fix build without pg promise variables (#2996)

* remove .env * Remove app_env from dockerfile * make metadata env variable optional * fix tests without .env * move getDb from top level to be inside methods * add dockerignore * Remove NEXT_PUBLIC_BASEPATH since it is determined at build time anyways * Set base path as env variable again, but not configurable
CDCgov · Dec 10, 2024 · bc6cf1e · bc6cf1e
1 parent a2ef121
commit bc6cf1e
Show file tree

Hide file tree

Showing 14 changed files with 48 additions and 35 deletions.
diff --git a/containers/ecr-viewer/.dockerignore b/containers/ecr-viewer/.dockerignore
@@ -0,0 +1,10 @@
+.next
+.github
+.env
+docker-compose.yml
+Dockerfile
+node_modules
+seed-scripts
+cypress
+design-review
+.swc
diff --git a/containers/ecr-viewer/.env b/containers/ecr-viewer/.env
diff --git a/containers/ecr-viewer/Dockerfile b/containers/ecr-viewer/Dockerfile
@@ -1,8 +1,5 @@
 FROM node:18-alpine AS base
 
-ARG APP_ENV
-ENV APP_ENV=${APP_ENV}
-
 # Install dependencies only when needed
 FROM base AS deps
 # Check https://github.com/nodejs/docker-node/tree/b4117f9333da4138b03a546ec926ef50a31506c3#nodealpine to understand why libc6-compat might be needed.

diff --git a/containers/ecr-viewer/docker-compose.yml b/containers/ecr-viewer/docker-compose.yml
@@ -19,8 +19,7 @@ services:
       - AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY:-xyz}
       - AZURE_STORAGE_CONNECTION_STRING=DefaultEndpointsProtocol=http;AccountName=devstoreaccount1;AccountKey=Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==;BlobEndpoint=http://azure-storage:10000/devstoreaccount1;
       - AZURE_CONTAINER_NAME=${AZURE_CONTAINER_NAME:-ecr-viewer-files}
-      - NEXT_PUBLIC_NON_INTEGRATED_VIEWER=${NEXT_PUBLIC_NON_INTEGRATED_VIEWER:-false}
-      - NEXT_PUBLIC_BASEPATH=${NEXT_PUBLIC_BASEPATH:-/ecr-viewer}
+      - NEXT_PUBLIC_NON_INTEGRATED_VIEWER=${NEXT_PUBLIC_NON_INTEGRATED_VIEWER:-true}
       - METADATA_DATABASE_SCHEMA=${METADATA_DATABASE_SCHEMA:-core}
       - SQL_SERVER_USER=${SQL_SERVER_USER}
       - SQL_SERVER_PASSWORD=${SQL_SERVER_PASSWORD}

diff --git a/containers/ecr-viewer/environment.d.ts b/containers/ecr-viewer/environment.d.ts
@@ -13,8 +13,8 @@ namespace NodeJS {
     ECR_BUCKET_NAME: string;
     GITHUB_ID: string;
     GITHUB_SECRET: string;
-    METADATA_DATABASE_SCHEMA: "core" | "extended";
-    METADATA_DATABASE_TYPE: "postgres" | "sqlserver";
+    METADATA_DATABASE_SCHEMA?: "core" | "extended";
+    METADATA_DATABASE_TYPE?: "postgres" | "sqlserver";
     NBS_PUB_KEY: string;
     NEXT_PUBLIC_NON_INTEGRATED_VIEWER: "true" | "false";
     NEXT_RUNTIME: string;

diff --git a/containers/ecr-viewer/next.config.js b/containers/ecr-viewer/next.config.js
@@ -1,5 +1,6 @@
 /** @type {import('next').NextConfig} */
 const path = require("path");
+const basePath = "/ecr-viewer";
 
 const nextConfig = {
   sassOptions: {
@@ -20,10 +21,10 @@ const nextConfig = {
     ];
   },
   output: "standalone",
-  basePath:
-    process.env.NODE_ENV === "production"
-      ? process.env.NEXT_PUBLIC_BASEPATH
-      : "",
+  basePath: process.env.NODE_ENV === "production" ? basePath : "",
+  env: {
+    BASE_PATH: basePath,
+  },
 };
 
 module.exports = nextConfig;
diff --git a/containers/ecr-viewer/src/app/api/fhir-data/fhir-data-service.ts b/containers/ecr-viewer/src/app/api/fhir-data/fhir-data-service.ts
@@ -9,14 +9,13 @@ import { loadYamlConfig, streamToJson } from "../utils";
 import { getDB } from "../services/postgres_db";
 import { s3Client } from "../services/s3Client";
 
-const { database, pgPromise } = getDB();
-
 /**
  * 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.
  */
 export const get_postgres = async (request: NextRequest) => {
+  const { database, pgPromise } = getDB();
   const params = request.nextUrl.searchParams;
   const ecr_id = params.get("id") ? params.get("id") : null;
   const mappings = loadYamlConfig();

diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts
@@ -10,8 +10,6 @@ import { BundleExtendedMetadata, BundleMetadata } from "./types";
 import { s3Client } from "../services/s3Client";
 import { get_pool } from "../services/sqlserver_db";
 
-const { database, pgPromise } = getDB();
-
 /**
  * Saves a FHIR bundle to a postgres database.
  * @async
@@ -22,6 +20,7 @@ const { database, pgPromise } = getDB();
  * @throws {Error} Throws an error if the FHIR bundle cannot be saved to postgress.
  */
 export const saveToPostgres = async (fhirBundle: Bundle, ecrId: string) => {
+  const { database, pgPromise } = getDB();
   const { ParameterizedQuery: PQ } = pgPromise;
   const addFhir = new PQ({
     text: "INSERT INTO fhir VALUES ($1, $2) RETURNING ecr_id",
@@ -435,6 +434,7 @@ export const saveMetadataToPostgres = async (
   metadata: BundleMetadata,
   ecrId: string,
 ) => {
+  const { database, pgPromise } = getDB();
   const { ParameterizedQuery: PQ } = pgPromise;
 
   try {

diff --git a/containers/ecr-viewer/src/app/components/EcrTableClient.tsx b/containers/ecr-viewer/src/app/components/EcrTableClient.tsx
@@ -9,7 +9,7 @@ import { range } from "../view-data/utils/utils";
 import classNames from "classnames";
 
 const basePath =
-  process.env.NODE_ENV === "production" ? process.env.NEXT_PUBLIC_BASEPATH : "";
+  process.env.NODE_ENV === "production" ? process.env.BASE_PATH : "";
 
 type EcrTableClientProps = {
   data: EcrDisplay[];

diff --git a/containers/ecr-viewer/src/app/services/listEcrDataService.ts b/containers/ecr-viewer/src/app/services/listEcrDataService.ts
@@ -6,8 +6,6 @@ import {
 import { get_pool } from "../api/services/sqlserver_db";
 import { getDB } from "../api/services/postgres_db";
 
-const { database, pgPromise } = getDB();
-
 export interface CoreMetadataModel {
   eicr_id: string;
   data_source: "DB" | "S3";
@@ -96,6 +94,7 @@ async function listEcrDataPostgres(
   searchTerm?: string,
   filterConditions?: string[],
 ): Promise<EcrDisplay[]> {
+  const { database } = getDB();
   const list = await database.manyOrNone<CoreMetadataModel>(
     "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, ed.report_date,  ARRAY_AGG(DISTINCT erc.condition) AS conditions, ARRAY_AGG(DISTINCT ers.rule_summary) AS rule_summaries FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id WHERE $[whereClause] GROUP BY ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date $[sortStatement] OFFSET $[startIndex] ROWS FETCH NEXT $[itemsPerPage] ROWS ONLY",
     {
@@ -236,6 +235,7 @@ const getTotalEcrCountPostgres = async (
   searchTerm?: string,
   filterConditions?: string[],
 ): Promise<number> => {
+  const { database } = getDB();
   let number = await database.one(
     "SELECT count(DISTINCT ed.eICR_ID) FROM ecr_data as ed LEFT JOIN ecr_rr_conditions erc on ed.eICR_ID = erc.eICR_ID WHERE $[whereClause]",
     {
@@ -315,6 +315,7 @@ const generateWhereStatementSqlServer = (
 export const generateSearchStatement = (searchTerm?: string) => ({
   rawType: true,
   toPostgres: () => {
+    const { pgPromise } = getDB();
     const searchFields = ["ed.patient_name_first", "ed.patient_name_last"];
     return searchFields
       .map((field) => {
@@ -352,6 +353,7 @@ export const generateFilterConditionsStatement = (
 ) => ({
   rawType: true,
   toPostgres: () => {
+    const { pgPromise } = getDB();
     if (!filterConditions) {
       return pgPromise.as.format("NULL IS NULL");
     }
@@ -396,6 +398,7 @@ export const generateSortStatement = (
 ) => ({
   rawType: true,
   toPostgres: () => {
+    const { pgPromise } = getDB();
     // Valid columns and directions
     const validColumns = ["patient", "date_created", "report_date"];
     const validDirections = ["ASC", "DESC"];

diff --git a/containers/ecr-viewer/src/app/tests/components/LoadingComponent.test.tsx b/containers/ecr-viewer/src/app/tests/components/LoadingComponent.test.tsx
@@ -7,6 +7,7 @@ describe("Snapshot test for EcrLoadingSkeleton", () => {
   let container: HTMLElement;
 
   beforeAll(() => {
+    process.env.NEXT_PUBLIC_NON_INTEGRATED_VIEWER = "true";
     const mockIntersectionObserver = jest.fn();
     mockIntersectionObserver.mockReturnValue({
       observe: () => null,
@@ -15,7 +16,11 @@ describe("Snapshot test for EcrLoadingSkeleton", () => {
     });
     window.IntersectionObserver = mockIntersectionObserver;
 
-    container = render(<EcrLoadingSkeleton />).container;
+    ({ container } = render(<EcrLoadingSkeleton />));
+  });
+
+  afterAll(() => {
+    process.env.NEXT_PUBLIC_NON_INTEGRATED_VIEWER = "false";
   });
   it("should match snapshot", () => {
     expect(container).toMatchSnapshot();

diff --git a/containers/ecr-viewer/src/app/tests/components/SideNav.test.tsx b/containers/ecr-viewer/src/app/tests/components/SideNav.test.tsx
@@ -18,6 +18,14 @@ describe("SectionConfig", () => {
     window.IntersectionObserver = mockIntersectionObserver;
   });
 
+  beforeAll(() => {
+    process.env.NEXT_PUBLIC_NON_INTEGRATED_VIEWER = "true";
+  });
+
+  afterAll(() => {
+    process.env.NEXT_PUBLIC_NON_INTEGRATED_VIEWER = "false";
+  });
+
   it("should create an instance with correct title and id", () => {
     const section = new SectionConfig("Test Section");
     expect(section.title).toBe("Test Section");

diff --git a/containers/ecr-viewer/src/app/tests/listEcrDataService.test.tsx b/containers/ecr-viewer/src/app/tests/listEcrDataService.test.tsx
@@ -104,6 +104,12 @@ describe("listEcrDataService", () => {
   });
 
   describe("list Ecr data with postgres", () => {
+    beforeAll(() => {
+      process.env.METADATA_DATABASE_TYPE = "postgres";
+    });
+    afterAll(() => {
+      delete process.env.METADATA_DATABASE_TYPE;
+    });
     it("should return empty array when no data is found", async () => {
       let startIndex = 0;
       let itemsPerPage = 25;

diff --git a/containers/orchestration/docker-compose.yml b/containers/orchestration/docker-compose.yml
@@ -33,6 +33,7 @@ services:
       - SOURCE=postgres
       - DATABASE_URL=postgres://postgres:pw@postgres:5432/ecr_viewer_db
       - APP_ENV=test
+      - NEXT_PUBLIC_NON_INTEGRATED_VIEWER=true
   orchestration-service:
     platform: linux/amd64
     build: