Merge branch 'development'

CHANGELOG.md

@@ -9,6 +9,29 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 
 \-
 
+## [0.44.1] - 2024-09-24
+
+### Added
+
+- `/api/v1/otus/:id/inventory/keys` a list of keys scoped to or containing the Otu
+- `otu_id` to ObservationMatrix, to facilitate setting scope and indexing of multi-entry keys
+- `is_public` flag to ObservationMatrix
+
+### Changed
+
+- Revert strict `verbatim_field_number` validation [#4061]
+- Renamed CollectingEvent `verbatim_trip_code` to `verbatim_field_number` [#4058]
+
+### Fixed
+
+- DwC `eventDate` should not be populated without an explict year reference [#4053]
+- DwC `month` should not be populated when range-provided [#4055]
+
+[#4053]: https://github.com/SpeciesFileGroup/taxonworks/issues/4053
+[#4055]: https://github.com/SpeciesFileGroup/taxonworks/issues/4055
+[#4058]: https://github.com/SpeciesFileGroup/taxonworks/issues/4058
+[#4061]: https://github.com/SpeciesFileGroup/taxonworks/issues/4061
+
 ## [0.44.0] - 2024-09-17
 
 ### Added
@@ -4836,7 +4859,8 @@ _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/v0.44.0..development
+[unreleased]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.44.1..development
+[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
 [0.43.3]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.43.2...v0.43.3
 [0.43.2]: https://github.com/SpeciesFileGroup/taxonworks/compare/v0.43.1...v0.43.2

Gemfile.lock

@@ -217,7 +217,7 @@ GEM
     drb (2.2.1)
     dropzonejs-rails (0.8.5)
       rails (> 3.1)
-    dwc_agent (3.1.5.0)
+    dwc_agent (3.2.0.0)
       namae (~> 1)
       namecase (~> 2)
     erubi (1.13.0)
@@ -233,8 +233,9 @@ GEM
       railties (>= 5.0.0)
     faker (3.4.2)
       i18n (>= 1.8.11, < 2)
-    faraday (2.11.0)
+    faraday (2.12.0)
       faraday-net_http (>= 2.0, < 3.4)
+      json
       logger
     faraday-excon (2.2.0)
       excon (>= 0.109.0)
@@ -427,7 +428,7 @@ GEM
     psych (5.1.2)
       stringio
     public_suffix (6.0.1)
-    puma (6.4.2)
+    puma (6.4.3)
       nio4r (~> 2.0)
     racc (1.8.1)
     rack (2.2.9)
@@ -577,7 +578,7 @@ GEM
     rubocop-performance (1.22.1)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rails (2.26.1)
+    rubocop-rails (2.26.2)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.52.0, < 2.0)
@@ -609,7 +610,7 @@ GEM
       rdoc (>= 5.0)
     seedbank (0.5.0)
       rake (>= 10.0)
-    selenium-webdriver (4.24.0)
+    selenium-webdriver (4.25.0)
       base64 (~> 0.2)
       logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)

app/controllers/observation_matrices_controller.rb

@@ -354,7 +354,11 @@ def set_observation_matrix
   end
 
   def observation_matrix_params
-    params.require(:observation_matrix).permit(:name)
+    params.require(:observation_matrix).permit(
+      :name,
+      :otu_id,
+      :is_public
+    )
   end
 
   def nexus_import_options_params
@@ -468,4 +472,4 @@ def nexus_dimensions_okay(nf)
     false
   end
 
-end
+end

app/controllers/otus_controller.rb

@@ -5,7 +5,7 @@ class OtusController < ApplicationController
     :show, :edit, :update, :destroy, :collection_objects, :navigation,
     :breadcrumbs, :timeline, :coordinate, :distribution,
     :api_show, :api_taxonomy_inventory, :api_type_material_inventory,
-    :api_nomenclature_citations, :api_distribution, :api_content, :api_dwc_inventory, :api_dwc_gallery ]
+    :api_nomenclature_citations, :api_distribution, :api_content, :api_dwc_inventory, :api_dwc_gallery, :api_key_inventory ]
 
   after_action -> { set_pagination_headers(:otus) }, only: [:index, :api_index], if: :json_request?
 
@@ -313,6 +313,11 @@ def api_autocomplete
     render '/otus/api/v1/autocomplete'
   end
 
+  # GET /api/v1/otus/:id/inventory/keys
+  def api_key_inventory
+    render json: helpers.otu_key_inventory(@otu)
+  end
+
   # GET /api/v1/otus/:id/inventory/taxonomy
   def api_taxonomy_inventory
     render '/otus/api/v1/inventory/taxonomy'

app/helpers/otus_helper.rb

@@ -348,4 +348,17 @@ def dwc_gallery_data(otu)
     r
   end
 
+  def otu_key_inventory(otu, is_public: true)
+    return {
+      observation_matrices: {
+        scoped: otu.in_scope_observation_matrices.where(is_public:).select(:id, :name).inject({}){|hsh, m| hsh[m.id] = m.name; hsh;} || {} ,
+        in: otu.observation_matrices.where(is_public:).select(:id, :name).inject({}){|hsh, m| hsh[m.id] = m.name; hsh;} || {},
+      },
+      leads: {
+        scoped: otu.leads.where(parent_id: nil, is_public:).select(:id, :text).inject({}){|hsh, m| hsh[m.id] = m.text; hsh;} || {},
+        in:  otu.leads.where.not(parent_id: nil).where(is_public: true).select(:id, :text).inject({}){|hsh, m| hsh[m.id] = m.text; hsh;} || {},
+      }
+    }
+  end
+
 end

app/javascript/vue/adapters/makeCollectingEvent.js

@@ -11,7 +11,7 @@ export function makeCollectingEvent (ceData = {}) {
     verbatimLongitude: ceData.verbatim_longitude,
     verbatimLatitude: ceData.verbatim_latitude,
     verbatimGeolocationUncertainty: ceData.verbatim_geolocation_uncertainty,
-    verbatimTripIdentifier: ceData.verbatim_trip_identifier,
+    verbatimFieldNumber: ceData.verbatim_field_number,
     verbatimCollectors: ceData.verbatim_collectors,
     verbatimMethod: ceData.verbatim_method,
     verbatimHabitat: ceData.verbatim_habitat,

app/javascript/vue/adapters/payload/makeCollectionObjectPayload.js

@@ -10,7 +10,7 @@ export function makeCollectingEventPayload (ceData) {
     verbatim_longitude: ceData.verbatimLongitude,
     verbatim_latitude: ceData.verbatimLatitude,
     verbatim_geolocation_uncertainty: ceData.verbatimGeolocationUncertainty,
-    verbatim_trip_identifier: ceData.verbatimTripIdentifier,
+    verbatim_field_number: ceData.verbatimFieldNumber,
     verbatim_collectors: ceData.verbatimCollectors,
     verbatim_method: ceData.verbatimMethod,
     verbatim_habitat: ceData.verbatimHabitat,

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

@@ -35,7 +35,7 @@
 <script setup>
 import { computed, ref, onBeforeMount } from 'vue'
 import { vTabkey } from '@/directives'
-import VToggle from '@/tasks/observation_matrices/new/components/newMatrix/switch.vue'
+import VToggle from '@/tasks/observation_matrices/new/components/Matrix/switch.vue'
 import FacetContainer from '@/components/Filter/Facets/FacetContainer.vue'
 
 const TYPE_PARAMETERS = {

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

@@ -46,7 +46,7 @@
 </template>
 
 <script>
-import SwitchButtom from '@/tasks/observation_matrices/new/components/newMatrix/switch.vue'
+import SwitchButtom from '@/tasks/observation_matrices/new/components/Matrix/switch.vue'
 import SmartSelector from '@/components/ui/SmartSelector'
 import DisplayList from '@/components/displayList'
 import FacetContainer from '@/components/Filter/Facets/FacetContainer.vue'

app/javascript/vue/components/Form/FormCollectingEvent/components/map/PrintLabel.vue

@@ -112,7 +112,7 @@ function generateLabel() {
     ...generateParsedLabel()
   )
 
-  const AtStart = ['TripIdentifier', 'TripCode']
+  const AtStart = ['FieldNumber', 'TripCode']
 
   const sortedObjectLabelKeys = sortArrayByArray(
     Object.keys(objectLabels),

app/javascript/vue/components/Form/FormCollectingEvent/components/verbatim/TripIdentifier.vue → app/javascript/vue/components/Form/FormCollectingEvent/components/verbatim/FieldNumber.vue

@@ -1,12 +1,16 @@
 <template>
   <div class="field label-above">
-    <label>Trip identifier</label>
+    <label>Field number</label>
     <textarea
       class="full_width"
       type="text"
       rows="3"
-      v-model="collectingEvent.verbatim_trip_identifier"
-      @change="() => { collectingEvent.isUnsaved = true }"
+      v-model="collectingEvent.verbatim_field_number"
+      @change="
+        () => {
+          collectingEvent.isUnsaved = true
+        }
+      "
     />
   </div>
 </template>

app/javascript/vue/components/Form/FormCollectingEvent/const/components.js

@@ -8,7 +8,7 @@ import Latitude from '../components/verbatim/Latitude.vue'
 import Locality from '../components/verbatim/Locality.vue'
 import Longitude from '../components/verbatim/Longitude.vue'
 import Method from '../components/verbatim/Method.vue'
-import TripIdentifier from '../components/verbatim/TripIdentifier.vue'
+import FieldNumber from '../components/verbatim/FieldNumber.vue'
 import Dates from '../components/parsed/Dates.vue'
 import Elevation from '../components/parsed/Elevation.vue'
 import GeographicArea from '../components/parsed/GeographicArea.vue'
@@ -36,7 +36,7 @@ const ComponentVerbatim = {
   Datum: 'Datum',
   Collectors: 'Collectors',
   Method: 'Method',
-  TripIdentifier: 'TripIdentifier'
+  FieldNumber: 'FieldNumber'
 }
 
 const ComponentParse = {
@@ -70,7 +70,7 @@ const VueComponents = {
   [ComponentVerbatim.VerbatimElevation]: VerbatimElevation,
   [ComponentVerbatim.Datum]: Datum,
   [ComponentVerbatim.Method]: Method,
-  [ComponentVerbatim.TripIdentifier]: TripIdentifier,
+  [ComponentVerbatim.FieldNumber]: FieldNumber,
   [ComponentParse.Dates]: Dates,
   [ComponentParse.Elevation]: Elevation,
   [ComponentParse.GeographicArea]: GeographicArea,

app/javascript/vue/components/Form/FormCollectingEvent/helpers/verbatimProperties.js

@@ -9,5 +9,5 @@ export const verbatimProperties = {
   DateComponent: 'verbatim_date',
   Collectors: 'verbatim_collectors',
   Method: 'verbatim_method',
-  TripIdentifier: 'verbatim_trip_identifier'
+  FieldNumber: 'verbatim_field_number'
 }

app/javascript/vue/components/radials/ce/components/VerbatimSlice.vue

@@ -86,7 +86,7 @@ const VERBATIM_FIELDS = {
   verbatim_datum: 'input',
   verbatim_collectors: 'textarea',
   verbatim_method: 'input',
-  verbatim_trip_identifier: 'input'
+  verbatim_field_number: 'input'
 }
 
 const props = defineProps({

app/javascript/vue/components/ui/Autocomplete.vue

@@ -13,26 +13,27 @@ headers to be used in the call. Using it will override the common headers
 <template>
   <div class="vue-autocomplete">
     <input
-      :id="inputId"
+      type="text"
       ref="autofocus"
+      :id="inputId"
       :style="inputStyle"
-      class="vue-autocomplete-input normal-input"
-      type="text"
       :placeholder="placeholder"
-      @input="checkTime(), sendType()"
+      :autofocus="autofocus"
+      :disabled="disabled"
       v-model="type"
       v-bind="inputAttributes"
+      autocomplete="off"
+      :class="[
+        'vue-autocomplete-input normal-input',
+        spinner && 'ui-autocomplete-loading',
+        !spinner && 'vue-autocomplete-input-search',
+        inputClass
+      ]"
+      @input="checkTime(), sendType()"
       @keydown.down="downKey"
       @keydown.up="upKey"
       @keydown.enter="enterKey"
       @keyup="sendKeyEvent"
-      autocomplete="off"
-      :autofocus="autofocus"
-      :disabled="disabled"
-      :class="{
-        'ui-autocomplete-loading': spinner,
-        'vue-autocomplete-input-search': !spinner
-      }"
     />
     <ul
       class="vue-autocomplete-list"
@@ -166,6 +167,11 @@ export default {
       default: 'value'
     },
 
+    inputClass: {
+      type: Array,
+      default: () => []
+    },
+
     inputStyle: {
       type: Object,
       default: () => ({})

app/javascript/vue/constants/modelTypes.js

@@ -33,6 +33,7 @@ export const LOAN = 'Loan'
 export const LOT = 'Lot'
 export const NOTE = 'Note'
 export const OBSERVATION = 'Observation'
+export const OBSERVATION_MATRIX = 'ObservationMatrix'
 export const OTU = 'Otu'
 export const PEOPLE = 'People'
 export const PERSON = 'Person'

app/javascript/vue/factory/CollectingEvent.js

@@ -10,7 +10,7 @@ export default () => ({
   verbatim_longitude: undefined,
   verbatim_latitude: undefined,
   verbatim_geolocation_uncertainty: undefined,
-  verbatim_trip_identifier: undefined,
+  verbatim_field_number: undefined,
   verbatim_collectors: undefined,
   verbatim_method: undefined,
   verbatim_habitat: undefined,

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

@@ -14,7 +14,7 @@ const permitParams = {
     verbatim_longitude: String,
     verbatim_latitude: String,
     verbatim_geolocation_uncertainty: String,
-    verbatim_trip_identifier: String,
+    verbatim_field_number: String,
     verbatim_collectors: String,
     verbatim_method: String,
     geographic_area_id: String,

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

@@ -5,7 +5,8 @@ const controller = 'observation_matrices'
 const permitParams = {
   observation_matrix: {
     name: String,
-    otu_id: Array
+    otu_id: Number,
+    is_public: Boolean
   }
 }
 

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

@@ -1,10 +1,13 @@
-import baseCRUD, {annotations} from './base'
+import baseCRUD from './base'
+import { ajaxCall } from '@/helpers'
 
 const controller = 'observation_matrix_columns'
 const permitParams = {
   observation_matrix_column: Object
 }
 
 export const ObservationMatrixColumn = {
-  ...baseCRUD(controller, permitParams)
+  ...baseCRUD(controller, permitParams),
+
+  sort: (ids) => ajaxCall('patch', `/${controller}/sort`, { ids })
 }

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

@@ -1,10 +1,13 @@
 import baseCRUD, { annotations } from './base'
+import { ajaxCall } from '@/helpers'
 
 const permitParams = {
   observation_matrix_row: Object
 }
 
 export const ObservationMatrixRow = {
   ...baseCRUD('observation_matrix_rows', permitParams),
-  ...annotations('observation_matrix_rows')
+  ...annotations('observation_matrix_rows'),
+
+  sort: (ids) => ajaxCall('patch', '/observation_matrix_rows/sort', { ids })
 }

app/javascript/vue/shared/Filter/constants/collectingEvent.js

@@ -8,7 +8,7 @@ export const COLLECTING_EVENT_PROPERTIES = [
   'verbatim_longitude',
   'verbatim_latitude',
   'verbatim_geolocation_uncertainty',
-  'verbatim_trip_identifier',
+  'verbatim_field_number',
   'verbatim_collectors',
   'verbatim_method',
   'geographic_area_id',

app/javascript/vue/tasks/biological_associations/biological_associations_graph/components/ModalGraph.vue

@@ -26,7 +26,7 @@
 </template>
 
 <script setup>
-import { ref, onMounted } from 'vue'
+import { ref, nextTick, onMounted } from 'vue'
 import VModal from '@/components/ui/Modal.vue'
 import VBtn from '@/components/ui/VBtn/index.vue'
 
@@ -47,6 +47,8 @@ function handleUpdateName() {
 }
 
 onMounted(() => {
-  inputName.value.focus()
+  nextTick(() => {
+    inputName.value.focus()
+  })
 })
 </script>