feat: support additional atlas fields on backend (#410) (#412)

__tests__/api-atlases-create.test.ts

@@ -25,7 +25,10 @@ jest.mock("../app/services/cellxgene");
 jest.mock("../app/utils/pg-app-connect-config");
 
 const NEW_ATLAS_DATA: NewAtlasData = {
+  cellxgeneAtlasCollection: "7a223dd3-a422-4f4b-a437-90b9a3b00ba8",
+  codeLinks: [{ url: "https://example.com/new-atlas-foo" }],
   description: "foo bar baz baz foo bar",
+  highlights: "bar foo baz baz baz foo",
   integrationLead: [],
   network: "eye",
   shortName: "test",
@@ -260,6 +263,51 @@ describe("/api/atlases/create", () => {
     ).toEqual(400);
   });
 
+  it("returns error 400 when cellxgene id is not a uuid", async () => {
+    expect(
+      (
+        await doCreateTest(
+          USER_CONTENT_ADMIN,
+          {
+            ...NEW_ATLAS_DATA,
+            cellxgeneAtlasCollection: "not-a-uuid",
+          },
+          true
+        )
+      )._getStatusCode()
+    ).toEqual(400);
+  });
+
+  it("returns error 400 when link url is not a url", async () => {
+    expect(
+      (
+        await doCreateTest(
+          USER_CONTENT_ADMIN,
+          {
+            ...NEW_ATLAS_DATA,
+            codeLinks: [{ url: "not-a-url" }],
+          },
+          true
+        )
+      )._getStatusCode()
+    ).toEqual(400);
+  });
+
+  it("returns error 400 when highlights are too long", async () => {
+    expect(
+      (
+        await doCreateTest(
+          USER_CONTENT_ADMIN,
+          {
+            ...NEW_ATLAS_DATA,
+            highlights: "x".repeat(10001),
+          },
+          true
+        )
+      )._getStatusCode()
+    ).toEqual(400);
+  });
+
   it("creates and returns atlas entry with no integration leads", async () => {
     await testSuccessfulCreate(NEW_ATLAS_DATA);
   });
@@ -291,9 +339,16 @@ async function testSuccessfulCreate(atlasData: NewAtlasData): Promise<void> {
   expect(newAtlasFromDb.target_completion).toEqual(
     atlasData.targetCompletion ? new Date(atlasData.targetCompletion) : null
   );
+  expect(newAtlasFromDb.overview.cellxgeneAtlasCollection).toEqual(
+    atlasData.cellxgeneAtlasCollection ?? null
+  );
+  expect(newAtlasFromDb.overview.codeLinks).toEqual(atlasData.codeLinks ?? []);
   expect(newAtlasFromDb.overview.description).toEqual(
     atlasData.description ?? ""
   );
+  expect(newAtlasFromDb.overview.highlights).toEqual(
+    atlasData.highlights ?? ""
+  );
   expect(newAtlasFromDb.overview.integrationLead).toEqual(
     atlasData.integrationLead
   );

__tests__/api-atlases-id.test.ts

@@ -82,8 +82,10 @@ const ATLAS_DRAFT_EDIT: AtlasEditData = {
   wave: "3",
 };
 
-const ATLAS_PUBLIC_EDIT_NO_TARGET_COMPLETION: AtlasEditData = {
+const ATLAS_PUBLIC_EDIT_NO_TARGET_COMPLETION_OR_CELLXGENE: AtlasEditData = {
+  codeLinks: ATLAS_DRAFT.codeLinks,
   description: ATLAS_DRAFT.description,
+  highlights: ATLAS_DRAFT.highlights,
   integrationLead: ATLAS_DRAFT.integrationLead,
   network: ATLAS_DRAFT.network,
   shortName: ATLAS_DRAFT.shortName,
@@ -92,6 +94,8 @@ const ATLAS_PUBLIC_EDIT_NO_TARGET_COMPLETION: AtlasEditData = {
 };
 
 const ATLAS_WITH_MISC_SOURCE_STUDIES_EDIT: AtlasEditData = {
+  cellxgeneAtlasCollection:
+    ATLAS_WITH_MISC_SOURCE_STUDIES.cellxgeneAtlasCollection,
   integrationLead: ATLAS_WITH_MISC_SOURCE_STUDIES.integrationLead,
   network: ATLAS_WITH_MISC_SOURCE_STUDIES.network,
   shortName: ATLAS_WITH_MISC_SOURCE_STUDIES.shortName,
@@ -388,16 +392,16 @@ describe(TEST_ROUTE, () => {
     await testSuccessfulEdit(ATLAS_DRAFT, ATLAS_DRAFT_EDIT, 2);
   });
 
-  it("PUT updates and returns atlas entry with target completion removed", async () => {
+  it("PUT updates and returns atlas entry with target completion and CELLxGENE collection removed", async () => {
     const updatedAtlas = await testSuccessfulEdit(
       ATLAS_PUBLIC,
-      ATLAS_PUBLIC_EDIT_NO_TARGET_COMPLETION,
+      ATLAS_PUBLIC_EDIT_NO_TARGET_COMPLETION_OR_CELLXGENE,
       0
     );
     expect(updatedAtlas.target_completion).toBeNull();
   });
 
-  it("PUT updates and returns atlas entry with description removed", async () => {
+  it("PUT updates and returns atlas entry with description, code links, and highlights removed", async () => {
     const updatedAtlas = await testSuccessfulEdit(
       ATLAS_WITH_MISC_SOURCE_STUDIES,
       ATLAS_WITH_MISC_SOURCE_STUDIES_EDIT,
@@ -430,7 +434,12 @@ async function testSuccessfulEdit(
 
   const updatedOverview = updatedAtlasFromDb.overview;
 
+  expect(updatedOverview.cellxgeneAtlasCollection).toEqual(
+    editData.cellxgeneAtlasCollection ?? null
+  );
+  expect(updatedOverview.codeLinks).toEqual(editData.codeLinks ?? []);
   expect(updatedOverview.description).toEqual(editData.description ?? "");
+  expect(updatedOverview.highlights).toEqual(editData.highlights ?? "");
   expect(updatedOverview.integrationLead).toEqual(editData.integrationLead);
   expect(updatedOverview.network).toEqual(editData.network);
   expect(updatedOverview.shortName).toEqual(editData.shortName);

app/apis/catalog/hca-atlas-tracker/common/entities.ts

@@ -6,9 +6,12 @@ export type APIValue = (typeof API)[APIKey];
 
 export interface HCAAtlasTrackerListAtlas {
   bioNetwork: NetworkKey;
+  cellxgeneAtlasCollection: string | null;
+  codeLinks: LinkInfo[];
   completedTaskCount: number;
   componentAtlasCount: number;
   description: string;
+  highlights: string;
   id: string;
   integrationLeadEmail: IntegrationLead["email"][];
   integrationLeadName: IntegrationLead["name"][];
@@ -27,9 +30,12 @@ export interface HCAAtlasTrackerListAtlas {
 
 export interface HCAAtlasTrackerAtlas {
   bioNetwork: NetworkKey;
+  cellxgeneAtlasCollection: string | null;
+  codeLinks: LinkInfo[];
   completedTaskCount: number;
   componentAtlasCount: number;
   description: string;
+  highlights: string;
   id: string;
   integrationLead: IntegrationLead[];
   publication: {
@@ -217,8 +223,11 @@ export interface HCAAtlasTrackerDBAtlasWithComponentAtlases
 }
 
 export interface HCAAtlasTrackerDBAtlasOverview {
+  cellxgeneAtlasCollection: string | null;
+  codeLinks: LinkInfo[];
   completedTaskCount: number;
   description: string;
+  highlights: string;
   integrationLead: IntegrationLead[];
   network: NetworkKey;
   shortName: string;
@@ -455,6 +464,11 @@ export interface IntegrationLead {
   name: string;
 }
 
+export interface LinkInfo {
+  label?: string;
+  url: string;
+}
+
 export type SourceDatasetId = string;
 
 export type SourceStudyId = string;

app/apis/catalog/hca-atlas-tracker/common/schema.ts

@@ -16,7 +16,15 @@ import { ROLE } from "./entities";
  * Schema for data used to create a new atlas.
  */
 export const newAtlasSchema = object({
+  cellxgeneAtlasCollection: string().uuid().nullable(),
+  codeLinks: array().of(
+    object({
+      label: string(),
+      url: string().url().required(),
+    }).required()
+  ),
   description: string().max(10000),
+  highlights: string().max(10000),
   integrationLead: array()
     .of(
       object({

app/apis/catalog/hca-atlas-tracker/common/utils.ts

@@ -43,9 +43,12 @@ export function atlasInputMapper(
 ): HCAAtlasTrackerListAtlas {
   return {
     bioNetwork: apiAtlas.bioNetwork,
+    cellxgeneAtlasCollection: apiAtlas.cellxgeneAtlasCollection,
+    codeLinks: apiAtlas.codeLinks,
     completedTaskCount: apiAtlas.completedTaskCount,
     componentAtlasCount: apiAtlas.componentAtlasCount,
     description: apiAtlas.description,
+    highlights: apiAtlas.highlights,
     id: apiAtlas.id,
     integrationLeadEmail: apiAtlas.integrationLead.map(({ email }) => email),
     integrationLeadName: apiAtlas.integrationLead.map(({ name }) => name),
@@ -68,9 +71,12 @@ export function dbAtlasToApiAtlas(
 ): HCAAtlasTrackerAtlas {
   return {
     bioNetwork: dbAtlas.overview.network,
+    cellxgeneAtlasCollection: dbAtlas.overview.cellxgeneAtlasCollection,
+    codeLinks: dbAtlas.overview.codeLinks,
     completedTaskCount: dbAtlas.overview.completedTaskCount,
     componentAtlasCount: dbAtlas.component_atlas_count,
     description: dbAtlas.overview.description,
+    highlights: dbAtlas.overview.highlights,
     id: dbAtlas.id,
     integrationLead: dbAtlas.overview.integrationLead,
     publication: {

app/services/atlases.ts

@@ -83,7 +83,10 @@ export async function atlasInputDataToDbData(
 ): Promise<AtlasInputDbData> {
   return {
     overviewData: {
+      cellxgeneAtlasCollection: inputData.cellxgeneAtlasCollection ?? null,
+      codeLinks: inputData.codeLinks ?? [],
       description: inputData.description ?? "",
+      highlights: inputData.highlights ?? "",
       integrationLead: inputData.integrationLead,
       network: inputData.network,
       shortName: inputData.shortName,

migrations/1723321794859_atlas-highlights-code-cellxgene.ts

@@ -0,0 +1,13 @@
+import { MigrationBuilder } from "node-pg-migrate";
+
+export function up(pgm: MigrationBuilder): void {
+  pgm.sql(
+    `UPDATE hat.atlases SET overview=overview||'{"cellxgeneAtlasCollection":null,"codeLinks":[],"highlights":""}'`
+  );
+}
+
+export function down(pgm: MigrationBuilder): void {
+  pgm.sql(
+    `UPDATE hat.atlases SET overview=overview-'cellxgeneAtlasCollection'-'codeLinks'-'highlights'`
+  );
+}

testing/constants.ts

@@ -1537,7 +1537,10 @@ export const INTEGRATION_LEAD_BAZ_BAZ = {
 };
 
 export const ATLAS_DRAFT: TestAtlas = {
+  cellxgeneAtlasCollection: null,
+  codeLinks: [],
   description: "bar baz baz foo baz",
+  highlights: "",
   id: ATLAS_ID_DRAFT,
   integrationLead: [
     {
@@ -1562,7 +1565,10 @@ export const ATLAS_DRAFT: TestAtlas = {
 };
 
 export const ATLAS_PUBLIC: TestAtlas = {
+  cellxgeneAtlasCollection: "354564bb-52cb-4dea-8e2e-d3d707ca3b87",
+  codeLinks: [{ label: "foo", url: "https://example.com/atlas-public-foo" }],
   description: "foo foo bar bar foo",
+  highlights: "bar foo baz foo foo bar baz",
   id: ATLAS_ID_PUBLIC,
   integrationLead: [
     {
@@ -1584,7 +1590,10 @@ export const ATLAS_PUBLIC: TestAtlas = {
 };
 
 export const ATLAS_WITH_IL: TestAtlas = {
+  cellxgeneAtlasCollection: null,
+  codeLinks: [],
   description: "foo baz bar baz foo baz",
+  highlights: "",
   id: "798b563d-16ff-438a-8e15-77be05b1f8ec",
   integrationLead: [INTEGRATION_LEAD_BAZ],
   network: "heart",
@@ -1596,7 +1605,12 @@ export const ATLAS_WITH_IL: TestAtlas = {
 };
 
 export const ATLAS_WITH_MISC_SOURCE_STUDIES: TestAtlas = {
+  cellxgeneAtlasCollection: "5aa910ee-23d7-419e-b2a4-8362dc058426",
+  codeLinks: [
+    { url: "https://example.com/atlas-with-misc-source-studies-foo" },
+  ],
   description: "bar foo bar bar foo baz",
+  highlights: "foo foo foo foo bar foo bar",
   id: ATLAS_ID_WITH_MISC_SOURCE_STUDIES,
   integrationLead: [INTEGRATION_LEAD_BAZ_BAZ],
   network: "adipose",
@@ -1623,7 +1637,10 @@ export const ATLAS_WITH_MISC_SOURCE_STUDIES: TestAtlas = {
 };
 
 export const ATLAS_WITH_SOURCE_STUDY_VALIDATIONS_A: TestAtlas = {
+  cellxgeneAtlasCollection: null,
+  codeLinks: [],
   description: "foo baz baz bar foo bar",
+  highlights: "",
   id: "7ce0814d-606c-475b-942a-0f72ff8c5c0b",
   integrationLead: [],
   network: "organoid",
@@ -1641,7 +1658,10 @@ export const ATLAS_WITH_SOURCE_STUDY_VALIDATIONS_A: TestAtlas = {
 };
 
 export const ATLAS_WITH_SOURCE_STUDY_VALIDATIONS_B: TestAtlas = {
+  cellxgeneAtlasCollection: null,
+  codeLinks: [],
   description: "baz foo baz foo bar bar foo",
+  highlights: "",
   id: "9766683a-3c8d-4ec8-b8b5-3fceb8fe0d31",
   integrationLead: [],
   network: "gut",

testing/entities.ts

@@ -3,6 +3,7 @@ import {
   DOI_STATUS,
   HCAAtlasTrackerDBUnpublishedSourceStudyInfo,
   IntegrationLead,
+  LinkInfo,
   NetworkKey,
   PublicationInfo,
   ROLE,
@@ -20,7 +21,10 @@ export interface TestUser {
 }
 
 export interface TestAtlas {
+  cellxgeneAtlasCollection: string | null;
+  codeLinks: LinkInfo[];
   description: string;
+  highlights: string;
   id: string;
   integrationLead: IntegrationLead[];
   network: NetworkKey;

testing/utils.ts

@@ -55,8 +55,11 @@ export function makeTestAtlasOverview(
   atlas: TestAtlas
 ): HCAAtlasTrackerDBAtlasOverview {
   return {
+    cellxgeneAtlasCollection: atlas.cellxgeneAtlasCollection,
+    codeLinks: atlas.codeLinks,
     completedTaskCount: 0,
     description: atlas.description,
+    highlights: atlas.highlights,
     integrationLead: atlas.integrationLead,
     network: atlas.network,
     shortName: atlas.shortName,
@@ -258,7 +261,12 @@ export function expectApiAtlasToMatchTest(
   apiAtlas: HCAAtlasTrackerAtlas,
   testAtlas: TestAtlas
 ): void {
+  expect(apiAtlas.cellxgeneAtlasCollection).toEqual(
+    testAtlas.cellxgeneAtlasCollection
+  );
+  expect(apiAtlas.codeLinks).toEqual(testAtlas.codeLinks);
   expect(apiAtlas.description).toEqual(testAtlas.description);
+  expect(apiAtlas.highlights).toEqual(testAtlas.highlights);
   expect(apiAtlas.id).toEqual(testAtlas.id);
   expect(apiAtlas.integrationLead).toEqual(testAtlas.integrationLead);
   expect(apiAtlas.bioNetwork).toEqual(testAtlas.network);