Merge branch 'development'

CHANGELOG.md

@@ -9,6 +9,53 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.12.10] - 2020-07-07
+
+### Added
+- Smart selection source on new combination and citations annotator
+- Parsed verbatim label on comprehensive specimen digitization task
+- Soft validation in timeline on Browse OTUs [#1593]
+- Topic facet in Filter Sources task [#1589]
+- Counts on type specimen and specimen records sections on Browse OTUs
+- Collecting method parsing in verbatim label text
+
+### Changed
+- Replaced vue-resource package by axios
+- Disabled parallel upload on new image task [#1596]
+- Default verbatim fields order on comprehensive specimen digitization
+- Set radius error in verbatim georeference [#1602]
+- Timeline filter.
+- Missing High classification ranks on classfication autocomplete on new taxon name [#1595]
+- Date and geo-coordinates parsing improvements
+- Also update cached taxon name fields when Adjective or Participle is selected
+- Repositories and Serials smart selectors' recent entries optimizations
+
+### Fixed
+- Filter collecting events was passing a wrong (changed name) parameters and structure for maps and geographic area
+- Not showing up people list after a crossref source [#1597]
+- Scroller in georeferences map modal
+- Grid Digitizer task failing to update containerized specimens matched by identifiers [#1601]
+- Specimen not associate with genus after create it in type section on new taxon name [#1604]
+- Volume field only accepted numbers [#1606]
+- Smart selectors not remove the previous selection after press new on New source task [#1605]
+- Georeference methods `latitude` returning longitude and `longitude` latitude
+- Smart selector overrides custom list after lists are loaded [#1608]
+- Duplicate shortcut, using the same one for comprehensive specimen digitization and clipboard [#1612]
+- Typo in taxon name relationship soft validation message.
+
+[#1589]: https://github.com/SpeciesFileGroup/taxonworks/issues/1589
+[#1593]: https://github.com/SpeciesFileGroup/taxonworks/issues/1593
+[#1595]: https://github.com/SpeciesFileGroup/taxonworks/issues/1595
+[#1596]: https://github.com/SpeciesFileGroup/taxonworks/issues/1596
+[#1597]: https://github.com/SpeciesFileGroup/taxonworks/issues/1597
+[#1601]: https://github.com/SpeciesFileGroup/taxonworks/issues/1601
+[#1602]: https://github.com/SpeciesFileGroup/taxonworks/issues/1602
+[#1604]: https://github.com/SpeciesFileGroup/taxonworks/issues/1604
+[#1605]: https://github.com/SpeciesFileGroup/taxonworks/issues/1605
+[#1606]: https://github.com/SpeciesFileGroup/taxonworks/issues/1606
+[#1608]: https://github.com/SpeciesFileGroup/taxonworks/issues/1608
+[#1612]: https://github.com/SpeciesFileGroup/taxonworks/issues/1612
+
 ## [0.12.9] - 2020-07-01
 
 ### Added
@@ -177,7 +224,8 @@ 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/v0.12.9...development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.10...development
+[0.12.10]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.9...v0.12.10
 [0.12.9]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.12.8...v0.12.9
 [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

app/assets/javascripts/views/tasks/nomenclature/browse.js

@@ -58,7 +58,7 @@ Object.assign(TW.views.tasks.nomenclature.browse, {
           window.open('/tasks/nomenclature/new_taxon_name?taxon_name_id=' + taxonId, '_self');
         });
 
-        TW.workbench.keyboard.createShortcut((navigator.platform.indexOf('Mac') > -1 ? 'ctrl' : 'alt') + "+c", "Comprehensive specimen digitization", "Browse nomenclature", function () {
+        TW.workbench.keyboard.createShortcut((navigator.platform.indexOf('Mac') > -1 ? 'ctrl' : 'alt') + "+e", "Comprehensive specimen digitization", "Browse nomenclature", function () {
           window.open('/tasks/accessions/comprehensive?taxon_name_id=' + taxonId, '_self');
         });
 

app/controllers/collecting_events_controller.rb

@@ -136,7 +136,10 @@ def download
   def parse_verbatim_label
     if params[:verbatim_label]
       render json: {date: Utilities::Dates.date_regex_from_verbatim_label(params[:verbatim_label]),
-                    geo: Utilities::Geo.coordinates_regex_from_verbatim_label(params[:verbatim_label])}.to_json
+                    geo: Utilities::Geo.coordinates_regex_from_verbatim_label(params[:verbatim_label]),
+                    elevation: Utilities::Elevation.elevation_regex_from_verbatim_label(params[:verbatim_label]),
+                    collecting_method: Utilities::CollectingMethods.method_regex_from_verbatim_label(params[:verbatim_label]),
+                  }.to_json
     end
   end
 
@@ -276,9 +279,11 @@ def filter_params
       :start_date, # used in date range
       :end_date,   # used in date range
       :partial_overlap_dates,
+      :spatial_geographic_areas,
       keyword_ids: [],
       spatial_geographic_area_ids: [],
-      otu_ids: [],
+      geographic_area_ids: [],
+      otu_ids: []
     )
   end
 

app/controllers/sources_controller.rb

@@ -246,7 +246,8 @@ def filter_params
       :year_start,
       author_ids: [],
       citation_object_type: [],
-      keyword_ids: []
+      keyword_ids: [],
+      topic_ids: []
     )
   end
 

app/javascript/vue/components/autocomplete.vue

@@ -79,7 +79,8 @@ export default {
       getRequest: 0,
       type: this.sendLabel,
       json: [],
-      current: -1
+      current: -1,
+      requestId: Math.random().toString(36).substr(2, 5)
     }
   },
 
@@ -334,15 +335,8 @@ export default {
         this.showList = (this.json.length > 0)
       } else {
         AjaxCall('get', this.ajaxUrl(), {
-          before: (request) => {
-            if(Object.keys(this.headers).length) {
-              request.headers.map = this.headers
-            }
-            if (this.previousRequest) {
-              this.previousRequest.abort()
-            }
-            this.previousRequest = request
-          }}).then(response => {
+          requestId: this.requestId
+        }).then(response => {
           this.json = this.getNested(response.body, this.nested)
           this.showList = (this.json.length > 0)
           this.spinner = false

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

@@ -5,15 +5,31 @@
       maxHeight: '80vh',
       overflowY: 'scroll'
   }">
-    <div 
+    <div class="horizontal-left-content margin-medium-top margin-medium-bottom">
+      <manually-component
+        class="margin-small-right"
+        @create="saveGeoreference"/>
+      <geolocate-component
+        class="margin-small-right"
+        @create="createGEOLocate"/>
+      <button
+        type="button"
+        v-if="verbatimLat && verbatimLng"
+        :disabled="verbatimGeoreferenceAlreadyCreated"
+        @click="createVerbatimShape"
+        class="button normal-input button-submit">
+        Create georeference from verbatim
+      </button>
+    </div>
+    <div
       :style="{
         height: height,
         width: width
     }">
       <spinner-component
         v-if="showSpinner || !collectingEventId"
         :legend="!collectingEventId ? 'Need collecting event ID' : 'Saving...'"/>
-      <map-component 
+      <map-component
         ref="leaflet"
         v-if="show"
         :height="height"
@@ -43,8 +59,8 @@
         v-if="verbatimLat && verbatimLng"
         :disabled="verbatimGeoreferenceAlreadyCreated"
         @click="createVerbatimShape"
-        class="button normal-input button-submit separate-bottom separate-top">
-        Create georeference from verbatim 
+        class="button normal-input button-submit">
+        Create georeference from verbatim
       </button>
     </div>
     <display-list
@@ -96,6 +112,10 @@ export default {
       required: false,
       default: 0
     },
+    geolocationUncertainty: {
+      type: [String, Number],
+      default: undefined
+    },
     verbatimLng: {
       type: [Number, String],
       default: 0
@@ -119,11 +139,7 @@ export default {
   },
   computed: {
     verbatimGeoreferenceAlreadyCreated () {
-      return this.georeferences.find(item => {
-        return item.geo_json.geometry.type === 'Point' &&
-          Number(item.geo_json.geometry.coordinates[0]) === Number(this.verbatimLng) &&
-          Number(item.geo_json.geometry.coordinates[1]) === Number(this.verbatimLat)
-      })
+      return this.georeferences.find(item => { return item.type === 'Georeference::VerbatimData' })
     }
   },
   data () {
@@ -253,7 +269,8 @@ export default {
         georeference: {
           geographic_item_attributes: { shape: JSON.stringify(shape) },
           collecting_event_id: this.collectingEventId,
-          type: 'Georeference::VerbatimData'
+          type: 'Georeference::VerbatimData',
+          error_radius: this.geolocationUncertainty
         }
       }
       this.showSpinner = true

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

@@ -5,6 +5,7 @@
         <tr>
           <th>Georeference ID</th>
           <th>Shape</th>
+          <th>Coordinates</th>
           <th>Error radius</th>
           <th>Type</th>
           <th></th>
@@ -19,7 +20,7 @@
           class="list-complete-item">
           <td>{{ item.id }}</td>
           <td>{{ item.geo_json.geometry.type }}</td>
-
+          <td>{{ getCoordinates(item.geo_json.geometry.coordinates) }}</td>
           <td>
             <edit-in-place 
               v-model="item.error_radius"
@@ -92,6 +93,9 @@ export default {
       } else {
         this.$emit('delete', item)
       }
+    },
+    getCoordinates (coordinates) {
+      return coordinates.map(coordinate => Array.isArray(coordinate) ? coordinate.map(item => item.slice(0, 2)) : coordinate)
     }
   }
 }

app/javascript/vue/components/radials/annotator/components/citations/new.vue

@@ -1,35 +1,43 @@
 <template>
   <div>
     <div class="separate-bottom inline">
-      <autocomplete
-        url="/sources/autocomplete"
-        label="label"
-        min="2"
-        :send-label="autocompleteLabel"
-        @getItem="citation.source_id = $event.id"
-        placeholder="Select a source"
-        param="term"/>
-      <input
-        type="text"
-        class="normal-input inline pages separate-left"
-        v-model="citation.pages"
-        placeholder="Pages">
-    </div>
-    <div class="flex-separate separate-bottom">
-      <label class="inline middle">
-        <input
-          v-model="citation.is_original"
-          type="checkbox">
-        Is original (does not apply to topics)
-      </label>
-      <default-element
-        class="separate-left"
-        label="source"
-        type="Source"
-        @getLabel="autocompleteLabel = $event"
-        @getId="citation.source_id = $event"
-        section="Sources"
-      />
+      <smart-selector
+        class="full_width"
+        model="sources"
+        ref="smartSelector"
+        pin-section="Sources"
+        pin-type="Source"
+        @selected="citation.source_id = $event.id"
+        v-model="source">
+        <div slot="footer">
+          <div
+            v-if="source"
+            class="horizontal-left-content margin-small-bottom">
+            <span
+              v-html="source.object_tag"/>
+            <span
+              class="button circle-button btn-delete button-default"
+              @click="unsetSource"/>
+          </div>
+          <ul class="no_bullets context-menu">
+            <li>
+              <input
+                type="text"
+                class="normal-input inline pages"
+                v-model="citation.pages"
+                placeholder="Pages">
+            </li>
+            <li>
+              <label class="inline middle">
+                <input
+                  v-model="citation.is_original"
+                  type="checkbox">
+                Is original (does not apply to topics)
+              </label>
+            </li>
+          </ul>
+        </div>
+      </smart-selector>
     </div>
     <div class="separate-bottom">
       <button
@@ -43,13 +51,11 @@
 </template>
 
 <script>
-  import DefaultElement from 'components/getDefaultPin.vue'
-  import Autocomplete from 'components/autocomplete.vue'
+  import SmartSelector from 'components/smartSelector'
 
   export default {
     components: {
-      DefaultElement,
-      Autocomplete
+      SmartSelector
     },
     props: {
       globalId: {
@@ -64,8 +70,8 @@
     },
     data() {
       return {
-        autocompleteLabel: undefined,
-        citation: this.newCitation()
+        citation: this.newCitation(),
+        source: undefined
       }
     },
     methods: {
@@ -81,7 +87,11 @@
       sendCitation() {
         this.$emit('create', this.citation)
         this.citation = this.newCitation()
-        this.autocompleteLabel = undefined
+        this.source = undefined
+      },
+      unsetSource () {
+        this.citation.source_id = undefined,
+        this.source = undefined
       }
     }
   }