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feat: move anvil identity tags back to columns and add a file download menu (#5000) #5001

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feat: move anvil identity tags back to columns and add a file download menu (#5000) #5001

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58 changes: 14 additions & 44 deletions __tests__/viewModelBuilders/activity-identity.test.tsx
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Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
import type { AggregatedDataset } from "../../app/apis/azul/anvil-cmg/common/aggregatedEntities";
import type { ActivityEntity } from "../../app/apis/azul/anvil-cmg/common/entities";
import type { ActivitiesResponse } from "../../app/apis/azul/anvil-cmg/common/responses";
import { buildActivityIdentity } from "../../app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders";
import { getChipLabels } from "./utils/identityCell";
import {
buildActivityIdentity,
buildActivityType,
} from "../../app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders";

const DATASET_TITLE = "Test Dataset Title";
const DOCUMENT_ID = "test-document-id";
Expand Down Expand Up @@ -33,50 +35,18 @@ const createMockActivitiesResponse = (
}) as ActivitiesResponse;

describe("buildActivityIdentity", () => {
it("renders the document ID as a plain text title", () => {
const { title } = buildActivityIdentity(createMockActivitiesResponse());
expect(title).toEqual({ label: DOCUMENT_ID, url: "" });
});

it("renders an activity type chip", () => {
expect(
getChipLabels(buildActivityIdentity(createMockActivitiesResponse()).chips)
).toEqual(["activity type Sequencing"]);
});

it("renders an activity type chip for the Unknown activity type", () => {
const response = createMockActivitiesResponse({ activity_type: "Unknown" });
expect(getChipLabels(buildActivityIdentity(response).chips)).toEqual([
"activity type Unknown",
]);
});

it.each([
["null", null as unknown as string],
["unspecified", "Unspecified"],
])("renders no chips when the activity type is %s", (_, value) => {
const response = createMockActivitiesResponse({ activity_type: value });
expect(buildActivityIdentity(response).chips).toEqual([]);
});

it("renders the dataset title as a plain text subtitle", () => {
const { subtitle } = buildActivityIdentity(createMockActivitiesResponse());
expect(subtitle).toEqual({ label: DATASET_TITLE, url: "" });
});

it("renders the dataset count as the subtitle when there is more than one dataset", () => {
const response = createMockActivitiesResponse({}, [
{ dataset_id: ["dataset-a"], title: ["Dataset A"] },
{ dataset_id: ["dataset-b"], title: ["Dataset B"] },
]);
expect(buildActivityIdentity(response).subtitle).toEqual({
label: "2 datasets",
url: "",
it("renders the document ID as a plain text title, clamped to two lines, with no chips or subtitle", () => {
expect(buildActivityIdentity(createMockActivitiesResponse())).toEqual({
maxLines: 2,
title: { label: DOCUMENT_ID, url: "" },
});
});
});

it("omits the subtitle when there are no datasets", () => {
const response = createMockActivitiesResponse({}, []);
expect(buildActivityIdentity(response).subtitle).toBeUndefined();
describe("buildActivityType", () => {
it("renders the activity type", () => {
expect(buildActivityType(createMockActivitiesResponse()).value).toBe(
"Sequencing"
);
});
});
115 changes: 21 additions & 94 deletions __tests__/viewModelBuilders/biosample-identity.test.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,14 @@ import type {
} from "../../app/apis/azul/anvil-cmg/common/aggregatedEntities";
import type { BioSampleEntity } from "../../app/apis/azul/anvil-cmg/common/entities";
import type { BioSamplesResponse } from "../../app/apis/azul/anvil-cmg/common/responses";
import { buildBioSampleIdentity } from "../../app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders";
import { getChipLabels } from "./utils/identityCell";
import {
buildAnatomicalSite,
buildBioSampleIdentity,
buildBioSampleType,
} from "../../app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders";

const BIOSAMPLE_ID = "test-biosample-id";
const DATASET_TITLE = "Test Dataset Title";
const UNSPECIFIED_CASES: [string, null | string][] = [
["null", null],
["unspecified", "Unspecified"],
];

/**
* Creates a mock BioSamplesResponse for testing.
Expand Down Expand Up @@ -43,98 +42,26 @@ const createMockBioSamplesResponse = (
}) as BioSamplesResponse;

describe("buildBioSampleIdentity", () => {
it("renders the biosample ID as a plain text title", () => {
const { title } = buildBioSampleIdentity(createMockBioSamplesResponse());
expect(title).toEqual({ label: BIOSAMPLE_ID, url: "" });
});

it("renders biosample type, anatomical site, then organism type chips", () => {
const response = createMockBioSamplesResponse({}, [
{ organism_type: ["Human"] },
{ organism_type: ["Mouse"] },
]);
expect(getChipLabels(buildBioSampleIdentity(response).chips)).toEqual([
"biosample type Tissue",
"anatomical site Blood",
"organism type Human",
"organism type Mouse",
]);
});

it.each(UNSPECIFIED_CASES)(
"omits the biosample type chip when the biosample type is %s",
(_, value) => {
const response = createMockBioSamplesResponse({ biosample_type: value });
expect(getChipLabels(buildBioSampleIdentity(response).chips)).toEqual([
"anatomical site Blood",
"organism type Human",
]);
}
);

it.each(UNSPECIFIED_CASES)(
"omits the anatomical site chip when the anatomical site is %s",
(_, value) => {
const response = createMockBioSamplesResponse({ anatomical_site: value });
expect(getChipLabels(buildBioSampleIdentity(response).chips)).toEqual([
"biosample type Tissue",
"organism type Human",
]);
}
);

it.each([
["empty", []],
["null", [null]],
["unspecified", ["Unspecified"]],
])("omits organism type chips when the organism type is %s", (_, value) => {
const response = createMockBioSamplesResponse({}, [
{ organism_type: value },
]);
expect(getChipLabels(buildBioSampleIdentity(response).chips)).toEqual([
"biosample type Tissue",
"anatomical site Blood",
]);
});

it("renders one organism type chip per unique organism type across donors", () => {
const response = createMockBioSamplesResponse({}, [
{ organism_type: ["Human"] },
{ organism_type: ["Human"] },
]);
expect(getChipLabels(buildBioSampleIdentity(response).chips)).toEqual([
"biosample type Tissue",
"anatomical site Blood",
"organism type Human",
]);
it("renders the biosample ID as a plain text title, clamped to two lines, with no chips or subtitle", () => {
expect(buildBioSampleIdentity(createMockBioSamplesResponse())).toEqual({
maxLines: 2,
title: { label: BIOSAMPLE_ID, url: "" },
});
});
});

it("renders no chips when every biosample field is unspecified", () => {
const response = createMockBioSamplesResponse(
{ anatomical_site: null, biosample_type: null },
[]
describe("buildAnatomicalSite", () => {
it("renders the anatomical site", () => {
expect(buildAnatomicalSite(createMockBioSamplesResponse()).value).toBe(
"Blood"
);
expect(buildBioSampleIdentity(response).chips).toEqual([]);
});

it("renders the dataset title as a plain text subtitle", () => {
const { subtitle } = buildBioSampleIdentity(createMockBioSamplesResponse());
expect(subtitle).toEqual({ label: DATASET_TITLE, url: "" });
});

it("renders the dataset count as the subtitle when there is more than one dataset", () => {
const response = createMockBioSamplesResponse({}, undefined, [
{ dataset_id: ["dataset-a"], title: ["Dataset A"] },
{ dataset_id: ["dataset-b"], title: ["Dataset B"] },
]);
expect(buildBioSampleIdentity(response).subtitle).toEqual({
label: "2 datasets",
url: "",
});
});
});

it("omits the subtitle when there are no datasets", () => {
const response = createMockBioSamplesResponse({}, undefined, []);
expect(buildBioSampleIdentity(response).subtitle).toBeUndefined();
describe("buildBioSampleType", () => {
it("renders the biosample type", () => {
expect(buildBioSampleType(createMockBioSamplesResponse()).value).toBe(
"Tissue"
);
});
});
93 changes: 27 additions & 66 deletions __tests__/viewModelBuilders/buildFileDownload.test.ts
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
import { AzulFileDownloadProps } from "@databiosphere/findable-ui/lib/components/Index/components/AzulFileDownload/azulFileDownload";
import { ReactElement } from "react";
import { FilesResponse } from "../../app/apis/azul/anvil-cmg/common/responses";
import { buildFileDownloadWithTooltip } from "../../app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders";
import { buildFileDownloadMenu } from "../../app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders";

/**
* Creates a mock FilesResponse with configurable file and dataset values.
Expand Down Expand Up @@ -52,6 +50,7 @@ const createMockFilesResponse = (
file_format: "bam",
file_id: "file-123",
file_name: "sample.bam",
file_path: "folder/sample.bam",
file_size: 1024,
file_type: "Analysis",
...overrides,
Expand All @@ -64,19 +63,17 @@ const createMockFilesResponse = (
],
});

describe("buildFileDownload", () => {
describe("buildFileDownloadMenu", () => {
describe("url prop based on azul_mirror_uri", () => {
it("returns undefined url when azul_mirror_uri is null", () => {
const response = createMockFilesResponse({
azul_mirror_uri: null,
azul_url: "https://service.azul.data/repository/files/file-123",
});

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props.url
).toBeUndefined();
expect(result.url).toBeUndefined();
});

it("returns undefined url when azul_mirror_uri is empty string", () => {
Expand All @@ -85,11 +82,9 @@ describe("buildFileDownload", () => {
azul_url: "https://service.azul.data/repository/files/file-123",
});

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props.url
).toBeUndefined();
expect(result.url).toBeUndefined();
});

it("returns azul_url when azul_mirror_uri has a value", () => {
Expand All @@ -99,11 +94,9 @@ describe("buildFileDownload", () => {
azul_url: azulUrl,
});

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props.url
).toBe(azulUrl);
expect(result.url).toBe(azulUrl);
});

it("returns azul_url value exactly as provided when mirror uri exists", () => {
Expand All @@ -114,11 +107,9 @@ describe("buildFileDownload", () => {
azul_url: azulUrl,
});

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props.url
).toBe(azulUrl);
expect(result.url).toBe(azulUrl);
});
});

Expand All @@ -128,12 +119,9 @@ describe("buildFileDownload", () => {
file_name: "my-sample-file.bam",
});

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props
.entityName
).toBe("my-sample-file.bam");
expect(result.entityName).toBe("my-sample-file.bam");
});

it("returns correct relatedEntityId from dataset_id", () => {
Expand All @@ -142,12 +130,9 @@ describe("buildFileDownload", () => {
{ dataset_id: ["my-dataset-id-123"] }
);

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props
.relatedEntityId
).toBe("my-dataset-id-123");
expect(result.relatedEntityId).toBe("my-dataset-id-123");
});

it("returns correct relatedEntityName from dataset title", () => {
Expand All @@ -156,39 +141,17 @@ describe("buildFileDownload", () => {
{ title: ["My Research Dataset"] }
);

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props
.relatedEntityName
).toBe("My Research Dataset");
expect(result.relatedEntityName).toBe("My Research Dataset");
});
});

describe("tooltip title", () => {
it("returns tooltip message when download is disabled", () => {
const response = createMockFilesResponse({
azul_mirror_uri: null,
});

const result = buildFileDownloadWithTooltip(response);

expect(result.title).toBe(
"Direct file downloads are currently only available for open-access files."
);
});
describe("drsUri", () => {
it("returns the file's DRS URI", () => {
const result = buildFileDownloadMenu(createMockFilesResponse());

it("returns enabled tooltip message when download is available", () => {
const response = createMockFilesResponse({
azul_mirror_uri: "s3://bucket/path/to/file.bam",
azul_url: "https://service.azul.data/repository/files/file-123",
});

const result = buildFileDownloadWithTooltip(response);

expect(result.title).toBe(
"This open-access file is freely downloadable from AWS Open Data, with no data transfer fees."
);
expect(result.drsUri).toBe("drs://data.azul/file-123");
});
});

Expand All @@ -206,11 +169,10 @@ describe("buildFileDownload", () => {
}
);

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props
).toEqual({
expect(result).toEqual({
drsUri: "drs://data.azul/file-123",
entityName: "research-data.bam",
relatedEntityId: "dataset-abc",
relatedEntityName: "Genomics Research Project",
Expand All @@ -231,11 +193,10 @@ describe("buildFileDownload", () => {
}
);

const result = buildFileDownloadWithTooltip(response);
const result = buildFileDownloadMenu(response);

expect(
(result.children as ReactElement<AzulFileDownloadProps>).props
).toEqual({
expect(result).toEqual({
drsUri: "drs://data.azul/file-123",
entityName: "research-data.bam",
relatedEntityId: "dataset-abc",
relatedEntityName: "Genomics Research Project",
Expand Down
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