Merge branch 'development'

CHANGELOG.md

@@ -9,11 +9,34 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.40.5] - 2024-04-25
+
+### Added
+
+- `/api/v1/taxon_name_relationships.csv` endpoint
+
+###  Changed
+
+- Dwca `otu_name` only includes Otu#name, never anything else.
+- `api/v1/otus/autocomplete` now more acurately returns the label of the matching term, i.e. Combinations are supported in rendering [https://github.com/SpeciesFileGroup/taxonpages/issues/193]
+- Update Ruby gems
+
+### Fixed
+
+- Quick forms: Lock buttons don't work on Biological associations.
+- Week in review task [#3926]
+- Missing Image metadata breaks radial
+- Basic endemism task had a broken link out
+- Prevent raise on bad polygon (LinearRing) Georeferences
+
+
+[#3926]: https://github.com/SpeciesFileGroup/taxonworks/issues/3926
+
 ## [0.40.4] - 2024-04-21
 
 ### Added
 
-- User estimated time tracking at the per-project level 
+- User estimated time tracking at the per-project level
 - Orphaned DwcOccurrence and DelayedJob job metadata to admin Health report
 
 ### Changed
@@ -4527,7 +4550,8 @@ _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/v0.40.4...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.5...development
+[0.40.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.4...v0.40.5
 [0.40.4]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.3...v0.40.4
 [0.40.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.2...v0.40.3
 [0.40.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.40.1...v0.40.2

Gemfile.lock

@@ -380,7 +380,7 @@ GEM
     paperclip-meta (3.1.0)
       paperclip (>= 5.0)
     parallel (1.24.0)
-    parallel_tests (4.6.1)
+    parallel_tests (4.7.0)
       parallel
     parser (3.3.0.5)
       ast (~> 2.4.1)
@@ -526,7 +526,7 @@ GEM
       rspec-support (~> 3.10)
     rspec-support (3.13.1)
     rtesseract (3.1.3)
-    rubocop (1.63.2)
+    rubocop (1.63.3)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -605,7 +605,7 @@ GEM
     spreadsheet (1.3.1)
       bigdecimal
       ruby-ole
-    spring (4.2.0)
+    spring (4.2.1)
     spring-commands-rspec (1.0.4)
       spring (>= 0.9.1)
     sprockets (3.7.3)

app/controllers/otus_controller.rb

@@ -302,12 +302,13 @@ def autocomplete
 
   # GET /api/v1/otus/autocomplete
   def api_autocomplete
-    @otus = ::Queries::Otu::Autocomplete.new(
+    @otu_metadata = ::Queries::Otu::Autocomplete.new(
       params.require(:term),
       project_id: sessions_current_project_id,
       with_taxon_name: params[:with_taxon_name],
       having_taxon_name_only: params[:having_taxon_name_only]
-    ).api_autocomplete
+    ).api_autocomplete_extended
+
 
     render '/otus/api/v1/autocomplete'
   end

app/controllers/taxon_name_relationships_controller.rb

@@ -117,12 +117,23 @@ def taxon_name_relationship_types
 
   # GET /api/v1/taxon_name_relationships
   def api_index
-    @taxon_name_relationships = Queries::TaxonNameRelationship::Filter.new(params.merge!(api: true)).all
+    q = Queries::TaxonNameRelationship::Filter.new(params.merge!(api: true)).all
       .where(project_id: sessions_current_project_id)
       .order('taxon_name_relationships.id')
-      .page(params[:page])
-      .per(params[:per])
-    render '/taxon_name_relationships/api/v1/index'
+
+    respond_to do |format|
+      format.json {
+        @taxon_name_relationships = q.all.page(params[:page]).per(params[:per])
+        render '/taxon_name_relationships/api/v1/index'
+      }
+      format.csv {
+        @taxon_name_relationships = q
+        send_data Export::CSV.generate_csv(
+          @taxon_name_relationships,
+          exclude_columns: %w{updated_by_id created_by_id project_id},
+        ), type: 'text', filename: "taxon_names_relationships_#{DateTime.now}.tsv"
+      }
+    end
   end
 
   # GET /api/v1/taxon_name_relationships/:id

app/controllers/taxon_names_controller.rb

@@ -245,9 +245,9 @@ def api_index
 
     respond_to do |format|
       format.json {
-       @taxon_names = q.page(params[:page]).per(params[:per])
-       render '/taxon_names/api/v1/index'
-     }
+        @taxon_names = q.page(params[:page]).per(params[:per])
+        render '/taxon_names/api/v1/index'
+      }
       format.csv {
         @taxon_names = q
         send_data Export::CSV.generate_csv(

app/helpers/graph_helper.rb

@@ -2,11 +2,11 @@ module GraphHelper
 
   def week_in_review(weeks)
     h = {
-      metadata: { 
+      metadata: {
         weeks_ago: weeks,
       },
       data: []
-    }  
+    }
 
     %w{otus taxon_names collection_objects collecting_events biological_associations asserted_distributions type_materials images documents descriptors observations contents}.each do |i|
 
@@ -21,10 +21,9 @@ def week_in_review(weeks)
       h[:data].push g
     end
 
-    h  
+    h
   end
 
-
   def objects_graph(object_scope)
     g = initialize_graph(nil, nil, nil)
 
@@ -41,7 +40,6 @@ def objects_graph(object_scope)
     g
   end
 
-
   def object_graph(object)
     return nil if object.nil?
 

app/helpers/otus_helper.rb

@@ -22,6 +22,17 @@ def otu_tag_elements(otu)
     ].compact
   end
 
+  # Used exclusively in /api/v1/otus/autocomplete
+  def otu_extended_autocomplete_tag(target)
+    if target.kind_of?(Otu)
+      otu_tag(target)
+    else # TaxonName
+      a = [ tag.span( full_taxon_name_tag(target).html_safe, class: :otu_tag_taxon_name, title: target.id) ]
+      a.push taxon_name_type_short_tag(target)
+      tag.span( a.compact.join(' ').html_safe, class: :otu_tag )
+    end
+  end
+
   # @return [String]
   #    no HTML inside <input>
   def otu_autocomplete_selected_tag(otu)
@@ -226,11 +237,11 @@ def aggregate_geo_json(otu, target, cached_map_type = 'CachedMapItem::WebLevel1'
 
     if gj = otu.cached_map_geo_json(cached_map_type)
 
-     i = 
+     i =
        {
          **gj,
         # 'type' => gj['type'],  # 'Feature',
-        
+
         'properties' => {
           'base' => {
             'type' => 'Otu',
@@ -243,7 +254,6 @@ def aggregate_geo_json(otu, target, cached_map_type = 'CachedMapItem::WebLevel1'
         }
       }
 
-
      if gj.keys.include?('coordinates')
        i['coordinates'] = gj['coordinates'] # was 'coordinates' TODO: might not work
      elsif gj.keys.include?('geometries')

app/helpers/projects_helper.rb

@@ -138,10 +138,8 @@ def image_cumulative_gb_per_year
     cumulative_gb_per_year(Image.group_by_year(:created_at, format: '%Y').sum(:image_file_file_size))
   end
 
-
   def week_in_review_graphs(weeks)
     content_tag(:div, '', 'data-weeks-ago': weeks, 'data-weeks-review': true)
   end
 
-
 end

app/javascript/vue/components/Filter/Facets/shared/FacetDataAttribute/AddValue.vue

@@ -1,6 +1,6 @@
 <template>
   <div>
-    <label>Value</label>
+    <label>{{ label }}</label>
     <div class="field">
       <textarea
         v-model="text"
@@ -34,6 +34,13 @@
 import { ref } from 'vue'
 import VBtn from '@/components/ui/VBtn/index.vue'
 
+defineProps({
+  label: {
+    type: String,
+    default: 'Value'
+  }
+})
+
 const emit = defineEmits('add')
 
 const exact = ref()

app/javascript/vue/components/Filter/Facets/shared/FacetImportAttribute/FacetImportAttribute.vue

@@ -18,6 +18,7 @@
     />
     <hr class="divisor full_width" />
     <AddValue
+      label="Value (any predicate)"
       @add="
         (value) => {
           values.push(value)

app/javascript/vue/components/radials/object/components/biological_relationships/biological_relationships_annotator.vue

@@ -19,7 +19,7 @@
       :klass="BIOLOGICAL_ASSOCIATION"
       lock-button
       use-session
-      @lock="lockSource = $event"
+      @lock="lock.source = $event"
     />
 
     <DisplayList
@@ -64,7 +64,7 @@
             small
           />
         </VBtn>
-        <LockComponent v-model="lockRelationship" />
+        <LockComponent v-model="lock.relationship" />
       </h3>
       <h3
         class="subtle relationship-title"
@@ -268,10 +268,11 @@ function reset() {
   }
   biologicalRelation.value = undefined
   flip.value = false
-  citation.value = {
-    ...makeEmptyCitation(),
-    source_id: lock.source ? citation.value.source_id : undefined,
-    pages: lock.source ? citation.value.pages : undefined
+
+  if (lock.source) {
+    citation.value.id = undefined
+  } else {
+    citation.value = makeEmptyCitation()
   }
 }
 
@@ -305,14 +306,16 @@ function saveAssociation() {
       )
     : BiologicalAssociation.create(payload)
 
-  saveRequest.then(({ body }) => {
-    addToList(body)
-    reset()
-    TW.workbench.alert.create(
-      'Biological association was successfully saved.',
-      'notice'
-    )
-  })
+  saveRequest
+    .then(({ body }) => {
+      addToList(body)
+      reset()
+      TW.workbench.alert.create(
+        'Biological association was successfully saved.',
+        'notice'
+      )
+    })
+    .catch(() => {})
 }
 
 function removeItem(item) {

app/javascript/vue/routes/endpoints/base.js

@@ -39,17 +39,16 @@ export default (model, permitParams) => ({
   async all(params = {}, { useFilter } = {}) {
     const makeRequest = useFilter ? this.filter : this.where
     const maxPer = params.per || 500
-    const requests = [
-      await makeRequest({
-        ...params,
-        per: maxPer
-      })
-    ]
+    const payload = {
+      ...params,
+      per: maxPer
+    }
+    const requests = [await makeRequest(payload)]
     const { totalPages } = getPagination(requests[0])
 
     if (totalPages > 1) {
       for (let page = 2; page <= totalPages; page++) {
-        requests.push(makeRequest({ params: { ...params, page } }))
+        requests.push(makeRequest({ ...payload, page }))
       }
     }
 

app/javascript/vue/tasks/collecting_events/filter/constants/layouts.js

@@ -33,7 +33,7 @@ export const LAYOUTS = {
         'cached_level1_geographic_name',
         'cached_level2_geographic_name',
         'verbatim_locality',
-        'verbatim_latititude',
+        'verbatim_latitude',
         'verbatim_longitude',
         'verbatim_geolocation_uncertainty',
         'minimum_elevation',