[FIX] sync curation extraction

compose/neurosynth-frontend/cypress/e2e/workflows/ingestion/Ingestion.cy.tsx

@@ -37,7 +37,7 @@ describe('Ingestion', () => {
             fixture: 'IngestionFixtures/annotationsPutFixture',
         }).as('annotationFixture');
 
-        cy.intercept('POST', `**/api/base-studies/`, {
+        cy.intercept('POST', '**/api/base-studies*', {
             fixture: 'IngestionFixtures/baseStudiesFixture',
         }).as('baseStudiesFixture');
     });

compose/neurosynth-frontend/src/helpers/Extraction.helpers.spec.ts

@@ -0,0 +1,43 @@
+import { describe, expect, it } from 'vitest';
+import { mapStubsToStudysetPayload } from './Extraction.helpers';
+import { BaseStudyReturn, StudyReturn } from 'neurostore-typescript-sdk';
+
+const makeBaseStudy = (id: string, versionIds: string[]): BaseStudyReturn => ({
+    id,
+    versions: versionIds.map<StudyReturn>((vid, idx) => ({
+        id: vid,
+        updated_at: idx.toString(), // for sorting fallback
+    })),
+});
+
+describe('mapStubsToStudysetPayload', () => {
+    it('zips stubs to base studies by index and carries stub UUIDs', () => {
+        const stubs = [{ id: 'stub-1' }, { id: 'stub-2' }];
+        const baseStudies: Array<BaseStudyReturn> = [makeBaseStudy('bs1', ['v1a']), makeBaseStudy('bs2', ['v2a'])];
+
+        const payload = mapStubsToStudysetPayload(stubs, baseStudies);
+        expect(payload).toEqual([
+            { id: 'v1a', curation_stub_uuid: 'stub-1' },
+            { id: 'v2a', curation_stub_uuid: 'stub-2' },
+        ]);
+    });
+
+    it('prefers an existing study ID when present', () => {
+        const stubs = [{ id: 'stub-1' }];
+        const existing = new Set<string>(['existing-id']);
+        const baseStudies: Array<BaseStudyReturn> = [makeBaseStudy('bs1', ['existing-id', 'new-id'])];
+
+        const payload = mapStubsToStudysetPayload(stubs, baseStudies, existing);
+        expect(payload[0]).toEqual({ id: 'existing-id', curation_stub_uuid: 'stub-1' });
+    });
+
+    it('returns the locked existing mapping even if ingest lacks that version', () => {
+        const stubs = [{ id: 'stub-1' }];
+        // ingest returned only a different version
+        const baseStudies: Array<BaseStudyReturn> = [makeBaseStudy('bs1', ['different-id'])];
+        const lockedMap = new Map<string, string>([['stub-1', 'existing-id']]);
+
+        const payload = mapStubsToStudysetPayload(stubs, baseStudies, undefined, lockedMap);
+        expect(payload[0]).toEqual({ id: 'existing-id', curation_stub_uuid: 'stub-1' });
+    });
+});

compose/neurosynth-frontend/src/helpers/Extraction.helpers.tsx

@@ -1,5 +1,6 @@
-import { StudyReturn, BaseStudy } from 'neurostore-typescript-sdk';
+import { StudyReturn, BaseStudy, BaseStudyReturn } from 'neurostore-typescript-sdk';
 import { lastUpdatedAtSortFn } from 'helpers/utils';
+import { ICurationStubStudy } from 'pages/Curation/Curation.types';
 
 export const selectBestBaseStudyVersion = (baseStudyVersions: Array<StudyReturn>) => {
     const sortedVersion = [...baseStudyVersions.sort(lastUpdatedAtSortFn)];
@@ -8,11 +9,50 @@ export const selectBestBaseStudyVersion = (baseStudyVersions: Array<StudyReturn>
 
 export const selectBestVersionsForStudyset = (baseStudies: Array<BaseStudy>): string[] => {
     const selectedVersions = baseStudies.map((baseStudy) => {
-        const studyVersion = selectBestBaseStudyVersion(
-            (baseStudy?.versions || []) as StudyReturn[]
-        );
+        const studyVersion = selectBestBaseStudyVersion((baseStudy?.versions || []) as StudyReturn[]);
         return studyVersion.id as string;
     });
 
     return selectedVersions;
 };
+
+type StubLike = Pick<ICurationStubStudy, 'id'>;
+
+export const mapStubsToStudysetPayload = (
+    stubs: Array<StubLike>,
+    stubBaseStudies: Array<BaseStudyReturn>,
+    existingStudyIds?: Set<string>,
+    lockedStubToStudyId?: Map<string, string>
+): Array<{ id: string; curation_stub_uuid: string }> => {
+    const payload: Array<{ id: string; curation_stub_uuid: string }> = [];
+
+    stubs.forEach((stub, idx) => {
+        const lockedStudyId = lockedStubToStudyId?.get(stub.id);
+        if (lockedStudyId) {
+            payload.push({
+                id: lockedStudyId,
+                curation_stub_uuid: stub.id,
+            });
+            return;
+        }
+
+        const stubBaseStudy = stubBaseStudies[idx];
+        if (!stubBaseStudy) return;
+
+        const versions = Array.isArray(stubBaseStudy.versions) ? (stubBaseStudy.versions as Array<StudyReturn>) : [];
+
+        // Prefer a version that already exists in the studyset
+        const foundVersion = versions.find((studyVersion) => existingStudyIds?.has(studyVersion.id || ''));
+
+        const chosenVersion = foundVersion || selectBestBaseStudyVersion(versions);
+
+        if (chosenVersion?.id) {
+            payload.push({
+                id: chosenVersion.id,
+                curation_stub_uuid: stub.id,
+            });
+        }
+    });
+
+    return payload;
+};

compose/neurosynth-frontend/src/hooks/__mocks__/index.ts

@@ -67,19 +67,6 @@ const useCreateMetaAnalysis = vi.fn().mockReturnValue({
     createMetaAnalysis: vi.fn().mockReturnValue(Promise.resolve()),
 });
 
-const useGetStudysets = vi.fn().mockReturnValue({
-    error: undefined,
-    isLoading: false,
-    isError: false,
-    data: {
-        metadata: {
-            total_count: 100,
-            unique_count: 100,
-        },
-        results: mockStudysets(),
-    },
-});
-
 const useCreateStudyset = vi.fn().mockReturnValue({
     // isLoading: false,
     // isError: false,
@@ -211,7 +198,6 @@ export {
     useGetFullText,
     useGetStudyById,
     useGetStudysetById,
-    useGetStudysets,
     useInputValidation,
     useIsMounted,
     useUpdateAnalysis,

compose/neurosynth-frontend/src/hooks/index.ts

@@ -29,7 +29,6 @@ import useGetStudysetById from './studysets/useGetStudysetById';
 import useCreateAnnotation from './analyses/useCreateAnnotation';
 import useCreateStudy from './studies/useCreateStudy';
 import useCreateProject from './projects/useCreateProject';
-import useGetStudysets from './studysets/useGetStudysets';
 import useDeleteStudyset from './studysets/useDeleteStudyset';
 import useGetBaseStudies from './studies/useGetBaseStudies';
 import useGetStudyById from './studies/useGetStudyById';
@@ -69,7 +68,6 @@ export {
     // META-ANALYSIS RESULTS
     useGetMetaAnalysisResultById,
     // STUDYSETS
-    useGetStudysets,
     useGetStudysetById,
     useCreateStudyset,
     useDeleteStudyset,

compose/neurosynth-frontend/src/hooks/projects/useCreateProject.tsx

@@ -8,7 +8,14 @@ const useCreateProject = () => {
     const queryClient = useQueryClient();
     const { enqueueSnackbar } = useSnackbar();
     return useMutation<AxiosResponse<ProjectReturn>, AxiosError, Project, unknown>(
-        (project) => API.NeurosynthServices.ProjectsService.projectsPost(project),
+        (project) =>
+            // Signature: projectsPost(sourceId?, copyAnnotations?, project)
+            // Explicitly pass `undefined` for the optional query params so the payload is treated as the body argument.
+            API.NeurosynthServices.ProjectsService.projectsPost(
+                undefined, // sourceId
+                undefined, // copyAnnotations
+                project
+            ),
         {
             onSuccess: () => {
                 // update queries

compose/neurosynth-frontend/src/hooks/studies/useGetBaseStudies.tsx

@@ -4,6 +4,21 @@ import API from 'utils/api';
 
 export const baseStudiesSearchHelper = (searchCriteria: Partial<SearchCriteria>) => {
     return API.NeurostoreServices.StudiesService.baseStudiesGet(
+        searchCriteria.isNested,
+        undefined, // year_min
+        undefined, // x
+        undefined, // y
+        undefined, // z
+        undefined, // radius
+        undefined, // year_max
+        undefined, // feature_filter
+        undefined, // pipeline_config
+        undefined, // feature_display
+        undefined, // semantic_search
+        undefined, // pipeline_config_id
+        undefined, // distance_threshold
+        undefined, // overall_cap
+        undefined, // feature_flatten
         searchCriteria.genericSearchStr || undefined,
         searchCriteria.sortBy === SortBy.RELEVANCE ? undefined : searchCriteria.sortBy,
         searchCriteria.pageOfResults,
@@ -14,6 +29,7 @@ export const baseStudiesSearchHelper = (searchCriteria: Partial<SearchCriteria>)
         searchCriteria.authorSearch || undefined,
         'group',
         searchCriteria.dataType === SearchDataType.ALL ? 'both' : searchCriteria.dataType,
+        undefined, // is_oa
         searchCriteria.journalSearch || undefined,
         searchCriteria.pmid,
         searchCriteria.doi,

compose/neurosynth-frontend/src/hooks/studysets/useCreateStudyset.tsx

@@ -6,7 +6,7 @@ import API from 'utils/api';
 const useCreateStudyset = () => {
     const queryClient = useQueryClient();
     return useMutation<AxiosResponse<StudysetReturn>, AxiosError, StudysetRequest, unknown>(
-        (studyset) => API.NeurostoreServices.StudySetsService.studysetsPost(studyset),
+        (studyset) => API.NeurostoreServices.StudySetsService.studysetsPost(undefined, undefined, undefined, studyset),
         {
             onSuccess: () => {
                 // update study

compose/neurosynth-frontend/src/hooks/studysets/useGetStudysetById.tsx

@@ -3,7 +3,8 @@ import { StudyReturn, StudysetReturn } from 'neurostore-typescript-sdk';
 import { useSnackbar } from 'notistack';
 import { useQuery } from 'react-query';
 import API from 'utils/api';
-import { STUDYSET_QUERY_STRING } from './useGetStudysets';
+
+export const STUDYSET_QUERY_STRING = 'studysets';
 
 const useGetStudysetById = (studysetId?: string, nested?: boolean) => {
     const { enqueueSnackbar } = useSnackbar();
@@ -17,7 +18,7 @@ const useGetStudysetById = (studysetId?: string, nested?: boolean) => {
         () => API.NeurostoreServices.StudySetsService.studysetsIdGet(studysetId || '', nested),
         {
             enabled: !!studysetId,
-            onError: (err) => {
+            onError: () => {
                 enqueueSnackbar('there was an error retrieving the studyset', { variant: 'error' });
             },
             select: (res) => {

compose/neurosynth-frontend/src/hooks/studysets/useUpdateStudyset.tsx

@@ -15,18 +15,14 @@ const useUpdateStudyset = () => {
             studyset: StudysetRequest;
         },
         unknown
-    >(
-        (args) =>
-            API.NeurostoreServices.StudySetsService.studysetsIdPut(args.studysetId, args.studyset),
-        {
-            onSuccess: () => {
-                queryClient.invalidateQueries('studysets');
-            },
-            onError: () => {
-                enqueueSnackbar('there was an error updating the studyset', { variant: 'error' });
-            },
-        }
-    );
+    >((args) => API.NeurostoreServices.StudySetsService.studysetsIdPut(args.studysetId, args.studyset), {
+        onSuccess: () => {
+            queryClient.invalidateQueries('studysets');
+        },
+        onError: () => {
+            enqueueSnackbar('there was an error updating the studyset', { variant: 'error' });
+        },
+    });
 };
 
 export default useUpdateStudyset;

compose/neurosynth-frontend/src/pages/Extraction/components/ExtractionOutOfSync.styles.ts

@@ -9,6 +9,7 @@ const ExtractionOutOfSyncStyles: Style = {
         marginBottom: '1rem',
         position: 'sticky',
         top: '1.5rem',
+        marginTop: '1rem',
         zIndex: 10,
     },
 };