feat: [lungmap] add lungmap projects to google datasets catalog (#4808)

__tests__/utils/schemaOrg/anvilDataset.test.ts

@@ -0,0 +1,182 @@
+import type { DatasetsResponse } from "../../../app/apis/azul/anvil-cmg/common/responses";
+import { buildAnvilDatasetJsonLd } from "../../../app/utils/schemaOrg/anvilDataset";
+import { DESCRIPTION_LENGTH } from "../../../app/utils/schemaOrg/constants";
+
+const BROWSER_URL = "https://explore.anvilproject.org";
+
+/**
+ * Builds a minimal valid AnVIL datasets response with optional overrides for
+ * top-level (dataset) and aggregated (activity/biosample/donor/file/library/
+ * diagnosis) fields.
+ * @param overrides - Partial overrides applied to the base response.
+ * @returns A `DatasetsResponse` shape suitable for builder tests.
+ */
+function makeDatasetsResponse(
+  overrides: Partial<DatasetsResponse> = {}
+): DatasetsResponse {
+  return {
+    activities: [],
+    biosamples: [],
+    datasets: [
+      {
+        accessible: true,
+        consent_group: ["NRES"],
+        dataset_id: "uuid-1",
+        description:
+          "A multi-cohort study of rare disease across many donors and biosamples.",
+        duos_id: null,
+        registered_identifier: [],
+        title: "Rare disease dataset",
+      },
+    ],
+    diagnoses: [],
+    donors: [],
+    entryId: "abc",
+    files: [],
+    libraries: [],
+    status: 200,
+    ...overrides,
+  } as unknown as DatasetsResponse;
+}
+
+describe("buildAnvilDatasetJsonLd", () => {
+  it("returns undefined when no dataset is present", () => {
+    const response = makeDatasetsResponse({ datasets: [] });
+    expect(buildAnvilDatasetJsonLd(response, BROWSER_URL)).toBeUndefined();
+  });
+
+  it("populates required Schema.org Dataset fields", () => {
+    const result = buildAnvilDatasetJsonLd(makeDatasetsResponse(), BROWSER_URL);
+    expect(result).toBeDefined();
+    expect(result!["@context"]).toBe("https://schema.org");
+    expect(result!["@type"]).toBe("Dataset");
+    expect(result!.name).toBe("Rare disease dataset");
+    expect(result!.description).toBe(
+      "A multi-cohort study of rare disease across many donors and biosamples."
+    );
+    expect(result!.url).toBe(`${BROWSER_URL}/datasets/uuid-1`);
+    expect(result!.identifier).toEqual(["uuid-1"]);
+    expect(result!.isAccessibleForFree).toBe(true);
+    expect(result!.includedInDataCatalog).toEqual({
+      "@type": "DataCatalog",
+      name: "AnVIL Data Explorer",
+      url: BROWSER_URL,
+    });
+  });
+
+  it("falls back to dataset_id when title is empty", () => {
+    const response = makeDatasetsResponse();
+    response.datasets[0].title = "";
+    const result = buildAnvilDatasetJsonLd(response, BROWSER_URL);
+    expect(result!.name).toBe("uuid-1");
+  });
+
+  it("strips HTML tags from description", () => {
+    const response = makeDatasetsResponse();
+    response.datasets[0].description =
+      "<p>Single-cell <strong>RNA-seq</strong> data across many donors and tissues.</p>";
+    const result = buildAnvilDatasetJsonLd(response, BROWSER_URL);
+    expect(result!.description).toBe(
+      "Single-cell RNA-seq data across many donors and tissues."
+    );
+  });
+
+  it("truncates descriptions over 5000 characters and appends an ellipsis", () => {
+    const longDescription = "a".repeat(DESCRIPTION_LENGTH.MAX + 200);
+    const response = makeDatasetsResponse();
+    response.datasets[0].description = longDescription;
+    const result = buildAnvilDatasetJsonLd(response, BROWSER_URL);
+    expect(result!.description).toHaveLength(DESCRIPTION_LENGTH.MAX);
+    expect(result!.description.endsWith("…")).toBe(true);
+  });
+
+  it("pads short descriptions with name and catalog context to meet the 50-char minimum", () => {
+    const response = makeDatasetsResponse();
+    response.datasets[0].description = "Short.";
+    const result = buildAnvilDatasetJsonLd(response, BROWSER_URL);
+    expect(result!.description).toBe(
+      "Rare disease dataset — Short. — AnVIL Data Explorer dataset."
+    );
+    expect(result!.description.length).toBeGreaterThanOrEqual(
+      DESCRIPTION_LENGTH.MIN
+    );
+  });
+
+  it("falls back to dataset name plus catalog context when description is missing", () => {
+    const response = makeDatasetsResponse();
+    response.datasets[0].description = undefined;
+    const result = buildAnvilDatasetJsonLd(response, BROWSER_URL);
+    expect(result!.description).toBe(
+      "Rare disease dataset — AnVIL Data Explorer dataset."
+    );
+    expect(result!.description.length).toBeGreaterThanOrEqual(
+      DESCRIPTION_LENGTH.MIN
+    );
+  });
+
+  it("includes registered_identifier values in identifier and dbGaP study URLs in sameAs", () => {
+    const response = makeDatasetsResponse();
+    response.datasets[0].registered_identifier = [
+      "phs000123",
+      "phs000456",
+      null,
+    ];
+    const result = buildAnvilDatasetJsonLd(response, BROWSER_URL);
+    expect(result!.identifier).toEqual(["uuid-1", "phs000123", "phs000456"]);
+    expect(result!.sameAs).toEqual([
+      "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000123",
+      "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000456",
+    ]);
+  });
+
+  it("omits sameAs when there are no registered identifiers", () => {
+    const result = buildAnvilDatasetJsonLd(makeDatasetsResponse(), BROWSER_URL);
+    expect(result!.sameAs).toBeUndefined();
+  });
+
+  it("builds deduplicated keywords from activity, biosample, donor, diagnosis, file, and library fields", () => {
+    const response = makeDatasetsResponse({
+      activities: [
+        { activity_type: ["sequencing"], data_modality: ["genomic"] },
+      ],
+      biosamples: [{ anatomical_site: ["brain"], biosample_type: ["tissue"] }],
+      diagnoses: [{ disease: ["epilepsy"], phenotype: [] }],
+      donors: [
+        {
+          organism_type: ["Homo sapiens"],
+          phenotypic_sex: ["female"],
+          reported_ethnicity: ["asian"],
+        },
+      ],
+      files: [
+        {
+          data_modality: ["genomic"],
+          file_format: ["fastq", "bam"],
+          file_id: "f1",
+          file_type: "sequencing",
+        },
+      ],
+      libraries: [{ prep_material_name: ["DNA"] }],
+    } as unknown as Partial<DatasetsResponse>);
+    const result = buildAnvilDatasetJsonLd(response, BROWSER_URL);
+    expect(result!.keywords).toEqual([
+      "sequencing",
+      "genomic",
+      "brain",
+      "tissue",
+      "Homo sapiens",
+      "female",
+      "asian",
+      "epilepsy",
+      "fastq",
+      "bam",
+      "DNA",
+    ]);
+  });
+
+  it("omits keywords and sameAs when sources are empty", () => {
+    const result = buildAnvilDatasetJsonLd(makeDatasetsResponse(), BROWSER_URL);
+    expect(result!.keywords).toBeUndefined();
+    expect(result!.sameAs).toBeUndefined();
+  });
+});