Merge branch 'development'

CHANGELOG.md

@@ -7,10 +7,33 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 ## [unreleased]
 
+\-
+
+## [0.44.3] - 2024-10-03
+
+### Added
+
+- `dwc_occurrence_id[]` param to dwc_gallery endpoint
+- Image matrix link to radial linker and radial matrix
+
+### Fixed
+
+- Date received facet on loans [#4067]
+- `api/v1/images/975145cf4d25d7ed35893170abc2e852` style calls finding images by id, not fingerprint [#3918]
+
+### Changed
+
+- Updated Ruby gems
+- In DwC Import Otu `name` is now only set via use of `identificationQualifier`
+
+[#3918]: https://github.com/SpeciesFileGroup/taxonworks/issues/3918
+[#4067]: https://github.com/SpeciesFileGroup/taxonworks/issues/4067
+
 ## [0.44.2] - 2024-09-27
 
 ### Added
 
+- Columns in filter results can be copied to clipboard
 - Sort by identifier match option [#4065]
 - `/collection_objects/123/dwc_compact` - DwC fields for those populated [#3994]
 - Pagination to `/api/v1/otus/:otu_id/inventory/dwc_gallery`
@@ -4877,7 +4900,8 @@ _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/v0.44.2..development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.44.3..development
+[0.44.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.44.2...v0.44.3
 [0.44.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.44.1...v0.44.2
 [0.44.1]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.44.0...v0.44.1
 [0.44.0]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.43.3...v0.44.0

Gemfile.lock

@@ -224,7 +224,7 @@ GEM
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
-    excon (0.111.0)
+    excon (0.112.0)
     execjs (2.8.1)
     factory_bot (6.5.0)
       activesupport (>= 5.0.0)
@@ -264,8 +264,8 @@ GEM
     gpx (1.2.0)
       nokogiri (~> 1.7)
       rake
-    groupdate (6.4.0)
-      activesupport (>= 6.1)
+    groupdate (6.5.0)
+      activesupport (>= 7)
     guard (2.18.1)
       formatador (>= 0.2.4)
       listen (>= 2.7, < 4.0)
@@ -292,7 +292,7 @@ GEM
     indefinite_article (0.2.5)
       activesupport
     io-console (0.7.2)
-    irb (1.14.0)
+    irb (1.14.1)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
     jbuilder (2.13.0)
@@ -347,9 +347,10 @@ GEM
     marcel (1.0.4)
     matrix (0.4.2)
     method_source (1.1.0)
-    mime-types (3.5.2)
+    mime-types (3.6.0)
+      logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0903)
+    mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
     minitest (5.25.1)
     modularity (3.0.1)
@@ -507,7 +508,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.7)
+    rexml (3.3.8)
     rgb (0.1.2)
     rgeo (3.0.1)
     rgeo-activerecord (7.0.1)
@@ -543,7 +544,7 @@ GEM
     rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-mocks (3.13.1)
+    rspec-mocks (3.13.2)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-rails (6.1.5)
@@ -703,7 +704,7 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webmock (3.23.1)
+    webmock (3.24.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)

app/controllers/images_controller.rb

@@ -45,7 +45,7 @@ def api_index
 
   # GET /api/v1/images/:id
   def api_show
-    @image = Image.where(project_id: sessions_current_project_id).find_by(id: params[:id])
+    @image = Image.where(project_id: sessions_current_project_id).find_by(id: params.permit(id: :integer)[:id])
     @image ||= Image.where(project_id: sessions_current_project_id).find_by(image_file_fingerprint: params[:id])
 
     render plain: 'Not found. You may need to add a &project_token= param to the URL currently in your address bar to access these data. See https://api.taxonworks.org/ for more.', status: :not_found and return if @image.nil?

app/controllers/otus_controller.rb

@@ -333,11 +333,14 @@ def api_dwc_inventory
         type: 'text',
         filename: "dwc_#{helpers.label_for_otu(@otu).gsub(/\W/,'_')}_#{DateTime.now}.csv"
       end
+
       format.json do
         if params[:page].blank? && params[:per].blank?
           render json: DwcOccurrence.scoped_by_otu(@otu).to_json
         else # only apply if provided, do not fall back to default scope
-          render json: DwcOccurrence.scoped_by_otu(@otu).page(params[:page]).per(params[:per]).to_json
+          r = DwcOccurrence.scoped_by_otu(@otu).page(params[:page]).per(params[:per])
+          assign_pagination(r)
+          render json: r.to_json
         end
       end
     end
@@ -346,7 +349,8 @@ def api_dwc_inventory
   # GET /api/v1/otus/:id/inventory/dwc_gallery.json?per=1&page=2
   def api_dwc_gallery
     # see otus_helper
-    @data = helpers.dwc_gallery_data(@otu)
+
+    @data = helpers.dwc_gallery_data(@otu, dwc_occurrence_id: params[:dwc_occurrence_id])
     render '/otus/api/v1/inventory/dwc_gallery'
   end
 

app/helpers/otus_helper.rb

@@ -328,15 +328,21 @@ def ranked_otu_table(otus)
 
   # @return Hash
   #   { dwc_occurrence_id: [ image1, image2 ... ], ... }
-  def dwc_gallery_data(otu, pagination_headers: true)
+  def dwc_gallery_data(otu, dwc_occurrence_id: [], pagination_headers: true)
     a = DwcOccurrence.scoped_by_otu(otu)
       .select(:id, :dwc_occurrence_object_id, :dwc_occurrence_object_type)
-      .page(params[:page])
-      .per(params[:per])
+
+    dwc_ids = [dwc_occurrence_id].flatten.compact.uniq
+
+    if dwc_ids.any?
+      a = a.where(id: dwc_ids)
+    end
+
+    a = a.page(params[:page]).per(params[:per])
 
     # Somehwhat of a janky pattern, probably needs to be
     # moved into Controller.
-    assign_pagination(a) if  pagination_headers
+    assign_pagination(a) if pagination_headers
 
     b = Image.with(dwc_scope: a)
       .joins("JOIN depictions d on d.image_id = images.id" )

app/javascript/vue/components/radials/linker/constants/links.js

@@ -49,6 +49,14 @@ export const TASK_FILTER_IMAGES = {
   link: '/tasks/images/filter'
 }
 
+export const TASK_IMAGE_MATRIX = {
+  label: 'Image matrix',
+  link: '/tasks/matrix_image/matrix_image/index',
+  parseParams: ({ params }) => ({
+    otu_filter: params.otu_id?.join('|')
+  })
+}
+
 export const TASK_BIOLOGICAL_ASSOCIATION_EXTENSION = {
   label: 'DwC Extension Preview',
   link: '/tasks/biological_associations/dwc_extension_preview'

app/javascript/vue/components/radials/linker/links/Otu.js

@@ -1,9 +1,10 @@
 import {
   TASK_CACHED_MAP_ITEM,
-  TASK_FIELD_SYNCHRONIZE
+  TASK_FIELD_SYNCHRONIZE,
+  TASK_IMAGE_MATRIX
 } from '../constants/links'
 
 export const Otu = {
   all: [TASK_CACHED_MAP_ITEM, TASK_FIELD_SYNCHRONIZE],
-  ids: [TASK_CACHED_MAP_ITEM, TASK_FIELD_SYNCHRONIZE]
+  ids: [TASK_CACHED_MAP_ITEM, TASK_FIELD_SYNCHRONIZE, TASK_IMAGE_MATRIX]
 }

app/javascript/vue/components/radials/linker/radial.vue

@@ -104,18 +104,12 @@ const menuOptions = computed(() => {
   const slices = []
 
   filterLinks.value.forEach((item) => {
-    const filteredParameters = filterEmptyParams(
-      isOnlyIds.value ? getParametersForId() : getParametersForAll(item.params)
-    )
-
-    const parameters = item.queryParam
-      ? { [QUERY_PARAM[props.objectType]]: filteredParameters }
-      : filteredParameters
+    const parameters = getLinkParameters(item)
 
     const link =
       item.link + '?' + qs.stringify(parameters, { arrayFormat: 'brackets' })
 
-    if (Object.values(filteredParameters).some(Boolean)) {
+    if (Object.values(parameters).some(Boolean)) {
       if (item.post) {
         slices.push(addSlice({ label: item.label }))
       } else if (link.length > MAX_LINK_SIZE) {
@@ -208,14 +202,21 @@ function getItemByName(name) {
 }
 
 function getLinkParameters(item) {
+  const { queryParam, parseParams } = item
   const filteredParameters = filterEmptyParams(
     isOnlyIds.value ? getParametersForId() : getParametersForAll()
   )
-  const parameters = item.queryParam
+
+  const params = queryParam
     ? { [QUERY_PARAM[props.objectType]]: filteredParameters }
     : filteredParameters
 
-  return parameters
+  const args = {
+    params,
+    objectType: props.objectType
+  }
+
+  return typeof parseParams === 'function' ? parseParams(args) : params
 }
 
 function setParametersFor({ name }) {

app/javascript/vue/components/radials/matrix/components/ImageMatrix.vue

@@ -0,0 +1,26 @@
+<template>
+  <ButtonImageMatrix
+    class="button normal-input button-default"
+    :disabled="!ids.length"
+    @click="() => openImageMatrix(ids)"
+  />
+</template>
+
+<script setup>
+import { RouteNames } from '@/routes/routes'
+import ButtonImageMatrix from '@/tasks/observation_matrices/dashboard/components/buttonImageMatrix.vue'
+
+defineProps({
+  ids: {
+    type: Object,
+    required: true
+  }
+})
+
+function openImageMatrix(ids) {
+  window.open(
+    `${RouteNames.ImageMatrix}?otu_filter=${ids.join('|')}&view=true`,
+    '_blank'
+  )
+}
+</script>

app/javascript/vue/components/radials/matrix/radial.vue

@@ -9,19 +9,33 @@
 </template>
 
 <script setup>
+import { OTU } from '@/constants'
 import { useAttrs } from 'vue'
 import RadialBatch from '@/components/radials/shared/RadialBatch.vue'
 import AddSlice from './components/AddSlice.vue'
 import AddNewSlice from './components/AddNewSlice.vue'
+import ImageMatrix from './components/ImageMatrix.vue'
+
+const attrs = useAttrs()
+const props = defineProps({
+  objectType: {
+    type: String,
+    default: undefined
+  }
+})
 
 const SLICES = {
   'Add to an existing matrix': AddSlice,
   'Add to a new matrix': AddNewSlice
 }
 
+if (attrs.ids && props.objectType === OTU) {
+  Object.assign(SLICES, {
+    'View image matrix': ImageMatrix
+  })
+}
+
 defineOptions({
   name: 'RadialMatrix'
 })
-
-const attrs = useAttrs()
 </script>

app/javascript/vue/directives/help.js

@@ -10,7 +10,7 @@ function getLabelFromPath(json, path) {
   const properties = path.split('.')
 
   properties.forEach((property) => {
-    json = json[property]
+    json = json?.[property]
   })
 
   return json

app/javascript/vue/routes/routes.js

@@ -52,6 +52,7 @@ const RouteNames = {
   NewCollectingEvent: '/tasks/collecting_events/new_collecting_event',
   NewContainer: '/tasks/containers/new_container',
   NewCombination: '/tasks/nomenclature/new_combination',
+  NewDescriptor: '/tasks/descriptors/new_descriptor',
   NewExtract: '/tasks/extracts/new_extract',
   NewLead: '/tasks/leads/new_lead',
   NewNamespace: '/tasks/namespaces/new_namespace',

app/javascript/vue/tasks/collecting_events/new_collecting_event/components/CollectingEventForm.vue

@@ -85,9 +85,14 @@ export default {
         const store = this.preferences.layout[this.keyStorage]
         if (
           store &&
-          Object.keys(this.componentsOrder).every(
-            (key) => store[key].length === this.componentsOrder[key].length
-          )
+          Object.keys(this.componentsOrder).every((key) => {
+            const section = this.componentsOrder[key]
+
+            return (
+              store[key]?.length === section.length &&
+              section.every((item) => store[key].includes(item))
+            )
+          })
         ) {
           this.componentsOrder = store
         }