feat: add set id to core schema (#3082)

* add set id to core schema * add set_id to core schema * add eicr_set_id to bundle metadata and save it to db * add save metadata to postgres tests
CDCgov · Dec 23, 2024 · 0fa0ec6 · 0fa0ec6
1 parent 0f6cfda
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diff --git a/containers/ecr-viewer/sql/core.sql b/containers/ecr-viewer/sql/core.sql
@@ -2,6 +2,7 @@ CREATE EXTENSION IF NOT EXISTS "uuid-ossp";
 
 CREATE TABLE ecr_data (
   eICR_ID VARCHAR(200) PRIMARY KEY,
+  set_id VARCHAR(255),
   data_source VARCHAR(2), -- S3 or DB
   fhir_reference_link VARCHAR(500), -- Link to the ecr fhir bundle
   patient_name_first VARCHAR(100),

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
@@ -493,14 +493,15 @@ export const saveMetadataToPostgres = async (
     await database.tx(async (t) => {
       // Insert main ECR metadata
       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)",
+        text: "INSERT INTO ecr_data (eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date, set_id) VALUES ($1, $2, $3, $4, $5, $6, $7)",
         values: [
           ecrId,
           metadata.last_name,
           metadata.first_name,
           metadata.birth_date,
           "DB",
           metadata.report_date,
+          metadata.eicr_set_id,
         ],
       });
 

diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/types.ts
@@ -84,6 +84,7 @@ export interface BundleMetadata {
   first_name: string;
   birth_date: string;
   data_source: string;
+  eicr_set_id: string | undefined;
   rr: RR[] | undefined;
   report_date: string;
 }
diff --git a/containers/ecr-viewer/src/app/tests/save-fhir-data-service.test.tsx b/containers/ecr-viewer/src/app/tests/save-fhir-data-service.test.tsx
@@ -0,0 +1,173 @@
+/**
+ * @jest-environment node
+ */
+
+import { saveMetadataToPostgres } from "../api/save-fhir-data/save-fhir-data-service";
+import { BundleMetadata } from "../api/save-fhir-data/types";
+import { getDB } from "../api/services/postgres_db";
+
+jest.mock("../api/services/postgres_db", () => ({
+  getDB: jest.fn(),
+}));
+
+describe("saveMetadataToPostgres", () => {
+  const mockTransaction = {
+    query: jest.fn(),
+    none: jest.fn(),
+    one: jest.fn(),
+  };
+
+  const baseMetadata: BundleMetadata = {
+    last_name: "lname",
+    first_name: "fname",
+    birth_date: "01/01/2000",
+    data_source: "s3",
+    eicr_set_id: "1234",
+    rr: [],
+    report_date: "12/20/2024",
+  };
+
+  const saveEcrDataQuery =
+    "INSERT INTO ecr_data (eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date, set_id) VALUES ($1, $2, $3, $4, $5, $6, $7)";
+  const saveRRConditionsQuery =
+    "INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition) VALUES (uuid_generate_v4(), $1, $2) RETURNING uuid";
+  const saveRRSummaryQuery =
+    "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary) VALUES (uuid_generate_v4(), $1, $2)";
+  beforeEach(() => {
+    const mockDatabase = {
+      tx: jest.fn(),
+    };
+
+    mockDatabase.tx.mockImplementation(async (callback) => {
+      return callback(mockTransaction);
+    });
+
+    (getDB as jest.Mock).mockReturnValue({
+      database: mockDatabase,
+      pgPromise: {
+        ParameterizedQuery: jest
+          .fn()
+          .mockImplementation(({ text, values }: any) => ({
+            text,
+            values,
+          })),
+      },
+    });
+  });
+
+  afterEach(() => {
+    jest.resetAllMocks();
+  });
+  it("should save without any rr", async () => {
+    const resp = await saveMetadataToPostgres(baseMetadata, "1-2-3-4");
+
+    expect(resp.message).toEqual("Success. Saved metadata to database.");
+    expect(resp.status).toEqual(200);
+    expect(mockTransaction.one).not.toHaveBeenCalled();
+    expect(mockTransaction.none).toHaveBeenCalledExactlyOnceWith({
+      text: saveEcrDataQuery,
+      values: [
+        "1-2-3-4",
+        "lname",
+        "fname",
+        "01/01/2000",
+        "DB",
+        "12/20/2024",
+        "1234",
+      ],
+    });
+  });
+
+  it("should save with rr without rule summaries", async () => {
+    const metadata: BundleMetadata = {
+      ...baseMetadata,
+      rr: [
+        {
+          condition: "flu",
+          rule_summaries: [],
+        },
+      ],
+    };
+
+    mockTransaction.one.mockReturnValue({ uuid: "return-id-1" });
+
+    const resp = await saveMetadataToPostgres(metadata, "1-2-3-4");
+
+    expect(resp.message).toEqual("Success. Saved metadata to database.");
+    expect(resp.status).toEqual(200);
+    expect(mockTransaction.one).toHaveBeenCalledExactlyOnceWith({
+      text: saveRRConditionsQuery,
+      values: ["1-2-3-4", "flu"],
+    });
+    expect(mockTransaction.none).toHaveBeenCalledExactlyOnceWith({
+      text: saveEcrDataQuery,
+      values: [
+        "1-2-3-4",
+        "lname",
+        "fname",
+        "01/01/2000",
+        "DB",
+        "12/20/2024",
+        "1234",
+      ],
+    });
+  });
+
+  it("should save with rr with rule summaries", async () => {
+    const metadata: BundleMetadata = {
+      ...baseMetadata,
+      rr: [
+        {
+          condition: "flu",
+          rule_summaries: [{ summary: "fever" }, { summary: "influenza" }],
+        },
+      ],
+    };
+
+    mockTransaction.one.mockReturnValueOnce({ uuid: "return-id-1" });
+
+    const resp = await saveMetadataToPostgres(metadata, "1-2-3-4");
+
+    expect(resp.message).toEqual("Success. Saved metadata to database.");
+    expect(resp.status).toEqual(200);
+    expect(mockTransaction.one).toHaveBeenCalledExactlyOnceWith({
+      text: saveRRConditionsQuery,
+      values: ["1-2-3-4", "flu"],
+    });
+    expect(mockTransaction.none).toHaveBeenCalledTimes(3);
+    expect(mockTransaction.none).toHaveBeenNthCalledWith(1, {
+      text: saveEcrDataQuery,
+      values: [
+        "1-2-3-4",
+        "lname",
+        "fname",
+        "01/01/2000",
+        "DB",
+        "12/20/2024",
+        "1234",
+      ],
+    });
+
+    expect(mockTransaction.none).toHaveBeenNthCalledWith(2, {
+      text: saveRRSummaryQuery,
+      values: ["return-id-1", "fever"],
+    });
+    expect(mockTransaction.none).toHaveBeenNthCalledWith(3, {
+      text: saveRRSummaryQuery,
+      values: ["return-id-1", "influenza"],
+    });
+  });
+
+  it("should return an error when db save fails", async () => {
+    jest.spyOn(console, "error").mockImplementation(() => {});
+
+    mockTransaction.none.mockRejectedValue({ error: "Connection timed out" });
+
+    const resp = await saveMetadataToPostgres(baseMetadata, "1-2-3-4");
+
+    expect(resp.message).toEqual("Failed to insert metadata to database.");
+    expect(resp.status).toEqual(500);
+    expect(mockTransaction.none).toHaveBeenCalledOnce();
+    expect(mockTransaction.one).not.toHaveBeenCalled();
+  });
+});
diff --git a/containers/message-parser/app/default_schemas/core.json b/containers/message-parser/app/default_schemas/core.json
@@ -4,6 +4,11 @@
     "data_type": "string",
     "nullable": false
   },
+  "eicr_set_id": {
+    "fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition').identifier.where(type.coding.code = '55751-2').where(use='official').value",
+    "data_type": "string",
+    "nullable": true
+  },
   "last_name": {
     "fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').name.first().family",
     "data_type": "string",