Merge branch 'release-deps' into dependabot/npm_and_yarn/sveltejs/kit…

…-2.11.1
hms-dbmi · Dec 19, 2024 · deead31 · deead31
2 parents 77354ce + d2cf110
commit deead31
Show file tree

Hide file tree

Showing 5 changed files with 141 additions and 110 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -20,7 +20,7 @@
     "@skeletonlabs/skeleton": "2.10.3",
     "@skeletonlabs/tw-plugin": "0.4.0",
     "@sveltejs/adapter-auto": "^3.2.4",
-    "@sveltejs/adapter-node": "^2.1.2",
+    "@sveltejs/adapter-node": "^5.2.10",
     "@sveltejs/kit": "^2.11.1",
     "@sveltejs/vite-plugin-svelte": "^3.1.0",
     "@tailwindcss/forms": "0.5.7",

diff --git a/src/lib/components/datatable/accessories/Rows.svelte b/src/lib/components/datatable/accessories/Rows.svelte
@@ -3,7 +3,7 @@
   import { DataHandler as RemoteHander } from '@vincjo/datatables/remote';
   export let handler: DataHandler | RemoteHander;
   export let options: number[] = [5, 10, 20, 50];
-  const rowsPerPage = handler.getRowsPerPage();
+  $: rowsPerPage = handler.getRowsPerPage();
   const setRowsPerPage = () => {
     handler.setPage(1);
     if (handler instanceof RemoteHander) {

diff --git a/src/lib/components/explorer/export/ExportStepper.svelte b/src/lib/components/explorer/export/ExportStepper.svelte
@@ -27,6 +27,7 @@
   import { branding, features, settings, resources } from '$lib/configuration';
   import { searchDictionary } from '$lib/services/dictionary';
   import type { ExportInterface } from '$lib/models/Export';
+  import { onMount } from 'svelte';
   export let query: QueryRequestInterface;
   export let showTreeStep = false;
   export let rows: ExportRowInterface[] = [];
@@ -42,6 +43,7 @@
   let sampleIds = false;
   let lastExports: ExportRowInterface[] = [];
   let loadingSampleIds = false;
+  let checkingSampleIds = false;
   $: datasetId = '';
   $: canDownload = true;
   $: apiExport = false;
@@ -51,6 +53,39 @@
     { dataElement: 'type', label: 'Type', sort: true },
   ];
 
+  onMount(async () => {
+    const exportedSampleIds = $exports.filter((e: ExportInterface) =>
+      e.conceptPath.includes('SAMPLE_ID'),
+    );
+    if (exportedSampleIds.length > 0) {
+      checkingSampleIds = true;
+      const genomicConcepts = await getGenomicConcepts();
+      if (genomicConcepts.length > 0) {
+        // Find sample IDs that match genomic concepts
+        const matchingSampleIds = exportedSampleIds.filter((sampleId) =>
+          genomicConcepts.some((concept) => concept.conceptPath === sampleId.conceptPath),
+        );
+        sampleIds = matchingSampleIds.length === genomicConcepts.length;
+        checkingSampleIds = false;
+        if (sampleIds) {
+          lastExports = matchingSampleIds.map((item) => ({
+            ref: item,
+            variableId: item.conceptPath,
+            variableName: item.display,
+            description: item.searchResult?.description,
+            type: item.searchResult?.type,
+            selected: true,
+          })) as ExportRowInterface[];
+        }
+      } else {
+        sampleIds = false;
+        checkingSampleIds = false;
+      }
+    } else {
+      sampleIds = false;
+    }
+  });
+
   const MAX_DATA_POINTS_FOR_EXPORT = settings.maxDataPointsForExport || 1000000;
 
   function openConfirmationModal() {
@@ -209,6 +244,40 @@
     return totalDataPoints > MAX_DATA_POINTS_FOR_EXPORT;
   }
 
+  async function getGenomicConcepts() {
+    const concepts = await searchDictionary(
+      '',
+      [
+        {
+          name: 'data_source_genomic',
+          category: 'data_source',
+          display: 'Genomic',
+          description: 'Associated with genomic data',
+          count: 0,
+        },
+      ],
+      { pageNumber: 0, pageSize: 10000 },
+    );
+
+    if (concepts.content.length === 0) {
+      return [];
+    }
+
+    // Get sample ID counts via cross counts query
+    const crossCountQuery = new Query(structuredClone(query.query));
+    crossCountQuery.expectedResultType = 'CROSS_COUNT';
+    const crossCountFields = concepts.content.map((concept) => concept.conceptPath);
+    crossCountQuery.setCrossCountFields(crossCountFields);
+
+    const crossCountResponse: Record<string, number> = await api.post('picsure/query/sync', {
+      query: crossCountQuery,
+      resourceUUID: resources.hpds,
+    });
+
+    // Filter and return only concepts with counts > 0
+    return concepts.content.filter((concept) => crossCountResponse[concept.conceptPath] > 0);
+  }
+
   async function toggleSampleIds() {
     try {
       loadingSampleIds = true;
@@ -217,72 +286,42 @@
           (e) => e.ref,
         ) as ExportInterface[];
         removeExports(exportsToRemove || []);
-        rows = rows.filter((r) => !lastExports.includes(r));
+        rows = rows.filter((r) => !lastExports.some((le) => le.variableId === r.variableId));
         return;
       }
 
-      // Get genomic concepts from dictionary
-      const concepts = await searchDictionary(
-        '',
-        [
-          {
-            name: 'data_source_genomic',
-            category: 'data_source',
-            display: 'Genomic',
-            description: 'Associated with genomic data',
-            count: 0,
-          },
-        ],
-        { pageNumber: 0, pageSize: 10000 },
-      );
-
-      if (concepts.content.length === 0) {
-        return;
-      }
-
-      // Get sample ID counts via cross counts query
-      const crossCountQuery = new Query(structuredClone(query.query));
-      crossCountQuery.expectedResultType = 'CROSS_COUNT';
-      const crossCountFields = concepts.content.map((concept) => concept.conceptPath);
-      crossCountQuery.setCrossCountFields(crossCountFields);
-
-      const crossCountResponse: Record<string, number> = await api.post('picsure/query/sync', {
-        query: crossCountQuery,
-        resourceUUID: resources.hpds,
-      });
-
-      // Filter to paths with counts > 0
-      const conceptPathsToAdd = Object.entries(crossCountResponse)
-        // eslint-disable-next-line @typescript-eslint/no-unused-vars
-        .filter(([_, count]) => count > 0)
-        .map(([path]) => path);
+      const genomicConcepts = await getGenomicConcepts();
 
-      // Create new exports for each path
-      const newExports = conceptPathsToAdd.map((path) => {
-        const concept = concepts.content.find((c) => c.conceptPath === path);
-        return {
-          id: uuidv4(),
-          searchResult: concept,
-          display: concept?.display || '',
-          conceptPath: concept?.conceptPath || '',
-        } as ExportInterface;
-      });
+      // Create new exports for each concept
+      const newExports = genomicConcepts.map(
+        (concept) =>
+          ({
+            id: uuidv4(),
+            searchResult: concept,
+            display: concept?.display || '',
+            conceptPath: concept?.conceptPath || '',
+          }) as ExportInterface,
+      );
 
       // Add exports and create corresponding rows
       addExports(newExports);
       const newRows = newExports.map(
         (e) =>
           ({
             ref: e,
-            variableId: e.id,
-            variableName: e.display,
+            variableId: e?.searchResult?.conceptPath,
+            variableName: e?.display,
             description: e?.searchResult?.description,
-            type: e?.searchResult.type,
+            type: e?.searchResult?.type,
             selected: true,
           }) as ExportRowInterface,
       );
-
-      rows = [...rows, ...newRows];
+      //Remove duplicates
+      rows = Array.from(
+        [...rows, ...newRows]
+          .reduce((map, row) => map.set(row.variableId, row), new Map())
+          .values(),
+      );
       lastExports = newRows;
     } catch (error) {
       console.error('Error in toggleSampleIds', error);
@@ -357,14 +396,18 @@
                   class="flex items-center"
                   data-testid="sample-ids-label"
                 >
-                  <input
-                    type="checkbox"
-                    class="mr-1 &[aria-disabled=“true”]:opacity-75"
-                    data-testid="sample-ids-checkbox"
-                    id="sample-ids-checkbox"
-                    bind:checked={sampleIds}
-                    on:change={toggleSampleIds}
-                  />
+                  {#if checkingSampleIds}
+                    <ProgressRadial width="w-4" />
+                  {:else}
+                    <input
+                      type="checkbox"
+                      class="mr-1 &[aria-disabled=“true”]:opacity-75"
+                      data-testid="sample-ids-checkbox"
+                      id="sample-ids-checkbox"
+                      bind:checked={sampleIds}
+                      on:change={toggleSampleIds}
+                    />
+                  {/if}
                   <span>Include sample identifiers</span>
                 </label>
               </div>

diff --git a/src/lib/stores/Export.ts b/src/lib/stores/Export.ts
@@ -6,7 +6,7 @@ const exports: Writable<ExportInterface[]> = writable([]);
 
 function addExport(exportedField: ExportInterface) {
   const currentExports = get(exports);
-  if (currentExports.some((e: ExportInterface) => e.id === exportedField.id)) {
+  if (currentExports.some((e: ExportInterface) => e.conceptPath === exportedField.conceptPath)) {
     return;
   }
   exports.set([...currentExports, exportedField]);
@@ -16,7 +16,8 @@ function addExport(exportedField: ExportInterface) {
 function addExports(exportedFields: ExportInterface[]) {
   const currentExports = get(exports);
   const newExports = exportedFields.filter(
-    (e: ExportInterface) => !currentExports.some((ce: ExportInterface) => ce.id === e.id),
+    (e: ExportInterface) =>
+      !currentExports.some((ce: ExportInterface) => ce.conceptPath === e.conceptPath),
   );
   exports.set([...currentExports, ...newExports]);
 }
@@ -32,7 +33,11 @@ function removeExport(uuid: string) {
 
 function removeExports(exportsToRemove: ExportInterface[]) {
   const currentExports = get(exports);
-  exports.set(currentExports.filter((e: ExportInterface) => !exportsToRemove.includes(e)));
+  exports.set(
+    currentExports.filter(
+      (e: ExportInterface) => !exportsToRemove.some((re) => re.conceptPath === e.conceptPath),
+    ),
+  );
 }
 
 export function clearExports() {