Conditions Endpoint

containers/ecr-viewer/docker-compose.yml

@@ -19,6 +19,10 @@ 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}
     profiles:
       - ecr-viewer
 

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

@@ -2,6 +2,14 @@
 
 /opt/mssql/bin/sqlservr &
 
+# Wait for SQL Server to start up
+until /opt/mssql-tools18/bin/sqlcmd -S localhost -U sa -P $MSSQL_SA_PASSWORD -Q "SELECT 1" -C &>/dev/null; do
+    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/seed-scripts/sql/extended.sql

@@ -0,0 +1,86 @@
+CREATE TABLE ECR_DATA
+(
+    eICR_ID                  VARCHAR(200) PRIMARY KEY,
+    set_id                   VARCHAR(255),
+    fhir_reference_link      VARCHAR(255),
+    last_name                VARCHAR(255),
+    first_name               VARCHAR(255),
+    birth_date               DATE,
+    gender                   VARCHAR(50),
+    birth_sex                VARCHAR(50),
+    gender_identity          VARCHAR(50),
+    race                     VARCHAR(255),
+    ethnicity                VARCHAR(255),
+    street_address_1         VARCHAR(255),
+    street_address_2         VARCHAR(255),
+    state                    VARCHAR(50),
+    zip_code                 VARCHAR(20),
+    latitude                 FLOAT,
+    longitude                FLOAT,
+    homelessness_status      VARCHAR(255),
+    disabilities             VARCHAR(255),
+    tribal_affiliation       VARCHAR(255),
+    tribal_enrollment_status VARCHAR(255),
+    current_job_title        VARCHAR(255),
+    current_job_industry     VARCHAR(255),
+    usual_occupation         VARCHAR(255),
+    usual_industry           VARCHAR(255),
+    preferred_language       VARCHAR(255),
+    pregnancy_status         VARCHAR(255),
+    rr_id                    VARCHAR(255),
+    processing_status        VARCHAR(255),
+    eicr_version_number      VARCHAR(50),
+    authoring_date           DATE,
+    authoring_time           TIME,
+    authoring_provider       VARCHAR(255),
+    provider_id              VARCHAR(255),
+    facility_id              VARCHAR(255),
+    facility_name            VARCHAR(255),
+    encounter_type           VARCHAR(255),
+    encounter_start_date     DATE,
+    encounter_start_time     TIME,
+    encounter_end_date       DATE,
+    encounter_end_time       TIME,
+    reason_for_visit         VARCHAR(MAX),
+    active_problems          VARCHAR(MAX)
+);
+
+CREATE TABLE ecr_rr_conditions
+(
+    UUID      VARCHAR(200) PRIMARY KEY,
+    eICR_ID   VARCHAR(200) NOT NULL REFERENCES ECR_DATA (eICR_ID),
+    condition VARCHAR(MAX)
+);
+
+CREATE TABLE ecr_rr_rule_summaries
+(
+    UUID                 VARCHAR(200) PRIMARY KEY,
+    ECR_RR_CONDITIONS_ID VARCHAR(200) REFERENCES ecr_rr_conditions (UUID),
+    rule_summary         VARCHAR(MAX)
+);
+
+
+CREATE TABLE ecr_labs
+(
+    UUID                                   VARCHAR(200) PRIMARY KEY,
+    eICR_ID                                VARCHAR(200) REFERENCES ECR_DATA (eICR_ID),
+    test_type                              VARCHAR(255),
+    test_type_code                         VARCHAR(50),
+    test_type_system                       VARCHAR(MAX),
+    test_result_qualitative                VARCHAR(MAX),
+    test_result_quantitative               FLOAT,
+    test_result_units                      VARCHAR(50),
+    test_result_code                       VARCHAR(50),
+    test_result_code_display               VARCHAR(255),
+    test_result_code_system                VARCHAR(50),
+    test_result_interpretation             VARCHAR(255),
+    test_result_interpretation_code        VARCHAR(50),
+    test_result_interpretation_system      VARCHAR(255),
+    test_result_reference_range_low_value  FLOAT,
+    test_result_reference_range_low_units  VARCHAR(50),
+    test_result_reference_range_high_value FLOAT,
+    test_result_reference_range_high_units VARCHAR(50),
+    specimen_type                          VARCHAR(255),
+    specimen_collection_date               DATE,
+    performing_lab                         VARCHAR(255)
+);

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

@@ -0,0 +1,19 @@
+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 source" }, { status: 500 });
+  }
+}

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

@@ -0,0 +1,65 @@
+import pgPromise from "pg-promise";
+import { database } from "../services/db";
+import { NextResponse } from "next/server";
+import sql from "mssql";
+/**
+ * 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 () => {
+  console.log("Get conditions from postgres");
+
+  const { ParameterizedQuery: PQ } = pgPromise;
+
+  try {
+    const response = await database.tx(async (t) => {
+      const getConditions = new PQ({
+        text: 'SELECT DISTINCT "condition" FROM ecr_rr_conditions',
+      });
+
+      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 () => {
+  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,
+    },
+  });
+
+  try {
+    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 ",
+    );
+    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/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;
-  }
+  let 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

@@ -175,14 +175,22 @@ export const saveMetadataToSqlServer = async (
   metadata: BundleExtendedMetadata,
   ecrId: string,
 ) => {
-  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,
-    },
-  });
+  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 || "localhost",
+      options: {
+        trustServerCertificate: true,
+      },
+    });
+  } catch (error: any) {
+    return NextResponse.json(
+      { message: "Failed to connect to SQL Server. " + error.message },
+      { status: 500 },
+    );
+  }
 
   const transaction = new sql.Transaction(pool);
   await transaction.begin();
@@ -290,10 +298,14 @@ export const saveMetadataToSqlServer = async (
             .input("eICR_ID", sql.VarChar(200), metadata.eicr_id)
             .input("test_type", sql.VarChar(200), lab.test_type)
             .input("test_type_code", sql.VarChar(50), lab.test_type_code)
-            .input("test_type_system", sql.VarChar(50), lab.test_type_system)
+            .input(
+              "test_type_system",
+              sql.VarChar(sql.MAX),
+              lab.test_type_system,
+            )
             .input(
               "test_result_qualitative",
-              sql.VarChar(255),
+              sql.VarChar(sql.MAX),
               lab.test_result_qualitative,
             )
             .input(
@@ -383,6 +395,7 @@ export const saveMetadataToSqlServer = async (
         { status: 200 },
       );
     } catch (error: any) {
+      console.log(metadata);
       console.error("Error inserting metadata to database:", error);
 
       // Rollback the transaction if any error occurs
@@ -494,18 +507,21 @@ export const saveWithMetadata = async (
   saveSource: string,
   metadata: BundleMetadata | BundleExtendedMetadata,
 ) => {
+  console.log("Saving FHIR data with metadata");
   let fhirDataResult;
   let metadataResult;
   const metadataSaveLocation = process.env.METADATA_DATABASE_TYPE;
   try {
     fhirDataResult = await saveFhirData(fhirBundle, ecrId, saveSource);
 
     if (metadataSaveLocation == "postgres") {
+      console.log("Saving metadata to Postgres");
       metadataResult = await saveMetadataToPostgres(
         metadata as BundleMetadata,
         ecrId,
       );
     } else if (metadataSaveLocation == "sqlserver") {
+      console.log("Saving metadata to SQL Server");
       metadataResult = await saveMetadataToSqlServer(
         metadata as BundleExtendedMetadata,
         ecrId,