Merge branch 'dev' into 35416-Add-Quality-Contol-table-to-MolecularAn…

…alysisRun-view
AAFC-BICoE · Dec 18, 2024 · 7e566a3 · 7e566a3
2 parents 7e3f031 + 52968b0
commit 7e566a3
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Showing 14 changed files with 415 additions and 127 deletions.
diff --git a/packages/common-ui/lib/list-page/useElasticSearchDistinctTerm.tsx b/packages/common-ui/lib/list-page/useElasticSearchDistinctTerm.tsx
@@ -1,50 +1,57 @@
 import Bodybuilder from "bodybuilder";
-import { castArray } from "lodash";
+import { castArray, pick } from "lodash";
 import { useEffect, useState } from "react";
 import { useApiClient, useQueryBuilderContext } from "..";
-
 const TOTAL_SUGGESTIONS: number = 100;
 const FILTER_AGGREGATION_NAME: string = "included_type_filter";
 const AGGREGATION_NAME: string = "term_aggregation";
 const NEST_AGGREGATION_NAME: string = "included_aggregation";
-
 interface QuerySuggestionFieldProps {
   /** The string you want elastic search to use. */
   fieldName?: string;
-
   /** If the field is a relationship, we need to know the type to filter it. */
   relationshipType?: string;
-
   /** The index you want elastic search to perform the search on */
   indexName: string;
-
   /** Used to determine if ".keyword" should be appended to the field name.  */
   keywordMultiFieldSupport: boolean;
-}
 
+  /** Used to determine if field is an array in the back end.  */
+  isFieldArray?: boolean;
+
+  /** User input used to query against */
+  inputValue?: string;
+
+  /** Group to be queried to only show the users most used values. */
+  groupNames?: string[];
+
+  /** Number of suggestions */
+  size?: number;
+}
 export function useElasticSearchDistinctTerm({
   fieldName,
   relationshipType,
   indexName,
-  keywordMultiFieldSupport
+  keywordMultiFieldSupport,
+  isFieldArray = false,
+  inputValue,
+  groupNames,
+  size
 }: QuerySuggestionFieldProps) {
   const { apiClient } = useApiClient();
-
   const [suggestions, setSuggestions] = useState<string[]>([]);
-
-  const { groups } = useQueryBuilderContext();
-
+  const { groups } = groupNames
+    ? { groups: groupNames }
+    : useQueryBuilderContext();
   // Every time the textEntered has changed, perform a new request for new suggestions.
   useEffect(() => {
     if (!fieldName) return;
     queryElasticSearchForSuggestions();
-  }, [fieldName, relationshipType, groups]);
-
+  }, [fieldName, relationshipType, groups, inputValue]);
   async function queryElasticSearchForSuggestions() {
     // Use bodybuilder to generate the query to send to elastic search.
     const builder = Bodybuilder();
     builder.size(0);
-
     // Group needs to be queried to only show the users most used values.
     if (groups && groups.length !== 0) {
       // terms is used to be able to support multiple groups.
@@ -54,7 +61,6 @@ export function useElasticSearchDistinctTerm({
         castArray(groups)
       );
     }
-
     // If the field has a relationship type, we need to do a nested query to filter it.
     if (relationshipType) {
       builder.aggregation(
@@ -83,16 +89,27 @@ export function useElasticSearchDistinctTerm({
       );
     } else {
       // If it's an attribute, no need to use nested filters.
-      builder.aggregation(
-        "terms",
-        fieldName + (keywordMultiFieldSupport ? ".keyword" : ""),
-        {
-          size: TOTAL_SUGGESTIONS
-        },
-        AGGREGATION_NAME
-      );
+      if (isFieldArray) {
+        builder.aggregation(
+          "terms",
+          fieldName + (keywordMultiFieldSupport ? ".keyword" : ""),
+          {
+            size: size ?? TOTAL_SUGGESTIONS,
+            include: `.*${inputValue}.*`
+          },
+          AGGREGATION_NAME
+        );
+      } else {
+        builder.aggregation(
+          "terms",
+          fieldName + (keywordMultiFieldSupport ? ".keyword" : ""),
+          {
+            size: TOTAL_SUGGESTIONS
+          },
+          AGGREGATION_NAME
+        );
+      }
     }
-
     await apiClient.axios
       .post(`search-api/search-ws/search`, builder.build(), {
         params: {
@@ -115,9 +132,7 @@ export function useElasticSearchDistinctTerm({
           }
           return undefined;
         };
-
         let suggestionArray: string[] | undefined;
-
         // The path to the results in the response changes if it contains the nested aggregation.
         if (relationshipType) {
           suggestionArray = findTermAggregationKey(
@@ -136,7 +151,6 @@ export function useElasticSearchDistinctTerm({
             AGGREGATION_NAME
           )?.buckets?.map((bucket) => bucket.key);
         }
-
         if (suggestionArray !== undefined) {
           setSuggestions(suggestionArray);
         } else {
@@ -149,6 +163,5 @@ export function useElasticSearchDistinctTerm({
         setSuggestions([]);
       });
   }
-
   return suggestions;
 }
diff --git a/packages/dina-ui/components/collection/collecting-event/CollectingEventFormLayout.tsx b/packages/dina-ui/components/collection/collecting-event/CollectingEventFormLayout.tsx
@@ -15,6 +15,7 @@ import {
   StringArrayField,
   TextField,
   TextFieldWithCoordButtons,
+  Tooltip,
   filterBy,
   useDinaFormContext,
   useInstanceContext
@@ -32,7 +33,8 @@ import {
   NotPubliclyReleasableWarning,
   ParseVerbatimToRangeButton,
   PersonSelectField,
-  TagsAndRestrictionsSection
+  TagsAndRestrictionsSection,
+  TagSelectReadOnly
 } from "../..";
 import { ManagedAttributesEditor } from "../../";
 import { DinaMessage, useDinaIntl } from "../../../intl/dina-ui-intl";
@@ -602,7 +604,20 @@ export function CollectingEventFormLayout({
         sectionName="general-section"
       >
         <NotPubliclyReleasableWarning />
-        <TagsAndRestrictionsSection resourcePath="collection-api/collecting-event" />
+        {readOnly ? (
+          <TagSelectReadOnly />
+        ) : (
+          <Tooltip
+            id="collecting_event_tag_info"
+            disableSpanMargin={true}
+            visibleElement={
+              <TagsAndRestrictionsSection
+                resourcePath="collection-api/collecting-event"
+                indexName="dina_material_sample_index"
+              />
+            }
+          />
+        )}
       </DinaFormSection>
       <div className="row mb-3">
         <div className="col-md-12">

diff --git a/packages/dina-ui/components/collection/material-sample/MaterialSampleForm.tsx b/packages/dina-ui/components/collection/material-sample/MaterialSampleForm.tsx
@@ -472,7 +472,10 @@ export function MaterialSampleForm({
                   <CollectionSelectSection resourcePath="collection-api/collection" />
                   <ProjectSelectSection resourcePath="collection-api/project" />
                   <AssemblageSelectSection resourcePath="collection-api/assemblage" />
-                  <TagsAndRestrictionsSection resourcePath="collection-api/material-sample" />
+                  <TagsAndRestrictionsSection
+                    resourcePath="collection-api/material-sample"
+                    indexName="dina_material_sample_index"
+                  />
                 </div>
                 <div className="col-md-4">
                   <NotPubliclyReleasableSection />

diff --git a/...ges/dina-ui/components/molecular-analysis/useMetagenomicsWorkflowMolecularAnalysisRun.tsx b/...ges/dina-ui/components/molecular-analysis/useMetagenomicsWorkflowMolecularAnalysisRun.tsx
@@ -234,9 +234,14 @@ export function useMetagenomicsWorkflowMolecularAnalysisRun({
   const { bulkGet, save } = useApiClient();
   const { formatMessage } = useDinaIntl();
   const { compareByStringAndNumber } = useStringComparator();
+  // Map of MolecularAnalysisRunItem {id:name}
+  const [molecularAnalysisRunItemNames, setMolecularAnalysisRunItemNames] =
+    useState<Record<string, string>>({});
   const columns = getMolecularAnalysisRunColumns(
     compareByStringAndNumber,
-    "metagenomics-batch-item"
+    "metagenomics-batch-item",
+    setMolecularAnalysisRunItemNames,
+    !editMode
   );
 
   // Used to display if the network calls are still in progress.
@@ -253,8 +258,13 @@ export function useMetagenomicsWorkflowMolecularAnalysisRun({
   const [sequencingRunItems, setSequencingRunItems] =
     useState<SequencingRunItem[]>();
 
+  // Used to determine if the resource needs to be reloaded.
+  const [reloadResource, setReloadResource] = useState<number>(Date.now());
+
   // Network Requests, starting with the SeqReaction
-  useQuery<MetagenomicsBatchItem[]>(
+  const { loading: loadingMetagenomicsBatchItems } = useQuery<
+    MetagenomicsBatchItem[]
+  >(
     {
       filter: filterBy([], {
         extraFilters: [
@@ -271,6 +281,7 @@ export function useMetagenomicsWorkflowMolecularAnalysisRun({
         "indexI5,indexI7,pcrBatchItem,molecularAnalysisRunItem,molecularAnalysisRunItem.run"
     },
     {
+      deps: [reloadResource],
       onSuccess: async ({ data: metagenomicsBatchItems }) => {
         /**
          * Go through each of the MetagenomicsBatchItems and retrieve the Molecular Analysis Run. There
@@ -390,21 +401,29 @@ export function useMetagenomicsWorkflowMolecularAnalysisRun({
 
       // Create a MolecularAnalysisRunitem for each MetagenomicsBatchItem.
       const molecularAnalysisRunItemSaveArgs: SaveArgs<MolecularAnalysisRunItem>[] =
-        sequencingRunItems.map(() => ({
-          type: "molecular-analysis-run-item",
-          resource: {
+        sequencingRunItems.map((item) => {
+          const molecularAnalysisRunItemName = item.materialSampleSummary?.id
+            ? molecularAnalysisRunItemNames[item.materialSampleSummary?.id]
+            : undefined;
+          return {
             type: "molecular-analysis-run-item",
-            usageType: "metagenomics-batch-item",
-            relationships: {
-              run: {
-                data: {
-                  id: savedMolecularAnalysisRun[0].id,
-                  type: "molecular-analysis-run"
+            resource: {
+              type: "molecular-analysis-run-item",
+              usageType: "metagenomics-batch-item",
+              ...(molecularAnalysisRunItemName && {
+                name: molecularAnalysisRunItemName
+              }),
+              relationships: {
+                run: {
+                  data: {
+                    id: savedMolecularAnalysisRun[0].id,
+                    type: "molecular-analysis-run"
+                  }
                 }
               }
-            }
-          } as any
-        }));
+            } as any
+          };
+        });
       const savedMolecularAnalysisRunItem = await save(
         molecularAnalysisRunItemSaveArgs,
         { apiBaseUrl: "/seqdb-api" }
@@ -481,10 +500,37 @@ export function useMetagenomicsWorkflowMolecularAnalysisRun({
         apiBaseUrl: "/seqdb-api"
       });
 
+      // Update existing MolecularAnalysisRunItem names
+      if (sequencingRunItems) {
+        const molecularAnalysisRunItemSaveArgs: SaveArgs<MolecularAnalysisRunItem>[] =
+          [];
+        sequencingRunItems.forEach((item) => {
+          const molecularAnalysisRunItemName = item.materialSampleSummary?.id
+            ? molecularAnalysisRunItemNames[item.materialSampleSummary?.id]
+            : undefined;
+          if (molecularAnalysisRunItemName) {
+            molecularAnalysisRunItemSaveArgs.push({
+              type: "molecular-analysis-run-item",
+              resource: {
+                id: item.molecularAnalysisRunItemId,
+                type: "molecular-analysis-run-item",
+                name: molecularAnalysisRunItemName
+              }
+            });
+          }
+        });
+        if (molecularAnalysisRunItemSaveArgs.length) {
+          await save(molecularAnalysisRunItemSaveArgs, {
+            apiBaseUrl: "/seqdb-api"
+          });
+        }
+      }
+
       // Go back to view mode once completed.
       setPerformSave(false);
       setEditMode(false);
       setLoading(false);
+      setReloadResource(Date.now());
     } catch (error) {
       console.error("Error updating sequencing run: ", error);
       setPerformSave(false);
@@ -527,7 +573,7 @@ export function useMetagenomicsWorkflowMolecularAnalysisRun({
   }, [performSave, loading]);
 
   return {
-    loading,
+    loading: loading || loadingMetagenomicsBatchItems,
     errorMessage,
     multipleRunWarning,
     sequencingRunName,