John conroy/publication collection aggs HMP-270

CHANGELOG-publication-collection-aggs.md

@@ -0,0 +1 @@
+- Get publication summary data types and organs from associated collection if applicable.

context/app/static/js/components/publications/AggsList/AggsList.jsx

@@ -2,10 +2,14 @@ import React from 'react';
 
 import BulletedList from 'js/shared-styles/lists/bulleted-lists/BulletedList';
 import BulletedListItem from 'js/shared-styles/lists/bulleted-lists/BulletedListItem';
-import { useAncestorSearchAggs } from './hooks';
+import { usePublicationDatasetsAggs } from './hooks';
 
-function AggsList({ uuid, field }) {
-  const { searchData } = useAncestorSearchAggs(uuid, field);
+function AggsList({ uuid, field, associatedCollectionUUID }) {
+  const { searchData } = usePublicationDatasetsAggs({
+    descendantUUID: uuid,
+    aggsField: field,
+    associatedCollectionUUID,
+  });
 
   const buckets = searchData?.aggregations?.[field]?.buckets;
 

context/app/static/js/components/publications/AggsList/hooks.js

@@ -1,26 +1,46 @@
-import { useMemo } from 'react';
+import useSearchData, { useSearchHits } from 'js/hooks/useSearchData';
+import { getAncestorsQuery, getIDsQuery } from 'js/helpers/queries';
 
-import useSearchData from 'js/hooks/useSearchData';
-import { getAncestorsQuery } from 'js/helpers/queries';
-
-function useAncestorSearchAggs(descendantUUID, aggsField) {
-  const query = useMemo(
-    () => ({
-      query: getAncestorsQuery(descendantUUID, 'dataset'),
-      aggs: {
-        [aggsField]: {
-          terms: {
-            field: `${aggsField}.keyword`,
-            size: 10000,
-          },
+function getAggsClause(aggsField) {
+  return {
+    aggs: {
+      [aggsField]: {
+        terms: {
+          field: `${aggsField}.keyword`,
+          size: 10000,
         },
       },
-      size: 0,
-    }),
-    [aggsField, descendantUUID],
-  );
+    },
+    size: 0,
+  };
+}
+
+function getCollectionDatasetsQuery(collectionUUID) {
+  return {
+    query: getIDsQuery(collectionUUID),
+    _source: 'datasets.uuid',
+    size: 10000,
+  };
+}
+
+function usePublicationDatasetsAggs({ descendantUUID, aggsField, associatedCollectionUUID }) {
+  const { searchHits: collectionDatasets } = useSearchHits(getCollectionDatasetsQuery(associatedCollectionUUID));
+
+  const collectionDatasetsUUIDs =
+    // eslint-disable-next-line no-underscore-dangle
+    collectionDatasets.length > 0 ? collectionDatasets[0]?._source?.datasets.map(({ uuid }) => uuid) : [];
+
+  const query = associatedCollectionUUID
+    ? {
+        query: getIDsQuery(collectionDatasetsUUIDs),
+        ...getAggsClause(aggsField),
+      }
+    : {
+        query: getAncestorsQuery(descendantUUID, 'dataset'),
+        ...getAggsClause(aggsField),
+      };
 
   return useSearchData(query);
 }
 
-export { useAncestorSearchAggs };
+export { usePublicationDatasetsAggs };

context/app/static/js/components/publications/PublicationSummary/PublicationSummary.jsx

@@ -27,6 +27,7 @@ function PublicationSummary({
   hubmap_id,
   publication_date,
   publication_status: isPublished,
+  associatedCollectionUUID,
 }) {
   const hasDOI = Boolean(publication_doi);
   const doiURL = `https://doi.org/${publication_doi}`;
@@ -74,15 +75,19 @@ function PublicationSummary({
           childContainerComponent="div"
           data-testid="publication-data-types"
         >
-          <AggsList uuid={uuid} field="mapped_data_types" />
+          <AggsList uuid={uuid} field="mapped_data_types" associatedCollectionUUID={associatedCollectionUUID} />
         </LabelledSectionText>
         <LabelledSectionText
           label="Organs"
           bottomSpacing={2}
           childContainerComponent="div"
           data-testid="publication-organs"
         >
-          <AggsList uuid={uuid} field="mapped_organ" />
+          <AggsList
+            uuid={uuid}
+            field="origin_samples.mapped_organ"
+            associatedCollectionUUID={associatedCollectionUUID}
+          />
         </LabelledSectionText>
         <LabelledSectionText
           label={isPublished ? 'Publication Date' : 'Preprint Date'}

context/app/static/js/pages/Publication/Publication.jsx

@@ -52,7 +52,12 @@ function Publication({ publication, vignette_json }) {
 
   return (
     <DetailLayout sectionOrder={sectionOrder}>
-      <PublicationSummary {...publication} status={combinedStatus} hasDOI={hasDOI} />
+      <PublicationSummary
+        {...publication}
+        status={combinedStatus}
+        hasDOI={hasDOI}
+        associatedCollectionUUID={associatedCollectionUUID}
+      />
       <PublicationsDataSection
         uuid={uuid}
         datasetUUIDs={ancestor_ids}