Merge branch 'development'

CHANGELOG.md

@@ -7,10 +7,34 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
+\-
+
+## [0.41.1] - 2024-05-10
+
+### Added
+
+- An extended biological associations API endpoint [#3944]
+
+### Fixed
+
+- Empty `higherClassification` included ""
+- Resaving Image resets height/width and original filename
+- New image from Data raising from path error
+- Filters: JSON request URL overflows container when too long
+- PDF Button is missing in Filter Sources
+- DwC Import task: Replace dialog shows `undefined` instead the current value
+- Radial annotator: Data attributes can't be deleted from the list
+- Radial quick forms: Collecting event slice doesn't render correctly
+- CSD: In some cases, the locking mechanism does not work correctly [#3941]
+
+[#3941]: https://github.com/SpeciesFileGroup/taxonworks/issues/3941
+[#3944]: https://github.com/SpeciesFileGroup/taxonworks/issues/3944
+
 ## [0.41.0] - 2024-05-02
 
 ### Added
 
+- Filter nomenclature: Local and global identifiers facets [#3942]
 - Field synchronizer task- batch edit (regex too), update and syncronize columns and between columns
 - `misspelling` option to API `taxon_name_relationship_set[]`
 
@@ -27,6 +51,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#3821]: https://github.com/SpeciesFileGroup/taxonworks/issues/3821
 [#3933]: https://github.com/SpeciesFileGroup/taxonworks/issues/3833
+[#3942]: https://github.com/SpeciesFileGroup/taxonworks/issues/3942
 
 ## [0.40.6] - 2024-04-30
 
@@ -4584,7 +4609,8 @@ _Special thanks to Tom Klein for his amazing open-source contributions on this r
 - 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/v0.41.0..development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.41.1..development
+[0.41.1]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.41.0...v0.41.1
 [0.41.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.6...v0.41.0
 [0.40.6]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.5...v0.40.6
 [0.40.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.4...v0.40.5

Gemfile

@@ -168,7 +168,9 @@ gem 'parallel_tests', group: [:development, :test]
 
 group :development do
   # gem "ruby-lsp", "~> 0.4.1", require: false
-
+
+  gem 'thruster' 
+
   # gem 'tunemygc'
   gem 'ruby-prof', '~> 1.2'
   gem 'better_errors', '~> 2.9'

Gemfile.lock

@@ -82,7 +82,7 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    Ascii85 (1.1.0)
+    Ascii85 (1.1.1)
     actioncable (6.1.7.7)
       actionpack (= 6.1.7.7)
       activesupport (= 6.1.7.7)
@@ -168,7 +168,7 @@ GEM
     bibtex-ruby (6.1.0)
       latex-decode (~> 0.0)
       racc (~> 1.7)
-    bigdecimal (3.1.7)
+    bigdecimal (3.1.8)
     bindex (0.8.1)
     binding_of_caller (1.0.1)
       debug_inspector (>= 1.2.0)
@@ -288,7 +288,7 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
-    i18n (1.14.4)
+    i18n (1.14.5)
       concurrent-ruby (~> 1.0)
     indefinite_article (0.2.5)
       activesupport
@@ -339,7 +339,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0507)
     mimemagic (0.3.10)
       nokogiri (~> 1)
       rake
@@ -353,7 +353,7 @@ GEM
     nenv (0.3.0)
     net-http (0.4.1)
       uri
-    net-imap (0.4.10)
+    net-imap (0.4.11)
       date
       net-protocol
     net-pop (0.1.2)
@@ -363,7 +363,7 @@ GEM
     net-smtp (0.3.4)
       net-protocol
     netrc (0.11.0)
-    nio4r (2.7.1)
+    nio4r (2.7.3)
     nokogiri (1.16.4-x86_64-darwin)
       racc (~> 1.4)
     nokogiri (1.16.4-x86_64-linux)
@@ -513,7 +513,7 @@ GEM
     rspec-expectations (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-mocks (3.13.0)
+    rspec-mocks (3.13.1)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-rails (5.1.2)
@@ -526,7 +526,7 @@ GEM
       rspec-support (~> 3.10)
     rspec-support (3.13.1)
     rtesseract (3.1.3)
-    rubocop (1.63.4)
+    rubocop (1.63.5)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -554,7 +554,7 @@ GEM
       rack (>= 1.1)
       rubocop (>= 1.33.0, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (2.29.1)
+    rubocop-rspec (2.29.2)
       rubocop (~> 1.40)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
@@ -632,6 +632,8 @@ GEM
     terrapin (0.6.0)
       climate_control (>= 0.0.3, < 1.0)
     thor (1.2.2)
+    thruster (0.1.4-x86_64-darwin)
+    thruster (0.1.4-x86_64-linux)
     tilt (2.3.0)
     timecop (0.9.8)
     timeliness (0.4.5)
@@ -808,6 +810,7 @@ DEPENDENCIES
   taxonifi (~> 0.6.0)
   term-ansicolor (~> 1.6)
   thor (~> 1.2)
+  thruster
   timecop (~> 0.9.1)
   turbolinks (~> 5.2.0)
   tzinfo-data (~> 1.2019)

app/assets/stylesheets/views/tasks/matrix/observation_matrices.scss

@@ -1,5 +1,5 @@
 #observation_matrices {
-  margin-top:50px;
+  margin-top: 50px;
   .otu_column {
     min-width: 400px;
   }
@@ -22,6 +22,7 @@
   min-width: 70px;
   position: relative;
   text-align: left;
+  background-color: transparent;
 }
 
 #vue-interactive-keys {
@@ -31,7 +32,7 @@
   .header-bar {
     width: 100%;
     height: 50px;
-    border-bottom: 1px solid #CCCCCC;
+    border-bottom: 1px solid #cccccc;
     background-color: white;
   }
 
@@ -41,7 +42,7 @@
     grid-template-rows: repeat(2, 1fr);
     grid-column-gap: 0px;
     grid-row-gap: 0px;
-    background-color: #CCCCCC;
+    background-color: #cccccc;
     grid-gap: 1px;
   }
   .grid-icon {
@@ -55,41 +56,47 @@
     background-color: white;
     overflow: scroll;
   }
-  
+
   .layout-mode-1 {
-    .descriptors-view { 
-      grid-area: 1 / 1 / 2 / 3; 
+    .descriptors-view {
+      grid-area: 1 / 1 / 2 / 3;
     }
-    .taxa-remaining { 
-      grid-area: 2 / 1 / 3 / 2; 
+    .taxa-remaining {
+      grid-area: 2 / 1 / 3 / 2;
     }
-    .taxa-eliminated { 
+    .taxa-eliminated {
       grid-area: 2 / 2 / 3 / 3;
     }
   }
-  
+
   .layout-mode-2 {
-    .descriptors-view  { 
-      grid-area: 1 / 1 / 3 / 2; 
+    .descriptors-view {
+      grid-area: 1 / 1 / 3 / 2;
     }
-    .taxa-remaining { 
-      grid-area: 1 / 2 / 2 / 3; 
+    .taxa-remaining {
+      grid-area: 1 / 2 / 2 / 3;
     }
-    .taxa-eliminated { 
-      grid-area: 2 / 2 / 3 / 3; 
+    .taxa-eliminated {
+      grid-area: 2 / 2 / 3 / 3;
     }
   }
 
   .full-height {
     height: 100%;
   }
 
-  .mainfont { color: #004050;}
-  .red { color: #C00000; }
-  .redbold { color: #C00000; font-weight: bold; }
+  .mainfont {
+    color: #004050;
+  }
+  .red {
+    color: #c00000;
+  }
+  .redbold {
+    color: #c00000;
+    font-weight: bold;
+  }
 
   .i3 {
-    box-shadow: 0px 2px 2px 0px rgba(0,0,0,0.2);
+    box-shadow: 0px 2px 2px 0px rgba(0, 0, 0, 0.2);
   }
-
-}
+}

app/controllers/biological_associations_controller.rb

@@ -149,6 +149,24 @@ def api_index_simple
     end
   end
 
+  def api_index_extended
+    @biological_associations = ::Queries::BiologicalAssociation::Filter.new(params.merge!(api: true))
+      .all
+      .where(project_id: sessions_current_project_id)
+      .order('biological_associations.id')
+      .page(params[:page])
+      .per(params[:per])
+
+    respond_to do |format|
+      format.json  { render '/biological_associations/api/v1/extended' and return }
+      format.csv {
+        send_data Export::CSV::BiologicalAssociations::Extended.csv(@biological_associations),
+        type: 'text',
+        filename: "biological_associations_extended_#{DateTime.now}.tsv"
+      }
+    end
+  end
+
   # PATCH /biological_associations/batch_update.json?biological_association_query=<>&biological_association={}
   def batch_update
     if r = BiologicalAssociation.batch_update(

app/helpers/biological_associations_helper.rb

@@ -61,4 +61,34 @@ def simple_hash(biological_associations)
     h
   end
 
+  def extended_hash(biological_associations)
+    h = []
+
+    biological_associations.each do |b|
+      types = biological_relationship_types(b.biological_relationship)
+
+      r = %I{order family genus}.inject({}) { |hsh, r| hsh[('subject_' + r.to_s).to_sym] = [b.biological_association_subject.taxonomy[r.to_s]].flatten.compact.join(' '); hsh }
+       r.merge!(
+        id: b.id,
+        subject_id: b.biological_association_subject_id,
+        subject_taxon_name_id: b.biological_association_subject.taxon_name_id,
+        subject_type: b.biological_association_subject_type,
+        subject: label_for(b.biological_association_subject),
+        subject_properties: types[:subject].join('|').presence,
+        biological_relationship_id: b.biological_relationship_id,
+        biological_relationships: label_for(b.biological_relationship),
+        object_properties: types[:object].join('|').presence,
+        object_id: b.biological_association_object_id,
+        object_taxon_name_id: b.biological_association_object.taxon_name_id,
+        object_type: b.biological_association_object_type,
+        object: label_for(b.biological_association_object),
+      )
+
+       r.merge! %I{order family genus}.inject({}) { |hsh, r| hsh[('object_' + r.to_s).to_sym] = [b.biological_association_object.taxonomy[r.to_s]].flatten.compact.join(' '); hsh }
+     h.push r
+    end
+
+    h
+  end
+
 end

app/javascript/vue/components/layout/Filter/FilterJsonRequestPanel.vue

@@ -1,7 +1,7 @@
 <template>
   <div class="panel content">
-    <div class="flex-separate middle">
-      <span> JSON Request: {{ queryString }} </span>
+    <div class="flex-separate middle gap-small">
+      <span class="word_break"> JSON Request: {{ queryString }} </span>
       <ButtonClipboard :text="queryString" />
     </div>
   </div>

app/javascript/vue/components/layout/Filter/FilterLayout.vue

@@ -308,8 +308,4 @@ onBeforeUnmount(() => {
   grid-template-columns: 400px 1fr;
   gap: 1em;
 }
-
-:deep(.btn-delete) {
-  background-color: #5d9ece;
-}
 </style>

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

@@ -75,7 +75,11 @@
 <script setup>
 import { computed, ref } from 'vue'
 import { ControlledVocabularyTerm, DataAttribute } from '@/routes/endpoints'
-import { IMPORT_ATTRIBUTE, PREDICATE } from '@/constants'
+import {
+  DATA_ATTRIBUTE_INTERNAL_ATTRIBUTE,
+  IMPORT_ATTRIBUTE,
+  PREDICATE
+} from '@/constants'
 import { useSlice } from '@/components/radials/composables'
 import VBtn from '@/components/ui/VBtn/index.vue'
 import TableList from './shared/tableList'
@@ -132,7 +136,7 @@ function saveDataAttribute() {
   const payload = {
     data_attribute: {
       id: currentId,
-      type: 'InternalAttribute',
+      type: DATA_ATTRIBUTE_INTERNAL_ATTRIBUTE,
       value: text.value,
       controlled_vocabulary_term_id: predicate.value.id,
       annotated_global_entity: decodeURIComponent(props.globalId)
@@ -150,7 +154,7 @@ function saveDataAttribute() {
 }
 
 function removeItem(item) {
-  DataAttribute.destroy(item).then((_) => {
+  DataAttribute.destroy(item.id).then((_) => {
     removeFromList(item)
   })
 }