Merge branch 'development'

CHANGELOG.md

@@ -9,6 +9,31 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.12.8] - 2020-06-29
+
+### Added
+- Set autofocus on source and geographic area in OTU radial asserted distribution form
+- `/otus/123/coordinate.json` endpoint - all OTUs coordinate with this one (refs [#1585])
+- Autosave on new asserted distribution task
+
+### Changed
+- Unauthorized json response
+- Better error handle for vue-autocomplete
+- Replaced old method to handle ajax call in all tasks
+- Updated relationships filter param on new taxon name task (refs [#1584])
+- ControlledVocabularyTerm model no longer requires SKOS with URI (refs [#1562], [#1561])
+- Improved sorting of objects in the Browse Nomenclatue task
+- Updated dwc-archive gem to version 1.1.1
+
+### Fixed
+- Topic `select_optimized` controller method crash
+- Recent list of biological associations not working due to the use of incorrect table
+
+[#1561]: https://github.com/SpeciesFileGroup/taxonworks/issues/1561
+[#1562]: https://github.com/SpeciesFileGroup/taxonworks/issues/1562
+[#1584]: https://github.com/SpeciesFileGroup/taxonworks/issues/1584
+[#1585]: https://github.com/SpeciesFileGroup/taxonworks/issues/1585
+
 ## [0.12.7] - 2020-06-26
 
 ### Added
@@ -137,7 +162,8 @@ 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/v0.12.7...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.8...development
+[0.12.8]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.7...v0.12.8
 [0.12.7]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.6...v0.12.7
 [0.12.6]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.5...v0.12.6
 [0.12.5]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.4...v0.12.5

Gemfile

@@ -95,7 +95,7 @@ gem 'rgb'
 # "Bio" and SFG gems
 gem 'taxonifi', '~> 0.5.5'
 gem 'sqed', '0.5.8'
-gem 'dwc-archive', '~> 1.0.1'
+gem 'dwc-archive', '~> 1.1.1'
 gem 'biodiversity', '~> 4.0', '>= 4.0.3'
 gem 'ruby-units', '~> 2.3.0', require: 'ruby_units/namespaced'
 

Gemfile.lock

@@ -152,9 +152,9 @@ GEM
     docile (1.3.2)
     dropzonejs-rails (0.8.4)
       rails (> 3.1)
-    dwc-archive (1.0.1)
-      nokogiri (~> 1.8)
-      parsley-store (~> 0.3)
+    dwc-archive (1.1.1)
+      biodiversity (~> 4)
+      nokogiri (~> 1.10)
     erubi (1.9.0)
     etc (1.1.0)
     exception_notification (4.4.1)
@@ -300,7 +300,6 @@ GEM
     parser (2.7.1.4)
       ast (~> 2.4.1)
     parslet (2.0.0)
-    parsley-store (0.3.4)
     passenger (6.0.5)
       etc
       rack
@@ -580,7 +579,7 @@ DEPENDENCIES
   database_cleaner (~> 1.8)
   delayed_job_active_record (~> 4.1.3)
   dropzonejs-rails (~> 0.8.1)
-  dwc-archive (~> 1.0.1)
+  dwc-archive (~> 1.1.1)
   exception_notification (~> 4.4)
   execjs (~> 2.7.0)
   factory_bot_rails (~> 5.1, >= 5.1.1)

app/controllers/asserted_distributions_controller.rb

@@ -143,7 +143,8 @@ def set_asserted_distribution
 
   def asserted_distribution_params
     params.require(:asserted_distribution).permit(
-      :otu_id, :geographic_area_id,
+      :otu_id,
+      :geographic_area_id,
       :is_absent,
       otu_attributes: [:id, :_destroy, :name, :taxon_name_id],
       origin_citation_attributes: [:id, :_destroy, :source_id, :pages],

app/controllers/otus_controller.rb

@@ -1,7 +1,7 @@
 class OtusController < ApplicationController
   include DataControllerConfiguration::ProjectDataControllerConfiguration
 
-  before_action :set_otu, only: [:show, :edit, :update, :destroy, :collection_objects, :navigation, :breadcrumbs, :timeline]
+  before_action :set_otu, only: [:show, :edit, :update, :destroy, :collection_objects, :navigation, :breadcrumbs, :timeline, :coordinate]
   after_action -> { set_pagination_headers(:otus) }, only: [:index], if: :json_request? 
 
   # GET /otus
@@ -45,6 +45,12 @@ def timeline
   def navigation
   end
 
+  # GET /otus/1/coordinate.json
+  def coordinate
+    @otus = Otu.coordinate_otus(@otu.id)
+    render :index
+  end
+
   # GET /otus/1/navigation.json
   def breadcrumbs 
     render json: :not_found and return if @otu.nil?

app/controllers/taxon_name_relationships_controller.rb

@@ -2,6 +2,7 @@ class TaxonNameRelationshipsController < ApplicationController
   include DataControllerConfiguration::ProjectDataControllerConfiguration
 
   before_action :set_taxon_name_relationship, only: [:show, :edit, :update, :destroy]
+  after_action -> { set_pagination_headers(:taxon_name_relationships) }, only: [:index], if: :json_request?
 
   # GET /taxon_name_relationships
   # GET /taxon_name_relationships.json
@@ -13,8 +14,7 @@ def index
         render '/shared/data/all/index'
       end
       format.json {
-        @taxon_name_relationships = TaxonNameRelationship.where(filter_sql)
-                                      .with_project_id(sessions_current_project_id)
+        @taxon_name_relationships = Queries::TaxonNameRelationship::Filter.new(filter_params).all.page(params[:page]).per(params[:per] || 500)
       }
     end
   end
@@ -121,9 +121,13 @@ def taxon_name_relationship_params
     )
   end
 
-  def filter_sql
-    h = params.permit(:taxon_name_id, :as_object, :as_subject, of_types: []).to_h.symbolize_keys
-    Queries::TaxonNameRelationshipsFilterQuery.new(**h).where_sql
+  def filter_params
+    params.permit(
+      :taxon_name_id,
+      :as_object, :as_subject,
+      taxon_name_relationship_type: [],
+      taxon_name_relationship_set: []
+    ).to_h.symbolize_keys.merge(project_id: sessions_current_project_id)
   end
 
 end

app/helpers/workbench/sessions_helper.rb

@@ -150,7 +150,7 @@ def require_sign_in_and_project_selection
     unless (sessions_signed_in? or @api_request) && sessions_project_selected?
       respond_to do |format|
         format.html { redirect_to root_url, notice: 'Whoa there, sign in and select a project first.'  }
-        format.json { render(json: {success: false}, status: :unauthorized) && return } # TODO: bad request, not unauthorized
+        format.json { render json: { error: 'Whoa there, sign in and select a project first.' }, status: :unauthorized } # TODO: bad request, not unauthorized
       end
     end
   end

app/javascript/vue/components/autocomplete.vue

@@ -67,6 +67,9 @@ Parameters:
 </template>
 
 <script>
+
+import AjaxCall from 'helpers/ajaxCall'
+
 export default {
   data: function () {
     return {
@@ -330,9 +333,8 @@ export default {
         this.searchEnd = true
         this.showList = (this.json.length > 0)
       } else {
-
-        this.$http.get(this.ajaxUrl(), {
-          before (request) {
+        AjaxCall('get', this.ajaxUrl(), {
+          before: (request) => {
             if(Object.keys(this.headers).length) {
               request.headers.map = this.headers
             }
@@ -341,8 +343,7 @@ export default {
             }
             this.previousRequest = request
           }}).then(response => {
-            this.json = this.getNested(response.body, this.nested)
-          
+          this.json = this.getNested(response.body, this.nested)
           this.showList = (this.json.length > 0)
           this.spinner = false
           this.searchEnd = true
@@ -360,6 +361,9 @@ export default {
     },
     activeSpinner: function () {
       return 'ui-autocomplete-loading'
+    },
+    setFocus () {
+      this.$refs.autofocus.focus()
     }
   }
 }

app/javascript/vue/components/defaultCitation.vue

@@ -39,6 +39,7 @@
 
 <script>
 import { TippyComponent } from 'vue-tippy'
+import AjaxCall from 'helpers/ajaxCall'
 
 export default {
   components: {
@@ -79,7 +80,7 @@ export default {
           annotated_global_entity: this.globalId
         }
       }
-      this.$http.post('/citations', citationItem).then(response => {
+      AjaxCall('post', '/citations', citationItem).then(response => {
         this.citationItem = response.body
         this.created = true
         TW.workbench.alert.create('Citation item was successfully created.', 'notice')
@@ -92,7 +93,7 @@ export default {
 				annotated_global_entity: this.globalId,
 				_destroy: true
 			}
-      this.$http.delete(`/citations/${this.citationItem.id}`, { citation: citation }).then(response => {
+      AjaxCall('delete', `/citations/${this.citationItem.id}`, { citation: citation }).then(response => {
         this.created = false
         TW.workbench.alert.create('Citation item was successfully destroyed.', 'notice')
       })

app/javascript/vue/components/defaultConfidence.vue

@@ -41,6 +41,7 @@
 <script>
 
 import { TippyComponent } from 'vue-tippy'
+import AjaxCall from 'helpers/ajaxCall'
 
 export default {
   components: {
@@ -102,7 +103,7 @@ export default {
         global_id: this.globalId,
         confidence_level_id: this.keyId
       }
-      this.$http.get('/confidences/exists', { params: params }).then(response => {
+      AjaxCall('get', '/confidences/exists', { params: params }).then(response => {
         if(response.body) {
           this.created = true
           this.confidenceItem = response.body
@@ -118,7 +119,7 @@ export default {
         confidence_level_id: [this.keyId],
         per: 100
       }
-      this.$http.get('/confidences', { params: params }).then(response => {
+      AjaxCall('get', '/confidences', { params: params }).then(response => {
         this.confidenceCount = response.body.length
       })
     },
@@ -129,7 +130,7 @@ export default {
           annotated_global_entity: this.globalId
         }
       }
-      this.$http.post('/confidences', ConfidenceItem).then(response => {
+      AjaxCall('post', '/confidences', ConfidenceItem).then(response => {
         this.confidenceItem = response.body
         this.created = true
         TW.workbench.alert.create('Confidence item was successfully created.', 'notice')
@@ -140,7 +141,7 @@ export default {
 				annotated_global_entity: this.globalId,
 				_destroy: true
 			}
-      this.$http.delete(`/confidences/${this.confidenceItem.id}`, { confidence: confidence }).then(response => {
+      AjaxCall('delete', `/confidences/${this.confidenceItem.id}`, { confidence: confidence }).then(response => {
         this.created = false
         TW.workbench.alert.create('Confidence item was successfully destroyed.', 'notice')
       })

app/javascript/vue/components/defaultTag.vue

@@ -38,6 +38,7 @@
 
 <script>
 import { TippyComponent } from 'vue-tippy'
+import AjaxCall from 'helpers/ajaxCall'
 
 export default {
   components: {
@@ -101,7 +102,7 @@ export default {
         global_id: this.globalId,
         keyword_id: this.keyId
       }
-      this.$http.get('/tags/exists', { params: params }).then(response => {
+      AjaxCall('get', '/tags/exists', { params: params }).then(response => {
         if (response.body) {
           this.created = true
         } else {
@@ -115,7 +116,7 @@ export default {
         keyword_id: [this.keyId],
         per: 100
       }
-      this.$http.get('/tags', { params: params }).then(response => {
+      AjaxCall('get', '/tags', { params: params }).then(response => {
         this.countTag = response.body.length
       })
     },
@@ -126,7 +127,7 @@ export default {
           annotated_global_entity: this.globalId
         }
       }
-      this.$http.post('/tags', tagItem).then(response => {
+      AjaxCall('post', '/tags', tagItem).then(response => {
         this.tagItem = response.body
         this.created = true
         TW.workbench.alert.create('Tag item was successfully created.', 'notice')
@@ -137,7 +138,7 @@ export default {
 				annotated_global_entity: this.globalId,
 				_destroy: true
 			}
-      this.$http.delete(`/tags/${this.tagItem.id}`, { tag: tag }).then(response => {
+      AjaxCall('delete', `/tags/${this.tagItem.id}`, { tag: tag }).then(response => {
         this.created = false
         TW.workbench.alert.create('Tag item was successfully destroyed.', 'notice')
       })

app/javascript/vue/components/georeferences/georeferences.vue

@@ -63,6 +63,7 @@ import DisplayList from './list'
 import convertDMS from 'helpers/parseDMS.js'
 import ManuallyComponent from './manuallyComponent'
 import GeolocateComponent from './geolocateComponent'
+import AjaxCall from 'helpers/ajaxCall'
 
 export default {
   components: {
@@ -157,7 +158,7 @@ export default {
       }
       this.showSpinner = true
      
-      this.$http.patch(`/georeferences/${shape.id}.json`, { georeference: georeference }).then(response => {
+      AjaxCall('patch', `/georeferences/${shape.id}.json`, { georeference: georeference }).then(response => {
         this.showSpinner = false
         this.$emit('updated', response.body)
         this.getGeoreferences()
@@ -176,7 +177,7 @@ export default {
         }
       }
       this.showSpinner = true
-      this.$http.post('/georeferences.json', data).then(response => {
+      AjaxCall('post', '/georeferences.json', data).then(response => {
         this.showSpinner = false
         if(response.body.error_radius) {
           response.body.geo_json.properties.radius = response.body.error_radius
@@ -201,7 +202,7 @@ export default {
 
       this.showSpinner = true
      
-      this.$http.patch(`/georeferences/${georeference.id}.json`, { georeference: georeference }).then(response => {
+      AjaxCall('patch', `/georeferences/${georeference.id}.json`, { georeference: georeference }).then(response => {
         const index = this.georeferences.findIndex(geo => { return geo.id == response.body.id })
         this.showSpinner = false
         this.georeferences[index] = response.body
@@ -212,7 +213,7 @@ export default {
       
     },
     getGeoreferences() {
-      this.$http.get(`/georeferences.json?collecting_event_id=${this.collectingEventId}`).then(response => {
+      AjaxCall('get', `/georeferences.json?collecting_event_id=${this.collectingEventId}`).then(response => {
         this.georeferences = response.body
         this.populateShapes()
         this.$emit('onGeoreferences', this.georeferences)
@@ -231,7 +232,7 @@ export default {
       })
     },
     removeGeoreference(geo) {
-      this.$http.delete(`/georeferences/${geo.id}.json`).then(() => {
+      AjaxCall('delete', `/georeferences/${geo.id}.json`).then(() => {
         this.georeferences.splice(this.georeferences.findIndex((item => {
           return item.id === geo.id
         })), 1)
@@ -256,7 +257,7 @@ export default {
         }
       }
       this.showSpinner = true
-      this.$http.post('/georeferences.json', data).then(response => {
+      AjaxCall('post', '/georeferences.json', data).then(response => {
         this.showSpinner = false
         this.georeferences.push(response.body)
         this.populateShapes()
@@ -267,13 +268,12 @@ export default {
       })
     },
     createGEOLocate(iframe_data) {
-
       this.showSpinner = true
-      this.$http.post('/georeferences.json', { georeference: {
-          iframe_response: iframe_data,
-          collecting_event_id: this.collectingEventId,
-          type: 'Georeference::GeoLocate'
-        }}).then(response => {
+      AjaxCall('post', '/georeferences.json', { georeference: {
+        iframe_response: iframe_data,
+        collecting_event_id: this.collectingEventId,
+        type: 'Georeference::GeoLocate'
+      }}).then(response => {
         this.showSpinner = false
         this.georeferences.push(response.body)
         this.populateShapes()