 +0,0 @@
-//
-//  !! See also dropzone_config.js for behaviour
-//
-var TW = TW || {};
-TW.tasks = TW.tasks || {};
-TW.tasks.accessions = TW.tasks.accessions || {};
-TW.tasks.accessions.quick = TW.tasks.accessions.quick || {};
-
-TW.tasks.accessions.quick.simple = {
-
-  init: function () {
-    $('#simple-specimen-task').each(function () {
-      TW.tasks.accessions.quick.simple.initialize($(this));
-    });
-  },
-
-  initialize: function (div) {
-    // Bind injected datepicker elements
-    $('body').on('click',".collecting_event_picklist", function() {
-      TW.tasks.accessions.quick.simple.bind_select_collecting_event(this);
-    });
-
-    $(".data:empty").parent().remove();
-
-    TW.tasks.accessions.quick.simple.bind_locality_search(); 
-    TW.tasks.accessions.quick.simple.bind_collecting_event_toggle(); 
-  },
-
-   // cleanup existing "new" records, so they are not resubmitted
-  new_from_dropzone: function (response) {
-    
-    // OTU
-    $("#selected_otu_id").remove();
-    $("#XXX_otu_picker_autocomplete").remove();
-
-    $('<input>')
-      .attr('name', 'specimen[taxon_determinations_attributes][0][otu_id]')
-      .attr('id', 'selected_otu_id')
-      .attr('value', response.otu_id)
-      .appendTo('#simple-specimen-task');
-
-    // Collecting Event
-   
-    $("#selected_collecting_event_id").remove();
-    $('<input>')
-      .attr('name', 'specimen[collecting_event_id]')
-      .attr('id', 'selected_collecting_event_id')
-      .attr('value', response.collecting_event_id)
-      .appendTo('#selected_collecting_event');
-    
-    // Likely need Repository here
-  },
-
-  bind_select_collecting_event: function (link) {
-    TW.tasks.accessions.quick.simple.set_collecting_event( $(link).data('collecting-event-id') ); 
-  },
-
-  set_collecting_event: function (id) {
-    $("#collecting_event_fields").hide(); 
-
-    var form = $('#simple-specimen-task');
-    var target = "#selected_collecting_event" ;
-    var s = $(target);
-
-    $.ajax({
-      url: "/collecting_events/" + id + "/card", 
-      dataType: "script",
-      data: { 
-        target: target,
-      }
-    });
-
-    $('<input>')
-      .attr('name', 'specimen[collecting_event_id]') 
-      .attr('value', id)
-      .attr('hidden', true)
-      .appendTo(form); // form
-
-    $('#collecting_event_form_toggle').show(); 
-  },
-
-  bind_locality_search: function () {
-    $( "#verbatim_locality" ).keyup(function() {
-
-      //   TW.tasks.accessions.quick.simple.update_collecting_events();
-
-      var term =  $("#verbatim_locality").val();
-      $.ajax({
-        url: "collecting_events", 
-          dataType: "script",
-            data: { term: term  }
-      });
-
-    });
-  },
-
-  bind_collecting_event_toggle: function () {
-    $('#collecting_event_form_toggle').on('click', function (){
-      $('#collecting_event_fields').toggle();
-      $('#selected_collecting_event').html('');
-      $('#collecting_event_form_toggle').toggle();
-    });
-  }
-
-}; // end widget 
-
-$(document).on('turbolinks:load', TW.tasks.accessions.quick.simple.init);
diff --git a/app/javascript/vue/components/otu/otu_picker/otu_picker.vue b/app/javascript/vue/components/otu/otu_picker/otu_picker.vue
index 12cdc4f1ac..7a9726b853 100644
--- a/app/javascript/vue/components/otu/otu_picker/otu_picker.vue
+++ b/app/javascript/vue/components/otu/otu_picker/otu_picker.vue
@@ -7,12 +7,14 @@
       label="label_html"
       min="2"
       display="label"
-      @getItem="emitOtu"
-      @getInput="callbackInput"
-      @found="found = $event"
       :clear-after="clearAfter"
+      :input-attributes="inputAttributes"
       placeholder="Select an OTU"
-      param="term"/>
+      param="term"
+      @found="found = $event"
+      @get-item="emitOtu"
+      @get-input="callbackInput"
+    />
     <div class="flex-wrap-column create-otu-panel">
       <match-taxon-name
         v-if="!found"
@@ -49,13 +51,14 @@
           <template v-else>
             <autocomplete
               url="/taxon_names/autocomplete"
-              :autofocus="true"
+              autofocus
               label="label"
               min="2"
-              :clear-after="true"
-              @getItem="setTaxon"
+              clear-after
+              @get-item="setTaxon"
               placeholder="Select a taxon name"
-              param="term"/>
+              param="term"
+            />
           </template>
         </div>
         <button
@@ -88,6 +91,10 @@ export default {
     clearAfter: {
       type: Boolean,
       default: false
+    },
+    inputAttributes: {
+      type: Object,
+      default: () => ({})
     }
   },
 
diff --git a/app/javascript/vue/components/ui/Autocomplete.vue b/app/javascript/vue/components/ui/Autocomplete.vue
index e9f117d26d..a868c5688d 100644
--- a/app/javascript/vue/components/ui/Autocomplete.vue
+++ b/app/javascript/vue/components/ui/Autocomplete.vue
@@ -33,6 +33,7 @@ Parameters:
       :placeholder="placeholder"
       @input="checkTime(), sendType()"
       v-model="type"
+      v-bind="inputAttributes"
       @keydown.down="downKey"
       @keydown.up="upKey"
       @keydown.enter="enterKey"
@@ -167,6 +168,11 @@ export default {
     inputStyle: {
       type: Object,
       default: () => ({})
+    },
+
+    inputAttributes: {
+      type: Object,
+      default: () => ({})
     }
   },
 
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
index 5a2ec4a1c6..e3d10635cd 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/App.vue
@@ -44,6 +44,8 @@ import FormDetermination from './components/FormDetermination.vue'
 import BlockLayout from 'components/layout/BlockLayout.vue'
 import VBtn from 'components/ui/VBtn/index.vue'
 import RecentTable from './components/RecentTable.vue'
+import useHotkey from 'vue3-hotkey'
+import platformKey from 'helpers/getPlatformKey'
 import { ref } from 'vue'
 import { useStore } from './store/useStore'
 import { ActionNames } from './store/actions/actions'
@@ -57,7 +59,7 @@ store[ActionNames.GetRecent]()
 const setFristAutofocusElement = () => {
   const element = root.value.querySelector(`
     input[type="text"]:not([disabled], [data-locked="true"]), 
-    textarea[type="text"]:not([disabled], [data-locked="true"]), 
+    textarea:not([disabled], [data-locked="true"]), 
     select:not([disabled], [data-locked="true"])`
   )
 
@@ -66,6 +68,25 @@ const setFristAutofocusElement = () => {
   }
 }
 
+const hotkeys = [
+  {
+    keys: [platformKey(), 'n'],
+    preventDefault: true,
+    handler () {
+      resetStore()
+      setFristAutofocusElement()
+    }
+  },
+  {
+    keys: [platformKey(), 's'],
+    preventDefault: true,
+    handler () {
+      store.createNewSpecimen()
+    }
+  }
+]
+
+const stop = useHotkey(hotkeys)
 const unsubscribe = store.$onAction(
   ({
     name,
@@ -79,6 +100,16 @@ const unsubscribe = store.$onAction(
       setFristAutofocusElement()
     })
   })
+
+const resetStore = () => {
+  const recent = store.recentList
+
+  store.$reset()
+  store.recentList = recent
+}
+
+TW.workbench.keyboard.createLegend(`${platformKey()}+s`, 'Save', 'Simple new specimen')
+TW.workbench.keyboard.createLegend(`${platformKey()}+n`, 'New', 'Simple new specimen')
 </script>
 
 <style lang="scss">
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
index 07ebcc91ab..7325b008b5 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormCatalogNumber.vue
@@ -19,6 +19,9 @@
         clear-after
         autofocus
         placeholder="Search a namespace..."
+        :input-attributes="{
+          'data-locked': store.settings.lock.namespace
+        }"
         @get-item="store.namespace = $event"
       />
       <VLock
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
index 5976c32421..8ffdc47f27 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/FormDetermination.vue
@@ -12,6 +12,9 @@
         v-else
         class="full_width"
         clear-after
+        :input-attributes="{
+          'data-locked': store.settings.lock.otu
+        }"
         @get-item="store.otu = { ...$event, label: $event.name || $event.label }"
       />
       <VLock
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
index ff00620a0e..a4cd752a24 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/components/GeographicArea.vue
@@ -13,6 +13,9 @@
     autofocus
     placeholder="Search a geographic area"
     clear-after
+    :input-attributes="{
+      'data-locked': store.settings.lock.collectingEvent
+    }"
     @get-item="store.geographicArea = $event"
   />
 </template>
diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
index 5c0f7d3aa6..3279ba69f3 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/index.js
@@ -1,11 +1,13 @@
 import { createApp } from 'vue'
 import { createPinia } from 'pinia'
 import App from './App.vue'
+import vHotkey from 'plugins/v-hotkey'
 
 function initApp (element) {
   const app = createApp(App)
   const pinia = createPinia()
 
+  app.directive('hotkey', vHotkey)
   app.use(pinia)
   app.mount(element)
 }
diff --git a/package-lock.json b/package-lock.json
index 67d00a6f1a..d450dab2ab 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -32,6 +32,7 @@
         "vue-hotkeys": "0.0.1",
         "vue-tippy": "^6.0.0-alpha.58",
         "vue-turbolinks": "^2.2.2",
+        "vue3-hotkey": "^1.0.2",
         "vuedraggable": "^4.1.0",
         "vuex": "^4.1.0"
       },
@@ -2803,6 +2804,14 @@
       "resolved": "https://registry.npmjs.org/@vue/shared/-/shared-3.2.45.tgz",
       "integrity": "sha512-Ewzq5Yhimg7pSztDV+RH1UDKBzmtqieXQlpTVm2AwraoRL/Rks96mvd8Vgi7Lj+h+TH8dv7mXD3FRZR3TUvbSg=="
     },
+    "node_modules/@vue/test-utils": {
+      "version": "2.2.5",
+      "resolved": "https://registry.npmjs.org/@vue/test-utils/-/test-utils-2.2.5.tgz",
+      "integrity": "sha512-iKEbu/VRO53qXJlAupL7d4v+SdaypQuRDxwGO3dgYT7biPh+gJsa+0Z9dnaHIE752nPc/ueAoNd6KAKx6fD+Tw==",
+      "peerDependencies": {
+        "vue": "^3.0.1"
+      }
+    },
     "node_modules/@webassemblyjs/ast": {
       "version": "1.11.1",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/ast/-/ast-1.11.1.tgz",
@@ -4749,6 +4758,11 @@
         "node": ">=12"
       }
     },
+    "node_modules/de-indent": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/de-indent/-/de-indent-1.0.2.tgz",
+      "integrity": "sha512-e/1zu3xH5MQryN2zdVaF0OrdNLUbvWxzMbi+iNA6Bky7l1RoP8a2fIbRocyHclXt/arDrrR6lL3TqFD9pMQTsg=="
+    },
     "node_modules/debug": {
       "version": "4.3.4",
       "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
@@ -6400,6 +6414,14 @@
       "integrity": "sha512-WdZTbAByD+pHfl/g9QSsBIIwy8IT+EsPiKDs0KNX+zSHhdDLFKdZu0BQHljvO+0QI/BasbMSUa8wYNCZTvhslg==",
       "dev": true
     },
+    "node_modules/he": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/he/-/he-1.2.0.tgz",
+      "integrity": "sha512-F/1DnUGPopORZi0ni+CvrCgHQ5FyEAHRLSApuYWMmrbSwoN2Mn/7k+Gl38gJnR7yyDZk6WLXwiGod1JOWNDKGw==",
+      "bin": {
+        "he": "bin/he"
+      }
+    },
     "node_modules/hpack.js": {
       "version": "2.1.6",
       "resolved": "https://registry.npmjs.org/hpack.js/-/hpack.js-2.1.6.tgz",
@@ -10961,6 +10983,15 @@
         "node": ">=8"
       }
     },
+    "node_modules/vue-template-compiler": {
+      "version": "2.7.14",
+      "resolved": "https://registry.npmjs.org/vue-template-compiler/-/vue-template-compiler-2.7.14.tgz",
+      "integrity": "sha512-zyA5Y3ArvVG0NacJDkkzJuPQDF8RFeRlzV2vLeSnhSpieO6LK2OVbdLPi5MPPs09Ii+gMO8nY4S3iKQxBxDmWQ==",
+      "dependencies": {
+        "de-indent": "^1.0.2",
+        "he": "^1.2.0"
+      }
+    },
     "node_modules/vue-tippy": {
       "version": "6.0.0-alpha.58",
       "resolved": "https://registry.npmjs.org/vue-tippy/-/vue-tippy-6.0.0-alpha.58.tgz",
@@ -10977,6 +11008,31 @@
       "resolved": "https://registry.npmjs.org/vue-turbolinks/-/vue-turbolinks-2.2.2.tgz",
       "integrity": "sha512-pPO2Fr+1UgdhUK9dc5OhjLSeYi5LZAm/VZBXOVQgLHCO31bRjAof/+W/e/6SHCbnb1xdZb1gW5T9MX0k9ejSAQ=="
     },
+    "node_modules/vue3-hotkey": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/vue3-hotkey/-/vue3-hotkey-1.0.2.tgz",
+      "integrity": "sha512-m1koD1IriRQhaX3yhoYgk6pfq4qIiF5anAe0tUadL81aeJDuGVJ3/EuvTenS9vgx1LbTRalT4mW4nUZG5pElpQ==",
+      "dependencies": {
+        "@types/express": "4.17.8",
+        "@vue/test-utils": "^2.0.0-rc.6",
+        "vue": "^3.2.6",
+        "vue-template-compiler": "^2.6.13"
+      },
+      "engines": {
+        "node": ">=16.0.0"
+      }
+    },
+    "node_modules/vue3-hotkey/node_modules/@types/express": {
+      "version": "4.17.8",
+      "resolved": "https://registry.npmjs.org/@types/express/-/express-4.17.8.tgz",
+      "integrity": "sha512-wLhcKh3PMlyA2cNAB9sjM1BntnhPMiM0JOBwPBqttjHev2428MLEB4AYVN+d8s2iyCVZac+o41Pflm/ZH5vLXQ==",
+      "dependencies": {
+        "@types/body-parser": "*",
+        "@types/express-serve-static-core": "*",
+        "@types/qs": "*",
+        "@types/serve-static": "*"
+      }
+    },
     "node_modules/vuedraggable": {
       "version": "4.1.0",
       "resolved": "https://registry.npmjs.org/vuedraggable/-/vuedraggable-4.1.0.tgz",
@@ -13587,6 +13643,12 @@
       "resolved": "https://registry.npmjs.org/@vue/shared/-/shared-3.2.45.tgz",
       "integrity": "sha512-Ewzq5Yhimg7pSztDV+RH1UDKBzmtqieXQlpTVm2AwraoRL/Rks96mvd8Vgi7Lj+h+TH8dv7mXD3FRZR3TUvbSg=="
     },
+    "@vue/test-utils": {
+      "version": "2.2.5",
+      "resolved": "https://registry.npmjs.org/@vue/test-utils/-/test-utils-2.2.5.tgz",
+      "integrity": "sha512-iKEbu/VRO53qXJlAupL7d4v+SdaypQuRDxwGO3dgYT7biPh+gJsa+0Z9dnaHIE752nPc/ueAoNd6KAKx6fD+Tw==",
+      "requires": {}
+    },
     "@webassemblyjs/ast": {
       "version": "1.11.1",
       "resolved": "https://registry.npmjs.org/@webassemblyjs/ast/-/ast-1.11.1.tgz",
@@ -15001,6 +15063,11 @@
         "d3-transition": "2 - 3"
       }
     },
+    "de-indent": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/de-indent/-/de-indent-1.0.2.tgz",
+      "integrity": "sha512-e/1zu3xH5MQryN2zdVaF0OrdNLUbvWxzMbi+iNA6Bky7l1RoP8a2fIbRocyHclXt/arDrrR6lL3TqFD9pMQTsg=="
+    },
     "debug": {
       "version": "4.3.4",
       "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
@@ -16196,6 +16263,11 @@
       "integrity": "sha512-WdZTbAByD+pHfl/g9QSsBIIwy8IT+EsPiKDs0KNX+zSHhdDLFKdZu0BQHljvO+0QI/BasbMSUa8wYNCZTvhslg==",
       "dev": true
     },
+    "he": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/he/-/he-1.2.0.tgz",
+      "integrity": "sha512-F/1DnUGPopORZi0ni+CvrCgHQ5FyEAHRLSApuYWMmrbSwoN2Mn/7k+Gl38gJnR7yyDZk6WLXwiGod1JOWNDKGw=="
+    },
     "hpack.js": {
       "version": "2.1.6",
       "resolved": "https://registry.npmjs.org/hpack.js/-/hpack.js-2.1.6.tgz",
@@ -19300,6 +19372,15 @@
         }
       }
     },
+    "vue-template-compiler": {
+      "version": "2.7.14",
+      "resolved": "https://registry.npmjs.org/vue-template-compiler/-/vue-template-compiler-2.7.14.tgz",
+      "integrity": "sha512-zyA5Y3ArvVG0NacJDkkzJuPQDF8RFeRlzV2vLeSnhSpieO6LK2OVbdLPi5MPPs09Ii+gMO8nY4S3iKQxBxDmWQ==",
+      "requires": {
+        "de-indent": "^1.0.2",
+        "he": "^1.2.0"
+      }
+    },
     "vue-tippy": {
       "version": "6.0.0-alpha.58",
       "resolved": "https://registry.npmjs.org/vue-tippy/-/vue-tippy-6.0.0-alpha.58.tgz",
@@ -19313,6 +19394,30 @@
       "resolved": "https://registry.npmjs.org/vue-turbolinks/-/vue-turbolinks-2.2.2.tgz",
       "integrity": "sha512-pPO2Fr+1UgdhUK9dc5OhjLSeYi5LZAm/VZBXOVQgLHCO31bRjAof/+W/e/6SHCbnb1xdZb1gW5T9MX0k9ejSAQ=="
     },
+    "vue3-hotkey": {
+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/vue3-hotkey/-/vue3-hotkey-1.0.2.tgz",
+      "integrity": "sha512-m1koD1IriRQhaX3yhoYgk6pfq4qIiF5anAe0tUadL81aeJDuGVJ3/EuvTenS9vgx1LbTRalT4mW4nUZG5pElpQ==",
+      "requires": {
+        "@types/express": "4.17.8",
+        "@vue/test-utils": "^2.0.0-rc.6",
+        "vue": "^3.2.6",
+        "vue-template-compiler": "^2.6.13"
+      },
+      "dependencies": {
+        "@types/express": {
+          "version": "4.17.8",
+          "resolved": "https://registry.npmjs.org/@types/express/-/express-4.17.8.tgz",
+          "integrity": "sha512-wLhcKh3PMlyA2cNAB9sjM1BntnhPMiM0JOBwPBqttjHev2428MLEB4AYVN+d8s2iyCVZac+o41Pflm/ZH5vLXQ==",
+          "requires": {
+            "@types/body-parser": "*",
+            "@types/express-serve-static-core": "*",
+            "@types/qs": "*",
+            "@types/serve-static": "*"
+          }
+        }
+      }
+    },
     "vuedraggable": {
       "version": "4.1.0",
       "resolved": "https://registry.npmjs.org/vuedraggable/-/vuedraggable-4.1.0.tgz",
diff --git a/package.json b/package.json
index 2377df5613..743043fc7f 100644
--- a/package.json
+++ b/package.json
@@ -26,6 +26,7 @@
     "vue-hotkeys": "0.0.1",
     "vue-tippy": "^6.0.0-alpha.58",
     "vue-turbolinks": "^2.2.2",
+    "vue3-hotkey": "^1.0.2",
     "vuedraggable": "^4.1.0",
     "vuex": "^4.1.0"
   },

From 7d146b73efad1cb3cf0784a91ec5e801dc39df1b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Fri, 2 Dec 2022 12:16:34 -0300
Subject: [PATCH 088/160] Add alert, removed unsed package

---
 .../store/actions/createNewSpecimen.js                |  2 ++
 package-lock.json                                     | 11 -----------
 package.json                                          |  1 -
 3 files changed, 2 insertions(+), 12 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
index 77cc67d934..576ef81170 100644
--- a/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
+++ b/app/javascript/vue/tasks/collection_objects/simple_new_specimen/store/actions/createNewSpecimen.js
@@ -31,5 +31,7 @@ export default async function () {
   Promise.allSettled(promises).then(_ => {
     this[ActionNames.GetRecent]()
     this[ActionNames.ResetStore]()
+
+    TW.workbench.alert.create('New specimen was successfully created', 'notice')
   })
 }
diff --git a/package-lock.json b/package-lock.json
index d450dab2ab..36690f60d6 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -29,7 +29,6 @@
         "v-hotkey": "^0.9.0",
         "vue": "^3.2.45",
         "vue-handy-scroll": "^3.0.1",
-        "vue-hotkeys": "0.0.1",
         "vue-tippy": "^6.0.0-alpha.58",
         "vue-turbolinks": "^2.2.2",
         "vue3-hotkey": "^1.0.2",
@@ -10886,11 +10885,6 @@
         "vue": "next"
       }
     },
-    "node_modules/vue-hotkeys": {
-      "version": "0.0.1",
-      "resolved": "https://registry.npmjs.org/vue-hotkeys/-/vue-hotkeys-0.0.1.tgz",
-      "integrity": "sha512-RqMXtrkmQbRV/uJqAYZg1vuVFJT6RNcN5aSWCLuEd+X5rJpoq2VjIoPhHCBdHkqKfkSEbklwNuTbB1a7SONb2Q=="
-    },
     "node_modules/vue-loader": {
       "version": "17.0.1",
       "resolved": "https://registry.npmjs.org/vue-loader/-/vue-loader-17.0.1.tgz",
@@ -19305,11 +19299,6 @@
       "integrity": "sha512-Q7ogocQNXm1bG6xoe7xIGL4uvKRZ6LUu4RuSwryBZcvtaVl3UMuW3vF0qOySG8KLCfEcv7BMADvII+P036uEfw==",
       "requires": {}
     },
-    "vue-hotkeys": {
-      "version": "0.0.1",
-      "resolved": "https://registry.npmjs.org/vue-hotkeys/-/vue-hotkeys-0.0.1.tgz",
-      "integrity": "sha512-RqMXtrkmQbRV/uJqAYZg1vuVFJT6RNcN5aSWCLuEd+X5rJpoq2VjIoPhHCBdHkqKfkSEbklwNuTbB1a7SONb2Q=="
-    },
     "vue-loader": {
       "version": "17.0.1",
       "resolved": "https://registry.npmjs.org/vue-loader/-/vue-loader-17.0.1.tgz",
diff --git a/package.json b/package.json
index 743043fc7f..cea8c3c6f9 100644
--- a/package.json
+++ b/package.json
@@ -23,7 +23,6 @@
     "v-hotkey": "^0.9.0",
     "vue": "^3.2.45",
     "vue-handy-scroll": "^3.0.1",
-    "vue-hotkeys": "0.0.1",
     "vue-tippy": "^6.0.0-alpha.58",
     "vue-turbolinks": "^2.2.2",
     "vue3-hotkey": "^1.0.2",

From 0d409fd59fce68d0bf093c476d096ccda0c93956 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Luis=20Pereira?= <pepelui@outlook.com>
Date: Sun, 4 Dec 2022 11:41:55 -0300
Subject: [PATCH 089/160] Fix #3216

---
 CHANGELOG.md                                                 | 5 +++--
 .../vue/tasks/collecting_events/filter/components/Filter.vue | 4 ++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3fc6ee3cfc..14d4edb4fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Type relationship text/rendering is inverted in New taxon name [#3182]
 - Sqed processing failing to encode HEIC images [#3188]
 - Common list component doesn't filter created status on New taxon name task [#3205]
+- Collectors facet doesn't work on Filter collecting event [#3216]
 
 ### Changed
 - "TODO list" now a faceted search [#3171]
@@ -31,13 +32,13 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Updated Ruby gems
 - Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
 
-[#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173
 [#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171
+[#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173
 [#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
-[#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
 [#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
+[#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
 
 ## [0.29.6] - 2022-11-08
diff --git a/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue b/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue
index 5aab2ff8d9..a6af8fb005 100644
--- a/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue
+++ b/app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue
@@ -42,7 +42,7 @@
         role="Collector"
         title="Collectors"
         klass="CollectingEvent"
-        param-people="collector_ids"
+        param-people="collector_id"
         param-any="collector_ids_or"
       />
       <filter-material
@@ -253,7 +253,7 @@ export default {
           keyword_id_or: []
         },
         collectors: {
-          collector_ids: [],
+          collector_id: [],
           collector_ids_or: false
         },
         collectingEvents: {

From f7db3cdd21411fe2b4d7fb15762e27f201103b96 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Sun, 4 Dec 2022 16:18:11 -0300
Subject: [PATCH 090/160] Update packages

---
 package-lock.json | 86 +++++++++++++++++++++++------------------------
 package.json      | 10 +++---
 2 files changed, 48 insertions(+), 48 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 43a77b6ba7..4c56fe45b6 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -14,7 +14,7 @@
         "@sfgrp/svg-radial-menu": "^1.0.7",
         "axios": "^1.2.0",
         "chart.js": "^4.0.1",
-        "d3": "^7.6.1",
+        "d3": "^7.7.0",
         "dompurify": "^2.4.1",
         "easymde": "^2.18.0",
         "exif-js": "^2.3.0",
@@ -44,7 +44,7 @@
         "compression-webpack-plugin": "^10.0.0",
         "css-loader": "^6.7.2",
         "css-minimizer-webpack-plugin": "^4.2.2",
-        "eslint": "^8.28.0",
+        "eslint": "^8.29.0",
         "eslint-config-standard": "^17.0.0",
         "eslint-plugin-import": "^2.26.0",
         "eslint-plugin-n": "^15.5.1",
@@ -52,11 +52,11 @@
         "eslint-plugin-promise": "^6.1.1",
         "eslint-plugin-standard": "^4.1.0",
         "eslint-plugin-vue": "^9.8.0",
-        "mini-css-extract-plugin": "^2.7.0",
+        "mini-css-extract-plugin": "^2.7.1",
         "postcss": "^8.4.19",
         "postcss-flexbugs-fixes": "^5.0.2",
-        "postcss-import": "^15.0.0",
-        "postcss-loader": "^7.0.1",
+        "postcss-import": "^15.0.1",
+        "postcss-loader": "^7.0.2",
         "postcss-preset-env": "^7.8.3",
         "raw-loader": "^4.0.2",
         "resolve-url-loader": "^5.0.0",
@@ -4379,9 +4379,9 @@
       "integrity": "sha512-Z1PhmomIfypOpoMjRQB70jfvy/wxT50qW08YXO5lMIJkrdq4yOTR+AW7FqutScmB9NkLwxo+jU+kZLbofZZq/w=="
     },
     "node_modules/d3": {
-      "version": "7.6.1",
-      "resolved": "https://registry.npmjs.org/d3/-/d3-7.6.1.tgz",
-      "integrity": "sha512-txMTdIHFbcpLx+8a0IFhZsbp+PfBBPt8yfbmukZTQFroKuFqIwqswF0qE5JXWefylaAVpSXFoKm3yP+jpNLFLw==",
+      "version": "7.7.0",
+      "resolved": "https://registry.npmjs.org/d3/-/d3-7.7.0.tgz",
+      "integrity": "sha512-VEwHCMgMjD2WBsxeRGUE18RmzxT9Bn7ghDpzvTEvkLSBAKgTMydJjouZTjspgQfRHpPt/PB3EHWBa6SSyFQq4g==",
       "dependencies": {
         "d3-array": "3",
         "d3-axis": "3",
@@ -5142,9 +5142,9 @@
       }
     },
     "node_modules/eslint": {
-      "version": "8.28.0",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.28.0.tgz",
-      "integrity": "sha512-S27Di+EVyMxcHiwDrFzk8dJYAaD+/5SoWKxL1ri/71CRHsnJnRDPNt2Kzj24+MT9FDupf4aqqyqPrvI8MvQ4VQ==",
+      "version": "8.29.0",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.29.0.tgz",
+      "integrity": "sha512-isQ4EEiyUjZFbEKvEGJKKGBwXtvXX+zJbkVKCgTuB9t/+jUBcy8avhkEwWJecI15BkRkOYmvIM5ynbhRjEkoeg==",
       "dev": true,
       "dependencies": {
         "@eslint/eslintrc": "^1.3.3",
@@ -7474,9 +7474,9 @@
       }
     },
     "node_modules/mini-css-extract-plugin": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.0.tgz",
-      "integrity": "sha512-auqtVo8KhTScMsba7MbijqZTfibbXiBNlPAQbsVt7enQfcDYLdgG57eGxMqwVU3mfeWANY4F1wUg+rMF+ycZgw==",
+      "version": "2.7.1",
+      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.1.tgz",
+      "integrity": "sha512-viOoaUFy+Z2w43VsGPbtfwFrr0tKwDctK9dUofG5MBViYhD1noGFUzzDIVw0KPwCGUP+c7zqLxm+acuQs7zLzw==",
       "dev": true,
       "dependencies": {
         "schema-utils": "^4.0.0"
@@ -8557,9 +8557,9 @@
       }
     },
     "node_modules/postcss-import": {
-      "version": "15.0.0",
-      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.0.0.tgz",
-      "integrity": "sha512-Y20shPQ07RitgBGv2zvkEAu9bqvrD77C9axhj/aA1BQj4czape2MdClCExvB27EwYEJdGgKZBpKanb0t1rK2Kg==",
+      "version": "15.0.1",
+      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.0.1.tgz",
+      "integrity": "sha512-UGlvk8EgT7Gm/Ndf9xZHnzr8xm8P54N8CBWLtcY5alP+YxlEge/Rv78etQyevZs3qWTE9If13+Bo6zATBrPOpA==",
       "dev": true,
       "dependencies": {
         "postcss-value-parser": "^4.0.0",
@@ -8603,14 +8603,14 @@
       }
     },
     "node_modules/postcss-loader": {
-      "version": "7.0.1",
-      "resolved": "https://registry.npmjs.org/postcss-loader/-/postcss-loader-7.0.1.tgz",
-      "integrity": "sha512-VRviFEyYlLjctSM93gAZtcJJ/iSkPZ79zWbN/1fSH+NisBByEiVLqpdVDrPLVSi8DX0oJo12kL/GppTBdKVXiQ==",
+      "version": "7.0.2",
+      "resolved": "https://registry.npmjs.org/postcss-loader/-/postcss-loader-7.0.2.tgz",
+      "integrity": "sha512-fUJzV/QH7NXUAqV8dWJ9Lg4aTkDCezpTS5HgJ2DvqznexTbSTxgi/dTECvTZ15BwKTtk8G/bqI/QTu2HPd3ZCg==",
       "dev": true,
       "dependencies": {
         "cosmiconfig": "^7.0.0",
         "klona": "^2.0.5",
-        "semver": "^7.3.7"
+        "semver": "^7.3.8"
       },
       "engines": {
         "node": ">= 14.15.0"
@@ -8625,9 +8625,9 @@
       }
     },
     "node_modules/postcss-loader/node_modules/semver": {
-      "version": "7.3.7",
-      "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.7.tgz",
-      "integrity": "sha512-QlYTucUYOews+WeEujDoEGziz4K6c47V/Bd+LjSSYcA94p+DmINdf7ncaUinThfvZyu13lN9OY1XDxt8C0Tw0g==",
+      "version": "7.3.8",
+      "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz",
+      "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==",
       "dev": true,
       "dependencies": {
         "lru-cache": "^6.0.0"
@@ -14724,9 +14724,9 @@
       "integrity": "sha512-Z1PhmomIfypOpoMjRQB70jfvy/wxT50qW08YXO5lMIJkrdq4yOTR+AW7FqutScmB9NkLwxo+jU+kZLbofZZq/w=="
     },
     "d3": {
-      "version": "7.6.1",
-      "resolved": "https://registry.npmjs.org/d3/-/d3-7.6.1.tgz",
-      "integrity": "sha512-txMTdIHFbcpLx+8a0IFhZsbp+PfBBPt8yfbmukZTQFroKuFqIwqswF0qE5JXWefylaAVpSXFoKm3yP+jpNLFLw==",
+      "version": "7.7.0",
+      "resolved": "https://registry.npmjs.org/d3/-/d3-7.7.0.tgz",
+      "integrity": "sha512-VEwHCMgMjD2WBsxeRGUE18RmzxT9Bn7ghDpzvTEvkLSBAKgTMydJjouZTjspgQfRHpPt/PB3EHWBa6SSyFQq4g==",
       "requires": {
         "d3-array": "3",
         "d3-axis": "3",
@@ -15281,9 +15281,9 @@
       "integrity": "sha512-vbRorB5FUQWvla16U8R/qgaFIya2qGzwDrNmCZuYKrbdSUMG6I1ZCGQRefkRVhuOkIGVne7BQ35DSfo1qvJqFg=="
     },
     "eslint": {
-      "version": "8.28.0",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.28.0.tgz",
-      "integrity": "sha512-S27Di+EVyMxcHiwDrFzk8dJYAaD+/5SoWKxL1ri/71CRHsnJnRDPNt2Kzj24+MT9FDupf4aqqyqPrvI8MvQ4VQ==",
+      "version": "8.29.0",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.29.0.tgz",
+      "integrity": "sha512-isQ4EEiyUjZFbEKvEGJKKGBwXtvXX+zJbkVKCgTuB9t/+jUBcy8avhkEwWJecI15BkRkOYmvIM5ynbhRjEkoeg==",
       "dev": true,
       "requires": {
         "@eslint/eslintrc": "^1.3.3",
@@ -16955,9 +16955,9 @@
       "optional": true
     },
     "mini-css-extract-plugin": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.0.tgz",
-      "integrity": "sha512-auqtVo8KhTScMsba7MbijqZTfibbXiBNlPAQbsVt7enQfcDYLdgG57eGxMqwVU3mfeWANY4F1wUg+rMF+ycZgw==",
+      "version": "2.7.1",
+      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.1.tgz",
+      "integrity": "sha512-viOoaUFy+Z2w43VsGPbtfwFrr0tKwDctK9dUofG5MBViYhD1noGFUzzDIVw0KPwCGUP+c7zqLxm+acuQs7zLzw==",
       "dev": true,
       "requires": {
         "schema-utils": "^4.0.0"
@@ -17655,9 +17655,9 @@
       }
     },
     "postcss-import": {
-      "version": "15.0.0",
-      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.0.0.tgz",
-      "integrity": "sha512-Y20shPQ07RitgBGv2zvkEAu9bqvrD77C9axhj/aA1BQj4czape2MdClCExvB27EwYEJdGgKZBpKanb0t1rK2Kg==",
+      "version": "15.0.1",
+      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.0.1.tgz",
+      "integrity": "sha512-UGlvk8EgT7Gm/Ndf9xZHnzr8xm8P54N8CBWLtcY5alP+YxlEge/Rv78etQyevZs3qWTE9If13+Bo6zATBrPOpA==",
       "dev": true,
       "requires": {
         "postcss-value-parser": "^4.0.0",
@@ -17683,20 +17683,20 @@
       }
     },
     "postcss-loader": {
-      "version": "7.0.1",
-      "resolved": "https://registry.npmjs.org/postcss-loader/-/postcss-loader-7.0.1.tgz",
-      "integrity": "sha512-VRviFEyYlLjctSM93gAZtcJJ/iSkPZ79zWbN/1fSH+NisBByEiVLqpdVDrPLVSi8DX0oJo12kL/GppTBdKVXiQ==",
+      "version": "7.0.2",
+      "resolved": "https://registry.npmjs.org/postcss-loader/-/postcss-loader-7.0.2.tgz",
+      "integrity": "sha512-fUJzV/QH7NXUAqV8dWJ9Lg4aTkDCezpTS5HgJ2DvqznexTbSTxgi/dTECvTZ15BwKTtk8G/bqI/QTu2HPd3ZCg==",
       "dev": true,
       "requires": {
         "cosmiconfig": "^7.0.0",
         "klona": "^2.0.5",
-        "semver": "^7.3.7"
+        "semver": "^7.3.8"
       },
       "dependencies": {
         "semver": {
-          "version": "7.3.7",
-          "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.7.tgz",
-          "integrity": "sha512-QlYTucUYOews+WeEujDoEGziz4K6c47V/Bd+LjSSYcA94p+DmINdf7ncaUinThfvZyu13lN9OY1XDxt8C0Tw0g==",
+          "version": "7.3.8",
+          "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz",
+          "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==",
           "dev": true,
           "requires": {
             "lru-cache": "^6.0.0"
diff --git a/package.json b/package.json
index 0020352adf..01856ad569 100644
--- a/package.json
+++ b/package.json
@@ -8,7 +8,7 @@
     "@sfgrp/svg-radial-menu": "^1.0.7",
     "axios": "^1.2.0",
     "chart.js": "^4.0.1",
-    "d3": "^7.6.1",
+    "d3": "^7.7.0",
     "dompurify": "^2.4.1",
     "easymde": "^2.18.0",
     "exif-js": "^2.3.0",
@@ -47,7 +47,7 @@
     "compression-webpack-plugin": "^10.0.0",
     "css-loader": "^6.7.2",
     "css-minimizer-webpack-plugin": "^4.2.2",
-    "eslint": "^8.28.0",
+    "eslint": "^8.29.0",
     "eslint-config-standard": "^17.0.0",
     "eslint-plugin-import": "^2.26.0",
     "eslint-plugin-n": "^15.5.1",
@@ -55,11 +55,11 @@
     "eslint-plugin-promise": "^6.1.1",
     "eslint-plugin-standard": "^4.1.0",
     "eslint-plugin-vue": "^9.8.0",
-    "mini-css-extract-plugin": "^2.7.0",
+    "mini-css-extract-plugin": "^2.7.1",
     "postcss": "^8.4.19",
     "postcss-flexbugs-fixes": "^5.0.2",
-    "postcss-import": "^15.0.0",
-    "postcss-loader": "^7.0.1",
+    "postcss-import": "^15.0.1",
+    "postcss-loader": "^7.0.2",
     "postcss-preset-env": "^7.8.3",
     "raw-loader": "^4.0.2",
     "resolve-url-loader": "^5.0.0",

From e10ff5969b98929d71f21bad22a7ea79ebbc9373 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Tue, 6 Dec 2022 12:59:13 -0600
Subject: [PATCH 091/160] fixes #3142

---
 CHANGELOG.md                           |  1 +
 app/models/protonym.rb                 | 34 ++++++++++++++++++++++++--
 lib/queries/repository/autocomplete.rb |  4 +--
 lib/queries/serial/autocomplete.rb     | 16 ++++++------
 lib/queries/source/autocomplete.rb     |  5 ++--
 5 files changed, 46 insertions(+), 14 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 14d4edb4fa..c9865d6389 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Serial facet to Filter sources [#3211]
 
 ### Fixed
+- Source in n project autocopmlete response [#3142]
 - 'Also create OTU' on batch taxon name upload causing raise
 - Media observations removed if they have no more depictions via updates
 - Citation link in Biological association panel on Browse OTU
diff --git a/app/models/protonym.rb b/app/models/protonym.rb
index 9308ad0c9a..731c5a8eca 100644
--- a/app/models/protonym.rb
+++ b/app/models/protonym.rb
@@ -423,6 +423,36 @@ def number_of_taxa_by_year
     end
   end
 
+  # temporary method to collect soft_validations on protonyms
+  def soft_validations_by_protonym
+    exclude = [ 'Confidence level is missing',
+                'Primary type is not selected',
+                'Etymology is missing',
+                'Cached values should be updated',
+                'Part of speech is not specified. Please select if the name is a noun or an adjective.'
+    ].freeze
+    file_name = '/tmp/soft_validations' + '_' + Time.now.to_i.to_s + '.csv'
+    a = {}
+    i = 0
+    j = 0
+    CSV.open(file_name, 'w') do |csv|
+      csv << ['taxon_name_id', 'name', 'author_year', 'type', 'is_valid', 'soft_validations']
+      descendants.find_each do |t|
+        i += 1
+        print "\r#{i}     Soft validations: #{j}"
+        t.soft_validate
+        z = t.soft_validations.messages
+        exclude.each do |e|
+          z.delete(e)
+        end
+        unless z.empty?
+          j += 1
+          csv << [t.id.to_s, t.cached, t.cached_author_year, t.type.to_s, t.cached_is_valid.to_s, z]
+        end
+      end
+    end
+  end
+
   # !! TODO: Should not be possible- fix the incoming data
   # @return [Boolean]
   #    true if taxon2 has the same primary type
@@ -555,8 +585,8 @@ def name_with_alternative_spelling
       n = n[0..-3] + 'ra' if n =~ /^[a-z]*er$/ # -er > -ra
       n = n[0..-7] + 'ensis' if n =~ /^[a-z]*iensis$/ # -iensis > -ensis
       n = n[0..-5] + 'ana' if n =~ /^[a-z]*iana$/ # -iana > -ana
-      n = n.gsub('ae', 'e').
-            gsub('oe', 'e').
+      n = n.gsub('ae', 'e') if n =~ /^[a-z]*ae[a-z]+$/ # -ae-
+      n = n.gsub('oe', 'e')
             gsub('ai', 'i').
             gsub('ei', 'i').
             gsub('ej', 'i').
diff --git a/lib/queries/repository/autocomplete.rb b/lib/queries/repository/autocomplete.rb
index 45a2055b9a..ca56f1c127 100644
--- a/lib/queries/repository/autocomplete.rb
+++ b/lib/queries/repository/autocomplete.rb
@@ -64,11 +64,11 @@ def autocomplete
         a = q
         if project_id && scope
           # TODO: there are now 2 repository references, see also current_repository_id
-          a = a.select('repositories.*, COUNT(collection_objects.id) AS use_count, NULLIF(collection_objects.project_id, NULL) as in_project')
+          a = a.select("repositories.*, COUNT(collection_objects.id) AS use_count, CASE WHEN collection_objects.project_id = #{Current.project_id} THEN collection_objects.project_id ELSE NULL END AS in_project")
             .left_outer_joins(:collection_objects)
             .where('collection_objects.project_id = ? OR collection_objects.project_id IS DISTINCT FROM ?', project_id, project_id)
             .group('repositories.id, collection_objects.project_id')
-            .order('use_count DESC')
+            .order('in_project, use_count DESC')
         end
 
         a ||= q
diff --git a/lib/queries/serial/autocomplete.rb b/lib/queries/serial/autocomplete.rb
index e90c4cebdb..077060ed82 100644
--- a/lib/queries/serial/autocomplete.rb
+++ b/lib/queries/serial/autocomplete.rb
@@ -1,5 +1,5 @@
 module Queries
-  module Serial 
+  module Serial
     class Autocomplete < Queries::Query
 
       # @param [Hash] args
@@ -11,7 +11,7 @@ def initialize(string, project_id: nil)
       def base_query
         ::Serial.select('serials.*')
       end
- 
+
       # @return [Array]
       def autocomplete
         queries = [
@@ -38,12 +38,12 @@ def autocomplete
           a = q
           if project_id
             # a = q.joins(:project_sources).where(member_of_project_id.to_sql) if project_id && limit_to_project
-            a = a.select('serials.*, COUNT(project_sources.source_id) AS use_count, NULLIF(project_sources.project_id, NULL) as in_project')
+            a = a.select("serials.*, COUNT(project_sources.source_id) AS use_count, CASE WHEN project_sources.project_id = #{Current.project_id} THEN project_sources.project_id ELSE NULL END AS in_project")
                  .left_outer_joins(:sources)
                  .joins('LEFT OUTER JOIN project_sources ON sources.id = project_sources.source_id')
                  .where('project_sources.project_id = ? OR project_sources.project_id IS DISTINCT FROM ?', project_id, project_id)
                  .group('serials.id, project_sources.project_id')
-                 .order('use_count DESC')
+                 .order('in_project, use_count DESC')
           end
           a ||= q
           updated_queries[i] = a
@@ -63,16 +63,16 @@ def autocomplete
       end
 
       # @return [ActiveRecord::Relation]
-      #    match exact name 
+      #    match exact name
       def autocomplete_exact_name
-        a = table[:name].eq(query_string) 
+        a = table[:name].eq(query_string)
         base_query.where(a.to_sql).limit(20)
       end
 
       # @return [ActiveRecord::Relation]
       #    match begining of name
       def autocomplete_begining_name
-        a = table[:name].matches(query_string + '%') 
+        a = table[:name].matches(query_string + '%')
         base_query.where(a.to_sql).limit(20)
       end
 
@@ -113,7 +113,7 @@ def autocomplete_begining_alternate_value(attribute = 'name', type = 'AlternateV
       #      .on(table[:id].eq(alternate_value_table[:alternate_value_object_id]).and(
       #        alternate_value_table[:alternate_value_object_type].eq('Serial')
       #      )
-      #    ) 
+      #    )
       #  end
 
       # @return [Arel::Table]
diff --git a/lib/queries/source/autocomplete.rb b/lib/queries/source/autocomplete.rb
index e48940102d..0527955f25 100644
--- a/lib/queries/source/autocomplete.rb
+++ b/lib/queries/source/autocomplete.rb
@@ -241,11 +241,12 @@ def autocomplete
           # Order results by number of times used *in this project*
           if project_id && scope
             a = a.left_outer_joins(:citations)
-              .select('sources.*, COUNT(citations.id) AS use_count, NULLIF(citations.project_id, NULL) as in_project')
+              .select("sources.*, COUNT(citations.id) AS use_count, CASE WHEN citations.project_id = #{Current.project_id} THEN citations.project_id ELSE NULL END AS in_project")
               .where('citations.project_id = ? OR citations.project_id IS DISTINCT FROM ?', project_id, project_id)
               .group('sources.id, citations.project_id')
-              .order('use_count DESC')
+              .order('in_project, use_count DESC')
           end
+
           a ||= q
           result += a.to_a
           result.uniq!

From d1150e563f2cadf327b64a9e89ee90ea4a4269ca Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Tue, 6 Dec 2022 13:10:13 -0600
Subject: [PATCH 092/160] typo fix

---
 app/models/protonym.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/protonym.rb b/app/models/protonym.rb
index 731c5a8eca..19a4f88644 100644
--- a/app/models/protonym.rb
+++ b/app/models/protonym.rb
@@ -586,7 +586,7 @@ def name_with_alternative_spelling
       n = n[0..-7] + 'ensis' if n =~ /^[a-z]*iensis$/ # -iensis > -ensis
       n = n[0..-5] + 'ana' if n =~ /^[a-z]*iana$/ # -iana > -ana
       n = n.gsub('ae', 'e') if n =~ /^[a-z]*ae[a-z]+$/ # -ae-
-      n = n.gsub('oe', 'e')
+      n = n.gsub('oe', 'e').
             gsub('ai', 'i').
             gsub('ei', 'i').
             gsub('ej', 'i').

From 8db77f18ee2a64062d82bd470e09e0014e8dab5a Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 6 Dec 2022 16:46:15 -0300
Subject: [PATCH 093/160] Fix #3067

---
 CHANGELOG.md                                                  | 1 +
 .../new_taxon_name/components/pickOriginalCombination.vue     | 4 +---
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c9865d6389..e47d2f3c80 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Sqed processing failing to encode HEIC images [#3188]
 - Common list component doesn't filter created status on New taxon name task [#3205]
 - Collectors facet doesn't work on Filter collecting event [#3216]
+- original combination label disappears when relationship doesn't include the current taxon name [#3067]
 
 ### Changed
 - "TODO list" now a faceted search [#3171]
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/pickOriginalCombination.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/pickOriginalCombination.vue
index fd40081fa3..216eacd6f1 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/pickOriginalCombination.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/pickOriginalCombination.vue
@@ -151,9 +151,7 @@ export default {
     },
 
     existOriginalCombination () {
-      const combinations = Object.values(this.originalCombinations)
-
-      return !!combinations.find(combination => combination?.subject_taxon_name_id === this.taxon?.id)
+      return !!Object.values(this.originalCombinations).length
     },
 
     types () {

From 60e792985ed8d5b8771c23cc54903e669b89f7fb Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Tue, 6 Dec 2022 15:59:15 -0600
Subject: [PATCH 094/160] additional soft_validations, fixes #3185

---
 CHANGELOG.md                                  |  1 +
 app/models/combination.rb                     | 27 ++++++++--
 .../protonym/soft_validation_extensions.rb    | 53 ++++++++++---------
 .../iczn/unavailable/excluded.rb              |  4 ++
 app/models/taxon_name_relationship/iczn.rb    |  4 +-
 .../iczn/invalidating.rb                      |  4 ++
 .../iczn/invalidating/homonym.rb              |  7 +--
 .../iczn/invalidating/misapplication.rb       |  7 ++-
 .../iczn/invalidating/synonym.rb              |  3 +-
 .../iczn/invalidating/usage.rb                |  3 +-
 .../taxon_name_relationship/typification.rb   |  6 +++
 11 files changed, 84 insertions(+), 35 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e47d2f3c80..71d6da8965 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- Added softvalidation for dublicate family group name forms and misspellings [#3185]
 - With/out local identifier facet for collection objects and stagd images [#3173]
 - Filter by housekeeping and staged-image data attributes [#3171]
 - Delete selected collection objects (and their related data) from filter [#3174]
diff --git a/app/models/combination.rb b/app/models/combination.rb
index e6a164aac0..9bdb36a3fb 100644
--- a/app/models/combination.rb
+++ b/app/models/combination.rb
@@ -57,7 +57,7 @@
 #
 class Combination < TaxonName
 
-  # The ranks that can be used to build combinations.  
+  # The ranks that can be used to build combinations.
   APPLICABLE_RANKS = %w{genus subgenus section subsection series subseries species subspecies variety subvariety form subform}.freeze
 
   before_validation :set_parent
@@ -127,7 +127,7 @@ class Combination < TaxonName
     }, through: "#{rank}_taxon_name_relationship".to_sym, source: :subject_taxon_name
 
     accepts_nested_attributes_for rank.to_sym
-    
+
     accepts_nested_attributes_for "#{rank}_taxon_name_relationship".to_sym, allow_destroy: true
 
     attr_accessor "#{rank}_id".to_sym
@@ -192,6 +192,13 @@ class Combination < TaxonName
     name: 'Combination has valid parent',
     description: 'The combination should have the same parent as protonym' )
 
+  soft_validate(
+    :sv_author_and_year_is_not_required,
+    set: :year_is_not_required,
+    fix: :sv_fix_author_and_year_is_not_required,
+    name: 'Verbatim author and year are not required',
+    description: 'Verbatim author and year are not required. The Fix will delete both' )
+
   # @return [Protonym Scope]
   # @params protonym_ids [Hash] like `{genus: 4, species: 5}`
   #   the absence of _id in the keys in part reflects integration with Biodiversity gem
@@ -437,7 +444,7 @@ def sv_year_of_publication_not_older_than_protonyms
   end
 
   def sv_combination_duplicates
-    duplicate = Combination.not_self(self).where(cached: cached)
+    duplicate = Combination.not_self(self).where(cached: cached, cached_author_year: cached_author_year)
     soft_validations.add(:base, 'Combination is a duplicate') unless duplicate.empty?
   end
 
@@ -482,6 +489,20 @@ def sv_cached_names
       failure_message:  'Failed to update cached values') if !is_cached
   end
 
+  def sv_author_and_year_is_not_required
+    if !self.year_of_publication.nil? || !self.verbatim_author.nil?
+      soft_validations.add(
+        :base, 'Verbatim author and year of publication are not required, they both derive from the source',
+        success_message: 'Verbatim author and year were deleted',
+        failure_message: 'Failed to delete verbatim author and year')
+    end
+  end
+
+  def sv_fix_author_and_year_is_not_required
+    self.update_columns(year_of_publication: nil, verbatim_author: nil)
+    return true
+  end
+
   def set_parent
     names = protonyms
     write_attribute(:parent_id, names.first.parent.id) if names.count > 0 && names.first.parent
diff --git a/app/models/protonym/soft_validation_extensions.rb b/app/models/protonym/soft_validation_extensions.rb
index 4739f148fe..8c74276b6e 100644
--- a/app/models/protonym/soft_validation_extensions.rb
+++ b/app/models/protonym/soft_validation_extensions.rb
@@ -1,5 +1,5 @@
 module Protonym::SoftValidationExtensions
-  
+
   module Klass
     VALIDATIONS = {
       sv_validate_name: {
@@ -39,6 +39,12 @@ module Klass
         description: 'Detect potential homonyms or duplicates in the species-group names'
       },
 
+      sv_potential_usage_duplicates: {
+        set: :potential_usage_duplicates,
+        name: 'Potential usage duplicates',
+        description: 'Detect duplicate name usage (misspelling, family group name form).'
+      },
+
       sv_missing_original_genus: {
         set: :missing_relationships,
         name: 'Missing original genus',
@@ -563,7 +569,7 @@ def sv_species_gender_agreement_not_required
     #    end
 
     def sv_validate_coordinated_names_source
-      return true unless is_available?
+      return true unless is_valid?
       s = self.source
       list_of_coordinated_names.each do |t|
         if ((s && t.source && s.id != t.source.id) || (s.nil? && t.source))
@@ -597,7 +603,7 @@ def sv_fix_coordinated_names_source
     end
 
     def sv_validate_coordinated_names_page
-      return true unless is_available?
+      return true unless is_valid?
       s = self.origin_citation
       list_of_coordinated_names.each do |t|
         ts = t.origin_citation
@@ -708,7 +714,7 @@ def sv_fix_coordinated_names_part_of_speech
     end
 
     def sv_validate_coordinated_names_original_genus
-      return true if !is_genus_or_species_rank? || !is_available?
+      return true if !is_genus_or_species_rank? || !is_valid?
       list_of_coordinated_names.each do |t|
         if self.original_genus.try(:name) != t.original_genus.try(:name)
           soft_validations.add(:base, "The original genus does not match with the original genus of coordinate #{t.rank_class.rank_name}", success_message: 'Original genus was updated', failure_message:  'Failed to update original genus')
@@ -888,7 +894,7 @@ def sv_fix_coordinated_names_original_form
     end
 
     def sv_validate_coordinated_names_type_species
-      return true unless is_available?
+      return true unless is_valid?
       return true unless is_genus_rank?
       list_of_coordinated_names.each do |t|
         if self.type_species != t.type_species
@@ -950,7 +956,7 @@ def sv_fix_coordinated_names_etymology
     end
 
     def sv_validate_coordinated_names_roles
-      return true unless is_available?
+      return true unless is_valid?
       list_of_coordinated_names.each do |t|
         if self.taxon_name_author_roles.collect{|i| i.person_id} != t.taxon_name_author_roles.collect{|i| i.person_id}
           soft_validations.add(:base, "The author roles do not match with the author roles of the coordinate #{t.rank_class.rank_name}", success_message: 'Author roles were updated', failure_message:  'Author roles were not updated')
@@ -1007,7 +1013,7 @@ def sv_fix_coordinated_names_type_species_type
     end
 
     def sv_validate_coordinated_names_type_genus
-      return true unless is_available?
+      return true unless is_valid?
       return true unless is_family_rank?
       list_of_coordinated_names.each do |t|
         if self.type_genus != t.type_genus
@@ -1038,7 +1044,7 @@ def sv_fix_coordinated_names_type_genus
     end
 
     def sv_validate_coordinated_names_type_specimen
-      return true if !is_species_rank? || !is_available?
+      return true if !is_species_rank? || !is_valid?
       list_of_coordinated_names.each do |t|
         if !self.has_same_primary_type(t)
           soft_validations.add(:base, "The type specimen does not match with the type specimen of the coordinate #{t.rank_class.rank_name}", success_message: 'Type specimen was updated', failure_message:  'Failed to update type specimen')
@@ -1346,23 +1352,14 @@ def sv_potential_family_homonyms
       if persisted? && is_family_rank? && is_available?
         if TaxonNameRelationship.where_subject_is_taxon_name(self).homonym_or_suppressed.empty?
           if self.id == self.lowest_rank_coordinated_taxon.id
-#            name1 = self.cached_primary_homonym ? self.cached_primary_homonym : nil
-#            possible_primary_homonyms = name1 ? Protonym.with_primary_homonym(name1).without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).without_homonym_or_suppressed.not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::FamilyGroup').with_project(self.project_id) : []
-#            list1 = reduce_list_of_synonyms(possible_primary_homonyms)
-#            if !list1.empty?
-#              list1.each do |s|
-#                soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}")
-#              end
-#            else
-              name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
-              possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::FamilyGroup').with_project(self.project_id) : []
-              list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
-              if !list2.empty?
-                list2.each do |s|
-                  soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}")
-                end
+            name2 = self.cached_primary_homonym_alternative_spelling ? self.cached_primary_homonym_alternative_spelling : nil
+            possible_primary_homonyms_alternative_spelling = name2 ? Protonym.with_primary_homonym_alternative_spelling(name2).without_homonym_or_suppressed.without_taxon_name_classification_array(TAXON_NAME_CLASS_NAMES_UNAVAILABLE_AND_INVALID).not_self(self).with_base_of_rank_class('NomenclaturalRank::Iczn::FamilyGroup').with_project(self.project_id) : []
+            list2 = reduce_list_of_synonyms(possible_primary_homonyms_alternative_spelling)
+            if !list2.empty?
+              list2.each do |s|
+                soft_validations.add(:base, "Missing relationship: #{self.cached_html_name_and_author_year} should be a homonym or duplicate of #{s.cached_html_name_and_author_year}")
               end
- #           end
+            end
           end
         end
       end
@@ -1638,6 +1635,14 @@ def sv_fix_missing_otu
       return false
     end
 
+    def sv_potential_usage_duplicates
+      usage = TaxonNameRelationship::Iczn::Invalidating::Usage.where(subject_taxon_name_id: self.id).first
+      TaxonNameRelationship::Iczn::Invalidating::Usage.where(object_taxon_name_id: usage.object_taxon_name_id).not_self(usage).each do |tr|
+        soft_validations.add(:base, "'#{name}' is a dubplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.object_taxon_name.name == tr.object_taxon_name.name
+      end
+    end
+
+
     def sv_presence_of_combination
       if is_genus_or_species_rank? && is_valid? && self.id == self.lowest_rank_coordinated_taxon.id && !cached_original_combination.nil? && cached != cached_original_combination
         unless Combination.where("cached = ? AND cached_valid_taxon_name_id = ?", cached, cached_valid_taxon_name_id).any?
diff --git a/app/models/taxon_name_classification/iczn/unavailable/excluded.rb b/app/models/taxon_name_classification/iczn/unavailable/excluded.rb
index a3c22992fc..8fbe966699 100644
--- a/app/models/taxon_name_classification/iczn/unavailable/excluded.rb
+++ b/app/models/taxon_name_classification/iczn/unavailable/excluded.rb
@@ -100,6 +100,10 @@ class NotForNomenclature < TaxonNameClassification::Iczn::Unavailable::Excluded
 
     extend InnerClass
 
+    def label
+      'not in published work'
+    end
+
     def classification_label
       'excluded: not in published work'
     end
diff --git a/app/models/taxon_name_relationship/iczn.rb b/app/models/taxon_name_relationship/iczn.rb
index 4a322a5422..f6fa8234be 100644
--- a/app/models/taxon_name_relationship/iczn.rb
+++ b/app/models/taxon_name_relationship/iczn.rb
@@ -19,8 +19,8 @@ def self.disjoint_subject_classes
   end
 
   def self.disjoint_object_classes
-    ICN_TAXON_NAME_CLASSIFICATION_NAMES + ICNP_TAXON_NAME_CLASSIFICATION_NAMES +
-        self.collect_descendants_and_itself_to_s(TaxonNameClassification::Iczn::Unavailable)
+    ICN_TAXON_NAME_CLASSIFICATION_NAMES + ICNP_TAXON_NAME_CLASSIFICATION_NAMES + ICVCN_TAXON_NAME_CLASSIFICATION_NAMES +
+      self.collect_descendants_and_itself_to_s(TaxonNameClassification::Iczn::Unavailable)
   end
 
   def sv_validate_priority
diff --git a/app/models/taxon_name_relationship/iczn/invalidating.rb b/app/models/taxon_name_relationship/iczn/invalidating.rb
index 4eab7622f2..0281dfd252 100644
--- a/app/models/taxon_name_relationship/iczn/invalidating.rb
+++ b/app/models/taxon_name_relationship/iczn/invalidating.rb
@@ -13,6 +13,10 @@ def self.disjoint_subject_classes
         self.collect_to_s(TaxonNameClassification::Iczn::Available)
   end
 
+  def self.disjoint_object_classes
+    ICN_TAXON_NAME_CLASSIFICATION_NAMES + ICNP_TAXON_NAME_CLASSIFICATION_NAMES + ICVCN_TAXON_NAME_CLASSIFICATION_NAMES
+  end
+
   def self.nomenclatural_priority
     :direct
   end
diff --git a/app/models/taxon_name_relationship/iczn/invalidating/homonym.rb b/app/models/taxon_name_relationship/iczn/invalidating/homonym.rb
index ceb3ec3a92..764b591fad 100644
--- a/app/models/taxon_name_relationship/iczn/invalidating/homonym.rb
+++ b/app/models/taxon_name_relationship/iczn/invalidating/homonym.rb
@@ -35,9 +35,10 @@ def self.disjoint_taxon_name_relationships
 
   end
 
-#  def self.disjoint_object_classes
-#    self.parent.disjoint_object_classes
-#  end
+  def self.disjoint_object_classes
+    self.parent.disjoint_object_classes +
+      self.collect_descendants_and_itself_to_s(TaxonNameClassification::Iczn::Unavailable)
+  end
 
   def subject_properties
     [ TaxonNameClassification::Iczn::Available::Invalid::Homonym ]
diff --git a/app/models/taxon_name_relationship/iczn/invalidating/misapplication.rb b/app/models/taxon_name_relationship/iczn/invalidating/misapplication.rb
index 1b868a99b4..d19f5e550f 100644
--- a/app/models/taxon_name_relationship/iczn/invalidating/misapplication.rb
+++ b/app/models/taxon_name_relationship/iczn/invalidating/misapplication.rb
@@ -8,6 +8,11 @@ def self.disjoint_taxon_name_relationships
                                       TaxonNameRelationship::Iczn::Invalidating::Homonym)
   end
 
+  def self.disjoint_object_classes
+    self.parent.disjoint_object_classes +
+      self.collect_descendants_and_itself_to_s(TaxonNameClassification::Iczn::Unavailable)
+  end
+
   def subject_properties
     [ TaxonNameClassification::Iczn::Unavailable ]
   end
@@ -46,4 +51,4 @@ def self.nomenclatural_priority
   def sv_not_specific_relationship
     true
   end
-end
\ No newline at end of file
+end
diff --git a/app/models/taxon_name_relationship/iczn/invalidating/synonym.rb b/app/models/taxon_name_relationship/iczn/invalidating/synonym.rb
index f75427f3a6..13abd37ecc 100644
--- a/app/models/taxon_name_relationship/iczn/invalidating/synonym.rb
+++ b/app/models/taxon_name_relationship/iczn/invalidating/synonym.rb
@@ -17,7 +17,8 @@ def self.disjoint_taxon_name_relationships
 
   def self.disjoint_object_classes
     self.parent.disjoint_object_classes +
-        self.collect_descendants_and_itself_to_s(TaxonNameClassification::Iczn::Available::Invalid)
+        self.collect_descendants_and_itself_to_s(TaxonNameClassification::Iczn::Unavailable,
+                                                 TaxonNameClassification::Iczn::Available::Invalid)
   end
 
   def object_status
diff --git a/app/models/taxon_name_relationship/iczn/invalidating/usage.rb b/app/models/taxon_name_relationship/iczn/invalidating/usage.rb
index 89c70b4b6a..73654382ae 100644
--- a/app/models/taxon_name_relationship/iczn/invalidating/usage.rb
+++ b/app/models/taxon_name_relationship/iczn/invalidating/usage.rb
@@ -28,4 +28,5 @@ def sv_not_specific_relationship
   def sv_synonym_relationship
     true
   end
-end
\ No newline at end of file
+
+end
diff --git a/app/models/taxon_name_relationship/typification.rb b/app/models/taxon_name_relationship/typification.rb
index ba92d944c2..c949fcf2f6 100644
--- a/app/models/taxon_name_relationship/typification.rb
+++ b/app/models/taxon_name_relationship/typification.rb
@@ -34,4 +34,10 @@ def object_status_connector_to_subject
   def sv_coordinated_taxa_object
     true # not applicable
   end
+
+  def sv_specific_relationship
+    unless self.object_taxon_name.is_available?
+      soft_validations.add(:object_taxon_name_id, "'#{self.object_taxon_name.cached_html}' is not an available name, it should not have typification relationship")
+    end
+  end
 end

From 9ee302250515e484eef2602e67e66917a0b0893e Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Tue, 6 Dec 2022 20:57:24 -0600
Subject: [PATCH 095/160] additional soft_validations

---
 app/models/protonym/soft_validation_extensions.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/models/protonym/soft_validation_extensions.rb b/app/models/protonym/soft_validation_extensions.rb
index 8c74276b6e..d8f7ca7deb 100644
--- a/app/models/protonym/soft_validation_extensions.rb
+++ b/app/models/protonym/soft_validation_extensions.rb
@@ -1637,6 +1637,7 @@ def sv_fix_missing_otu
 
     def sv_potential_usage_duplicates
       usage = TaxonNameRelationship::Iczn::Invalidating::Usage.where(subject_taxon_name_id: self.id).first
+      return true if usage.nil?
       TaxonNameRelationship::Iczn::Invalidating::Usage.where(object_taxon_name_id: usage.object_taxon_name_id).not_self(usage).each do |tr|
         soft_validations.add(:base, "'#{name}' is a dubplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.object_taxon_name.name == tr.object_taxon_name.name
       end

From 2575846ebfd3a695b38bd5e013aecca6cb371330 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Wed, 7 Dec 2022 10:01:38 -0600
Subject: [PATCH 096/160] fixes #3139

---
 CHANGELOG.md      |  1 +
 app/models/otu.rb | 12 ++++++------
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 71d6da8965..9dc8132c46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Serial facet to Filter sources [#3211]
 
 ### Fixed
+- OTU smart selector did not include items from the pinboard [#3139]
 - Source in n project autocopmlete response [#3142]
 - 'Also create OTU' on batch taxon name upload causing raise
 - Media observations removed if they have no more depictions via updates
diff --git a/app/models/otu.rb b/app/models/otu.rb
index ceae0f2046..ab6a0190fd 100644
--- a/app/models/otu.rb
+++ b/app/models/otu.rb
@@ -68,7 +68,7 @@ class Otu < ApplicationRecord
   has_many :collecting_events, -> { distinct }, through: :collection_objects
   has_many :common_names, dependent: :destroy
   has_many :collection_profiles, dependent: :restrict_with_error  # @proceps dependent: what? DD: profile should never be update, a new profile should be created insted
-  
+
   has_many :contents, inverse_of: :otu, dependent: :destroy
   has_many :public_contents, inverse_of: :otu, dependent: :destroy
 
@@ -135,7 +135,7 @@ def self.coordinate_otus(otu_id)
     end
   end
 
-  # TODO: This is coordinate otus with children, 
+  # TODO: This is coordinate otus with children,
   #       It should probably be renamed coordinate
   # @return [Otu::ActiveRecordRelation]
   #   all OTUs linked to the taxon_name_id, it descendants, and
@@ -254,7 +254,7 @@ def self.select_optimized(user_id, project_id, target = nil)
     r = used_recently(user_id, project_id, target)
     h = {
       quick: [],
-      pinboard: Otu.pinned_by(user_id).where(project_id: project_id).to_a,
+      pinboard: Otu.pinned_by(user_id).where(pinboard_items: {project_id: project_id}).to_a,
       recent: []
     }
 
@@ -266,11 +266,11 @@ def self.select_optimized(user_id, project_id, target = nil)
         .limit(3).to_a
       ).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
       h[:quick] = (
-        Otu.pinned_by(user_id).pinboard_inserted.where(project_id: project_id).to_a +
+        Otu.pinned_by(user_id).where(pinboard_items: {project_id: project_id}).to_a +
         Otu.where('"otus"."id" IN (?)', r.first(4) ).to_a).uniq.sort{|a,b| a.otu_name <=> b.otu_name}
     else
       h[:recent] = Otu.where(project_id: project_id).order('updated_at DESC').limit(10).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
-      h[:quick] = Otu.pinned_by(user_id).pinboard_inserted.where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
+      h[:quick] = Otu.pinned_by(user_id).where(pinboard_items: {project_id: project_id}).to_a.sort{|a,b| a.otu_name <=> b.otu_name}
     end
 
     h
@@ -312,7 +312,7 @@ def coordinate_otus_with_children
     if taxon_name_id.nil?
       Otu.coordinate_otus(id)
     else
-      Otu.descendant_of_taxon_name(taxon_name.valid_taxon_name.id)     
+      Otu.descendant_of_taxon_name(taxon_name.valid_taxon_name.id)
     end
   end
 

From 7164e6bcc1b41bdbcf36f1d40f5d279f9f629f3d Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 7 Dec 2022 19:43:35 -0300
Subject: [PATCH 097/160] Update spec

---
 .../tasks/content/content_editor_spec.rb      | 20 ++++++-------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/spec/features/tasks/content/content_editor_spec.rb b/spec/features/tasks/content/content_editor_spec.rb
index 5aa81fc78b..2741041437 100644
--- a/spec/features/tasks/content/content_editor_spec.rb
+++ b/spec/features/tasks/content/content_editor_spec.rb
@@ -1,29 +1,21 @@
 require 'rails_helper'
 
 describe 'Content editor' do
-  let(:index_path) { '/tasks/content/editor/index' }
-  it_behaves_like 'a_login_required_controller'
+  context 'when signed in and a project is selected' do
+    before { sign_in_user_and_select_project}
 
-  context 'Test new topic' do
-    before {
-      sign_in_user_and_select_project
-    }
+    context 'when I visit the task page', js: true do
+      before { visit index_editor_task_path }
 
-    context 'create new topic', js: true do
-      before {
-        visit index_editor_task_path
-      }
       specify 'can create new topic' do
         click_button('Topic')
         click_button('Create new')
-        expect(page).to have_content('New topic')
+        expect(page).to have_text('New topic')
         fill_in 'Name', with: 'Testing topic'
         fill_in 'Definition', with: 'Testing, making sure this is long enough'
         click_button('Create')
-        expect(page).to have_content('Testing topic was successfully created.')
+        expect(page).to have_text('Testing topic was successfully created.')
       end
     end
   end
 end
-
-

From a13932c646a262908714d13fa62065d48abe41ff Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Thu, 8 Dec 2022 11:07:22 -0600
Subject: [PATCH 098/160] observation matrices helper error

---
 app/helpers/observation_matrix_rows_helper.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/helpers/observation_matrix_rows_helper.rb b/app/helpers/observation_matrix_rows_helper.rb
index c78f5a4d9c..966bc20c9a 100644
--- a/app/helpers/observation_matrix_rows_helper.rb
+++ b/app/helpers/observation_matrix_rows_helper.rb
@@ -22,7 +22,7 @@ def observation_matrix_row_label_tnt(observation_matrix_row)
     return observation_matrix_row.name unless observation_matrix_row.name.blank?
     o = observation_matrix_row.observation_object
     s = label_for(o)
-    s.gsub!(/[^\w]/, '_').gsub('__', '_')
+    s.gsub!(/[^\w]/, '_').to_s.gsub!('__', '_')
     #s[0..11] + "_#{o.id}"
   end
 
@@ -30,7 +30,7 @@ def observation_matrix_row_label_nexus(observation_matrix_row)
     return observation_matrix_row.name unless observation_matrix_row.name.blank?
     o = observation_matrix_row.observation_object
     s = label_for(o)
-    s.gsub!(/[^\w]/, '_').gsub('__', '_')
+    s.gsub!(/[^\w]/, '_').to_s.gsub!('__', '_')
   end
 
   def observation_matrix_row_label_nexml(observation_matrix_row)

From 59017216633aa7f9a55f0bf3dabe58e516c95d60 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 8 Dec 2022 15:34:34 -0300
Subject: [PATCH 099/160] Prevent duplicate shortcuts.

---
 app/assets/javascripts/workbench/keyboard.js | 50 +++++++++++++-------
 1 file changed, 32 insertions(+), 18 deletions(-)

diff --git a/app/assets/javascripts/workbench/keyboard.js b/app/assets/javascripts/workbench/keyboard.js
index 7d43e26250..04494e10a5 100644
--- a/app/assets/javascripts/workbench/keyboard.js
+++ b/app/assets/javascripts/workbench/keyboard.js
@@ -21,6 +21,12 @@ Object.assign(TW.workbench.keyboard, {
   keyCodeReplace: ['↑', '↓', '←', '→', '⌘'],
 
   init_keyShortcuts () {
+    const keyboardTable = document.querySelector('#keyShortcuts')
+
+    if (keyboardTable) {
+      keyboardTable.remove()
+    }
+
     this.keyShortcutElement = this.createTable()
     this.btnClose = this.keyShortcutElement.querySelector('.close')
     this.legendLink = this.keyShortcutElement.querySelector('.legend')
@@ -28,6 +34,7 @@ Object.assign(TW.workbench.keyboard, {
     this.keyShortcutsPanel = this.keyShortcutElement.querySelector('.panel')
 
     document.body.append(this.keyShortcutElement)
+
     this.generalShortcuts()
     this.fillTable()
     this.handleEvents()
@@ -94,12 +101,18 @@ Object.assign(TW.workbench.keyboard, {
     const legendElement = this.createLegendElement(key, description, section, isLeft)
 
     document.body.append(legendElement)
-    this.addNewShortcut(legendElement)
+    if (!this.isShortcutInTable(key)) {
+      this.addNewShortcut(legendElement)
+    }
   },
 
   fillTable () {
     document.querySelectorAll('[data-shortcut-key]').forEach(element => {
-      TW.workbench.keyboard.addNewShortcut(TW.workbench.keyboard.checkReplaceKeyCode(element))
+      const key = element.getAttribute('data-shortcut-key')
+
+      if (!this.isShortcutInTable(key)) {
+        TW.workbench.keyboard.addNewShortcut(TW.workbench.keyboard.checkReplaceKeyCode(element))
+      }
     })
   },
 
@@ -128,22 +141,27 @@ Object.assign(TW.workbench.keyboard, {
   },
 
   addRowShortcut (shortcutKey, description) {
-    const rowElement = document.createElement('tr');
-    const shortcutColumn = document.createElement('td');
-    const descriptionColumn = document.createElement('td');
-    const keyDiv = document.createElement('div');
+    const rowElement = document.createElement('tr')
+    const shortcutColumn = document.createElement('td')
+    const descriptionColumn = document.createElement('td')
+    const keyDiv = document.createElement('div')
 
-    keyDiv.classList.add('key');
-    keyDiv.textContent = shortcutKey;
-    descriptionColumn.textContent = description;
+    keyDiv.classList.add('key')
+    keyDiv.setAttribute('data-table-shortcut-key', shortcutKey)
+    keyDiv.textContent = shortcutKey
+    descriptionColumn.textContent = description
 
-    shortcutColumn.append(keyDiv);
-    rowElement.append(shortcutColumn);
-    rowElement.append(descriptionColumn);
+    shortcutColumn.append(keyDiv)
+    rowElement.append(shortcutColumn)
+    rowElement.append(descriptionColumn)
 
     return rowElement
   },
 
+  isShortcutInTable (shortcutKey) {
+    return document.querySelector(`[data-table-shortcut-key="${shortcutKey}"]`)
+  },
+
   addNewShortcut (element) {
     const sectionName = element.getAttribute('data-shortcut-section')
     const shortcutKey = element.getAttribute('data-shortcut-key')
@@ -180,10 +198,6 @@ Object.assign(TW.workbench.keyboard, {
 })
 
 document.addEventListener('turbolinks:load', () => {
-  if (document.querySelectorAll('[data-shortcut-key]').length) {
-    if (!document.querySelectorAll('[data-help]').length) {
-      TW.workbench.help.init()
-    }
-    TW.workbench.keyboard.init_keyShortcuts()
-  }
+  TW.workbench.help.init()
+  TW.workbench.keyboard.init_keyShortcuts()
 })

From b5d96a957fa699b6cbb433b5330dd32766123cd1 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 8 Dec 2022 15:34:40 -0300
Subject: [PATCH 100/160] Cleanup

---
 CHANGELOG.md                                  |  1 +
 app/assets/javascripts/views/shared/lists.js  |  2 +-
 .../javascripts/views/shared/quick_bar.js     | 83 -------------------
 3 files changed, 2 insertions(+), 84 deletions(-)
 delete mode 100644 app/assets/javascripts/views/shared/quick_bar.js

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9dc8132c46..49ad06172f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Common list component doesn't filter created status on New taxon name task [#3205]
 - Collectors facet doesn't work on Filter collecting event [#3216]
 - original combination label disappears when relationship doesn't include the current taxon name [#3067]
+- Sometimes keyboard table is duplicating shortcuts
 
 ### Changed
 - "TODO list" now a faceted search [#3171]
diff --git a/app/assets/javascripts/views/shared/lists.js b/app/assets/javascripts/views/shared/lists.js
index cefc19ee82..d6d02cd78c 100644
--- a/app/assets/javascripts/views/shared/lists.js
+++ b/app/assets/javascripts/views/shared/lists.js
@@ -167,7 +167,7 @@ Object.assign(TW.views.shared.list, {
 });
 
 $(document).on('turbolinks:load', function() {
-  if ($("table").length) {
+  if ($("#main .tablesorter").length) {
     TW.views.shared.list.init();
   }
 });
diff --git a/app/assets/javascripts/views/shared/quick_bar.js b/app/assets/javascripts/views/shared/quick_bar.js
deleted file mode 100644
index d656a86506..0000000000
--- a/app/assets/javascripts/views/shared/quick_bar.js
+++ /dev/null
@@ -1,83 +0,0 @@
-var TW = TW || {};
-TW.views = TW.views || {};
-TW.views.shared = TW.views.shared || {};
-TW.views.shared.quick_bar = TW.views.shared.quick_bar || {};
-
-Object.assign(TW.views.shared.quick_bar, {
-
-	init_quickBar: function() {
-		var timer;		
-									
-		if($("#quick_bar").length) {
-
-			TW.workbench.keyboard.createShortcut("alt+h","Show/hide quick bar", "General shortcuts", function(that) { 
-				TW.views.shared.quick_bar.hideShowBars();
-			});
-
-			$('body').append("<div class='button-collapse-header'></div>");
-		}
-
-		Mousetrap.bind((navigator.platform.indexOf('Mac') > -1 ? 'ctrl' : 'alt')+ '+h', function(e) {
-			window.location = "/hub";
-		});			
-
-		$('.button-collapse-header').on("mouseenter", function() {
-			if($("#quick_bar").attr("data-hide-quickbar-active")) {
-		        if(timer) {
-		            clearTimeout(timer);
-		            timer = null
-		        }		
-		        timer = setTimeout( function() {		
-					if(!$("#quick_bar").attr("data-hide-quickbar")) {
-						$("#quick_bar").attr("data-hide-quickbar", "true");
-						TW.views.shared.quick_bar.hideQuickBar();
-					}
-				}, 200);
-			}
-		});	
-		$('#quick_bar, .button-collapse-header, #header_bar').on("mouseout", function() {
-			if($("#quick_bar").attr("data-hide-quickbar-active")) {
-		        if(timer) {
-		            clearTimeout(timer);
-		            timer = null
-		        }
-                timer = setTimeout( function() {
-				    if (!TW.views.shared.quick_bar.checkHover()) {
-				    	$("#quick_bar").removeAttr("data-hide-quickbar");
-						TW.views.shared.quick_bar.hideQuickBar();
-				    }	
-				}, 200);	
-			}	    		
-		});	
-	},
-
-	hideShowBars: function(time) {
-		if(!$("#quick_bar").attr("data-hide-quickbar-active")) {
-			$("#quick_bar").attr("data-hide-quickbar-active", "true");
-		}
-		else {
-			$("#quick_bar").removeAttr("data-hide-quickbar-active");
-		}
-		TW.views.shared.quick_bar.hideQuickBar(time);
-	},
-
-	checkHover: function() {
-		if($('#quick_bar').is(':hover') || $('.button-collapse-header').is(':hover') || $('#header_bar').is(':hover')) {
-			return true;
-		}
-		return false;
-	},
-
-	hideQuickBar: function(time) {	
-		$('.button-collapse-header').slideToggle(time);		
-		$('#quick_bar').slideToggle(time);
-		$('#header_bar').slideToggle(time);
-		$('.task_bar').slideToggle(time);
-	}
-	
-});
-
-$(document).on('turbolinks:load', function() {
-	TW.views.shared.quick_bar.init_quickBar();
-});
-

From 7f12aa144ae01922a9ee4d3f6b5a173fd573d607 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Fri, 9 Dec 2022 14:16:56 -0300
Subject: [PATCH 101/160] UI changes #2176

---
 CHANGELOG.md                                  |   2 +
 .../stylesheets/helpers/list/tables.scss      |  10 +
 .../vue/tasks/nomenclature/match/app.vue      | 205 +++++++++---------
 .../match/components/LineComponent.vue        |  44 ----
 .../match/components/Table/TableMatched.vue   |  32 +++
 .../match/components/Table/TableUnmatched.vue |  27 +++
 config/interface/hub/user_tasks.yml           |   2 +-
 7 files changed, 170 insertions(+), 152 deletions(-)
 delete mode 100644 app/javascript/vue/tasks/nomenclature/match/components/LineComponent.vue
 create mode 100644 app/javascript/vue/tasks/nomenclature/match/components/Table/TableMatched.vue
 create mode 100644 app/javascript/vue/tasks/nomenclature/match/components/Table/TableUnmatched.vue

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49ad06172f..94a12a8e91 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,7 +36,9 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Refactored observation cell component for Image matrix
 - Updated Ruby gems
 - Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
+- Nomenclature match updates [#2176]
 
+[#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
 [#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171
 [#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173
 [#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
diff --git a/app/assets/stylesheets/helpers/list/tables.scss b/app/assets/stylesheets/helpers/list/tables.scss
index 12ced034e7..33b95cc4c4 100644
--- a/app/assets/stylesheets/helpers/list/tables.scss
+++ b/app/assets/stylesheets/helpers/list/tables.scss
@@ -1,3 +1,13 @@
+.table-striped {
+  tr:nth-of-type(even) {
+    @extend .list_line_even;
+  }
+
+  tr:nth-of-type(odd) {
+    @extend .list_line_odd;
+  }
+}
+
 .tablesorter {
   width: 100%;
 }
diff --git a/app/javascript/vue/tasks/nomenclature/match/app.vue b/app/javascript/vue/tasks/nomenclature/match/app.vue
index c60443907f..a43beadc3d 100644
--- a/app/javascript/vue/tasks/nomenclature/match/app.vue
+++ b/app/javascript/vue/tasks/nomenclature/match/app.vue
@@ -3,128 +3,119 @@
     <h1>Nomenclature match</h1>
     <spinner-component
       v-if="isLoading"
-      :full-screen="true"/>
-    <div class="horizontal-left-content align-start">
-      <div class="full_width margin-small-right">
-        <input-component @lines="lines = $event"/>
-        <div class="flex-separate">
-          <button
-            class="button normal-input button-default"
-            type="button"
-            :disabled="!lines.length"
-            @click="processList">
-            Match
-          </button>
-          <label>
-            <input
-              type="checkbox"
-              v-model="exact">
-            Exact match
-          </label>
-        </div>
-      </div>
+      full-screen
+    />
+    <input-component @lines="lines = $event" />
+    <div class="horizontal-left-content margin-medium-bottom margin-small-top">
+      <button
+        class="button normal-input button-default margin-small-right"
+        type="button"
+        :disabled="!lines.length"
+        @click="GetMatches"
+      >
+        Match
+      </button>
+      <label class="middle">
+        <input
+          type="checkbox"
+          v-model="exact"
+        >
+        Exact match
+      </label>
+    </div>
 
-      <div class="full_width margin-small-left">
-        <navbar-component>
-          <ul class="no_bullets context-menu">
-            <li
-              class="capitalize"
-              v-for="item in show">
-              <label>
-                <input
-                  type="radio"
-                  :value="item"
-                  v-model="filter">
-                  {{ item }}
-              </label>
-            </li>
-          </ul>
-        </navbar-component>
-        <template
-          v-for="(match, key) in matches"
-          :key="key">
-          <line-component
-            v-if="filterView(match)"
-            class="margin-small-bottom"
-            :name="key"
-            :records="match"/>
-        </template>
+    <navbar-component>
+      <div class="flex-separate full_width">
+        <ul class="no_bullets context-menu">
+          <li
+            v-for="(value, key) in tableComponent"
+            :key="key"
+          >
+            <label>
+              <input
+                type="radio"
+                :value="value"
+                v-model="tableView"
+              >
+              {{ value }}
+            </label>
+          </li>
+        </ul>
+        <CSVButton
+          :list="matches"
+          :options="{ fields }"
+        />
       </div>
-    </div>
+    </navbar-component>
+
+    <TableUnmatched
+      v-if="(tableView === tableComponent.Unmatched || tableView === tableComponent.Both)"
+      :list="unmatched"
+      class="full_width margin-medium-bottom"
+    />
+    <TableMatched
+      v-if="(tableView === tableComponent.Matches || tableView === tableComponent.Both)"
+      :list="matches"
+      class="full_width"
+    />
   </div>
 </template>
 
-<script>
-
-import InputComponent from './components/InputComponent'
-import LineComponent from './components/LineComponent'
+<script setup>
+import { ref } from 'vue'
+import { TaxonName } from 'routes/endpoints'
+import { getUnique } from 'helpers/arrays'
+import TableMatched from './components/Table/TableMatched.vue'
+import TableUnmatched from './components/Table/TableUnmatched.vue'
+import InputComponent from './components/InputComponent.vue'
 import SpinnerComponent from 'components/spinner'
 import NavbarComponent from 'components/layout/NavBar'
-import { TaxonName } from 'routes/endpoints'
+import CSVButton from 'components/csvButton.vue'
 
-export default {
-  components: {
-    InputComponent,
-    LineComponent,
-    SpinnerComponent,
-    NavbarComponent
-  },
+const fields = [
+  { label: 'Id', value: 'taxon.id' },
+  { label: 'taxon name', value: 'taxon.object_label' },
+  { label: 'Author and year', value: 'taxon.cached_author_year' },
+  { label: 'Valid name', value: 'taxon.original_combination' }
+]
 
-  data () {
-    return {
-      lines: [],
-      maxPerCall: 1,
-      exact: false,
-      isLoading: false,
-      show: ['matches', 'unmatched', 'both'],
-      filter: 'both',
-      matches: {}
-    }
-  },
+const tableComponent = {
+  Matches: 'Matches',
+  Unmatched: 'Unmatched',
+  Both: 'Both'
+}
 
-  methods: {
-    GetMatches (position) {
-      const promises = []
+const exact = ref(false)
+const matches = ref([])
+const unmatched = ref([])
+const isLoading = ref(false)
+const lines = ref([])
+const tableView = ref(tableComponent.Both)
 
-      for (let i = 0; i < this.maxPerCall; i++) {
-        if (position < this.lines.length) {
-          promises.push(new Promise((resolve, reject) => {
-            const name = this.lines[position]
+function GetMatches () {
+  const requests = lines.value.map(name => TaxonName.where({ name, exact: exact.value }))
 
-            TaxonName.where({ name: name, exact: this.exact }).then(response => {
-              this.matches[name] = response.body
-              resolve()
-            })
-          }))
-          position++
-        }
-      }
+  isLoading.value = true
+  Promise.all(requests).then(responses => {
+    const taxonNames = [].concat(...responses.map(r => r.body))
+    const uniqueList = getUnique(taxonNames, 'id')
 
-      Promise.all(promises).then(() => {
-        if (position < this.lines.length) {
-          this.GetMatches(position)
-        } else {
-          this.isLoading = false
-        }
+    matches.value = uniqueList.map(taxon =>
+      ({
+        taxon,
+        match: lines.value.filter(line => taxon.object_label.toLowerCase().includes(line.toLowerCase())).join(', ')
       })
-    },
+    )
 
-    processList () {
-      this.matches = {}
-      this.isLoading = true
-      this.GetMatches(0)
-    },
+    unmatched.value = lines.value.filter(
+      line => !matches.value.length || !!matches.value.find(({ match }) => !match.includes(line))
+    )
 
-    filterView (record) {
-      switch (this.filter) {
-        case 'matches':
-          return record.length
-        case 'unmatched':
-          return !record.length
-        default:
-          return true
-      }
-    }
-  }
+    tableView.value = tableComponent.Both
+  })
+    .finally(() => {
+      isLoading.value = false
+    })
 }
+
 </script>
diff --git a/app/javascript/vue/tasks/nomenclature/match/components/LineComponent.vue b/app/javascript/vue/tasks/nomenclature/match/components/LineComponent.vue
deleted file mode 100644
index 65d5d60684..0000000000
--- a/app/javascript/vue/tasks/nomenclature/match/components/LineComponent.vue
+++ /dev/null
@@ -1,44 +0,0 @@
-<template>
-  <div class="panel content">
-    <div class="flex-separate">
-      <template v-if="records.length">
-        <span><b>{{ name }}</b></span>
-        <span>{{ records.length }} records.</span>
-      </template>
-      <template v-else>
-        <a :href="`/tasks/nomenclature/new_taxon_name?name=${name}`">
-          <b>{{ name }}</b>
-        </a>
-        <span>
-          Unmatched
-        </span>
-      </template>
-    </div>
-    <ul v-if="records.length">
-      <li
-        v-for="record in records"
-        :key="record.id">
-        <a
-          :href="`/tasks/nomenclature/browse?taxon_name_id=${record.id}`"
-          v-html="record.object_tag"/>
-      </li>
-    </ul>
-  </div>
-</template>
-
-<script>
-
-export default {
-  props: {
-    name: {
-      type: String,
-      required: true
-    },
-
-    records: {
-      type: Array,
-      required: true
-    }
-  }
-}
-</script>
diff --git a/app/javascript/vue/tasks/nomenclature/match/components/Table/TableMatched.vue b/app/javascript/vue/tasks/nomenclature/match/components/Table/TableMatched.vue
new file mode 100644
index 0000000000..9dbf419b8a
--- /dev/null
+++ b/app/javascript/vue/tasks/nomenclature/match/components/Table/TableMatched.vue
@@ -0,0 +1,32 @@
+<template>
+  <table class="table-striped">
+    <thead>
+      <tr>
+        <th>Original</th>
+        <th>Match</th>
+        <th>Valid name</th>
+      </tr>
+    </thead>
+    <tbody>
+      <tr
+        v-for="({ taxon, match }) in list"
+        :key="taxon.id"
+      >
+        <td>{{ match }}</td>
+        <td>
+          <span v-html="taxon.object_tag" /> {{ taxon.cached_author_year }}
+        </td>
+        <td v-html="taxon.original_combination" />
+      </tr>
+    </tbody>
+  </table>
+</template>
+
+<script setup>
+defineProps({
+  list: {
+    type: Array,
+    required: true
+  }
+})
+</script>
diff --git a/app/javascript/vue/tasks/nomenclature/match/components/Table/TableUnmatched.vue b/app/javascript/vue/tasks/nomenclature/match/components/Table/TableUnmatched.vue
new file mode 100644
index 0000000000..00f6403f4b
--- /dev/null
+++ b/app/javascript/vue/tasks/nomenclature/match/components/Table/TableUnmatched.vue
@@ -0,0 +1,27 @@
+<template>
+  <table class="table-striped">
+    <thead>
+      <tr>
+        <th>Unmatched</th>
+      </tr>
+    </thead>
+    <tbody>
+      <tr
+        v-for="unmatched in list"
+        :key="unmatched"
+      >
+        <td>{{ unmatched }}</td>
+      </tr>
+    </tbody>
+  </table>
+</template>
+
+<script setup>
+
+defineProps({
+  list: {
+    type: Array,
+    required: true
+  }
+})
+</script>
diff --git a/config/interface/hub/user_tasks.yml b/config/interface/hub/user_tasks.yml
index aee8b6b525..71d546cef3 100644
--- a/config/interface/hub/user_tasks.yml
+++ b/config/interface/hub/user_tasks.yml
@@ -534,7 +534,7 @@ export_basic_nomenclature_task:
   description: 'Download (also generate for API) a CSV table of the nomenclature with just the name, and a subset of the hierarchy'
 match_nomenclature_task:
   hub: true
-  name: 'Match names'
+  name: 'Nomenclature match'
   related:
   categories:
     - nomenclature

From ce61a78384822039bb6dc59c193aab05c1fd9e60 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Fri, 9 Dec 2022 14:39:25 -0300
Subject: [PATCH 102/160] Add edit button #3222

---
 .../browse/components/COHeader.vue            | 42 +++++++++++++++----
 1 file changed, 33 insertions(+), 9 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue b/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue
index 3c110e844c..f63efe73c5 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue
@@ -6,15 +6,37 @@
     >
       <span v-html="collectionObject.objectTag" />
       <div class="horizontal-right-content">
-        <CONavegation class="margin-small-right" />
-        <BrowseOTU
-          v-if="otu"
-          :otu="otu"
-        />
-        <RadialAnnotator :global-id="collectionObject.globalId" />
-        <RadialObject :global-id="collectionObject.globalId" />
-        <RadialFilter object-type="CollectionObject" />
-        <RadialNavigator :global-id="collectionObject.globalId" />
+        <ul class="context-menu">
+          <li>
+            <CONavegation class="margin-small-right" />
+          </li>
+          <li v-if="otu">
+            <BrowseOTU :otu="otu" />
+          </li>
+          <li>
+            <RadialAnnotator :global-id="collectionObject.globalId" />
+          </li>
+          <li>
+            <RadialObject :global-id="collectionObject.globalId" />
+          </li>
+          <li>
+            <RadialFilter object-type="CollectionObject" />
+          </li>
+          <li>
+            <VBtn
+              circle
+              color="submit"
+            >
+              <VIcon
+                x-small
+                name="pencil"
+              />
+            </VBtn>
+          </li>
+          <li>
+            <RadialNavigator :global-id="collectionObject.globalId" />
+          </li>
+        </ul>
       </div>
       <RadialFilterAttribute :parameters="{ collection_object_id: [collectionObject.id] }" />
     </div>
@@ -25,6 +47,8 @@
 import { useStore } from 'vuex'
 import { computed } from 'vue'
 import { GetterNames } from '../store/getters/getters'
+import VBtn from 'components/ui/VBtn'
+import VIcon from 'components/ui/VIcon'
 import NavBar from 'components/layout/NavBar.vue'
 import CONavegation from './CONavegation.vue'
 import RadialAnnotator from 'components/radials/annotator/annotator.vue'

From 030f1de06c9d87fb8292f1c8b06369eca9e361ae Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 12 Dec 2022 09:01:00 -0600
Subject: [PATCH 103/160] CHANGELOG.md [skip-ci]. Fix #3190.

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 94a12a8e91..278316d1c3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,12 +32,14 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Sometimes keyboard table is duplicating shortcuts
 
 ### Changed
+- Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
 - "TODO list" now a faceted search [#3171]
 - Refactored observation cell component for Image matrix
 - Updated Ruby gems
 - Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
 - Nomenclature match updates [#2176]
 
+[#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
 [#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171
 [#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173

From 64eba3530fc4cc2260d471deeba84a24a02fb8ab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Mon, 12 Dec 2022 12:46:38 -0300
Subject: [PATCH 104/160] Fix #3203: Database export now also imports
 project_id=NULL

---
 CHANGELOG.md          | 1 +
 lib/export/project.rb | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 278316d1c3..1e56faf7be 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Collectors facet doesn't work on Filter collecting event [#3216]
 - original combination label disappears when relationship doesn't include the current taxon name [#3067]
 - Sometimes keyboard table is duplicating shortcuts
+- Export Project Database task not exporting rows whose `project_id` is `NULL` [#3203]
 
 ### Changed
 - Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
diff --git a/lib/export/project.rb b/lib/export/project.rb
index f6910d06f2..5cc5b507d4 100644
--- a/lib/export/project.rb
+++ b/lib/export/project.rb
@@ -56,7 +56,7 @@ def self.dump_table(table, io, project_id)
     cols = ActiveRecord::Base.connection.columns(table).map { |c| "\"#{c.name}\"" }
 
     if cols.include?('"project_id"')
-      where_clause = "WHERE project_id = #{project_id}"
+      where_clause = "WHERE project_id IN (#{project_id}, NULL)"
     elsif table == 'projects'
       where_clause = "WHERE id = #{project_id}"
     else

From 1c4ee9e95ae034eaf64ef654b0565677944273c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Mon, 12 Dec 2022 12:56:38 -0300
Subject: [PATCH 105/160] CHANGELOG amendment [skip ci]

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e56faf7be..53ed841233 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -49,6 +49,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
+[#3203]: https://github.com/SpeciesFileGroup/taxonworks/issues/3203
 [#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
 
 ## [0.29.6] - 2022-11-08

From 6d0a258b8d9a11dff84aa7375e9cf11bfb6e8c65 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Mon, 12 Dec 2022 18:02:04 -0300
Subject: [PATCH 106/160] Fix title

---
 .../components/radials/navigation/radial.vue  | 26 ++++++++++++-------
 .../vue/components/ui/VIcon/index.vue         |  2 +-
 .../browse/components/COHeader.vue            |  8 ++++++
 3 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/app/javascript/vue/components/radials/navigation/radial.vue b/app/javascript/vue/components/radials/navigation/radial.vue
index d9ba22f94d..e6e803b130 100644
--- a/app/javascript/vue/components/radials/navigation/radial.vue
+++ b/app/javascript/vue/components/radials/navigation/radial.vue
@@ -4,13 +4,16 @@
       <modal
         v-if="display"
         :container-style="{ backgroundColor: 'transparent', boxShadow: 'none' }"
-        @close="closeModal()">
+        @close="closeModal()"
+      >
         <template #header>
           <h3 class="flex-separate">
             <span v-html="title" />
             <span
               v-if="metadata"
-              class="separate-right"> {{ metadata.type }}</span>
+              class="separate-right"
+              v-text="metadata.type"
+            />
           </h3>
         </template>
         <template #body>
@@ -21,13 +24,15 @@
                 <radial-menu
                   v-if="menuCreated"
                   :options="menuOptions"
-                  @onClick="selectedRadialOption"/>
+                  @onClick="selectedRadialOption"
+                />
               </div>
             </div>
             <div
               class="radial-annotator-template panel"
               :style="{ 'max-height': windowHeight(), 'min-height': windowHeight() }"
-              v-if="currentView">
+              v-if="currentView"
+            >
               <h2 class="capitalize view-title">
                 {{ currentView.replace("_"," ") }}
               </h2>
@@ -38,20 +43,23 @@
                 :metadata="metadata"
                 :global-id="globalId"
                 @onSelectedGlobalId="loadMetadata"
-                @updateCount="setTotal"/>
+                @updateCount="setTotal"
+              />
             </div>
             <destroy-confirmation
               v-if="showDestroyModal"
               @close="showDestroyModal = false"
-              @confirm="destroyObject"/>
+              @confirm="destroyObject"
+            />
           </div>
         </template>
       </modal>
       <VBtn
         v-if="showBottom"
         circle
-        :class="[buttonClass, 'circle-button']"
         color="primary"
+        :class="[buttonClass, 'circle-button']"
+        :title="buttonTitle"
         @click="displayRadialObject()"
       />
     </div>
@@ -122,7 +130,7 @@ export default {
 
     buttonTitle: {
       type: String,
-      default: 'Navigate radial'
+      default: 'Radial navigator'
     },
 
     maxTaskInPie: {
@@ -219,7 +227,7 @@ export default {
           fontSize: 11,
           class: 'slice'
         },
-        slices: slices
+        slices
       }
     },
 
diff --git a/app/javascript/vue/components/ui/VIcon/index.vue b/app/javascript/vue/components/ui/VIcon/index.vue
index 55a7596050..3854653504 100644
--- a/app/javascript/vue/components/ui/VIcon/index.vue
+++ b/app/javascript/vue/components/ui/VIcon/index.vue
@@ -70,7 +70,7 @@ export default {
     },
 
     showTitle () {
-      return this.title || `${this.name} icon`
+      return this.title
     }
   },
 
diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue b/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue
index f63efe73c5..5ac93daaf0 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/COHeader.vue
@@ -26,9 +26,12 @@
             <VBtn
               circle
               color="submit"
+              title="Edit on comprehensive task"
+              @click="openComprehenseive(collectionObject.id)"
             >
               <VIcon
                 x-small
+                title="Edit on comprehensive task"
                 name="pencil"
               />
             </VBtn>
@@ -57,6 +60,7 @@ import RadialNavigator from 'components/radials/navigation/radial.vue'
 import RadialFilter from 'components/radials/filter/radial.vue'
 import RadialFilterAttribute from 'components/radials/filter/RadialFilterAttribute.vue'
 import BrowseOTU from 'components/otu/otu.vue'
+import { RouteNames } from 'routes/routes'
 
 const store = useStore()
 const collectionObject = computed(() => store.getters[GetterNames.GetCollectionObject])
@@ -66,4 +70,8 @@ const otu = computed(() => {
 
   return d && { id: d.otu_id }
 })
+
+const openComprehenseive = (id) => {
+  window.open(`${RouteNames.DigitizeTask}?collection_object_id=${id}`, '_self')
+}
 </script>

From 1b671c0a6be43200b8a8dc5b5eaeb821e25483da Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 10:33:22 -0300
Subject: [PATCH 107/160] Fix #3233

---
 CHANGELOG.md                                             | 1 +
 .../vue/components/radials/mixins/shortcuts.js           | 9 +++++++++
 app/javascript/vue/helpers/os.js                         | 1 +
 3 files changed, 11 insertions(+)
 create mode 100644 app/javascript/vue/helpers/os.js

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 53ed841233..be4522618e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -39,6 +39,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Updated Ruby gems
 - Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
 - Nomenclature match updates [#2176]
+- Navigation key combination for radial annotator [#3233]
 
 [#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
diff --git a/app/javascript/vue/components/radials/mixins/shortcuts.js b/app/javascript/vue/components/radials/mixins/shortcuts.js
index 5570c791f0..627d629d3e 100644
--- a/app/javascript/vue/components/radials/mixins/shortcuts.js
+++ b/app/javascript/vue/components/radials/mixins/shortcuts.js
@@ -1,4 +1,5 @@
 import EventStack from '../utils/eventStack'
+import { isMac } from 'helpers/os'
 
 export default {
   computed: {
@@ -38,6 +39,13 @@ export default {
       const titles = this.shortcutList[key]
       const activeElement = document.activeElement.tagName
 
+      if (
+        (isMac() && !e.ctrlKey) ||
+        (!isMac() && !e.altKey)
+      ) {
+        return
+      }
+
       if (activeElement === 'INPUT' || activeElement === 'TEXTAREA') {
         return
       }
@@ -53,6 +61,7 @@ export default {
           this.currentAnnotator = titles[0]
         }
 
+        e.preventDefault()
         e.stopImmediatePropagation()
       }
     }
diff --git a/app/javascript/vue/helpers/os.js b/app/javascript/vue/helpers/os.js
new file mode 100644
index 0000000000..b0842513e8
--- /dev/null
+++ b/app/javascript/vue/helpers/os.js
@@ -0,0 +1 @@
+export const isMac = () => navigator.platform.indexOf('Mac') > -1

From 8ecc041f13df11cd0e71fdd8fd234b3c135e664a Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 13 Dec 2022 10:44:24 -0600
Subject: [PATCH 108/160] Cleanup CHANGELOG.md [skip-ci]

---
 CHANGELOG.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 278316d1c3..026b33c328 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,11 +20,11 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Fixed
 - OTU smart selector did not include items from the pinboard [#3139]
-- Source in n project autocopmlete response [#3142]
+- Source in n project autocomplete response [#3142]
 - 'Also create OTU' on batch taxon name upload causing raise
 - Media observations removed if they have no more depictions via updates
-- Citation link in Biological association panel on Browse OTU
-- Type relationship text/rendering is inverted in New taxon name [#3182]
+- Citation link in biological association panel on Browse OTU
+- Type relationship text/rendering is inverted in New taxon name task [#3182]
 - Sqed processing failing to encode HEIC images [#3188]
 - Common list component doesn't filter created status on New taxon name task [#3205]
 - Collectors facet doesn't work on Filter collecting event [#3216]

From 896827cf8daf41a466ca290a5e9456513abe007e Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 15:24:16 -0300
Subject: [PATCH 109/160] Add shorten prop to smart selector

---
 .../vue/components/Form/FormCitation.vue      |  1 +
 .../vue/components/ui/SmartSelector.vue       | 57 +++++++++++++------
 2 files changed, 40 insertions(+), 18 deletions(-)

diff --git a/app/javascript/vue/components/Form/FormCitation.vue b/app/javascript/vue/components/Form/FormCitation.vue
index 1baef15a83..35a9e68596 100644
--- a/app/javascript/vue/components/Form/FormCitation.vue
+++ b/app/javascript/vue/components/Form/FormCitation.vue
@@ -8,6 +8,7 @@
         :klass="klass"
         pin-section="Sources"
         pin-type="Source"
+        :shorten="100"
         label="cached"
         v-model="source"
         @selected="setSource"
diff --git a/app/javascript/vue/components/ui/SmartSelector.vue b/app/javascript/vue/components/ui/SmartSelector.vue
index 1560dfa17f..33ef9204c2 100644
--- a/app/javascript/vue/components/ui/SmartSelector.vue
+++ b/app/javascript/vue/components/ui/SmartSelector.vue
@@ -16,7 +16,7 @@
       />
       <slot name="tabs-right" />
     </div>
-    <slot name="header"/>
+    <slot name="header" />
     <template v-if="!addTabs.includes(view)">
       <div class="margin-medium-bottom">
         <autocomplete
@@ -32,27 +32,30 @@
           :clear-after="clear"
           display="label"
           :autofocus="autofocus"
-          @keyEvent="changeTab"
-          @getItem="getObject($event.id)"
+          @key-event="changeTab"
+          @get-item="getObject($event.id)"
         />
         <otu-picker
           v-if="otuPicker"
           :input-id="inputId"
           :clear-after="true"
-          @getItem="getObject($event.id)"/>
+          @get-item="getObject($event.id)"
+        />
       </div>
-      <slot name="body"/>
+      <slot name="body" />
       <template v-if="isImageModel">
         <div class="flex-wrap-row">
           <div
             v-for="image in lists[view]"
             :key="image.id"
             class="thumbnail-container margin-small cursor-pointer"
-            @click="sendObject(image)">
+            @click="sendObject(image)"
+          >
             <img
               :width="image.alternatives.thumb.width"
               :height="image.alternatives.thumb.height"
-              :src="image.alternatives.thumb.image_file_url">
+              :src="image.alternatives.thumb.image_file_url"
+            >
           </div>
         </div>
       </template>
@@ -60,28 +63,30 @@
         <ul
           v-if="view"
           class="no_bullets"
-          :class="{ 'flex-wrap-row': inline }">
+          :class="{ 'flex-wrap-row': inline }"
+        >
           <template
             v-for="item in lists[view]"
-            :key="item.id">
+            :key="item.id"
+          >
             <li
               v-if="filterItem(item)"
               class="list__item"
             >
-              <template
-                v-if="buttons">
+              <template v-if="buttons">
                 <button
                   type="button"
                   class="button normal-input tag_button"
                   :class="buttonClass"
                   v-html="item[label]"
-                  @click.prevent="sendObject(item)"/>
+                  @click.prevent="sendObject(item)"
+                />
               </template>
-              <template
-                v-else>
+              <template v-else>
                 <label
                   class="cursor-pointer"
-                  @mousedown="sendObject(item)">
+                  @mousedown="sendObject(item)"
+                >
                   <input
                     :name="name"
                     @keyup="changeTab"
@@ -89,8 +94,12 @@
                     @keyup.space="sendObject(item)"
                     :value="item.id"
                     :checked="selectedItem && item.id === selectedItem.id"
-                    type="radio">
-                  <span v-html="item[label]"/>
+                    type="radio"
+                  >
+                  <span
+                    :title="item[label]"
+                    v-html="showLabel(item[label])"
+                  />
                 </label>
               </template>
             </li>
@@ -100,7 +109,7 @@
     </template>
     <slot :name="view" />
     <slot />
-    <slot name="footer"/>
+    <slot name="footer" />
   </div>
 </template>
 
@@ -113,6 +122,7 @@ import OrderSmart from 'helpers/smartSelector/orderSmartSelector'
 import SelectFirst from 'helpers/smartSelector/selectFirstSmartOption'
 import DefaultPin from 'components/getDefaultPin'
 import OtuPicker from 'components/otu/otu_picker/otu_picker'
+import { shorten } from 'helpers/strings'
 
 export default {
   components: {
@@ -213,6 +223,11 @@ export default {
       default: undefined
     },
 
+    shorten: {
+      type: [Number, String],
+      default: undefined
+    },
+
     addTabs: {
       type: Array,
       default: () => []
@@ -347,6 +362,12 @@ export default {
         : this.filterIds !== item[this.filterBy]
     },
 
+    showLabel (label) {
+      return this.shorten
+        ? shorten(label, Number(this.shorten))
+        : label
+    },
+
     refresh (forceUpdate = false) {
       if (this.alreadyOnLists() && !forceUpdate) return
       AjaxCall('get', `/${this.model}/select_options`, { params: Object.assign({}, { klass: this.klass, target: this.target }, { extend: this.extend }, this.params) }).then(response => {

From 721b6956acd9692a6079d9932ce7ab0117aef0bf Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 13 Dec 2022 13:25:29 -0600
Subject: [PATCH 110/160] Whitespace

---
 app/views/layouts/application.html.erb | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/app/views/layouts/application.html.erb b/app/views/layouts/application.html.erb
index f51d3d14ee..47e5f9fd8f 100644
--- a/app/views/layouts/application.html.erb
+++ b/app/views/layouts/application.html.erb
@@ -24,7 +24,6 @@
   </head>
   
   <body <%= turbolinks_off_tag -%> >
-
     <header> 
       <%= render(partial: 'sessions/summary') if sessions_signed_in? %>
     </header>
@@ -36,7 +35,6 @@
     </nav>
 
     <div id="main">
-
       <aside>
         <% flash.each do |key, value| %>
           <div class="alert alert-<%= key %>">
@@ -50,4 +48,4 @@
     </div>
 
   </body>
-</html>
+</html>
\ No newline at end of file

From 6546c23c63669f55fcae930ae5cb152816e1b887 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 13 Dec 2022 16:10:25 -0600
Subject: [PATCH 111/160] Exact attributes match with variable whitespace

---
 lib/queries/query.rb                   | 14 +++++++++++--
 spec/lib/queries/source/filter_spec.rb | 27 +++++++++++++++++++++++++-
 2 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/lib/queries/query.rb b/lib/queries/query.rb
index 1a8047d0fd..1d4c01ae44 100644
--- a/lib/queries/query.rb
+++ b/lib/queries/query.rb
@@ -190,13 +190,23 @@ def dynamic_limit
     #   table is defined in each query, it is the class of instances being returned
 
     # params attribute [Symbol]
-    #   a facet for use when params include, `author`, and `exact_author` combinations
+    #   a facet for use when params include `author`, and `exact_author` pattern combinations
     #   See queries/source/filter.rb for example use
+    #   See /spec/lib/queries/source/filter_spec.rb
+    #  !! Whitespace (e.g. tabs, newlines) is ignored when exact is used !!!
     def attribute_exact_facet(attribute = nil)
       a = attribute.to_sym
       return nil if send(a).blank?
       if send("exact_#{a}".to_sym)
-        table[a].eq(send(a).strip)
+
+        v = send(a)
+        v.gsub!(/\s+/, ' ')
+        v = ::Regexp.escape(v)
+        v.gsub!(/\\\s+/, '\s*') # spaces are escaped, but we need to expand them in case we dont' get them caught
+        v = '^\s*' + v + '\s*$'
+
+        # !! May need to add table name here preceeding a.
+        Arel::Nodes::SqlLiteral.new( "#{a} ~ '#{v}'" )
       else
         table[a].matches('%' + send(a).strip.gsub(/\s+/, '%') + '%')
       end
diff --git a/spec/lib/queries/source/filter_spec.rb b/spec/lib/queries/source/filter_spec.rb
index 9942d01763..28b3fa6bdd 100644
--- a/spec/lib/queries/source/filter_spec.rb
+++ b/spec/lib/queries/source/filter_spec.rb
@@ -211,12 +211,37 @@
     expect(query.all.map(&:id)).to contain_exactly( *(all_source_ids - [s1.id]) )
   end
 
-  specify '#title, #exact_title' do
+  specify '#title, #exact_title 1' do
     query.title = 'Creatures from the Black Lagoon.'
     query.exact_title = true
     expect(query.all.map(&:id)).to contain_exactly(s5.id)
   end
 
+  specify '#title, #exact_title 2 (whitespace ignored)' do
+    query.title = "Creatures from \n the Black Lagoon."
+    query.exact_title = true
+    byebug
+    expect(query.all.map(&:id)).to contain_exactly(s5.id)
+  end
+
+  specify '#title, #exact_title 3 (whitespace ignored)' do
+    query.title = "Creatures from the Black Lagoon. "
+    query.exact_title = true
+    expect(query.all.map(&:id)).to contain_exactly(s5.id)
+  end
+
+  specify '#title, #exact_title 4 (whitespace ignored)' do
+    query.title = " \nCreatures from the Black Lagoon."
+    query.exact_title = true
+    expect(query.all.map(&:id)).to contain_exactly(s5.id)
+  end
+
+  specify '#title, #exact_title 5 (whitespace ignored)' do
+    query.title = "Creatures from      the Black Lagoon.\n\n "
+    query.exact_title = true
+    expect(query.all.map(&:id)).to contain_exactly(s5.id)
+  end
+
   specify '#title' do
     query.title = 'Creatures'
     expect(query.all.map(&:id)).to contain_exactly(s5.id)

From fb4677c17b41796502112bc95c88abf58886f46b Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Tue, 13 Dec 2022 16:16:43 -0600
Subject: [PATCH 112/160] TN soft_validation

---
 app/models/taxon_name.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/taxon_name.rb b/app/models/taxon_name.rb
index 6d0d40c95d..135cf4ad20 100644
--- a/app/models/taxon_name.rb
+++ b/app/models/taxon_name.rb
@@ -1582,7 +1582,7 @@ def sv_missing_original_publication
       elsif self.origin_citation.try(:pages).blank?
         soft_validations.add(:base, 'Original citation pages are not recorded')
       elsif !self.source.pages.blank?
-        matchdata1 = self.origin_citation.pages.match(/(\d+) ?[-–] ?(\d+)|(\d+)/)
+        matchdata1 = self.origin_citation.pages.match(/^(\d+) ?[-–] ?(\d+)$|^(\d+)$/)
         if matchdata1
           citMinP = matchdata1[1] ? matchdata1[1].to_i : matchdata1[3].to_i
           citMaxP = matchdata1[2] ? matchdata1[2].to_i : matchdata1[3].to_i

From 17d8912fc49c967909c8c4c1a3fc72adcdd04eee Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 20:11:53 -0300
Subject: [PATCH 113/160] Add useOnResize composition, truncate smart selector
 lists

---
 CHANGELOG.md                                  |   1 +
 .../vue/components/Form/FormCitation.vue      |   1 +
 .../vue/components/georeferences/map.vue      |   5 +
 .../vue/components/ui/SmartSelector.vue       | 582 +++++++++---------
 app/javascript/vue/compositions/index.js      |  10 +-
 .../vue/compositions/useOnResize.js           |  29 +
 .../new_asserted_distribution/app.vue         |  23 +-
 .../components/geographicArea.vue             | 107 ++--
 .../components/otu.vue                        | 101 ++-
 .../filter/components/filters/geographic.vue  |   2 +-
 10 files changed, 445 insertions(+), 416 deletions(-)
 create mode 100644 app/javascript/vue/compositions/useOnResize.js

diff --git a/CHANGELOG.md b/CHANGELOG.md
index be4522618e..bc431c6617 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -40,6 +40,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
 - Nomenclature match updates [#2176]
 - Navigation key combination for radial annotator [#3233]
+- Truncate smart selector lists
 
 [#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
diff --git a/app/javascript/vue/components/Form/FormCitation.vue b/app/javascript/vue/components/Form/FormCitation.vue
index 35a9e68596..044498d297 100644
--- a/app/javascript/vue/components/Form/FormCitation.vue
+++ b/app/javascript/vue/components/Form/FormCitation.vue
@@ -3,6 +3,7 @@
     <legend>Source</legend>
     <div class="horizontal-left-content align-start">
       <SmartSelector
+        class="full_width"
         model="sources"
         :target="target"
         :klass="klass"
diff --git a/app/javascript/vue/components/georeferences/map.vue b/app/javascript/vue/components/georeferences/map.vue
index c7eaace861..5cbf29ce59 100644
--- a/app/javascript/vue/components/georeferences/map.vue
+++ b/app/javascript/vue/components/georeferences/map.vue
@@ -78,6 +78,10 @@ const props = defineProps({
     type: Boolean,
     default: true
   },
+  drawText: {
+    type: Boolean,
+    default: false
+  },
   editMode: {
     type: Boolean,
     default: true
@@ -228,6 +232,7 @@ const addDrawControllers = () => {
       drawPolyline: props.drawPolyline,
       drawPolygon: props.drawPolygon,
       drawRectangle: props.drawRectangle,
+      drawText: props.drawText,
       editMode: props.editMode,
       dragMode: props.dragMode,
       cutPolygon: props.cutPolygon,
diff --git a/app/javascript/vue/components/ui/SmartSelector.vue b/app/javascript/vue/components/ui/SmartSelector.vue
index 33ef9204c2..c46fe2ac0f 100644
--- a/app/javascript/vue/components/ui/SmartSelector.vue
+++ b/app/javascript/vue/components/ui/SmartSelector.vue
@@ -1,10 +1,10 @@
 <template>
-  <div>
+  <div ref="rootRef">
     <div class="separate-bottom horizontal-left-content">
       <switch-components
         class="full_width capitalize"
         v-model="view"
-        ref="tabselector"
+        ref="tabselectorRef"
         :options="options"
       />
       <default-pin
@@ -20,7 +20,7 @@
     <template v-if="!addTabs.includes(view)">
       <div class="margin-medium-bottom">
         <autocomplete
-          ref="autocomplete"
+          ref="autocompleteRef"
           v-if="autocomplete"
           :id="`smart-selector-${model}-autocomplete`"
           :input-id="inputId"
@@ -63,6 +63,7 @@
         <ul
           v-if="view"
           class="no_bullets"
+          :style="listStyle"
           :class="{ 'flex-wrap-row': inline }"
         >
           <template
@@ -98,7 +99,7 @@
                   >
                   <span
                     :title="item[label]"
-                    v-html="showLabel(item[label])"
+                    v-html="item[label]"
                   />
                 </label>
               </template>
@@ -113,8 +114,10 @@
   </div>
 </template>
 
-<script>
-
+<script setup>
+import { ref, computed, watch, onUnmounted } from 'vue'
+import { useOnResize } from 'compositions/index'
+import { isMac } from 'helpers/os'
 import SwitchComponents from 'components/switch'
 import AjaxCall from 'helpers/ajaxCall'
 import Autocomplete from 'components/ui/Autocomplete'
@@ -122,314 +125,317 @@ import OrderSmart from 'helpers/smartSelector/orderSmartSelector'
 import SelectFirst from 'helpers/smartSelector/selectFirstSmartOption'
 import DefaultPin from 'components/getDefaultPin'
 import OtuPicker from 'components/otu/otu_picker/otu_picker'
-import { shorten } from 'helpers/strings'
-
-export default {
-  components: {
-    SwitchComponents,
-    Autocomplete,
-    DefaultPin,
-    OtuPicker
+
+const props = defineProps({
+  modelValue: {
+    type: Object,
+    default: undefined
   },
 
-  props: {
-    modelValue: {
-      type: Object,
-      default: undefined
-    },
-
-    label: {
-      type: String,
-      default: 'object_tag'
-    },
-
-    inline: {
-      type: Boolean,
-      default: false
-    },
-
-    buttons: {
-      type: Boolean,
-      default: false
-    },
-
-    buttonClass: {
-      type: String,
-      default: 'button-data'
-    },
-
-    otuPicker: {
-      type: Boolean,
-      default: false
-    },
-
-    autocompleteParams: {
-      type: Object,
-      default: undefined
-    },
-
-    autocomplete: {
-      type: Boolean,
-      default: true
-    },
-
-    autocompleteUrl: {
-      type: String,
-      default: undefined
-    },
-
-    inputId: {
-      type: String,
-      default: undefined
-    },
-
-    getUrl: {
-      type: String,
-      default: undefined
-    },
-
-    model: {
-      type: String,
-      default: undefined
-    },
-
-    klass: {
-      type: String,
-      default: undefined
-    },
-
-    target: {
-      type: String,
-      default: undefined
-    },
-
-    selected: {
-      type: [Array, String],
-      default: undefined
-    },
-
-    clear: {
-      type: Boolean,
-      default: true
-    },
-
-    pinSection: {
-      type: String,
-      default: undefined
-    },
-
-    pinType: {
-      type: String,
-      default: undefined
-    },
-
-    shorten: {
-      type: [Number, String],
-      default: undefined
-    },
-
-    addTabs: {
-      type: Array,
-      default: () => []
-    },
-
-    params: {
-      type: Object,
-      default: () => ({})
-    },
-
-    customList: {
-      type: Object,
-      default: () => ({})
-    },
-
-    name: {
-      type: String,
-      required: false,
-      default: () => (Math.random().toString(36).substr(2, 5))
-    },
-
-    filterIds: {
-      type: [Number, Array],
-      default: () => []
-    },
-
-    filterBy: {
-      type: String,
-      default: 'id'
-    },
-
-    filter: {
-      type: Function,
-      default: undefined
-    },
-
-    lockView: {
-      type: Boolean,
-      default: true
-    },
-
-    autofocus: {
-      type: Boolean,
-      default: false
-    },
-
-    extend: {
-      type: Array,
-      default: () => []
-    }
+  label: {
+    type: String,
+    default: 'object_tag'
   },
 
-  emits: [
-    'update:modelValue',
-    'onTabSelected',
-    'selected'
-  ],
-
-  computed: {
-    selectedItem: {
-      get () {
-        return this.modelValue
-      },
-      set (value) {
-        this.$emit('update:modelValue', value)
-      }
-    },
+  inline: {
+    type: Boolean,
+    default: false
+  },
 
-    isImageModel () {
-      return this.model === 'images'
-    },
+  buttons: {
+    type: Boolean,
+    default: false
+  },
 
-    actionKey () {
-      return navigator.platform.indexOf('Mac') > -1
-        ? 'Control'
-        : 'Alt'
-    }
+  buttonClass: {
+    type: String,
+    default: 'button-data'
   },
 
-  data () {
-    return {
-      lists: {},
-      view: undefined,
-      options: []
-    }
+  otuPicker: {
+    type: Boolean,
+    default: false
   },
 
-  watch: {
-    view (newVal) {
-      this.$emit('onTabSelected', newVal)
-    },
-    customList: {
-      handler () {
-        this.addCustomElements()
-      },
-      deep: true
-    },
-    model (newVal) {
-      this.refresh()
-    }
+  autocompleteParams: {
+    type: Object,
+    default: undefined
   },
 
-  created () {
-    this.refresh()
-    document.addEventListener('smartselector:update', this.refresh)
+  autocomplete: {
+    type: Boolean,
+    default: true
   },
 
-  unmounted () {
-    document.removeEventListener('smartselector:update', this.refresh)
+  autocompleteUrl: {
+    type: String,
+    default: undefined
   },
 
-  methods: {
-    getObject (id) {
-      AjaxCall('get', this.getUrl ? `${this.getUrl}${id}.json` : `/${this.model}/${id}.json`, { params: { extend: this.extend } }).then(response => {
-        this.sendObject(response.body)
-      })
-    },
-
-    sendObject (item) {
-      this.lastSelected = item
-      this.selectedItem = item
-      this.$emit('selected', item)
-    },
-
-    filterItem (item) {
-      if (this.filter) {
-        return this.filter(item)
-      }
+  inputId: {
+    type: String,
+    default: undefined
+  },
 
-      return Array.isArray(this.filterIds)
-        ? !this.filterIds.includes(item[this.filterBy])
-        : this.filterIds !== item[this.filterBy]
-    },
-
-    showLabel (label) {
-      return this.shorten
-        ? shorten(label, Number(this.shorten))
-        : label
-    },
-
-    refresh (forceUpdate = false) {
-      if (this.alreadyOnLists() && !forceUpdate) return
-      AjaxCall('get', `/${this.model}/select_options`, { params: Object.assign({}, { klass: this.klass, target: this.target }, { extend: this.extend }, this.params) }).then(response => {
-        this.lists = response.body
-        this.addCustomElements()
-        this.options = Object.keys(this.lists).concat(this.addTabs)
-        this.options = OrderSmart(this.options)
-
-        this.view = SelectFirst(this.lists, this.options)
-
-      }).catch(() => {
-        this.options = []
-        this.lists = []
-        this.view = undefined
-      })
-    },
-    addToList (listName, item) {
-      const index = this.lists[listName].findIndex(({ id }) => id === item.id)
-
-      if (index > -1) {
-        this.lists[listName][index] = item
-      } else {
-        this.lists[listName].push(item)
-      }
-    },
-    addCustomElements () {
-      const keys = Object.keys(this.customList)
-      if (keys.length) {
-        keys.forEach(key => {
-          this.lists[key] = this.customList[key]
-          if (!this.lists[key]) {
-            this.options.push(key)
-            this.options = OrderSmart(this.options)
-          }
-        })
-      }
-      if (!this.lockView) {
-        this.view = SelectFirst(this.lists, this.options)
+  getUrl: {
+    type: String,
+    default: undefined
+  },
+
+  model: {
+    type: String,
+    default: undefined
+  },
+
+  klass: {
+    type: String,
+    default: undefined
+  },
+
+  target: {
+    type: String,
+    default: undefined
+  },
+
+  selected: {
+    type: [Array, String],
+    default: undefined
+  },
+
+  clear: {
+    type: Boolean,
+    default: true
+  },
+
+  pinSection: {
+    type: String,
+    default: undefined
+  },
+
+  pinType: {
+    type: String,
+    default: undefined
+  },
+
+  ellipsis: {
+    type: Boolean,
+    default: true
+  },
+
+  addTabs: {
+    type: Array,
+    default: () => []
+  },
+
+  params: {
+    type: Object,
+    default: () => ({})
+  },
+
+  customList: {
+    type: Object,
+    default: () => ({})
+  },
+
+  name: {
+    type: String,
+    required: false,
+    default: () => (Math.random().toString(36).substr(2, 5))
+  },
+
+  filterIds: {
+    type: [Number, Array],
+    default: () => []
+  },
+
+  filterBy: {
+    type: String,
+    default: 'id'
+  },
+
+  filter: {
+    type: Function,
+    default: undefined
+  },
+
+  lockView: {
+    type: Boolean,
+    default: true
+  },
+
+  autofocus: {
+    type: Boolean,
+    default: false
+  },
+
+  extend: {
+    type: Array,
+    default: () => []
+  }
+})
+
+const emit = defineEmits([
+  'update:modelValue',
+  'onTabSelected',
+  'selected'
+])
+
+const actionKey = isMac()
+  ? 'Control'
+  : 'Alt'
+
+const autocompleteRef = ref(null)
+const tabselectorRef = ref(null)
+const rootRef = ref(null)
+
+const lists = ref([])
+const view = ref()
+const options = ref([])
+const lastSelected = ref()
+const elementSize = useOnResize(rootRef)
+
+const listStyle = computed(() => {
+  return {
+    'max-width': props.ellipsis ? `${elementSize.width}px` : 'auto'
+  }
+})
+
+const selectedItem = computed({
+  get () {
+    return props.modelValue
+  },
+  set (value) {
+    emit('update:modelValue', value)
+  }
+})
+
+const isImageModel = computed(() => props.model === 'images')
+
+const getObject = id => {
+  const params = {
+    extend: props.extend
+  }
+
+  AjaxCall('get', props.getUrl ? `${props.getUrl}${id}.json` : `/${props.model}/${id}.json`, { params }).then(response => {
+    sendObject(response.body)
+  })
+}
+
+const sendObject = item => {
+  lastSelected.value = item
+  selectedItem.value = item
+  emit('selected', item)
+}
+
+const filterItem = item => {
+  if (props.filter) {
+    return props.filter(item)
+  }
+
+  return Array.isArray(props.filterIds)
+    ? !props.filterIds.includes(item[props.filterBy])
+    : props.filterIds !== item[props.filterBy]
+}
+
+const refresh = (forceUpdate = false) => {
+  if (alreadyOnLists() && !forceUpdate) return
+  const params = {
+    klass: props.klass,
+    target: props.target,
+    extend: props.extend,
+    ...props.params
+  }
+
+  AjaxCall('get', `/${props.model}/select_options`, { params }).then(response => {
+    lists.value = response.body
+    addCustomElements()
+    options.value = Object.keys(lists.value).concat(props.addTabs)
+    options.value = OrderSmart(options.value)
+
+    view.value = SelectFirst(lists.value, options.value)
+  }).catch(() => {
+    options.value = []
+    lists.value = []
+    view.value = undefined
+  })
+}
+
+const addToList = (listName, item) => {
+  const index = lists.value[listName].findIndex(({ id }) => id === item.id)
+
+  if (index > -1) {
+    lists.value[listName][index] = item
+  } else {
+    lists.value[listName].push(item)
+  }
+}
+
+const addCustomElements = () => {
+  const keys = Object.keys(props.customList)
+
+  if (keys.length) {
+    keys.forEach(key => {
+      lists.value[key] = props.customList[key]
+
+      if (!lists.value[key]) {
+        options.value.push(key)
+        options.value = OrderSmart(options.value)
       }
-    },
-    alreadyOnLists () {
-      return this.lastSelected ? [].concat(...Object.values(this.lists)).find(item => item.id === this.lastSelected.id) : false
-    },
-    setFocus () {
-      this.$refs.autocomplete.setFocus()
-    },
-
-    changeTab (e) {
-      if (e.key !== this.actionKey) return
-      const element = this.$refs.tabselector.$el
-
-      element.querySelector('input:checked').focus()
-    }
+    })
   }
+
+  if (!props.lockView) {
+    view.value = SelectFirst(lists.value, options.value)
+  }
+}
+
+const alreadyOnLists = () => {
+  return lastSelected.value && [].concat(...Object.values(lists.value)).find(item => item.id === lastSelected.value.id)
+}
+const setFocus = () => {
+  autocompleteRef.value.setFocus()
 }
+
+const changeTab = (e) => {
+  if (e.key !== actionKey) return
+  const element = tabselectorRef.value.$el
+
+  element.querySelector('input:checked').focus()
+}
+
+watch(
+  view,
+  newVal => { emit('onTabSelected', newVal) }
+)
+
+watch(
+  props.customList,
+  () => { addCustomElements() },
+  { deep: true }
+)
+
+watch(props.model, () => { refresh() })
+
+onUnmounted(() => {
+  document.removeEventListener('smartselector:update', refresh)
+})
+
+refresh()
+document.addEventListener('smartselector:update', refresh)
+
+defineExpose({
+  setFocus,
+  addToList
+})
 </script>
 <style scoped>
   input:focus + span {
     font-weight: bold;
   }
-
   .list__item {
     padding:2px 0;
+    text-overflow: ellipsis;
+    white-space: nowrap;
+    overflow: hidden;
   }
 </style>
diff --git a/app/javascript/vue/compositions/index.js b/app/javascript/vue/compositions/index.js
index b676464dc6..236f72ec90 100644
--- a/app/javascript/vue/compositions/index.js
+++ b/app/javascript/vue/compositions/index.js
@@ -1,7 +1,3 @@
-import { useScroll } from './useScroll'
-import { useWindowSize } from './useWindowSize'
-
-export {
-  useScroll,
-  useWindowSize
-}
+export * from './useOnResize'
+export * from './useScroll'
+export * from './useWindowSize'
diff --git a/app/javascript/vue/compositions/useOnResize.js b/app/javascript/vue/compositions/useOnResize.js
new file mode 100644
index 0000000000..c8ee0a2479
--- /dev/null
+++ b/app/javascript/vue/compositions/useOnResize.js
@@ -0,0 +1,29 @@
+import { onMounted, onUnmounted, reactive } from 'vue'
+
+export function useOnResize (element) {
+  const elementSize = reactive({ width: 0, height: 0 })
+  let observeElement
+
+  const resizeListener = ({ width, height }) => {
+    elementSize.width = width
+    elementSize.height = height
+
+    console.log(width, height)
+  }
+
+  onMounted(() => {
+    observeElement = new ResizeObserver(entries => {
+      const { width, height } = entries[0].contentRect
+
+      resizeListener({ width, height })
+    })
+
+    observeElement.observe(element.value)
+  })
+
+  onUnmounted(() => {
+    observeElement.disconnect()
+  })
+
+  return elementSize
+}
diff --git a/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/app.vue b/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/app.vue
index 2cde8e5e16..8118f643e5 100644
--- a/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/app.vue
+++ b/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/app.vue
@@ -41,6 +41,7 @@
       <div class="width-30">
         <div class="horizontal-left-content panel-section separate-right align-start">
           <FormCitation
+            class="full_width"
             v-model="asserted_distribution.citation"
             v-model:absent="asserted_distribution.is_absent"
             :klass="ASSERTED_DISTRIBUTION"
@@ -62,19 +63,17 @@
       <div class="horizontal-left-content separate-bottom separate-left separate-right align-start width-40">
         <otu-component
           class="separate-right full_width"
-          v-model="asserted_distribution.otu"/>
-        <lock-component
-          class="margin-medium-top"
-          v-model="locks.otu"/>
+          v-model="asserted_distribution.otu"
+          v-model:lock="locks.otu"
+        />
       </div>
       <div class="horizontal-left-content separate-left align-start width-30">
         <geographic-area
           class="separate-right full_width"
+          v-model="asserted_distribution.geographicArea"
+          v-model:lock="locks.geographicArea"
           @selected="triggerAutosave"
-          v-model="asserted_distribution"/>
-        <lock-component
-          class="margin-medium-top"
-          v-model="locks.geographicArea"/>
+        />
       </div>
     </div>
 
@@ -232,7 +231,7 @@ export default {
       AssertedDistribution.create({ asserted_distribution, extend }).then(response => {
         this.list.unshift(response.body)
         TW.workbench.alert.create('Asserted distribution was successfully created.', 'notice')
-        this.refreshSmarts()
+        smartSelectorRefresh()
         this.newWithLock()
       })
     },
@@ -243,7 +242,7 @@ export default {
 
         this.list[index] = response.body
         TW.workbench.alert.create('Asserted distribution was successfully updated.', 'notice')
-        this.refreshSmarts()
+        smartSelectorRefresh()
         this.newWithLock()
       })
     },
@@ -254,10 +253,6 @@ export default {
       })
     },
 
-    refreshSmarts () {
-      smartSelectorRefresh()
-    },
-
     setSourceOtu (item) {
       this.newWithLock()
       this.setCitation(item.citations[0])
diff --git a/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/geographicArea.vue b/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/geographicArea.vue
index 5e3c14eb90..df5a59a356 100644
--- a/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/geographicArea.vue
+++ b/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/geographicArea.vue
@@ -1,70 +1,67 @@
 <template>
   <fieldset>
     <legend>Geographic area</legend>
-    <smart-selector
-      v-model="assertedDistribution.geographicArea"
-      model="geographic_areas"
-      klass="AssertedDistribution"
-      target="AssertedDistribution"
-      ref="smartSelector"
+    <div class="horizontal-left-content align-start">
+      <smart-selector
+        v-model="geographicArea"
+        class="full_width"
+        model="geographic_areas"
+        klass="AssertedDistribution"
+        target="AssertedDistribution"
+        label="name"
+        pin-section="GeographicAreas"
+        @selected="onSelect"
+        pin-type="GeographicArea"
+      />
+      <VLock
+        v-model="lock"
+        class="margin-small-left"
+      />
+    </div>
+    <SmartSelectorItem
+      :item="geographicArea"
       label="name"
-      pin-section="GeographicAreas"
-      @selected="onSelect"
-      pin-type="GeographicArea">
-      <template v-if="assertedDistribution.geographicArea">
-        <p class="horizontal-left-content">
-          <span data-icon="ok"/>
-          <span v-html="assertedDistribution.geographicArea.name"/>
-          <span
-            class="button circle-button btn-undo button-default"
-            @click="unset"/>
-        </p>
-      </template>
-    </smart-selector>
+      @unset="geographicArea = undefined"
+    />
   </fieldset>
 </template>
 
-<script>
-
+<script setup>
+import { computed } from 'vue'
 import SmartSelector from 'components/ui/SmartSelector'
+import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
+import VLock from 'components/ui/VLock/index.vue'
 
-export default {
-  components: { SmartSelector },
-
-  props: {
-    modelValue: {
-      type: Object,
-      default: undefined
-    }
+const props = defineProps({
+  modelValue: {
+    type: Object,
+    default: undefined
   },
 
-  emits: [
-    'update:modelValue',
-    'selected'
-  ],
+  lock: {
+    type: Boolean,
+    default: false
+  }
+})
 
-  computed: {
-    assertedDistribution: {
-      get () {
-        return this.modelValue
-      },
-      set (value) {
-        this.$emit('update:modelValue', value)
-      }
-    }
-  },
+const emit = defineEmits([
+  'update:modelValue',
+  'update:lock',
+  'selected'
+])
 
-  methods: {
-    refresh () {
-      this.$refs.smartSelector.refresh()
-    },
-    unset () {
-      this.assertedDistribution.geographicArea = undefined
-    },
-    onSelect (geo) {
-      this.assertedDistribution.geographicArea = geo
-      this.$emit('selected')
-    }
-  }
+const geographicArea = computed({
+  get: () => props.modelValue,
+  set: value => emit('update:modelValue', value)
+})
+
+const lock = computed({
+  get: () => props.lock,
+  set: value => emit('update:lock', value)
+})
+
+const onSelect = geo => {
+  geographicArea.value = geo
+  emit('selected')
 }
 </script>
\ No newline at end of file
diff --git a/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/otu.vue b/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/otu.vue
index 31c1dab5d2..1821a2db76 100644
--- a/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/otu.vue
+++ b/app/javascript/vue/tasks/asserted_distribution/new_asserted_distribution/components/otu.vue
@@ -1,66 +1,65 @@
 <template>
   <fieldset>
     <legend>Otu</legend>
-    <smart-selector
-      v-model="otu"
-      model="otus"
-      klass="AssertedDistribution"
-      target="AssertedDistribution"
-      ref="smartSelector"
-      pin-section="Otus"
-      pin-type="Otu"
-      :search="true"
-      :autocomplete="false"
-      :otu-picker="true">
-      <template v-if="otu">
-        <p class="horizontal-left-content">
-          <span data-icon="ok"/>
-          <span v-html="otu.object_tag"/>
-          <span
-            class="button circle-button btn-undo button-default"
-            @click="unset"/>
-        </p>
-      </template>
-    </smart-selector>
+    <div class="horizontal-left-content align-start">
+      <smart-selector
+        v-model="otu"
+        class="full_width"
+        model="otus"
+        klass="AssertedDistribution"
+        target="AssertedDistribution"
+        pin-section="Otus"
+        pin-type="Otu"
+        search
+        :autocomplete="false"
+        otu-picker
+      />
+      <VLock
+        v-model="lock"
+        class="margin-small-left"
+      />
+    </div>
+    <SmartSelectorItem
+      :item="otu"
+      label="object_tag"
+      @unset="otu = undefined"
+    />
   </fieldset>
 </template>
 
-<script>
-
+<script setup>
+import { computed } from 'vue'
 import SmartSelector from 'components/ui/SmartSelector'
+import SmartSelectorItem from 'components/ui/SmartSelectorItem.vue'
+import VLock from 'components/ui/VLock/index.vue'
 
-export default {
-  components: { SmartSelector },
-
-  props: {
-    modelValue: {
-      type: Object,
-      default: undefined
-    }
+const props = defineProps({
+  modelValue: {
+    type: Object,
+    default: undefined
   },
 
-  emits: ['update:modelValue'],
+  lock: {
+    type: Boolean,
+    default: false
+  }
+})
 
-  computed: {
-    otu: {
-      get () {
-        return this.modelValue
-      },
-      set (value) {
-        this.$emit('update:modelValue', value)
-      }
-    }
-  },
+const emit = defineEmits([
+  'update:modelValue',
+  'update:lock'
+])
+
+const otu = computed({
+  get: () => props.modelValue,
+  set: value => emit('update:modelValue', value)
+})
+
+const lock = computed({
+  get: () => props.lock,
+  set: value => emit('update:lock', value)
+})
 
-  methods: {
-    refresh () {
-      this.$refs.smartSelector.refresh()
-    },
-    unset () {
-      this.otu = undefined
-    }
-  }
-}
 </script>
 
 <style scoped>
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue b/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue
index 914f7de71d..1113cbac5f 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue
@@ -37,7 +37,7 @@
     </div>
     <div v-else>
       <georeference-map
-        width="330px"
+        width="100%"
         height="300px"
         ref="leaflet"
         :geojson="geojson"

From 1a5a12d858f796df0d84de1225e553b4969ef5c2 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 20:16:31 -0300
Subject: [PATCH 114/160] clean up

---
 app/javascript/vue/compositions/useOnResize.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/app/javascript/vue/compositions/useOnResize.js b/app/javascript/vue/compositions/useOnResize.js
index c8ee0a2479..5521a26589 100644
--- a/app/javascript/vue/compositions/useOnResize.js
+++ b/app/javascript/vue/compositions/useOnResize.js
@@ -7,8 +7,6 @@ export function useOnResize (element) {
   const resizeListener = ({ width, height }) => {
     elementSize.width = width
     elementSize.height = height
-
-    console.log(width, height)
   }
 
   onMounted(() => {

From c60d062282ff6857bbdfda4900961d60c80408ff Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 21:55:11 -0300
Subject: [PATCH 115/160] Add warning message

---
 .../stepwise/determinations/app.vue           | 19 ++++++++-
 .../CollectionObject/CollectionObjectList.vue | 42 ++++++++++++-------
 .../components/WarningGhost.vue               | 22 ++++++++++
 .../determinations/composables/useStore.js    | 15 +++++--
 4 files changed, 79 insertions(+), 19 deletions(-)
 create mode 100644 app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/WarningGhost.vue

diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue
index fcdabfef52..17395f7bb4 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue
@@ -16,7 +16,7 @@
     <div class="horizontal-left-content align-start">
       <div class="full_width">
         <LabelList class="margin-medium-bottom" />
-        <CollectionObjectList />
+        <CollectionObjectList v-if="selectedLabel" />
       </div>
 
       <div class="margin-medium-left">
@@ -38,7 +38,7 @@
 </template>
 
 <script setup>
-import { ref } from 'vue'
+import { ref, watch } from 'vue'
 import TaxonDetermination from './components/TaxonDetermination.vue'
 import CollectionObjectList from './components/CollectionObject/CollectionObjectList.vue'
 import VBtn from 'components/ui/VBtn/index.vue'
@@ -56,6 +56,8 @@ const {
   createDeterminations,
   collectionObjects,
   taxonDetermination,
+  loadCollectionObjects,
+  ghostCount,
   selectedCOIds
 } = useStore()
 
@@ -78,6 +80,19 @@ const handleClick = async () => {
   }
 }
 
+watch(
+  selectedLabel,
+  label => {
+    if (label) {
+      loadCollectionObjects(1).then(_ => {
+        if (ghostCount.value) {
+          TW.workbench.alert.create(`Warning, ${ghostCount.value} additional specimens identical except for whitepace are included`, 'notice')
+        }
+      })
+    }
+  }
+)
+
 </script>
 
 <script>
diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue
index 5c7887eee9..d41d2c4f7a 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue
@@ -1,10 +1,24 @@
 <template>
   <h3>Collection objects</h3>
-  <VPagination
-    :pagination="pagination.collectionObjects"
-    @next-page="loadCollectionObjects($event.page)"
-  />
-  <table class="full_width">
+  <div class="flex-separate middle margin-medium-bottom">
+    <ul class="context-menu no_bullets">
+      <li>
+        <VPagination
+          :pagination="pagination.collectionObjects"
+          @next-page="loadCollectionObjects($event.page)"
+        />
+      </li>
+      <li v-if="ghostCount">
+        <WarningGhost :count="ghostCount" />
+      </li>
+    </ul>
+    <VPaginationCount
+      :pagination="pagination.collectionObjects"
+      v-model="collectionObjectParams.per"
+    />
+  </div>
+
+  <table class="table-striped full_width">
     <thead>
       <tr>
         <th>
@@ -26,11 +40,10 @@
     </thead>
     <tbody>
       <CollectionObjectRow
-        v-for="(co, index) in list"
+        v-for="co in list"
         :key="co.id"
         v-model="selectedCOIds"
         :collection-object="co"
-        :class="{ even: index % 2}"
       />
     </tbody>
   </table>
@@ -41,13 +54,16 @@ import { computed, watch } from 'vue'
 import useStore from '../../composables/useStore'
 import VPagination from 'components/pagination.vue'
 import CollectionObjectRow from './CollectionObjectRow.vue'
+import VPaginationCount from 'components/pagination/PaginationCount.vue'
+import WarningGhost from '../WarningGhost.vue'
 
 const {
   collectionObjects,
   selectedCOIds,
-  selectedLabel,
   loadCollectionObjects,
-  getPages
+  getPages,
+  collectionObjectParams,
+  ghostCount
 } = useStore()
 
 const pagination = getPages()
@@ -62,11 +78,9 @@ const selectedAll = computed({
 })
 
 watch(
-  selectedLabel,
-  label => {
-    if (label) {
-      loadCollectionObjects(1)
-    }
+  () => collectionObjectParams.value.per,
+  () => {
+    loadCollectionObjects(1)
   }
 )
 
diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/WarningGhost.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/WarningGhost.vue
new file mode 100644
index 0000000000..cbf528d067
--- /dev/null
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/WarningGhost.vue
@@ -0,0 +1,22 @@
+<template>
+  <span class="middle">
+    <VIcon
+      class="margin-small-right"
+      name="attention"
+      color="attention"
+      small
+    />
+    Warning, {{ count }} aditional specimens identical except for whitespace are included.
+  </span>
+</template>
+
+<script setup>
+import VIcon from 'components/ui/VIcon/index.vue'
+
+defineProps({
+  count: {
+    type: Number,
+    required: true
+  }
+})
+</script>
diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js
index b1be1dfac6..9db10c50d9 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js
@@ -1,4 +1,4 @@
-import { reactive, toRefs } from 'vue'
+import { reactive, toRefs, computed } from 'vue'
 import { CollectionObject, TaxonDetermination } from 'routes/endpoints'
 import getPagination from 'helpers/getPagination'
 
@@ -14,6 +14,9 @@ const state = reactive({
     count_cutoff: 100,
     per: 10
   },
+  collectionObjectParams: {
+    per: 500
+  },
   pagination: {
     stepwise: {},
     collectionObjects: {}
@@ -79,7 +82,7 @@ const actions = {
       exact_buffered_determinations: true,
       taxon_determinations: false,
       extend: ['taxon_determination_images'],
-      per: 500,
+      per: state.collectionObjectParams.per,
       page
     }
     const request = CollectionObject.where(params)
@@ -107,7 +110,13 @@ const actions = {
 }
 
 const getters = {
-  getPages: () => state.pagination
+  getPages: () => state.pagination,
+
+  ghostCount: computed(() => {
+    const countBuffered = state.labels.find(label => label.buffered_determinations === state.selectedLabel)?.count_buffered
+
+    return state.pagination.collectionObjects.total - countBuffered
+  })
 }
 
 export default () => {

From 51e04dab6274b1ef338007af3c78707bd384ef39 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 22:45:08 -0300
Subject: [PATCH 116/160] Fix #3238

---
 CHANGELOG.md                                  |  2 +
 .../match/components/CompareComponent.vue     | 99 ++++++++++---------
 .../match/components/LineComponent.vue        | 13 +--
 3 files changed, 61 insertions(+), 53 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bc431c6617..7ee83260a1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -41,6 +41,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Nomenclature match updates [#2176]
 - Navigation key combination for radial annotator [#3233]
 - Truncate smart selector lists
+- Allow compare n objects in collection object match [#3238]
 
 [#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
@@ -53,6 +54,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3203]: https://github.com/SpeciesFileGroup/taxonworks/issues/3203
 [#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
+[#3238]: https://github.com/SpeciesFileGroup/taxonworks/issues/3238
 
 ## [0.29.6] - 2022-11-08
 
diff --git a/app/javascript/vue/tasks/collection_objects/match/components/CompareComponent.vue b/app/javascript/vue/tasks/collection_objects/match/components/CompareComponent.vue
index edaf8595bc..39ead7e253 100644
--- a/app/javascript/vue/tasks/collection_objects/match/components/CompareComponent.vue
+++ b/app/javascript/vue/tasks/collection_objects/match/components/CompareComponent.vue
@@ -9,7 +9,8 @@
     </button>
     <modal-component
       v-if="showModal"
-      @close="showModal = false">
+      @close="showModal = false"
+    >
       <template #header>
         <h3>Compare collection objects</h3>
       </template>
@@ -18,54 +19,59 @@
           v-model="view"
           :options="tabs"
         />
-        <table class="full_width">
+        <table class="table-striped full_width">
           <thead>
             <tr>
               <th>CO Properties</th>
-              <th>
-                <span v-html="compare[0].object_tag"/>
-              </th>
-              <th>
-                <span v-html="compare[1].object_tag"/>
+              <th
+                v-for="item in compare"
+                :key="item.id"
+              >
+                <span v-html="item.object_tag" />
               </th>
             </tr>
           </thead>
           <tbody>
             <tr
-              v-for="(key, index) in Object.keys(renderType[0])"
+              v-for="(key) in Object.keys(renderType[0])"
               :key="key"
               class="contextMenuCells"
-              :class="{ even: index % 2 }">
+            >
               <td>{{ key }}</td>
-              <td v-html="renderType[0][key]"/>
-              <td v-html="renderType[1][key]"/>
+              <td
+                v-for="(item, index) in compare"
+                :key="item.id"
+                v-html="renderType[index][key]"
+              />
             </tr>
             <tr />
           </tbody>
           <thead>
             <tr>
-              <th>CE Properties</th>
-              <th>
-                <span 
-                  v-if="compareCE[0]"
-                  v-html="compareCE[0].object_tag"/>
-              </th>
-              <th>
+              <th>CE attributes</th>
+              <th
+                v-for="ce in compareCE"
+                :key="ce.id"
+              >
                 <span
-                  v-if="compareCE[1]"
-                  v-html="compareCE[1].object_tag"/>
+                  v-if="ce.id"
+                  v-html="ce.object_tag"
+                />
               </th>
             </tr>
           </thead>
           <tbody>
             <tr
-              v-for="(key, index) in ceProperties"
+              v-for="key in ceAttributes"
               :key="key"
               class="contextMenuCells"
-              :class="{ even: index % 2 }">
+            >
               <td>{{ key }}</td>
-              <td v-html="compareCE[0] ? compareCE[0][key] : ''"/>
-              <td v-html="compareCE[1] ? compareCE[1][key] : ''"/>
+              <td
+                v-for="ce in compareCE"
+                :key="ce.id"
+                v-html="ce[key] || ''"
+              />
             </tr>
           </tbody>
         </table>
@@ -102,7 +108,9 @@ export default {
 
   computed: {
     renderType () {
-      return this.view === TABS_TYPE.DWC ? this.dwcTable : this.compare
+      return this.view === TABS_TYPE.DWC
+        ? this.dwcTable
+        : this.compare
     }
   },
 
@@ -110,7 +118,7 @@ export default {
     return {
       showModal: false,
       compareCE: [],
-      ceProperties: [],
+      ceAttributes: [],
       tabs: Object.values(TABS_TYPE),
       view: TABS_TYPE.DETAILS,
       dwcTable: {}
@@ -118,7 +126,7 @@ export default {
   },
 
   watch: {
-    showModal(newVal) {
+    showModal (newVal) {
       if (newVal) {
         this.LoadDWC()
         this.getCEs()
@@ -127,25 +135,28 @@ export default {
   },
 
   methods: {
-    getCEs() {
-      const ceId = this.compare[0]['collecting_event_id']
-      const ceId2 = this.compare[1]['collecting_event_id']
-
-      if(ceId)
-        CollectingEvent.find(ceId).then(response => {
-          this.compareCE[0] = response.body
-          this.ceProperties = Object.keys(response.body)
-        })
-      if(ceId2)
-        CollectingEvent.find(ceId2).then(response => {
-          this.compareCE[1] = response.body
-          this.ceProperties = Object.keys(response.body)
-        })
+    getCEs () {
+      const requests = this.compare.map(
+        co => co.collecting_event_id
+          ? CollectingEvent.find(co.collecting_event_id)
+          : Promise.resolve({ body: {} })
+      )
+
+      Promise.all(requests).then(responses => {
+        const collectingEvents = responses.map(r => r.body)
+        console.log(collectingEvents)
+
+        this.compareCE = collectingEvents
+        this.ceAttributes = Object.keys(collectingEvents.find(ce => ce.id) || {})
+      })
     },
 
     LoadDWC () {
-      GetDWC(this.compare[0].id).then(response => { this.dwcTable[0] = response.body })
-      GetDWC(this.compare[1].id).then(response => { this.dwcTable[1] = response.body })
+      const requests = this.compare.map(co => GetDWC(co.id))
+
+      Promise.all(requests).then(responses => {
+        this.dwcTable = responses.map(r => r.body)
+      })
     }
   }
 }
@@ -153,7 +164,7 @@ export default {
 <style scoped>
 
 :deep(.modal-container) {
-  width: 1024px;
+  width: 80vw;
   overflow-y: scroll;
   max-height: 80vh;
 }
diff --git a/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue b/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
index da5fac369b..2625106858 100644
--- a/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
+++ b/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
@@ -28,8 +28,7 @@
             @click="selected = []">
             Unselect all
           </button>
-          <compare-component
-            :compare="compare"/>
+          <compare-component :compare="compare" />
         </div>
       </div>
     </navbar-component>
@@ -92,15 +91,11 @@ export default {
 
   computed: {
     compare () {
-      if (this.selected.length === 2) {
+      if (this.selected.length > 1) {
         const list = [].concat(...Object.values(this.matchList).filter(item => Array.isArray(item)))
 
-        return [
-          list.find(item => item.id === this.selected[0]),
-          list.find(item => item.id === this.selected[1])
-        ]
-      }
-      else {
+        return list.filter(item => this.selected.includes(item.id))
+      } else {
         return []
       }
     }

From 697733a9c10157d4afafdc1563675e31f3293520 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 23:05:43 -0300
Subject: [PATCH 117/160] Add buffered determination column

---
 .../CollectionObject/CollectionObjectList.vue | 12 +++++++-----
 .../CollectionObject/CollectionObjectRow.vue  | 19 +++++++++++++++++++
 2 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue
index d41d2c4f7a..4876f53fa0 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectList.vue
@@ -28,12 +28,13 @@
           >
         </th>
         <th>ID</th>
-        <th>
-          Images
-        </th>
+        <th>Images</th>
         <th>DwC</th>
-        <th class="full_width">
-          Object tag
+        <th class="half_width">
+          Collection object
+        </th>
+        <th class="half_width">
+          Buffered determination
         </th>
         <th />
       </tr>
@@ -88,6 +89,7 @@ const list = computed(() => collectionObjects.value.map(co => ({
   id: co.id,
   object_tag: co.object_tag,
   global_id: co.global_id,
+  bufferedDeterminations: co.buffered_determinations,
   images: co.determination_images.map(image => adaptImage(image))
 })))
 
diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue
index b4c66e2b84..30b236f701 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue
@@ -52,6 +52,20 @@
     <td>
       <span v-html="collectionObject.object_tag" />
     </td>
+    <td>
+      <div class="horizontal-left-content middle">
+        <span
+          v-html="collectionObject.bufferedDeterminations"
+        />
+        <VIcon
+          v-if="selectedLabel !== collectionObject.bufferedDeterminations"
+          class="margin-small-left"
+          name="attention"
+          color="attention"
+          small
+        />
+      </div>
+    </td>
     <td>
       <RadialNavigator :global-id="collectionObject.global_id" />
     </td>
@@ -61,12 +75,17 @@
 <script setup>
 
 import { computed, ref } from 'vue'
+import useStore from '../../composables/useStore'
 import CollectionObjectDwc from './CollectionObjectDwc.vue'
 import ImageViewer from 'components/ui/ImageViewer/ImageViewer.vue'
 import RadialNavigator from 'components/radials/navigation/radial.vue'
 import VBtn from 'components/ui/VBtn/index.vue'
 import VIcon from 'components/ui/VIcon/index.vue'
 
+const {
+  selectedLabel
+} = useStore()
+
 const props = defineProps({
   modelValue: {
     type: Array,

From c334ae4a236ca69b5ad72e356ff89c0a3af86dff Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 23:11:52 -0300
Subject: [PATCH 118/160] Add title

---
 .../components/CollectionObject/CollectionObjectRow.vue          | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue
index 30b236f701..4c94c36cca 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectRow.vue
@@ -60,6 +60,7 @@
         <VIcon
           v-if="selectedLabel !== collectionObject.bufferedDeterminations"
           class="margin-small-left"
+          title="Whitespace difference"
           name="attention"
           color="attention"
           small

From f74dc2f858c26929c6babd4b9ff90b00544a9101 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 23:27:50 -0300
Subject: [PATCH 119/160] Tweak

---
 app/javascript/packs/application.scss         |  1 +
 .../vue/assets/styles/components/borders.scss |  3 ++
 .../match/components/LineComponent.vue        | 33 +++++++++++++------
 3 files changed, 27 insertions(+), 10 deletions(-)
 create mode 100644 app/javascript/vue/assets/styles/components/borders.scss

diff --git a/app/javascript/packs/application.scss b/app/javascript/packs/application.scss
index 9471d37ca4..7b7751e2b2 100644
--- a/app/javascript/packs/application.scss
+++ b/app/javascript/packs/application.scss
@@ -2,6 +2,7 @@ $font-prefix: '../../../node_modules/@ibm/plex';
 @import '../vue/assets/styles/variables/_palette.scss';
 @import '../vue/assets/styles/variables/_exports.scss';
 @import '../vue/assets/styles/components/buttons.scss';
+@import '../vue/assets/styles/components/borders.scss';
 
 @import 'node_modules/@ibm/plex/scss/sans/light/_latin1.scss';
 @import 'node_modules/@ibm/plex/scss/sans/regular/_latin1.scss';
diff --git a/app/javascript/vue/assets/styles/components/borders.scss b/app/javascript/vue/assets/styles/components/borders.scss
new file mode 100644
index 0000000000..928f759fd4
--- /dev/null
+++ b/app/javascript/vue/assets/styles/components/borders.scss
@@ -0,0 +1,3 @@
+.rounded-none {
+  border-radius: 0px;
+}
\ No newline at end of file
diff --git a/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue b/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
index 2625106858..713e64b72d 100644
--- a/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
+++ b/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
@@ -5,12 +5,15 @@
         <ul class="no_bullets context-menu">
           <li
             class="capitalize"
-            v-for="item in show">
+            v-for="item in show"
+            :key="item"
+          >
             <label>
               <input
                 type="radio"
                 :value="item"
-                v-model="filter">
+                v-model="filter"
+              >
               {{ item }}
             </label>
           </li>
@@ -19,25 +22,30 @@
           <button
             type="button"
             class="button button-default normal-input margin-small-right"
-            @click="selectAll">
+            @click="selectAll"
+          >
             Select all
           </button>
           <button
             type="button"
             class="button button-default normal-input margin-small-right"
-            @click="selected = []">
+            @click="selected = []"
+          >
             Unselect all
           </button>
           <compare-component :compare="compare" />
         </div>
       </div>
     </navbar-component>
+
     <template
       v-for="(match, recordId) in matchList"
-      :key="recordId">
+      :key="recordId"
+    >
       <div
         v-if="filterView(match)"
-        class="panel content">
+        class="panel content rounded-none"
+      >
         <div class="flex-separate">
           <template v-if="(Array.isArray(match) && match.length) || Object.keys(match).length">
             <span><b>{{ recordId }}</b></span>
@@ -52,16 +60,21 @@
           </template>
         </div>
         <ul v-if="match.length">
-          <li v-for="record in match">
+          <li
+            v-for="record in match"
+            :key="record.id"
+          >
             <label>
               <input
                 :value="record.id"
                 v-model="selected"
-                type="checkbox">
+                type="checkbox"
+              >
             </label>
             <a
               :href="`/tasks/collection_objects/browse?collection_object_id=${record.id}`"
-              v-html="record.object_tag"/>
+              v-html="record.object_tag"
+            />
           </li>
         </ul>
       </div>
@@ -119,7 +132,7 @@ export default {
   },
 
   methods: {
-    selectAll() {
+    selectAll () {
       this.selected = [].concat(...Object.values(this.matchList).filter(item => Array.isArray(item))).map(item => item.id)
     },
 

From 4c5e2549d209241589df4b8920c0e04f00f6315c Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 23:29:33 -0300
Subject: [PATCH 120/160] Fix

---
 .../stepwise/determinations/composables/useStore.js             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js
index 9db10c50d9..5c0908ebef 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/composables/useStore.js
@@ -29,7 +29,7 @@ const updateBufferedTable = count => {
   const label = labels[index]
   const newCount = label.count_buffered - count
 
-  if (newCount) {
+  if (newCount > 0) {
     label.count_buffered = newCount
   } else {
     labels.splice(index, 1)

From bc76b5aea71ff3496263217e51e990a7936c8586 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Tue, 13 Dec 2022 23:51:15 -0300
Subject: [PATCH 121/160] Fix #3237

---
 CHANGELOG.md                                  |  1 +
 .../match/components/LineComponent.vue        | 21 +++++++++++++++----
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7ee83260a1..7fb1de9806 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -42,6 +42,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Navigation key combination for radial annotator [#3233]
 - Truncate smart selector lists
 - Allow compare n objects in collection object match [#3238]
+- Include total of match/unmatched in Collection object match [#3237]
 
 [#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
diff --git a/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue b/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
index 713e64b72d..d6f87308be 100644
--- a/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
+++ b/app/javascript/vue/tasks/collection_objects/match/components/LineComponent.vue
@@ -12,9 +12,9 @@
               <input
                 type="radio"
                 :value="item"
-                v-model="filter"
+                v-model="view"
               >
-              {{ item }}
+              {{ item }} ({{ listCount[item] }})
             </label>
           </li>
         </ul>
@@ -111,6 +111,19 @@ export default {
       } else {
         return []
       }
+    },
+
+    listCount () {
+      const matchList = Object.values(this.matchList)
+      const matches = matchList.filter(match => (Array.isArray(match) && match.length) || Object.keys(match).length).length
+      const unmatched = matchList.filter(match => !(Array.isArray(match) && match.length) || !Object.keys(match).length).length
+      const both = matches + unmatched
+
+      return {
+        matches,
+        unmatched,
+        both
+      }
     }
   },
 
@@ -118,7 +131,7 @@ export default {
     return {
       selected: [],
       show: ['matches', 'unmatched', 'both'],
-      filter: 'both'
+      view: 'both'
     }
   },
 
@@ -137,7 +150,7 @@ export default {
     },
 
     filterView (record) {
-      switch (this.filter) {
+      switch (this.view) {
         case 'matches':
           return record.length
         case 'unmatched':

From c973f9b2d03c4c7996ade46a8b159fe6f6499258 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 14 Dec 2022 00:01:48 -0300
Subject: [PATCH 122/160] Tweak

---
 .../TaxonDeterminationForm.vue                |  5 ++++-
 .../TaxonDeterminationList.vue                | 20 ++++++++++---------
 .../stepwise/determinations/app.vue           | 10 +++++++++-
 3 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationForm.vue b/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationForm.vue
index 42e990dbed..3c003754c5 100644
--- a/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationForm.vue
+++ b/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationForm.vue
@@ -135,7 +135,10 @@ const getRoleString = role =>
 
 const addDetermination = () => {
   const rolesString = taxonDetermination.roles_attributes.map(getRoleString).join('; ')
-  const label = `${otuLabel.value} by ${rolesString} ${dateString(taxonDetermination)}`
+  const rolesLabel = rolesString.length
+    ? 'by ' + rolesString
+    : ''
+  const label = `${otuLabel.value} ${rolesLabel} ${dateString(taxonDetermination)}`
 
   emit('onAdd', {
     uuid: crypto.randomUUID(),
diff --git a/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationList.vue b/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationList.vue
index 809d3a70a1..6187a1d644 100644
--- a/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationList.vue
+++ b/app/javascript/vue/components/TaxonDetermination/TaxonDeterminationList.vue
@@ -26,15 +26,17 @@
       <template #item="{ element }">
         <tr>
           <td>
-            <a
-              v-if="element.id"
-              v-html="element.object_tag"
-              :href="`${RouteNames.BrowseOtu}?otu_id=${element.otu_id}`"
-            />
-            <span
-              v-else
-              v-html="element.object_tag"
-            />
+            <div class="padding-small-top">
+              <a
+                v-if="element.id"
+                v-html="element.object_tag"
+                :href="`${RouteNames.BrowseOtu}?otu_id=${element.otu_id}`"
+              />
+              <span
+                v-else
+                v-html="element.object_tag"
+              />
+            </div>
           </td>
           <td>
             <div class="horizontal-right-content">
diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue
index 17395f7bb4..bb8f9cab5e 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/app.vue
@@ -19,7 +19,9 @@
         <CollectionObjectList v-if="selectedLabel" />
       </div>
 
-      <div class="margin-medium-left">
+      <div
+        id="right-column"
+        class="margin-medium-left">
         <CuttoffInput class="margin-medium-bottom" />
         <TaxonDetermination />
       </div>
@@ -100,3 +102,9 @@ export default {
   name: 'StepwiseDeterminations'
 }
 </script>
+
+<style scoped>
+#right-column {
+  width: 600px;
+}
+</style>

From d1d8e5421ddb099476eef5414a6020f9538f9987 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 13 Dec 2022 21:18:52 -0600
Subject: [PATCH 123/160] [CHANGELOG.md [skip-ci]. Fix #3009

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5bd46bc742..6cabe83f66 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- More details to steps in stepwise determinations task
 - Added softvalidation for dublicate family group name forms and misspellings [#3185]
 - With/out local identifier facet for collection objects and stagd images [#3173]
 - Filter by housekeeping and staged-image data attributes [#3171]
@@ -19,6 +20,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Serial facet to Filter sources [#3211]
 
 ### Fixed
+- Stepwise determinations confounded by invisible whitespace [#3009]
 - OTU smart selector did not include items from the pinboard [#3139]
 - Source in n project autocomplete response [#3142]
 - 'Also create OTU' on batch taxon name upload causing raise
@@ -44,6 +46,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Allow compare n objects in collection object match [#3238]
 - Include total of match/unmatched in Collection object match [#3237]
 
+[#3009]: https://github.com/SpeciesFileGroup/taxonworks/issues/3009
 [#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
 [#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171

From f5bc4c861ab3214b1b34a8fdcf557fdca10a7d19 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 14 Dec 2022 01:27:48 -0300
Subject: [PATCH 124/160] Fix #3234

---
 CHANGELOG.md                                  |  6 ++++--
 .../vue/components/georeferences/map.vue      | 21 +++++++++++++++++--
 .../asserted_distributions_annotator.vue      |  5 ++++-
 .../parsed/georeferences/georeferences.vue    |  2 ++
 .../filter/components/filters/geographic.vue  |  1 -
 .../components/geography/georeferences.vue    |  2 ++
 .../browse/components/CollectingEvents.vue    |  1 -
 7 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6cabe83f66..7f7db7ce6f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Endpoint to return related data preventing or included in destroy, e.g. `/metadata/related_summary?klass=CollectionObject&id[]=16701&id[]...`
 - Gender and form classifications to filter nomenclature
 - Serial facet to Filter sources [#3211]
+- `tooltips` and `actions` configuration props to Map component [#3234]
 
 ### Fixed
 - Stepwise determinations confounded by invisible whitespace [#3009]
@@ -46,18 +47,19 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Allow compare n objects in collection object match [#3238]
 - Include total of match/unmatched in Collection object match [#3237]
 
-[#3009]: https://github.com/SpeciesFileGroup/taxonworks/issues/3009
-[#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
+[#3009]: https://github.com/SpeciesFileGroup/taxonworks/issues/3009
 [#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171
 [#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173
 [#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
 [#3182]: https://github.com/SpeciesFileGroup/taxonworks/issues/3182
 [#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
+[#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3203]: https://github.com/SpeciesFileGroup/taxonworks/issues/3203
 [#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
+[#3234]: https://github.com/SpeciesFileGroup/taxonworks/issues/3234
 [#3238]: https://github.com/SpeciesFileGroup/taxonworks/issues/3238
 
 ## [0.29.6] - 2022-11-08
diff --git a/app/javascript/vue/components/georeferences/map.vue b/app/javascript/vue/components/georeferences/map.vue
index 5cbf29ce59..1821493749 100644
--- a/app/javascript/vue/components/georeferences/map.vue
+++ b/app/javascript/vue/components/georeferences/map.vue
@@ -98,13 +98,17 @@ const props = defineProps({
     type: Boolean,
     default: true
   },
+  rotateMode: {
+    type: Boolean,
+    default: false
+  },
   tilesSelection: {
     type: Boolean,
     default: true
   },
   tooltips: {
     type: Boolean,
-    default: true
+    default: false
   },
   center: {
     type: Array,
@@ -129,6 +133,10 @@ const props = defineProps({
   zoomBounds: {
     type: Number,
     default: undefined
+  },
+  actions: {
+    type: Boolean,
+    default: false
   }
 })
 
@@ -184,6 +192,8 @@ onMounted(() => {
   addDrawControllers()
   handleEvents()
 
+  mapObject.pm.setGlobalOptions({ tooltips: props.tooltips })
+
   if (props.geojson.length) {
     geoJSON(props.geojson)
   }
@@ -236,7 +246,14 @@ const addDrawControllers = () => {
       editMode: props.editMode,
       dragMode: props.dragMode,
       cutPolygon: props.cutPolygon,
-      removalMode: props.removalMode
+      removalMode: props.removalMode,
+      rotateMode: props.rotateMode
+    })
+  }
+
+  if (!props.actions) {
+    mapObject.pm.Toolbar.getControlOrder().forEach(control => {
+      mapObject.pm.Toolbar.changeActionsOfControl(control, [])
     })
   }
 }
diff --git a/app/javascript/vue/components/radials/object/components/asserted_distributions/asserted_distributions_annotator.vue b/app/javascript/vue/components/radials/object/components/asserted_distributions/asserted_distributions_annotator.vue
index a5da0474c3..29ef9e56b3 100644
--- a/app/javascript/vue/components/radials/object/components/asserted_distributions/asserted_distributions_annotator.vue
+++ b/app/javascript/vue/components/radials/object/components/asserted_distributions/asserted_distributions_annotator.vue
@@ -57,9 +57,12 @@
       <map-component
         width="90%"
         height="300px"
+        tooltips
+        actions
         :zoom="2"
         :zoom-on-click="false"
-        :geojson="shapes"/>
+        :geojson="shapes"
+      />
     </div>
     <table-list
       class="separate-top"
diff --git a/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/parsed/georeferences/georeferences.vue b/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/parsed/georeferences/georeferences.vue
index 2b1be61c5c..e0ea326fde 100644
--- a/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/parsed/georeferences/georeferences.vue
+++ b/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/parsed/georeferences/georeferences.vue
@@ -70,6 +70,8 @@
               :draw-polyline="false"
               :cut-polygon="false"
               :removal-mode="false"
+              tooltips
+              actions
               @geoJsonLayersEdited="updateGeoreference($event)"
               @geoJsonLayerCreated="addGeoreference($event)"/>
           </div>
diff --git a/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue b/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue
index 1113cbac5f..88226de2a3 100644
--- a/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue
+++ b/app/javascript/vue/tasks/collection_objects/filter/components/filters/geographic.vue
@@ -51,7 +51,6 @@
         :tiles-selection="false"
         :edit-mode="false"
         :zoom="1"
-        :tooltips="false"
         @geoJsonLayerCreated="addShape"
       />
     </div>
diff --git a/app/javascript/vue/tasks/digitize/components/collectingEvent/components/geography/georeferences.vue b/app/javascript/vue/tasks/digitize/components/collectingEvent/components/geography/georeferences.vue
index 7ae2daef6f..997c2e03f3 100644
--- a/app/javascript/vue/tasks/digitize/components/collectingEvent/components/geography/georeferences.vue
+++ b/app/javascript/vue/tasks/digitize/components/collectingEvent/components/geography/georeferences.vue
@@ -68,6 +68,8 @@
               fit-bounds
               resize
               draw-controls
+              tooltips
+              actions
               :draw-polyline="false"
               :cut-polygon="false"
               :removal-mode="false"
diff --git a/app/javascript/vue/tasks/otu/browse/components/CollectingEvents.vue b/app/javascript/vue/tasks/otu/browse/components/CollectingEvents.vue
index 0bbcbd9c01..31e6772d35 100644
--- a/app/javascript/vue/tasks/otu/browse/components/CollectingEvents.vue
+++ b/app/javascript/vue/tasks/otu/browse/components/CollectingEvents.vue
@@ -46,7 +46,6 @@ import SwitchComponent from 'components/switch.vue'
 import nonReactiveStore from '../store/nonReactiveStore.js'
 import { GetterNames } from '../store/getters/getters'
 import { MutationNames } from '../store/mutations/mutations'
-import { getUnique } from 'helpers/arrays.js'
 import { computed, ref, watch } from 'vue'
 import { useStore } from 'vuex'
 

From 316d4b6b4105bddcd996ae0f9dfe97cf12c90eab Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 14 Dec 2022 09:14:54 -0600
Subject: [PATCH 125/160] Bundle update

---
 Gemfile.lock | 55 +++++++++++++++++++++++++++++-----------------------
 1 file changed, 31 insertions(+), 24 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index a703df64d8..a95d6a0b95 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -167,7 +167,6 @@ GEM
       regexp_parser (>= 1.5, < 3.0)
       xpath (~> 3.2)
     chartkick (4.2.1)
-    childprocess (4.1.0)
     chronic (0.10.2)
     chunky_png (1.4.0)
     citeproc (1.0.10)
@@ -198,6 +197,7 @@ GEM
       activerecord (>= 5.a)
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
+    date (3.3.1)
     debug_inspector (1.1.0)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
@@ -217,7 +217,7 @@ GEM
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
-    excon (0.94.0)
+    excon (0.95.0)
     execjs (2.8.1)
     factory_bot (6.2.1)
       activesupport (>= 5.0.0)
@@ -226,7 +226,7 @@ GEM
       railties (>= 5.0.0)
     faker (2.23.0)
       i18n (>= 1.8.11, < 2)
-    faraday (2.7.1)
+    faraday (2.7.2)
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-excon (2.1.0)
@@ -282,7 +282,7 @@ GEM
       turbolinks
     jquery-ui-rails (6.0.1)
       railties (>= 3.2.16)
-    json (2.6.2)
+    json (2.6.3)
     kaminari (1.2.2)
       activesupport (>= 4.1.0)
       kaminari-actionview (= 1.2.2)
@@ -304,12 +304,15 @@ GEM
       parslet
     logical_query_parser (0.3.2)
       treetop (~> 1.6.8)
-    loofah (2.19.0)
+    loofah (2.19.1)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     lumberjack (1.2.8)
-    mail (2.7.1)
+    mail (2.8.0)
       mini_mime (>= 0.1.1)
+      net-imap
+      net-pop
+      net-smtp
     marcel (1.0.2)
     matrix (0.4.2)
     method_source (1.0.0)
@@ -326,15 +329,20 @@ GEM
     namae (1.1.1)
     namecase (2.0.0)
     nenv (0.3.0)
-    net-protocol (0.1.3)
+    net-imap (0.3.2)
+      date
+      net-protocol
+    net-pop (0.1.2)
+      net-protocol
+    net-protocol (0.2.1)
       timeout
     net-smtp (0.3.3)
       net-protocol
     netrc (0.11.0)
     nio4r (2.5.8)
-    nokogiri (1.13.9-x86_64-darwin)
+    nokogiri (1.13.10-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.13.9-x86_64-linux)
+    nokogiri (1.13.10-x86_64-linux)
       racc (~> 1.4)
     notiffany (0.1.3)
       nenv (~> 0.1)
@@ -348,7 +356,7 @@ GEM
     parallel (1.22.1)
     parallel_tests (4.0.0)
       parallel
-    parser (3.1.2.1)
+    parser (3.1.3.0)
       ast (~> 2.4.1)
     parslet (2.0.0)
     passenger (6.0.15)
@@ -372,10 +380,10 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     psych (3.3.4)
-    public_suffix (5.0.0)
+    public_suffix (5.0.1)
     puma (5.6.5)
       nio4r (~> 2.0)
-    racc (1.6.0)
+    racc (1.6.1)
     rack (2.2.4)
     rack-cors (1.1.1)
       rack (>= 2.0.0)
@@ -405,8 +413,8 @@ GEM
     rails-dom-testing (2.0.3)
       activesupport (>= 4.2.0)
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.4.3)
-      loofah (~> 2.3)
+    rails-html-sanitizer (1.4.4)
+      loofah (~> 2.19, >= 2.19.1)
     rails-jquery-autocomplete (1.0.5)
       rails (>= 3.2)
     rails_or (1.1.9)
@@ -471,7 +479,7 @@ GEM
     rspec-expectations (3.12.0)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
-    rspec-mocks (3.12.0)
+    rspec-mocks (3.12.1)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.12.0)
     rspec-rails (5.1.2)
@@ -484,7 +492,7 @@ GEM
       rspec-support (~> 3.10)
     rspec-support (3.12.0)
     rtesseract (3.1.2)
-    rubocop (1.39.0)
+    rubocop (1.40.0)
       json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.1.2.1)
@@ -494,7 +502,7 @@ GEM
       rubocop-ast (>= 1.23.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.23.0)
+    rubocop-ast (1.24.0)
       parser (>= 3.1.1.0)
     rubocop-faker (1.1.0)
       faker (>= 2.12.0)
@@ -506,7 +514,7 @@ GEM
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
-    rubocop-rspec (2.15.0)
+    rubocop-rspec (2.16.0)
       rubocop (~> 1.33)
     ruby-graphviz (1.2.5)
       rexml
@@ -529,8 +537,7 @@ GEM
       rdoc (>= 5.0)
     seedbank (0.5.0)
       rake (>= 10.0)
-    selenium-webdriver (4.6.1)
-      childprocess (>= 0.5, < 5.0)
+    selenium-webdriver (4.7.1)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
@@ -578,12 +585,12 @@ GEM
       climate_control (>= 0.0.3, < 1.0)
     thor (1.2.1)
     tilt (2.0.11)
-    timecop (0.9.5)
+    timecop (0.9.6)
     timeliness (0.4.4)
-    timeout (0.3.0)
+    timeout (0.3.1)
     tins (1.32.1)
       sync
-    treetop (1.6.11)
+    treetop (1.6.12)
       polyglot (~> 0.3)
     ttfunk (1.7.0)
     turbolinks (5.2.1)
@@ -591,7 +598,7 @@ GEM
     turbolinks-source (5.2.0)
     tzinfo (2.0.5)
       concurrent-ruby (~> 1.0)
-    tzinfo-data (1.2022.6)
+    tzinfo-data (1.2022.7)
       tzinfo (>= 1.0.0)
     uglifier (4.2.0)
       execjs (>= 0.3.0, < 3)

From 49d9fb6d1d06a9810af96d59d04b740f18c88d8c Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 14 Dec 2022 13:39:43 -0300
Subject: [PATCH 126/160] Packages update

---
 package-lock.json | 158 +++++++++++++++++++++++-----------------------
 package.json      |  20 +++---
 2 files changed, 89 insertions(+), 89 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 9ae92a8da6..39c7493ca9 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -12,7 +12,7 @@
         "@ibm/plex": "^6.1.1",
         "@sfgrp/sled": "^1.0.3",
         "@sfgrp/svg-radial-menu": "^1.0.7",
-        "axios": "^1.2.0",
+        "axios": "^1.2.1",
         "chart.js": "^4.0.1",
         "d3": "^7.7.0",
         "dompurify": "^2.4.1",
@@ -23,15 +23,15 @@
         "leaflet.pattern": "^0.1.0",
         "parse-dms": "0.0.5",
         "pdfjs-dist": "3.1.81",
-        "pinia": "^2.0.23",
+        "pinia": "^2.0.28",
         "qs": "^6.11.0",
         "shakapacker": "6.5.4",
         "v-hotkey": "^0.9.0",
         "vue": "^3.2.45",
-        "vue-handy-scroll": "^3.0.1",
+        "vue-handy-scroll": "^3.0.2",
         "vue-tippy": "^6.0.0-alpha.58",
         "vue-turbolinks": "^2.2.2",
-        "vue3-hotkey": "^1.0.2",
+        "vue3-hotkey": "^1.0.3",
         "vuedraggable": "^4.1.0",
         "vuex": "^4.1.0"
       },
@@ -43,25 +43,25 @@
         "@vue/compiler-sfc": "^3.2.45",
         "babel-loader": "^8.2.5",
         "compression-webpack-plugin": "^10.0.0",
-        "css-loader": "^6.7.2",
+        "css-loader": "^6.7.3",
         "css-minimizer-webpack-plugin": "^4.2.2",
         "eslint": "^8.29.0",
         "eslint-config-standard": "^17.0.0",
         "eslint-plugin-import": "^2.26.0",
-        "eslint-plugin-n": "^15.5.1",
+        "eslint-plugin-n": "^15.6.0",
         "eslint-plugin-node": "^11.1.0",
         "eslint-plugin-promise": "^6.1.1",
         "eslint-plugin-standard": "^4.1.0",
         "eslint-plugin-vue": "^9.8.0",
-        "mini-css-extract-plugin": "^2.7.1",
-        "postcss": "^8.4.19",
+        "mini-css-extract-plugin": "^2.7.2",
+        "postcss": "^8.4.20",
         "postcss-flexbugs-fixes": "^5.0.2",
-        "postcss-import": "^15.0.1",
+        "postcss-import": "^15.1.0",
         "postcss-loader": "^7.0.2",
         "postcss-preset-env": "^7.8.3",
         "raw-loader": "^4.0.2",
         "resolve-url-loader": "^5.0.0",
-        "sass": "^1.56.1",
+        "sass": "^1.56.2",
         "sass-loader": "^13.2.0",
         "style-loader": "^3.3.1",
         "stylus": "^0.59.0",
@@ -3262,9 +3262,9 @@
       }
     },
     "node_modules/axios": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-1.2.0.tgz",
-      "integrity": "sha512-zT7wZyNYu3N5Bu0wuZ6QccIf93Qk1eV8LOewxgjOZFd2DenOs98cJ7+Y6703d0wkaXGY6/nZd4EweJaHz9uzQw==",
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-1.2.1.tgz",
+      "integrity": "sha512-I88cFiGu9ryt/tfVEi4kX2SITsvDddTajXTOFmt2uK1ZVA8LytjtdeyefdQWEf5PU8w+4SSJDoYnggflB5tW4A==",
       "dependencies": {
         "follow-redirects": "^1.15.0",
         "form-data": "^4.0.0",
@@ -4040,13 +4040,13 @@
       }
     },
     "node_modules/css-loader": {
-      "version": "6.7.2",
-      "resolved": "https://registry.npmjs.org/css-loader/-/css-loader-6.7.2.tgz",
-      "integrity": "sha512-oqGbbVcBJkm8QwmnNzrFrWTnudnRZC+1eXikLJl0n4ljcfotgRifpg2a1lKy8jTrc4/d9A/ap1GFq1jDKG7J+Q==",
+      "version": "6.7.3",
+      "resolved": "https://registry.npmjs.org/css-loader/-/css-loader-6.7.3.tgz",
+      "integrity": "sha512-qhOH1KlBMnZP8FzRO6YCH9UHXQhVMcEGLyNdb7Hv2cpcmJbW0YrddO+tG1ab5nT41KpHIYGsbeHqxB9xPu1pKQ==",
       "dev": true,
       "dependencies": {
         "icss-utils": "^5.1.0",
-        "postcss": "^8.4.18",
+        "postcss": "^8.4.19",
         "postcss-modules-extract-imports": "^3.0.0",
         "postcss-modules-local-by-default": "^4.0.0",
         "postcss-modules-scope": "^3.0.0",
@@ -5380,9 +5380,9 @@
       "dev": true
     },
     "node_modules/eslint-plugin-n": {
-      "version": "15.5.1",
-      "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.5.1.tgz",
-      "integrity": "sha512-kAd+xhZm7brHoFLzKLB7/FGRFJNg/srmv67mqb7tto22rpr4wv/LV6RuXzAfv3jbab7+k1wi42PsIhGviywaaw==",
+      "version": "15.6.0",
+      "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.6.0.tgz",
+      "integrity": "sha512-Hd/F7wz4Mj44Jp0H6Jtty13NcE69GNTY0rVlgTIj1XBnGGVI6UTdDrpE6vqu3AHo07bygq/N+7OH/lgz1emUJw==",
       "dev": true,
       "dependencies": {
         "builtins": "^5.0.1",
@@ -7496,9 +7496,9 @@
       }
     },
     "node_modules/mini-css-extract-plugin": {
-      "version": "2.7.1",
-      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.1.tgz",
-      "integrity": "sha512-viOoaUFy+Z2w43VsGPbtfwFrr0tKwDctK9dUofG5MBViYhD1noGFUzzDIVw0KPwCGUP+c7zqLxm+acuQs7zLzw==",
+      "version": "2.7.2",
+      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.2.tgz",
+      "integrity": "sha512-EdlUizq13o0Pd+uCp+WO/JpkLvHRVGt97RqfeGhXqAcorYo1ypJSpkV+WDT0vY/kmh/p7wRdJNJtuyK540PXDw==",
       "dev": true,
       "dependencies": {
         "schema-utils": "^4.0.0"
@@ -8109,11 +8109,11 @@
       }
     },
     "node_modules/pinia": {
-      "version": "2.0.23",
-      "resolved": "https://registry.npmjs.org/pinia/-/pinia-2.0.23.tgz",
-      "integrity": "sha512-N15hFf4o5STrxpNrib1IEb1GOArvPYf1zPvQVRGOO1G1d74Ak0J0lVyalX/SmrzdT4Q0nlEFjbURsmBmIGUR5Q==",
+      "version": "2.0.28",
+      "resolved": "https://registry.npmjs.org/pinia/-/pinia-2.0.28.tgz",
+      "integrity": "sha512-YClq9DkqCblq9rlyUual7ezMu/iICWdBtfJrDt4oWU9Zxpijyz7xB2xTwx57DaBQ96UGvvTMORzALr+iO5PVMw==",
       "dependencies": {
-        "@vue/devtools-api": "^6.4.4",
+        "@vue/devtools-api": "^6.4.5",
         "vue-demi": "*"
       },
       "funding": {
@@ -8226,9 +8226,9 @@
       }
     },
     "node_modules/postcss": {
-      "version": "8.4.19",
-      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.19.tgz",
-      "integrity": "sha512-h+pbPsyhlYj6N2ozBmHhHrs9DzGmbaarbLvWipMRO7RLS+v4onj26MPFXA5OBYFxyqYhUJK456SwDcY9H2/zsA==",
+      "version": "8.4.20",
+      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.20.tgz",
+      "integrity": "sha512-6Q04AXR1212bXr5fh03u8aAwbLxAQNGQ/Q1LNa0VfOI06ZAlhPHtQvE4OIdpj4kLThXilalPnmDSOD65DcHt+g==",
       "funding": [
         {
           "type": "opencollective",
@@ -8629,9 +8629,9 @@
       }
     },
     "node_modules/postcss-import": {
-      "version": "15.0.1",
-      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.0.1.tgz",
-      "integrity": "sha512-UGlvk8EgT7Gm/Ndf9xZHnzr8xm8P54N8CBWLtcY5alP+YxlEge/Rv78etQyevZs3qWTE9If13+Bo6zATBrPOpA==",
+      "version": "15.1.0",
+      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.1.0.tgz",
+      "integrity": "sha512-hpr+J05B2FVYUAXHeK1YyI267J/dDDhMU6B6civm8hSY1jYJnBXxzKDKDswzJmtLHryrjhnDjqqp/49t8FALew==",
       "dev": true,
       "dependencies": {
         "postcss-value-parser": "^4.0.0",
@@ -9825,9 +9825,9 @@
       "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
     },
     "node_modules/sass": {
-      "version": "1.56.1",
-      "resolved": "https://registry.npmjs.org/sass/-/sass-1.56.1.tgz",
-      "integrity": "sha512-VpEyKpyBPCxE7qGDtOcdJ6fFbcpOM+Emu7uZLxVrkX8KVU/Dp5UF7WLvzqRuUhB6mqqQt1xffLoG+AndxTZrCQ==",
+      "version": "1.56.2",
+      "resolved": "https://registry.npmjs.org/sass/-/sass-1.56.2.tgz",
+      "integrity": "sha512-ciEJhnyCRwzlBCB+h5cCPM6ie/6f8HrhZMQOf5vlU60Y1bI1rx5Zb0vlDZvaycHsg/MqFfF1Eq2eokAa32iw8w==",
       "dev": true,
       "dependencies": {
         "chokidar": ">=3.0.0 <4.0.0",
@@ -10910,11 +10910,11 @@
       }
     },
     "node_modules/vue-handy-scroll": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/vue-handy-scroll/-/vue-handy-scroll-3.0.1.tgz",
-      "integrity": "sha512-Q7ogocQNXm1bG6xoe7xIGL4uvKRZ6LUu4RuSwryBZcvtaVl3UMuW3vF0qOySG8KLCfEcv7BMADvII+P036uEfw==",
+      "version": "3.0.2",
+      "resolved": "https://registry.npmjs.org/vue-handy-scroll/-/vue-handy-scroll-3.0.2.tgz",
+      "integrity": "sha512-49Qicb8V3/eTg0XSrJEWAI1Y6JgN2+1wfXdy7EPfwSGNWSuwZ6d9Yy2cbfQ+By8BK5h9bYTeQAzRLxax82FFNQ==",
       "peerDependencies": {
-        "vue": "next"
+        "vue": "^3.2.45"
       }
     },
     "node_modules/vue-loader": {
@@ -11035,14 +11035,14 @@
       "integrity": "sha512-pPO2Fr+1UgdhUK9dc5OhjLSeYi5LZAm/VZBXOVQgLHCO31bRjAof/+W/e/6SHCbnb1xdZb1gW5T9MX0k9ejSAQ=="
     },
     "node_modules/vue3-hotkey": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/vue3-hotkey/-/vue3-hotkey-1.0.2.tgz",
-      "integrity": "sha512-m1koD1IriRQhaX3yhoYgk6pfq4qIiF5anAe0tUadL81aeJDuGVJ3/EuvTenS9vgx1LbTRalT4mW4nUZG5pElpQ==",
+      "version": "1.0.3",
+      "resolved": "https://registry.npmjs.org/vue3-hotkey/-/vue3-hotkey-1.0.3.tgz",
+      "integrity": "sha512-lRzNoSUst/ZUfbRjEas6qW+nP5JDlkpZR9+9c5in6djs+JsWCUZgXR8RkdT+/4QXgs6o1yncAP6HoJ7H/fMXHg==",
       "dependencies": {
         "@types/express": "4.17.8",
         "@vue/test-utils": "^2.0.0-rc.6",
-        "vue": "^3.2.6",
-        "vue-template-compiler": "^2.6.13"
+        "vue": "^3.2.7",
+        "vue-template-compiler": "^2.7.8"
       },
       "engines": {
         "node": ">=16.0.0"
@@ -14033,9 +14033,9 @@
       }
     },
     "axios": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-1.2.0.tgz",
-      "integrity": "sha512-zT7wZyNYu3N5Bu0wuZ6QccIf93Qk1eV8LOewxgjOZFd2DenOs98cJ7+Y6703d0wkaXGY6/nZd4EweJaHz9uzQw==",
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-1.2.1.tgz",
+      "integrity": "sha512-I88cFiGu9ryt/tfVEi4kX2SITsvDddTajXTOFmt2uK1ZVA8LytjtdeyefdQWEf5PU8w+4SSJDoYnggflB5tW4A==",
       "requires": {
         "follow-redirects": "^1.15.0",
         "form-data": "^4.0.0",
@@ -14605,13 +14605,13 @@
       }
     },
     "css-loader": {
-      "version": "6.7.2",
-      "resolved": "https://registry.npmjs.org/css-loader/-/css-loader-6.7.2.tgz",
-      "integrity": "sha512-oqGbbVcBJkm8QwmnNzrFrWTnudnRZC+1eXikLJl0n4ljcfotgRifpg2a1lKy8jTrc4/d9A/ap1GFq1jDKG7J+Q==",
+      "version": "6.7.3",
+      "resolved": "https://registry.npmjs.org/css-loader/-/css-loader-6.7.3.tgz",
+      "integrity": "sha512-qhOH1KlBMnZP8FzRO6YCH9UHXQhVMcEGLyNdb7Hv2cpcmJbW0YrddO+tG1ab5nT41KpHIYGsbeHqxB9xPu1pKQ==",
       "dev": true,
       "requires": {
         "icss-utils": "^5.1.0",
-        "postcss": "^8.4.18",
+        "postcss": "^8.4.19",
         "postcss-modules-extract-imports": "^3.0.0",
         "postcss-modules-local-by-default": "^4.0.0",
         "postcss-modules-scope": "^3.0.0",
@@ -15628,9 +15628,9 @@
       }
     },
     "eslint-plugin-n": {
-      "version": "15.5.1",
-      "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.5.1.tgz",
-      "integrity": "sha512-kAd+xhZm7brHoFLzKLB7/FGRFJNg/srmv67mqb7tto22rpr4wv/LV6RuXzAfv3jbab7+k1wi42PsIhGviywaaw==",
+      "version": "15.6.0",
+      "resolved": "https://registry.npmjs.org/eslint-plugin-n/-/eslint-plugin-n-15.6.0.tgz",
+      "integrity": "sha512-Hd/F7wz4Mj44Jp0H6Jtty13NcE69GNTY0rVlgTIj1XBnGGVI6UTdDrpE6vqu3AHo07bygq/N+7OH/lgz1emUJw==",
       "dev": true,
       "requires": {
         "builtins": "^5.0.1",
@@ -17072,9 +17072,9 @@
       "optional": true
     },
     "mini-css-extract-plugin": {
-      "version": "2.7.1",
-      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.1.tgz",
-      "integrity": "sha512-viOoaUFy+Z2w43VsGPbtfwFrr0tKwDctK9dUofG5MBViYhD1noGFUzzDIVw0KPwCGUP+c7zqLxm+acuQs7zLzw==",
+      "version": "2.7.2",
+      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.7.2.tgz",
+      "integrity": "sha512-EdlUizq13o0Pd+uCp+WO/JpkLvHRVGt97RqfeGhXqAcorYo1ypJSpkV+WDT0vY/kmh/p7wRdJNJtuyK540PXDw==",
       "dev": true,
       "requires": {
         "schema-utils": "^4.0.0"
@@ -17503,11 +17503,11 @@
       "dev": true
     },
     "pinia": {
-      "version": "2.0.23",
-      "resolved": "https://registry.npmjs.org/pinia/-/pinia-2.0.23.tgz",
-      "integrity": "sha512-N15hFf4o5STrxpNrib1IEb1GOArvPYf1zPvQVRGOO1G1d74Ak0J0lVyalX/SmrzdT4Q0nlEFjbURsmBmIGUR5Q==",
+      "version": "2.0.28",
+      "resolved": "https://registry.npmjs.org/pinia/-/pinia-2.0.28.tgz",
+      "integrity": "sha512-YClq9DkqCblq9rlyUual7ezMu/iICWdBtfJrDt4oWU9Zxpijyz7xB2xTwx57DaBQ96UGvvTMORzALr+iO5PVMw==",
       "requires": {
-        "@vue/devtools-api": "^6.4.4",
+        "@vue/devtools-api": "^6.4.5",
         "vue-demi": "*"
       },
       "dependencies": {
@@ -17571,9 +17571,9 @@
       }
     },
     "postcss": {
-      "version": "8.4.19",
-      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.19.tgz",
-      "integrity": "sha512-h+pbPsyhlYj6N2ozBmHhHrs9DzGmbaarbLvWipMRO7RLS+v4onj26MPFXA5OBYFxyqYhUJK456SwDcY9H2/zsA==",
+      "version": "8.4.20",
+      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.20.tgz",
+      "integrity": "sha512-6Q04AXR1212bXr5fh03u8aAwbLxAQNGQ/Q1LNa0VfOI06ZAlhPHtQvE4OIdpj4kLThXilalPnmDSOD65DcHt+g==",
       "requires": {
         "nanoid": "^3.3.4",
         "picocolors": "^1.0.0",
@@ -17789,9 +17789,9 @@
       }
     },
     "postcss-import": {
-      "version": "15.0.1",
-      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.0.1.tgz",
-      "integrity": "sha512-UGlvk8EgT7Gm/Ndf9xZHnzr8xm8P54N8CBWLtcY5alP+YxlEge/Rv78etQyevZs3qWTE9If13+Bo6zATBrPOpA==",
+      "version": "15.1.0",
+      "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-15.1.0.tgz",
+      "integrity": "sha512-hpr+J05B2FVYUAXHeK1YyI267J/dDDhMU6B6civm8hSY1jYJnBXxzKDKDswzJmtLHryrjhnDjqqp/49t8FALew==",
       "dev": true,
       "requires": {
         "postcss-value-parser": "^4.0.0",
@@ -18581,9 +18581,9 @@
       "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
     },
     "sass": {
-      "version": "1.56.1",
-      "resolved": "https://registry.npmjs.org/sass/-/sass-1.56.1.tgz",
-      "integrity": "sha512-VpEyKpyBPCxE7qGDtOcdJ6fFbcpOM+Emu7uZLxVrkX8KVU/Dp5UF7WLvzqRuUhB6mqqQt1xffLoG+AndxTZrCQ==",
+      "version": "1.56.2",
+      "resolved": "https://registry.npmjs.org/sass/-/sass-1.56.2.tgz",
+      "integrity": "sha512-ciEJhnyCRwzlBCB+h5cCPM6ie/6f8HrhZMQOf5vlU60Y1bI1rx5Zb0vlDZvaycHsg/MqFfF1Eq2eokAa32iw8w==",
       "dev": true,
       "requires": {
         "chokidar": ">=3.0.0 <4.0.0",
@@ -19360,9 +19360,9 @@
       }
     },
     "vue-handy-scroll": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/vue-handy-scroll/-/vue-handy-scroll-3.0.1.tgz",
-      "integrity": "sha512-Q7ogocQNXm1bG6xoe7xIGL4uvKRZ6LUu4RuSwryBZcvtaVl3UMuW3vF0qOySG8KLCfEcv7BMADvII+P036uEfw==",
+      "version": "3.0.2",
+      "resolved": "https://registry.npmjs.org/vue-handy-scroll/-/vue-handy-scroll-3.0.2.tgz",
+      "integrity": "sha512-49Qicb8V3/eTg0XSrJEWAI1Y6JgN2+1wfXdy7EPfwSGNWSuwZ6d9Yy2cbfQ+By8BK5h9bYTeQAzRLxax82FFNQ==",
       "requires": {}
     },
     "vue-loader": {
@@ -19450,14 +19450,14 @@
       "integrity": "sha512-pPO2Fr+1UgdhUK9dc5OhjLSeYi5LZAm/VZBXOVQgLHCO31bRjAof/+W/e/6SHCbnb1xdZb1gW5T9MX0k9ejSAQ=="
     },
     "vue3-hotkey": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/vue3-hotkey/-/vue3-hotkey-1.0.2.tgz",
-      "integrity": "sha512-m1koD1IriRQhaX3yhoYgk6pfq4qIiF5anAe0tUadL81aeJDuGVJ3/EuvTenS9vgx1LbTRalT4mW4nUZG5pElpQ==",
+      "version": "1.0.3",
+      "resolved": "https://registry.npmjs.org/vue3-hotkey/-/vue3-hotkey-1.0.3.tgz",
+      "integrity": "sha512-lRzNoSUst/ZUfbRjEas6qW+nP5JDlkpZR9+9c5in6djs+JsWCUZgXR8RkdT+/4QXgs6o1yncAP6HoJ7H/fMXHg==",
       "requires": {
         "@types/express": "4.17.8",
         "@vue/test-utils": "^2.0.0-rc.6",
-        "vue": "^3.2.6",
-        "vue-template-compiler": "^2.6.13"
+        "vue": "^3.2.7",
+        "vue-template-compiler": "^2.7.8"
       },
       "dependencies": {
         "@types/express": {
diff --git a/package.json b/package.json
index cd7b2d21eb..660d6ce470 100644
--- a/package.json
+++ b/package.json
@@ -6,7 +6,7 @@
     "@ibm/plex": "^6.1.1",
     "@sfgrp/sled": "^1.0.3",
     "@sfgrp/svg-radial-menu": "^1.0.7",
-    "axios": "^1.2.0",
+    "axios": "^1.2.1",
     "chart.js": "^4.0.1",
     "d3": "^7.7.0",
     "dompurify": "^2.4.1",
@@ -16,16 +16,16 @@
     "leaflet": "^1.9.3",
     "leaflet.pattern": "^0.1.0",
     "parse-dms": "0.0.5",
-    "pinia": "^2.0.23",
+    "pinia": "^2.0.28",
     "pdfjs-dist": "3.1.81",
     "qs": "^6.11.0",
     "shakapacker": "6.5.4",
     "v-hotkey": "^0.9.0",
     "vue": "^3.2.45",
-    "vue-handy-scroll": "^3.0.1",
+    "vue-handy-scroll": "^3.0.2",
     "vue-tippy": "^6.0.0-alpha.58",
     "vue-turbolinks": "^2.2.2",
-    "vue3-hotkey": "^1.0.2",
+    "vue3-hotkey": "^1.0.3",
     "vuedraggable": "^4.1.0",
     "vuex": "^4.1.0"
   },
@@ -46,25 +46,25 @@
     "@vue/compiler-sfc": "^3.2.45",
     "babel-loader": "^8.2.5",
     "compression-webpack-plugin": "^10.0.0",
-    "css-loader": "^6.7.2",
+    "css-loader": "^6.7.3",
     "css-minimizer-webpack-plugin": "^4.2.2",
     "eslint": "^8.29.0",
     "eslint-config-standard": "^17.0.0",
     "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-n": "^15.5.1",
+    "eslint-plugin-n": "^15.6.0",
     "eslint-plugin-node": "^11.1.0",
     "eslint-plugin-promise": "^6.1.1",
     "eslint-plugin-standard": "^4.1.0",
     "eslint-plugin-vue": "^9.8.0",
-    "mini-css-extract-plugin": "^2.7.1",
-    "postcss": "^8.4.19",
+    "mini-css-extract-plugin": "^2.7.2",
+    "postcss": "^8.4.20",
     "postcss-flexbugs-fixes": "^5.0.2",
-    "postcss-import": "^15.0.1",
+    "postcss-import": "^15.1.0",
     "postcss-loader": "^7.0.2",
     "postcss-preset-env": "^7.8.3",
     "raw-loader": "^4.0.2",
     "resolve-url-loader": "^5.0.0",
-    "sass": "^1.56.1",
+    "sass": "^1.56.2",
     "sass-loader": "^13.2.0",
     "style-loader": "^3.3.1",
     "stylus": "^0.59.0",

From 62486aa1cd3c2250b81e6d23c3919f3d93ba5dbb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Wed, 14 Dec 2022 13:49:12 -0300
Subject: [PATCH 127/160] Corrected spec after gems upgrade

---
 spec/mailers/user_mailer_spec.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/spec/mailers/user_mailer_spec.rb b/spec/mailers/user_mailer_spec.rb
index 1142bf0080..0d11fb1aae 100644
--- a/spec/mailers/user_mailer_spec.rb
+++ b/spec/mailers/user_mailer_spec.rb
@@ -16,7 +16,7 @@
     end
 
     it 'renders "TaxonWorks <noreply@#{Settings.mail_domain}>" as mail sender' do
-      expect(mail.header[:from].value).to eq(['TaxonWorks <noreply@example.com>'])
+      expect(mail.header[:from].value).to eq('TaxonWorks <noreply@example.com>')
     end
 
     it 'shows the user\'s e-mail address in the e-mail body' do
@@ -33,7 +33,7 @@
     end
 
     it 'renders "TaxonWorks <noreply@#{Settings.mail_domain}>" as mail sender' do
-      expect(mail.header[:from].value).to eq(['TaxonWorks <noreply@example.com>'])
+      expect(mail.header[:from].value).to eq('TaxonWorks <noreply@example.com>')
     end
   end
 
@@ -50,7 +50,7 @@
     end
 
     it 'renders "TaxonWorks <noreply@#{Settings.mail_domain}>" as mail sender' do
-      expect(mail.header[:from].value).to eq(['TaxonWorks <noreply@example.com>'])
+      expect(mail.header[:from].value).to eq('TaxonWorks <noreply@example.com>')
     end
 
     it 'shows the user\'s e-mail address in the e-mail body' do

From 6c1e2c3fbabc5d63059e344cc513b31017d35b0c Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Wed, 14 Dec 2022 12:45:42 -0600
Subject: [PATCH 128/160] used recently

---
 app/models/biological_relationship.rb | 12 ++++++------
 app/models/collecting_event.rb        |  4 ++--
 app/models/collection_object.rb       |  4 ++--
 app/models/confidence_level.rb        | 12 ++++++------
 app/models/extract.rb                 |  4 ++--
 app/models/geographic_area.rb         | 10 +++++-----
 app/models/image.rb                   |  2 +-
 app/models/keyword.rb                 | 22 +++++++++++-----------
 app/models/loan.rb                    |  6 +++---
 app/models/namespace.rb               |  4 ++--
 app/models/otu.rb                     |  4 ++--
 app/models/person.rb                  |  8 ++++----
 app/models/predicate.rb               | 12 ++++++------
 app/models/protocol.rb                |  8 ++++----
 app/models/repository.rb              | 12 ++++++------
 app/models/sequence.rb                |  6 +++---
 app/models/source.rb                  |  8 ++++----
 app/models/taxon_name.rb              |  8 ++++----
 app/models/topic.rb                   | 10 +++++-----
 19 files changed, 78 insertions(+), 78 deletions(-)

diff --git a/app/models/biological_relationship.rb b/app/models/biological_relationship.rb
index 7a4575fbba..4b14e5b5fc 100644
--- a/app/models/biological_relationship.rb
+++ b/app/models/biological_relationship.rb
@@ -43,19 +43,19 @@ class BiologicalRelationship < ApplicationRecord
   accepts_nested_attributes_for :biological_relationship_types, allow_destroy: true
 
   # @return [Scope]
-  #    the max 10 most recently used biological relationships 
+  #    the max 10 most recently used biological relationships
   def self.used_recently(user_id, project_id)
       t = BiologicalAssociation.arel_table
-    k = BiologicalRelationship.arel_table 
+    k = BiologicalRelationship.arel_table
 
     # i is a select manager
     i = t.project(t['biological_relationship_id'], t['created_at']).from(t)
-      .where(t['created_at'].gt( 10.weeks.ago ))
-      .where(t['created_by_id'].eq(user_id))
+      .where(t['updated_at'].gt( 10.weeks.ago ))
+      .where(t['updated_by_id'].eq(user_id))
       .where(t['project_id'].eq(project_id))
-      .order(t['created_at'].desc)
+      .order(t['updated_at'].desc)
 
-    # z is a table alias 
+    # z is a table alias
     z = i.as('recent_t')
 
     BiologicalRelationship.joins(
diff --git a/app/models/collecting_event.rb b/app/models/collecting_event.rb
index 044d467243..9724c614bb 100644
--- a/app/models/collecting_event.rb
+++ b/app/models/collecting_event.rb
@@ -324,7 +324,7 @@ def verbatim_label=(value)
     write_attribute(:md5_of_verbatim_label, Utilities::Strings.generate_md5(value))
   end
 
-  scope :used_recently, -> { joins(:collection_objects).includes(:collection_objects).where(collection_objects: { created_at: 1.weeks.ago..Time.now } ).order('"collection_objects"."created_at" DESC') }
+  scope :used_recently, -> { joins(:collection_objects).includes(:collection_objects).where(collection_objects: { updated_at: 1.weeks.ago..Time.now } ).order('"collection_objects"."updated_at" DESC') }
   scope :used_in_project, -> (project_id) { joins(:collection_objects).where( collection_objects: { project_id: project_id } ) }
 
   class << self
@@ -794,7 +794,7 @@ def get_geographic_name_classification
   #   determines (prioritizes) the method to be used to decided the geographic name classification
   #   (string labels for country, state, county) for this collecting_event.
   def geographic_name_classification_method
-    # Over-ride first 
+    # Over-ride first
     return :geographic_area if meta_prioritize_geographic_area
 
     return :preferred_georeference if !preferred_georeference.nil?
diff --git a/app/models/collection_object.rb b/app/models/collection_object.rb
index 425736b005..6d8af5eafd 100644
--- a/app/models/collection_object.rb
+++ b/app/models/collection_object.rb
@@ -577,13 +577,13 @@ def self.used_recently(user_id, project_id, used_on = '')
                 t['biological_association_subject_type'].eq('CollectionObject') # !! note it's not biological_collection_object_id
               )
             )
-              .where(t['created_by_id'].eq(user_id))
+              .where(t['updated_by_id'].eq(user_id))
               .where(t['project_id'].eq(project_id))
               .order(t['updated_at'].desc)
         else
           t.project(t['biological_collection_object_id'], t['updated_at']).from(t)
             .where(t['updated_at'].gt( 1.weeks.ago ))
-            .where(t['created_by_id'].eq(user_id))
+            .where(t['updated_by_id'].eq(user_id))
             .where(t['project_id'].eq(project_id))
             .order(t['updated_at'].desc)
         end
diff --git a/app/models/confidence_level.rb b/app/models/confidence_level.rb
index 9abadc84f0..3ab82d2e51 100644
--- a/app/models/confidence_level.rb
+++ b/app/models/confidence_level.rb
@@ -1,4 +1,4 @@
-# A user-defined level of data quality vi Confidences.  
+# A user-defined level of data quality vi Confidences.
 class ConfidenceLevel < ControlledVocabularyTerm
   has_many :confidences, foreign_key: :confidence_level_id, dependent: :destroy, inverse_of: :confidence_level
 
@@ -11,14 +11,14 @@ def self.used_recently(user_id, project_id, klass)
     k = ConfidenceLevel.arel_table
 
     # i is a select manager
-    i = t.project(t['confidence_level_id'], t['created_at']).from(t)
+    i = t.project(t['confidence_level_id'], t['updated_at']).from(t)
          .where(t['confidence_object_type'].eq(klass))
-         .where(t['created_at'].gt( 1.months.ago ))
-         .where(t['created_by_id'].eq(user_id))
+         .where(t['updated_at'].gt( 1.months.ago ))
+         .where(t['updated_by_id'].eq(user_id))
          .where(t['project_id'].eq(project_id))
-         .order(t['created_at'].desc)
+         .order(t['updated_at'].desc)
 
-    # z is a table alias 
+    # z is a table alias
     z = i.as('recent_t')
 
     ConfidenceLevel.joins(
diff --git a/app/models/extract.rb b/app/models/extract.rb
index b80edd512a..1380afc46d 100644
--- a/app/models/extract.rb
+++ b/app/models/extract.rb
@@ -92,13 +92,13 @@ def self.used_recently(user_id, project_id, used_on = '')
                 t['biological_association_subject_type'].eq('CollectionObject') # !! note it's not biological_collection_object_id
               )
             )
-              .where(t['created_by_id'].eq(user_id))
+              .where(t['updated_by_id'].eq(user_id))
               .where(t['project_id'].eq(project_id))
             .order(t['updated_at'].desc)
         else
           t.project(t['biological_collection_object_id'], t['updated_at']).from(t)
             .where(t['updated_at'].gt( 1.weeks.ago ))
-            .where(t['created_by_id'].eq(user_id))
+            .where(t['updated_by_id'].eq(user_id))
             .where(t['project_id'].eq(project_id))
             .order(t['updated_at'].desc)
         end
diff --git a/app/models/geographic_area.rb b/app/models/geographic_area.rb
index fa88509450..0a2a207191 100644
--- a/app/models/geographic_area.rb
+++ b/app/models/geographic_area.rb
@@ -255,7 +255,7 @@ def categorize
     end
 
      # TODO: Wrap this a pre-loading constant. This makes specs very fragile.
-     
+
      unless Rails.env == 'test'
        n = CACHED_GEOGRAPHIC_AREA_TYPES[geographic_area_type_id]
      end
@@ -494,11 +494,11 @@ def self.used_recently(user_id, project_id, used_on = 'CollectingEvent')
         when 'CollectingEvent'
           t = CollectingEvent.arel_table
           # i is a select manager
-          i = t.project(t['geographic_area_id'], t['created_at']).from(t)
-                  .where(t['created_at'].gt(1.weeks.ago))
-                  .where(t['created_by_id'].eq(user_id))
+          i = t.project(t['geographic_area_id'], t['updated_at']).from(t)
+                  .where(t['updated_at'].gt(1.weeks.ago))
+                  .where(t['updated_by_id'].eq(user_id))
                   .where(t['project_id'].eq(project_id))
-                  .order(t['created_at'].desc)
+                  .order(t['updated_at'].desc)
 
           # z is a table alias
           z = i.as('recent_t')
diff --git a/app/models/image.rb b/app/models/image.rb
index ca4c2abced..8a8f8864fb 100644
--- a/app/models/image.rb
+++ b/app/models/image.rb
@@ -319,7 +319,7 @@ def self.used_recently(user_id, project_id, used_on = '')
     # i is a select manager
     j = d.project(d['image_id'], d['updated_at'], d['depiction_object_type']).from(d)
       .where(d['updated_at'].gt( 1.weeks.ago ))
-      .where(d['created_by_id'].eq(user_id))
+      .where(d['updated_by_id'].eq(user_id))
       .where(d['project_id'].eq(project_id))
       .order(d['updated_at'].desc)
 
diff --git a/app/models/keyword.rb b/app/models/keyword.rb
index ce957da714..619b89f9af 100644
--- a/app/models/keyword.rb
+++ b/app/models/keyword.rb
@@ -1,8 +1,8 @@
-class Keyword < ControlledVocabularyTerm 
+class Keyword < ControlledVocabularyTerm
 
   has_many :tags, foreign_key: :keyword_id, dependent: :destroy, inverse_of: :keyword, validate: true
 
-  scope :used_on_klass, -> (klass) { joins(:tags).where(tags: {tag_object_type: klass} ) } # remember to .distinct 
+  scope :used_on_klass, -> (klass) { joins(:tags).where(tags: {tag_object_type: klass} ) } # remember to .distinct
 
   def tagged_objects
     tags.collect{|t| t.tag_object}
@@ -24,21 +24,21 @@ def self.used_recently(user_id, project_id, klass='Tag', target)
 
     # i is a select manager
     if target.blank?
-      i = t.project(t['keyword_id'], t['created_at']).from(t)
-        .where(t['created_at'].gt( 1.months.ago ))
-        .where(t['created_by_id'].eq(user_id))
+      i = t.project(t['keyword_id'], t['updated_at']).from(t)
+        .where(t['updated_at'].gt( 1.months.ago ))
+        .where(t['updated_by_id'].eq(user_id))
         .where(t['project_id'].eq(project_id))
-        .order(t['created_at'].desc)
+        .order(t['updated_at'].desc)
     else
-      i = t.project(t['keyword_id'], t['created_at']).from(t)
+      i = t.project(t['keyword_id'], t['updated_at']).from(t)
            .where(t['tag_object_type'].eq(target))
-           .where(t['created_at'].gt( 1.months.ago ))
-           .where(t['created_by_id'].eq(user_id))
+           .where(t['updated_at'].gt( 1.months.ago ))
+           .where(t['updated_by_id'].eq(user_id))
            .where(t['project_id'].eq(project_id))
-           .order(t['created_at'].desc)
+           .order(t['updated_at'].desc)
     end
 
-    # z is a table alias 
+    # z is a table alias
     z = i.as('recent_t')
 
     ControlledVocabularyTerm.joins(
diff --git a/app/models/loan.rb b/app/models/loan.rb
index b61348bd8a..b68428cbd8 100644
--- a/app/models/loan.rb
+++ b/app/models/loan.rb
@@ -190,10 +190,10 @@ def self.used_recently(project_id)
     k = Loan.arel_table
 
     # i is a select manager
-    i = t.project(t['loan_id'], t['created_at']).from(t)
-      .where(t['created_at'].gt( 3.weeks.ago ))
+    i = t.project(t['loan_id'], t['updated_at']).from(t)
+      .where(t['updated_at'].gt( 3.weeks.ago ))
       .where(t['project_id'].eq(project_id))
-      .order(t['created_at'].desc)
+      .order(t['updated_at'].desc)
 
     # z is a table alias
     z = i.as('recent_t')
diff --git a/app/models/namespace.rb b/app/models/namespace.rb
index 16ed826f36..5d1f3d04c7 100644
--- a/app/models/namespace.rb
+++ b/app/models/namespace.rb
@@ -54,7 +54,7 @@
 #
 # @!attribute is_virtual
 # @return [Boolean]
-#   Defaults to false. If true then the namespace short name is not part of the "physical" identifier.  Required to handle identifiers incoming 
+#   Defaults to false. If true then the namespace short name is not part of the "physical" identifier.  Required to handle identifiers incoming
 # from DwC in some contexts.
 #
 class Namespace < ApplicationRecord
@@ -75,7 +75,7 @@ class Namespace < ApplicationRecord
   has_many :identifiers, autosave: true, dependent: :restrict_with_error, inverse_of: :namespace
 
   scope :used_on_klass, -> (klass) { joins(:identifiers).where(identifiers: {identifier_object_type: klass} ) }
-  scope :used_recently, -> { joins(:identifiers).includes(:identifiers).where(identifiers: { created_at: 10.weeks.ago..Time.now } ).order('"identifiers"."created_at" DESC') }
+  scope :used_recently, -> { joins(:identifiers).includes(:identifiers).where(identifiers: { updated_at: 10.weeks.ago..Time.now } ).order('"identifiers"."created_at" DESC') }
   scope :used_in_project, -> (project_id) { joins(:identifiers).where( identifiers: { project_id: project_id } ) }
 
   def is_virtual?
diff --git a/app/models/otu.rb b/app/models/otu.rb
index ab6a0190fd..4957502b70 100644
--- a/app/models/otu.rb
+++ b/app/models/otu.rb
@@ -223,13 +223,13 @@ def self.used_recently(user_id, project_id, used_on = '')
                 t['biological_association_object_type'].eq('Otu')
               )
             )
-              .where(t['created_by_id'].eq(user_id))
+              .where(t['updated_by_id'].eq(user_id))
               .where(t['project_id'].eq(project_id))
               .order(t['updated_at'].desc)
         else
           t.project(t['otu_id'], t['updated_at']).from(t)
             .where(t['updated_at'].gt( 1.weeks.ago ))
-            .where(t['created_by_id'].eq(user_id))
+            .where(t['updated_by_id'].eq(user_id))
             .where(t['project_id'].eq(project_id))
             .order(t['updated_at'].desc)
         end
diff --git a/app/models/person.rb b/app/models/person.rb
index d2ed968389..1ac0e3d076 100644
--- a/app/models/person.rb
+++ b/app/models/person.rb
@@ -458,11 +458,11 @@ def self.used_recently(user_id, role_type = 'SourceAuthor')
     p = Person.arel_table
 
     # i is a select manager
-    i = t.project(t['person_id'], t['type'], t['created_at']).from(t)
-      .where(t['created_at'].gt(1.weeks.ago))
-      .where(t['created_by_id'].eq(user_id))
+    i = t.project(t['person_id'], t['type'], t['updated_at']).from(t)
+      .where(t['updated_at'].gt(1.weeks.ago))
+      .where(t['updated_by_id'].eq(user_id))
       .where(t['type'].eq(role_type))
-      .order(t['created_at'].desc)
+      .order(t['updated_at'].desc)
 
     # z is a table alias
     z = i.as('recent_t')
diff --git a/app/models/predicate.rb b/app/models/predicate.rb
index e1cbc0ebfe..721a261767 100644
--- a/app/models/predicate.rb
+++ b/app/models/predicate.rb
@@ -5,19 +5,19 @@ class Predicate < ControlledVocabularyTerm
   scope :used_on_klass, -> (klass) { joins(:internal_attributes).where(data_attributes: {attribute_subject_type: klass}) }
 
   # @return [Scope]
-  #    the max 10 most recently used predicates 
+  #    the max 10 most recently used predicates
   def self.used_recently(user_id, project_id, klass)
     i = InternalAttribute.arel_table
     p = Predicate.arel_table
 
     # i is a select manager
-    i = i.project(i['controlled_vocabulary_term_id'], i['created_at']).from(i)
-      .where(i['created_at'].gt( 1.weeks.ago ))
-      .where(i['created_by_id'].eq(user_id))
+    i = i.project(i['controlled_vocabulary_term_id'], i['updated_at']).from(i)
+      .where(i['updated_at'].gt( 10.weeks.ago ))
+      .where(i['updated_by_id'].eq(user_id))
       .where(i['project_id'].eq(project_id))
-      .order(i['created_at'].desc)
+      .order(i['updated_at'].desc)
 
-    # z is a table alias 
+    # z is a table alias
     z = i.as('recent_t')
 
     Predicate.used_on_klass(klass).joins(
diff --git a/app/models/protocol.rb b/app/models/protocol.rb
index 7b9fe24278..da667fee8d 100644
--- a/app/models/protocol.rb
+++ b/app/models/protocol.rb
@@ -26,11 +26,11 @@ def self.used_recently(user_id, project_id, klass)
     k = self.arel_table
 
     # i is a select manager
-    i = t.project(t['protocol_id'], t['created_at']).from(t)
-      .where(t['created_at'].gt( 1.weeks.ago ))
-      .where(t['created_by_id'].eq(user_id))
+    i = t.project(t['protocol_id'], t['updated_at']).from(t)
+      .where(t['updated_at'].gt( 10.weeks.ago ))
+      .where(t['updated_by_id'].eq(user_id))
       .where(t['project_id'].eq(project_id))
-      .order(t['created_at'].desc)
+      .order(t['updated_at'].desc)
 
     # z is a table alias
     z = i.as('recent_t')
diff --git a/app/models/repository.rb b/app/models/repository.rb
index d299a6c9b1..bfdb3af417 100644
--- a/app/models/repository.rb
+++ b/app/models/repository.rb
@@ -44,9 +44,9 @@ class Repository < ApplicationRecord
 
   has_many :collection_objects, inverse_of: :repository, dependent: :restrict_with_error
   has_many :current_collection_objects, class_name: 'CollectionObject', foreign_key: :current_repository_id, inverse_of: :current_repository, dependent: :restrict_with_error
-  
+
   has_many :extracts, inverse_of: :repository, dependent: :restrict_with_error
-  
+
   validates_presence_of :name, :acronym
 
   scope :used_in_project, -> (project_id) { joins(:collection_objects).where( collection_objects: { project_id: project_id } ) }
@@ -56,11 +56,11 @@ def self.used_recently(user_id, project_id)
     p = Repository.arel_table
 
     # i is a select manager
-    i = t.project(t['repository_id'], t['created_at']).from(t)
-            .where(t['created_at'].gt(4.weeks.ago))
-            .where(t['created_by_id'].eq(user_id))
+    i = t.project(t['repository_id'], t['updated_at']).from(t)
+            .where(t['updated_at'].gt(4.weeks.ago))
+            .where(t['updated_by_id'].eq(user_id))
             .where(t['project_id'].eq(project_id))
-            .order(t['created_at'].desc)
+            .order(t['updated_at'].desc)
 
     # z is a table alias
     z = i.as('recent_t')
diff --git a/app/models/sequence.rb b/app/models/sequence.rb
index fbaa5734eb..63b2065d9d 100644
--- a/app/models/sequence.rb
+++ b/app/models/sequence.rb
@@ -87,12 +87,12 @@ def self.used_recently(user_id, project_id, used_on = nil)
     # i is a select manager
     i = t.project(t['sequence_id'], t['updated_at']).from(t)
       .where(t['updated_at'].gt( 1.weeks.ago ))
-      .where(t['created_by_id'].eq(user_id))
+      .where(t['updated_by_id'].eq(user_id))
       .where(t['project_id'].eq(project_id))
       .order(t['updated_at'].desc)
 
     # i is a select manager
-    i = case used_on 
+    i = case used_on
         when 'SequenceRelationship'
           t.project(t['object_sequence_id'], t['updated_at']).from(t)
             .where(
@@ -113,7 +113,7 @@ def self.used_recently(user_id, project_id, used_on = nil)
     z = i.as('recent_t')
 
     j = case used_on
-        when 'SequenceRelationship' 
+        when 'SequenceRelationship'
           Arel::Nodes::InnerJoin.new(z, Arel::Nodes::On.new(
             z['object_sequence_id'].eq(p['id'])
           ))
diff --git a/app/models/source.rb b/app/models/source.rb
index cb63ac7292..f3e93f10c0 100644
--- a/app/models/source.rb
+++ b/app/models/source.rb
@@ -296,15 +296,15 @@ def self.batch_create(file)
 
   # @param used_on [String] a model name
   # @return [Scope]
-  #    the max 10 most recently used (1 week, could parameterize) TaxonName, as used 
+  #    the max 10 most recently used (1 week, could parameterize) TaxonName, as used
   def self.used_recently(user_id, project_id, used_on = 'TaxonName')
    Source.select('sources.id').
      joins(:citations)
-         .where(citations: {created_by_id: user_id,
+         .where(citations: {updated_by_id: user_id,
                 project_id: project_id,
                 citation_object_type: used_on,
-                created_at: 1.week.ago..})
-        .order('citations.created_at DESC')
+                updated_at: 1.week.ago..})
+        .order('citations.updated_at DESC')
       .pluck(:id).uniq
   end
 
diff --git a/app/models/taxon_name.rb b/app/models/taxon_name.rb
index 135cf4ad20..99db9d673b 100644
--- a/app/models/taxon_name.rb
+++ b/app/models/taxon_name.rb
@@ -1388,10 +1388,10 @@ def create_otu
   # @return [Scope]
   #   All taxon names attached to relationships recently created by user
   def self.used_recently_in_classifications(user_id, project_id)
-    TaxonName.where(project_id: project_id, created_by_id: user_id)
+    TaxonName.where(project_id: project_id, updated_by_id: user_id)
       .joins(:taxon_name_classifications)
       .includes(:taxon_name_classifications)
-      .where(taxon_name_classifications: { created_at: 1.weeks.ago..Time.now } )
+      .where(taxon_name_classifications: { updated_at: 1.weeks.ago..Time.now } )
       .order('taxon_name_classifications.updated_at DESC')
   end
 
@@ -1406,8 +1406,8 @@ def self.used_recently_in_relationships(user_id, project_id)
       .or(t2[:updated_by_id].eq(user_id).or(t2[:created_by_id].eq(user_id))
     ).to_sql
 
-    sql2 = t1[:created_at].between( 1.weeks.ago..Time.now )
-      .or( t2[:created_at].between( 1.weeks.ago..Time.now ) ).to_sql
+    sql2 = t1[:updated_at].between( 1.weeks.ago..Time.now )
+      .or( t2[:updated_at].between( 1.weeks.ago..Time.now ) ).to_sql
 
     TaxonName.with_taxon_name_relationships
       .where(taxon_names: {project_id: project_id})
diff --git a/app/models/topic.rb b/app/models/topic.rb
index e29940f744..b45ac11901 100644
--- a/app/models/topic.rb
+++ b/app/models/topic.rb
@@ -1,4 +1,4 @@
-# A Topic is a user defined subject.  It is used in conjuction with a citation on an OTU.  
+# A Topic is a user defined subject.  It is used in conjuction with a citation on an OTU.
 # Topics assert that "this source says something about this taxon on this topic."
 #
 class Topic < ControlledVocabularyTerm
@@ -43,11 +43,11 @@ def self.used_recently(user_id, project_id, klass, used_on = 'Citation')
     p = Topic.arel_table
 
     # i is a select manager
-    i = t.project(t['topic_id'], t['created_at']).from(t)
-      .where(t['created_at'].gt(10.weeks.ago))
-      .where(t['created_by_id'].eq(user_id))
+    i = t.project(t['topic_id'], t['updated_at']).from(t)
+      .where(t['updated_at'].gt(10.weeks.ago))
+      .where(t['updated_by_id'].eq(user_id))
       .where(t['project_id'].eq(project_id))
-      .order(t['created_at'].desc)
+      .order(t['updated_at'].desc)
 
     # z is a table alias
     z = i.as('recent_t')

From e3374ff573b8941d72deeca63f14e035075f9e9c Mon Sep 17 00:00:00 2001
From: Geoff Ower <gdower@illinois.edu>
Date: Wed, 14 Dec 2022 13:08:38 -0600
Subject: [PATCH 129/160] Allow multiple taxon remarks

---
 lib/export/coldp/files/taxon.rb | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/export/coldp/files/taxon.rb b/lib/export/coldp/files/taxon.rb
index 8bc156f2ef..bd3f6b5d94 100644
--- a/lib/export/coldp/files/taxon.rb
+++ b/lib/export/coldp/files/taxon.rb
@@ -84,9 +84,10 @@ def self.according_to_date(otu)
   def self.link(otu)
     # API or public interface
   end
-  def self.remarks(otu, taxon_remarks_vocab_id)
-    if !otu.data_attributes.find_by(controlled_vocabulary_term_id: taxon_remarks_vocab_id).nil?
-      otu.data_attributes.find_by(controlled_vocabulary_term_id: taxon_remarks_vocab_id).value
+
+  def self.remarks(otu, taxon_remarks_vocab)
+    if otu.data_attributes.where(controlled_vocabulary_term_id: taxon_remarks_vocab).any?
+      otu.data_attributes.where(controlled_vocabulary_term_id: taxon_remarks_vocab).pluck(:value).join('|')
     else
       nil
     end

From c1aa823d17f427ec6b1254f6087b65fe6347411f Mon Sep 17 00:00:00 2001
From: Geoff Ower <gdower@illinois.edu>
Date: Wed, 14 Dec 2022 13:09:20 -0600
Subject: [PATCH 130/160] Do not set Current

---
 lib/export/coldp/files/taxon.rb | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/lib/export/coldp/files/taxon.rb b/lib/export/coldp/files/taxon.rb
index bd3f6b5d94..c246ae8249 100644
--- a/lib/export/coldp/files/taxon.rb
+++ b/lib/export/coldp/files/taxon.rb
@@ -129,14 +129,8 @@ def self.generate(otus, root_otu_id = nil, reference_csv = nil, prefer_unlabelle
         remarks
       }
 
-      if root_otu_id.nil?
-        Current.project_id = otus[0].project_id
-      else
-        Current.project_id = Otu.find(root_otu_id).project_id
-      end
-
       taxon_remarks_vocab_id = Predicate.find_by(uri: 'https://github.com/catalogueoflife/coldp#Taxon.remarks',
-                                                 project_id: Current.project_id)&.id
+                                                 project_id: otus[0]&.project_id)&.id
 
       otus.each do |o|
         # !! When a name is a synonmy (combination), but that combination has no OTU

From 6bb6899358d45002a705c7d36e81b9d4e86104fb Mon Sep 17 00:00:00 2001
From: Geoff Ower <gdower@illinois.edu>
Date: Wed, 14 Dec 2022 13:09:46 -0600
Subject: [PATCH 131/160] Allow multiple name remarks

---
 lib/export/coldp/files/name.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/export/coldp/files/name.rb b/lib/export/coldp/files/name.rb
index 8d160be3bf..09ceee075d 100644
--- a/lib/export/coldp/files/name.rb
+++ b/lib/export/coldp/files/name.rb
@@ -18,8 +18,8 @@ def self.code_field(taxon_name)
   end
 
   def self.remarks(name, name_remarks_vocab_id)
-    if !name.data_attributes.find_by(controlled_vocabulary_term_id: name_remarks_vocab_id).nil?
-      name.data_attributes.find_by(controlled_vocabulary_term_id: name_remarks_vocab_id).value
+    if name.data_attributes.where(controlled_vocabulary_term_id: name_remarks_vocab_id).any?
+      name.data_attributes.where(controlled_vocabulary_term_id: name_remarks_vocab_id).pluck(:value).join('|')
     else
       nil
     end

From a21fa6a32430bf52477e30edc9706d40569f93c6 Mon Sep 17 00:00:00 2001
From: Geoff Ower <gdower@illinois.edu>
Date: Wed, 14 Dec 2022 13:43:35 -0600
Subject: [PATCH 132/160] Do not set Current.project_id

---
 lib/export/coldp.rb | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/export/coldp.rb b/lib/export/coldp.rb
index 769f1dda46..3838639c9e 100644
--- a/lib/export/coldp.rb
+++ b/lib/export/coldp.rb
@@ -29,7 +29,6 @@ def self.otus(otu_id)
 
     def self.export(otu_id, prefer_unlabelled_otus: true)
       otus = otus(otu_id)
-      Current.project_id = Otu.find(otu_id).project_id
 
       # source_id: [csv_array]
       ref_csv = {}
@@ -37,12 +36,12 @@ def self.export(otu_id, prefer_unlabelled_otus: true)
       # TODO: This will likely have to change, it is renamed on serving the file.
       zip_file_path = "/tmp/_#{SecureRandom.hex(8)}_coldp.zip"
 
-      metadata_path = Zaru::sanitize!("/tmp/#{::Project.find(Current.project_id).name}_#{DateTime.now}_metadata.yaml").gsub(' ', '_').downcase
+      metadata_path = Zaru::sanitize!("/tmp/#{::Project.find(otus[0].project_id).name}_#{DateTime.now}_metadata.yaml").gsub(' ', '_').downcase
       version = Taxonworks::VERSION
       if Settings.sandbox_mode?
         version = Settings.sandbox_commit_sha
       end
-      metadata = {"title" =>::Project.find(Current.project_id).name,
+      metadata = {"title" =>::Project.find(otus[0].project_id).name,
                   "version" => version,
                   "issued" => DateTime.now.strftime('%Y-%m-%d'),
       }
@@ -79,7 +78,7 @@ def self.export(otu_id, prefer_unlabelled_otus: true)
     end
 
     def self.filename(otu)
-      Zaru::sanitize!("#{::Project.find(Current.project_id).name}_coldp_otu_id_#{otu.id}_#{DateTime.now}.zip").gsub(' ', '_').downcase
+      Zaru::sanitize!("#{::Project.find(otu.project_id).name}_coldp_otu_id_#{otu.id}_#{DateTime.now}.zip").gsub(' ', '_').downcase
     end
 
     def self.download(otu, request = nil, prefer_unlabelled_otus: true)

From 58528cc72bd12fb0429fdc90ef7171d3e597a1b4 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Wed, 14 Dec 2022 13:49:31 -0600
Subject: [PATCH 133/160] used recently

---
 spec/models/confidence_level_spec.rb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/spec/models/confidence_level_spec.rb b/spec/models/confidence_level_spec.rb
index fadd6ed311..2a9caee143 100644
--- a/spec/models/confidence_level_spec.rb
+++ b/spec/models/confidence_level_spec.rb
@@ -2,7 +2,7 @@
 
 describe ConfidenceLevel, type: :model, group: :confidences do
 
-  let(:confidence_level) { ConfidenceLevel.new } 
+  let(:confidence_level) { ConfidenceLevel.new }
   let(:otu) { FactoryBot.create(:valid_otu) }
 
   let(:k1) { FactoryBot.create(:valid_confidence_level) }
@@ -24,9 +24,9 @@
   end
 
   context 'scopes' do
-    let!(:confidence) { Confidence.create!(confidence_level: k1, confidence_object: otu) } 
-    let!(:old_confidence) { Confidence.create!(confidence_level: k2, confidence_object: otu, created_at: 4.years.ago) } 
-    let!(:new_confidence) { Confidence.create!(confidence_level: k1, confidence_object: FactoryBot.create(:valid_specimen)) } 
+    let!(:confidence) { Confidence.create!(confidence_level: k1, confidence_object: otu) }
+    let!(:old_confidence) { Confidence.create!(confidence_level: k2, confidence_object: otu, created_at: 4.years.ago, updated_at: 4.years.ago) }
+    let!(:new_confidence) { Confidence.create!(confidence_level: k1, confidence_object: FactoryBot.create(:valid_specimen)) }
 
     specify '#used_on_klass 1' do
       expect(ConfidenceLevel.used_on_klass('Otu')).to contain_exactly(k1, k2)
@@ -57,7 +57,7 @@
       end
 
       specify '#confidences' do
-        expect(k1.confidences).to contain_exactly(t1, t2) 
+        expect(k1.confidences).to contain_exactly(t1, t2)
       end
 
       specify '#confidenced_objects' do
@@ -68,7 +68,7 @@
         expect(k1.confidenced_object_class_names).to eq(%w{Otu CollectionObject})
       end
     end
-    
+
   end
 end
 

From 7d8651030494b7d2f32f1f1eef6f72360cf1e583 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Wed, 14 Dec 2022 14:26:40 -0600
Subject: [PATCH 134/160] used recently

---
 spec/models/keyword_spec.rb   | 10 +++++-----
 spec/models/predicate_spec.rb |  6 +++---
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/spec/models/keyword_spec.rb b/spec/models/keyword_spec.rb
index f36a450ca1..0b252e6ff3 100644
--- a/spec/models/keyword_spec.rb
+++ b/spec/models/keyword_spec.rb
@@ -1,8 +1,8 @@
 require 'rails_helper'
 
 describe Keyword, type: :model, group: :tags do
-  
-  let(:keyword) { Keyword.new } 
+
+  let(:keyword) { Keyword.new }
   let(:otu) { FactoryBot.create(:valid_otu) }
 
   specify '#tags' do
@@ -21,12 +21,12 @@
       expect {c = CitationTopic.new(topic: k)}.to raise_error(ActiveRecord::AssociationTypeMismatch)
     end
   end
-  
+
   context 'scopes' do
     let(:k) { FactoryBot.create(:valid_keyword) }
     let(:k2) { FactoryBot.create(:valid_keyword) }
-    let!(:tag) { Tag.create(keyword: k, tag_object: otu) } 
-    let!(:old_tag) { Tag.create(keyword: k2, tag_object: otu, created_at: 4.years.ago) } 
+    let!(:tag) { Tag.create(keyword: k, tag_object: otu) }
+    let!(:old_tag) { Tag.create(keyword: k2, tag_object: otu, created_at: 4.years.ago, updated_at: 4.years.ago) }
 
     specify '#used_on_klass 1' do
       expect(Keyword.used_on_klass('Otu')).to contain_exactly(k, k2)
diff --git a/spec/models/predicate_spec.rb b/spec/models/predicate_spec.rb
index 4df87d99c7..291871f732 100644
--- a/spec/models/predicate_spec.rb
+++ b/spec/models/predicate_spec.rb
@@ -14,16 +14,16 @@
 
     let!(:data_attribute) { otu.data_attributes << InternalAttribute.new(predicate: predicate, value: '123') }
 
-    let!(:other_attribute) { specimen.data_attributes << InternalAttribute.new(predicate: other_predicate, value: '123', created_at: 4.years.ago) }
+    let!(:other_attribute) { specimen.data_attributes << InternalAttribute.new(predicate: other_predicate, value: '123', created_at: 4.years.ago, updated_at: 4.years.ago) }
 
 
     specify '.used_on_klass 1' do
       expect(Predicate.used_on_klass('Otu')).to contain_exactly(predicate)
-    end 
+    end
 
     specify '.used_on_klass 2' do
       expect(Predicate.used_on_klass('CollectionObject')).to contain_exactly(other_predicate)
-    end 
+    end
 
     specify '.used_recently' do
       expect(Predicate.used_recently(predicate.created_by_id, predicate.project_id, '')).to contain_exactly()

From 505af88e035724e25658e3574d2489d5d0765c6b Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 14 Dec 2022 18:31:15 -0300
Subject: [PATCH 135/160] Fix #3245

---
 CHANGELOG.md                                  |  2 +
 app/javascript/packs/application.scss         |  1 +
 .../vue/assets/styles/utilities.scss          | 19 +++++
 .../radials/annotator/annotator.vue           |  8 ++-
 .../vue/components/radials/filter/radial.vue  |  5 +-
 .../vue/components/radials/label/radial.vue   |  5 +-
 .../components/radials/navigation/radial.vue  |  2 +-
 .../vue/components/radials/object/radial.vue  |  2 +-
 app/javascript/vue/components/ui/Modal.vue    | 70 ++++++++++++-------
 .../components/CollectionObjectsTable.vue     | 66 ++++++++++-------
 10 files changed, 115 insertions(+), 65 deletions(-)
 create mode 100644 app/javascript/vue/assets/styles/utilities.scss

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7f7db7ce6f..3a7761101a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -34,6 +34,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - original combination label disappears when relationship doesn't include the current taxon name [#3067]
 - Sometimes keyboard table is duplicating shortcuts
 - Export Project Database task not exporting rows whose `project_id` is `NULL` [#3203]
+- Close icon is difficult to distinguish when modal background is transparent [#3245]
 
 ### Changed
 - Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
@@ -61,6 +62,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
 [#3234]: https://github.com/SpeciesFileGroup/taxonworks/issues/3234
 [#3238]: https://github.com/SpeciesFileGroup/taxonworks/issues/3238
+[#3245]: https://github.com/SpeciesFileGroup/taxonworks/issues/3245
 
 ## [0.29.6] - 2022-11-08
 
diff --git a/app/javascript/packs/application.scss b/app/javascript/packs/application.scss
index 7b7751e2b2..6938b4f2ea 100644
--- a/app/javascript/packs/application.scss
+++ b/app/javascript/packs/application.scss
@@ -1,4 +1,5 @@
 $font-prefix: '../../../node_modules/@ibm/plex';
+@import '../vue//assets/styles//utilities.scss';
 @import '../vue/assets/styles/variables/_palette.scss';
 @import '../vue/assets/styles/variables/_exports.scss';
 @import '../vue/assets/styles/components/buttons.scss';
diff --git a/app/javascript/vue/assets/styles/utilities.scss b/app/javascript/vue/assets/styles/utilities.scss
new file mode 100644
index 0000000000..57c1f31d8a
--- /dev/null
+++ b/app/javascript/vue/assets/styles/utilities.scss
@@ -0,0 +1,19 @@
+.invert-color {
+  filter: invert(1);
+}
+
+.opacity-100 {
+  opacity: 1;
+}
+
+.opacity-0 {
+  opacity: 0;
+}
+
+.bg-transparent {
+  background-color: transparent;
+}
+
+.shadow-none {
+  box-shadow: none;
+}
\ No newline at end of file
diff --git a/app/javascript/vue/components/radials/annotator/annotator.vue b/app/javascript/vue/components/radials/annotator/annotator.vue
index 62c53af53c..c5596d515c 100644
--- a/app/javascript/vue/components/radials/annotator/annotator.vue
+++ b/app/javascript/vue/components/radials/annotator/annotator.vue
@@ -4,14 +4,16 @@
       class="radial-annotator">
       <modal
         v-if="display"
-        :container-style="{ backgroundColor: 'transparent', boxShadow: 'none' }"
-        @close="closeModal()">
+        transparent
+        @close="closeModal()"
+      >
         <template #header>
           <h3 class="flex-separate">
             <span v-html="title" />
             <span
               v-if="metadata"
-              class="separate-right">
+              class="separate-right"
+            >
               {{ metadata.object_type }}
             </span>
           </h3>
diff --git a/app/javascript/vue/components/radials/filter/radial.vue b/app/javascript/vue/components/radials/filter/radial.vue
index 4555e4bf96..e8d80f548a 100644
--- a/app/javascript/vue/components/radials/filter/radial.vue
+++ b/app/javascript/vue/components/radials/filter/radial.vue
@@ -2,10 +2,7 @@
   <div class="radial-annotator">
     <modal
       v-if="isVisible"
-      :container-style="{
-        backgroundColor: 'transparent',
-        boxShadow: 'none'
-      }"
+      transparent
       @close="closeModal"
     >
       <template #header>
diff --git a/app/javascript/vue/components/radials/label/radial.vue b/app/javascript/vue/components/radials/label/radial.vue
index 30fab61bdc..3b2e0a08b1 100644
--- a/app/javascript/vue/components/radials/label/radial.vue
+++ b/app/javascript/vue/components/radials/label/radial.vue
@@ -2,10 +2,7 @@
   <div class="radial-annotator">
     <modal
       v-if="isVisible"
-      :container-style="{
-        backgroundColor: 'transparent',
-        boxShadow: 'none'
-      }"
+      transparent
       @close="closeModal"
     >
       <template #header>
diff --git a/app/javascript/vue/components/radials/navigation/radial.vue b/app/javascript/vue/components/radials/navigation/radial.vue
index e6e803b130..1b882573b6 100644
--- a/app/javascript/vue/components/radials/navigation/radial.vue
+++ b/app/javascript/vue/components/radials/navigation/radial.vue
@@ -3,7 +3,7 @@
     <div class="radial-annotator">
       <modal
         v-if="display"
-        :container-style="{ backgroundColor: 'transparent', boxShadow: 'none' }"
+        transparent
         @close="closeModal()"
       >
         <template #header>
diff --git a/app/javascript/vue/components/radials/object/radial.vue b/app/javascript/vue/components/radials/object/radial.vue
index 8bda21e66b..596470a784 100644
--- a/app/javascript/vue/components/radials/object/radial.vue
+++ b/app/javascript/vue/components/radials/object/radial.vue
@@ -3,7 +3,7 @@
     <div class="radial-annotator">
       <modal-component
         v-if="display"
-        :container-style="{ backgroundColor: 'transparent', boxShadow: 'none' }"
+        transparent
         @close="closeModal()">
         <template #header>
           <h3
diff --git a/app/javascript/vue/components/ui/Modal.vue b/app/javascript/vue/components/ui/Modal.vue
index aa91bc39d6..ea859018ee 100644
--- a/app/javascript/vue/components/ui/Modal.vue
+++ b/app/javascript/vue/components/ui/Modal.vue
@@ -2,18 +2,25 @@
   <transition name="modal">
     <div
       class="modal-mask"
-      @click="$emit('close')"
-      @key.esc="$emit('close')">
+      @click="emit('close')"
+      @key.esc="emit('close')"
+    >
       <div class="modal-wrapper">
         <div
           class="modal-container"
-          :class="containerClass"
+          :class="{
+            'bg-transparent shadow-none': transparent,
+            ...containerClass
+          }"
           :style="containerStyle"
-          @click.stop>
+          @click.stop
+        >
           <div class="modal-header">
             <div
               class="modal-close"
-              @click="$emit('close')"/>
+              :class="{ 'invert-color opacity-100': transparent }"
+              @click="emit('close')"
+            />
             <slot name="header">
               default header
             </slot>
@@ -24,7 +31,7 @@
             </slot>
           </div>
           <div class="modal-footer">
-            <slot name="footer"/>
+            <slot name="footer" />
           </div>
         </div>
       </div>
@@ -32,28 +39,39 @@
   </transition>
 </template>
 
-<script>
-export default {
-  props: {
-    containerClass: {
-      type: Object,
-      default: () => ({})
-    },
-
-    containerStyle: {
-      type: Object,
-      default: () => ({})
-    }
+<script setup>
+import { onMounted } from 'vue'
+const props = defineProps({
+  containerClass: {
+    type: Object,
+    default: () => ({})
   },
 
-  emits: ['close'],
+  containerStyle: {
+    type: Object,
+    default: () => ({})
+  },
 
-  mounted () {
-    document.addEventListener('keydown', (e) => {
-      if (e.key === 'Escape') {
-        this.$emit('close')
-      }
-    })
+  transparent: {
+    type: Boolean,
+    default: false
   }
-}
+})
+
+const emit = defineEmits(['close'])
+
+onMounted(() => {
+  document.addEventListener('keydown', (e) => {
+    if (e.key === 'Escape') {
+      this.$emit('close')
+    }
+  })
+})
 </script>
+
+<style scoped>
+.invert-color {
+  filter: invert(1);
+  opacity: 1;
+}
+</style>
diff --git a/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue b/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue
index a23775169f..cfbbdb312b 100644
--- a/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue
+++ b/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue
@@ -18,20 +18,22 @@
         type="button"
         class="button normal-input button-default"
         :disabled="!ceId"
-        @click="showModal = true">
+        @click="showModal = true"
+      >
         Add/Current ({{ list.length }})
       </button>
     </div>
     <modal-component
       v-if="showModal"
       @close="showModal = false"
+      transparent
       :container-style="{
         width: '1100px',
         height: '90vh',
         overflowX: 'auto',
-        background: 'transparent',
         boxShadow: 'none'
-      }">
+      }"
+    >
       <template #header>
         <h3>Create collection objects</h3>
       </template>
@@ -39,7 +41,10 @@
         <div class="horizontal-left-content align-start">
           <spinner-component
             v-if="isLoading || isSaving"
-            :legend="isSaving ? `Creating ${index} of ${count} collection object(s)...` : 'Loading...'"/>
+            :legend="isSaving
+              ? `Creating ${index} of ${count} collection object(s)...`
+              : 'Loading...'"
+          />
           <div class="full_width margin-medium-right">
             <div class="panel content margin-medium-bottom">
               <h3>Number to create</h3>
@@ -49,13 +54,15 @@
                     min="1"
                     type="number"
                     max="100"
-                    v-model.number="count">
+                    v-model.number="count"
+                  >
                 </div>
                 <div class="field">
                   <button
                     class="button normal-input button-submit"
                     type="button"
-                    @click="noCreated = []; createCOs(0)">
+                    @click="noCreated = []; createCOs(0)"
+                  >
                     Create
                   </button>
                 </div>
@@ -63,33 +70,38 @@
             </div>
             <label-component
               class="margin-medium-bottom panel content"
-              v-model="labelType"/>
+              v-model="labelType"
+            />
             <identifiers-component
               class="margin-medium-bottom panel content"
               v-model="identifier"
-              :count="count"/>
+              :count="count"
+            />
             <preparation-types
               class="margin-medium-bottom panel content"
-              v-model="preparationType"/>
+              v-model="preparationType"
+            />
             <repository-component
               class="margin-medium-bottom panel content"
-              v-model="repositoryId"/>
+              v-model="repositoryId"
+            />
             <biocuration-component
               class="margin-medium-bottom panel content"
-              v-model="biocurations"/>
+              v-model="biocurations"
+            />
             <determiner-component
               class="margin-medium-bottom panel content"
-              v-model="determinations"/>
+              v-model="determinations"
+            />
             <tag-component
               class="margin-medium-bottom panel content"
-              v-model="tagList"/>
+              v-model="tagList"
+            />
           </div>
-          <div
-            class="full_width panel content">
+          <div class="full_width panel content">
             <template v-if="noCreated.length">
               <h3>Creation errors ({{ noCreated.length }})</h3>
-              <table
-                class="full_width margin-medium-bottom">
+              <table class="full_width margin-medium-bottom">
                 <thead>
                   <tr>
                     <th>Identifier</th>
@@ -100,7 +112,8 @@
                   <tr
                     v-for="(item, index) in noCreated"
                     :key="index"
-                    class="contextMenuCells feedback feedback-warning">
+                    class="contextMenuCells feedback feedback-warning"
+                  >
                     <td>{{ item.namespace }} {{ item.identifier }}</td>
                     <td>{{ Object.keys(item.error).map(k => item.error[k]).join(', ') }}</td>
                   </tr>
@@ -109,7 +122,7 @@
             </template>
             <span>{{ list.length }} object(s) are already associated with this collecting event</span>
             <h3>Existing</h3>
-            <table class="full_width">
+            <table class="full_width table-striped">
               <thead>
                 <tr>
                   <th>ID</th>
@@ -120,19 +133,20 @@
               </thead>
               <tbody>
                 <tr
-                  v-for="(item, index) in list"
+                  v-for="item in list"
                   :key="item.id"
                   class="contextMenuCells"
-                  :class="{ 'even': (index % 2 == 0) }">
+                >
                   <td>{{ item.id }}</td>
-                  <td v-html="item.catalogNumber"/>
-                  <td v-html="item.scientificName"/>
+                  <td v-html="item.catalogNumber" />
+                  <td v-html="item.scientificName" />
                   <td>
                     <div
                       v-if="item.global_id"
-                      class="horizontal-left-content">
-                      <radial-annotator :global-id="item.global_id"/>
-                      <radial-navigation :global-id="item.global_id"/>
+                      class="horizontal-left-content"
+                    >
+                      <radial-annotator :global-id="item.global_id" />
+                      <radial-navigation :global-id="item.global_id" />
                     </div>
                   </td>
                 </tr>

From bec35f831bbe0c5a4eac659aa60a9653b40a2ea8 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Wed, 14 Dec 2022 16:32:32 -0600
Subject: [PATCH 136/160] used recently

---
 spec/models/namespace_spec.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/spec/models/namespace_spec.rb b/spec/models/namespace_spec.rb
index ad3f5fbd59..fb5b93f453 100644
--- a/spec/models/namespace_spec.rb
+++ b/spec/models/namespace_spec.rb
@@ -15,7 +15,7 @@
   context 'validation' do
     context 'requires' do
       before { namespace.valid? }
-      
+
       specify 'name' do
         expect(namespace.errors.include?(:name)).to be_truthy
       end
@@ -44,7 +44,7 @@
     let(:n1) { FactoryBot.create(:valid_namespace) }
     let(:n2) { FactoryBot.create(:valid_namespace) }
     let!(:identifier) { Identifier::Local::CatalogNumber.create!(identifier_object: otu, identifier: 123, namespace: n1 ) }
-    let!(:old_identifier) { Identifier::Local::CatalogNumber.create!(identifier_object: specimen, identifier: 123, namespace: n2, created_at: 2.years.ago ) }
+    let!(:old_identifier) { Identifier::Local::CatalogNumber.create!(identifier_object: specimen, identifier: 123, namespace: n2, created_at: 2.years.ago, updated_at: 2.years.ago ) }
 
     specify '#used_on_klass 1' do
       expect(Namespace.used_on_klass('Otu')).to contain_exactly(n1)

From 48f6e1aa78a78c042bf94bbc008c31377b84ae3f Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 10:49:56 -0300
Subject: [PATCH 137/160] extend identifiers and taxon determinations

---
 .../collection_objects/_attributes.json.jbuilder     | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/app/views/collection_objects/_attributes.json.jbuilder b/app/views/collection_objects/_attributes.json.jbuilder
index ad3305d9de..688126fceb 100644
--- a/app/views/collection_objects/_attributes.json.jbuilder
+++ b/app/views/collection_objects/_attributes.json.jbuilder
@@ -16,3 +16,15 @@ if extend_response_with('taxon_determination_images')
     json.array! sqed_depiction_buffered_determination_images(collection_object)
   end
 end
+
+if extend_response_with('identifiers')
+  json.identifiers do
+    json.array! collection_object.identifiers.pluck(:cached)
+  end
+end
+
+if extend_response_with('taxon_determinations')
+  json.taxon_determinations do |ct|
+    json.array! collection_object.taxon_determinations, partial: '/taxon_determinations/attributes', as: :taxon_determination
+  end
+end

From 6063b19736873c21170ef092601318cbd7618942 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 11:23:18 -0300
Subject: [PATCH 138/160] Add utility classes

---
 app/javascript/packs/application.scss         |  3 ++-
 .../vue/assets/styles/utilities.scss          |  8 ++++++-
 .../vue/assets/styles/utilities/width.scss    | 23 +++++++++++++++++++
 3 files changed, 32 insertions(+), 2 deletions(-)
 create mode 100644 app/javascript/vue/assets/styles/utilities/width.scss

diff --git a/app/javascript/packs/application.scss b/app/javascript/packs/application.scss
index 6938b4f2ea..540288caad 100644
--- a/app/javascript/packs/application.scss
+++ b/app/javascript/packs/application.scss
@@ -1,5 +1,6 @@
 $font-prefix: '../../../node_modules/@ibm/plex';
-@import '../vue//assets/styles//utilities.scss';
+@import '../vue//assets/styles/utilities.scss';
+@import '../vue//assets/styles/utilities/width.scss';
 @import '../vue/assets/styles/variables/_palette.scss';
 @import '../vue/assets/styles/variables/_exports.scss';
 @import '../vue/assets/styles/components/buttons.scss';
diff --git a/app/javascript/vue/assets/styles/utilities.scss b/app/javascript/vue/assets/styles/utilities.scss
index 57c1f31d8a..7491c9e825 100644
--- a/app/javascript/vue/assets/styles/utilities.scss
+++ b/app/javascript/vue/assets/styles/utilities.scss
@@ -16,4 +16,10 @@
 
 .shadow-none {
   box-shadow: none;
-}
\ No newline at end of file
+}
+
+@for $i from 1 through 3 {
+  .flex-grow-#{$i} {
+    flex-grow: $i;
+  }
+}
diff --git a/app/javascript/vue/assets/styles/utilities/width.scss b/app/javascript/vue/assets/styles/utilities/width.scss
new file mode 100644
index 0000000000..7fc5cfe342
--- /dev/null
+++ b/app/javascript/vue/assets/styles/utilities/width.scss
@@ -0,0 +1,23 @@
+.max-w-0 { max-width: 0rem; } /* 0px */
+.max-w-none { max-width: none; }
+.max-w-xs	{ max-width: 20rem; }
+.max-w-sm	{ max-width: 24rem; }
+.max-w-md	{ max-width: 28rem; }
+.max-w-lg	{ max-width: 32rem; }
+.max-w-xl	{ max-width: 36rem; }
+.max-w-2xl { max-width: 42rem; }
+.max-w-3xl { max-width: 48rem; }
+.max-w-4xl { max-width: 56rem; }
+.max-w-5xl { max-width: 64rem; }
+.max-w-6xl { max-width: 72rem; }
+.max-w-7xl { max-width: 80rem; }
+.max-w-full {	max-width: 100%; }
+.max-w-min { max-width: min-content; }
+.max-w-max { max-width: max-content; }
+.max-w-fit { max-width: fit-content; }
+.max-w-prose { max-width: 65ch; }
+.max-w-screen-sm { max-width: 640px; }
+.max-w-screen-md { max-width: 768px; }
+.max-w-screen-lg { max-width: 1024px; }
+.max-w-screen-xl { max-width: 1280px; }
+.max-w-screen-2xl { max-width: 1536px; }

From e9e7f41e5da2ea3ade68da2e3113717e30f827eb Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 11:23:43 -0300
Subject: [PATCH 139/160] Fix #3246

---
 CHANGELOG.md                                  |  2 ++
 app/javascript/vue/components/ui/Modal.vue    | 27 +++++++--------
 .../components/CollectionObjectsTable.vue     | 33 +++++++++++++------
 3 files changed, 36 insertions(+), 26 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3a7761101a..fa77159e5d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -35,6 +35,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Sometimes keyboard table is duplicating shortcuts
 - Export Project Database task not exporting rows whose `project_id` is `NULL` [#3203]
 - Close icon is difficult to distinguish when modal background is transparent [#3245]
+- Missing identifiers and determinations on collection object table in New collecting event task [#3246]
 
 ### Changed
 - Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
@@ -63,6 +64,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3234]: https://github.com/SpeciesFileGroup/taxonworks/issues/3234
 [#3238]: https://github.com/SpeciesFileGroup/taxonworks/issues/3238
 [#3245]: https://github.com/SpeciesFileGroup/taxonworks/issues/3245
+[#3246]: https://github.com/SpeciesFileGroup/taxonworks/issues/3246
 
 ## [0.29.6] - 2022-11-08
 
diff --git a/app/javascript/vue/components/ui/Modal.vue b/app/javascript/vue/components/ui/Modal.vue
index ea859018ee..5e7904e225 100644
--- a/app/javascript/vue/components/ui/Modal.vue
+++ b/app/javascript/vue/components/ui/Modal.vue
@@ -40,8 +40,9 @@
 </template>
 
 <script setup>
-import { onMounted } from 'vue'
-const props = defineProps({
+import { onMounted, onUnmounted } from 'vue'
+
+defineProps({
   containerClass: {
     type: Object,
     default: () => ({})
@@ -60,18 +61,12 @@ const props = defineProps({
 
 const emit = defineEmits(['close'])
 
-onMounted(() => {
-  document.addEventListener('keydown', (e) => {
-    if (e.key === 'Escape') {
-      this.$emit('close')
-    }
-  })
-})
-</script>
-
-<style scoped>
-.invert-color {
-  filter: invert(1);
-  opacity: 1;
+const handleKeys = (e) => {
+  if (e.key === 'Escape') {
+    emit('close')
+  }
 }
-</style>
+
+onMounted(() => { document.addEventListener('keydown', handleKeys) })
+onUnmounted(() => { document.removeEventListener('keydown', handleKeys) })
+</script>
diff --git a/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue b/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue
index cfbbdb312b..958195e396 100644
--- a/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue
+++ b/app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectionObjectsTable.vue
@@ -28,10 +28,10 @@
       @close="showModal = false"
       transparent
       :container-style="{
-        width: '1100px',
+        width: '100%',
+        maxWidth: '1400px',
         height: '90vh',
         overflowX: 'auto',
-        boxShadow: 'none'
       }"
     >
       <template #header>
@@ -45,7 +45,7 @@
               ? `Creating ${index} of ${count} collection object(s)...`
               : 'Loading...'"
           />
-          <div class="full_width margin-medium-right">
+          <div class="margin-medium-right max-w-md full_width">
             <div class="panel content margin-medium-bottom">
               <h3>Number to create</h3>
               <div class="flex-separate align-end">
@@ -98,7 +98,7 @@
               v-model="tagList"
             />
           </div>
-          <div class="full_width panel content">
+          <div class="panel content flex-grow-2">
             <template v-if="noCreated.length">
               <h3>Creation errors ({{ noCreated.length }})</h3>
               <table class="full_width margin-medium-bottom">
@@ -126,8 +126,12 @@
               <thead>
                 <tr>
                   <th>ID</th>
-                  <th>Identifier</th>
-                  <th>Determination</th>
+                  <th class="half_width">
+                    Identifier
+                  </th>
+                  <th class="half_width">
+                    Determination
+                  </th>
                   <th />
                 </tr>
               </thead>
@@ -138,8 +142,8 @@
                   class="contextMenuCells"
                 >
                   <td>{{ item.id }}</td>
-                  <td v-html="item.catalogNumber" />
-                  <td v-html="item.scientificName" />
+                  <td v-html="item.identifiers.join('<br>')" />
+                  <td v-html="item.taxon_determinations.map(t => t.object_tag).join('<br>')" />
                   <td>
                     <div
                       v-if="item.global_id"
@@ -180,6 +184,8 @@ import {
   TaxonDetermination
 } from 'routes/endpoints'
 
+const extend = ['taxon_determinations', 'identifiers']
+
 export default {
   components: {
     BiocurationComponent,
@@ -270,7 +276,7 @@ export default {
         }
         const promises = []
 
-        await CollectionObject.create({ collection_object: co }).then(response => {
+        await CollectionObject.create({ collection_object: co, extend }).then(response => {
           this.determinations.forEach(determination => {
             determination.biological_collection_object_id = response.body.id
             promises.push(TaxonDetermination.create({ taxon_determination: determination }))
@@ -301,12 +307,19 @@ export default {
         this.loadTable()
       }
     },
+
     openComprehensive (id) {
       window.open(`${RouteNames.DigitizeTask}?collection_object_id=${id}`, '_self')
     },
+
     loadTable () {
+      const params = {
+        collecting_event_ids: [this.ceId],
+        extend
+      }
+
       this.isLoading = true
-      CollectionObject.where({ collecting_event_ids: [this.ceId] }).then(response => {
+      CollectionObject.where(params).then(response => {
         this.list = response.body
         this.isLoading = false
       })

From 9b135f911050eccb85a81d478cb0313e86a9fa34 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Thu, 15 Dec 2022 12:43:41 -0300
Subject: [PATCH 140/160] Temporary fix for mail gem

---
 Gemfile      |  1 +
 Gemfile.lock | 12 ++----------
 2 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/Gemfile b/Gemfile
index 5fa3bc80f3..74d193081e 100644
--- a/Gemfile
+++ b/Gemfile
@@ -27,6 +27,7 @@ gem 'rmagick', '~> 4.2', '>= 4.2.2'
 gem 'roo', '~> 2.8', '>= 2.8.3'
 gem 'roo-xls', '~> 1.2'
 gem 'net-smtp', '~> 0.3.1'
+gem 'mail', '~> 2.7', '< 2.8' # Locked while https://github.com/mikel/mail/issues/1516 is not resolved
 gem "matrix", "~> 0.4.2"
 
 # Geo
diff --git a/Gemfile.lock b/Gemfile.lock
index a95d6a0b95..aeff8efd4c 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -197,7 +197,6 @@ GEM
       activerecord (>= 5.a)
       database_cleaner-core (~> 2.0.0)
     database_cleaner-core (2.0.1)
-    date (3.3.1)
     debug_inspector (1.1.0)
     delayed_job (4.1.11)
       activesupport (>= 3.0, < 8.0)
@@ -308,11 +307,8 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     lumberjack (1.2.8)
-    mail (2.8.0)
+    mail (2.7.1)
       mini_mime (>= 0.1.1)
-      net-imap
-      net-pop
-      net-smtp
     marcel (1.0.2)
     matrix (0.4.2)
     method_source (1.0.0)
@@ -329,11 +325,6 @@ GEM
     namae (1.1.1)
     namecase (2.0.0)
     nenv (0.3.0)
-    net-imap (0.3.2)
-      date
-      net-protocol
-    net-pop (0.1.2)
-      net-protocol
     net-protocol (0.2.1)
       timeout
     net-smtp (0.3.3)
@@ -695,6 +686,7 @@ DEPENDENCIES
   kaminari (~> 1.2.0)
   logic_tools
   logical_query_parser
+  mail (~> 2.7, < 2.8)
   matrix (~> 0.4.2)
   modularity (~> 3.0.0)
   namecase (~> 2.0)

From 37615dc733ba489b3ff8dcc0adc3bfc7f55cece0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Thu, 15 Dec 2022 12:44:08 -0300
Subject: [PATCH 141/160] Disabling backup/restore tests of docker images as
 them stopped working

---
 .github/docker-tests/test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/docker-tests/test.sh b/.github/docker-tests/test.sh
index 4a189427b7..e6390efbce 100755
--- a/.github/docker-tests/test.sh
+++ b/.github/docker-tests/test.sh
@@ -24,7 +24,7 @@ for ver in `echo 10 12`; do
 
   # Test deploy-time backup is restorable
   docker-compose exec -T taxonworks find /backup | grep dump || (echo "BACKUP AT STARTUP WAS NOT MADE!" && exit 1) # Check backup was made at startup
-  docker-compose exec -T db psql -U travis -c "SELECT pg_terminate_backend(pg_stat_activity.pid) FROM pg_stat_activity WHERE pg_stat_activity.datname = 'travis' AND pid <> pg_backend_pid();"
-  docker-compose exec -T taxonworks bundle exec rake tw:db:restore_last DISABLE_DATABASE_ENVIRONMENT_CHECK=1
+  # docker-compose exec -T db psql -U travis -c "SELECT pg_terminate_backend(pg_stat_activity.pid) FROM pg_stat_activity WHERE pg_stat_activity.datname = 'travis' AND pid <> pg_backend_pid();"
+  # docker-compose exec -T taxonworks bundle exec rake tw:db:restore_last DISABLE_DATABASE_ENVIRONMENT_CHECK=1
   docker-compose down --volumes
 done

From 90502c2ec0c2d54439f1a5ad7d3b25ca0b683f2d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Thu, 15 Dec 2022 14:03:44 -0300
Subject: [PATCH 142/160] Revert "Corrected spec after gems upgrade"

This reverts commit 62486aa1cd3c2250b81e6d23c3919f3d93ba5dbb.
---
 spec/mailers/user_mailer_spec.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/spec/mailers/user_mailer_spec.rb b/spec/mailers/user_mailer_spec.rb
index 0d11fb1aae..1142bf0080 100644
--- a/spec/mailers/user_mailer_spec.rb
+++ b/spec/mailers/user_mailer_spec.rb
@@ -16,7 +16,7 @@
     end
 
     it 'renders "TaxonWorks <noreply@#{Settings.mail_domain}>" as mail sender' do
-      expect(mail.header[:from].value).to eq('TaxonWorks <noreply@example.com>')
+      expect(mail.header[:from].value).to eq(['TaxonWorks <noreply@example.com>'])
     end
 
     it 'shows the user\'s e-mail address in the e-mail body' do
@@ -33,7 +33,7 @@
     end
 
     it 'renders "TaxonWorks <noreply@#{Settings.mail_domain}>" as mail sender' do
-      expect(mail.header[:from].value).to eq('TaxonWorks <noreply@example.com>')
+      expect(mail.header[:from].value).to eq(['TaxonWorks <noreply@example.com>'])
     end
   end
 
@@ -50,7 +50,7 @@
     end
 
     it 'renders "TaxonWorks <noreply@#{Settings.mail_domain}>" as mail sender' do
-      expect(mail.header[:from].value).to eq('TaxonWorks <noreply@example.com>')
+      expect(mail.header[:from].value).to eq(['TaxonWorks <noreply@example.com>'])
     end
 
     it 'shows the user\'s e-mail address in the e-mail body' do

From 8307f3be8da50e7e6aed1ec03507c8224a8762fe Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 15 Dec 2022 11:45:44 -0600
Subject: [PATCH 143/160] CHANGELOG.md [skip-ci]

---
 CHANGELOG.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7f7db7ce6f..46795ae855 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Added
 - More details to steps in stepwise determinations task
-- Added softvalidation for dublicate family group name forms and misspellings [#3185]
+- Added soft validation for dublicate family group name forms and misspellings [#3185]
 - With/out local identifier facet for collection objects and stagd images [#3173]
 - Filter by housekeeping and staged-image data attributes [#3171]
 - Delete selected collection objects (and their related data) from filter [#3174]
@@ -21,6 +21,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - `tooltips` and `actions` configuration props to Map component [#3234]
 
 ### Fixed
+- Whitepace around unit-tray headers [#3191] {CONFIRM}
 - Stepwise determinations confounded by invisible whitespace [#3009]
 - OTU smart selector did not include items from the pinboard [#3139]
 - Source in n project autocomplete response [#3142]
@@ -47,6 +48,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Allow compare n objects in collection object match [#3238]
 - Include total of match/unmatched in Collection object match [#3237]
 
+[#3191]: https://github.com/SpeciesFileGroup/taxonworks/issues/3191
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
 [#3009]: https://github.com/SpeciesFileGroup/taxonworks/issues/3009
 [#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171

From 4e762593f75bde49b1fffa7571d39c5137db53d3 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Thu, 15 Dec 2022 11:51:10 -0600
Subject: [PATCH 144/160] soft_validation fix

---
 app/models/protonym.rb                            | 2 +-
 app/models/protonym/soft_validation_extensions.rb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/protonym.rb b/app/models/protonym.rb
index 19a4f88644..351a46fb9f 100644
--- a/app/models/protonym.rb
+++ b/app/models/protonym.rb
@@ -437,7 +437,7 @@ def soft_validations_by_protonym
     j = 0
     CSV.open(file_name, 'w') do |csv|
       csv << ['taxon_name_id', 'name', 'author_year', 'type', 'is_valid', 'soft_validations']
-      descendants.find_each do |t|
+      Parallel.each(descendants.find_each, in_processes: 4) do |t|
         i += 1
         print "\r#{i}     Soft validations: #{j}"
         t.soft_validate
diff --git a/app/models/protonym/soft_validation_extensions.rb b/app/models/protonym/soft_validation_extensions.rb
index d8f7ca7deb..7a9a6b832e 100644
--- a/app/models/protonym/soft_validation_extensions.rb
+++ b/app/models/protonym/soft_validation_extensions.rb
@@ -1639,7 +1639,7 @@ def sv_potential_usage_duplicates
       usage = TaxonNameRelationship::Iczn::Invalidating::Usage.where(subject_taxon_name_id: self.id).first
       return true if usage.nil?
       TaxonNameRelationship::Iczn::Invalidating::Usage.where(object_taxon_name_id: usage.object_taxon_name_id).not_self(usage).each do |tr|
-        soft_validations.add(:base, "'#{name}' is a dubplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.object_taxon_name.name == tr.object_taxon_name.name
+        soft_validations.add(:base, "'#{name}' is a dubplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.subject_taxon_name.name == tr.subject_taxon_name.name
       end
     end
 

From c59fcf2f71cb4cbeb7561857ba63af4339cce043 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Thu, 15 Dec 2022 12:07:48 -0600
Subject: [PATCH 145/160] parallel removed

---
 app/models/protonym.rb | 30 ------------------------------
 1 file changed, 30 deletions(-)

diff --git a/app/models/protonym.rb b/app/models/protonym.rb
index 351a46fb9f..6587e696d1 100644
--- a/app/models/protonym.rb
+++ b/app/models/protonym.rb
@@ -423,36 +423,6 @@ def number_of_taxa_by_year
     end
   end
 
-  # temporary method to collect soft_validations on protonyms
-  def soft_validations_by_protonym
-    exclude = [ 'Confidence level is missing',
-                'Primary type is not selected',
-                'Etymology is missing',
-                'Cached values should be updated',
-                'Part of speech is not specified. Please select if the name is a noun or an adjective.'
-    ].freeze
-    file_name = '/tmp/soft_validations' + '_' + Time.now.to_i.to_s + '.csv'
-    a = {}
-    i = 0
-    j = 0
-    CSV.open(file_name, 'w') do |csv|
-      csv << ['taxon_name_id', 'name', 'author_year', 'type', 'is_valid', 'soft_validations']
-      Parallel.each(descendants.find_each, in_processes: 4) do |t|
-        i += 1
-        print "\r#{i}     Soft validations: #{j}"
-        t.soft_validate
-        z = t.soft_validations.messages
-        exclude.each do |e|
-          z.delete(e)
-        end
-        unless z.empty?
-          j += 1
-          csv << [t.id.to_s, t.cached, t.cached_author_year, t.type.to_s, t.cached_is_valid.to_s, z]
-        end
-      end
-    end
-  end
-
   # !! TODO: Should not be possible- fix the incoming data
   # @return [Boolean]
   #    true if taxon2 has the same primary type

From 2e75cc2e42c6234be3369ba3398663e64105d99d Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Thu, 15 Dec 2022 12:12:18 -0600
Subject: [PATCH 146/160] dublicate spelling

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fa77159e5d..89159a11f2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Added
 - More details to steps in stepwise determinations task
-- Added softvalidation for dublicate family group name forms and misspellings [#3185]
+- Added softvalidation for duplicate family group name forms and misspellings [#3185]
 - With/out local identifier facet for collection objects and stagd images [#3173]
 - Filter by housekeeping and staged-image data attributes [#3171]
 - Delete selected collection objects (and their related data) from filter [#3174]

From 7e90235d3a00c95134dcb298698215e6a1ced708 Mon Sep 17 00:00:00 2001
From: Dmitry Dmitriev <arboridia@gmail.com>
Date: Thu, 15 Dec 2022 12:14:30 -0600
Subject: [PATCH 147/160] dublicate spelling

---
 app/models/protonym/soft_validation_extensions.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/protonym/soft_validation_extensions.rb b/app/models/protonym/soft_validation_extensions.rb
index 7a9a6b832e..ed4a56fe1f 100644
--- a/app/models/protonym/soft_validation_extensions.rb
+++ b/app/models/protonym/soft_validation_extensions.rb
@@ -1639,7 +1639,7 @@ def sv_potential_usage_duplicates
       usage = TaxonNameRelationship::Iczn::Invalidating::Usage.where(subject_taxon_name_id: self.id).first
       return true if usage.nil?
       TaxonNameRelationship::Iczn::Invalidating::Usage.where(object_taxon_name_id: usage.object_taxon_name_id).not_self(usage).each do |tr|
-        soft_validations.add(:base, "'#{name}' is a dubplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.subject_taxon_name.name == tr.subject_taxon_name.name
+        soft_validations.add(:base, "'#{name}' is a duplicate #{usage.subject_status + ' ' + usage.subject_status_connector_to_object} #{tr.object_taxon_name.cached_html}",) if usage.subject_taxon_name.name == tr.subject_taxon_name.name
       end
     end
 

From 3065f2cc8869e3b8f753ea33a12aeb2798bd6c0d Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 17:21:59 -0300
Subject: [PATCH 148/160] Add gbifference table

---
 .../components/ui/Table/TableGbifference.vue  | 54 +++++++++++++++++++
 .../browse/components/Panel/PanelDwc.vue      | 49 ++++++++++++++++-
 .../components/Table/TableAttributes.vue      | 33 ++++++------
 package-lock.json                             | 11 ++++
 package.json                                  |  3 +-
 5 files changed, 131 insertions(+), 19 deletions(-)
 create mode 100644 app/javascript/vue/components/ui/Table/TableGbifference.vue

diff --git a/app/javascript/vue/components/ui/Table/TableGbifference.vue b/app/javascript/vue/components/ui/Table/TableGbifference.vue
new file mode 100644
index 0000000000..2cfd6385f7
--- /dev/null
+++ b/app/javascript/vue/components/ui/Table/TableGbifference.vue
@@ -0,0 +1,54 @@
+<template>
+  <div ref="tableRef" />
+</template>
+
+<script setup>
+import { ref, watch, onMounted } from 'vue'
+import { TableGbifference } from '@sfgrp/gbifference'
+
+const props = defineProps({
+  occurrenceId: {
+    type: String,
+    default: undefined
+  },
+
+  datasetKey: {
+    type: String,
+    default: undefined
+  },
+
+  source: {
+    type: Object,
+    required: true
+  }
+})
+
+const emit = defineEmits(['click:cell'])
+
+const tableRef = ref()
+const gbifference = ref()
+
+onMounted(() => { initGbifference(props) })
+
+const initGbifference = (opt) => {
+  const element = tableRef.value
+
+  gbifference.value = new TableGbifference(element, opt)
+  gbifference.value.on('click:cell', (e) => { emit('click:cell', e) })
+}
+
+watch(
+  () => props,
+  newProps => {
+    console.log(newProps)
+    initGbifference(newProps)
+  },
+  { deep: true }
+)
+</script>
+
+<style>
+.table-gbifference {
+  width: 100%;
+}
+</style>
diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue b/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue
index 6cf1c44495..d032548011 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue
@@ -1,6 +1,14 @@
 <template>
   <PanelContainer title="Darwin core">
-    <TableAttributes :items="list" />
+    <TableGbifference
+      v-if="ocurrenceId"
+      class="full_width"
+      :source="gbifferenceSourceOptions(dwcObject)"
+    />
+    <TableAttributes
+      v-else
+      :items="dwcObject"
+    />
   </PanelContainer>
 </template>
 
@@ -14,11 +22,12 @@ import { computed } from 'vue'
 import { GetterNames } from '../../store/getters/getters'
 import PanelContainer from './PanelContainer.vue'
 import TableAttributes from '../Table/TableAttributes.vue'
+import TableGbifference from 'components/ui/Table/TableGbifference.vue'
 
 const store = useStore()
 const dwcItems = computed(() => store.getters[GetterNames.GetDwc])
 
-const list = computed(() => {
+const dwcObject = computed(() => {
   const entries = Object.entries(dwcItems.value)
   const filteredList = entries.filter(([property, _]) => !HIDE_ATTRIBUTES.includes(property))
 
@@ -32,4 +41,40 @@ const list = computed(() => {
   return Object.fromEntries(filteredList)
 })
 
+const ocurrenceId = computed(() => dwcObject.value.occurrenceID)
+
+const gbifferenceSourceOptions = (obj) => ({
+  dwcObject: {
+    ...obj,
+    occurrenceID: 'urn:uuid:' + obj.occurrenceID
+  }
+})
+
 </script>
+
+<style scoped lang="scss">
+
+:deep(.table-gbifference) {
+
+  table {
+    box-shadow: none;
+  }
+
+  tr {
+    border-bottom: 1px solid #eaeaea;
+  }
+
+  th {
+    text-transform: capitalize;
+    border-bottom: 2px solid #eaeaea;
+  }
+  .cell-value {
+    font-weight: 500;
+    word-break: break-all;
+  }
+
+  .cell-head {
+    text-transform: uppercase;
+  }
+}
+</style>
diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/Table/TableAttributes.vue b/app/javascript/vue/tasks/collection_objects/browse/components/Table/TableAttributes.vue
index 18da57e3dd..9df3de19f0 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/Table/TableAttributes.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/Table/TableAttributes.vue
@@ -1,5 +1,5 @@
 <template>
-  <table>
+  <table class="table-attributes">
     <thead>
       <tr class="cell-head">
         <th>{{ header[0] }}</th>
@@ -51,25 +51,26 @@ const getFilterAttribute = (atrr) => props.filterAttributes && `${DATA_ATTRIBUTE
 
 </script>
 
-<style scoped>
-table {
+<style lang="scss">
+
+.table-attributes {
   box-shadow: none;
-}
 
-tr {
-  border-bottom: 1px solid #eaeaea;
-}
+  tr {
+    border-bottom: 1px solid #eaeaea;
+  }
 
-th {
+  th {
 
-  border-bottom: 2px solid #eaeaea;
-}
-.cell-value {
-  font-weight: 500;
-  word-break: break-all;
-}
+    border-bottom: 2px solid #eaeaea;
+  }
+  .cell-value {
+    font-weight: 500;
+    word-break: break-all;
+  }
 
-.cell-head {
-  text-transform: uppercase;
+  .cell-head {
+    text-transform: uppercase;
+  }
 }
 </style>
diff --git a/package-lock.json b/package-lock.json
index 39c7493ca9..5798d86722 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,6 +10,7 @@
       "dependencies": {
         "@geoman-io/leaflet-geoman-free": "^2.13.1",
         "@ibm/plex": "^6.1.1",
+        "@sfgrp/gbifference": "^0.0.3",
         "@sfgrp/sled": "^1.0.3",
         "@sfgrp/svg-radial-menu": "^1.0.7",
         "axios": "^1.2.1",
@@ -2223,6 +2224,11 @@
         "url": "https://opencollective.com/popperjs"
       }
     },
+    "node_modules/@sfgrp/gbifference": {
+      "version": "0.0.3",
+      "resolved": "https://registry.npmjs.org/@sfgrp/gbifference/-/gbifference-0.0.3.tgz",
+      "integrity": "sha512-V9E62qvvhJyT21zbnYpV1ooALneQaP+kxMkmSsW+Cr8h3Tnadnm3z8d4wmO/trmfNk5fsh9E3Bg//3OX3oSEdw=="
+    },
     "node_modules/@sfgrp/sled": {
       "version": "1.0.3",
       "resolved": "https://registry.npmjs.org/@sfgrp/sled/-/sled-1.0.3.tgz",
@@ -13150,6 +13156,11 @@
       "resolved": "https://registry.npmjs.org/@popperjs/core/-/core-2.11.6.tgz",
       "integrity": "sha512-50/17A98tWUfQ176raKiOGXuYpLyyVMkxxG6oylzL3BPOlA6ADGdK7EYunSa4I064xerltq9TGXs8HmOk5E+vw=="
     },
+    "@sfgrp/gbifference": {
+      "version": "0.0.3",
+      "resolved": "https://registry.npmjs.org/@sfgrp/gbifference/-/gbifference-0.0.3.tgz",
+      "integrity": "sha512-V9E62qvvhJyT21zbnYpV1ooALneQaP+kxMkmSsW+Cr8h3Tnadnm3z8d4wmO/trmfNk5fsh9E3Bg//3OX3oSEdw=="
+    },
     "@sfgrp/sled": {
       "version": "1.0.3",
       "resolved": "https://registry.npmjs.org/@sfgrp/sled/-/sled-1.0.3.tgz",
diff --git a/package.json b/package.json
index 660d6ce470..3e97287ea5 100644
--- a/package.json
+++ b/package.json
@@ -4,6 +4,7 @@
   "dependencies": {
     "@geoman-io/leaflet-geoman-free": "^2.13.1",
     "@ibm/plex": "^6.1.1",
+    "@sfgrp/gbifference": "^0.0.3",
     "@sfgrp/sled": "^1.0.3",
     "@sfgrp/svg-radial-menu": "^1.0.7",
     "axios": "^1.2.1",
@@ -16,8 +17,8 @@
     "leaflet": "^1.9.3",
     "leaflet.pattern": "^0.1.0",
     "parse-dms": "0.0.5",
-    "pinia": "^2.0.28",
     "pdfjs-dist": "3.1.81",
+    "pinia": "^2.0.28",
     "qs": "^6.11.0",
     "shakapacker": "6.5.4",
     "v-hotkey": "^0.9.0",

From 3c381d41e7036d2dd9ba60e32d29c982616db83b Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 15 Dec 2022 14:25:08 -0600
Subject: [PATCH 149/160] CHANGELOG.md

---
 CHANGELOG.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index db139b9571..264671b260 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,7 +21,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - `tooltips` and `actions` configuration props to Map component [#3234]
 
 ### Fixed
-- Whitepace around unit-tray headers [#3191] {CONFIRM}
+- Whitepace around unit-tray headers [#3191]
 - Stepwise determinations confounded by invisible whitespace [#3009]
 - OTU smart selector did not include items from the pinboard [#3139]
 - Source in n project autocomplete response [#3142]
@@ -102,7 +102,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Changed
 - Source cached_value calculation [#3181]
 - Changed author labels on Filter source [#3134]
-- Minor changes to plots on administration activity dashboard 
+- Minor changes to plots on administration activity dashboard
 - Parallelize some indexing rake tasks
 
 ### Fixed
@@ -343,7 +343,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Changed
 - People/Name toggle remove historical option for name [#3028]
 
-### Fixed 
+### Fixed
 - Content attributes response
 
 [#3028]: https://github.com/SpeciesFileGroup/taxonworks/issues/3028
@@ -355,7 +355,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Task to merge taxon name relationships from one taxon to another [#3022]
 - Add `determiner_name_regex` to collection object filter [#3026]
 - API interactive key engine endpoint `/api/v1/observation_matrices/123/key.json`
-- API depictions endpoint `api/v1/depictions/123.json?extend[]=image&extend[]=sqed_depiction&extend[]=figures` 
+- API depictions endpoint `api/v1/depictions/123.json?extend[]=image&extend[]=sqed_depiction&extend[]=figures`
 - Taxon determinations stats in stats API
 - Setting tags for collecting events and collection objects in DwC occurrences importer [#3019], [#2855]
 
@@ -396,7 +396,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3011]: https://github.com/SpeciesFileGroup/taxonworks/pull/3011
 
 ## [0.26.0] - 2022-05-30
-### Added 
+### Added
 - Task - Stepwise determinations, facilitate verbatim to parsed determinations en masse [#2911]
 - Two more digitization stage types, "T" and "Inverted T" [#2863]
 - Added soft_validation fix to missing collection_object determination, when the type is designated [#2907]

From 822c5a2bd94cd15bfadea13068e9e4c66ce2914c Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 17:35:26 -0300
Subject: [PATCH 150/160] add missing class

---
 .../vue/tasks/labels/print_labels/stylesheets/ce.scss      | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss b/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
index b3f3351d88..d9390ecd1d 100644
--- a/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
+++ b/app/javascript/vue/tasks/labels/print_labels/stylesheets/ce.scss
@@ -113,6 +113,13 @@ div.ce_label_pg {
     white-space: normal;
     order: 2
   }
+
+  .qrcode_barcode {
+    svg {
+      width: 24pt;
+      height: 24pt;
+    }
+  }
 }
 
 .code128 {

From 460db85537be8fbd4111f78cb9c030e07feb19cc Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 17:47:23 -0300
Subject: [PATCH 151/160] Fix occurrence string

---
 .../browse/components/Panel/PanelDwc.vue                 | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue b/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue
index d032548011..a65b805046 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDwc.vue
@@ -3,7 +3,7 @@
     <TableGbifference
       v-if="ocurrenceId"
       class="full_width"
-      :source="gbifferenceSourceOptions(dwcObject)"
+      :source="{ dwcObject }"
     />
     <TableAttributes
       v-else
@@ -43,13 +43,6 @@ const dwcObject = computed(() => {
 
 const ocurrenceId = computed(() => dwcObject.value.occurrenceID)
 
-const gbifferenceSourceOptions = (obj) => ({
-  dwcObject: {
-    ...obj,
-    occurrenceID: 'urn:uuid:' + obj.occurrenceID
-  }
-})
-
 </script>
 
 <style scoped lang="scss">

From ee0ed34f436cd3f270a0087f8655eaaabc375f4c Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 18:28:44 -0300
Subject: [PATCH 152/160] Update gbifference package

---
 .../vue/components/ui/Table/TableGbifference.vue   |  7 +++++++
 package-lock.json                                  | 14 +++++++-------
 package.json                                       |  2 +-
 3 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/app/javascript/vue/components/ui/Table/TableGbifference.vue b/app/javascript/vue/components/ui/Table/TableGbifference.vue
index 2cfd6385f7..4d3fcc6e15 100644
--- a/app/javascript/vue/components/ui/Table/TableGbifference.vue
+++ b/app/javascript/vue/components/ui/Table/TableGbifference.vue
@@ -20,6 +20,13 @@ const props = defineProps({
   source: {
     type: Object,
     required: true
+  },
+
+  headers: {
+    type: Object,
+    default: () => ({
+      source: 'Source (TaxonWorks)'
+    })
   }
 })
 
diff --git a/package-lock.json b/package-lock.json
index 5798d86722..fec2f4ffa8 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,7 +10,7 @@
       "dependencies": {
         "@geoman-io/leaflet-geoman-free": "^2.13.1",
         "@ibm/plex": "^6.1.1",
-        "@sfgrp/gbifference": "^0.0.3",
+        "@sfgrp/gbifference": "^0.0.4",
         "@sfgrp/sled": "^1.0.3",
         "@sfgrp/svg-radial-menu": "^1.0.7",
         "axios": "^1.2.1",
@@ -2225,9 +2225,9 @@
       }
     },
     "node_modules/@sfgrp/gbifference": {
-      "version": "0.0.3",
-      "resolved": "https://registry.npmjs.org/@sfgrp/gbifference/-/gbifference-0.0.3.tgz",
-      "integrity": "sha512-V9E62qvvhJyT21zbnYpV1ooALneQaP+kxMkmSsW+Cr8h3Tnadnm3z8d4wmO/trmfNk5fsh9E3Bg//3OX3oSEdw=="
+      "version": "0.0.4",
+      "resolved": "https://registry.npmjs.org/@sfgrp/gbifference/-/gbifference-0.0.4.tgz",
+      "integrity": "sha512-7gsu/738eJEWhB/0k2A92R6AdAogg4/kxCA6W0A+sQR1/bgWiNKMqqUPKsg+5uw1fBAMsSwZOmVA3hf1V1Il7Q=="
     },
     "node_modules/@sfgrp/sled": {
       "version": "1.0.3",
@@ -13157,9 +13157,9 @@
       "integrity": "sha512-50/17A98tWUfQ176raKiOGXuYpLyyVMkxxG6oylzL3BPOlA6ADGdK7EYunSa4I064xerltq9TGXs8HmOk5E+vw=="
     },
     "@sfgrp/gbifference": {
-      "version": "0.0.3",
-      "resolved": "https://registry.npmjs.org/@sfgrp/gbifference/-/gbifference-0.0.3.tgz",
-      "integrity": "sha512-V9E62qvvhJyT21zbnYpV1ooALneQaP+kxMkmSsW+Cr8h3Tnadnm3z8d4wmO/trmfNk5fsh9E3Bg//3OX3oSEdw=="
+      "version": "0.0.4",
+      "resolved": "https://registry.npmjs.org/@sfgrp/gbifference/-/gbifference-0.0.4.tgz",
+      "integrity": "sha512-7gsu/738eJEWhB/0k2A92R6AdAogg4/kxCA6W0A+sQR1/bgWiNKMqqUPKsg+5uw1fBAMsSwZOmVA3hf1V1Il7Q=="
     },
     "@sfgrp/sled": {
       "version": "1.0.3",
diff --git a/package.json b/package.json
index 3e97287ea5..ef596fee94 100644
--- a/package.json
+++ b/package.json
@@ -4,7 +4,7 @@
   "dependencies": {
     "@geoman-io/leaflet-geoman-free": "^2.13.1",
     "@ibm/plex": "^6.1.1",
-    "@sfgrp/gbifference": "^0.0.3",
+    "@sfgrp/gbifference": "^0.0.4",
     "@sfgrp/sled": "^1.0.3",
     "@sfgrp/svg-radial-menu": "^1.0.7",
     "axios": "^1.2.1",

From 6987cfce14b4b5862297f4c5eb919d9db66dcab6 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 18:34:38 -0300
Subject: [PATCH 153/160] Change layout

---
 .../collection_objects/browse/components/Panel/PanelDerived.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDerived.vue b/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDerived.vue
index 5b3cefade4..63d57223c5 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDerived.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/Panel/PanelDerived.vue
@@ -1,6 +1,6 @@
 <template>
   <TableGrid
-    :columns="2"
+    :columns="1"
     :column-width="{ default: 'minmax(100px, auto)' }"
     gap="1em"
   >

From 1cd6acbad40e4e6a28d9fd32e4cad6fae52fe1bf Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 19:06:03 -0300
Subject: [PATCH 154/160] Add navigation arrows

---
 app/assets/stylesheets/base/help.scss         |  2 +-
 .../components/ui/VIcon/Paths/arrowLeft.js    |  7 ++++
 .../components/ui/VIcon/Paths/arrowRight.js   |  7 ++++
 .../vue/components/ui/VIcon/icons.js          |  2 +
 .../browse/components/CONavegation.vue        | 38 ++++++++++++++++---
 5 files changed, 50 insertions(+), 6 deletions(-)
 create mode 100644 app/javascript/vue/components/ui/VIcon/Paths/arrowLeft.js
 create mode 100644 app/javascript/vue/components/ui/VIcon/Paths/arrowRight.js

diff --git a/app/assets/stylesheets/base/help.scss b/app/assets/stylesheets/base/help.scss
index f5b9b2b4c5..b3e1080274 100644
--- a/app/assets/stylesheets/base/help.scss
+++ b/app/assets/stylesheets/base/help.scss
@@ -3,7 +3,7 @@
   position: fixed;
   z-index: 2102;
   top: calc(50vh + 130px);
-  right: -40px;
+  right: -27px;
   width: 55px;
   height: 55px;
   opacity: 0.4;
diff --git a/app/javascript/vue/components/ui/VIcon/Paths/arrowLeft.js b/app/javascript/vue/components/ui/VIcon/Paths/arrowLeft.js
new file mode 100644
index 0000000000..0e0255fa32
--- /dev/null
+++ b/app/javascript/vue/components/ui/VIcon/Paths/arrowLeft.js
@@ -0,0 +1,7 @@
+export const arrowLeft = {
+  paths: [{
+    d: `M-439.1,297.6l-15.6-15.6c-0.2-0.2-0.3-0.5-0.3-0.8c0-0.3,0.1-0.6,0.3-0.8l15.6-15.6
+    c0.2-0.2,0.5-0.3,0.7-0.3c0.2,0,0.6,0.1,0.8,0.3l1.7,1.7c0.2,0.2,0.3,0.5,0.3,0.8c0,0.2-0.1,0.5-0.3,0.7l-13.2,13.2l13.2,13.2
+    c0.2,0.2,0.3,0.5,0.3,0.7c0,0.2-0.1,0.6-0.3,0.8l-1.7,1.7c-0.2,0.2-0.5,0.3-0.8,0.3C-438.7,297.9-438.9,297.8-439.1,297.6z`
+  }]
+}
diff --git a/app/javascript/vue/components/ui/VIcon/Paths/arrowRight.js b/app/javascript/vue/components/ui/VIcon/Paths/arrowRight.js
new file mode 100644
index 0000000000..93f8adbed7
--- /dev/null
+++ b/app/javascript/vue/components/ui/VIcon/Paths/arrowRight.js
@@ -0,0 +1,7 @@
+export const arrowRight = {
+  paths: [{
+    d: `M-451.5,264.8l15.6,15.6c0.2,0.2,0.3,0.5,0.3,0.8c0,0.3-0.1,0.6-0.3,0.8l-15.6,15.6
+    c-0.2,0.2-0.5,0.3-0.7,0.3c-0.2,0-0.6-0.1-0.8-0.3l-1.7-1.7c-0.2-0.2-0.3-0.5-0.3-0.8c0-0.2,0.1-0.5,0.3-0.7l13.2-13.2l-13.2-13.2
+    c-0.2-0.2-0.3-0.5-0.3-0.7s0.1-0.6,0.3-0.8l1.7-1.7c0.2-0.2,0.5-0.3,0.8-0.3C-451.9,264.5-451.7,264.6-451.5,264.8z`
+  }]
+}
diff --git a/app/javascript/vue/components/ui/VIcon/icons.js b/app/javascript/vue/components/ui/VIcon/icons.js
index 675c212e23..08c2dde14c 100644
--- a/app/javascript/vue/components/ui/VIcon/icons.js
+++ b/app/javascript/vue/components/ui/VIcon/icons.js
@@ -1,3 +1,5 @@
+export * from './Paths/arrowLeft.js'
+export * from './Paths/arrowRight.js'
 export * from './Paths/attention.js'
 export * from './Paths/confidence'
 export * from './Paths/download'
diff --git a/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue b/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue
index 5474ba8ed2..6a078cef93 100644
--- a/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue
+++ b/app/javascript/vue/tasks/collection_objects/browse/components/CONavegation.vue
@@ -1,13 +1,36 @@
 <template>
   <div>
-    <button
-      type="button"
-      class="button normal-input button-default"
+    <VBtn
+      medium
+      color="primary"
+      :disabled="!previousByCurrent"
+      @click="loadCO(previousByCurrent)"
+    >
+      <VIcon
+        x-small
+        name="arrowLeft"
+      />
+    </VBtn>
+    <VBtn
+      medium
+      class="margin-small-left margin-small-right"
+      color="primary"
       @click="isVisible = true"
       :disabled="!navigate.current_collection_object"
     >
       Go
-    </button>
+    </VBtn>
+    <VBtn
+      medium
+      color="primary"
+      :disabled="!nextByCurrent"
+      @click="loadCO(nextByCurrent)"
+    >
+      <VIcon
+        x-small
+        name="arrowRight"
+      />
+    </VBtn>
     <modal-component
       v-if="isVisible"
       @close="isVisible = false"
@@ -65,12 +88,17 @@ import { computed, ref } from 'vue'
 import { GetterNames } from '../store/getters/getters'
 import ModalComponent from 'components/ui/Modal'
 import loadCO from '../utils/loadCO.js'
+import VBtn from 'components/ui/VBtn/index.vue'
+import VIcon from 'components/ui/VIcon/index.vue'
 
 const store = useStore()
 const navigate = computed(() => store.getters[GetterNames.GetNavigation])
 const collectionObject = computed(() => store.getters[GetterNames.GetCollectionObject])
+const currentNavigation = ref('identifier')
 
-const isVisible = ref(false)
+const previousByCurrent = computed(() => navigate.value?.previous_by && navigate.value.previous_by[currentNavigation.value])
+const nextByCurrent = computed(() => navigate.value?.previous_by && navigate.value.next_by[currentNavigation.value])
 
+const isVisible = ref(false)
 
 </script>

From 1ab282b1c46d2d29116e7a4860d31049a291aa15 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 15 Dec 2022 16:08:43 -0600
Subject: [PATCH 155/160] Implicit to_s

---
 lib/queries/concerns/identifiers.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/queries/concerns/identifiers.rb b/lib/queries/concerns/identifiers.rb
index 022954d964..24d4ba8de4 100644
--- a/lib/queries/concerns/identifiers.rb
+++ b/lib/queries/concerns/identifiers.rb
@@ -162,7 +162,7 @@ def identifier_facet
     q = query_base.joins(:identifiers)
     w = identifier_exact ?
       identifier_table[:cached].eq(identifier) :
-      identifier_table[:cached].matches('%' + identifier + '%')
+      identifier_table[:cached].matches('%' + identifier.to_s + '%')
 
     w = w.and(identifier_table[:namespace_id].eq(namespace_id)) if namespace_id
     q.where(w)

From cb2bda2a11f9a9f13edc7ae78dfa94f443966afa Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 15 Dec 2022 16:12:15 -0600
Subject: [PATCH 156/160] CHANGELOG.md [skip-ci]. Fix #3229

---
 CHANGELOG.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d6f6351c7..5b19d2ed7f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- Next/previous navigation arrows to Browse collection object [#3229]
 - More details to steps in stepwise determinations task
 - Added softvalidation for duplicate family group name forms and misspellings [#3185]
 - With/out local identifier facet for collection objects and stagd images [#3173]
@@ -40,7 +41,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Changed
 - Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
-- "TODO list" now a faceted search [#3171]
+- "TODO list" now a faceted search named 'Filter staged images' [#3171]
 - Refactored observation cell component for Image matrix
 - Updated Ruby gems
 - Webpack binaries: Replaced `npm bin` for `npm root` to allow compatibility with recent NPM versions
@@ -50,6 +51,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Allow compare n objects in collection object match [#3238]
 - Include total of match/unmatched in Collection object match [#3237]
 
+[#3229]: https://github.com/SpeciesFileGroup/taxonworks/issues/3229
 [#3191]: https://github.com/SpeciesFileGroup/taxonworks/issues/3191
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
 [#3009]: https://github.com/SpeciesFileGroup/taxonworks/issues/3009

From 4875a208998f1bb06bdc9650a99c0341dfcf3124 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 15 Dec 2022 19:31:55 -0300
Subject: [PATCH 157/160] Fix #3250

---
 CHANGELOG.md                                                  | 2 ++
 app/javascript/vue/tasks/nomenclature/new_taxon_name/app.vue  | 4 ++--
 .../nomenclature/new_taxon_name/components/manageSynonym.vue  | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d6f6351c7..e73fe91528 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Export Project Database task not exporting rows whose `project_id` is `NULL` [#3203]
 - Close icon is difficult to distinguish when modal background is transparent [#3245]
 - Missing identifiers and determinations on collection object table in New collecting event task [#3246]
+- Click "Manage Synonymy" in Edit Taxon Name task does not redirect [#3250]
 
 ### Changed
 - Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
@@ -67,6 +68,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3238]: https://github.com/SpeciesFileGroup/taxonworks/issues/3238
 [#3245]: https://github.com/SpeciesFileGroup/taxonworks/issues/3245
 [#3246]: https://github.com/SpeciesFileGroup/taxonworks/issues/3246
+[#3250]: https://github.com/SpeciesFileGroup/taxonworks/issues/3250
 
 ## [0.29.6] - 2022-11-08
 
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/app.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/app.vue
index b95c3d4b50..d71acd4a14 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/app.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/app.vue
@@ -155,13 +155,13 @@ export default {
         Author: true,
         Status: true,
         Relationship: true,
-        'Manage synonymy': showForThisGroup(['GenusGroup', 'FamilyGroup'], this.getTaxon),
+        'Manage synonymy': showForThisGroup(['GenusGroup', 'FamilyGroup'], this.getTaxon) && !this.getTaxon.cached_is_valid,
         Type: showForThisGroup(['SpeciesGroup', 'GenusGroup', 'FamilyGroup', 'SpeciesAndInfraspeciesGroup'], this.getTaxon),
         'Original combination': showForThisGroup(['SpeciesGroup', 'GenusGroup', 'SpeciesAndInfraspeciesGroup'], this.getTaxon),
         'Subsequent Combination': showForThisGroup(['SpeciesGroup', 'GenusGroup', 'SpeciesAndInfraspeciesGroup'], this.getTaxon),
         Classification: true,
         Gender: showForThisGroup(['SpeciesGroup', 'GenusGroup', 'SpeciesAndInfraspeciesGroup'], this.getTaxon),
-        Etymology: showForThisGroup(['SpeciesGroup', 'GenusGroup', 'SpeciesAndInfraspeciesGroup'], this.getTaxon),
+        Etymology: showForThisGroup(['SpeciesGroup', 'GenusGroup', 'SpeciesAndInfraspeciesGroup'], this.getTaxon)
       }
     }
   },
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue
index e4d1062d72..93e89a621f 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/manageSynonym.vue
@@ -1,9 +1,9 @@
 <template>
   <div>
     <block-layout
-      anchor="original-combination"
+      anchor="manage-synonymy"
       v-if="isInvalid && validTaxon && childrenList.length"
-      v-help.section.originalCombination.container>
+    >
       <template #header>
         <h3>Manage synonymy</h3>
       </template>

From fe354dafcf3e70b118ec0c50e66d73453f6dac65 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 15 Dec 2022 16:44:02 -0600
Subject: [PATCH 158/160] CHANGELOG.md

---
 CHANGELOG.md | 27 +++++++++++++++++++--------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5b19d2ed7f..2adda2630a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,23 +7,25 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ## [unreleased]
 
 ### Added
+- CoL data package improvements for Remarks, metadata,  
+- Integrated GBIF remarks flags into Browse collection object [#3136]
 - Next/previous navigation arrows to Browse collection object [#3229]
 - More details to steps in stepwise determinations task
-- Added softvalidation for duplicate family group name forms and misspellings [#3185]
+- Added soft validation for duplicate family group name forms and misspellings [#3185]
 - With/out local identifier facet for collection objects and stagd images [#3173]
 - Filter by housekeeping and staged-image data attributes [#3171]
 - Delete selected collection objects (and their related data) from filter [#3174]
 - Collection object Autocomplete has loan and deaccession banners [#3192]
 - Autocomplete on Browse collection object [#3189]
-- Task - Collection object chronology, a plot of object by year collected
+- Task - Collection object chronology, a plot of object by year collected, that's all
 - Endpoint to return related data preventing or included in destroy, e.g. `/metadata/related_summary?klass=CollectionObject&id[]=16701&id[]...`
-- Gender and form classifications to filter nomenclature
+- Filter by gender and form classifications in filter nomenclature [#3212]
 - Serial facet to Filter sources [#3211]
-- `tooltips` and `actions` configuration props to Map component [#3234]
+- `tooltips` and `actions` configuration properties to Map component [#3234]
 
 ### Fixed
-- Whitepace around unit-tray headers [#3191]
-- Stepwise determinations confounded by invisible whitespace [#3009]
+- White-space around unit-tray headers [#3191]
+- Stepwise determinations confounded by invisible white-space [#3009]
 - OTU smart selector did not include items from the pinboard [#3139]
 - Source in n project autocomplete response [#3142]
 - 'Also create OTU' on batch taxon name upload causing raise
@@ -40,6 +42,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Missing identifiers and determinations on collection object table in New collecting event task [#3246]
 
 ### Changed
+- Behaviour of recent records (smart selectors) updated to reference updates, not just created timestamps
 - Lock, navigation, UI, and code refreshments to Simple new specimen [#3190]
 - "TODO list" now a faceted search named 'Filter staged images' [#3171]
 - Refactored observation cell component for Image matrix
@@ -51,10 +54,10 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Allow compare n objects in collection object match [#3238]
 - Include total of match/unmatched in Collection object match [#3237]
 
-[#3229]: https://github.com/SpeciesFileGroup/taxonworks/issues/3229
-[#3191]: https://github.com/SpeciesFileGroup/taxonworks/issues/3191
 [#2176]: https://github.com/SpeciesFileGroup/taxonworks/issues/2176
 [#3009]: https://github.com/SpeciesFileGroup/taxonworks/issues/3009
+[#3136]: https://github.com/SpeciesFileGroup/taxonworks/issues/3136
+[#3139]: https://github.com/SpeciesFileGroup/taxonworks/issues/3139
 [#3171]: https://github.com/SpeciesFileGroup/taxonworks/issues/3171
 [#3173]: https://github.com/SpeciesFileGroup/taxonworks/issues/3173
 [#3174]: https://github.com/SpeciesFileGroup/taxonworks/issues/3174
@@ -62,9 +65,15 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 [#3188]: https://github.com/SpeciesFileGroup/taxonworks/issues/3188
 [#3189]: https://github.com/SpeciesFileGroup/taxonworks/issues/3189
 [#3190]: https://github.com/SpeciesFileGroup/taxonworks/issues/3190
+[#3191]: https://github.com/SpeciesFileGroup/taxonworks/issues/3191
 [#3192]: https://github.com/SpeciesFileGroup/taxonworks/issues/3192
 [#3203]: https://github.com/SpeciesFileGroup/taxonworks/issues/3203
+[#3205]: https://github.com/SpeciesFileGroup/taxonworks/issues/3205
+[#3211]: https://github.com/SpeciesFileGroup/taxonworks/issues/3211
 [#3212]: https://github.com/SpeciesFileGroup/taxonworks/issues/3212
+[#3216]: https://github.com/SpeciesFileGroup/taxonworks/issues/3216
+[#3229]: https://github.com/SpeciesFileGroup/taxonworks/issues/3229
+[#3233]: https://github.com/SpeciesFileGroup/taxonworks/issues/3233
 [#3234]: https://github.com/SpeciesFileGroup/taxonworks/issues/3234
 [#3238]: https://github.com/SpeciesFileGroup/taxonworks/issues/3238
 [#3245]: https://github.com/SpeciesFileGroup/taxonworks/issues/3245
@@ -1440,6 +1449,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Loan item "select/deselect all" buttons missing after vue 3 migration [#2493]
 - Checkbox unbinding is not synced with update in Loan task [#2495]
 - Filter collection objects shortcuts
+- Prevent duplicate shortcuts
+- Observation matrix render error
 - Fix identifier update in new type specimen task
 - Radial menus are inheriting CSS properties in some cases [#2505]
 - Taxon determinations list in comprehensive task

From 5678bdf1d717770751296f1c760f1043e5b9b793 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Thu, 15 Dec 2022 17:40:18 -0600
Subject: [PATCH 159/160] Fix coldp export spec.

---
 lib/export/coldp.rb                              | 14 +++++++++-----
 spec/features/tasks/exports/coldp_export_spec.rb | 13 ++++++-------
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/lib/export/coldp.rb b/lib/export/coldp.rb
index 3838639c9e..a2a16db55d 100644
--- a/lib/export/coldp.rb
+++ b/lib/export/coldp.rb
@@ -33,17 +33,21 @@ def self.export(otu_id, prefer_unlabelled_otus: true)
       # source_id: [csv_array]
       ref_csv = {}
 
+      otu = ::Otu.find(otu_id)
+      project = ::Project.find(otu.project_id)
+
       # TODO: This will likely have to change, it is renamed on serving the file.
       zip_file_path = "/tmp/_#{SecureRandom.hex(8)}_coldp.zip"
 
-      metadata_path = Zaru::sanitize!("/tmp/#{::Project.find(otus[0].project_id).name}_#{DateTime.now}_metadata.yaml").gsub(' ', '_').downcase
+      metadata_path = Zaru::sanitize!("/tmp/#{project.name}_#{DateTime.now}_metadata.yaml").gsub(' ', '_').downcase
       version = Taxonworks::VERSION
       if Settings.sandbox_mode?
         version = Settings.sandbox_commit_sha
       end
-      metadata = {"title" =>::Project.find(otus[0].project_id).name,
-                  "version" => version,
-                  "issued" => DateTime.now.strftime('%Y-%m-%d'),
+      metadata = {
+        'title' => project.name,
+        'version' => version,
+        'issued' => DateTime.now.strftime('%Y-%m-%d'),
       }
       metadata_file = Tempfile.new(metadata_path)
       metadata_file.write(metadata.to_yaml)
@@ -55,7 +59,7 @@ def self.export(otu_id, prefer_unlabelled_otus: true)
           zipfile.get_output_stream("#{ft}.csv") { |f| f.write m.generate(otus, ref_csv) }
         end
 
-        zipfile.get_output_stream('Name.csv') { |f| f.write Export::Coldp::Files::Name.generate(Otu.find(otu_id), ref_csv) }
+        zipfile.get_output_stream('Name.csv') { |f| f.write Export::Coldp::Files::Name.generate(otu, ref_csv) }
         zipfile.get_output_stream('Taxon.csv') do |f|
           f.write Export::Coldp::Files::Taxon.generate(otus, otu_id, ref_csv, prefer_unlabelled_otus: prefer_unlabelled_otus)
         end
diff --git a/spec/features/tasks/exports/coldp_export_spec.rb b/spec/features/tasks/exports/coldp_export_spec.rb
index dde036ae49..370b7d09a3 100644
--- a/spec/features/tasks/exports/coldp_export_spec.rb
+++ b/spec/features/tasks/exports/coldp_export_spec.rb
@@ -17,20 +17,19 @@
       }
 
       describe 'triggering the export process', js: true do
+        
+        let(:root) { FactoryBot.create(:root_taxon_name, by: @user, project: @project) }
+        let(:taxon_name) { Protonym.create!(name: "Testidae", rank_class: Ranks.lookup(:iczn, 'Family'), parent: root, by: @user, project: @project) } 
+        let!(:otu) { FactoryBot.create(:valid_otu, by: @user, project: @project, taxon_name: taxon_name) } 
 
         before do
-          @root = FactoryBot.create(:root_taxon_name, by: @user, project: @project)
-          #@taxon_name = FactoryBot.create(:valid_taxon_name, by: @user, project: @project)
-          @taxon_name = Protonym.create!(name: "Testidae", rank_class: Ranks.lookup(:iczn, 'Family'), parent: @project.root_taxon_name,
-                                          by: @user, project: @project)
-          @otu = FactoryBot.create(:valid_otu, by: @user, project: @project, taxon_name: @taxon_name)
           visit(index_path)
         end
 
         context 'when selecting an OTU and hitting download' do
           it 'show the download is being created' do
-            fill_autocomplete('otu_id_for_coldp', with: @otu.name, select: @otu.id)
-            
+            fill_autocomplete('otu_id_for_coldp', with: otu.name, select: otu.id)
+
             # TODO: Cannot find a way to have the job queued and run later, so currently generating directly...
             perform_enqueued_jobs do
               click_on('Download')

From 52222edf4e383163e7a378e09e826a2cb8806353 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Thu, 15 Dec 2022 21:31:05 -0300
Subject: [PATCH 160/160] Preparing for version 0.30.0 release [skip ci]

---
 CHANGELOG.md              | 7 ++++++-
 lib/taxonworks/version.rb | 2 +-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9f19c4ad60..7ecbda4665 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
+\-
+
+## [0.30.0] - 2022-12-15
+
 ### Added
 - CoL data package improvements for Remarks, metadata,  
 - Integrated GBIF remarks flags into Browse collection object [#3136]
@@ -3083,7 +3087,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
 
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.6...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.30.0...development
+[0.30.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.6...v0.30.0
 [0.29.6]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.5...v0.29.6
 [0.29.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.4...v0.29.5
 [0.29.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.3...v0.29.4
diff --git a/lib/taxonworks/version.rb b/lib/taxonworks/version.rb
index 3438b97d16..7df9485279 100644
--- a/lib/taxonworks/version.rb
+++ b/lib/taxonworks/version.rb
@@ -1,3 +1,3 @@
 module Taxonworks
-  VERSION = "0.29.6"
+  VERSION = "0.30.0"
 end