Fixing MLLP port setup and adding MLLP testing for #27 (#28)

* Mllp work

* Updates

* Config fix

* attempted workflow fix

* Openhim config fix

* version bump and workflow fix

* Small fix

.github/workflows/main.yml

@@ -121,7 +121,10 @@ jobs:
 
       - name: Show containers
         run: docker-compose -f "ci.docker-compose.yml" ps
-
+
+      - name: Show OpenHIM Log
+        run: docker-compose -f "ci.docker-compose.yml" logs openhim-core
+
       # Newman Container Approach
       - name: Run General Tests Collection
         env: 
@@ -138,6 +141,9 @@ jobs:
           POSTMAN_COLLECTION: https://www.getpostman.com/collections/2ee8ebff39c078bac256
         run: docker-compose -f ci.docker-compose.yml up --exit-code-from newman newman
 
+      - name: Run MLLP Tests
+        run: docker-compose -f ci.docker-compose.yml up --exit-code-from mllp_tests mllp_tests
+
       - name: Show SHR Log
         run: docker-compose -f "ci.docker-compose.yml" logs shr
 
@@ -157,11 +163,13 @@ jobs:
 
       - name: Publish Docker image
         uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        if: github.event_name == 'release'
         with:
           context: .
           push: true
           tags: ${{ steps.meta.outputs.tags }},${{ env.REGISTRY }}/${{ steps.string.outputs.lowercase }}:${{steps.package-version.outputs.current-version}} 
           labels: ${{ steps.meta.outputs.labels }}
           cache-from: type=gha
           cache-to: type=gha,mode=max
-          build-args: NODE_AUTH_TOKEN=${{ secrets.NPM_TOKEN }}          
+          build-args: NODE_AUTH_TOKEN=${{ secrets.NPM_TOKEN }}          
+

.github/workflows/script/build-test.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
-docker build ./ -t test-image:latest --build-args NODE_AUTH_TOKEN
+docker build --build-arg NODE_AUTH_TOKEN=$env:NODE_AUTH_TOKEN ./ -t test-image:latest 
+
 docker-compose -f ci.docker-compose.yml pull shr-fhir openhim-core mongo-db newman kafka zookeeper
 docker-compose -f ci.docker-compose.yml up -d shr-fhir mongo-db openhim-core kafka zookeeper
 
@@ -14,6 +15,8 @@ docker-compose -f ci.docker-compose.yml up -d shr
 
 docker-compose -f ci.docker-compose.yml ps
 
+docker-compose -f ci.docker-compose.yml up mllp_tests
+
 declare -a tests=("https://www.getpostman.com/collections/481bb6cc8e1e964fd8bd" 
                 "https://www.getpostman.com/collections/ff5183adca5b5e720338" 
                 "https://www.getpostman.com/collections/2ee8ebff39c078bac256"
@@ -27,4 +30,5 @@ do
    docker-compose -f ci.docker-compose.yml up --exit-code-from newman newman 
 done
 
+
 # docker-compose -f ci.docker-compose.yml down -v

Dockerfile

@@ -46,6 +46,7 @@ ARG NODE_ENV=docker
 ENV NODE_ENV=$NODE_ENV
 
 EXPOSE 3000
+EXPOSE 3001
 
-CMD sh -c './wait-for shr=-fhir:8080 -- '
+CMD sh -c './wait-for shr-fhir:8080 -- '
 ENTRYPOINT node dist/app.js

ci.docker-compose.yml

@@ -6,11 +6,10 @@ services:
     container_name: shr
     hostname: shr
     image: test-image:latest
-    ports:
-      - 3000:3000
-      - 3001:3001
     environment:
       - NODE_ENV=docker
+    ports:
+      - 3001:3001
     volumes:
       - ./config/config_ci.json:/app/config/config_docker.json
       - ./config/mediator_ci.json:/app/config/mediator_docker.json
@@ -55,7 +54,7 @@ services:
   # OpenHIM Config
   openhim-config:
     container_name: openhim-config
-    image: ghcr.io/i-tech-uw/openhim-config:latest
+    image: ghcr.io/i-tech-uw/openhim-config:v0.0.0
     volumes:
       - ./config/openhim/ci-openhim-config.json:/app/test-openhim-config.json
 
@@ -68,6 +67,13 @@ services:
       - ./.postman:/.postman
     entrypoint: newman run $POSTMAN_COLLECTION -e /.postman/ci.postman_environment.json --insecure --timeout-request 10000 --delay-request 10000
 
+  # MLLP Tests
+  mllp_tests:
+    container_name: mllp_tests
+    image: ghcr.io/b-techbw/mllp-tester:main
+    volumes:
+      - ./test/mllp:/test
+
   # Task Runner
   zookeeper:
     image: 'bitnami/zookeeper:latest'
@@ -78,10 +84,12 @@ services:
     image: 'bitnami/kafka:latest'
     hostname: kafka
     container_name: kafka
+    ports:
+      - 9092:9092
     environment:
       - KAFKA_BROKER_ID=1
       - KAFKA_CFG_LISTENERS=PLAINTEXT://:9092
-      - KAFKA_CFG_ADVERTISED_LISTENERS=PLAINTEXT://kafka:9092
+      - KAFKA_CFG_ADVERTISED_LISTENERS=PLAINTEXT://localhost:9092
       - KAFKA_CFG_ZOOKEEPER_CONNECT=zookeeper:2181
       - ALLOW_PLAINTEXT_LISTENER=yes
       - KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE=true

config/config_ci.json

@@ -16,8 +16,5 @@
     "mpiURL": "https://openhim-core:5000/CR/fhir",
     "baseURL": "http://shr-fhir:8080/fhir"
   },
-  "fhirConverterUrl": "https://openhim-core:5000/72f",
-  "taskRunner": {
-    "brokers" : ["kafka:9092"]
-  }
+  "fhirConverterUrl": "https://openhim-core:5000/72f"
 }

config/config_development.json

@@ -22,6 +22,6 @@
   },
   "fhirConverterUrl": "http://localhost:5001/72f",
   "taskRunner": {
-    "workers" : ["localhost:9092"]
+    "brokers" : ["localhost:9092"]
   }
 }

dev.docker-compose.yml

@@ -115,12 +115,24 @@ services:
   # OpenHIM Config
   openhim-config:
     container_name: openhim-config
-    image: ghcr.io/i-tech-uw/openhim-config:latest
+    image: ghcr.io/i-tech-uw/openhim-config:v0.0.0
     volumes:
       - ./config/openhim/dev-openhim-config.json:/app/test-openhim-config.json
     profiles: ["dev"]
     networks:
       - hie
+
+  # MLLP Testing
+  mllp_tests:
+    container_name: mllp_tests
+    image: ghcr.io/b-techbw/mllp-tester:main
+    networks:
+      - hie
+    volumes:
+      - ./test/mllp:/test
+    # tty: true
+    # stdin_open: true
+    # entrypoint: bash
 volumes:
   mongo-data:
   hapi-data:

package.json

@@ -1,6 +1,6 @@
 {
   "name": "shared-health-registry",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "description": "Open Implementation of an OpenHIE Shared Health Record",
   "main": "app.js",
   "scripts": {
@@ -20,7 +20,7 @@
   "license": "ISC",
   "dependencies": {
     "@ahryman40k/ts-fhir-types": "^4.0.34",
-    "@b-techbw/mllp": "^3.0.1",
+    "@b-techbw/mllp": ">=3.0.6",
     "@types/got": "^9.6.12",
     "acorn": ">=7.1.1",
     "async": "^3.1.0",

src/app.ts

@@ -26,9 +26,7 @@ if (require.main === module) {
   }
 
   // TODO: Extract to separate project / package
-  if (true) { //config.get("app:taskRunner:brokers")) {
-
+  if (config.get("taskRunner:brokers")) {
     run().catch(logger.error)
-
   }
 }

src/routes/hl7.ts

@@ -23,7 +23,7 @@ router.post('/oru', async (req: Request, res: Response) => {
     return res.status(200).json(resultBundle)
 
   } catch (error) {
-    logger.error(`Could not translate and save ORU message to SHR!\n${error}`)
+    logger.error(`/oru: failed!\n${error}`)
     return res.status(500).json(error)
   }
 

src/server/kafkaWorkers.ts

@@ -4,6 +4,7 @@ import logger from '../lib/winston'
 import { LaboratoryWorkflowsBw } from '../workflows/lab-bw';
 import { IBundle } from '@ahryman40k/ts-fhir-types/lib/R4';
 import { saveLabBundle } from "../hapi/lab";
+import { Consumer } from "kafkajs";
 const errorTypes = ['unhandledRejection', 'uncaughtException']
 const signalTraps: NodeJS.Signals[] = ['SIGTERM', 'SIGINT', 'SIGUSR2'] 
 
@@ -20,6 +21,8 @@ const signalTraps: NodeJS.Signals[] = ['SIGTERM', 'SIGINT', 'SIGUSR2']
  */
 
 export async function run() {
+    let k: Consumer = consumer
+
     await consumer.connect()
 
     await consumer.subscribe({ topic: "map-concepts", fromBeginning: true })

src/workflows/hl7.ts

@@ -6,8 +6,18 @@ import URI from "urijs";
 import { saveLabBundle } from "../hapi/lab";
 import config from "../lib/config";
 import logger from "../lib/winston";
+import { IBundle, BundleTypeKind } from '@ahryman40k/ts-fhir-types/lib/R4';
 export default class Hl7Workflows {
-
+  private static errorBundle: IBundle = {
+    resourceType: "Bundle",
+    type: BundleTypeKind._transactionResponse,
+    entry: [{
+      response: {
+        status: "500 Server Error"
+      }
+    }]
+  }
+
   // GET Lab Orders via HL7v2 over HTTP - ORU Message
   static async saveOruMessage(hl7Msg: string): Promise<R4.IBundle> {
     try {
@@ -34,8 +44,7 @@ export default class Hl7Workflows {
 
     } catch (error: any) {
       logger.error(`Could not translate and save ORU message!\n${JSON.stringify(error)}`)
-
-      throw new Error(`Could not translate ORU message!\n${JSON.stringify(error)}`)
+      return this.errorBundle
     }
   }
 
@@ -65,8 +74,7 @@ export default class Hl7Workflows {
 
     } catch (error: any) {
       logger.error(`Could not translate and save ORU message!\n${JSON.stringify(error)}`)
-
-      throw new Error(`Could not translate ORU message!\n${JSON.stringify(error)}`)
+      return this.errorBundle
     }
   }
 
@@ -101,4 +109,4 @@ export default class Hl7Workflows {
       }
     } while (nextExists);
   }
-}
+}

test/mllp/messages/example-adt.hl7

@@ -0,0 +1,10 @@
+MSH|^~\&|||||202109211304||ADT^A04|54200|D|2.4|||AL|NE|
+EVN||202109211304|||MT^MEDITECH|202109211304|
+PID|1||GG00001280^^^^MR^GGC~OMANG123^^^^SS^GGC~GG1403^^^^PI^GGC~MOH0004687^^^^HUB^GGC||Test^ADT^Message^^^^L||19790921|F|||PLOT 123^^Gaborone^B^0101||00267891608025|||S||XG0000002195|
+NK1|1|Test^Test|BR^Brother|Plot 123^^Gaborone^B^0101|00267891608029||NOK|
+PV1|1|O|HGGMMO|RF|||K^Naicker^Kalvin^^^^^^^^^^XX|||||||||||CLI||U|||||||||||||||||||GGC||REG|||202109211304|
+PV2|||||||||||1||||||||||||||RF|||||||||||N|
+ROL|1|AD|AT|K^Naicker^Kalvin^^^^^^^^^^XX|
+ROL|2|AD|PP|GENPRI00^Doctor^Private^^^^^^^^^^XX|
+GT1|1||Test^ADT^Message||PLOT 123^^Gaborone^B^0101|00267891608025|||||SF|OMANG123|
+IN1|1|Citizens||Citizens|Botswana Government^Ministry of Health^Gaborone^B^0101|

test/mllp/messages/example-oru.hl7

@@ -0,0 +1,9 @@
+MSH|^~\&|LAB|GGC|||202106101550||ORU^R01|165293.1|D|
+PID|1|TEST0062404|GG00042482^^^^MR^GGC~GG5714^^^^PI^GGC~TEST0062404^^^^HUB^GGC||Murambi^Tawanda||19880616|M||CT|Plot 1011^^Gaborone^Botswana^00267|||||M|| ZG0000044218|
+OBR|1|MOH001^LAB|68222^LAB|COVID^SARS-CoV-2 PCR^L|||202106031400|||||||202106101545||ZZHGGMMO^Healthpost^Mmopane||00049731||||||LAB|F||^^^^^R|
+OBX|1|ST|SARS-CoV-2 PCR^SARS-CoV-2 PCR^L||INCONCLUSIVE|||N||A^S|F||||GNHL^National Health Laboratory^L|
+OBX|2|ST|S-Cov-2 RVW^SARS-CoV-2 PCR REVIEW^L||.|||N||A^S|F|||202106101549|GNHL^National Health Laboratory^L|
+NTE|1|
+NTE|2|
+NTE|3||SARS-CoV-2 PCR Tests Authorised by: MEDITECH|
+NTE|4||Authorised Date: 10/06/21 1549|

test/mllp/tests.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+hostname="shr"
+port=3001
+
+for hl7File in messages/*
+do
+  echo "Testing $hl7File"
+  lines=""
+
+  while IFS='' read -r LINE || [ -n "${LINE}" ]; do
+      LINE=`echo $LINE | sed -e 's/^[[:space:]]*//'`
+      echo "processing line: ${LINE}"
+      lines="${lines}${LINE}\x0d"
+  done < $hl7File
+
+  msg="\x0b${lines}\x1c\x0d"
+
+  echo $hostname
+  echo $msg
+
+  echo -ne $msg | socat - TCP:$hostname:$port
+done