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refactor: move dispatching logic into fhir-data-service, dry out code #3130

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refactor: move dispatching logic into fhir-data-service, dry out code #3130

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f121c45
refactor: move dispatching logic into fhir-data-service, dry out code
mcmcgrath13 Jan 15, 2025
7acd790
Update containers/ecr-viewer/src/app/api/fhir-data/fhir-data-service.ts
mcmcgrath13 Jan 15, 2025
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110 changes: 74 additions & 36 deletions containers/ecr-viewer/src/app/api/fhir-data/fhir-data-service.ts
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Original file line number Diff line number Diff line change
@@ -1,57 +1,99 @@
import { NextRequest, NextResponse } from "next/server";
import { NextResponse } from "next/server";
import { GetObjectCommand } from "@aws-sdk/client-s3";
import {
BlobClient,
BlobDownloadResponseParsed,
BlobServiceClient,
} from "@azure/storage-blob";
import { loadYamlConfig, streamToJson } from "../utils";
import {
AZURE_SOURCE,
POSTGRES_SOURCE,
S3_SOURCE,
loadYamlConfig,
streamToJson,
} from "../utils";
import { getDB } from "../services/postgres_db";
import { s3Client } from "../services/s3Client";

const UNKNOWN_ECR_ID = "eCR ID not found";

type FhirDataResponse = {
payload: { fhirBundle: any } | { message: string };
status: number;
};

/**
* Get the fhir data for a given ECR ID
* @param ecr_id The id of the ecr to fetch
* @returns NextResponse with the ecr or error data
*/
export async function get_fhir_data(ecr_id: string | null) {
let res: FhirDataResponse;
if (process.env.SOURCE === S3_SOURCE) {
res = await get_s3(ecr_id);
} else if (process.env.SOURCE === AZURE_SOURCE) {
res = await get_azure(ecr_id);
} else if (process.env.SOURCE === POSTGRES_SOURCE) {
res = await get_postgres(ecr_id);
} else {
res = { payload: { message: "Invalid source" }, status: 500 };
}
const { status, payload } = res;
if (status !== 200) {
return NextResponse.json(payload, { status });
}

const mappings = loadYamlConfig();
if (!mappings) {
console.error("Unable to load FHIR mappings");
return NextResponse.json(
{ message: "Internal system error" },
{ status: 500 },
);
}

return NextResponse.json(
{ ...payload, fhirPathMappings: mappings },
{ status },
);
}

/**
* Retrieves FHIR data from PostgreSQL database based on eCR ID.
* @param request - The NextRequest object containing the request information.
* @returns A promise resolving to a NextResponse object.
* @param ecr_id - The id of the ecr to fetch.
* @returns A promise resolving to the data and status.
*/
export const get_postgres = async (request: NextRequest) => {
export const get_postgres = async (
ecr_id: string | null,
): Promise<FhirDataResponse> => {
const { database, pgPromise } = getDB();
const params = request.nextUrl.searchParams;
const ecr_id = params.get("id") || null;
const mappings = loadYamlConfig();

const { ParameterizedQuery: PQ } = pgPromise;
const findFhir = new PQ({
text: "SELECT * FROM fhir WHERE ecr_id = $1",
values: [ecr_id],
});
try {
if (!mappings) throw Error("no mappings!");
const entry = await database.one(findFhir);
return NextResponse.json(
{ fhirBundle: entry.data, fhirPathMappings: mappings },
{ status: 200 },
);
return { payload: { fhirBundle: entry.data }, status: 200 };
} catch (error: any) {
console.error("Error fetching data:", error);
if (error.message == "No data returned from the query.") {
return NextResponse.json({ message: UNKNOWN_ECR_ID }, { status: 404 });
return { payload: { message: UNKNOWN_ECR_ID }, status: 404 };
} else {
return NextResponse.json({ message: error.message }, { status: 500 });
return { payload: { message: error.message }, status: 500 };
}
}
};

/**
* Retrieves FHIR data from S3 based on eCR ID.
* @param request - The NextRequest object containing the request information.
* @param ecr_id - The id of the ecr to fetch.
* @returns A promise resolving to a NextResponse object.
*/
export const get_s3 = async (request: NextRequest) => {
const params = request.nextUrl.searchParams;
const ecr_id = params.get("id");
export const get_s3 = async (
ecr_id: string | null,
): Promise<FhirDataResponse> => {
const bucketName = process.env.ECR_BUCKET_NAME;
const objectKey = `${ecr_id}.json`; // This could also come from the request, e.g., req.query.key

Expand All @@ -64,34 +106,30 @@ export const get_s3 = async (request: NextRequest) => {
const { Body } = await s3Client.send(command);
const content = await streamToJson(Body);

return NextResponse.json(
{ fhirBundle: content, fhirPathMappings: loadYamlConfig() },
{ status: 200 },
);
return { payload: { fhirBundle: content }, status: 200 };
} catch (error: any) {
console.error("S3 GetObject error:", error);
if (error?.Code === "NoSuchKey") {
return NextResponse.json({ message: UNKNOWN_ECR_ID }, { status: 404 });
return { payload: { message: UNKNOWN_ECR_ID }, status: 404 };
} else {
return NextResponse.json({ message: error.message }, { status: 500 });
return { payload: { message: error.message }, status: 500 };
}
}
};

/**
* Retrieves FHIR data from Azure Blob Storage based on eCR ID.
* @param request - The NextRequest object containing the request information.
* @param ecr_id - The id of the ecr to fetch.
* @returns A promise resolving to a NextResponse object.
*/
export const get_azure = async (request: NextRequest) => {
export const get_azure = async (
ecr_id: string | null,
): Promise<FhirDataResponse> => {
// TODO: Make this global after we get Azure access
const blobClient = BlobServiceClient.fromConnectionString(
process.env.AZURE_STORAGE_CONNECTION_STRING!,
);

const params = request.nextUrl.searchParams;
const ecr_id = params.get("id");

if (!process.env.AZURE_CONTAINER_NAME)
throw Error("Azure container name not found");

Expand All @@ -106,19 +144,19 @@ export const get_azure = async (request: NextRequest) => {
await blockBlobClient.download();
const content = await streamToJson(downloadResponse.readableStreamBody);

return NextResponse.json(
{ fhirBundle: content, fhirPathMappings: loadYamlConfig() },
{ status: 200 },
);
return {
payload: { fhirBundle: content },
status: 200,
};
} catch (error: any) {
console.error(
"Failed to download the FHIR data from Azure Blob Storage:",
error,
);
if (error?.statusCode === 404) {
return NextResponse.json({ message: UNKNOWN_ECR_ID }, { status: 404 });
return { payload: { message: UNKNOWN_ECR_ID }, status: 404 };
} else {
return NextResponse.json({ message: error.message }, { status: 500 });
return { payload: { message: error.message }, status: 500 };
}
}
};
17 changes: 5 additions & 12 deletions containers/ecr-viewer/src/app/api/fhir-data/route.ts
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
import { NextRequest, NextResponse } from "next/server";
import { get_s3, get_azure, get_postgres } from "./fhir-data-service";
import { S3_SOURCE, AZURE_SOURCE, POSTGRES_SOURCE } from "@/app/api/utils";
import { NextRequest } from "next/server";
import { get_fhir_data } from "./fhir-data-service";

/**
* Handles GET requests by fetching data from different sources based on the environment configuration.
Expand All @@ -13,13 +12,7 @@ import { S3_SOURCE, AZURE_SOURCE, POSTGRES_SOURCE } from "@/app/api/utils";
* may vary based on the source and is thus marked as `unknown`.
*/
export async function GET(request: NextRequest) {
if (process.env.SOURCE === S3_SOURCE) {
return get_s3(request);
} else if (process.env.SOURCE === AZURE_SOURCE) {
return await get_azure(request);
} else if (process.env.SOURCE === POSTGRES_SOURCE) {
return await get_postgres(request);
} else {
return NextResponse.json({ message: "Invalid source" }, { status: 500 });
}
const params = request.nextUrl.searchParams;
const ecr_id = params.get("id") || null;
return get_fhir_data(ecr_id);
}
69 changes: 6 additions & 63 deletions containers/ecr-viewer/src/app/tests/api/fhir-data/route.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -2,18 +2,12 @@
* @jest-environment node
*/
import { GET } from "@/app/api/fhir-data/route";
import {
get_postgres,
get_s3,
get_azure,
} from "@/app/api/fhir-data/fhir-data-service";
import { S3_SOURCE, AZURE_SOURCE, POSTGRES_SOURCE } from "@/app/api/utils";
import { get_fhir_data } from "@/app/api/fhir-data/fhir-data-service";
import { POSTGRES_SOURCE } from "@/app/api/utils";
import { NextRequest, NextResponse } from "next/server";

jest.mock("../../../api/fhir-data/fhir-data-service", () => ({
get_postgres: jest.fn(),
get_s3: jest.fn(),
get_azure: jest.fn(),
get_fhir_data: jest.fn(),
}));

const emptyResponse = { fhirBundle: [], fhirPathMappings: [] };
Expand All @@ -24,68 +18,17 @@ describe("GET fhir-data", () => {
jest.resetAllMocks();
});

it("should return a 200 response with postgres bundle when source is postgres", async () => {
process.env.SOURCE = POSTGRES_SOURCE;
(get_postgres as jest.Mock).mockResolvedValue(
NextResponse.json(emptyResponse, { status: 200 }),
);

const response = await GET(
new NextRequest(new URL("https://example.com/api/fhir-data?id=123")),
);

expect(get_postgres).toHaveBeenCalledOnce();
expect(get_s3).not.toHaveBeenCalled();
expect(get_azure).not.toHaveBeenCalled();
expect(response.status).toEqual(200);
expect(await response.json()).toEqual(emptyResponse);
});

it("should return a 200 response with s3 bundle when source is s3", async () => {
process.env.SOURCE = S3_SOURCE;
(get_s3 as jest.Mock).mockResolvedValue(
NextResponse.json(emptyResponse, { status: 200 }),
);

const response = await GET(
new NextRequest(new URL("https://example.com/api/fhir-data?id=123")),
);

expect(get_s3).toHaveBeenCalledOnce();
expect(get_postgres).not.toHaveBeenCalled();
expect(get_azure).not.toHaveBeenCalled();
expect(response.status).toEqual(200);
expect(await response.json()).toEqual(emptyResponse);
});

it("should return a 200 response with azure bundle when source is azure", async () => {
process.env.SOURCE = AZURE_SOURCE;
(get_azure as jest.Mock).mockResolvedValue(
it("should defer to get_fhir_data service function", async () => {
(get_fhir_data as jest.Mock).mockResolvedValue(
NextResponse.json(emptyResponse, { status: 200 }),
);

const response = await GET(
new NextRequest(new URL("https://example.com/api/fhir-data?id=123")),
);

expect(get_azure).toHaveBeenCalledOnce();
expect(get_s3).not.toHaveBeenCalled();
expect(get_postgres).not.toHaveBeenCalled();
expect(get_fhir_data).toHaveBeenCalledOnce();
expect(response.status).toEqual(200);
expect(await response.json()).toEqual(emptyResponse);
});

it("should return a 500 response when METADATA_DATABASE_TYPE is invalid", async () => {
(process.env.SOURCE as any) = "p0$+gre$";

const response = await GET(
new NextRequest(new URL("https://example.com/api/fhir-data?id=123")),
);

jest.spyOn(console, "error").mockImplementation();
expect(response.status).toEqual(500);
expect(await response.json()).toEqual({
message: "Invalid source",
});
});
});
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