Implement core metadata schema in the eCR viewer

.github/workflows/container-ecr-viewer.yaml

@@ -65,13 +65,9 @@ jobs:
         working-directory: ./containers/${{env.CONTAINER}} # Navigate to your Node.js app directory
         run: npm install
 
-      - name: Copy seed data
-        working-directory: ./containers/${{env.CONTAINER}}
-        run: cp ./cypress/assets/data.sql ./seed-scripts/sql
-
       - name: Start ${{env.CONTAINER}}
-        working-directory: ./containers/${{env.CONTAINER}}
-        run: docker compose --env-file .env.test up -d
+        working-directory: ./containers/${{env.CONTAINER}}/cypress
+        run: docker compose --env-file ../.env.test up -d
 
       - name: Wait for server to be ready
         run: |

containers/ecr-viewer/cypress.config.ts

@@ -9,5 +9,6 @@ export default defineConfig({
     env: {
       BASE_PATH: `${isDev ? "/" : "/ecr-viewer"}`,
     },
+    defaultCommandTimeout: 120000,
   },
 });

containers/ecr-viewer/cypress/docker-compose.yml

@@ -0,0 +1,32 @@
+services:
+  # PostgreSQL database
+  db:
+    image: "postgres:alpine"
+    ports:
+      - "5432:5432"
+    volumes:
+      - ../sql/core.sql:/docker-entrypoint-initdb.d/core.sql
+      - ../seed-scripts/sql/01-init.sql:/docker-entrypoint-initdb.d/01-init.sql
+      - ./assets/data.sql:/docker-entrypoint-initdb.d/data.sql
+      - ../seed-scripts/sql/.pgpass/:/usr/local/lib/.pgpass
+    environment:
+      - POSTGRES_USER=postgres
+      - PGUSER=postgres
+      - POSTGRES_PASSWORD=pw
+      - POSTGRES_DB=ecr_viewer_db
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready"]
+      interval: 2s
+      timeout: 5s
+      retries: 20
+
+  # Next.js app
+  ecr-viewer:
+    build:
+      context: ../../..
+      dockerfile: ./containers/ecr-viewer/Dockerfile
+    ports:
+      - "3000:3000"
+    environment:
+      - DATABASE_URL=${DATABASE_URL:-postgres://postgres:pw@db:5432/ecr_viewer_db}
+      - APP_ENV=${APP_ENV:-prod}

containers/ecr-viewer/docker-compose.yml

@@ -5,8 +5,8 @@ services:
     ports:
       - "5432:5432"
     volumes:
-      - ./sql/:/docker-entrypoint-initdb.d/
-      - ./seed-scripts/sql/:/docker-entrypoint-initdb.d/
+      - ./sql/core.sql:/docker-entrypoint-initdb.d/core.sql
+      - ./seed-scripts/sql/01-init.sql:/docker-entrypoint-initdb.d/01-init.sql
       - ./seed-scripts/sql/.pgpass/:/usr/local/lib/.pgpass
     environment:
       - POSTGRES_USER=postgres

containers/ecr-viewer/next-env.d.ts

@@ -2,4 +2,4 @@
 /// <reference types="next/image-types/global" />
 
 // NOTE: This file should not be edited
-// see https://nextjs.org/docs/basic-features/typescript for more information.
+// see https://nextjs.org/docs/app/building-your-application/configuring/typescript for more information.

containers/ecr-viewer/package.json

@@ -16,7 +16,7 @@
     "update-cypress-data": "docker compose -f ./seed-scripts/docker-compose-create-sql.yml up --build --abort-on-container-exit",
     "cypress:open": "cypress open",
     "cypress:run": "cypress run",
-    "cypress:run-local": "cp ./cypress/assets/data.sql ./seed-scripts/sql && docker compose --env-file .env.test up db -d && concurrently --kill-others 'npm run dev' 'npx wait-on http://localhost:3000 && NODE_ENV=dev cypress run ; docker compose down && rm ./seed-scripts/sql/data.sql'",
+    "cypress:run-local": "docker compose -f cypress/docker-compose.yml --env-file .env.test up db -d && concurrently --kill-others 'npm run dev' 'npx wait-on http://localhost:3000 && NODE_ENV=dev cypress run ; docker compose down'",
     "cypress:run-prod": "NODE_ENV=production cypress run"
   },
   "dependencies": {

containers/ecr-viewer/seed-scripts/create-e2e-sql.py

@@ -37,11 +37,22 @@ def save_sql_insert_metadata(metadata):
             rule_summary = parsed_values["rule_summary"]
             report_date = parsed_values["report_date"]
             data_source = "DB"
-            query = f"""INSERT INTO fhir_metadata (
-              ecr_id,patient_name_last,patient_name_first,patient_birth_date,data_source,reportable_condition,rule_summary,report_date
-            ) VALUES (
-              '{ecr_id}','{last_name}','{first_name}','{birth_date}','{data_source}','{reportable_condition}','{rule_summary}',{'NULL' if report_date is None else f"'{report_date}'"}
-            ) ON CONFLICT (ecr_id) DO NOTHING;\n"""
+            query = f"""WITH inserted_data AS (
+    INSERT INTO ecr_data (
+        eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date
+    ) VALUES (
+        '{ecr_id}', '{last_name}', '{first_name}', '{birth_date}', '{data_source}', {'NULL' if report_date is None else f"'{report_date}'"}
+    )
+    ON CONFLICT (eICR_ID) DO NOTHING
+    RETURNING eICR_ID
+), inserted_condition AS (
+    INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition)
+    VALUES (uuid_generate_v4(), (SELECT eICR_ID FROM inserted_data), '{reportable_condition}')
+    RETURNING uuid
+)
+INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary)
+VALUES (uuid_generate_v4(), (SELECT uuid FROM inserted_condition), '{rule_summary}')
+RETURNING (SELECT eICR_ID FROM inserted_data);"""
             output_file.write(query)
 
 

containers/ecr-viewer/seed-scripts/docker-compose.yml

@@ -126,8 +126,8 @@ services:
     ports:
       - "5432:5432"
     volumes:
-      - ../sql/:/docker-entrypoint-initdb.d/
-      - ./sql/:/docker-entrypoint-initdb.d/
+      - ./sql/01-init.sql:/docker-entrypoint-initdb.d/01-init.sql
+      - ../sql/core.sql:/docker-entrypoint-initdb.d/core.sql
       - ./sql/.pgpass/:/usr/local/lib/.pgpass
       - db:/var/lib/postgresql/data
     environment:

containers/ecr-viewer/seed-scripts/sql/01-init.sql

@@ -5,18 +5,4 @@ CREATE TABLE IF NOT EXISTS fhir (
   data JSONB NOT NULL,
   date_created TIMESTAMPTZ NOT NULL DEFAULT NOW(),
   PRIMARY KEY (ecr_id)
-);
-
-CREATE TABLE IF NOT EXISTS fhir_metadata(
-  ecr_id VARCHAR(200) NOT NULL,
-  data_source VARCHAR(2) NOT NULL, -- S3 or DB
-  data_link VARCHAR(500), -- Link to the data
-  patient_name_first VARCHAR(100) NOT NULL,
-  patient_name_last VARCHAR(100) NOT NULL,
-  patient_birth_date DATE NOT NULL,
-  reportable_condition VARCHAR(10000),
-  rule_summary VARCHAR(10000),
-  report_date DATE,
-  date_created TIMESTAMPTZ NOT NULL DEFAULT NOW(),
-  PRIMARY KEY (ecr_id)
-)
+);

containers/ecr-viewer/sql/core.sql

@@ -1,10 +1,13 @@
+CREATE EXTENSION IF NOT EXISTS "uuid-ossp";
+
 CREATE TABLE ecr_data (
   eICR_ID VARCHAR(200) PRIMARY KEY,
   data_source VARCHAR(2), -- S3 or DB
-  data_link VARCHAR(500), -- Link to the data
+  fhir_reference_link VARCHAR(500), -- Link to the ecr fhir bundle
   patient_name_first VARCHAR(100),
   patient_name_last VARCHAR(100),
   patient_birth_date DATE,
+  date_created TIMESTAMPTZ NOT NULL DEFAULT NOW(),
   report_date DATE
 );
 

containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts

@@ -192,7 +192,7 @@ export const saveFhirData = async (
  * @param metadata - The FHIR bundle metadata to be saved.
  * @param ecrId - The unique identifier for the Electronic Case Reporting (ECR) associated with the FHIR bundle.
  * @returns A promise that resolves when the FHIR bundle metadata is successfully saved to postgres.
- * @throws {Error} Throws an error if the FHIR bundle metadata cannot be saved to postgress.
+ * @throws {Error} Throws an error if the FHIR bundle metadata cannot be saved to postgres.
  */
 export const saveToMetadataPostgres = async (
   metadata: BundleMetadata,
@@ -203,25 +203,36 @@ export const saveToMetadataPostgres = async (
   const database = db(db_url);
 
   const { ParameterizedQuery: PQ } = pgPromise;
-  const addMetadata = new PQ({
-    text: "INSERT INTO fhir_metadata (ecr_id,patient_name_last,patient_name_first,patient_birth_date,data_source,reportable_condition,rule_summary,report_date) VALUES ($1, $2, $3, $4, $5, $6, $7, $8) RETURNING ecr_id",
+  const saveToEcrData = new PQ({
+    text: "INSERT INTO ecr_data (eICR_ID,patient_name_last,patient_name_first,patient_birth_date,data_source,report_date) VALUES ($1, $2, $3, $4, $5, $6) RETURNING eICR_ID",
     values: [
       ecrId,
-      metadata.first_name,
       metadata.last_name,
+      metadata.first_name,
       metadata.birth_date,
       "DB",
-      metadata.reportable_condition,
-      metadata.rule_summary,
       metadata.report_date,
     ],
   });
 
+  const saveRRConditions = new PQ({
+    text: "INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition) VALUES (uuid_generate_v4(), $1, $2) RETURNING uuid",
+    values: [ecrId, metadata.reportable_condition],
+  });
+
   try {
-    const saveECR = await database.one(addMetadata);
+    const saveECR = await database.one(saveToEcrData);
+    const savedRRCondition = await database.one(saveRRConditions);
+
+    const saveRRSummary = new PQ({
+      text: "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id,rule_summary) VALUES (uuid_generate_v4(), $1, $2)",
+      values: [savedRRCondition.uuid, metadata.rule_summary],
+    });
+
+    await database.none(saveRRSummary);
 
     return NextResponse.json(
-      { message: "Success. Saved metadata to database: " + saveECR.ecr_id },
+      { message: "Success. Saved metadata to database: " + saveECR.eICR_ID },
       { status: 200 },
     );
   } catch (error: any) {

containers/ecr-viewer/src/app/api/services/listEcrDataService.ts

@@ -12,7 +12,7 @@ export type EcrMetadataModel = {
   patient_name_first: string;
   patient_name_last: string;
   patient_birth_date: Date;
-  reportable_condition: string;
+  condition: string;
   rule_summary: string;
   report_date: Date;
   date_created: Date;
@@ -38,13 +38,13 @@ export async function listEcrData(
   startIndex: number,
   itemsPerPage: number,
 ): Promise<EcrDisplay[]> {
-  const fhirMetadataQuery =
-    "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET " +
+  const ecrDataQuery =
+    "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date 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 order by ed.report_date DESC OFFSET " +
     startIndex +
     " ROWS FETCH NEXT " +
     itemsPerPage +
     " ROWS ONLY";
-  let list = await database.manyOrNone<EcrMetadataModel>(fhirMetadataQuery);
+  let list = await database.manyOrNone<EcrMetadataModel>(ecrDataQuery);
   return processMetadata(list);
 }
 
@@ -64,7 +64,7 @@ export const processMetadata = (
       patient_date_of_birth: object.patient_birth_date
         ? formatDate(new Date(object.patient_birth_date!).toISOString())
         : "",
-      reportable_condition: object.reportable_condition || "",
+      reportable_condition: object.condition || "",
       rule_summary: object.rule_summary || "",
       date_created: object.date_created
         ? convertUTCToLocalString(
@@ -81,10 +81,10 @@ export const processMetadata = (
 };
 
 /**
- * Retrieves the total number of eCRs stored in the fhir table.
+ * Retrieves the total number of eCRs stored in the ecr_data table.
  * @returns A promise resolving to the total number of eCRs.
  */
 export const getTotalEcrCount = async (): Promise<number> => {
-  let number = await database.one("SELECT count(*) FROM fhir_metadata");
+  let number = await database.one("SELECT count(*) FROM ecr_data");
   return number.count;
 };

containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx

@@ -25,7 +25,7 @@ describe("listEcrDataService", () => {
           patient_name_last: "Person",
           patient_birth_date: new Date(),
           report_date: new Date(),
-          reportable_condition: "Long",
+          condition: "Long",
           rule_summary: "Longer",
           data_source: "DB",
           data: "",
@@ -38,7 +38,7 @@ describe("listEcrDataService", () => {
           patient_name_last: "Test",
           patient_birth_date: new Date(),
           report_date: new Date(),
-          reportable_condition: "Stuff",
+          condition: "Stuff",
           rule_summary: "Other stuff",
           data_source: "DB",
           data: "",
@@ -103,7 +103,7 @@ describe("listEcrDataService", () => {
       database.manyOrNone = jest.fn(() => Promise.resolve([]));
       const actual = await listEcrData(startIndex, itemsPerPage);
       expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith(
-        "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
+        "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date 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 order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
       );
       expect(actual).toBeEmpty();
     });
@@ -118,7 +118,7 @@ describe("listEcrDataService", () => {
             patient_name_first: "Billy",
             patient_name_last: "Bob",
             report_date: new Date("06/21/2024 8:00 AM EDT"),
-            reportable_condition: "stuff",
+            condition: "stuff",
             rule_summary: "yup",
             data: "",
             data_link: "",
@@ -132,7 +132,7 @@ describe("listEcrDataService", () => {
       const actual: EcrDisplay[] = await listEcrData(startIndex, itemsPerPage);
 
       expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith(
-        "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
+        "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date 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 order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
       );
       expect(actual).toEqual([
         {
@@ -158,7 +158,7 @@ describe("listEcrDataService", () => {
             patient_name_last: "lnam",
             patient_birth_date: new Date("1990-01-01T05:00:00.000Z"),
             report_date: new Date("2024-06-20T04:00:00.000Z"),
-            reportable_condition: "sick",
+            condition: "sick",
             rule_summary: "stuff",
             data: "",
             data_link: "",
@@ -171,7 +171,7 @@ describe("listEcrDataService", () => {
       let itemsPerPage = 25;
       const actual: EcrDisplay[] = await listEcrData(startIndex, itemsPerPage);
       expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith(
-        "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
+        "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date 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 order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
       );
       expect(actual).toEqual([
         {