Merge pull request #92 from mcode/dev

Merge dev for v0.11
mcode · Jun 19, 2023 · 1a5d26f · 1a5d26f
2 parents 615c7bf + 00879b0
commit 1a5d26f
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diff --git a/EndToEndSetupGuide.md b/EndToEndSetupGuide.md
@@ -13,6 +13,8 @@ Follow this guide if you would like to start each application without using Dock
 	- test-ehr
 - node
 	- REMS, pims, dtr, rems-smart-on-fhir, crd-request-generator
+- git
+	- On Windows 'Git Bash' was used for the command line interface
 
 ## Installation Order
 1. Clone each Repo
@@ -21,12 +23,13 @@ Follow this guide if you would like to start each application without using Dock
 
 ## Clone Repos
 ```
-git clone git@github.com:mcode/test-ehr.git
-git clone git@github.com:mcode/crd-request-generator.git
-git clone git@github.com:mcode/REMS.git
-git clone git@github.com:mcode/pims.git
-git clone git@github.com:mcode/dtr.git
-git clone git@github.com:mcode/rems-smart-on-fhir.git
+git clone https://github.com/mcode/test-ehr.git
+git clone https://github.com/mcode/crd-request-generator.git
+git clone https://github.com/mcode/REMS.git
+git clone https://github.com/mcode/pims.git
+git clone https://github.com/mcode/dtr.git
+git clone https://github.com/mcode/rems-smart-on-fhir.git
+git clone https://github.com/mcode/rems-smart-on-fhir.git
 ```
 
 ## Utilities
@@ -159,14 +162,32 @@ git clone git@github.com:mcode/rems-smart-on-fhir.git
 
 	`cd pims`
 
-- Setup
+- Backend
+	- Navigate to the backend directory
+		
+		`cd backend`
+	- Setup
 
-	`npm install`
+		`npm install`
+	- Run
 
-- Run
+		`npm start`
+		
+- Frontend
+	- Navigate to the frontend directory
 
-	`npm start`
+		`cd frontend`
+	- Setup
 
+		`npm install`
+	- Run
+		- Linux or Mac
+
+			`npm start`
+		- Windows
+
+			`PORT=5050 npm start`
+
 ### dtr
 - Navigate into directory already cloned from GitHub [www.github.com/mcode/dtr](https://www.github.com/mcode/dtr)
 
@@ -194,7 +215,11 @@ git clone git@github.com:mcode/rems-smart-on-fhir.git
 	`npm install`
 
 - Run
+	- Linux or Mac
 
-	`npm start`
+		`npm start`
+	- Windows
+
+		`PORT=4040 npm run start`
 
 
diff --git a/docker-compose-dev.yml b/docker-compose-dev.yml
@@ -40,7 +40,7 @@ services:
     image: mongo
     container_name: rems_dev_pims-remsadmin-mongo
     ports:
-      - '27017:27017' 
+      - '27017:27017'
     environment:
       MONGO_INITDB_ROOT_USERNAME: rems-admin-pims-root
       MONGO_INITDB_ROOT_PASSWORD: rems-admin-pims-password
@@ -56,7 +56,7 @@ services:
     environment:
       - REACT_APP_REMS_CONFIG=true
     ports:
-      - "3000:3000" 
+      - "3000:3000"
       - "3001:3001"
     volumes:
       - rems_dev_crd-request-generator-sync:/home/node/app/crd-request-generator:nocopy #  nocopy is important
@@ -114,16 +114,15 @@ services:
       dockerfile: Dockerfile.dev
     container_name: rems_dev_pims
     ports:
-      - "5050:5050" 
+      - "5050:5050"
       - "5051:5051"
     environment:
       REMS_ADMIN_BASE: http://rems-administrator:8090
-      MONGO_HOSTNAME: mongodb://pims_remsadmin_mongo:27017/pims
+      MONGO_URL: mongodb://pims_remsadmin_mongo:27017/pims
     volumes:
       - rems_dev_pims-sync:/home/node/app/pims:nocopy
       - rems_dev_pims-nodeModules:/home/node/app/pims/node_modules
       - rems_dev_pims-logs:/home/node/app/pims/logs
-
 
 volumes:
   rems_dev_test-ehr-sync:
@@ -139,7 +138,6 @@ volumes:
   rems_dev_rems-smart-on-fhir-sync:
     external: true
 
-
   rems_dev_keycloak-data:
   rems_dev_pims_remsadmin_mongo:
   rems_dev_test-ehr-gradle:
@@ -155,10 +153,11 @@ volumes:
   rems_dev_dtr-nodeModules:
   rems_dev_dtr-databaseData:
   rems_dev_dtr-logs:
-  rems_dev_pims-logs: 
-  rems_dev_pims-nodeModules: 
+  rems_dev_pims-logs:
+  rems_dev_pims-nodeModules:
   rems_dev_rems-nodeModules:
   rems_dev_rems-logs:
   rems_dev_rems-smart-on-fhir-nodeModules:
   rems_dev_rems-smart-on-fhir-logs:
 
+
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,7 +1,7 @@
 version: '3.6'
 services:
   keycloak:
-    container_name: rems_prod_keycloak  
+    container_name: rems_prod_keycloak
     # command: ["-Djboss.http.port=8180"]
     ports:
       - '8180:8080'
@@ -24,7 +24,6 @@ services:
     extra_hosts:
       - "host.docker.internal:host-gateway"
 
-
   # Create crd request generator container
   crd-request-generator: # Name of our service
     image: codexrems/crd-request-generator:REMSvCurrent
@@ -42,14 +41,15 @@ services:
     ports: # Port binding to host from docker container
       - "3005:3005" # Bind port 3000 of host to 3000 of container
 
+  # Create rems-smart-on-fhir container
   rems-smart-on-fhir:
     image: codexrems/rems-smart-on-fhir:REMSvCurrent
     container_name: rems_prod_rems-smart-on-fhir
     ports:
       - "4040:4040"
 
 
-  # # Create rems container
+  # Create rems container
   rems-administrator: # Name of our service
     image: codexrems/rems-administrator:REMSvCurrent
     container_name: rems_prod_rems
@@ -59,31 +59,30 @@ services:
       VSAC_API_KEY: ${VSAC_API_KEY}
       MONGO_URL: mongodb://rems-user:pass@pims_remsadmin_mongo:27017
 
+  # Create pims admin container
   pims_remsadmin_mongo:
     image: mongo
     container_name: rems_prod_pims-remsadmin-mongo
     ports:
-      - '27017:27017' 
+      - '27017:27017'
     environment:
       MONGO_INITDB_ROOT_USERNAME: rems-admin-pims-root
       MONGO_INITDB_ROOT_PASSWORD: rems-admin-pims-password
     volumes:
       - rems_prod_pims_remsadmin_mongo:/data/db
       - ./mongo-init.js:/docker-entrypoint-initdb.d/mongo-init.js
 
+  # Create pims container
   pims:
     image: codexrems/pims:REMSvCurrent
     container_name: rems_prod_pims
     environment:
       REMS_ADMIN_BASE: http://rems-administrator:8090
-      MONGO_HOSTNAME: mongodb://pims_remsadmin_mongo:27017/pims
+      MONGO_URL: mongodb://pims_remsadmin_mongo:27017/pims
     ports:
-      - "5050:5050" 
+      - "5050:5050"
       - "5051:5051"
 
-
-
-
 volumes:
   rems_prod_keycloak-data:
   rems_prod_pims_remsadmin_mongo:

diff --git a/src/hooks/rems.hook.ts b/src/hooks/rems.hook.ts
@@ -361,10 +361,15 @@ const handler = (req: TypedRequestBody, res: any) => {
             } else {
               // link is SMART
               // TODO: smart links should be built with discovered questionnaires, not hard coded ones
-              e.appContext = `${e.appContext}&order=${JSON.stringify(contextRequest)}&coverage=${
-                contextRequest.insurance?.[0].reference
-              }`;
-              card.addLink(e);
+              const newLink: Link = {
+                label: e.label,
+                url: e.url,
+                type: e.type,
+                appContext: `${e.appContext}&order=${JSON.stringify(contextRequest)}&coverage=${
+                  contextRequest.insurance?.[0].reference
+                }`
+              };
+              card.addLink(newLink);
             }
           });
           cardArray.push(card);

diff --git a/src/lib/etasu.ts b/src/lib/etasu.ts
@@ -18,12 +18,47 @@ router.get('/:drug', async (req: Request, res: Response) => {
 });
 
 router.get('/met/:caseId', async (req: Request, res: Response) => {
+  console.log('get etasu by caseId');
   res.send(await remsCaseCollection.findOne({ case_number: req.params.caseId }));
 });
 
+router.get(
+  '/met/patient/:patientFirstName/:patientLastName/:patientDOB/drugCode/:drugCode',
+  async (req: Request, res: Response) => {
+    console.log(
+      'get etasu by drug code and patient: ' +
+        req.params.patientFirstName +
+        ' ' +
+        req.params.patientLastName +
+        ' ' +
+        req.params.patientDOB +
+        ' - ' +
+        req.params.drugCode
+    );
+    const searchDict = {
+      patientFirstName: req.params.patientFirstName,
+      patientLastName: req.params.patientLastName,
+      patientDOB: req.params.patientDOB,
+      drugCode: req.params.drugCode
+    };
+
+    res.send(await remsCaseCollection.findOne(searchDict));
+  }
+);
+
 router.get(
   '/met/patient/:patientFirstName/:patientLastName/:patientDOB/drug/:drugName',
   async (req: Request, res: Response) => {
+    console.log(
+      'get etasu by drug name and patient: ' +
+        req.params.patientFirstName +
+        ' ' +
+        req.params.patientLastName +
+        ' ' +
+        req.params.patientDOB +
+        ' - ' +
+        req.params.drugName
+    );
     const searchDict = {
       patientFirstName: req.params.patientFirstName,
       patientLastName: req.params.patientLastName,