feat: return source dataset count from source study apis (#324) (#330)

clevercanary · Jun 21, 2024 · d23a5b4 · d23a5b4
1 parent fbdd9f9
commit d23a5b4
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Showing 10 changed files with 182 additions and 108 deletions.
diff --git a/__tests__/api-atlases-id-source-studies-create.test.ts b/__tests__/api-atlases-id-source-studies-create.test.ts
@@ -6,7 +6,6 @@ import {
   HCAAtlasTrackerSourceStudy,
   PublicationInfo,
 } from "../app/apis/catalog/hca-atlas-tracker/common/entities";
-import { dbSourceStudyToApiSourceStudy } from "../app/apis/catalog/hca-atlas-tracker/common/utils";
 import { endPgPool, query } from "../app/services/database";
 import createHandler from "../pages/api/atlases/[atlasId]/source-studies/create";
 import {
@@ -52,7 +51,10 @@ import {
   resetDatabase,
 } from "../testing/db-utils";
 import { TestAtlas, TestUser } from "../testing/entities";
-import { withConsoleErrorHiding } from "../testing/utils";
+import {
+  expectSourceStudyToMatch,
+  withConsoleErrorHiding,
+} from "../testing/utils";
 
 jest.mock("../app/services/user-profile");
 jest.mock("../app/utils/pg-app-connect-config");
@@ -230,14 +232,14 @@ describe("/api/atlases/[atlasId]/source-studies/create", () => {
   });
 
   it("creates, validates, and returns source study entry for journal publication", async () => {
-    const newStudy = await testSuccessfulCreate(
+    const { dbStudy } = await testSuccessfulCreate(
       ATLAS_DRAFT,
       NEW_STUDY_DATA,
       PUBLICATION_NORMAL,
       HCA_ID_NORMAL,
       CELLXGENE_ID_NORMAL
     );
-    const validations = await getValidationsByEntityId(newStudy.id);
+    const validations = await getValidationsByEntityId(dbStudy.id);
     expect(validations).not.toHaveLength(0);
   });
 
@@ -358,7 +360,7 @@ describe("/api/atlases/[atlasId]/source-studies/create", () => {
     expect(validationsBefore).not.toHaveLength(0);
     expect(validationsBefore[0].atlas_ids).toHaveLength(1);
     expect(validationsBefore[0].atlas_ids[0]).toEqual(ATLAS_DRAFT.id);
-    const dbStudy = await testSuccessfulCreate(
+    const { dbStudy } = await testSuccessfulCreate(
       ATLAS_PUBLIC,
       NEW_STUDY_DRAFT_OK,
       PUBLICATION_DRAFT_OK,
@@ -374,7 +376,7 @@ describe("/api/atlases/[atlasId]/source-studies/create", () => {
   });
 
   it("adds and returns source study that already exists via preprint DOI", async () => {
-    const dbStudy = await testSuccessfulCreate(
+    const { dbStudy } = await testSuccessfulCreate(
       ATLAS_DRAFT,
       NEW_STUDY_PUBLIC_WITH_PREPRINT_PREPRINT,
       PUBLICATION_PUBLIC_WITH_PREPRINT,
@@ -385,7 +387,7 @@ describe("/api/atlases/[atlasId]/source-studies/create", () => {
   });
 
   it("adds and returns source study that already exists via journal DOI", async () => {
-    const dbStudy = await testSuccessfulCreate(
+    const { dbStudy } = await testSuccessfulCreate(
       ATLAS_DRAFT,
       NEW_STUDY_PUBLIC_WITH_JOURNAL_JOURNAL,
       PUBLICATION_PUBLIC_WITH_JOURNAL,
@@ -406,15 +408,17 @@ describe("/api/atlases/[atlasId]/source-studies/create", () => {
     expect(fooBefore).toBeNull();
     expect(barBefore).toBeNull();
 
-    const dbStudy = await testSuccessfulCreate(
+    const { apiStudy } = await testSuccessfulCreate(
       ATLAS_DRAFT,
       NEW_STUDY_WITH_NEW_SOURCE_DATASETS,
       null,
       null,
       CELLXGENE_ID_WITH_NEW_SOURCE_DATASETS
     );
 
-    const studyDatasets = await getStudySourceDatasets(dbStudy.id);
+    expect(apiStudy.sourceDatasetCount).toEqual(2);
+
+    const studyDatasets = await getStudySourceDatasets(apiStudy.id);
 
     expect(studyDatasets).toHaveLength(2);
 
@@ -448,7 +452,10 @@ async function testSuccessfulCreate(
   expectedPublication: PublicationInfo | null,
   expectedHcaId: string | null,
   expectedCellxGeneId: string | null
-): Promise<HCAAtlasTrackerDBSourceStudy> {
+): Promise<{
+  apiStudy: HCAAtlasTrackerSourceStudy;
+  dbStudy: HCAAtlasTrackerDBSourceStudy;
+}> {
   const res = await doCreateTest(USER_CONTENT_ADMIN, atlas, newData);
   expect(res._getStatusCode()).toEqual(201);
   const newStudy: HCAAtlasTrackerSourceStudy = res._getJSONData();
@@ -472,7 +479,10 @@ async function testSuccessfulCreate(
     expectedHcaId,
     expectedCellxGeneId
   );
-  return newStudyFromDb;
+  return {
+    apiStudy: newStudy,
+    dbStudy: newStudyFromDb,
+  };
 }
 
 async function testSuccessfulUnpublishedCreate(
@@ -528,5 +538,5 @@ function expectDbStudyToMatch(
   expect(dbStudy.study_info.publication).toEqual(publication);
   expect(dbStudy.study_info.hcaProjectId).toEqual(hcaId);
   expect(dbStudy.study_info.cellxgeneCollectionId).toEqual(cellxgeneId);
-  expect(dbSourceStudyToApiSourceStudy(dbStudy)).toEqual(apiStudy);
+  expectSourceStudyToMatch(dbStudy, apiStudy);
 }
diff --git a/__tests__/api-atlases-id-source-studies-id.test.ts b/__tests__/api-atlases-id-source-studies-id.test.ts
@@ -6,7 +6,6 @@ import {
   HCAAtlasTrackerDBSourceStudy,
   HCAAtlasTrackerSourceStudy,
 } from "../app/apis/catalog/hca-atlas-tracker/common/entities";
-import { dbSourceStudyToApiSourceStudy } from "../app/apis/catalog/hca-atlas-tracker/common/utils";
 import { METHOD } from "../app/common/entities";
 import { endPgPool, query } from "../app/services/database";
 import studyHandler from "../pages/api/atlases/[atlasId]/source-studies/[sourceStudyId]";
@@ -38,6 +37,7 @@ import {
   TestUser,
 } from "../testing/entities";
 import {
+  expectSourceStudyToMatch,
   makeTestSourceStudyOverview,
   withConsoleErrorHiding,
 } from "../testing/utils";
@@ -288,7 +288,7 @@ describe("/api/atlases/[atlasId]/source-studies/[sourceStudyId]", () => {
     );
     expect(studyFromDb.study_info.hcaProjectId).toEqual(null);
     expect(studyFromDb.study_info.cellxgeneCollectionId).toEqual(null);
-    expect(dbSourceStudyToApiSourceStudy(studyFromDb)).toEqual(updatedStudy);
+    expectSourceStudyToMatch(studyFromDb, updatedStudy);
 
     const validationsAfter = await getValidationsByEntityId(
       SOURCE_STUDY_PUBLIC_NO_CROSSREF.id
@@ -369,6 +369,10 @@ describe("/api/atlases/[atlasId]/source-studies/[sourceStudyId]", () => {
     );
     expect(res._getStatusCode()).toEqual(200);
 
+    const updatedStudy = res._getJSONData() as HCAAtlasTrackerSourceStudy;
+
+    expect(updatedStudy.sourceDatasetCount).toEqual(4);
+
     const studyDatasetsAfter = await getStudySourceDatasets(
       SOURCE_STUDY_DRAFT_OK.id
     );

diff --git a/__tests__/api-atlases-id-source-studies.test.ts b/__tests__/api-atlases-id-source-studies.test.ts
@@ -20,6 +20,7 @@ import { TestPublishedSourceStudy, TestUser } from "../testing/entities";
 
 jest.mock("../app/services/user-profile");
 jest.mock("../app/services/hca-projects");
+jest.mock("../app/services/cellxgene");
 jest.mock("../app/utils/pg-app-connect-config");
 
 beforeAll(async () => {

diff --git a/app/apis/catalog/hca-atlas-tracker/common/entities.ts b/app/apis/catalog/hca-atlas-tracker/common/entities.ts
@@ -67,6 +67,7 @@ interface HCAAtlasTrackerSourceStudyCommon {
   doiStatus: DOI_STATUS;
   hcaProjectId: string | null;
   id: string;
+  sourceDatasetCount: number;
 }
 
 export interface HCAAtlasTrackerPublishedSourceStudy
@@ -231,6 +232,11 @@ export interface HCAAtlasTrackerDBUnpublishedSourceStudyInfo {
   unpublishedInfo: UnpublishedInfo;
 }
 
+export type HCAAtlasTrackerDBSourceStudyWithSourceDatasets =
+  HCAAtlasTrackerDBSourceStudy & {
+    source_dataset_count: number;
+  };
+
 export interface HCAAtlasTrackerDBSourceDataset {
   created_at: Date;
   id: string;

diff --git a/app/apis/catalog/hca-atlas-tracker/common/utils.ts b/app/apis/catalog/hca-atlas-tracker/common/utils.ts
@@ -8,6 +8,7 @@ import {
   HCAAtlasTrackerDBComponentAtlas,
   HCAAtlasTrackerDBSourceDatasetWithStudyProperties,
   HCAAtlasTrackerDBSourceStudy,
+  HCAAtlasTrackerDBSourceStudyWithSourceDatasets,
   HCAAtlasTrackerDBValidationWithAtlasProperties,
   HCAAtlasTrackerListAtlas,
   HCAAtlasTrackerListValidationRecord,
@@ -89,7 +90,7 @@ export function dbComponentAtlasToApiComponentAtlas(
 }
 
 export function dbSourceStudyToApiSourceStudy(
-  dbSourceStudy: HCAAtlasTrackerDBSourceStudy
+  dbSourceStudy: HCAAtlasTrackerDBSourceStudyWithSourceDatasets
 ): HCAAtlasTrackerSourceStudy {
   const {
     study_info: { capId, cellxgeneCollectionId, hcaProjectId, publication },
@@ -107,6 +108,7 @@ export function dbSourceStudyToApiSourceStudy(
       journal: null,
       publicationDate: null,
       referenceAuthor: unpublishedInfo.referenceAuthor,
+      sourceDatasetCount: dbSourceStudy.source_dataset_count,
       title: unpublishedInfo.title,
     };
   } else {
@@ -121,6 +123,7 @@ export function dbSourceStudyToApiSourceStudy(
       journal: publication?.journal ?? null,
       publicationDate: publication?.publicationDate ?? null,
       referenceAuthor: publication?.authors[0]?.name ?? null,
+      sourceDatasetCount: dbSourceStudy.source_dataset_count,
       title: publication?.title ?? null,
     };
   }
@@ -140,7 +143,7 @@ export function dbSourceDatasetToApiSourceDataset(
     disease: dbSourceDataset.sd_info.disease,
     doi: dbSourceDataset.doi,
     id: dbSourceDataset.id,
-    publicationString: getDbSourceDatasetCitation(dbSourceDataset),
+    publicationString: getDbEntityCitation(dbSourceDataset),
     sourceStudyId: dbSourceDataset.source_study_id,
     sourceStudyTitle:
       studyInfo.publication?.title ?? studyInfo.unpublishedInfo?.title ?? null,
@@ -186,19 +189,20 @@ export function getAtlasName(atlas: HCAAtlasTrackerAtlas): string {
 }
 
 /**
- * Returns the source dataset citation.
- * @param sourceDataset - Database model of source dataset with source study properties.
- * @returns Source dataset citation.
+ * Returns the entity's citation.
+ * @param entity - Database model of entity with source study properties.
+ * @returns citation for the associated source study.
  */
-function getDbSourceDatasetCitation(
-  sourceDataset: HCAAtlasTrackerDBSourceDatasetWithStudyProperties
+export function getDbEntityCitation(
+  entity:
+    | HCAAtlasTrackerDBSourceStudy
+    | HCAAtlasTrackerDBSourceDatasetWithStudyProperties
 ): string {
-  if (sourceDataset.doi === null) {
-    const { contactEmail, referenceAuthor } =
-      sourceDataset.study_info.unpublishedInfo;
+  if (entity.doi === null) {
+    const { contactEmail, referenceAuthor } = entity.study_info.unpublishedInfo;
     return getUnpublishedCitation(referenceAuthor, contactEmail);
   } else {
-    const studyInfo = sourceDataset.study_info;
+    const studyInfo = entity.study_info;
     const publication = studyInfo.publication;
     return getPublishedCitation(
       studyInfo.doiStatus,