Merge branch 'development'

.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

.ruby-version

@@ -1 +1 @@
-3.2.1
+3.2.2

CHANGELOG.md

@@ -9,11 +9,41 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.34.5] - 2023-09-26
+
+### Added
+
+- Cached map item report (linked from Filter OTUs)
+- Depictions list on Filter image
+
+### Changed
+
+- Calls to `/api/v1` have a new key/value signature
+- Staged image metadata field format from JSON to JSONB [#3446]
+- Updated Ruby gems
+
+### 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
+- 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]
+- 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
 
 ### 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`
@@ -3863,7 +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

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 (4.13.1)
       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

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;
 }
-

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

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

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

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
 

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 }
+      ),
+      (content_tag('div','', id: 'curation-issue-tracker-container') if sessions_current_project&.data_curation_issue_tracker_url)
+    ].join().html_safe
+  end
+
 end

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')

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

app/javascript/vue/components/radials/annotator/components/data_attribute_annotator.vue

@@ -48,17 +48,33 @@
       </VBtn>
     </div>
     <TableList
-      :list="list"
+      :list="internalAttributes"
       :header="['Name', 'Value', '']"
       :attributes="['predicate_name', 'value']"
       edit
       target-citations="data_attributes"
       @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: {

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'
+}

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 ]
 }