From d72a9fb3b54ecae0f78a95c86f8af0e6c51246eb Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 18 Sep 2023 10:24:04 -0500
Subject: [PATCH 01/29] Change json to jsonb for SqedDepiction.  Fix #3556

---
 CHANGELOG.md                                  | 11 +++++-
 app/models/image.rb                           |  7 +++-
 app/views/images/show.html.erb                |  8 +++++
 ...2_change_sqed_depictions_json_to_jsbonb.rb |  6 ++++
 db/schema.rb                                  | 35 ++++++++++---------
 5 files changed, 48 insertions(+), 19 deletions(-)
 create mode 100644 db/migrate/20230918143352_change_sqed_depictions_json_to_jsbonb.rb

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6f017232f9..3e853d8451 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,16 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
-\-
+
+### Changed
+
+- Staged image metadata field format from JSON to JSONB [#3446]
+
+### Fixed
+
+- Staged image queries failing when multiple facets used [#3556]
+
+[#3556]: https://github.com/SpeciesFileGroup/taxonworks/issues/3556
 
 ## [0.34.4] - 2023-09-15
 
diff --git a/app/models/image.rb b/app/models/image.rb
index 43721216e2..dddb2b5352 100644
--- a/app/models/image.rb
+++ b/app/models/image.rb
@@ -70,6 +70,7 @@ class Image < ApplicationRecord
     medium: { width: 300, height: 300 }
   }.freeze
 
+
   has_one :sled_image, dependent: :destroy
 
   has_many :depictions, inverse_of: :image, dependent: :restrict_with_error
@@ -98,7 +99,11 @@ class Image < ApplicationRecord
 
   accepts_nested_attributes_for :sled_image, allow_destroy: true
 
-    # @return [Boolean]
+  def sqed_depiction
+    depictions.joins(:sqed_depiction).first&.sqed_depiction
+  end
+
+  # @return [Boolean]
   def has_duplicate?
     Image.where(image_file_fingerprint: self.image_file_fingerprint).count > 1
   end
diff --git a/app/views/images/show.html.erb b/app/views/images/show.html.erb
index 605dd2f998..89b1086562 100644
--- a/app/views/images/show.html.erb
+++ b/app/views/images/show.html.erb
@@ -12,6 +12,14 @@
     <% end %>
     </ul>
   <% end %>
+
+  <% if @image.sqed_depiction -%>
+    <%= content_tag(:h3, 'SQED Depiction') -%>
+    <ul>
+    <%= tag.ul(tag.li(link_to 'Staged image', sqed_depiction_breakdown_task_path(id: @image.sqed_depiction))) %>
+    </ul>
+  <% end %>
+
 <% end %>
 
 <%= content_for :additional_navigation do %>
diff --git a/db/migrate/20230918143352_change_sqed_depictions_json_to_jsbonb.rb b/db/migrate/20230918143352_change_sqed_depictions_json_to_jsbonb.rb
new file mode 100644
index 0000000000..ec0f83fb0f
--- /dev/null
+++ b/db/migrate/20230918143352_change_sqed_depictions_json_to_jsbonb.rb
@@ -0,0 +1,6 @@
+class ChangeSqedDepictionsJsonToJsbonb < ActiveRecord::Migration[6.1]
+  def change  
+    change_column :sqed_depictions, :result_ocr, :jsonb, using: 'result_ocr::jsonb'
+    change_column :sqed_depictions, :result_boundary_coordinates, :jsonb, using: 'result_boundary_coordinates::jsonb'
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index 1cbfe27a87..bebcc0960f 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2023_09_11_214526) do
+ActiveRecord::Schema.define(version: 2023_09_18_143352) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "btree_gin"
@@ -436,8 +436,8 @@
   end
 
   create_table "confidences", id: :serial, force: :cascade do |t|
-    t.string "confidence_object_type", null: false
     t.integer "confidence_object_id", null: false
+    t.string "confidence_object_type", null: false
     t.integer "position", null: false
     t.integer "created_by_id", null: false
     t.integer "updated_by_id", null: false
@@ -669,8 +669,8 @@
   end
 
   create_table "documentation", id: :serial, force: :cascade do |t|
-    t.string "documentation_object_type", null: false
     t.integer "documentation_object_id", null: false
+    t.string "documentation_object_type", null: false
     t.integer "document_id", null: false
     t.integer "project_id", null: false
     t.integer "created_by_id", null: false
@@ -688,7 +688,7 @@
   create_table "documents", id: :serial, force: :cascade do |t|
     t.string "document_file_file_name", null: false
     t.string "document_file_content_type", null: false
-    t.bigint "document_file_file_size", null: false
+    t.integer "document_file_file_size", null: false
     t.datetime "document_file_updated_at", null: false
     t.integer "project_id", null: false
     t.integer "created_by_id", null: false
@@ -720,6 +720,7 @@
     t.boolean "is_public"
     t.string "type"
     t.integer "total_records"
+    t.string "sha2"
     t.index ["created_by_id"], name: "index_downloads_on_created_by_id"
     t.index ["filename"], name: "index_downloads_on_filename"
     t.index ["project_id"], name: "index_downloads_on_project_id"
@@ -897,8 +898,8 @@
     t.string "vernacularName"
     t.string "waterBody"
     t.string "year"
-    t.string "dwc_occurrence_object_type"
     t.integer "dwc_occurrence_object_id"
+    t.string "dwc_occurrence_object_type"
     t.integer "created_by_id", null: false
     t.integer "updated_by_id", null: false
     t.integer "project_id"
@@ -1097,7 +1098,7 @@
     t.datetime "updated_at", null: false
     t.string "image_file_file_name"
     t.string "image_file_content_type"
-    t.bigint "image_file_file_size"
+    t.integer "image_file_file_size"
     t.datetime "image_file_updated_at"
     t.integer "updated_by_id", null: false
     t.text "image_file_meta"
@@ -1178,8 +1179,8 @@
     t.integer "project_id", null: false
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
-    t.string "loan_item_object_type"
     t.integer "loan_item_object_id"
+    t.string "loan_item_object_type"
     t.integer "total"
     t.string "disposition"
     t.index ["created_by_id"], name: "index_loan_items_on_created_by_id"
@@ -1208,7 +1209,7 @@
     t.datetime "updated_at", null: false
     t.string "recipient_honorific"
     t.string "recipient_country"
-    t.text "lender_address", null: false
+    t.text "lender_address", default: "Lender's address not provided.", null: false
     t.boolean "is_gift"
     t.index ["created_by_id"], name: "index_loans_on_created_by_id"
     t.index ["project_id"], name: "index_loans_on_project_id"
@@ -1404,10 +1405,10 @@
   end
 
   create_table "origin_relationships", id: :serial, force: :cascade do |t|
-    t.string "old_object_type", null: false
     t.integer "old_object_id", null: false
-    t.string "new_object_type", null: false
+    t.string "old_object_type", null: false
     t.integer "new_object_id", null: false
+    t.string "new_object_type", null: false
     t.integer "position"
     t.integer "created_by_id", null: false
     t.integer "updated_by_id", null: false
@@ -1509,8 +1510,8 @@
   end
 
   create_table "pinboard_items", id: :serial, force: :cascade do |t|
-    t.string "pinned_object_type", null: false
     t.integer "pinned_object_id", null: false
+    t.string "pinned_object_type", null: false
     t.integer "user_id", null: false
     t.integer "project_id", null: false
     t.integer "position", null: false
@@ -1574,7 +1575,7 @@
     t.datetime "updated_at", null: false
     t.integer "created_by_id", null: false
     t.integer "updated_by_id", null: false
-    t.jsonb "preferences", default: "{}", null: false
+    t.jsonb "preferences", default: {}, null: false
     t.string "api_access_token"
     t.string "data_curation_issue_tracker_url"
     t.index ["created_by_id"], name: "index_projects_on_created_by_id"
@@ -1583,8 +1584,8 @@
 
   create_table "protocol_relationships", id: :serial, force: :cascade do |t|
     t.integer "protocol_id", null: false
-    t.string "protocol_relationship_object_type", null: false
     t.integer "protocol_relationship_object_id", null: false
+    t.string "protocol_relationship_object_type", null: false
     t.integer "position", null: false
     t.integer "created_by_id", null: false
     t.integer "updated_by_id", null: false
@@ -1843,15 +1844,15 @@
     t.string "boundary_finder", null: false
     t.boolean "has_border", null: false
     t.string "layout", null: false
-    t.jsonb "metadata_map", default: "{}", null: false
-    t.jsonb "specimen_coordinates", default: "{}", null: false
+    t.jsonb "metadata_map", default: {}, null: false
+    t.jsonb "specimen_coordinates", default: {}, null: false
     t.integer "project_id", null: false
     t.integer "created_by_id", null: false
     t.integer "updated_by_id", null: false
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
-    t.json "result_boundary_coordinates"
-    t.json "result_ocr"
+    t.jsonb "result_boundary_coordinates"
+    t.jsonb "result_ocr"
     t.datetime "in_progress"
     t.index ["depiction_id"], name: "index_sqed_depictions_on_depiction_id"
     t.index ["project_id"], name: "index_sqed_depictions_on_project_id"

From bcd905c55466087235389c575d96fd9b2a5d2155 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 18 Sep 2023 10:31:50 -0500
Subject: [PATCH 02/29] Comment on xml column [skip ci]

---
 lib/queries/depiction/filter.rb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/queries/depiction/filter.rb b/lib/queries/depiction/filter.rb
index c2eb1aa079..2520c91fb6 100644
--- a/lib/queries/depiction/filter.rb
+++ b/lib/queries/depiction/filter.rb
@@ -70,6 +70,10 @@ def depiction_object_id_facet
         table[:depiction_object_id].eq_any(depiction_object_id)
       end
 
+      # If we add merge_clauses then we likely have
+      # to deal with excluding the `xml` field from distinct+intersection calls
+      # via a custom base_query field.
+
       def and_clauses
         [
           depiction_id_facet,

From 9b2f82cb39741e2cc3019286e2a408d02483dd86 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 19 Sep 2023 10:03:19 -0500
Subject: [PATCH 03/29] Fix bug with ordering in OTUs filter.

---
 CHANGELOG.md                       | 1 +
 app/controllers/otus_controller.rb | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e853d8451..4467455966 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- Taxon name/otus filter order bug
 - Staged image queries failing when multiple facets used [#3556]
 
 [#3556]: https://github.com/SpeciesFileGroup/taxonworks/issues/3556
diff --git a/app/controllers/otus_controller.rb b/app/controllers/otus_controller.rb
index 079ae3c5b1..180a13db04 100644
--- a/app/controllers/otus_controller.rb
+++ b/app/controllers/otus_controller.rb
@@ -22,7 +22,7 @@ def index
           .page(params[:page])
           .per(params[:per])
           .eager_load(:taxon_name)
-          .order('taxon_names.cached, otus.name')
+          .order(:cached, 'otus.name')
       }
     end
   end

From 59d9283ed478f5d8fc8c726c8b4fd99aa8710a55 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 20 Sep 2023 12:22:49 -0300
Subject: [PATCH 04/29] Add depiction list on filter images

---
 CHANGELOG.md                                           |  5 ++++-
 app/javascript/vue/tasks/images/filter/app.vue         |  6 ++++--
 .../tasks/images/filter/components/DepictionList.vue   | 10 ++++++----
 .../vue/tasks/images/filter/components/image.vue       |  2 +-
 4 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4467455966..89333c1ddf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,9 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
+### Added
+
+- Depictions list on Filter image
 
 ### Changed
 
@@ -23,7 +26,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Added
 
-- ImportAttribute facets to various filters 
+- ImportAttribute facets to various filters
 - Project data curation issue tracking URL field (and to base API response) [#3550]
 - Manual option to regenerate derivative images on Show Image
 - API gallery endpoint `/depictions/gallery`
diff --git a/app/javascript/vue/tasks/images/filter/app.vue b/app/javascript/vue/tasks/images/filter/app.vue
index 78d5f50e4c..c6c4e6bb92 100644
--- a/app/javascript/vue/tasks/images/filter/app.vue
+++ b/app/javascript/vue/tasks/images/filter/app.vue
@@ -19,8 +19,9 @@
           v-if="list.length"
           class="horizontal-right-content"
         >
-          <span>|</span>
-          <div class="margin-small-left">
+          <span class="margin-small-left margin-small-right">|</span>
+          <div class="horizontal-left-content gap-small margin-small-left">
+            <DepictionList :image-id="selectedIds" />
             <SelectAll
               v-model="selectedIds"
               :ids="list.map(({ id }) => id)"
@@ -55,6 +56,7 @@ import ListComponent from './components/list'
 import SelectAll from '@/tasks/collection_objects/filter/components/selectAll.vue'
 import VSpinner from '@/components/spinner.vue'
 import useFilter from '@/shared/Filter/composition/useFilter.js'
+import DepictionList from './components/DepictionList.vue'
 import { IMAGE } from '@/constants/index.js'
 import { Image } from '@/routes/endpoints'
 
diff --git a/app/javascript/vue/tasks/images/filter/components/DepictionList.vue b/app/javascript/vue/tasks/images/filter/components/DepictionList.vue
index 56e622fb92..a1decd4d35 100644
--- a/app/javascript/vue/tasks/images/filter/components/DepictionList.vue
+++ b/app/javascript/vue/tasks/images/filter/components/DepictionList.vue
@@ -4,7 +4,8 @@
       v-if="isModalVisible"
       @close="isModalVisible = false"
       :container-style="{
-        maxWidth: '700px'
+        maxWidth: '700px',
+        width: '700px'
       }"
     >
       <template #header>
@@ -55,6 +56,7 @@
     <VBtn
       medium
       color="primary"
+      :disabled="!imageId.length"
       @click="isModalVisible = true"
     >
       Depictions
@@ -78,8 +80,8 @@ import RadialNavigator from '@/components/radials/navigation/radial.vue'
 
 const props = defineProps({
   imageId: {
-    type: Number,
-    required: true
+    type: Array,
+    default: () => []
   }
 })
 
@@ -92,7 +94,7 @@ watch(isModalVisible, (newVal) => {
     isLoading.value = true
 
     Depiction.filter({
-      image_id: [props.imageId]
+      image_id: props.imageId
     })
       .then(({ body }) => {
         list.value = body
diff --git a/app/javascript/vue/tasks/images/filter/components/image.vue b/app/javascript/vue/tasks/images/filter/components/image.vue
index 8532a1812d..224ca8d2ac 100644
--- a/app/javascript/vue/tasks/images/filter/components/image.vue
+++ b/app/javascript/vue/tasks/images/filter/components/image.vue
@@ -56,7 +56,7 @@
                 <RadialNavigation :global-id="image.global_id" />
               </li>
               <li>
-                <DepictionList :image-id="image.id" />
+                <DepictionList :image-id="[image.id]" />
               </li>
             </ul>
           </div>

From d3804ec77c96db6ded75e5b6ebefca232addb9cd Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 20 Sep 2023 15:58:11 -0300
Subject: [PATCH 05/29] Fix #3560

---
 CHANGELOG.md                                                    | 1 +
 .../annotator/components/citations/citation_annotator.vue       | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 89333c1ddf..18dee25b67 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 - Taxon name/otus filter order bug
 - Staged image queries failing when multiple facets used [#3556]
+- Citations list is truncated in Radial Annotator [#3560]
 
 [#3556]: https://github.com/SpeciesFileGroup/taxonworks/issues/3556
 
diff --git a/app/javascript/vue/components/radials/annotator/components/citations/citation_annotator.vue b/app/javascript/vue/components/radials/annotator/components/citations/citation_annotator.vue
index 6ae9f7b4c6..23171b127c 100644
--- a/app/javascript/vue/components/radials/annotator/components/citations/citation_annotator.vue
+++ b/app/javascript/vue/components/radials/annotator/components/citations/citation_annotator.vue
@@ -134,7 +134,7 @@ export default {
   },
 
   created() {
-    Citation.where({
+    Citation.all({
       citation_object_id: this.metadata.object_id,
       citation_object_type: this.metadata.object_type,
       extend: EXTEND_PARAMS

From d2678285dbb6ca8367b0e05bc1f4af0b072db93e Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 20 Sep 2023 16:47:09 -0500
Subject: [PATCH 06/29] Add Cached map item report from filter OTUs

Debug cached maps
---
 CHANGELOG.md                                  |  1 +
 .../tasks/cached_maps/report_controller.rb    | 10 +++++
 .../radials/linker/constants/links.js         |  5 +++
 .../components/radials/linker/links/Otu.js    |  9 ++++-
 .../cached_maps/report/items_by_otu.html.erb  | 40 +++++++++++++++++++
 config/routes/tasks.rb                        |  9 ++++-
 6 files changed, 71 insertions(+), 3 deletions(-)
 create mode 100644 app/controllers/tasks/cached_maps/report_controller.rb
 create mode 100644 app/views/tasks/cached_maps/report/items_by_otu.html.erb

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 18dee25b67..9604390c60 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Added
 
+- Cached map item report (linked from Filter OTUs)
 - Depictions list on Filter image
 
 ### Changed
diff --git a/app/controllers/tasks/cached_maps/report_controller.rb b/app/controllers/tasks/cached_maps/report_controller.rb
new file mode 100644
index 0000000000..513ad5532c
--- /dev/null
+++ b/app/controllers/tasks/cached_maps/report_controller.rb
@@ -0,0 +1,10 @@
+class Tasks::CachedMaps::ReportController < ApplicationController
+  include TaskControllerConfiguration
+
+  # GET
+  def items_by_otu
+    @otus = ::Queries::Otu::Filter.new(params).all.limit(10).page(params[:page]).per(params[:per])
+    @cached_map_items = CachedMapItem.where(otu: @otus).distinct.limit(500)
+  end
+
+end
diff --git a/app/javascript/vue/components/radials/linker/constants/links.js b/app/javascript/vue/components/radials/linker/constants/links.js
index 4908f17eee..744db31596 100644
--- a/app/javascript/vue/components/radials/linker/constants/links.js
+++ b/app/javascript/vue/components/radials/linker/constants/links.js
@@ -22,3 +22,8 @@ export const TASK_TAXON_NAME_STATS = {
   label: 'Chronology stats',
   link: '/tasks/taxon_names/stats/'
 }
+
+export const TASK_CACHED_MAP_ITEM = {
+  label: 'Cached map items',
+  link: '/tasks/cached_maps/report/items_by_otu'
+}
diff --git a/app/javascript/vue/components/radials/linker/links/Otu.js b/app/javascript/vue/components/radials/linker/links/Otu.js
index fd423f5e08..9c102e1619 100644
--- a/app/javascript/vue/components/radials/linker/links/Otu.js
+++ b/app/javascript/vue/components/radials/linker/links/Otu.js
@@ -1,4 +1,9 @@
+import {
+  TASK_CACHED_MAP_ITEM,
+} from '../constants/links'
+
+
 export const Otu = {
-  all: [],
-  ids: []
+  all: [ TASK_CACHED_MAP_ITEM ],
+  ids: [ TASK_CACHED_MAP_ITEM ]
 }
diff --git a/app/views/tasks/cached_maps/report/items_by_otu.html.erb b/app/views/tasks/cached_maps/report/items_by_otu.html.erb
new file mode 100644
index 0000000000..d579fe952a
--- /dev/null
+++ b/app/views/tasks/cached_maps/report/items_by_otu.html.erb
@@ -0,0 +1,40 @@
+<h1> Cached map items by OTU </h1>
+
+<%= tag.td(link_to('Back to Filter OTUs', filter_otus_task_path( ::Queries::Otu::Filter.new(params).params)) ) %>
+
+<%= tag.p 'This report lists individual items that make up one or more OTU cached maps', class: [:feedback, 'feedback-info'] %>
+
+<table>
+  <tr>
+    <%= tag.th('id') %>
+    <%= tag.th('OTU') %>
+    <%= tag.th('GeographicItem ID') %>
+    <%= tag.th('GeographicAreas (inferred!)') %>
+    <%= tag.th('Reference count') %>
+    <%= tag.th('Level 0 name') %>
+    <%= tag.th('Level 1 name') %>
+    <%= tag.th('Level 2 name') %>
+    <%# tag.th('recomputed - quick_cached_map_name_hierarchy') %>
+    <%# tag.th('recomputed - cached_map_name_hierarchy') %>
+    <%= tag.th('untranslated') %>
+    <%= tag.th('Is absent (not implemented)') %>
+  </tr>
+
+  <% @cached_map_items.find_each do |i| %>
+    <tr>
+      <%= tag.td(i.id) %>
+      <%= tag.td(link_to(otu_tag(i.otu), filter_otus_task_path(otu_id: i.otu_id) )) %>
+      <%= tag.td(link_to(i.geographic_item_id, geographic_item_path(i.geographic_item_id.to_s))) %>
+      <%= tag.td(i.geographic_item.geographic_areas.collect{|c| geographic_area_link(c)}.join.html_safe) %>
+      <%= tag.td(i.reference_count) %>
+
+      <%= tag.td(i.level0_geographic_name) %>
+      <%= tag.td(i.level1_geographic_name) %>
+      <%= tag.td(i.level2_geographic_name) %>
+      <%# tag.td(i.geographic_item.quick_geographic_name_hierarchy ) %>
+      <%# tag.td( CachedMapItem.cached_map_name_hierarchy(i.geographic_item_id)) %>
+      <%= tag.td(i.untranslated ? tag.em('True', class: [:feedback, 'feedback-thin', 'feedback-warning']) : nil  ) %>
+      <%= tag.td(i.is_absent) %>
+    </tr>
+  <% end %>
+</table>
diff --git a/config/routes/tasks.rb b/config/routes/tasks.rb
index b9606572d7..d546568d3b 100644
--- a/config/routes/tasks.rb
+++ b/config/routes/tasks.rb
@@ -1,4 +1,11 @@
 scope :tasks do
+
+  scope :cached_maps do
+    scope :report, controller: 'tasks/cached_maps/report' do
+      get :items_by_otu, as: 'cached_map_items_by_otus_task'
+    end
+  end
+
   scope :geographic_areas do
     scope :usage, controller: 'tasks/geographic_areas/usage' do
       get '/', action: :index, as: 'geographic_area_usage_task'
@@ -510,7 +517,7 @@
     end
 
     scope :filter, controller: 'tasks/otus/filter' do
-      get '/', action: :index, as: 'filter_otus_task' 
+      get '/', action: :index, as: 'filter_otus_task'
 
       # TODO: remove all
       #   get 'find', as: 'find_otus_task' # 'find_area_and_date_task'

From 9aa60319f7c2c03933d73d7484d8f8874cbee476 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Wed, 20 Sep 2023 17:01:54 -0500
Subject: [PATCH 07/29] Fix CO timeline data/time issue.

Fixes to CachedMap indexing of label values
---
 app/models/cached_map_item.rb               | 50 ++++++++-------------
 app/models/concerns/shared/maps.rb          | 13 ++++--
 app/models/geographic_area.rb               |  5 +++
 app/models/geographic_item.rb               |  7 +--
 lib/catalog/collection_object.rb            | 30 ++++++-------
 lib/catalog/collection_object/entry_item.rb |  4 +-
 lib/tasks/maintenance/cached/maps.rake      | 22 ++++++---
 7 files changed, 66 insertions(+), 65 deletions(-)

diff --git a/app/models/cached_map_item.rb b/app/models/cached_map_item.rb
index 5446743604..e9ebc2eb1f 100644
--- a/app/models/cached_map_item.rb
+++ b/app/models/cached_map_item.rb
@@ -56,50 +56,42 @@ class CachedMapItem < ApplicationRecord
   #   {country:, state:, county: }
   #  Check to see if a record is already present rather than-recalculate spatially
   #  CONSIDER: Use Reddis store to cache these results and look them up from there.
+  #
   def self.cached_map_name_hierarchy(geographic_item_id)
     h = CachedMapItem
-      .select(
-        'level0_geographic_name country, level1_geographic_name state, level2_geographic_name county'
-      )
+      .select('level0_geographic_name country, level1_geographic_name state, level2_geographic_name county')
         .where('level0_geographic_name IS NOT NULL OR level1_geographic_name IS NOT NULL OR level2_geographic_name IS NOT NULL')
         .find_by(geographic_item_id:) # finds first
         &.attributes
-        &.compact
+        &.compact!
 
-      return h if h.present?
+    return h.symbolize_keys if h.present?
 
-      GeographicItem.find(geographic_item_id).quick_geographic_name_hierarchy
+    GeographicItem.find(geographic_item_id).quick_geographic_name_hierarchy
   end
 
   def self.cached_map_geographic_items_by_otu(otu_scope = nil)
     return GeographicItem.none if otu_scope.nil?
 
-    s =
-      'WITH otu_scope AS (' + otu_scope.all.to_sql + ') ' +
+    s = 'WITH otu_scope AS (' + otu_scope.all.to_sql + ') ' +
       ::GeographicItem
-      .joins(
-        'JOIN cached_maps on cached_maps.geographic_item_id = geographic_items.id'
-      )
-        .joins(
-          'JOIN otu_scope as otu_scope1 on otu_scope1.id = cached_maps.otu_id'
-        )
-          .to_sql
+        .joins('JOIN cached_maps on cached_maps.geographic_item_id = geographic_items.id')
+        .joins( 'JOIN otu_scope as otu_scope1 on otu_scope1.id = cached_maps.otu_id').to_sql
 
-        ::GeographicItem.from('(' + s + ') as geographic_items').distinct
+    ::GeographicItem.from('(' + s + ') as geographic_items').distinct
   end
 
   # TODO: constantize
   def self.types_by_data_origin(data_origin = [])
     data_origin.each do |d|
-      a =
-        CachedMapItem
+      a = CachedMapItem
         .descendants
         .inject([]) do |ary, t|
           ary.push(t.name) if t::SOURCE_GAZETEERS.include?(d)
           ary
-        end
-          .compact
-          .uniq
+        end.compact!
+
+        a = a.uniq if a.present?
         return a if a.present?
     end
   end
@@ -148,7 +140,7 @@ def self.translate_by_alternate_shape(geographic_item_id, data_origin)
       .order(cached_total_area: :ASC) # smallest first
       .first
       &.id
-    return [a]
+      return [a]
     else
       []
     end
@@ -160,15 +152,10 @@ def self.translate_by_spatial_overlap(geographic_item_id, data_origin, percent_o
     return [] if geographic_item_id.blank?
     b = GeographicItem
       .joins(:geographic_areas_geographic_items)
-      .where(
-        ::GeographicItem
-      .joins(:geographic_areas_geographic_items)
       .where(geographic_areas_geographic_items: { data_origin: })
-      .within_radius_of_item_sql(geographic_item_id, 0.0)
-      )
-        .where(geographic_areas_geographic_items: { data_origin: })
-        .order('geographic_items.cached_total_area ASC')
-        .pluck(:id, :cached_total_area)
+      .where( GeographicItem.within_radius_of_item_sql(geographic_item_id, 0.0) )
+      .order('geographic_items.cached_total_area ASC')
+      .pluck(:id, :cached_total_area)
 
       gi = GeographicItem.select(:id, :cached_total_area).find(geographic_item_id)
       original_area = gi.cached_total_area
@@ -237,6 +224,7 @@ def self.translate_geographic_item_id(geographic_item_id, origin_type = nil, dat
     end
 
     a, debug = translate_by_spatial_overlap(geographic_item_id, data_origin, percent_overlap_cutoff)
+
     return a if a.present?
 
     []
@@ -284,11 +272,9 @@ def self.stubs(source_object, cached_map_type)
         h[:geographic_item_id] = [geographic_item_id]
         h[:untranslated] = true
       end
-
     end
 
     h[:otu_id] = otu_id
-
     h
   end
 end
diff --git a/app/models/concerns/shared/maps.rb b/app/models/concerns/shared/maps.rb
index de36c9b54f..830f9917d3 100644
--- a/app/models/concerns/shared/maps.rb
+++ b/app/models/concerns/shared/maps.rb
@@ -1,7 +1,7 @@
 ## Shared code for extending models that impact CachedMap creation (at present AssertedDistribution, Georeference).
 #
 # TODO:
-# - callbacks in all potentially altering models, e.g.: 
+# - callbacks in all potentially altering models, e.g.:
 #   * AssertedDistribution (geographic_area_id change, otu_id change)
 #   * GeographicItem (shape change) ?! necessary or we destroy/update !?
 #   * CollectionObject (collecting_event_id change)
@@ -11,7 +11,7 @@
 #   * GeographicArea - !?!@# (new/altered gazetters)
 #
 # - provide 2 shapes, absent/present when both there
-# - resolve "untranslated" when rendering 
+# - resolve "untranslated" when rendering
 #
 module Shared::Maps
   extend ActiveSupport::Concern
@@ -72,6 +72,10 @@ def remove_from_cached_map_items
       delay(queue: 'cached_map').deduct_from_cached_map_items
     end
 
+    # @param batch (Boolean)
+    #   true - skips setting geographic name labels (see followup tasks)
+    #   false - sets labels
+    #
     # Creates or increments a CachedMapItem and creates a CachedMapRegister for this object.
     # * !! Assumes this is the first time CachedMapItem is being indexed for this object.
     # * !! Does NOT check register.
@@ -104,8 +108,9 @@ def create_cached_map_items(batch = false)
                   # en-masse after processing.
                   unless batch
                     name_hierarchy[geographic_item_id] ||= CachedMapItem.cached_map_name_hierarchy(geographic_item_id)
-                    a.level0_geographic_name = name_hierarchy[geographic_item_id][:country],
-                    a.level1_geographic_name = name_hierarchy[geographic_item_id][:state],
+
+                    a.level0_geographic_name = name_hierarchy[geographic_item_id][:country]
+                    a.level1_geographic_name = name_hierarchy[geographic_item_id][:state]
                     a.level2_geographic_name = name_hierarchy[geographic_item_id][:county]
                   end
 
diff --git a/app/models/geographic_area.rb b/app/models/geographic_area.rb
index 1bee2eac1f..b355376579 100644
--- a/app/models/geographic_area.rb
+++ b/app/models/geographic_area.rb
@@ -354,6 +354,11 @@ def categorize_tdwg
 
   # @return [Hash]
   #   use the parent/child relationships of the this GeographicArea to return a country/state/county categorization
+  #   {
+  #     state: '',
+  #     country: '',
+  #     county: ''
+  #   }
   def geographic_name_classification
     v = {}
     self_and_ancestors.each do |a|
diff --git a/app/models/geographic_item.rb b/app/models/geographic_item.rb
index aa283980d4..1f5e8fe977 100644
--- a/app/models/geographic_item.rb
+++ b/app/models/geographic_item.rb
@@ -84,7 +84,6 @@ class GeographicItem < ApplicationRecord
   # ANTI_MERIDIAN = '0X0102000020E61000000200000000000000008066400000000000405640000000000080664000000000004056C0'
   ANTI_MERIDIAN = 'LINESTRING (180 89.0, 180 -89)'.freeze
 
-  has_one :cached_map, inverse_of: :geographic_item
   has_many :cached_map_items, inverse_of: :geographic_item
 
   has_many :geographic_areas_geographic_items, dependent: :destroy, inverse_of: :geographic_item
@@ -92,9 +91,7 @@ class GeographicItem < ApplicationRecord
   has_many :asserted_distributions, through: :geographic_areas
   has_many :geographic_area_types, through: :geographic_areas
   has_many :parent_geographic_areas, through: :geographic_areas, source: :parent
-  has_many :gadm_geographic_areas, class_name: 'GeographicArea', foreign_key: :gadm_geo_item_id
-  has_many :ne_geographic_areas, class_name: 'GeographicArea', foreign_key: :ne_geo_item_id
-  has_many :tdwg_geographic_areas, class_name: 'GeographicArea', foreign_key: :tdwg_geo_item_id
+
   has_many :georeferences, inverse_of: :geographic_item
   has_many :georeferences_through_error_geographic_item,
     class_name: 'Georeference', foreign_key: :error_geographic_item_id, inverse_of: :error_geographic_item
@@ -872,7 +869,7 @@ def st_multi(*geographic_item_ids)
   # of how the GeographicArea gazetteer is indexed.
   def quick_geographic_name_hierarchy
     geographic_areas.order(:id).each do |ga|
-      h = ga.geographic_name_classification # not quick enough
+      h = ga.geographic_name_classification # not quick enough !!
       return h if h.present?
     end
    return  {}
diff --git a/lib/catalog/collection_object.rb b/lib/catalog/collection_object.rb
index 05224ece48..d0c0054e62 100644
--- a/lib/catalog/collection_object.rb
+++ b/lib/catalog/collection_object.rb
@@ -43,33 +43,33 @@ class Catalog::CollectionObject < ::Catalog
   # Group the events so that they can be toggled
   FILTER_MAP = {
     born: :life,
-    died: :life, 
-    collected_on: :collecting_event, 
+    died: :life,
+    collected_on: :collecting_event,
     determined: :taxon_determinations,
     described: :observations,
     given_identifier: :annotations,
-    georeferenced: :collecting_event, 
+    georeferenced: :collecting_event,
     destroyed: :accessions,
-    placed_in_repository: :accessions, 
-    sent_for_loan: :loans, 
+    placed_in_repository: :accessions,
+    sent_for_loan: :loans,
     returned_from_loan: :loans,
-    updated_metadata: :annotations, 
-    added_note: :annotations, 
+    updated_metadata: :annotations,
+    added_note: :annotations,
     annotated: :annotations,
-    cited: :annotations, 
+    cited: :annotations,
     containerized: :accessions,
     extracted_from: :lab,
     sequenced: :lab,
     dissected: :lab,
     tagged: :annotations,
-    typified: nil, 
-    added_attribute: :annotations, 
+    typified: nil,
+    added_attribute: :annotations,
     biologically_classified: :biology,
-    fossilized_between:  :collecting_event, 
-    imaged: :images, 
-    metadata_depicted: :images, 
+    fossilized_between:  :collecting_event,
+    imaged: :images,
+    metadata_depicted: :images,
     collecting_event_metadata_depicted: :images,
-    collection_site_imaged: :collecting_event,  
+    collection_site_imaged: :collecting_event,
     biologically_associated: :biology,
     became_origin_of: :lab,
     originated_from: :lab,
@@ -130,7 +130,7 @@ def self.data_for(collection_object)
     end
 
     o.type_materials.each do |t|
-      date = t&.source&.nomenclature_date
+      date = t&.source&.nomenclature_date&.to_time
       data.items << Catalog::CollectionObject::EntryItem.new(type: :typified, object: t, start_date: date)
     end
 
diff --git a/lib/catalog/collection_object/entry_item.rb b/lib/catalog/collection_object/entry_item.rb
index f58e4450f3..3bf1a98f75 100644
--- a/lib/catalog/collection_object/entry_item.rb
+++ b/lib/catalog/collection_object/entry_item.rb
@@ -20,8 +20,8 @@ def initialize(object: nil, type: nil, start_date: nil, end_date: nil)
     raise TaxonWorks::Error, ':object is nil' if object.nil?
     raise TaxonWorks::Error, ':type is nil' if type.nil?
     raise TaxonWorks::Error, 'type is not in the list' if !Catalog::CollectionObject::EVENT_TYPES.include?(type)
-    raise TaxonWorks::Error, 'start_date is not a DateTime' if start_date && !start_date.kind_of?(Time)
-    raise TaxonWorks::Error, 'end_date is not a DateTime' if end_date && !end_date.kind_of?(Time)
+    raise TaxonWorks::Error, 'start_date is not a Time' if start_date && !start_date.kind_of?(Time)
+    raise TaxonWorks::Error, 'end_date is not a Time' if end_date && !end_date.kind_of?(Time)
 
     @object = object
     @start_date = start_date
diff --git a/lib/tasks/maintenance/cached/maps.rake b/lib/tasks/maintenance/cached/maps.rake
index 43fb488d45..4269e4fb23 100644
--- a/lib/tasks/maintenance/cached/maps.rake
+++ b/lib/tasks/maintenance/cached/maps.rake
@@ -63,15 +63,21 @@ namespace :tw do
           puts "Labelling #{items.count} CachedMapItems."
 
           Parallel.each(items.each, progress: 'labelling_geographic_items', in_processes: cached_rebuild_processes ) do |o|
-            h =  CachedMapItem.cached_map_name_hierarchy(o.geographic_item_id)
-            CachedMapItem.where(geographic_item_id: o.geographic_item_id)
-              .where.not(untranslated: true)
-              .update_all(
+
+            h = CachedMapItem.cached_map_name_hierarchy(o.geographic_item_id)
+
+            z = CachedMapItem.where(geographic_item_id: o.geographic_item_id)
+                  .where.not(untranslated: true)
+
+              puts 'Size: ' + z.size.to_s
+
+              z.update_all(
                 level0_geographic_name: h[:country],
                 level1_geographic_name: h[:state],
                 level2_geographic_name: h[:county]
               )
-              puts o.geographic_item_id
+
+            puts o.geographic_item_id
             puts h
           end
           puts 'Done labelling cached map items.'
@@ -97,12 +103,14 @@ namespace :tw do
 
           Parallel.each(otus.find_each, progress: 'build_cached_map_for_otu', in_processes: cached_rebuild_processes ) do |o|
             o.collecting_events.each do |ce|
+
+              # !! All georeferences, not just one
               ce.georeferences.where.missing(:cached_map_register).each do |g|
 
                 begin
                   CachedMapItem.transaction do
                     reconnected ||= Georeference.connection.reconnect! || true # https://github.com/grosser/parallel
-                    g.send(:create_cached_map_items)
+                    g.send(:create_cached_map_items, true)
                   end
                   true
                 rescue => exception
@@ -116,7 +124,7 @@ namespace :tw do
               begin
                 CachedMapItem.transaction do
                   reconnected ||= AssertedDistribution.connection.reconnect! || true # https://github.com/grosser/parallel
-                  ad.send(:create_cached_map_items)
+                  ad.send(:create_cached_map_items, true)
                 end
                 true
               rescue => exception

From 25628dc9f69baccbaf12ee77a9763eec16aa6d0e Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Wed, 20 Sep 2023 19:06:24 -0300
Subject: [PATCH 08/29] Fix dwc attributes table

---
 CHANGELOG.md                                  |  1 +
 .../CollectionObject/CollectionObjectDwc.vue  | 25 ++++++++++---------
 2 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9604390c60..6eb2662631 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Taxon name/otus filter order bug
 - Staged image queries failing when multiple facets used [#3556]
 - Citations list is truncated in Radial Annotator [#3560]
+- DwC attributes are now showing in Stepwise determinations task
 
 [#3556]: https://github.com/SpeciesFileGroup/taxonworks/issues/3556
 
diff --git a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectDwc.vue b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectDwc.vue
index c2c4926af6..c686347367 100644
--- a/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectDwc.vue
+++ b/app/javascript/vue/tasks/collection_objects/stepwise/determinations/components/CollectionObject/CollectionObjectDwc.vue
@@ -4,7 +4,7 @@
       <h3>DwC Attributes</h3>
     </template>
     <template #body>
-      <table class="full_width">
+      <table class="full_width table-striped">
         <thead>
           <tr>
             <th>Attribute</th>
@@ -13,13 +13,11 @@
         </thead>
         <tbody>
           <tr
-            v-for="(value, attr, index) in dwcAttributes"
-            :key="attr"
-            class="list-complete-item contextMenuCells"
-            :class="{ even: index % 2 }"
+            v-for="(value, index) in dwc?.column_headers"
+            :key="value"
           >
-            <td>{{ attr }}</td>
             <td>{{ value }}</td>
+            <td>{{ dwc.data[0][index] }}</td>
           </tr>
         </tbody>
       </table>
@@ -42,12 +40,15 @@ const props = defineProps({
 })
 
 const isLoading = ref(true)
-const dwcAttributes = ref({})
+const dwc = ref({})
 
-CollectionObject.find(props.collectionObjectId, {
-  extend: ['dwc_fields']
-}).then(({ body }) => {
-  isLoading.value = false
-  dwcAttributes.value = body.dwc
+CollectionObject.dwcIndex({
+  collection_object_id: [props.collectionObjectId]
 })
+  .then(({ body }) => {
+    dwc.value = body
+  })
+  .finally(() => {
+    isLoading.value = false
+  })
 </script>

From b254adc3fcd5c5b430b295543475a718f065a856 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Wed, 20 Sep 2023 20:47:18 -0300
Subject: [PATCH 09/29] Added hint that a task exists in create import dataset

---
 app/views/import_datasets/_form.html.erb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/app/views/import_datasets/_form.html.erb b/app/views/import_datasets/_form.html.erb
index f9fdc88524..b4bd53ddd7 100644
--- a/app/views/import_datasets/_form.html.erb
+++ b/app/views/import_datasets/_form.html.erb
@@ -1,3 +1,5 @@
+<p class="feedback feedback-info"> A task is available, use <%= link_to('Darwin Core Archive (DwC-A) import', dwca_import_task_path) -%>.</p>
+
 <%= form_for(@import_dataset.becomes(ImportDataset), multipart: true) do |f| %>
     <%= render 'shared/errors', object: @import_dataset.becomes(ImportDataset) %>
 

From 8f7a06bb57524d4332991f1079307094944545f7 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 21 Sep 2023 12:11:01 -0300
Subject: [PATCH 10/29] Add issue tracker

---
 app/assets/stylesheets/base/headers.scss      | 33 ++++----
 app/helpers/workbench/layout_helper.rb        | 12 +++
 app/javascript/packs/application.js           |  1 +
 .../vue/initializers/issue_tracker/App.vue    | 78 +++++++++++++++++++
 .../vue/initializers/issue_tracker/main.js    | 29 +++++++
 app/views/sessions/_summary.html.erb          | 15 +---
 6 files changed, 138 insertions(+), 30 deletions(-)
 create mode 100644 app/javascript/vue/initializers/issue_tracker/App.vue
 create mode 100644 app/javascript/vue/initializers/issue_tracker/main.js

diff --git a/app/assets/stylesheets/base/headers.scss b/app/assets/stylesheets/base/headers.scss
index 88302cf1ff..f5d79477cc 100644
--- a/app/assets/stylesheets/base/headers.scss
+++ b/app/assets/stylesheets/base/headers.scss
@@ -6,27 +6,25 @@
   background-color: $color-header;
   height: 60px;
 
-  #taxonworks {
-    .logo {
-      width: 160px;
-      height: 20px;
-      background-image: image-url('taxonworks-white.svg');
-      background-size: contain;
-      background-repeat: no-repeat;
-      background-position: left center;
-      padding: 0px;
-      text-decoration: none;
-    }
+  #taxonworks_logo {
+    width: 160px;
+    height: 20px;
+    background-image: image-url('taxonworks-white.svg');
+    background-size: contain;
+    background-repeat: no-repeat;
+    background-position: left center;
+    padding: 0px;
+    text-decoration: none;
   }
 
   #taxonworks_left {
     flex-grow: 1;
-    line-height: $font_small;
+  }
 
-    a {
-      color: white;
-      text-decoration: none;
-    }
+  #taxonworks_left > a {
+    color: white;
+    text-decoration: none;
+    line-height: $font_small;
   }
 
   #taxonworks_version {
@@ -43,7 +41,7 @@
   .horizontal_navbar {
     a {
       padding: 0px;
-      color: #FFF;
+      color: #fff;
     }
     li {
       padding-left: $standard_padding;
@@ -69,4 +67,3 @@
   padding-left: $standard_padding;
   padding-right: $standard_padding;
 }
-
diff --git a/app/helpers/workbench/layout_helper.rb b/app/helpers/workbench/layout_helper.rb
index 92a0cc6186..42645e56cf 100644
--- a/app/helpers/workbench/layout_helper.rb
+++ b/app/helpers/workbench/layout_helper.rb
@@ -27,4 +27,16 @@ def sandbox_details_tag
     end 
   end
 
+  def issue_tracker_tag
+    [
+      link_to(
+        'Issues', 
+        'https://github.com/SpeciesFileGroup/taxonworks/issues',
+        target: '_blank',
+        data: { 'curation-issue-tracker': sessions_current_project.data_curation_issue_tracker_url}
+      ),
+      sessions_current_project.data_curation_issue_tracker_url? ? content_tag('div','', id: 'curation-issue-tracker-container') : nil
+    ].join().html_safe
+  end
+
 end
diff --git a/app/javascript/packs/application.js b/app/javascript/packs/application.js
index a3f67783ce..cfd091b4f9 100644
--- a/app/javascript/packs/application.js
+++ b/app/javascript/packs/application.js
@@ -14,6 +14,7 @@ import 'leaflet/dist/leaflet.css'
 import 'tippy.js/dist/tippy.css'
 
 require('../vanilla/initializers/copyTable.js')
+require('../vue/initializers/issue_tracker/main.js')
 
 require('../vue/tasks/citations/otus/main.js')
 require('../vue/tasks/content/editor/main.js')
diff --git a/app/javascript/vue/initializers/issue_tracker/App.vue b/app/javascript/vue/initializers/issue_tracker/App.vue
new file mode 100644
index 0000000000..73fb57992e
--- /dev/null
+++ b/app/javascript/vue/initializers/issue_tracker/App.vue
@@ -0,0 +1,78 @@
+<template>
+  <VModal
+    v-if="isModalVisible"
+    @close="() => (isModalVisible = false)"
+    :container-style="{
+      width: '700px'
+    }"
+  >
+    <template #header>
+      <h3>Report a problem</h3>
+    </template>
+    <template #body>
+      <h4>My issue is with:</h4>
+      <ul>
+        <li
+          v-for="item in URLs"
+          :key="item.label"
+        >
+          <a
+            :href="item.url"
+            target="_blank"
+            :title="item.description"
+          >
+            {{ item.label }}
+          </a>
+          {{ item.description }}
+        </li>
+      </ul>
+    </template>
+  </VModal>
+</template>
+
+<script setup>
+import VModal from '@/components/ui/Modal.vue'
+import { ref, onMounted, onBeforeUnmount, defineOptions } from 'vue'
+
+defineOptions({
+  name: 'IssueTracker'
+})
+
+const props = defineProps({
+  element: {
+    type: HTMLElement,
+    required: true
+  }
+})
+
+const URLs = [
+  {
+    label: 'Data',
+    description:
+      "E.g. missing data that I'd like to add, misspellings, or invalid data",
+    url: props.element.getAttribute('data-curation-issue-tracker')
+  },
+  {
+    label: 'Website',
+    description:
+      'E.g. a link, task, or other feature is not working as expected',
+    url: 'https://github.com/SpeciesFileGroup/taxonworks/issues'
+  }
+]
+
+const isModalVisible = ref(false)
+
+function openModal(e) {
+  e.preventDefault()
+
+  isModalVisible.value = true
+}
+
+onMounted(() => {
+  props.element.addEventListener('click', openModal)
+})
+
+onBeforeUnmount(() => {
+  props.element.removeEventListener('click', openModal)
+})
+</script>
diff --git a/app/javascript/vue/initializers/issue_tracker/main.js b/app/javascript/vue/initializers/issue_tracker/main.js
new file mode 100644
index 0000000000..50d923d02c
--- /dev/null
+++ b/app/javascript/vue/initializers/issue_tracker/main.js
@@ -0,0 +1,29 @@
+import { createApp } from 'vue'
+import App from './App.vue'
+
+let app
+
+function init(linkElement) {
+  const containerElement = document.querySelector(
+    '#curation-issue-tracker-container'
+  )
+
+  app = createApp(App, {
+    element: linkElement
+  })
+  app.mount(containerElement)
+}
+
+document.addEventListener('turbolinks:load', () => {
+  const issueTrackerElement = document.querySelector(
+    '[data-curation-issue-tracker]'
+  )
+
+  if (issueTrackerElement) {
+    init(issueTrackerElement)
+  }
+})
+
+document.addEventListener('turbolinks:before-render', () => {
+  if (app) app.unmount()
+})
diff --git a/app/views/sessions/_summary.html.erb b/app/views/sessions/_summary.html.erb
index 916b0bb4bc..5a0691fd4a 100644
--- a/app/views/sessions/_summary.html.erb
+++ b/app/views/sessions/_summary.html.erb
@@ -2,20 +2,11 @@
   <div class="horizontal-left-content item item1">
     <div
       id="taxonworks_left"
-      class="horizontal-left-content align-end">
-      <div id="taxonworks">
-        <%= link_to(content_tag(:div, '', class: :logo), root_path) -%> 
-      </div>
-      <div>
+      class="horizontal-left-content align-end gap-small">
+        <%= link_to(content_tag(:div, '', id: :taxonworks_logo), root_path) -%> 
         <%= taxonworks_version_tag -%>
         <%= sandbox_details_tag -%>
-        <a
-          class="margin-small-left"
-          href="https://github.com/SpeciesFileGroup/taxonworks/issues"
-          target="_blank">
-          Issues
-        </a>
-      </ul>
+        <%= issue_tracker_tag %>
     </div>
   </div>
 

From 7bf5197de16a81348f4bc3bcf107c29f2a62f965 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Thu, 21 Sep 2023 17:27:53 -0300
Subject: [PATCH 11/29] Fix #3554

---
 CHANGELOG.md                                  |  1 +
 .../new_taxon_name/components/navHeader.vue   |  2 +-
 .../components/quickTaxonName.vue             | 30 ++++++++++++-------
 .../new_taxon_name/components/type.vue        |  2 +-
 4 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6eb2662631..cd963bdeb0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Staged image queries failing when multiple facets used [#3556]
 - Citations list is truncated in Radial Annotator [#3560]
 - DwC attributes are now showing in Stepwise determinations task
+- Quick taxon name only works for species [#3554]
 
 [#3556]: https://github.com/SpeciesFileGroup/taxonworks/issues/3556
 
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/navHeader.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/navHeader.vue
index dc0861f38c..b04b47b827 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/navHeader.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/navHeader.vue
@@ -1,5 +1,5 @@
 <template>
-  <nav-bar class="relative">
+  <nav-bar navbar-class="panel content relative">
     <div class="flex-separate">
       <ul class="no_bullets context-menu">
         <template
diff --git a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/quickTaxonName.vue b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/quickTaxonName.vue
index fd542fab76..c2ddf6b545 100644
--- a/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/quickTaxonName.vue
+++ b/app/javascript/vue/tasks/nomenclature/new_taxon_name/components/quickTaxonName.vue
@@ -13,17 +13,25 @@
     />
     <button
       type="button"
-      @click="showModal = true"
       class="button normal-input button-default margin-small-left"
+      @click="
+        () => {
+          showModal = true
+        }
+      "
     >
       New
     </button>
     <modal-component
       v-if="showModal"
-      @close="showModal = false"
+      @close="
+        () => {
+          showModal = false
+        }
+      "
     >
       <template #header>
-        <h3>Create new species taxon name</h3>
+        <h3>Create new {{ group }} taxon name</h3>
       </template>
       <template #body>
         <div>
@@ -88,10 +96,10 @@ export default {
     ranks() {
       return this.$store.getters[GetterNames.GetRankList][this.nomenclatureCode]
     },
-    speciesRank() {
-      return this.ranksList.find((rank) => {
-        return rank.endsWith('::Species')
-      })
+    childRank() {
+      return this.ranksList.find((rank) =>
+        rank.endsWith(this.group === 'genus' ? '::Genus' : '::Species')
+      )
     },
     taxon() {
       return this.$store.getters[GetterNames.GetTaxon]
@@ -133,13 +141,15 @@ export default {
       TaxonName.create({
         taxon_name: {
           name: this.name,
-          rank_class: this.speciesRank,
+          rank_class: this.childRank,
           parent_id: this.taxon.id,
           type: 'Protonym'
         }
-      }).then((response) => {
-        this.$emit('getItem', response.body)
       })
+        .then((response) => {
+          this.$emit('getItem', response.body)
+        })
+        .catch(() => {})
     }
   }
 }
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 b5f957b5e1..4b0b32d205 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
@@ -34,8 +34,8 @@
             ) &&
             (!GetRelationshipsCreated.length || editType)
           "
-          @get-item="addTaxonType"
           :group="childOfParent[getRankGroup.toLowerCase()]"
+          @get-item="addTaxonType"
         />
         <template
           v-if="

From 0773ea2b32100728f0774e46e23fd5b075715664 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Fri, 22 Sep 2023 10:35:01 -0300
Subject: [PATCH 12/29] Fix issue tracker tag

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

diff --git a/app/helpers/workbench/layout_helper.rb b/app/helpers/workbench/layout_helper.rb
index 42645e56cf..b5db85804b 100644
--- a/app/helpers/workbench/layout_helper.rb
+++ b/app/helpers/workbench/layout_helper.rb
@@ -33,9 +33,9 @@ def issue_tracker_tag
         'Issues', 
         'https://github.com/SpeciesFileGroup/taxonworks/issues',
         target: '_blank',
-        data: { 'curation-issue-tracker': sessions_current_project.data_curation_issue_tracker_url}
+        data: { 'curation-issue-tracker': sessions_current_project&.data_curation_issue_tracker_url }
       ),
-      sessions_current_project.data_curation_issue_tracker_url? ? content_tag('div','', id: 'curation-issue-tracker-container') : nil
+      (content_tag('div','', id: 'curation-issue-tracker-container') if sessions_current_project&.data_curation_issue_tracker_url)
     ].join().html_safe
   end
 

From b03e9a6fc8f07122d4c355a83c46a1a25caea078 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Fri, 22 Sep 2023 15:40:06 -0300
Subject: [PATCH 13/29] Update packages

---
 package-lock.json | 607 +++++++++++++++++++++++-----------------------
 package.json      |  14 +-
 2 files changed, 317 insertions(+), 304 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 5638cc91ac..674e62a4de 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -23,7 +23,7 @@
         "exif-js": "^2.3.0",
         "leaflet": "^1.9.4",
         "leaflet.pattern": "^0.1.0",
-        "marked": "^9.0.0",
+        "marked": "^9.0.3",
         "parse-dms": "0.0.5",
         "pdfjs-dist": "3.10.111",
         "pinia": "^2.1.6",
@@ -40,9 +40,9 @@
         "vuex": "^4.1.0"
       },
       "devDependencies": {
-        "@babel/core": "^7.22.19",
+        "@babel/core": "^7.22.20",
         "@babel/plugin-transform-runtime": "^7.22.15",
-        "@babel/preset-env": "^7.22.15",
+        "@babel/preset-env": "^7.22.20",
         "@babel/runtime": "^7.22.15",
         "@vue/compiler-sfc": "^3.3.4",
         "babel-loader": "^9.1.3",
@@ -58,20 +58,20 @@
         "eslint-plugin-standard": "^4.1.0",
         "eslint-plugin-vue": "^9.17.0",
         "mini-css-extract-plugin": "^2.7.6",
-        "postcss": "^8.4.29",
+        "postcss": "^8.4.30",
         "postcss-flexbugs-fixes": "^5.0.2",
         "postcss-import": "^15.1.0",
         "postcss-loader": "^7.3.3",
-        "postcss-preset-env": "^9.1.3",
+        "postcss-preset-env": "^9.1.4",
         "raw-loader": "^4.0.2",
         "resolve-url-loader": "^5.0.0",
-        "sass": "^1.67.0",
+        "sass": "^1.68.0",
         "sass-loader": "^13.3.2",
         "style-loader": "^3.3.3",
         "stylus": "^0.60.0",
         "stylus-loader": "^7.1.3",
         "terser-webpack-plugin": "^5.3.9",
-        "url": "^0.11.2",
+        "url": "^0.11.3",
         "vue-loader": "^17.2.2",
         "webpack": "^5.88.2",
         "webpack-assets-manifest": "^5.1.0",
@@ -121,27 +121,27 @@
       }
     },
     "node_modules/@babel/compat-data": {
-      "version": "7.22.9",
-      "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.22.9.tgz",
-      "integrity": "sha512-5UamI7xkUcJ3i9qVDS+KFDEK8/7oJ55/sJMB1Ge7IEapr7KfdfV/HErR+koZwOfd+SgtFKOKRhRakdg++DcJpQ==",
+      "version": "7.22.20",
+      "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.22.20.tgz",
+      "integrity": "sha512-BQYjKbpXjoXwFW5jGqiizJQQT/aC7pFm9Ok1OWssonuguICi264lbgMzRp2ZMmRSlfkX6DsWDDcsrctK8Rwfiw==",
       "engines": {
         "node": ">=6.9.0"
       }
     },
     "node_modules/@babel/core": {
-      "version": "7.22.19",
-      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.22.19.tgz",
-      "integrity": "sha512-Q8Yj5X4LHVYTbLCKVz0//2D2aDmHF4xzCdEttYvKOnWvErGsa6geHXD6w46x64n5tP69VfeH+IfSrdyH3MLhwA==",
+      "version": "7.22.20",
+      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.22.20.tgz",
+      "integrity": "sha512-Y6jd1ahLubuYweD/zJH+vvOY141v4f9igNQAQ+MBgq9JlHS2iTsZKn1aMsb3vGccZsXI16VzTBw52Xx0DWmtnA==",
       "dependencies": {
         "@ampproject/remapping": "^2.2.0",
         "@babel/code-frame": "^7.22.13",
         "@babel/generator": "^7.22.15",
         "@babel/helper-compilation-targets": "^7.22.15",
-        "@babel/helper-module-transforms": "^7.22.19",
+        "@babel/helper-module-transforms": "^7.22.20",
         "@babel/helpers": "^7.22.15",
         "@babel/parser": "^7.22.16",
         "@babel/template": "^7.22.15",
-        "@babel/traverse": "^7.22.19",
+        "@babel/traverse": "^7.22.20",
         "@babel/types": "^7.22.19",
         "convert-source-map": "^1.7.0",
         "debug": "^4.1.0",
@@ -288,9 +288,9 @@
       }
     },
     "node_modules/@babel/helper-environment-visitor": {
-      "version": "7.22.5",
-      "resolved": "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.5.tgz",
-      "integrity": "sha512-XGmhECfVA/5sAt+H+xpSg0mfrHq6FzNr9Oxh7PSEBBRUb/mL7Kz3NICXb194rCqAEdxkhPT1a88teizAFyvk8Q==",
+      "version": "7.22.20",
+      "resolved": "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz",
+      "integrity": "sha512-zfedSIzFhat/gFhWfHtgWvlec0nqB9YEIVrpuwjruLlXfUSnA8cJB0miHKwqDnQ7d32aKo2xt88/xZptwxbfhA==",
       "engines": {
         "node": ">=6.9.0"
       }
@@ -341,15 +341,15 @@
       }
     },
     "node_modules/@babel/helper-module-transforms": {
-      "version": "7.22.19",
-      "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.22.19.tgz",
-      "integrity": "sha512-m6h1cJvn+OJ+R3jOHp30faq5xKJ7VbjwDj5RGgHuRlU9hrMeKsGC+JpihkR5w1g7IfseCPPtZ0r7/hB4UKaYlA==",
+      "version": "7.22.20",
+      "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.22.20.tgz",
+      "integrity": "sha512-dLT7JVWIUUxKOs1UnJUBR3S70YK+pKX6AbJgB2vMIvEkZkrfJDbYDJesnPshtKV4LhDOR3Oc5YULeDizRek+5A==",
       "dependencies": {
-        "@babel/helper-environment-visitor": "^7.22.5",
+        "@babel/helper-environment-visitor": "^7.22.20",
         "@babel/helper-module-imports": "^7.22.15",
         "@babel/helper-simple-access": "^7.22.5",
         "@babel/helper-split-export-declaration": "^7.22.6",
-        "@babel/helper-validator-identifier": "^7.22.19"
+        "@babel/helper-validator-identifier": "^7.22.20"
       },
       "engines": {
         "node": ">=6.9.0"
@@ -451,9 +451,9 @@
       }
     },
     "node_modules/@babel/helper-validator-identifier": {
-      "version": "7.22.19",
-      "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.19.tgz",
-      "integrity": "sha512-Tinq7ybnEPFFXhlYOYFiSjespWQk0dq2dRNAiMdRTOYQzEGqnnNyrTxPYHP5r6wGjlF1rFgABdDV0g8EwD6Qbg==",
+      "version": "7.22.20",
+      "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.20.tgz",
+      "integrity": "sha512-Y4OZ+ytlatR8AI+8KZfKuL5urKp7qey08ha31L8b3BwewJAoJamTzyvxPR/5D+KkdJCGPq/+8TukHBlY10FX9A==",
       "engines": {
         "node": ">=6.9.0"
       }
@@ -1518,11 +1518,11 @@
       }
     },
     "node_modules/@babel/preset-env": {
-      "version": "7.22.15",
-      "resolved": "https://registry.npmjs.org/@babel/preset-env/-/preset-env-7.22.15.tgz",
-      "integrity": "sha512-tZFHr54GBkHk6hQuVA8w4Fmq+MSPsfvMG0vPnOYyTnJpyfMqybL8/MbNCPRT9zc2KBO2pe4tq15g6Uno4Jpoag==",
+      "version": "7.22.20",
+      "resolved": "https://registry.npmjs.org/@babel/preset-env/-/preset-env-7.22.20.tgz",
+      "integrity": "sha512-11MY04gGC4kSzlPHRfvVkNAZhUxOvm7DCJ37hPDnUENwe06npjIRAfInEMTGSb4LZK5ZgDFkv5hw0lGebHeTyg==",
       "dependencies": {
-        "@babel/compat-data": "^7.22.9",
+        "@babel/compat-data": "^7.22.20",
         "@babel/helper-compilation-targets": "^7.22.15",
         "@babel/helper-plugin-utils": "^7.22.5",
         "@babel/helper-validator-option": "^7.22.15",
@@ -1596,7 +1596,7 @@
         "@babel/plugin-transform-unicode-regex": "^7.22.5",
         "@babel/plugin-transform-unicode-sets-regex": "^7.22.5",
         "@babel/preset-modules": "0.1.6-no-external-plugins",
-        "@babel/types": "^7.22.15",
+        "@babel/types": "^7.22.19",
         "babel-plugin-polyfill-corejs2": "^0.4.5",
         "babel-plugin-polyfill-corejs3": "^0.8.3",
         "babel-plugin-polyfill-regenerator": "^0.5.2",
@@ -1653,13 +1653,13 @@
       }
     },
     "node_modules/@babel/traverse": {
-      "version": "7.22.19",
-      "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.22.19.tgz",
-      "integrity": "sha512-ZCcpVPK64krfdScRbpxF6xA5fz7IOsfMwx1tcACvCzt6JY+0aHkBk7eIU8FRDSZRU5Zei6Z4JfgAxN1bqXGECg==",
+      "version": "7.22.20",
+      "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.22.20.tgz",
+      "integrity": "sha512-eU260mPZbU7mZ0N+X10pxXhQFMGTeLb9eFS0mxehS8HZp9o1uSnFeWQuG1UPrlxgA7QoUzFhOnilHDp0AXCyHw==",
       "dependencies": {
         "@babel/code-frame": "^7.22.13",
         "@babel/generator": "^7.22.15",
-        "@babel/helper-environment-visitor": "^7.22.5",
+        "@babel/helper-environment-visitor": "^7.22.20",
         "@babel/helper-function-name": "^7.22.5",
         "@babel/helper-hoist-variables": "^7.22.5",
         "@babel/helper-split-export-declaration": "^7.22.6",
@@ -1868,9 +1868,9 @@
       }
     },
     "node_modules/@csstools/postcss-color-function": {
-      "version": "3.0.3",
-      "resolved": "https://registry.npmjs.org/@csstools/postcss-color-function/-/postcss-color-function-3.0.3.tgz",
-      "integrity": "sha512-5oNUbO89SX7BuSB0ZiUxDaQt4R2K3A+RQZlxNHOvghZJO/UqgomLPII6JkgrywLQ0Y4JDzbyNuwr0OKo2v0RsQ==",
+      "version": "3.0.4",
+      "resolved": "https://registry.npmjs.org/@csstools/postcss-color-function/-/postcss-color-function-3.0.4.tgz",
+      "integrity": "sha512-ZLi+nSb/u1Tt+zxB8MGE2rOkX7YhWGxM3pBQRz9nn8DIAKT84GkaeHGyVrxwCPBVdko/4nwqApC7YCeqgZxTAw==",
       "dev": true,
       "funding": [
         {
@@ -1886,7 +1886,7 @@
         "@csstools/css-color-parser": "^1.3.1",
         "@csstools/css-parser-algorithms": "^2.3.1",
         "@csstools/css-tokenizer": "^2.2.0",
-        "@csstools/postcss-progressive-custom-properties": "^3.0.0"
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         "css-blank-pseudo": "^6.0.0",
         "css-has-pseudo": "^6.0.0",
         "css-prefers-color-scheme": "^9.0.0",
-        "cssdb": "^7.7.1",
+        "cssdb": "^7.7.2",
         "postcss-attribute-case-insensitive": "^6.0.2",
         "postcss-clamp": "^4.1.0",
-        "postcss-color-functional-notation": "^6.0.0",
+        "postcss-color-functional-notation": "^6.0.1",
         "postcss-color-hex-alpha": "^9.0.2",
-        "postcss-color-rebeccapurple": "^9.0.0",
-        "postcss-custom-media": "^10.0.0",
-        "postcss-custom-properties": "^13.3.0",
-        "postcss-custom-selectors": "^7.1.4",
+        "postcss-color-rebeccapurple": "^9.0.1",
+        "postcss-custom-media": "^10.0.1",
+        "postcss-custom-properties": "^13.3.1",
+        "postcss-custom-selectors": "^7.1.5",
         "postcss-dir-pseudo-class": "^8.0.0",
-        "postcss-double-position-gradients": "^5.0.0",
+        "postcss-double-position-gradients": "^5.0.1",
         "postcss-focus-visible": "^9.0.0",
         "postcss-focus-within": "^8.0.0",
         "postcss-font-variant": "^5.0.0",
         "postcss-gap-properties": "^5.0.0",
-        "postcss-image-set-function": "^6.0.0",
-        "postcss-initial": "^4.0.1",
-        "postcss-lab-function": "^6.0.3",
+        "postcss-image-set-function": "^6.0.1",
+        "postcss-lab-function": "^6.0.4",
         "postcss-logical": "^7.0.0",
         "postcss-nesting": "^12.0.1",
         "postcss-opacity-percentage": "^2.0.0",
@@ -20289,9 +20302,9 @@
       "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
     },
     "sass": {
-      "version": "1.67.0",
-      "resolved": "https://registry.npmjs.org/sass/-/sass-1.67.0.tgz",
-      "integrity": "sha512-SVrO9ZeX/QQyEGtuZYCVxoeAL5vGlYjJ9p4i4HFuekWl8y/LtJ7tJc10Z+ck1c8xOuoBm2MYzcLfTAffD0pl/A==",
+      "version": "1.68.0",
+      "resolved": "https://registry.npmjs.org/sass/-/sass-1.68.0.tgz",
+      "integrity": "sha512-Lmj9lM/fef0nQswm1J2HJcEsBUba4wgNx2fea6yJHODREoMFnwRpZydBnX/RjyXw2REIwdkbqE4hrTo4qfDBUA==",
       "dev": true,
       "requires": {
         "chokidar": ">=3.0.0 <4.0.0",
@@ -21060,9 +21073,9 @@
       }
     },
     "url": {
-      "version": "0.11.2",
-      "resolved": "https://registry.npmjs.org/url/-/url-0.11.2.tgz",
-      "integrity": "sha512-7yIgNnrST44S7PJ5+jXbdIupfU1nWUdQJBFBeJRclPXiWgCvrSq5Frw8lr/i//n5sqDfzoKmBymMS81l4U/7cg==",
+      "version": "0.11.3",
+      "resolved": "https://registry.npmjs.org/url/-/url-0.11.3.tgz",
+      "integrity": "sha512-6hxOLGfZASQK/cijlZnZJTq8OXAkt/3YGfQX45vvMYXpZoo8NdWZcY73K108Jf759lS1Bv/8wXnHDTSz17dSRw==",
       "dev": true,
       "requires": {
         "punycode": "^1.4.1",
diff --git a/package.json b/package.json
index f42a7ced88..480457e80c 100644
--- a/package.json
+++ b/package.json
@@ -17,7 +17,7 @@
     "exif-js": "^2.3.0",
     "leaflet": "^1.9.4",
     "leaflet.pattern": "^0.1.0",
-    "marked": "^9.0.0",
+    "marked": "^9.0.3",
     "parse-dms": "0.0.5",
     "pdfjs-dist": "3.10.111",
     "pinia": "^2.1.6",
@@ -43,9 +43,9 @@
     "defaults"
   ],
   "devDependencies": {
-    "@babel/core": "^7.22.19",
+    "@babel/core": "^7.22.20",
     "@babel/plugin-transform-runtime": "^7.22.15",
-    "@babel/preset-env": "^7.22.15",
+    "@babel/preset-env": "^7.22.20",
     "@babel/runtime": "^7.22.15",
     "@vue/compiler-sfc": "^3.3.4",
     "babel-loader": "^9.1.3",
@@ -61,20 +61,20 @@
     "eslint-plugin-standard": "^4.1.0",
     "eslint-plugin-vue": "^9.17.0",
     "mini-css-extract-plugin": "^2.7.6",
-    "postcss": "^8.4.29",
+    "postcss": "^8.4.30",
     "postcss-flexbugs-fixes": "^5.0.2",
     "postcss-import": "^15.1.0",
     "postcss-loader": "^7.3.3",
-    "postcss-preset-env": "^9.1.3",
+    "postcss-preset-env": "^9.1.4",
     "raw-loader": "^4.0.2",
     "resolve-url-loader": "^5.0.0",
-    "sass": "^1.67.0",
+    "sass": "^1.68.0",
     "sass-loader": "^13.3.2",
     "style-loader": "^3.3.3",
     "stylus": "^0.60.0",
     "stylus-loader": "^7.1.3",
     "terser-webpack-plugin": "^5.3.9",
-    "url": "^0.11.2",
+    "url": "^0.11.3",
     "vue-loader": "^17.2.2",
     "webpack": "^5.88.2",
     "webpack-assets-manifest": "^5.1.0",

From f6177cd0c46e28deb2648d02d9665655ae04fc16 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Mon, 25 Sep 2023 15:25:36 -0300
Subject: [PATCH 14/29] Upgrade to Ruby 3.2.2

---
 .github/docker-tests/docker-image-test/Dockerfile | 2 +-
 .github/workflows/build.yml                       | 4 +---
 .ruby-version                                     | 2 +-
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/docker-tests/docker-image-test/Dockerfile b/.github/docker-tests/docker-image-test/Dockerfile
index 0f88ddd054..4ae4e6ea58 100644
--- a/.github/docker-tests/docker-image-test/Dockerfile
+++ b/.github/docker-tests/docker-image-test/Dockerfile
@@ -1,4 +1,4 @@
-FROM ruby:3.2.1
+FROM ruby:3.2.2
 
 RUN apt-get update 
 RUN apt-get install -y curl bzip2 unzip default-jre \
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 0342793ee9..3b742e813d 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -57,10 +57,8 @@ jobs:
     - name: Git checkout
       uses: actions/checkout@v3
     
-    - name: Set up Ruby 3.2
+    - name: Set up Ruby
       uses: ruby/setup-ruby@v1
-      with:
-        ruby-version: 3.2
         
     - name: Set up Ruby Bundler gems cache
       uses: actions/cache@v3
diff --git a/.ruby-version b/.ruby-version
index e4604e3afd..be94e6f53d 100644
--- a/.ruby-version
+++ b/.ruby-version
@@ -1 +1 @@
-3.2.1
+3.2.2

From 9fb15413bb6c6079db78ac0951bf6f5ea0190525 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Mon, 25 Sep 2023 17:06:27 -0300
Subject: [PATCH 15/29] Fix #3566

---
 CHANGELOG.md                                   | 4 ++++
 app/javascript/vue/tasks/images/filter/app.vue | 1 +
 2 files changed, 5 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd963bdeb0..059d0795ef 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,8 +23,12 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Citations list is truncated in Radial Annotator [#3560]
 - DwC attributes are now showing in Stepwise determinations task
 - Quick taxon name only works for species [#3554]
+- Filter Images: Change `per` doesn't update the table [#3566]
 
+[#3554]: https://github.com/SpeciesFileGroup/taxonworks/issues/3554
 [#3556]: https://github.com/SpeciesFileGroup/taxonworks/issues/3556
+[#3560]: https://github.com/SpeciesFileGroup/taxonworks/issues/3560
+[#3566]: https://github.com/SpeciesFileGroup/taxonworks/issues/3566
 
 ## [0.34.4] - 2023-09-15
 
diff --git a/app/javascript/vue/tasks/images/filter/app.vue b/app/javascript/vue/tasks/images/filter/app.vue
index c6c4e6bb92..15d22f499d 100644
--- a/app/javascript/vue/tasks/images/filter/app.vue
+++ b/app/javascript/vue/tasks/images/filter/app.vue
@@ -11,6 +11,7 @@
       v-model="parameters"
       v-model:append="append"
       @filter="makeFilterRequest({ ...parameters, page: 1 })"
+      @per="makeFilterRequest({ ...parameters, page: 1 })"
       @nextpage="loadPage"
       @reset="resetFilter"
     >

From 226eeae7cc328f98a844b7d50b5eddb410538b52 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 25 Sep 2023 15:13:12 -0500
Subject: [PATCH 16/29] Update /api/v1 signature

---
 CHANGELOG.md                              | 1 +
 app/views/api/v1/base/index.json.jbuilder | 5 +++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 059d0795ef..3e85ae0210 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Changed
 
+- Calls to `/api/v1` have a new key/value signature
 - Staged image metadata field format from JSON to JSONB [#3446]
 
 ### Fixed
diff --git a/app/views/api/v1/base/index.json.jbuilder b/app/views/api/v1/base/index.json.jbuilder
index 7ef2ad5470..96d1ef4597 100644
--- a/app/views/api/v1/base/index.json.jbuilder
+++ b/app/views/api/v1/base/index.json.jbuilder
@@ -1,8 +1,9 @@
 json.success true
 
 json.open_projects do
-  json.array! open_api_projects.pluck(:api_access_token, :name, :data_curation_issue_tracker_url) do |token, name, data_curation_issue_tracker_url|
-    json.set! token, name
+  json.array! open_api_projects.pluck(:api_access_token, :name, :data_curation_issue_tracker_url) do |project_token, name, data_curation_issue_tracker_url|
+    json.name name
+    json.project_token project_token
     json.data_curation_issue_tracker_url data_curation_issue_tracker_url
   end
 end

From a6485f9ae09a43336a45e245e27cb37b29e96862 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 25 Sep 2023 15:40:29 -0500
Subject: [PATCH 17/29] Fix api spec

---
 spec/requests/api/v1/base_spec.rb | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/spec/requests/api/v1/base_spec.rb b/spec/requests/api/v1/base_spec.rb
index 8752e31694..ee6f6fe0e6 100644
--- a/spec/requests/api/v1/base_spec.rb
+++ b/spec/requests/api/v1/base_spec.rb
@@ -11,9 +11,18 @@
 
     it_behaves_like 'a successful response'
 
-    specify 'open_projects' do
-      expect(JSON.parse(response.body).dig('open_projects').first).to include({project.api_access_token => project.name})
+    specify 'open_projects #name' do
+      expect(JSON.parse(response.body).dig('open_projects').first).to include({'name' => project.name})
     end
+
+    specify 'open_projects #project_token' do
+      expect(JSON.parse(response.body).dig('open_projects').first).to include({'project_token' => project.api_access_token})
+    end
+
+    specify 'open_projects #data_curation_issue_tracker_url' do
+      expect(JSON.parse(response.body).dig('open_projects').first).to include({'data_curation_issue_tracker_url' => nil})
+    end
+
   end
 
   context 'Invalid path' do

From 31ce8a702d8e0f8d51cfa228470e44adc930a05f Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 25 Sep 2023 15:47:57 -0500
Subject: [PATCH 18/29] Fix import predicate any value for predicate searches

---
 CHANGELOG.md                            | 1 +
 lib/queries/concerns/data_attributes.rb | 7 +++++++
 2 files changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e85ae0210..d7fc6e5182 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- ImportAttribute facet not working on any predicate searches
 - Taxon name/otus filter order bug
 - Staged image queries failing when multiple facets used [#3556]
 - Citations list is truncated in Radial Annotator [#3560]
diff --git a/lib/queries/concerns/data_attributes.rb b/lib/queries/concerns/data_attributes.rb
index 5f73684fa4..f3cd938cf9 100644
--- a/lib/queries/concerns/data_attributes.rb
+++ b/lib/queries/concerns/data_attributes.rb
@@ -195,6 +195,12 @@ def data_attribute_predicate_id_facet
     referenced_klass.joins(:internal_attributes).where(data_attributes: {controlled_vocabulary_term_id: data_attribute_predicate_id})
   end
 
+  def data_attribute_import_predicate_facet
+    return nil if data_attribute_import_predicate.empty?
+    referenced_klass.joins(:import_attributes).where(data_attributes: {import_predicate: data_attribute_import_predicate})
+  end
+
+
   def data_attribute_without_predicate_id_facet
     return nil if data_attribute_without_predicate_id.blank?
     not_these = referenced_klass.left_joins(:internal_attributes).where(data_attributes: {controlled_vocabulary_term_id: data_attribute_without_predicate_id})
@@ -334,6 +340,7 @@ def self.merge_clauses
     [
       :data_attribute_import_exact_pair_facet,
       :data_attribute_exact_pair_facet,
+      :data_attribute_import_predicate_facet,
       :data_attribute_predicate_id_facet,
       :data_attribute_wildcard_pair_facet,
       :data_attribute_import_wildcard_pair_facet,

From f08557170befc7ea2640ac2a58b370940d5ce137 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 25 Sep 2023 16:10:49 -0500
Subject: [PATCH 19/29] Fix chronology stats report

---
 CHANGELOG.md                      | 1 +
 app/helpers/taxon_names_helper.rb | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d7fc6e5182..e158a681e5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- Chronology stats report
 - ImportAttribute facet not working on any predicate searches
 - Taxon name/otus filter order bug
 - Staged image queries failing when multiple facets used [#3556]
diff --git a/app/helpers/taxon_names_helper.rb b/app/helpers/taxon_names_helper.rb
index 1325d4743d..db84b22ba3 100644
--- a/app/helpers/taxon_names_helper.rb
+++ b/app/helpers/taxon_names_helper.rb
@@ -501,7 +501,7 @@ def taxon_names_per_year(totals)
   end
 
   def taxon_names_by_year_count(names)
-    t = names.select('EXTRACT(YEAR FROM cached_nomenclature_date) AS year, COUNT(*) AS count').group('year').inject({}){|hsh, r| hsh[r.year.to_i] = r.count; hsh}
+    t = names.select('EXTRACT(YEAR FROM taxon_names.cached_nomenclature_date) AS year, COUNT(*) AS count').group('year').inject({}){|hsh, r| hsh[r.year.to_i] = r.count; hsh}
     t
   end
 

From 00c5d6c8a0859162c2bb2039304d83ac8a8834d2 Mon Sep 17 00:00:00 2001
From: jlpereira <pepelui@outlook.com>
Date: Mon, 25 Sep 2023 18:28:02 -0300
Subject: [PATCH 20/29] Add import attributes list

---
 .../components/data_attribute_annotator.vue   | 36 +++++++++++++++----
 app/javascript/vue/constants/modelTypes.js    |  1 +
 2 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/app/javascript/vue/components/radials/annotator/components/data_attribute_annotator.vue b/app/javascript/vue/components/radials/annotator/components/data_attribute_annotator.vue
index 804b83fa80..53a3e68eed 100644
--- a/app/javascript/vue/components/radials/annotator/components/data_attribute_annotator.vue
+++ b/app/javascript/vue/components/radials/annotator/components/data_attribute_annotator.vue
@@ -48,7 +48,7 @@
       </VBtn>
     </div>
     <TableList
-      :list="list"
+      :list="internalAttributes"
       :header="['Name', 'Value', '']"
       :attributes="['predicate_name', 'value']"
       edit
@@ -56,9 +56,25 @@
       @edit="setDataAttribute"
       @delete="removeItem"
     />
+
+    <div
+      v-if="importList.length"
+      class="margin-medium-top"
+    >
+      <h3>Import attributes</h3>
+      <TableList
+        :list="importList"
+        :header="['Name', 'Value', '']"
+        :attributes="['import_predicate', 'value']"
+        :destroy="false"
+      />
+    </div>
   </div>
 </template>
+
 <script>
+import { ControlledVocabularyTerm } from '@/routes/endpoints'
+import { IMPORT_ATTRIBUTE } from '@/constants'
 import { addToArray } from '@/helpers/arrays.js'
 import CRUD from '../request/crud.js'
 import AnnotatorExtend from '../components/annotatorExtend.js'
@@ -80,6 +96,14 @@ export default {
   computed: {
     validateFields() {
       return this.predicate && this.value.length
+    },
+
+    importList() {
+      return this.list.filter((item) => item.base_class === IMPORT_ATTRIBUTE)
+    },
+
+    internalAttributes() {
+      return this.list.filter((item) => item.base_class !== IMPORT_ATTRIBUTE)
     }
   },
 
@@ -92,12 +116,10 @@ export default {
     }
   },
 
-  mounted() {
-    this.getList(`/controlled_vocabulary_terms.json?type[]=Predicate`).then(
-      (response) => {
-        this.all = response.body
-      }
-    )
+  created() {
+    ControlledVocabularyTerm.where({ type: ['Predicate'] }).then((response) => {
+      this.all = response.body
+    })
   },
 
   methods: {
diff --git a/app/javascript/vue/constants/modelTypes.js b/app/javascript/vue/constants/modelTypes.js
index c25fc3ad26..6efd8c43d2 100644
--- a/app/javascript/vue/constants/modelTypes.js
+++ b/app/javascript/vue/constants/modelTypes.js
@@ -22,6 +22,7 @@ export const GEOREFERENCE = 'Georeference'
 export const GEOGRAPHIC_AREA = 'GeographicArea'
 export const IDENTIFIER = 'Identifier'
 export const IMAGE = 'Image'
+export const IMPORT_ATTRIBUTE = 'ImportAttribute'
 export const LOAN = 'Loan'
 export const LOT = 'Lot'
 export const NOTE = 'Note'

From 97bef02a40f34e1aea86ee8c96278825a6b2ba14 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Mon, 25 Sep 2023 16:31:20 -0500
Subject: [PATCH 21/29] Syntax [skip ci]

---
 app/controllers/import_datasets_controller.rb | 28 +++++-----
 app/models/import_dataset/darwin_core.rb      | 52 +++++++++----------
 2 files changed, 39 insertions(+), 41 deletions(-)

diff --git a/app/controllers/import_datasets_controller.rb b/app/controllers/import_datasets_controller.rb
index d9dceae597..9f7d118d0f 100644
--- a/app/controllers/import_datasets_controller.rb
+++ b/app/controllers/import_datasets_controller.rb
@@ -89,22 +89,20 @@ def destroy
 
   def list
     @import_datasets = ImportDataset.with_project_id(sessions_current_project_id).order(:id).page(params[:page])
-  end  
+  end
 
   private
-    # Use callbacks to share common setup or constraints between actions.
-    def set_import_dataset
-      @import_dataset = ImportDataset.where(project_id: sessions_current_project_id).find(params[:id])
-    end
+  def set_import_dataset
+    @import_dataset = ImportDataset.where(project_id: sessions_current_project_id).find(params[:id])
+  end
 
-    # Only allow a list of trusted parameters through.
-    def import_dataset_params
-      params.require(:import_dataset).permit(
-        :source,
-        :description,
-        import_settings: [
-          :nomenclatural_code,
-          :row_type
-        ])
-    end
+  def import_dataset_params
+    params.require(:import_dataset).permit(
+      :source,
+      :description,
+      import_settings: [
+        :nomenclatural_code,
+        :row_type
+      ])
+  end
 end
diff --git a/app/models/import_dataset/darwin_core.rb b/app/models/import_dataset/darwin_core.rb
index a3b928968c..6600133d4e 100644
--- a/app/models/import_dataset/darwin_core.rb
+++ b/app/models/import_dataset/darwin_core.rb
@@ -5,8 +5,8 @@ class ImportDataset::DarwinCore < ImportDataset
 
   before_destroy :destroy_namespace
 
-  CHECKLIST_ROW_TYPE = "http://rs.tdwg.org/dwc/terms/Taxon"
-  OCCURRENCES_ROW_TYPE = "http://rs.tdwg.org/dwc/terms/Occurrence"
+  CHECKLIST_ROW_TYPE = 'http://rs.tdwg.org/dwc/terms/Taxon'.freeze
+  OCCURRENCES_ROW_TYPE = 'http://rs.tdwg.org/dwc/terms/Occurrence'.freeze
 
   def initialize(params)
     import_settings = params&.delete(:import_settings)
@@ -44,7 +44,7 @@ def self.create_with_subtype_detection(params)
 
         ### Check all files are readable
         [dwc.core, *dwc.extensions].each do |table|
-          table.read { |data, errors| raise "Errors found when reading data" unless errors.empty? }
+          table.read { |data, errors| raise 'Errors found when reading data' unless errors.empty? }
         end
       else
         if path =~ /\.(xlsx?|ods)\z/i
@@ -56,9 +56,9 @@ def self.create_with_subtype_detection(params)
         row_type = params.dig(:import_settings, :row_type)
         if row_type
           core_type = row_type
-        elsif headers.include? "occurrenceID"
+        elsif headers.include? 'occurrenceID'
           core_type = OCCURRENCES_ROW_TYPE
-        elsif headers.include? "taxonID"
+        elsif headers.include? 'taxonID'
           core_type = CHECKLIST_ROW_TYPE
         end
       end
@@ -88,7 +88,7 @@ def start_import(&block)
       when 'Importing'
         self.metadata['import_uuid'] = SecureRandom.uuid if self.updated_at < 10.minutes.ago
       else
-        raise "Invalid initial state"
+        raise 'Invalid initial state'
       end
       save!
 
@@ -132,9 +132,9 @@ def import(max_time, max_records, retry_errored: false, filters: nil, record_id:
       retry_errored = self.metadata['import_retry_errored'] if retry_errored.nil?
       start_id = self.metadata['import_start_id'] if retry_errored
 
-      status = ["Ready"]
-      status << "Errored" if retry_errored
-      records = add_filters(core_records.where(status: status), filters).order(:id).limit(max_records) #.preload_fields
+      status = ['Ready']
+      status << 'Errored' if retry_errored
+      records = add_filters(core_records.where(status:), filters).order(:id).limit(max_records) #.preload_fields
 
       records = records.where(id: start_id..) if start_id
       records = core_records.where(id: record_id, status: %w{Ready Errored}) if record_id
@@ -142,7 +142,7 @@ def import(max_time, max_records, retry_errored: false, filters: nil, record_id:
       records = records.all
       start_time = Time.now - lock_time
 
-      dwc_data_attributes = project.preferences["model_predicate_sets"].map do |model, predicate_ids|
+      dwc_data_attributes = project.preferences['model_predicate_sets'].map do |model, predicate_ids|
         [model, Hash[
           *Predicate.where(id: predicate_ids)
             .select { |p| /^http:\/\/rs\.tdwg\.org\/dwc\/terms\/.*/ =~ p.uri }
@@ -184,33 +184,33 @@ def progress(filters: nil)
 
   # Stages DwC-A records into DB.
   def stage
-    if status == "Staging" # ActiveJob being retried could cause this state
+    if status == 'Staging' # ActiveJob being retried could cause this state
       transaction do
         core_records_fields.delete_all
         dataset_records.delete_all
       end
     end
 
-    update!(status: "Staging") if status == "Uploaded"
+    update!(status: 'Staging') if status == 'Uploaded'
 
-    if status != "Ready"
+    if status != 'Ready'
       perform_staging
-      update!(status: "Ready")
+      update!(status: 'Ready')
     end
   end
 
   # Sets import settings for this dataset
   def set_import_settings(import_settings)
-    metadata["import_settings"] ||= {}
-    import_settings.each { |k, v| metadata["import_settings"].merge!({k => v}) }
+    metadata['import_settings'] ||= {}
+    import_settings.each { |k, v| metadata['import_settings'].merge!({k => v}) }
 
-    metadata["import_settings"]
+    metadata['import_settings']
   end
 
   def get_core_record_identifier_namespace
-    id = metadata.dig("namespaces", "core")
+    id = metadata.dig('namespaces', 'core')
 
-    if id.nil? || (@core_record_identifier_namespace ||= Namespace.find_by(id: id)).nil?
+    if id.nil? || (@core_record_identifier_namespace ||= Namespace.find_by(id:)).nil?
       random = SecureRandom.hex(4)
       project_name = Project.find(Current.project_id).name
 
@@ -224,8 +224,8 @@ def get_core_record_identifier_namespace
       )
 
       metadata.deep_merge!({
-        "namespaces" => {
-          "core" => @core_record_identifier_namespace.id
+        'namespaces' => {
+          'core' => @core_record_identifier_namespace.id
         }
       })
       save!
@@ -235,7 +235,7 @@ def get_core_record_identifier_namespace
   end
 
   def default_nomenclatural_code
-    self.metadata.dig("import_settings", "nomenclatural_code")&.downcase&.to_sym || :iczn
+    self.metadata.dig('import_settings', 'nomenclatural_code')&.downcase&.to_sym || :iczn
   end
 
   protected
@@ -264,7 +264,7 @@ def get_records(source)
       records[:core] = records[:core].map { |r| r.to_h }
       headers[:core] = records[:core].first.to_h.keys
     else
-      raise "Unsupported input format"
+      raise 'Unsupported input format'
     end
 
     return records, headers
@@ -273,7 +273,7 @@ def get_records(source)
   def get_dwc_headers(table)
     headers = []
 
-    headers[table.id[:index]] = "id" if table.id
+    headers[table.id[:index]] = 'id' if table.id
     table.fields.each { |f| headers[f[:index]] = get_normalized_dwc_term(f) if f[:index] }
 
     table.read_header.first.each_with_index { |f, i| headers[i] ||= f.strip }
@@ -305,7 +305,7 @@ def get_field_mapping(field_name)
   private
 
   def get_fields_mapping
-    @fields_mapping ||= metadata["core_headers"]
+    @fields_mapping ||= metadata['core_headers']
       .reject(&:nil?)
       .each.with_index.inject({}) { |m, (h, i)| m.merge({ h.downcase => i, i => h}) }
   end
@@ -322,7 +322,7 @@ def get_normalized_dwc_term(field)
   end
 
   def destroy_namespace
-    Namespace.find_by(id: metadata["identifier_namespace"])&.destroy # If in use or gone no deletion happens
+    Namespace.find_by(id: metadata['identifier_namespace'])&.destroy # If in use or gone no deletion happens
   end
 
   def add_filters(records, filters)

From 1ef7ea7cd91833c5bc03e8270c95faff5d90d798 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Mon, 25 Sep 2023 19:00:27 -0300
Subject: [PATCH 22/29] Not upgrading Ruby for deliver tester at this time

---
 .github/docker-tests/docker-image-test/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/docker-tests/docker-image-test/Dockerfile b/.github/docker-tests/docker-image-test/Dockerfile
index 4ae4e6ea58..0f88ddd054 100644
--- a/.github/docker-tests/docker-image-test/Dockerfile
+++ b/.github/docker-tests/docker-image-test/Dockerfile
@@ -1,4 +1,4 @@
-FROM ruby:3.2.2
+FROM ruby:3.2.1
 
 RUN apt-get update 
 RUN apt-get install -y curl bzip2 unzip default-jre \

From 8887179276e5f77f1da73bfb216341672bed2c99 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Mon, 25 Sep 2023 19:15:14 -0300
Subject: [PATCH 23/29] Bundle update

---
 Gemfile.lock | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index ad29bc8362..bcf20d668c 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -219,7 +219,7 @@ GEM
       unf (>= 0.0.5, < 1.0.0)
     dropzonejs-rails (0.8.5)
       rails (> 3.1)
-    dwc_agent (3.0.11.0)
+    dwc_agent (3.0.13.0)
       namae (~> 1)
       namecase (~> 2)
     erubi (1.12.0)
@@ -245,7 +245,7 @@ GEM
     faraday-follow_redirects (0.3.0)
       faraday (>= 1, < 3)
     faraday-net_http (3.0.2)
-    ffi (1.15.5)
+    ffi (1.16.2)
     ffi-geos (2.4.0)
       ffi (>= 1.0.0)
     formatador (1.1.0)
@@ -394,7 +394,7 @@ GEM
       method_source (~> 1.0)
     psych (3.3.4)
     public_suffix (5.0.3)
-    puma (6.3.1)
+    puma (6.4.0)
       nio4r (~> 2.0)
     racc (1.7.1)
     rack (2.2.8)
@@ -524,21 +524,21 @@ GEM
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.29.0)
       parser (>= 3.2.1.0)
-    rubocop-capybara (2.18.0)
+    rubocop-capybara (2.19.0)
       rubocop (~> 1.41)
-    rubocop-factory_bot (2.23.1)
+    rubocop-factory_bot (2.24.0)
       rubocop (~> 1.33)
     rubocop-faker (1.1.0)
       faker (>= 2.12.0)
       rubocop (>= 0.82.0)
-    rubocop-performance (1.19.0)
+    rubocop-performance (1.19.1)
       rubocop (>= 1.7.0, < 2.0)
       rubocop-ast (>= 0.4.0)
     rubocop-rails (2.21.1)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
-    rubocop-rspec (2.24.0)
+    rubocop-rspec (2.24.1)
       rubocop (~> 1.33)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
@@ -563,7 +563,7 @@ GEM
       rdoc (>= 5.0)
     seedbank (0.5.0)
       rake (>= 10.0)
-    selenium-webdriver (4.12.0)
+    selenium-webdriver (4.13.0)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
@@ -646,7 +646,7 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    websocket (1.2.9)
+    websocket (1.2.10)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)
@@ -660,7 +660,7 @@ GEM
     xpath (3.2.0)
       nokogiri (~> 1.8)
     zaru (0.3.0)
-    zeitwerk (2.6.11)
+    zeitwerk (2.6.12)
     zip_tricks (5.6.0)
 
 PLATFORMS
@@ -800,4 +800,4 @@ RUBY VERSION
    ruby 3.2.1p31
 
 BUNDLED WITH
-   2.4.19
+   2.4.10

From 8e9c6d1c11e952936eb868e71ceab38a0080a827 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Mon, 25 Sep 2023 19:44:36 -0300
Subject: [PATCH 24/29] Updated libheif and libde265 assets reference

---
 exe/install-imagemagick7.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/exe/install-imagemagick7.sh b/exe/install-imagemagick7.sh
index 92adf0dd45..6faf9bdbe5 100755
--- a/exe/install-imagemagick7.sh
+++ b/exe/install-imagemagick7.sh
@@ -7,7 +7,7 @@ apt-get build-dep -y libmagickcore-dev
 
 cd /usr/src/
 
-[ ! -d libde265-* ] && curl -sL $(curl -s https://api.github.com/repos/strukturag/libde265/releases/latest | jq --raw-output '.assets[0] | .browser_download_url') | tar xzf - && \
+[ ! -d libde265-* ] && curl -sL $(curl -s https://api.github.com/repos/strukturag/libde265/releases/latest | jq --raw-output '.assets[1] | .browser_download_url') | tar xzf - && \
   cd libde265-* && \
   ./autogen.sh && \
   ./configure && \
@@ -18,7 +18,7 @@ make install
 cd ..
 
 [ ! -d libheif-* ] && \
-  curl -sL $(curl -s https://api.github.com/repos/strukturag/libheif/releases/latest | jq --raw-output '.assets[0] | .browser_download_url') | tar xzf - && \
+  curl -sL $(curl -s https://api.github.com/repos/strukturag/libheif/releases/latest | jq --raw-output '.assets[1] | .browser_download_url') | tar xzf - && \
   cd libheif-* && \
   mkdir -p build && cd build && \
   cmake .. && \

From c84e1f79e24a325be92b39d94bb9aa72a9fcbf91 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 26 Sep 2023 09:32:26 -0500
Subject: [PATCH 25/29] Fix BibTeX batch loader failing on empty entries

---
 CHANGELOG.md                                  |  1 +
 .../bibtex/bibtex_batch_preview.html.erb      | 39 ++++++++++---------
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c77b6cd742..6d79b0f4c4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ### Fixed
 
+- Batch import BibTeX failing on empty entries
 - Chronology stats report
 - ImportAttribute facet not working on any predicate searches
 - Taxon name/otus filter order bug
diff --git a/app/views/sources/batch_load/bibtex/bibtex_batch_preview.html.erb b/app/views/sources/batch_load/bibtex/bibtex_batch_preview.html.erb
index f6645e3bbd..929888f7fb 100644
--- a/app/views/sources/batch_load/bibtex/bibtex_batch_preview.html.erb
+++ b/app/views/sources/batch_load/bibtex/bibtex_batch_preview.html.erb
@@ -1,39 +1,42 @@
 <h2> BibTeX Batch Load Preview </h2>
 
-<p> Import includes <%= @sources.count -%> records. </p>
+<p> Import includes <%= @sources.compact.size -%> records. </p>
 
 <p> To complete this import, select the file again and click create:
   <%= form_tag create_bibtex_batch_load_sources_path, multipart: true do -%>
-      <%= file_field_tag :file -%>
-      <%= submit_tag 'Create' -%>
+    <%= file_field_tag :file -%>
+    <%= submit_tag 'Create' -%>
   <% end %>
 </p>
 
 <p> <span style='color:green'>Green</span> lines will be imported. If there are soft validation errors
 they will appear below the green line in <span style="color:brown">brown</span>.
-  <span style="color:red">Red</span> lines will not be imported and are followed by a list of the associated errors.
+<span style="color:red">Red</span> lines will not be imported and are followed by a list of the associated errors.
 </p>
 
 <ol>
   <% @sources.each_with_index do |s, i| %>
+    <% if s.blank? %>
+      <%= tag.li(tag.span('Empty or errored entry', class: [:feedback, 'feedback-thin', 'feedback-warning'])) %>  
+    <% else %>
       <% if s.valid? %>
-          <%= content_tag(:li, s.cached_string('html').html_safe, class: 'green') -%>
-          <% if s.soft_validations.messages.count > 0 %>
-              <ul>
-                <% s.soft_validations.messages.each do |e| %>
-                    <%= content_tag(:li, e.to_s.html_safe, class: 'brown') -%>
-                <% end %>
-              </ul>
-          <% end %>
-      <% else %>
-          <%= content_tag(:li, s.cached_string('html').html_safe, class: 'red') -%>
+        <%= tag.li(s.cached_string('html').html_safe, class: 'green') -%>
+        <% if s.soft_validations.messages.count > 0 %>
           <ul>
-            <% s.errors.messages.each do |e| %>
-                <%= content_tag(:li, e.to_s.html_safe) -%>
+            <% s.soft_validations.messages.each do |e| %>
+              <%= tag.li( e.to_s.html_safe, class: 'brown') -%>
             <% end %>
           </ul>
-
-<% end %>
+        <% end %>
+      <% else %>
+        <%= tag.li(s.cached_string('html').html_safe, class: 'red') -%>
+        <ul>
+          <% s.errors.messages.each do |e| %>
+            <%= tag.li(e.to_s.html_safe) -%>
+          <% end %>
+        </ul>
+      <% end %>
+    <% end %>
   <% end %>
 </ol>
 

From 317ce7e260ead851d38ff6870dd696b5011036c1 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 26 Sep 2023 09:32:47 -0500
Subject: [PATCH 26/29] Selenium webdriver patch bump

---
 Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index bcf20d668c..7e573818e4 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -563,7 +563,7 @@ GEM
       rdoc (>= 5.0)
     seedbank (0.5.0)
       rake (>= 10.0)
-    selenium-webdriver (4.13.0)
+    selenium-webdriver (4.13.1)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)

From e41ccd703a55e99fd697ea632e83a8024a45fb39 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 26 Sep 2023 12:18:38 -0500
Subject: [PATCH 27/29] Tweak /otus/autocomplete to simplify

---
 lib/queries/otu/autocomplete.rb | 40 ++++++++-------------------------
 1 file changed, 9 insertions(+), 31 deletions(-)

diff --git a/lib/queries/otu/autocomplete.rb b/lib/queries/otu/autocomplete.rb
index 7d995d99e2..3f764dc822 100644
--- a/lib/queries/otu/autocomplete.rb
+++ b/lib/queries/otu/autocomplete.rb
@@ -100,15 +100,12 @@ def autocomplete_taxon_name
         .order('id_order.row_num')
       end
 
-      # Maintains valid_taxon_name_id needed for API. Much over-kill on intermediate queries,
-      # needs refactor.
+      # Maintains valid_taxon_name_id needed for API.
       #
-      # TODO:
+      # Considerations:
       #   otus -> taxon names -> valid taxon name_id <- otu can return more OTUs than the original query
-      #      becuase there can be multiple OTUs for the valid name of an invalid original result
-      #
-      #  This means we can just go from an invalid otu to it's valid target, we'd have to select the first
-      #  target (distinct on).
+      #      because there can be multiple OTUs for the valid name of an invalid original result.
+      #      right now we pick the first valid OTU for the name with distinct on()
       #
       def api_autocomplete
         @with_taxon_name = true
@@ -118,31 +115,12 @@ def api_autocomplete
         # before priority ordering is applied. May require tuning.
         otus = compact_priorities( autocomplete_base.limit(30) )
 
-        otu_order = otus.map(&:id)
-
-        taxon_names = ::TaxonName.where(project_id:, id: otus.map(&:taxon_name_id).uniq) # pertinent names
-
-        s = 'WITH tns AS (' + taxon_names.that_is_valid.to_sql + ') ' +
-           ::Otu.joins('JOIN tns AS tns_o ON tns_o.id = otus.taxon_name_id')
-             .where(otus: {id: otu_order})
-             .select('DISTINCT ON(otus.id) otus.*, otus.id as otu_valid_id')
-             .to_sql
-
-        a = ::Otu.select('otus.*, otu_valid_id').from('(' + s + ') as otus')
-
-        # Invalid name matches
-        t = 'WITH tns_invalid AS (' + taxon_names.that_is_invalid.to_sql + ') ' +
-          ::Otu.joins('JOIN tns_invalid as tns_invalid1 ON tns_invalid1.id = otus.taxon_name_id')
-           .where(otus: {id: otu_order})
-           .joins('LEFT JOIN otus AS otus1 ON tns_invalid1.cached_valid_taxon_name_id = otus1.taxon_name_id')
-           .select('DISTINCT ON(otus1.id) otus.*, otus1.id AS otu_valid_id')
-           .to_sql
-
-        b = ::Otu.select('otus.*, otu_valid_id').from('(' + t + ') as otus')
+        otu_order = otus.map(&:id).uniq
 
-        # TODO? see alternate ordering approach in SQL in autocomplete_taxon_name
-        u = ::Otu.from("( (#{a.to_sql}) UNION (#{b.to_sql})) as otus")
-        f = ::Otu.from('(' + u.to_sql + ') as otus')
+        f = ::Otu.where(id: otu_order)
+              .joins('left join taxon_names t1 on otus.taxon_name_id = t1.id')
+              .joins('left join otus o2 on t1.cached_valid_taxon_name_id = o2.taxon_name_id AND t1.cached_is_valid = true')
+              .select('distinct on (otus.id) otus.id, otus.name, otus.taxon_name_id, COALESCE(o2.id, otus.id) as otu_valid_id')
 
         f.sort_by.with_index { |item, idx| [(otu_order.index(item.id) || 999), (idx || 999)] }
       end

From 30d69840433c8a4223ae5a7f0435ce6a37d1ded8 Mon Sep 17 00:00:00 2001
From: mjy <diapriid@gmail.com>
Date: Tue, 26 Sep 2023 12:19:08 -0500
Subject: [PATCH 28/29] Add project_id reference (should do nothing)

---
 lib/queries/otu/filter.rb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/lib/queries/otu/filter.rb b/lib/queries/otu/filter.rb
index f89649f149..62b39f429b 100644
--- a/lib/queries/otu/filter.rb
+++ b/lib/queries/otu/filter.rb
@@ -261,8 +261,8 @@ def from_wkt(wkt_shape)
         c = ::Queries::CollectingEvent::Filter.new(wkt: wkt_shape, project_id:)
         a = ::Queries::AssertedDistribution::Filter.new(wkt: wkt_shape, project_id:)
 
-        q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all)
-        q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all)
+        q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all, project_id:)
+        q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all, project_id:)
 
         referenced_klass_union([q1, q2]).distinct
       end
@@ -273,8 +273,8 @@ def geo_json_facet
         c = ::Queries::CollectingEvent::Filter.new(geo_json:, project_id:, radius:)
         a = ::Queries::AssertedDistribution::Filter.new(geo_json:, project_id:, radius:)
 
-        q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all)
-        q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all)
+        q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all, project_id:)
+        q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all, project_id:)
 
         referenced_klass_union([q1, q2]).distinct
       end

From 120e0f907003c0ec71f279ad1cbe178334f0f6dd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hern=C3=A1n=20Lucas=20Pereira?=
 <ellocodelassembler@gmail.com>
Date: Tue, 26 Sep 2023 19:32:03 -0300
Subject: [PATCH 29/29] Preparing for version 0.34.5 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 6d79b0f4c4..bdf41e1a27 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
+\-
+
+## [0.34.5] - 2023-09-26
+
 ### Added
 
 - Cached map item report (linked from Filter OTUs)
@@ -3889,7 +3893,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 - Loosing input page numbers when switching tabs on New Taxon Name task
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.4...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.5...development
+[0.34.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.4...v0.34.5
 [0.34.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.3...v0.34.4
 [0.34.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.2...v0.34.3
 [0.34.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.34.1...v0.34.2
diff --git a/lib/taxonworks/version.rb b/lib/taxonworks/version.rb
index 38074d941b..4a69921855 100644
--- a/lib/taxonworks/version.rb
+++ b/lib/taxonworks/version.rb
@@ -1,3 +1,3 @@
 module Taxonworks
-  VERSION = "0.34.4"
+  VERSION = "0.34.5"
 end