feat: add component atlas source dataset apis (#275) (#291)

* feat: add component atlas source dataset apis (#275)

* test: add tests for component atlas source dataset apis (#275)

* style: fix variable name (#275)

* chore: remove commented-out code (#275)

* feat: add component atlas source datasets get api (#275)

* test: add tests for component atlas source datasets get api (#275)

* feat: add component atlas individual source dataset api (#275)

* fix: remove inconsistent and unnecessary client parameter (#275)

__tests__/api-atlases-id-source-studies-id-source-datasets.test.ts

@@ -75,7 +75,7 @@ describe("/api/atlases/[id]/source-studies/[sourceStudyId]/source-datasets", ()
     );
     expect(res._getStatusCode()).toEqual(200);
     const sourceDatasets = res._getJSONData() as HCAAtlasTrackerSourceDataset[];
-    expect(sourceDatasets).toHaveLength(4);
+    expect(sourceDatasets).toHaveLength(8);
     expectSourceDatasetsToMatch(sourceDatasets, [
       SOURCE_DATASET_FOO,
       SOURCE_DATASET_BAR,
@@ -92,7 +92,7 @@ describe("/api/atlases/[id]/source-studies/[sourceStudyId]/source-datasets", ()
     );
     expect(res._getStatusCode()).toEqual(200);
     const sourceDatasets = res._getJSONData() as HCAAtlasTrackerSourceDataset[];
-    expect(sourceDatasets).toHaveLength(4);
+    expect(sourceDatasets).toHaveLength(8);
     expectSourceDatasetsToMatch(sourceDatasets, [
       SOURCE_DATASET_FOO,
       SOURCE_DATASET_BAR,

__tests__/update-cellxgene-source-datasets.test.ts

@@ -32,7 +32,7 @@ describe("updateCellxGeneSourceDatasets", () => {
       SOURCE_STUDY_WITH_SOURCE_DATASETS.id
     );
 
-    expect(sourceDatasetsBefore).toHaveLength(4);
+    expect(sourceDatasetsBefore).toHaveLength(8);
 
     expectSourceDatasetToMatch(
       findSourceDatasetById(
@@ -61,7 +61,7 @@ describe("updateCellxGeneSourceDatasets", () => {
       SOURCE_STUDY_WITH_SOURCE_DATASETS.id
     );
 
-    expect(sourceDatasetsAfter).toHaveLength(5);
+    expect(sourceDatasetsAfter).toHaveLength(9);
 
     expectSourceDatasetToMatch(
       findSourceDatasetById(

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

@@ -68,6 +68,27 @@ export const componentAtlasEditSchema = newComponentAtlasSchema;
 
 export type ComponentAtlasEditData = InferType<typeof componentAtlasEditSchema>;
 
+/**
+ * Schema for data used to add source datasets to a component atlas.
+ */
+export const componentAtlasAddSourceDatasetsSchema = object({
+  sourceDatasetIds: array(string().required()).required(),
+}).strict();
+
+export type ComponentAtlasAddSourceDatasetsData = InferType<
+  typeof componentAtlasAddSourceDatasetsSchema
+>;
+
+/**
+ * Schema for data used to remove source datasets from a component atlas.
+ */
+export const componentAtlasDeleteSourceDatasetsSchema =
+  componentAtlasAddSourceDatasetsSchema;
+
+export type ComponentAtlasDeleteSourceDatasetsData = InferType<
+  typeof componentAtlasDeleteSourceDatasetsSchema
+>;
+
 /**
  * Create schema that combines an unpublished source study schema and a published source study schema.
  * @param publishedSchema - Published source study schema.

app/services/component-atlases.ts

@@ -1,4 +1,4 @@
-import { NotFoundError } from "app/utils/api-handler";
+import { InvalidOperationError, NotFoundError } from "app/utils/api-handler";
 import {
   HCAAtlasTrackerDBComponentAtlas,
   HCAAtlasTrackerDBComponentAtlasInfo,
@@ -9,6 +9,7 @@ import {
 } from "../apis/catalog/hca-atlas-tracker/common/schema";
 import { confirmAtlasExists } from "./atlases";
 import { query } from "./database";
+import { confirmSourceDatasetsExist } from "./source-datasets";
 
 /**
  * Get all component atlases of the given atlas.
@@ -119,7 +120,91 @@ export async function deleteComponentAtlas(
     throw getComponentAtlasNotFoundError(atlasId, componentAtlasId);
 }
 
-function getComponentAtlasNotFoundError(
+/**
+ * Add the given source datasets to the specified comonent atlas.
+ * @param atlasId - Atlas that the component atlas is accessed through.
+ * @param componentAtlasId - Component atlas ID.
+ * @param sourceDatasetIds - IDs of source datasets to add.
+ */
+export async function addSourceDatasetsToComponentAtlas(
+  atlasId: string,
+  componentAtlasId: string,
+  sourceDatasetIds: string[]
+): Promise<void> {
+  await confirmSourceDatasetsExist(sourceDatasetIds);
+
+  const existingDatasetsResult = await query<{ array: string[] }>(
+    `
+      SELECT ARRAY(
+        SELECT sd_id FROM unnest(source_datasets) AS sd_id WHERE sd_id=ANY($1)
+      ) FROM hat.component_atlases WHERE id=$2 AND atlas_id=$3
+    `,
+    [sourceDatasetIds, componentAtlasId, atlasId]
+  );
+
+  if (existingDatasetsResult.rows.length === 0)
+    throw getComponentAtlasNotFoundError(atlasId, componentAtlasId);
+
+  const existingSpecifiedDatasets = existingDatasetsResult.rows[0].array;
+
+  if (existingSpecifiedDatasets.length !== 0)
+    throw new InvalidOperationError(
+      `Component atlas with ID ${componentAtlasId} already has source datasets with IDs: ${existingSpecifiedDatasets.join(
+        ", "
+      )}`
+    );
+
+  await query(
+    "UPDATE hat.component_atlases SET source_datasets=source_datasets||$1 WHERE id=$2",
+    [sourceDatasetIds, componentAtlasId]
+  );
+}
+
+/**
+ * Remove the given source datasets from the specified comonent atlas.
+ * @param atlasId - Atlas that the component atlas is accessed through.
+ * @param componentAtlasId - Component atlas ID.
+ * @param sourceDatasetIds - IDs of source datasets to remove.
+ */
+export async function deleteSourceDatasetsFromComponentAtlas(
+  atlasId: string,
+  componentAtlasId: string,
+  sourceDatasetIds: string[]
+): Promise<void> {
+  await confirmSourceDatasetsExist(sourceDatasetIds);
+
+  const missingDatasetsResult = await query<{ array: string[] }>(
+    `
+      SELECT ARRAY(
+        SELECT sd_id FROM unnest($1::uuid[]) AS sd_id WHERE NOT sd_id=ANY(source_datasets)
+      ) FROM hat.component_atlases WHERE id=$2 AND atlas_id=$3
+    `,
+    [sourceDatasetIds, componentAtlasId, atlasId]
+  );
+
+  if (missingDatasetsResult.rows.length === 0)
+    throw getComponentAtlasNotFoundError(atlasId, componentAtlasId);
+
+  const missingDatasets = missingDatasetsResult.rows[0].array;
+
+  if (missingDatasets.length !== 0)
+    throw new InvalidOperationError(
+      `Component atlas with ID ${componentAtlasId} doesn't have source datasets with IDs: ${missingDatasets.join(
+        ", "
+      )}`
+    );
+
+  await query(
+    `
+      UPDATE hat.component_atlases
+      SET source_datasets = ARRAY(SELECT unnest(source_datasets) EXCEPT SELECT unnest($1::uuid[]))
+      WHERE id=$2
+    `,
+    [sourceDatasetIds, componentAtlasId]
+  );
+}
+
+export function getComponentAtlasNotFoundError(
   atlasId: string,
   componentAtlasId: string
 ): NotFoundError {

app/services/source-datasets.ts

@@ -1,6 +1,7 @@
 import { CellxGeneDataset } from "app/utils/cellxgene-api";
 import pg from "pg";
 import {
+  HCAAtlasTrackerDBComponentAtlas,
   HCAAtlasTrackerDBSourceDataset,
   HCAAtlasTrackerDBSourceDatasetInfo,
   HCAAtlasTrackerDBSourceDatasetWithStudyProperties,
@@ -11,6 +12,7 @@ import {
 } from "../apis/catalog/hca-atlas-tracker/common/schema";
 import { InvalidOperationError, NotFoundError } from "../utils/api-handler";
 import { getCellxGeneDatasetsByCollectionId } from "./cellxgene";
+import { getComponentAtlasNotFoundError } from "./component-atlases";
 import { doTransaction, query } from "./database";
 import { confirmSourceStudyExistsOnAtlas } from "./source-studies";
 
@@ -33,6 +35,33 @@ export async function getSourceStudyDatasets(
   return queryResult.rows;
 }
 
+/**
+ * Get all source datasets of the given component atlas.
+ * @param atlasId - ID of the atlas that the component atlas is accesed through.
+ * @param componentAtlasId - Component atlas ID.
+ * @returns database-model source datasets.
+ */
+export async function getComponentAtlasDatasets(
+  atlasId: string,
+  componentAtlasId: string
+): Promise<HCAAtlasTrackerDBSourceDatasetWithStudyProperties[]> {
+  const componentAtlasResult = await query<
+    Pick<HCAAtlasTrackerDBComponentAtlas, "source_datasets">
+  >(
+    "SELECT source_datasets FROM hat.component_atlases WHERE id=$1 AND atlas_id=$2",
+    [componentAtlasId, atlasId]
+  );
+  if (componentAtlasResult.rows.length === 0)
+    throw getComponentAtlasNotFoundError(atlasId, componentAtlasId);
+  const sourceDatasetIds = componentAtlasResult.rows[0].source_datasets;
+  const queryResult =
+    await query<HCAAtlasTrackerDBSourceDatasetWithStudyProperties>(
+      "SELECT d.*, s.doi, s.study_info FROM hat.source_datasets d JOIN hat.source_studies s ON d.source_study_id = s.id WHERE d.id = ANY($1)",
+      [sourceDatasetIds]
+    );
+  return queryResult.rows;
+}
+
 /**
  * Get a source dataset.
  * @param atlasId - ID of the atlas that the source dataset is accessed through.
@@ -64,6 +93,40 @@ export async function getSourceDataset(
   return queryResult.rows[0];
 }
 
+/**
+ * Get a source dataset of a component atlas.
+ * @param atlasId - ID of the atlas that the source dataset is accessed through.
+ * @param componentAtlasId - ID of the component atlas that the source dataset is accessed through.
+ * @param sourceDatasetId - Source dataset ID.
+ * @returns database model of the source dataset.
+ */
+export async function getComponentAtlasSourceDataset(
+  atlasId: string,
+  componentAtlasId: string,
+  sourceDatasetId: string
+): Promise<HCAAtlasTrackerDBSourceDatasetWithStudyProperties> {
+  const { exists } = (
+    await query<{ exists: boolean }>(
+      "SELECT EXISTS(SELECT 1 FROM hat.component_atlases WHERE $1=ANY(source_datasets) AND id=$2 AND atlas_id=$3)",
+      [sourceDatasetId, componentAtlasId, atlasId]
+    )
+  ).rows[0];
+  if (!exists)
+    throw new NotFoundError(
+      `Source dataset with ID ${sourceDatasetId} doesn't exist on component atlas with ID ${componentAtlasId} on atlas with ID ${atlasId}`
+    );
+  const queryResult =
+    await query<HCAAtlasTrackerDBSourceDatasetWithStudyProperties>(
+      "SELECT d.*, s.doi, s.study_info FROM hat.source_datasets d JOIN hat.source_studies s ON d.source_study_id = s.id WHERE d.id = $1",
+      [sourceDatasetId]
+    );
+  if (queryResult.rows.length === 0)
+    throw new NotFoundError(
+      `Source dataset with ID ${sourceDatasetId} doesn't exist`
+    );
+  return queryResult.rows[0];
+}
+
 /**
  * Create a source dataset for the given source study.
  * @param atlasId - ID of the atlas that the source study is accessed through.
@@ -250,6 +313,26 @@ async function confirmSourceDatasetIsNonCellxGene(
     );
 }
 
+/**
+ * Check whether a list of dataset IDs exist, and throw an error if any don't.
+ * @param sourceDatasetIds - Source dataset IDs to check for.
+ */
+export async function confirmSourceDatasetsExist(
+  sourceDatasetIds: string[]
+): Promise<void> {
+  const queryResult = await query<Pick<HCAAtlasTrackerDBSourceDataset, "id">>(
+    "SELECT id FROM hat.source_datasets WHERE id=ANY($1)",
+    [sourceDatasetIds]
+  );
+  if (queryResult.rows.length < sourceDatasetIds.length) {
+    const foundIds = queryResult.rows.map((r) => r.id);
+    const missingIds = sourceDatasetIds.filter((id) => !foundIds.includes(id));
+    throw new InvalidOperationError(
+      `No source datasets exist with IDs: ${missingIds.join(", ")}`
+    );
+  }
+}
+
 function getSourceDatasetNotFoundError(
   sourceStudyId: string,
   sourceDatasetId: string

pages/api/atlases/[atlasId]/component-atlases/[componentAtlasId]/source-datasets.ts

@@ -0,0 +1,62 @@
+import { ROLE_GROUP } from "app/apis/catalog/hca-atlas-tracker/common/constants";
+import { ROLE } from "../../../../../../app/apis/catalog/hca-atlas-tracker/common/entities";
+import { componentAtlasAddSourceDatasetsSchema } from "../../../../../../app/apis/catalog/hca-atlas-tracker/common/schema";
+import { dbSourceDatasetToApiSourceDataset } from "../../../../../../app/apis/catalog/hca-atlas-tracker/common/utils";
+import { METHOD } from "../../../../../../app/common/entities";
+import {
+  addSourceDatasetsToComponentAtlas,
+  deleteSourceDatasetsFromComponentAtlas,
+} from "../../../../../../app/services/component-atlases";
+import { getComponentAtlasDatasets } from "../../../../../../app/services/source-datasets";
+import {
+  handleByMethod,
+  handler,
+  role,
+} from "../../../../../../app/utils/api-handler";
+
+const getHandler = handler(role(ROLE_GROUP.READ), async (req, res) => {
+  const atlasId = req.query.atlasId as string;
+  const componentAtlasId = req.query.componentAtlasId as string;
+  res
+    .status(200)
+    .json(
+      (await getComponentAtlasDatasets(atlasId, componentAtlasId)).map(
+        dbSourceDatasetToApiSourceDataset
+      )
+    );
+});
+
+const postHandler = handler(role(ROLE.CONTENT_ADMIN), async (req, res) => {
+  const atlasId = req.query.atlasId as string;
+  const componentAtlasId = req.query.componentAtlasId as string;
+  const { sourceDatasetIds } =
+    await componentAtlasAddSourceDatasetsSchema.validate(req.body);
+  await addSourceDatasetsToComponentAtlas(
+    atlasId,
+    componentAtlasId,
+    sourceDatasetIds
+  );
+  res.status(201).end();
+});
+
+const deleteHandler = handler(role(ROLE.CONTENT_ADMIN), async (req, res) => {
+  const atlasId = req.query.atlasId as string;
+  const componentAtlasId = req.query.componentAtlasId as string;
+  const { sourceDatasetIds } =
+    await componentAtlasAddSourceDatasetsSchema.validate(req.body);
+  await deleteSourceDatasetsFromComponentAtlas(
+    atlasId,
+    componentAtlasId,
+    sourceDatasetIds
+  );
+  res.status(200).end();
+});
+
+/**
+ * API route for adding or deleting multiple source datasets on a component atlas.
+ */
+export default handleByMethod({
+  [METHOD.GET]: getHandler,
+  [METHOD.POST]: postHandler,
+  [METHOD.DELETE]: deleteHandler,
+});