Conditions Endpoint (#2934)

* Conditions endpoint

* Fixes to get SQLServer to run, and fix SQL query

* Unit tests

* Revert the complete removal of saveSource

* Remove debug statements, reduce size of test_type_system

* Update tests with order by

* Centralize SQL Server pool, and extended.sql

* Removed renamed db.ts

* [pre-commit.ci] auto fixes from pre-commit hooks

* Update postgres_db name

* Correct postgres spelling

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Josh Nygaard <[email protected]>

containers/ecr-viewer/docker-compose.yml

@@ -10,7 +10,6 @@ services:
     environment:
       - APP_ENV=${APP_ENV:-test}
       - METADATA_DATABASE_TYPE=${METADATA_DATABASE_TYPE:-postgres}
-      - METADATA_DATABASE_SCHEMA=${METADATA_DATABASE_SCHEMA}
       - SOURCE=${SOURCE:-postgres}
       - DATABASE_URL=postgres://postgres:pw@postgres:5432/ecr_viewer_db
       - AWS_CUSTOM_ENDPOINT=http://aws-storage:4566
@@ -22,6 +21,7 @@ services:
       - AZURE_CONTAINER_NAME=${AZURE_CONTAINER_NAME:-ecr-viewer-files}
       - NEXT_PUBLIC_NON_INTEGRATED_VIEWER=${NEXT_PUBLIC_NON_INTEGRATED_VIEWER:-false}
       - NEXT_PUBLIC_BASEPATH=${NEXT_PUBLIC_BASEPATH:-/ecr-viewer}
+      - METADATA_DATABASE_SCHEMA=${METADATA_DATABASE_SCHEMA:-core}
       - SQL_SERVER_USER=${SQL_SERVER_USER}
       - SQL_SERVER_PASSWORD=${SQL_SERVER_PASSWORD}
       - SQL_SERVER_HOST=${SQL_SERVER_HOST:-sqlserver}
@@ -37,6 +37,7 @@ services:
       - ./sql/core.sql:/docker-entrypoint-initdb.d/core.sql
       - ./seed-scripts/sql/.pgpass/:/usr/local/lib/.pgpass
       - db:/var/lib/postgresql/data
+      - ./sql/extended.sql:/var/opt/mssql/scripts/extended.sql
     environment:
       - POSTGRES_USER=postgres
       - PGUSER=postgres

containers/ecr-viewer/seed-scripts/sql/entrypoint.sh

@@ -7,8 +7,9 @@ until /opt/mssql-tools18/bin/sqlcmd -S localhost -U sa -P $MSSQL_SA_PASSWORD -Q
     echo "Waiting for SQL Server to start..."
     sleep 1
 done
+echo "SQL Server ready."
 
 # Run your SQL script
 /opt/mssql-tools18/bin/sqlcmd -S localhost -U sa -P $MSSQL_SA_PASSWORD -d master -i /var/opt/mssql/scripts/extended.sql -C
 
-wait
+wait

containers/ecr-viewer/src/app/api/conditions/route.ts

@@ -0,0 +1,22 @@
+import { NextResponse } from "next/server";
+import { get_conditions_postgres, get_conditions_sqlserver } from "./service";
+
+/**
+ * Retrieves FHIR data from PostgreSQL database based on eCR ID.
+ * @returns A promise resolving to a NextResponse object.
+ */
+export async function GET() {
+  const metadataSaveLocation = process.env.METADATA_DATABASE_TYPE;
+
+  switch (metadataSaveLocation) {
+    case "postgres":
+      return await get_conditions_postgres();
+    case "sqlserver":
+      return await get_conditions_sqlserver();
+    default:
+      return NextResponse.json(
+        { message: "Invalid metadata save location: " + metadataSaveLocation },
+        { status: 500 },
+      );
+  }
+}

containers/ecr-viewer/src/app/api/conditions/service.ts

@@ -0,0 +1,63 @@
+import pgPromise from "pg-promise";
+import { database } from "../services/postgres_db";
+import { NextResponse } from "next/server";
+import sql from "mssql";
+import { get_pool } from "../services/sqlserver_db";
+/**
+ * Retrieves all unique conditions from the ecr_rr_conditions table in the PostgreSQL database.
+ * @returns A promise resolving to a NextResponse object.
+ * @throws An error if the connection to the PostgreSQL database fails.
+ */
+export const get_conditions_postgres = async () => {
+  const { ParameterizedQuery: PQ } = pgPromise;
+
+  try {
+    const response = await database.tx(async (t) => {
+      const getConditions = new PQ({
+        text: 'SELECT DISTINCT "condition" FROM ecr_rr_conditions ORDER BY "condition"',
+      });
+
+      const conditions = await t.any(getConditions);
+      return NextResponse.json(
+        conditions.map((c) => c.condition),
+        { status: 200 },
+      );
+    });
+
+    return response;
+  } catch (error: any) {
+    console.error("Error fetching data:", error);
+    return NextResponse.json({ message: error.message }, { status: 500 });
+  }
+};
+
+/**
+ * Retrieves all unique conditions from the ecr_rr_conditions table in the SQL Server database.
+ * @returns A promise resolving to a NextResponse object.
+ * @throws An error if the connection to the SQL Server database fails.
+ */
+export const get_conditions_sqlserver = async () => {
+  try {
+    let pool = await get_pool();
+    if (!pool) {
+      return NextResponse.json(
+        { message: "Failed to connect to SQL Server." },
+        { status: 500 },
+      );
+    }
+
+    const transaction = new sql.Transaction(pool);
+    await transaction.begin();
+    const request = new sql.Request(transaction);
+
+    const result = await request.query(
+      "SELECT DISTINCT erc.[condition] FROM ecr_rr_conditions erc ORDER BY erc.[condition]",
+    );
+    const conditions: string[] = result.recordset.map((row) => row.condition);
+
+    return NextResponse.json(conditions, { status: 200 });
+  } catch (error: any) {
+    console.error("Error fetching data:", error);
+    return NextResponse.json({ message: error.message }, { status: 500 });
+  }
+};

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

@@ -7,7 +7,7 @@ import {
   BlobServiceClient,
 } from "@azure/storage-blob";
 import { loadYamlConfig, streamToJson } from "../utils";
-import { database } from "../services/db";
+import { database } from "../services/postgres_db";
 import { s3Client } from "../services/s3Client";
 
 /**

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

@@ -10,13 +10,11 @@ import { S3_SOURCE, AZURE_SOURCE, POSTGRES_SOURCE } from "@/app/api/utils";
 export async function POST(request: NextRequest) {
   let requestBody;
   let fhirBundle;
-  let saveSource;
   let ecrId;
 
   try {
     requestBody = await request.json();
     fhirBundle = requestBody.fhirBundle;
-    saveSource = requestBody.saveSource;
     ecrId = requestBody.fhirBundle.entry[0].resource.id;
   } catch (error: any) {
     console.error("Error reading request body:", error);
@@ -36,9 +34,7 @@ export async function POST(request: NextRequest) {
     );
   }
 
-  if (!saveSource) {
-    saveSource = process.env.SOURCE;
-  }
+  const saveSource = requestBody.saveSource || process.env.SOURCE;
 
   if (
     [S3_SOURCE, AZURE_SOURCE, POSTGRES_SOURCE].includes(saveSource) == false

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

@@ -1,14 +1,15 @@
 import { BlobServiceClient } from "@azure/storage-blob";
 import { NextResponse } from "next/server";
 import pgPromise from "pg-promise";
-import { database, db_url } from "../services/db";
+import { database, db_url } from "../services/postgres_db";
 import { PutObjectCommand, PutObjectCommandOutput } from "@aws-sdk/client-s3";
 import { Bundle } from "fhir/r4";
 import { S3_SOURCE, AZURE_SOURCE, POSTGRES_SOURCE } from "@/app/api/utils";
 import sql from "mssql";
 import { randomUUID } from "crypto";
 import { BundleExtendedMetadata, BundleMetadata } from "./types";
 import { s3Client } from "../services/s3Client";
+import { get_pool } from "../services/sqlserver_db";
 
 /**
  * Saves a FHIR bundle to a postgres database.
@@ -175,19 +176,11 @@ export const saveMetadataToSqlServer = async (
   metadata: BundleExtendedMetadata,
   ecrId: string,
 ) => {
-  let pool;
-  try {
-    pool = await sql.connect({
-      user: process.env.SQL_SERVER_USER,
-      password: process.env.SQL_SERVER_PASSWORD,
-      server: process.env.SQL_SERVER_HOST,
-      options: {
-        trustServerCertificate: true,
-      },
-    });
-  } catch (error: any) {
+  let pool = await get_pool();
+
+  if (!pool) {
     return NextResponse.json(
-      { message: "Failed to connect to SQL Server. " + error.message },
+      { message: "Failed to connect to SQL Server." },
       { status: 500 },
     );
   }

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

@@ -1,4 +1,4 @@
-import { database } from "@/app/api/services/db";
+import { database } from "@/app/api/services/postgres_db";
 import {
   convertUTCToLocalString,
   formatDate,

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

@@ -0,0 +1,17 @@
+import sql from "mssql";
+
+/**
+ * Connect to the SQL Server database and return a connection pool.
+ * @returns A promise resolving to a connection pool.
+ */
+export const get_pool = async () => {
+  let pool = await sql.connect({
+    user: process.env.SQL_SERVER_USER,
+    password: process.env.SQL_SERVER_PASSWORD,
+    server: process.env.SQL_SERVER_HOST || "localhost",
+    options: {
+      trustServerCertificate: true,
+    },
+  });
+  return pool;
+};

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

@@ -11,7 +11,7 @@ import {
   generateFilterConditionsStatement,
   generateWhereStatement,
 } from "@/app/api/services/listEcrDataService";
-import { database } from "../services/db";
+import { database } from "../services/postgres_db";
 import {
   convertUTCToLocalString,
   formatDate,