Merge branch 'development'

CHANGELOG.md

@@ -8,6 +8,15 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.29.3] - 2022-09-13
+
+### Fixed
+- View image matrix button doesn't work in Interactive key task
+- Missing collectors parameters in Filter collecting events.
+- Pagination on Image Matrix task
+- Project Preferences task causing internal server errors
+- Boolean params not handled correctly on specific conditions in some filters
+
 ## [0.29.2] - 2022-09-08
 ### Added
 - Administration level project classification visualization [#3092]
@@ -2893,7 +2902,8 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 [#1532]: https://github.com/SpeciesFileGroup/taxonworks/issues/1532
 
-[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.2...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.3...development
+[0.29.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.2...v0.29.3
 [0.29.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.1...v0.29.2
 [0.29.1]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.29.0...v0.29.1
 [0.29.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.28.1...v0.29.0

Dockerfile.development

@@ -4,7 +4,7 @@ ARG BUNDLER_WORKERS=1
 # Install Firefox (for headless feature tests)
 RUN apt-get update && \
     apt-get install -y locales \
-                       libgtk-3-0 libgtk-3-dev libdbus-glib-1-2 libxt6 && \
+                       libgtk-3-0 libgtk-3-dev libdbus-glib-1-2 libxt6 libasound2 && \
     curl -sL 'https://download.mozilla.org/?product=firefox-latest&lang=en-US&os=linux64' | \
     tar -xjf - -C /usr/bin && \
     /usr/bin/firefox/firefox --version && \

app/controllers/collecting_events_controller.rb

@@ -307,6 +307,8 @@ def filter_params
       :end_date,   # used in date range
       :geo_json,
       :geographic_area_id,
+      :georeferences,
+      :geographic_area,
       :identifier,
       :identifier_end,
       :identifier_exact,
@@ -350,7 +352,9 @@ def api_params
       :depictions,
       :end_date, # used in date range
       :geo_json,
+      :georeferences,
       :geographic_area_id,
+      :geographic_area,
       :identifier,
       :identifier_end,
       :identifier_exact,

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

@@ -84,7 +84,7 @@ export const CollectingEvent = {
 
   clone: (id, params) => AjaxCall('post', `/${controller}/${id}/clone`, params),
 
-  filter: params => AjaxCall('post', `/${controller}/filter`, params),
+  filter: params => AjaxCall('post', `/${controller}/filter.json`, params),
 
   navigation: (id) => AjaxCall('get', `/${controller}/${id}/navigation`),
 

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

@@ -56,7 +56,7 @@ export const CollectionObject = {
 
   dwcIndex: (params) => AjaxCall('get', `/${controller}/dwc_index`, { params }),
 
-  filter: (params) => AjaxCall('post', `/${controller}/filter`, params),
+  filter: (params) => AjaxCall('post', `/${controller}/filter.json`, params),
 
   metadataBadge: (id) => AjaxCall('get', `/${controller}/${id}/metadata_badge`),
 

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

@@ -40,5 +40,5 @@ export const Extract = {
   ...baseCRUD(controller, permitParams),
   ...annotations(controller),
 
-  filter: params => AjaxCall('post', `/${controller}/filter`, params)
+  filter: params => AjaxCall('post', `/${controller}/filter.json`, params)
 }

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

@@ -29,5 +29,5 @@ export const Image = {
   ...baseCRUD(controller, permitParams),
   ...annotations(controller),
 
-  filter: params => AjaxCall('post', `/${controller}/filter`, params)
+  filter: params => AjaxCall('post', `/${controller}/filter.json`, params)
 }

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

@@ -25,7 +25,7 @@ export const People = {
 
   roles: id => AjaxCall('get', `/${controller}/${id}/roles.json`),
 
-  filter: params => AjaxCall('post', `/${controller}/filter`, params),
+  filter: params => AjaxCall('post', `/${controller}/filter.json`, params),
 
   merge: (id, params) => AjaxCall('post', `/people/${id}/merge`, params)
 }

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

@@ -73,7 +73,7 @@ export const Source = {
 
   clone: (id, params) => AjaxCall('post', `/${model}/${id}/clone`, params),
 
-  filter: params => AjaxCall('post', `/${model}/filter`, params),
+  filter: params => AjaxCall('post', `/${model}/filter.json`, params),
 
   parse: params => AjaxCall('get', `/${model}/parse.json`, { params })
 }

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

@@ -42,7 +42,7 @@ const permitParams = {
 export const TaxonName = {
   ...baseCRUD(model, permitParams),
 
-  filter: params => AjaxCall('post', `/${model}/filter`, params),
+  filter: params => AjaxCall('post', `/${model}/filter.json`, params),
 
   ranks: () => AjaxCall('get', `/${model}/ranks`),
 

app/javascript/vue/tasks/collecting_events/filter/components/Filter.vue

@@ -171,6 +171,7 @@ export default {
       if (this.emptyParams) return
       const params = this.filterEmptyParams({
         ...checkMatchIdentifiersParams(this.params.matchIdentifiers),
+        ...this.params.collectors,
         ...this.params.keywords,
         ...this.params.dataAttributes,
         ...this.params.identifier,
@@ -179,6 +180,7 @@ export default {
         ...this.params.byRecordsWith,
         ...this.params.user,
         ...this.params.settings,
+        ...this.params.types,
         ...this.flatObject(this.params.collectingEvents, 'fields')
       })
 

app/javascript/vue/tasks/interactive_keys/components/RowFilter.vue

@@ -3,7 +3,8 @@
     <button
       type="button"
       class="button normal-input button-default margin-small-bottom"
-      @click="setModelView(true)">
+      @click="setModelView(true)"
+    >
       Select
     </button>
     <modal-component
@@ -13,7 +14,8 @@
         width: '500px',
         overflow: 'scroll',
         maxHeight: '80vh'
-      }">
+      }"
+    >
       <template #header>
         <h3>Row filter</h3>
       </template>
@@ -22,37 +24,41 @@
           <button
             v-if="allSelected"
             type="button"
-            class="button normal-input button-default margin-small-bottom"
-            @click="unselectAll">
+            class="button normal-input button-default margin-small-bottom margin-small-right"
+            @click="unselectAll"
+          >
             Unselect all
           </button>
           <button
             v-else
             type="button"
-            class="button normal-input button-default margin-small-bottom"
-            @click="selectAll">
+            class="button normal-input button-default margin-small-bottom margin-small-right"
+            @click="selectAll"
+          >
             Select all
           </button>
           <button
             type="button"
-            class="button normal-input button-default"
-            @click="closeAndApply">
+            class="button normal-input button-default margin-small-right"
+            @click="closeAndApply"
+          >
             Apply filter
           </button>
-          <button-image-matrix
-            :otu-ids="otuIds"/>
+          <button-image-matrix :otu-ids="otuIds" />
         </div>
         <ul class="no_bullets">
           <li
             v-for="item in remaining"
             :key="item.object.id"
-            class="margin-small-bottom middle">
+            class="margin-small-bottom middle"
+          >
             <label>
               <input
                 v-model="selectedRows"
                 :value="item.object.id"
-                type="checkbox">
-              <span v-html="displayLabel(item.object)"/>
+                type="checkbox"
+              >
+              <span v-html="displayLabel(item.object)" />
             </label>
           </li>
         </ul>
@@ -62,25 +68,27 @@
           <button
             v-if="allSelected"
             type="button"
-            class="button normal-input button-default margin-small-bottom"
-            @click="unselectAll">
+            class="button normal-input button-default margin-small-bottom margin-small-right"
+            @click="unselectAll"
+          >
             Unselect all
           </button>
           <button
             v-else
             type="button"
-            class="button normal-input button-default margin-small-bottom"
-            @click="selectAll">
+            class="button normal-input button-default margin-small-bottom margin-small-right"
+            @click="selectAll"
+          >
             Select all
           </button>
           <button
             type="button"
-            class="button normal-input button-default"
-            @click="closeAndApply">
+            class="button normal-input button-default margin-small-right"
+            @click="closeAndApply"
+          >
             Apply filter
           </button>
-          <button-image-matrix
-            :otu-ids="otuIds"/>
+          <button-image-matrix :otu-ids="otuIds" />
         </div>
       </template>
     </modal-component>
@@ -125,11 +133,15 @@ export default {
     },
 
     otuIds () {
-      const objects = this.remaining
-        .map(item => item.object)
-        .filter(item => this.selectedRows.includes(item.id))
+      const ids = []
 
-      return objects.map(item => item.otu_id).filter(id => id)
+      this.remaining.forEach(({ object }) => {
+        if (this.selectedRows.includes(object.id)) {
+          ids.push(object.observation_object_id)
+        }
+      })
+
+      return ids
     },
 
     allSelected () {

app/javascript/vue/tasks/observation_matrices/image/app.vue

@@ -216,8 +216,9 @@ export default {
 
     loadPage ({ page }) {
       this.$store.dispatch(ActionNames.LoadObservationMatrix, {
-        observation_matrix_id: this.matrixId,
+        observation_matrix_id: this.matrixId || 0,
         page,
+        otu_filter: this.otuFilter,
         per: this.per
       })
       setParam(RouteNames.ImageMatrix, 'observation_matrix_id', this.matrixId)

app/models/source/verbatim.rb

@@ -48,7 +48,6 @@ def date
   def generate_bibtex
     return false if verbatim.blank?
     result = TaxonWorks::Vendor::Serrano.new_from_citation(citation: verbatim)
-    byebug
     if result.type == 'Source::Bibtex'
       result
     else

app/views/projects/show.json.jbuilder

@@ -1 +1 @@
-json.partial '/projects/attributes', project: @project
+json.partial! '/projects/attributes', project: @project

lib/queries/collecting_event/filter.rb

@@ -95,7 +95,6 @@ class Filter
       #  whether the CollectingEvent has associated CollectionObjects
       attr_accessor :collection_objects
 
-
       # @return Array
       # @param collection_object_id [Array, Integer, String]
       #    all collecting events matching collection objects
@@ -107,6 +106,18 @@ class Filter
       #   nil - not applied
       attr_accessor :depictions
 
+      # @return [True, False, nil]
+      #   true - georeferences
+      #   false - not georeferenced
+      #   nil - not applied
+      attr_accessor :georeferences
+
+      # @return [True, False, nil]
+      #   true - has geographic_area present
+      #   false - without geographic_area
+      #   nil - not applied
+      attr_accessor :geographic_area
+
       def initialize(params)
         # @spatial_geographic_area_ids = params[:spatial_geographic_areas].blank? ? [] : params[:spatial_geographic_area_ids]
 
@@ -116,6 +127,8 @@ def initialize(params)
         @collection_objects = boolean_param(params, :collection_objects )
         @collection_object_id = params[:collection_object_id]
         @depictions = boolean_param(params, :depictions)
+        @georeferences = boolean_param(params, :georeferences)
+        @geographic_area = boolean_param(params, :geographic_area)
         @geo_json = params[:geo_json]
         @geographic_area_id = params[:geographic_area_id]
         @in_labels = params[:in_labels]
@@ -183,6 +196,15 @@ def attribute_clauses
         c
       end
 
+      def geographic_area_facet
+        return nil if geographic_area.nil?
+        if geographic_area 
+          ::CollectingEvent.where.not(geographic_area_id: null).distinct
+        else
+          ::CollectingEvent.where(geographic_area_id: null).distinct
+        end
+      end
+
       def depictions_facet
         return nil if depictions.nil?
 
@@ -195,6 +217,18 @@ def depictions_facet
         end
       end
 
+      def georeferences_facet
+        return nil if georeferences.nil?
+
+        if georeferences
+          ::CollectingEvent.joins(:georeferences).distinct
+        else
+          ::CollectingEvent.left_outer_joins(:georeferences)
+            .where(georeferences: {id: nil})
+            .distinct
+        end
+      end
+
       # @return Scope
       def collection_objects_facet
         return nil if collection_objects.nil?
@@ -336,7 +370,9 @@ def base_merge_clauses
           data_attribute_predicate_facet,
           data_attribute_value_facet,
           data_attributes_facet,
+          geographic_area_facet,
           depictions_facet,
+          georeferences_facet,
           geo_json_facet,
           identifier_between_facet,
           identifier_facet,       # See Queries::Concerns::Identifiers

lib/queries/collection_object/filter.rb

@@ -215,7 +215,7 @@ class Filter < Queries::Query
 
       # @param [Hash] args are permitted params
       def initialize(params)
-        params.reject!{ |_k, v| v.blank? } # dump all entries with empty values
+        params.reject!{ |_k, v| v.nil? || (v == '') } # dump all entries with empty values
 
         # Only CollectingEvent fields are permitted now.
         # (Perhaps) TODO: allow concern attributes nested inside as well, e.g. show me all COs with this Tag on CE.

lib/queries/concerns/protocols.rb

@@ -31,7 +31,7 @@ def set_protocols_params(params)
     @protocol_id_and = params[:protocol_id_and].blank? ? [] : params[:protocol_id_and]
     @protocol_id_or = params[:protocol_id_or].blank? ? [] : params[:protocol_id_or]
 
-    @protocols = (params[:protocols]&.downcase == 'true' ? true : false) if !params[:protocols].nil?
+    @protocols = (params[:protocols]&.to_s&.downcase == 'true' ? true : false) if !params[:protocols].nil?
   end
 
   def protocol_id_and

lib/queries/concerns/tags.rb

@@ -33,7 +33,7 @@ def set_tags_params(params)
     @keyword_id_and = params[:keyword_id_and].blank? ? [] : params[:keyword_id_and]
     @keyword_id_or = params[:keyword_id_or].blank? ? [] : params[:keyword_id_or]
 
-    @tags = (params[:tags]&.downcase == 'true' ? true : false) if !params[:tags].nil?
+    @tags = (params[:tags]&.to_s&.downcase == 'true' ? true : false) if !params[:tags].nil?
   end
 
   def keyword_id_and