Merge pull request #4212 from SpeciesFileGroup/filter_field_occurrences

Filter field occurrences

CHANGELOG.md

@@ -10,6 +10,10 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Added
 
 - Append mode to multi update data attributes task [#4204]
+<<<<<<< HEAD
+- <in progress Batch add/remove Protocols>
+- Protocol `is_machine_output` attribute to facilitate MachineObservation types
+=======
 - Sticky navbar on browse nomenclature and collecting event
 - Move button to citations and depiction slices in radial annotator
 - Freeze column checkbox to filter tasks [#4220]
@@ -18,6 +22,7 @@ This project <em>does not yet</em> adheres to [Semantic Versioning](https://semv
 ### Changed
 
 - Add total to unmatched panel on Nomenclature match task
+>>>>>>> development
 
 [#4204]: https://github.com/SpeciesFileGroup/taxonworks/pull/4204
 [#4219]: https://github.com/SpeciesFileGroup/taxonworks/pull/4219

app/controllers/protocol_relationships_controller.rb

@@ -90,6 +90,22 @@ def search
     end
   end
 
+  # POST
+  def batch_by_filter_scope
+    if r = ProtocolRelationship.batch_by_filter_scope(
+        mode: params[:mode] || :add,
+        filter_query: params.require(:filter_query), # like filter_query: { otu_query: {}}
+        protocol_id: params.require(:protocol_id),
+        replace_protocol_id: params[:replace_protocol_id]
+    )
+      render json: r.to_json, status: :ok
+    else
+      render json: {}, status: :unprocessable_entity
+    end
+  end
+
+
+
   private
 
   def set_protocol_relationship

app/controllers/protocols_controller.rb

@@ -112,6 +112,6 @@ def set_protocol
   end
 
   def protocol_params
-    params.require(:protocol).permit(:name, :short_name, :description)
+    params.require(:protocol).permit(:name, :short_name, :description, :is_machine_output)
   end
 end

app/controllers/tasks/field_occurrences/filter_controller.rb

@@ -0,0 +1,4 @@
+class Tasks::FieldOccurrences::FilterController < ApplicationController
+  include TaskControllerConfiguration
+
+end

app/javascript/packs/application.js

@@ -120,3 +120,4 @@ import '../vue/tasks/biological_associations/new/main.js'
 import '../vue/tasks/otus/duplicates/main.js'
 import '../vue/tasks/field_occurrences/browse/main.js'
 import '../vue/tasks/data_attributes/multi_update/main.js'
+import '../vue/tasks/field_occurrences/filter/main.js'

app/javascript/vue/components/Filter/Facets/CollectionObject/FacetBiocurations.vue

@@ -30,7 +30,7 @@
 </template>
 
 <script setup>
-import { computed, ref, onBeforeMount } from 'vue'
+import { computed, ref, onBeforeMount, watch } from 'vue'
 import { ControlledVocabularyTerm } from '@/routes/endpoints'
 import { URLParamsToJSON } from '@/helpers/url/parse.js'
 import FacetContainer from '@/components/Filter/Facets/FacetContainer.vue'
@@ -61,4 +61,13 @@ onBeforeMount(() => {
     }
   )
 })
+
+watch(
+  () => params.value.biocuration_class_id,
+  (newVal) => {
+    if (!newVal) {
+      params.value.biocuration_class_id = []
+    }
+  }
+)
 </script>

app/javascript/vue/components/radials/filter/constants/filterLinks.js

@@ -10,6 +10,10 @@ export const FILTER_EXTRACT = {
   label: 'Extracts',
   link: '/tasks/extracts/filter'
 }
+export const FILTER_FIELD_OCCURRENCE = {
+  label: 'Field occurrences',
+  link: '/tasks/field_occurrences/filter'
+}
 export const FILTER_OTU = {
   label: 'OTUs',
   link: '/tasks/otus/filter'

app/javascript/vue/components/radials/filter/constants/idParams.js

@@ -8,6 +8,7 @@ import {
   DESCRIPTOR,
   DWC_OCCURRENCE,
   EXTRACT,
+  FIELD_OCCURRENCE,
   IMAGE,
   LOAN,
   OBSERVATION,
@@ -27,6 +28,7 @@ export const ID_PARAM_FOR = {
   [DESCRIPTOR]: 'descriptor_id',
   [DWC_OCCURRENCE]: 'dwc_occurrence_id',
   [EXTRACT]: 'extract_id',
+  [FIELD_OCCURRENCE]: 'field_occurrence_id',
   [IMAGE]: 'image_id',
   [LOAN]: 'loan_id',
   [OBSERVATION]: 'observation_id',

app/javascript/vue/components/radials/filter/constants/queryParam.js

@@ -5,6 +5,7 @@ import {
   COLLECTION_OBJECT,
   DESCRIPTOR,
   EXTRACT,
+  FIELD_OCCURRENCE,
   IMAGE,
   OTU,
   PEOPLE,
@@ -24,6 +25,7 @@ export const QUERY_PARAM = {
   [DESCRIPTOR]: 'descriptor_query',
   [DWC_OCCURRENCE]: 'dwc_occurrence_query',
   [EXTRACT]: 'extract_query',
+  [FIELD_OCCURRENCE]: 'field_occurrence_query',
   [IMAGE]: 'image_query',
   [OTU]: 'otu_query',
   [SOURCE]: 'source_query',

app/javascript/vue/components/radials/filter/links/BiologicalAssociation.js

@@ -4,7 +4,8 @@ import {
   FILTER_COLLECTION_OBJECT,
   FILTER_OTU,
   FILTER_SOURCE,
-  FILTER_TAXON_NAME
+  FILTER_TAXON_NAME,
+  FILTER_FIELD_OCCURRENCE
 } from '../constants/filterLinks'
 
 export const BiologicalAssociation = [
@@ -13,5 +14,6 @@ export const BiologicalAssociation = [
   FILTER_COLLECTION_OBJECT,
   FILTER_OTU,
   FILTER_SOURCE,
-  FILTER_TAXON_NAME
+  FILTER_TAXON_NAME,
+  FILTER_FIELD_OCCURRENCE
 ]

app/javascript/vue/components/radials/filter/links/CollectingEvent.js

@@ -2,19 +2,21 @@
 import {
   FILTER_BIOLOGICAL_ASSOCIATION,
   FILTER_COLLECTION_OBJECT,
+  FILTER_FIELD_OCCURRENCE,
   FILTER_OTU,
   FILTER_SOURCE,
   FILTER_TAXON_NAME,
   FILTER_IMAGE,
-  FILTER_DWC_OCCURRENCE,
+  FILTER_DWC_OCCURRENCE
 } from '../constants/filterLinks'
 
 export const CollectingEvent = [
   FILTER_BIOLOGICAL_ASSOCIATION,
   FILTER_COLLECTION_OBJECT,
+  FILTER_FIELD_OCCURRENCE,
   FILTER_OTU,
   FILTER_SOURCE,
   FILTER_TAXON_NAME,
   FILTER_IMAGE,
-  FILTER_DWC_OCCURRENCE,
+  FILTER_DWC_OCCURRENCE
 ]

app/javascript/vue/components/radials/filter/links/FieldOccurrence.js

@@ -0,0 +1,11 @@
+import {
+  FILTER_BIOLOGICAL_ASSOCIATION,
+  FILTER_COLLECTING_EVENT,
+  FILTER_OTU
+} from '../constants/filterLinks'
+
+export const FieldOccurrence = [
+  FILTER_BIOLOGICAL_ASSOCIATION,
+  FILTER_COLLECTING_EVENT,
+  FILTER_OTU
+]

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

@@ -11,6 +11,7 @@ import {
   FILTER_OBSERVATION,
   FILTER_SOURCE,
   FILTER_TAXON_NAME,
+  FILTER_FIELD_OCCURRENCE
 } from '../constants/filterLinks'
 
 export const Otu = [
@@ -21,9 +22,10 @@ export const Otu = [
   FILTER_CONTENT,
   FILTER_DESCRIPTOR,
   FILTER_EXTRACT,
+  FILTER_FIELD_OCCURRENCE,
   FILTER_IMAGE,
   FILTER_LOAN,
   FILTER_OBSERVATION,
   FILTER_SOURCE,
-  FILTER_TAXON_NAME,
+  FILTER_TAXON_NAME
 ]

app/javascript/vue/components/radials/filter/links/index.js

@@ -6,6 +6,7 @@ export * from './Content'
 export * from './Descriptor'
 export * from './DwcOccurrence'
 export * from './Extract'
+export * from './FieldOccurrence'
 export * from './Image'
 export * from './Loan'
 export * from './Observation'

app/javascript/vue/components/radials/mass/components/Annotator/Confidence/ConfidenceMain.vue

@@ -51,6 +51,7 @@
 import { ref, onBeforeMount, shallowRef } from 'vue'
 import { ControlledVocabularyTerm, Confidence } from '@/routes/endpoints'
 import { ID_PARAM_FOR } from '@/components/radials/filter/constants/idParams.js'
+import { QUERY_PARAM } from '@/components/radials/filter/constants/queryParam'
 import { CONFIDENCE_LEVEL } from '@/constants'
 import ConfidenceList from './ConfidenceList.vue'
 import ConfirmationModal from '@/components/ConfirmationModal.vue'
@@ -134,7 +135,9 @@ function makePayload(confidence) {
   return {
     mode: selectedMode.value.mode,
     confidence_level_id: confidence.id,
-    filter_query: props.parameters
+    filter_query: {
+      [QUERY_PARAM[props.objectType]]: props.parameters
+    }
   }
 }
 
@@ -143,7 +146,9 @@ function makeReplacePayload([replace, to]) {
     mode: selectedMode.value.mode,
     confidence_level_id: to.id,
     replace_confidence_level_id: replace.id,
-    filter_query: props.parameters
+    filter_query: {
+      [QUERY_PARAM[props.objectType]]: props.parameters
+    }
   }
 }
 </script>

app/javascript/vue/components/radials/mass/components/Annotator/Protocol/ProtocolList.vue

@@ -0,0 +1,34 @@
+<template>
+  <div
+    color="create"
+    class="flex-wrap-row gap-small margin-large-top"
+  >
+    <VBtn
+      v-for="item in list"
+      :key="item.id"
+      :color="color"
+      medium
+      @click="() => emit('select', item)"
+    >
+      <span v-html="item.object_tag" />
+    </VBtn>
+  </div>
+</template>
+
+<script setup>
+import VBtn from '@/components/ui/VBtn/index.vue'
+
+defineProps({
+  color: {
+    type: String,
+    default: 'primary'
+  },
+
+  list: {
+    type: Array,
+    default: () => []
+  }
+})
+
+const emit = defineEmits(['select'])
+</script>