Updated BW workflows for OpenMRS lab interoperability (#79)

Updates post-rebase IPMS Workflow updates Updating lab workflows with location mappings fix Bundle format fixes Workflow updates Workflow updates fixes Location workflow fixes Retries and logging of MLLP sender' Pilot updates Test fix Removed skipped tests svu update
I-TECH-UW · Oct 14, 2023 · 3667a80 · 3667a80
1 parent b0b978d
commit 3667a80
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diff --git a/.eslintcache b/.eslintcache
@@ -1 +1 @@
-[{"/u01/code/shared-health-record/src/lib/hl7MllpSender.ts":"1","/u01/code/shared-health-record/src/workflows/labWorkflowsBw.ts":"2","/u01/code/shared-health-record/src/workflows/__tests__/labWorkflowsBw.ts":"3"},{"size":1599,"mtime":1691536925750,"results":"4","hashOfConfig":"5"},{"size":30252,"mtime":1691536926174},{"size":3190,"mtime":1691537800246},{"filePath":"6","messages":"7","suppressedMessages":"8","errorCount":0,"fatalErrorCount":0,"warningCount":3,"fixableErrorCount":0,"fixableWarningCount":0,"source":null},"h0u5wi","/u01/code/shared-health-record/src/lib/hl7MllpSender.ts",["9","10","11"],[],{"ruleId":"12","severity":1,"message":"13","line":19,"column":40,"nodeType":"14","messageId":"15","endLine":19,"endColumn":43,"suggestions":"16"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":75,"nodeType":"14","messageId":"15","endLine":25,"endColumn":78,"suggestions":"17"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":89,"nodeType":"14","messageId":"15","endLine":25,"endColumn":92,"suggestions":"18"},"@typescript-eslint/no-explicit-any","Unexpected any. Specify a different type.","TSAnyKeyword","unexpectedAny",["19","20"],["21","22"],["23","24"],{"messageId":"25","fix":"26","desc":"27"},{"messageId":"28","fix":"29","desc":"30"},{"messageId":"25","fix":"31","desc":"27"},{"messageId":"28","fix":"32","desc":"30"},{"messageId":"25","fix":"33","desc":"27"},{"messageId":"28","fix":"34","desc":"30"},"suggestUnknown",{"range":"35","text":"36"},"Use `unknown` instead, this will force you to explicitly, and safely assert the type is correct.","suggestNever",{"range":"35","text":"37"},"Use `never` instead, this is useful when instantiating generic type parameters that you don't need to know the type of.",{"range":"38","text":"36"},{"range":"38","text":"37"},{"range":"39","text":"36"},{"range":"39","text":"37"},[453,456],"unknown","never",[752,755],[766,769]]
+[{"/u01/code/shared-health-record/src/lib/hl7MllpSender.ts":"1","/u01/code/shared-health-record/src/workflows/labWorkflowsBw.ts":"2","/u01/code/shared-health-record/src/workflows/__tests__/labWorkflowsBw.ts":"3"},{"size":1599,"mtime":1691536925750,"results":"4","hashOfConfig":"5"},{"size":30252,"mtime":1691536926174},{"size":3190,"mtime":1691537800246},{"filePath":"6","messages":"7","suppressedMessages":"8","errorCount":0,"fatalErrorCount":0,"warningCount":3,"fixableErrorCount":0,"fixableWarningCount":0,"source":null},"h0u5wi","/u01/code/shared-health-record/src/lib/hl7MllpSender.ts",["9","10","11"],[],{"ruleId":"12","severity":1,"message":"13","line":19,"column":40,"nodeType":"14","messageId":"15","endLine":19,"endColumn":43,"suggestions":"16"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":75,"nodeType":"14","messageId":"15","endLine":25,"endColumn":78,"suggestions":"17"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":89,"nodeType":"14","messageId":"15","endLine":25,"endColumn":92,"suggestions":"18"},"@typescript-eslint/no-explicit-any","Unexpected any. Specify a different type.","TSAnyKeyword","unexpectedAny",["19","20"],["21","22"],["23","24"],{"messageId":"25","fix":"26","desc":"27"},{"messageId":"28","fix":"29","desc":"30"},{"messageId":"25","fix":"31","desc":"27"},{"messageId":"28","fix":"32","desc":"30"},{"messageId":"25","fix":"33","desc":"27"},{"messageId":"28","fix":"34","desc":"30"},"suggestUnknown",{"range":"35","text":"36"},"Use `unknown` instead, this will force you to explicitly, and safely assert the type is correct.","suggestNever",{"range":"35","text":"37"},"Use `never` instead, this is useful when instantiating generic type parameters that you don't need to know the type of.",{"range":"38","text":"36"},{"range":"38","text":"37"},{"range":"39","text":"36"},{"range":"39","text":"37"},[453,456],"unknown","never",[752,755],[766,769]]
diff --git a/config/config_docker.json b/config/config_docker.json
@@ -6,14 +6,14 @@
   "mediator": {
     "api": {
       "username": "[email protected]",
-      "password": "HLh6eX4f?#tc4R@F",
+      "password": "openhim",
       "apiURL": "https://openhim-core:8080",
       "trustSelfSigned": true,
       "urn": "urn:mediator:shared-health-record"
     },
     "client": {
       "username": "shr-client",
-      "password": "k?f?NPJ9NRG3p3A9"
+      "password": "shr-client"
     }
   },
   "fhirServer": {
@@ -40,6 +40,7 @@
     "ipmsPatientTypeSystemUrl": "http://moh.bw.org/ext/ipms-patient-type",
     "ipmsPatientStatusSystemUrl": "http://moh.bw.org/ext/ipms-patient-status",
     "ipmsXLocationSystemUrl": "http://moh.bw.org/ext/ipms-xlocation",
+    "ipmsOrderTypeSystemUrl": "http://moh.bw.org/ext/ipms-order-type",
     "requestTimeout": 60000,
     "toIpmsAdtTemplate": "ADT_A04_TO_IPMS.hbs",
     "fromIpmsAdtTemplate": "ADT_A04_FROM_IPMS.hbs",

diff --git a/config/ipms_facility_mappings.xlsx b/config/ipms_facility_mappings.xlsx
diff --git a/config/ipms_facility_mappings_v0.xlsx b/config/ipms_facility_mappings_v0.xlsx
diff --git a/debug.docker-compose.yml b/debug.docker-compose.yml
@@ -19,7 +19,7 @@ services:
     restart: unless-stopped
     hostname: shr
     restart: unless-stopped
-    image: ghcr.io/i-tech-uw/shared-health-record:local
+    image: ghcr.io/i-tech-uw/shared-health-record:debug-2
     build:
       context: ./
       args:

diff --git a/src/lib/locationMap.ts b/src/lib/locationMap.ts
@@ -8,7 +8,6 @@ type FacilityMapping = {
   provider: string
   patientType: string
   patientStatus: string
-  futurePatientStatus: string
   xLocation: string
 }
 
@@ -22,23 +21,22 @@ async function getFacilityMappings() {
 
   const workbook = new Excel.Workbook()
   const content = await workbook.xlsx.readFile(locationMapFile)
-  const worksheet = content.getWorksheet('HIE')
+  const worksheet = content.getWorksheet('LIVE')
 
   const rowStartIndex = 2
-  const rowEndIndex = 11
+  const rowEndIndex = 90
 
   const rows = worksheet.getRows(rowStartIndex, rowEndIndex) ?? []
 
   const mappings = rows.map((row: Excel.Row): FacilityMapping => {
     return {
       index: parseInt(getCellValue(row, 1)),
-      orderingFacility: getCellValue(row, 2),
-      receivingFacility: getCellValue(row, 3),
-      provider: getCellValue(row, 5),
-      patientType: getCellValue(row, 6),
+      orderingFacility: getCellValue(row, 4),
+      receivingFacility: getCellValue(row, 2),
+      provider: getCellValue(row, 6),
+      patientType: getCellValue(row, 8),
       patientStatus: getCellValue(row, 7),
-      futurePatientStatus: getCellValue(row, 8),
-      xLocation: getCellValue(row, 9),
+      xLocation: getCellValue(row, 3),
     }
   })
 

diff --git a/src/server/__tests__/mllpAdapter.ts b/src/server/__tests__/mllpAdapter.ts
@@ -1,5 +1,5 @@
 import { BundleTypeKind, IBundle } from '@ahryman40k/ts-fhir-types/lib/R4'
-import { promises as fs } from 'fs'
+import fs from 'fs/promises'
 import path from 'path'
 import Hl7Workflows from '../../workflows/hl7WorkflowsBw'
 import MllpAdapter from '../mllpAdapter'

diff --git a/src/workflows/labWorkflowsBw.ts b/src/workflows/labWorkflowsBw.ts
@@ -133,6 +133,8 @@ export class LabWorkflowsBw extends LabWorkflows {
         default:
           break
       }
+      await new Promise(resolve => setTimeout(resolve, 300))
+
       return res
     } catch (e) {
       logger.error(e)
@@ -150,6 +152,7 @@ export class LabWorkflowsBw extends LabWorkflows {
           e.resource.code.coding &&
           e.resource.code.coding.length > 0
         ) {
+          logger.info`Translating ServiceRequest Codings`
           e.resource = await this.translateCoding(e.resource)
         }
       }
@@ -317,10 +320,14 @@ export class LabWorkflowsBw extends LabWorkflows {
         pimsCoding = this.getCoding(sr, config.get('bwConfig:pimsSystemUrl'))
         cielCoding = this.getCoding(sr, config.get('bwConfig:cielSystemUrl'))
 
+        logger.info(`PIMS Coding: ${JSON.stringify(pimsCoding)}`)
+        logger.info(`CIEL Coding: ${JSON.stringify(cielCoding)}`)
+
         if (pimsCoding && pimsCoding.code) {
           // Translate from PIMS to CIEL and IPMS
           ipmsCoding = await this.getIpmsCode(
             `/orgs/I-TECH-UW/sources/IPMSLAB/mappings?toConcept=${pimsCoding.code}&toConceptSource=PIMSLAB`,
+            pimsCoding.code,
           )
 
           if (ipmsCoding && ipmsCoding.code) {
@@ -340,16 +347,25 @@ export class LabWorkflowsBw extends LabWorkflows {
           // Translate from CIEL to IPMS
           ipmsCoding = await this.getIpmsCode(
             `/orgs/I-TECH-UW/sources/IPMSLAB/mappings?toConcept=${cielCoding.code}&toConceptSource=CIEL`,
+            cielCoding.code,
           )
         }
 
         // Add IPMS Coding
         if (ipmsCoding && ipmsCoding.code) {
-          sr.code.coding.push({
+          const ipmsOrderTypeExt = {
+            url: config.get('bwConfig:ipmsOrderTypeSystemUrl'),
+            valueString: ipmsCoding.hl7Flag,
+          }
+
+          const srCoding = {
             system: config.get('bwConfig:ipmsSystemUrl'),
             code: ipmsCoding.mnemonic,
             display: ipmsCoding.display,
-          })
+            extension: [ipmsOrderTypeExt],
+          }
+
+          sr.code.coding.push(srCoding)
         }
 
         // Get LOINC Coding
@@ -944,17 +960,23 @@ export class LabWorkflowsBw extends LabWorkflows {
     }
   }
 
-  private static async getIpmsCode(q: string) {
+  private static async getIpmsCode(q: string, c = '') {
     try {
       const ipmsMappings = await this.getOclMapping(q)
 
+      //logger.info(`IPMS Mappings: ${JSON.stringify(ipmsMappings)}`)
+
       // Prioritize "Broader Than Mappings"
       //TODO: Figure out if this is proper way to handle panels / broad to narrow
-      let mappingIndex = ipmsMappings.findIndex((x: any) => x.map_type == 'BROADER-THAN')
+      let mappingIndex = ipmsMappings.findIndex(
+        (x: any) => x.map_type == 'BROADER-THAN' && x.to_concept_code == c,
+      )
 
       // Fall back to "SAME AS"
       if (mappingIndex < 0) {
-        mappingIndex = ipmsMappings.findIndex((x: any) => x.map_type == 'SAME-AS')
+        mappingIndex = ipmsMappings.findIndex(
+          (x: any) => x.map_type == 'SAME-AS' && x.to_concept_code == c,
+        )
       }
 
       if (mappingIndex >= 0) {
@@ -963,12 +985,17 @@ export class LabWorkflowsBw extends LabWorkflows {
         const ipmsCodingInfo: any = await this.getOclMapping(
           `/orgs/I-TECH-UW/sources/IPMSLAB/concepts/${ipmsCode}`,
         )
-        let ipmsMnemonic
+        // logger.info(`IPMS Coding Info: ${JSON.stringify(ipmsCodingInfo)}`)
+        let ipmsMnemonic, hl7Flag
         if (ipmsCodingInfo) {
           ipmsMnemonic = ipmsCodingInfo.names.find((x: any) => x.name_type == 'Short').name
+          hl7Flag =
+            ipmsCodingInfo.extras && ipmsCodingInfo.extras.IPMS_HL7_ORM_TYPE
+              ? ipmsCodingInfo.extras.IPMS_HL7_ORM_TYPE
+              : 'LAB'
         }
 
-        return { code: ipmsCode, display: ipmsDisplay, mnemonic: ipmsMnemonic }
+        return { code: ipmsCode, display: ipmsDisplay, mnemonic: ipmsMnemonic, hl7Flag: hl7Flag }
       } else {
         return null
       }
@@ -982,6 +1009,8 @@ export class LabWorkflowsBw extends LabWorkflows {
     try {
       const codeMapping = await this.getOclMapping(q)
 
+      //logger.info(`Code Mapping: ${JSON.stringify(codeMapping)}`)
+
       if (codeMapping && codeMapping.length > 0) {
         return {
           code: codeMapping[0].to_concept_code,
@@ -999,7 +1028,20 @@ export class LabWorkflowsBw extends LabWorkflows {
   private static async getOclMapping(queryString: string): Promise<any[]> {
     const options = { timeout: config.get('bwConfig:requestTimeout') | 1000 }
 
+    logger.info(`${config.get('bwConfig:oclUrl')}${queryString}`)
+
     return got.get(`${config.get('bwConfig:oclUrl')}${queryString}`, options).json()
   }
+
+  private static async getOclConcept(conceptCode: string): Promise<any> {
+    const options = { timeout: config.get('bwConfig:requestTimeout') | 1000 }
+
+    return got
+      .get(
+        `${config.get('bwConfig:oclUrl')}/orgs/I-TECH-UW/sources/IPMSLAB/concepts/${conceptCode}`,
+        options,
+      )
+      .json()
+  }
 }
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		[{"/u01/code/shared-health-record/src/lib/hl7MllpSender.ts":"1","/u01/code/shared-health-record/src/workflows/labWorkflowsBw.ts":"2","/u01/code/shared-health-record/src/workflows/__tests__/labWorkflowsBw.ts":"3"},{"size":1599,"mtime":1691536925750,"results":"4","hashOfConfig":"5"},{"size":30252,"mtime":1691536926174},{"size":3190,"mtime":1691537800246},{"filePath":"6","messages":"7","suppressedMessages":"8","errorCount":0,"fatalErrorCount":0,"warningCount":3,"fixableErrorCount":0,"fixableWarningCount":0,"source":null},"h0u5wi","/u01/code/shared-health-record/src/lib/hl7MllpSender.ts",["9","10","11"],[],{"ruleId":"12","severity":1,"message":"13","line":19,"column":40,"nodeType":"14","messageId":"15","endLine":19,"endColumn":43,"suggestions":"16"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":75,"nodeType":"14","messageId":"15","endLine":25,"endColumn":78,"suggestions":"17"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":89,"nodeType":"14","messageId":"15","endLine":25,"endColumn":92,"suggestions":"18"},"@typescript-eslint/no-explicit-any","Unexpected any. Specify a different type.","TSAnyKeyword","unexpectedAny",["19","20"],["21","22"],["23","24"],{"messageId":"25","fix":"26","desc":"27"},{"messageId":"28","fix":"29","desc":"30"},{"messageId":"25","fix":"31","desc":"27"},{"messageId":"28","fix":"32","desc":"30"},{"messageId":"25","fix":"33","desc":"27"},{"messageId":"28","fix":"34","desc":"30"},"suggestUnknown",{"range":"35","text":"36"},"Use `unknown` instead, this will force you to explicitly, and safely assert the type is correct.","suggestNever",{"range":"35","text":"37"},"Use `never` instead, this is useful when instantiating generic type parameters that you don't need to know the type of.",{"range":"38","text":"36"},{"range":"38","text":"37"},{"range":"39","text":"36"},{"range":"39","text":"37"},[453,456],"unknown","never",[752,755],[766,769]]
		[{"/u01/code/shared-health-record/src/lib/hl7MllpSender.ts":"1","/u01/code/shared-health-record/src/workflows/labWorkflowsBw.ts":"2","/u01/code/shared-health-record/src/workflows/__tests__/labWorkflowsBw.ts":"3"},{"size":1599,"mtime":1691536925750,"results":"4","hashOfConfig":"5"},{"size":30252,"mtime":1691536926174},{"size":3190,"mtime":1691537800246},{"filePath":"6","messages":"7","suppressedMessages":"8","errorCount":0,"fatalErrorCount":0,"warningCount":3,"fixableErrorCount":0,"fixableWarningCount":0,"source":null},"h0u5wi","/u01/code/shared-health-record/src/lib/hl7MllpSender.ts",["9","10","11"],[],{"ruleId":"12","severity":1,"message":"13","line":19,"column":40,"nodeType":"14","messageId":"15","endLine":19,"endColumn":43,"suggestions":"16"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":75,"nodeType":"14","messageId":"15","endLine":25,"endColumn":78,"suggestions":"17"},{"ruleId":"12","severity":1,"message":"13","line":25,"column":89,"nodeType":"14","messageId":"15","endLine":25,"endColumn":92,"suggestions":"18"},"@typescript-eslint/no-explicit-any","Unexpected any. Specify a different type.","TSAnyKeyword","unexpectedAny",["19","20"],["21","22"],["23","24"],{"messageId":"25","fix":"26","desc":"27"},{"messageId":"28","fix":"29","desc":"30"},{"messageId":"25","fix":"31","desc":"27"},{"messageId":"28","fix":"32","desc":"30"},{"messageId":"25","fix":"33","desc":"27"},{"messageId":"28","fix":"34","desc":"30"},"suggestUnknown",{"range":"35","text":"36"},"Use `unknown` instead, this will force you to explicitly, and safely assert the type is correct.","suggestNever",{"range":"35","text":"37"},"Use `never` instead, this is useful when instantiating generic type parameters that you don't need to know the type of.",{"range":"38","text":"36"},{"range":"38","text":"37"},{"range":"39","text":"36"},{"range":"39","text":"37"},[453,456],"unknown","never",[752,755],[766,769]]