Update BW laboratory workflows for #34 (#35)

* Updated laboratory workflows support * Yarn update * TS fixes * Token update * Test fixes and updates
I-TECH-UW · Feb 5, 2022 · 9dbf315 · 9dbf315
1 parent 2f9cad8
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diff --git a/app.docker-compose.yml b/app.docker-compose.yml
diff --git a/ci.docker-compose.yml b/ci.docker-compose.yml
@@ -1,4 +1,4 @@
-version: '2.4'
+version: '3.9'
 
 # Docker Compose for Github CI setup
 services:
@@ -101,6 +101,15 @@ services:
       - zookeeper
     networks:
       - test
+  # HL7 Converter
+  fhir-converter:
+    container_name: fhir-converter
+    hostname: fhir-converter
+    restart: unless-stopped
+    image: ghcr.io/b-techbw/openhim-mediator-fhir-converter:v3.1.0
+    volumes:
+      - ./config/fhir-converter/config.json:/app/config.json
+
   # Not necessary
   openhim-console:
     image: jembi/openhim-console:latest

diff --git a/config/fhir-converter/config.json b/config/fhir-converter/config.json
@@ -0,0 +1,124 @@
+{
+    "auth": {
+      "secret": "23221o43-71bc-4247-86e4-ea21aaf89c28",
+      "tokenDuration": 5400
+    },
+    "logLevel": "info",
+    "app": {
+      "port": 2019
+    },
+    "mediator": {
+      "api": {
+        "username": "[email protected]",
+        "password": "openhim",
+        "apiURL": "https://openhim-core:8080",
+        "trustSelfSigned": true,
+        "urn": "urn:mediator:hl7v2tofhir_translator"
+      }
+    },
+    "mediatorConfig": {
+      "urn": "urn:mediator:hl7v2tofhir_translator",
+      "version": "2.3.4",
+      "name": "HL7v2 to FHIR Translator",
+      "description": "HL7v2 to FHIR Translator",
+      "defaultChannelConfig": [
+        {
+          "methods": [
+            "GET",
+            "POST",
+            "PUT",
+            "PATCH"
+          ],
+          "type": "http",
+          "whitelist": [],
+          "authType": "private",
+          "matchContentTypes": [],
+          "properties": [],
+          "txViewAcl": [],
+          "txViewFullAcl": [],
+          "txRerunAcl": [],
+          "status": "enabled",
+          "rewriteUrls": false,
+          "addAutoRewriteRules": true,
+          "autoRetryEnabled": false,
+          "autoRetryPeriodMinutes": 60,
+          "requestBody": true,
+          "responseBody": true,
+          "name": "HL7v2 Translator API Passthrough",
+          "description": "HL7v2 Translator API Passthrough",
+          "urlPattern": "^/72f/.*$",
+          "routes": [
+            {
+              "type": "http",
+              "status": "enabled",
+              "forwardAuthHeader": false,
+              "name": "Send to Translator ",
+              "secured": false,
+              "host": "fhir-converter",
+              "port": 2019,
+              "path": "",
+              "pathTransform": "s/72f/api/g",
+              "primary": true,
+              "username": "",
+              "password": ""
+            }
+          ],
+          "alerts": [],
+          "rewriteUrlsConfig": [],
+          "priority": 4
+        },
+        {
+          "methods": [
+            "POST"
+          ],
+          "type": "http",
+          "whitelist": [],
+          "authType": "private",
+          "matchContentTypes": [],
+          "properties": [],
+          "txViewAcl": [],
+          "txViewFullAcl": [],
+          "txRerunAcl": [],
+          "status": "enabled",
+          "rewriteUrls": false,
+          "addAutoRewriteRules": true,
+          "autoRetryEnabled": false,
+          "autoRetryPeriodMinutes": 60,
+          "requestBody": true,
+          "responseBody": true,
+          "name": "FHIR --> HL7v2 API",
+          "description": "FHIR to HL7v2 Translation",
+          "urlPattern": "^/f27/.*$",
+          "routes": [
+            {
+              "type": "http",
+              "status": "enabled",
+              "forwardAuthHeader": false,
+              "name": "Send to Translator ",
+              "secured": false,
+              "host": "fhir-converter",
+              "port": 2019,
+              "path": "",
+              "pathTransform": "s/f27/api\/convert\/fhir/g",
+              "primary": true,
+              "username": "",
+              "password": ""
+            }
+          ],
+          "priority": 5
+        }
+      ],
+      "endpoints": [
+        {
+          "name": "HL7v2 to FHIR Translator",
+          "host": "fhir-converter",
+          "port": 2019,
+          "type": "http",
+          "primary": true,
+          "forwardAuthHeader": false,
+          "status": "enabled",
+          "path": "api"
+        }
+      ]
+    }
+  }
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,7 +1,4 @@
-version: '2.4'
-
-## Port Assignments:
-##  See .env file
+version: '3.9'
 
 ## Container debugging: 
 # 1. append the following lines to desired container 
@@ -12,29 +9,56 @@ version: '2.4'
 #    stdin_open: true
 #    entrypoint: bash
 
-## Utility for booting up placeholder page:
-# `docker run --hostname openhim-placeholder --network shared-health-record_sedish --name openhim-placeholder -e MESSAGE=OPENHIM-PLACEHOLDER -e PORT=3000 -d docker.io/sroze/landing-page:latest`
-
 services:
+  # shr: Run natively using yarn, or see docker-compose.yml
   shr:
-    hostname: shr
     container_name: shr
-    build: ./
+    hostname: shr
+    build: .
     ports:
-      - "3000:3000"
-    restart: on-failure
+      - 3000:3000
     environment:
       - NODE_ENV=docker
+    volumes:
+      - ./config/config_development.json:/app/config/config_docker.json
+      - ./config/mediator_development.json:/app/config/mediator_docker.json
     networks:
-    - hie
+      - hie
+    profiles: ["shr"]
+
   shr-fhir:
-    image: "hapiproject/hapi:latest"
     container_name: shr-fhir
     hostname: shr-fhir
+    image: hapiproject/hapi:latest
     restart: unless-stopped
+    volumes:
+      - hapi-data:/data/hapi
+    networks:
+      - hie
+    profiles: ["dev"]
     ports:
-      - "8080:8080"
+      - 8090:8080
 
+  # Kafka Task Runners
+  zookeeper:
+    image: 'bitnami/zookeeper:latest'
+    hostname: zookeeper
+    environment:
+      - ALLOW_ANONYMOUS_LOGIN=yes
+  kafka:
+    image: 'bitnami/kafka:latest'
+    hostname: kafka
+    ports:
+      - '9092:9092'
+    environment:
+      - KAFKA_BROKER_ID=1
+      - KAFKA_CFG_LISTENERS=PLAINTEXT://:9092
+      - KAFKA_CFG_ADVERTISED_LISTENERS=PLAINTEXT://127.0.0.1:9092
+      - KAFKA_CFG_ZOOKEEPER_CONNECT=zookeeper:2181
+      - ALLOW_PLAINTEXT_LISTENER=yes
+      - KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE=true
+    volumes:
+      - /bitnami/kafka
 networks:
   hie:
     external: true

diff --git a/src/workflows/lab-bw.ts → src/lib/ipmsDataGen.ts b/src/workflows/lab-bw.ts → src/lib/ipmsDataGen.ts
@@ -1,102 +1,8 @@
-"use strict"
-
 import { R4 } from "@ahryman40k/ts-fhir-types";
-import got from "got";
-import logger from "../lib/winston";
-import { LaboratoryWorkflows } from "./lab";
 import { v4 as uuidv4 } from 'uuid';
-import { sendPayload } from "../lib/kafka"
-
-export class LaboratoryWorkflowsBw extends LaboratoryWorkflows {
-  static async handleBwLabOrder(orderBundle: R4.IBundle, resultBundle: R4.IBundle) {
-    try {
-      sendPayload({bundle: orderBundle, response: resultBundle}, "map-concepts")
-    } catch (e) {
-      logger.error(e)
-    }
-  }
-
-  // Add coding mappings info to bundle
-  static async addBwCodings(bundle: R4.IBundle): Promise<R4.IBundle> {
-    try {
-      for (const e of bundle.entry!) {
-        if (e.resource && e.resource.resourceType == "ServiceRequest" && e.resource.basedOn) {
-          e.resource = await this.translatePimsCoding(e.resource)
-        }
-      }
-    } catch (e) {
-      logger.error(e)
-    }
-
-    return bundle
-  }
-
-  // Add location info to bundle
-  static async addBwLocations(bundle: R4.IBundle): Promise<R4.IBundle> {
-    try {
-      for (const e of bundle.entry!) {
-        if (e.resource && e.resource.resourceType == "ServiceRequest" && e.resource.basedOn) {
-          e.resource = await this.translateLocations(e.resource)
-        }
-      }
-    } catch (e) {
-      logger.error(e)
-    }
-
-    return bundle
-  }
 
-
-  static async translatePimsCoding(sr: R4.IServiceRequest): Promise<R4.IServiceRequest> {
-    try {
-      let pimsCoding: R4.ICoding = <R4.ICoding>sr.code!.coding!.find(e => e.system &&
-        e.system == "https://api.openconceptlab.org/orgs/B-TECHBW/sources/PIMS-LAB-TEST-DICT/")
-      let pimsCode: string = pimsCoding.code!
-
-      let ipmsMapping: any = await got.get(`https://api.openconceptlab.org/orgs/B-TECHBW/sources/IPMS-LAB-TEST/mappings?toConcept=${pimsCode}&toConceptSource=PIMS-LAB-TEST-DICT`).json()
-      let ipmsCode: string = ipmsMapping[0].from_concept_code
-      if (ipmsMapping.length > 0) {
-        sr.code!.coding!.push({
-          system: "https://api.openconceptlab.org/orgs/B-TECHBW/sources/IPMS-LAB-TEST/",
-          code: ipmsCode,
-          display: ipmsMapping[0].from_concept_name_resolved
-        })
-      }
-
-      let cielMapping: any = await got.get(`https://api.openconceptlab.org/orgs/B-TECHBW/sources/IPMS-LAB-TEST/mappings/?toConceptSource=CIEL&fromConcept=${ipmsCode}`).json()
-      let cielCode: string = cielMapping[0].to_concept_code
-      if (cielMapping.length > 0) {
-        sr.code!.coding!.push({
-          system: "https://api.openconceptlab.org/orgs/CIEL/sources/CIEL/",
-          code: cielCode,
-          display: cielMapping[0].to_concept_name_resolved
-        })
-      }
-
-      let loincMapping = got.get(`https://api.openconceptlab.org/sources/CIEL/mappings/?toConceptSource=LOINC&fromConcept=${cielCode}&mapType=SAME-AS`).json()
-      loincMapping.catch(logger.error).then((lm: any) => {
-        if (lm.length > 0) {
-          let loinCode: string = lm[0].to_concept_code
-          sr.code!.coding!.push({
-            system: "https://api.openconceptlab.org/orgs/Regenstrief/sources/LOINC/",
-            code: loinCode
-          })
-        }
-      })
-
-    } catch (e) {
-      logger.error(`Could not translate ServiceRequest codings: \n ${e}`)
-    }
-    return sr
-  }
-
-  static async translateLocations(sr: R4.IServiceRequest): Promise<R4.IServiceRequest> {
-    logger.info("Not Implemented yet!")
-
-    return sr
-  }
-
-  static generateIpmsResults(entries: R4.IBundle_Entry[]): R4.IBundle_Entry[] {
+export class IpmsDataGen {
+    static generateIpmsResults(entries: R4.IBundle_Entry[]): R4.IBundle_Entry[] {
     let generatedResults: R4.IBundle_Entry[] = []
 
     for (let entry of entries) {
@@ -219,6 +125,4 @@ export class LaboratoryWorkflowsBw extends LaboratoryWorkflows {
       result: [{ reference: "Observation/" + obsId }]
     }
   }
-}
-
-
+}
diff --git a/src/routes/hl7.ts b/src/routes/hl7.ts
@@ -7,7 +7,7 @@ import got from "got/dist/source";
 import URI from "urijs";
 import config from "../lib/config";
 import logger from "../lib/winston";
-import Hl7Workflows from '../workflows/hl7';
+import Hl7WorkflowsBw from '../workflows/hl7WorkflowsBw';
 
 const querystring = require('querystring');
 
@@ -18,7 +18,7 @@ router.post('/oru', async (req: Request, res: Response) => {
   try {
     let hl7Msg = req.body.trim()
 
-    let resultBundle: R4.IBundle = await Hl7Workflows.saveOruMessage(hl7Msg)
+    let resultBundle: R4.IBundle = await Hl7WorkflowsBw.saveOruMessage(hl7Msg)
 
     return res.status(200).json(resultBundle)
 

diff --git a/src/routes/lab-bw.ts b/src/routes/lab-bw.ts
@@ -6,7 +6,7 @@ import { R4 } from '@ahryman40k/ts-fhir-types'
 import config from '../lib/config'
 import { invalidBundleMessage, invalidBundle } from "../lib/helpers"
 import { saveLabBundle } from '../hapi/lab';
-import { LaboratoryWorkflowsBw } from "../workflows/lab-bw"
+import { LabWorkflowsBw } from "../workflows/labWorkflowsBw"
 import { or } from "ip"
 
 export const router = express.Router()
@@ -26,7 +26,7 @@ router.all('/', async (req: Request, res: Response) => {
       let resultBundle: R4.IBundle = (await saveLabBundle(orderBundle))
 
       // Trigger Background Tasks
-      LaboratoryWorkflowsBw.handleBwLabOrder(orderBundle, resultBundle)
+      LabWorkflowsBw.handleBwLabOrder(orderBundle, resultBundle)
 
       return res.status(200).json(resultBundle)
     } catch (e) {