Merge branch 'main' into rob/2646-align-patient-info-population-betwe…

…en-design-and-dev

containers/ecr-viewer/seed-scripts/create-seed-data.py

@@ -14,7 +14,7 @@ def convert_files():
     :return: A list of fhir bundles
     """
     print("Converting files...")
-    subfolders = ["LA", "TN", "ME", "KY"]
+    subfolders = ["LA"]
     # Iterate over the subfolders
     for subfolder in subfolders:
         subfolder_path = os.path.join(BASEDIR, "baseECR", subfolder)

containers/tefca-viewer/README.md

@@ -1,16 +1,22 @@
-## Getting Started with TEFCA Viewer
+## Getting Started with Query Connector
 
 ### Introduction
 
-The DIBBs TEFCA Viewer app offers a REST API for searching for a patient and viewng information tied to your case investigation.
+The DIBBs Query Connector app offers a REST API for searching for a patient and viewing information tied to your case investigation.
 
-### Running TEFCA Viewer
+### Running Query Connector
 
-The TEFCA Viewer app can be run using Docker (or any other OCI container runtime e.g., Podman), or directly from the Node.js source code.
+The Query Connector app can be run using Docker (or any other OCI container runtime e.g., Podman), or directly from the Node.js source code.
+
+#### Obtaining an eRSD API Key
+
+Before running the Query Connector locally, you will need to obtain an API key for the electronic Reporting and Surveillance Distribution (eRSD). With the API key, you have access to 200+ pre-built queries for reportable conditions, e.g., chlamydia, influenza, hepatitis A, etc. These queries can be used and modified in the Query Connector app.
+
+To obtain a free API key, please visit https://ersd.aimsplatform.org/#/api-keys and follow the sign up instructions. Add your API key as an environment variable called `ERSD_API_KEY` in an `.env` file that can be accessed when running the Query Connector app.
 
 #### Running with Docker (Recommended)
 
-To run the TEFCA Viewer app with Docker, follow these steps.
+To run the Query Connector app with Docker, follow these steps.
 
 1. Confirm that you have Docker installed by running `docker -v`. If you do not see a response similar to what is shown below, follow [these instructions](https://docs.docker.com/get-docker/) to install Docker.
 
@@ -23,21 +29,21 @@ Docker version 20.10.21, build baeda1f
    1. If you're using an M1 Mac, you'll need to tell Docker to pull the non-Apple Silicon image using `docker pull --platform linux/amd64 ghcr.io/cdcgov/phdi/tefca-viewer:latest` since we don't have a image for Apple Silicon. If you're using this setup, there might be some issues with architecture incompatability that the team hasn't run into, so please flag if you run into something!
 3. Run the service with `docker run -p 3000:3000 tefca-viewer:latest`. If you're on a Windows machine, you may need to run `docker run -p 3000:3000 ghcr.io/cdcgov/phdi/tefca-viewer:latest` instead.
 
-Congratulations, the TEFCA Viewer app should now be running on `localhost:3000/tefca-viewer`!
+Congratulations, the Query Connector app should now be running on `localhost:3000/tefca-viewer`!
 
 #### Running from Node.js Source Code
 
-We recommend running the TEFCA Viewer app from a container, but if that is not feasible for a given use-case, it may also be run directly from Node using the steps below.
+We recommend running the Query Connector app from a container, but if that is not feasible for a given use-case, it may also be run directly from Node using the steps below.
 
 1. Ensure that both Git and Node 18.x or higher are installed.
 2. Clone the PHDI repository with `git clone https://github.com/CDCgov/phdi`.
 3. Navigate to `/phdi/containers/tefca-viewer/`.
-4. Install all of the Node dependencies for the TEFCA Viewer app with `npm install`.
-5. Run the TEFCA Viewer app on `localhost:3000` with `npm run dev`. If you are on a Windows Machine, you may need to run `npm run dev-win` instead.
+4. Install all of the Node dependencies for the Query Connector app with `npm install`.
+5. Run the Query Connector app on `localhost:3000` with `npm run dev`. If you are on a Windows Machine, you may need to run `npm run dev-win` instead.
 
 ### Building the Docker Image
 
-To build the Docker image for the TEFCA Viewer app from source instead of downloading it from the PHDI repository follow these steps.
+To build the Docker image for the Query Connector app from source instead of downloading it from the PHDI repository follow these steps.
 
 1. Ensure that both [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) and [Docker](https://docs.docker.com/get-docker/) are installed.
 2. Clone the PHDI repository with `git clone https://github.com/CDCgov/phdi`.
@@ -46,7 +52,7 @@ To build the Docker image for the TEFCA Viewer app from source instead of downlo
 
 ### Running via docker-compose (WIP)
 
-The TEFCA Viewer will eventually require other inputs from other DIBBs services. For now, this is a simplified docker compose file that starts the Node service. This can be run with `docker compose up --build`. See the [Docker Compose documentation](https://docs.docker.com/engine/reference/commandline/compose_up/) for additional information.
+The Query Connector will eventually require other inputs from other DIBBs services. For now, this is a simplified docker compose file that starts the Node service. This can be run with `docker compose up --build`. See the [Docker Compose documentation](https://docs.docker.com/engine/reference/commandline/compose_up/) for additional information.
 
 ### Developer Documentation
 

containers/tefca-viewer/docker-compose-dev.yaml

@@ -10,6 +10,8 @@ services:
       - POSTGRES_DB=tefca_db
       # Note: you must have a local .env file with the DATABASE_URL set to the following:
       # DATABASE_URL=postgresql://postgres:pw@localhost:5432/tefca_db
+      # Note: you must have a local .env file with the ERSD_API_KEY set to a key
+      # obtained from the ERSD API at https://ersd.aimsplatform.org/#/api-keys
     healthcheck:
       test: ["CMD-SHELL", "pg_isready -U postgres"]
       interval: 2s

containers/tefca-viewer/docker-compose.yaml

@@ -26,6 +26,8 @@ services:
     environment:
       - NODE_ENV=production
       - DATABASE_URL=postgres://postgres:pw@db:5432/tefca_db
+      # Note: you must have a local .env file with the ERSD_API_KEY set to a key
+      # obtained from the ERSD API at https://ersd.aimsplatform.org/#/api-keys
     depends_on:
       db:
         condition: service_healthy

containers/tefca-viewer/src/app/database-service.ts

@@ -1,6 +1,6 @@
 "use server";
 import { Pool, PoolConfig, QueryResultRow } from "pg";
-// import dotenv from "dotenv";
+import { Bundle, OperationOutcome } from "fhir/r4";
 import { ValueSetItem, valueSetTypeToClincalServiceTypeMap } from "./constants";
 
 const getQuerybyNameSQL = `
@@ -87,3 +87,35 @@ export const mapQueryRowsToValueSetItems = async (rows: QueryResultRow[]) => {
   });
   return vsItems;
 };
+
+/*
+ * The expected return type from the eRSD API.
+ */
+type ErsdResponse = Bundle | OperationOutcome;
+
+/**
+ * Fetches the eRSD Specification from the eRSD API. This function requires an API key
+ * to access the eRSD API. The API key can be obtained at https://ersd.aimsplatform.org/#/api-keys.
+ * @param eRSDVersion - The version of the eRSD specification to retrieve. Defaults to v2.
+ * @returns The eRSD Specification as a FHIR Bundle or an OperationOutcome if an error occurs.
+ */
+export async function getERSD(eRSDVersion: number = 2): Promise<ErsdResponse> {
+  const ERSD_API_KEY = process.env.ERSD_API_KEY;
+  const eRSDUrl = `https://ersd.aimsplatform.org/api/ersd/v${eRSDVersion}specification?format=json&api-key=${ERSD_API_KEY}`;
+  const response = await fetch(eRSDUrl);
+  if (response.status === 200) {
+    const data = (await response.json()) as Bundle;
+    return data;
+  } else {
+    return {
+      resourceType: "OperationOutcome",
+      issue: [
+        {
+          severity: "error",
+          code: "processing",
+          diagnostics: `Failed to retrieve data from eRSD: ${response.status} ${response.statusText}`,
+        },
+      ],
+    } as OperationOutcome;
+  }
+}