Location MFL Code Update

src/lib/helpers.ts

@@ -45,6 +45,24 @@ export async function hapiPassthrough(targetUri: any, res: Response): Promise<an
   }
 }
 
+export async function hapiGet(resource: string, options: any): Promise<any> {
+  const targetUri = config.get('fhirServer:baseURL') + '/' + resource
+
+  logger.info(`Getting ${targetUri}`)
+
+  // Merge options
+  const sendOptions = {...options, username: config.get('fhirServer:username'), password: config.get('fhirServer:password')}
+
+  try {
+    const result = got.get(targetUri, sendOptions)
+
+    return await result.json()
+  } catch (error) {
+    logger.error(`Could not get ${targetUri}:\n${JSON.stringify(error)}`)
+    return null
+  }
+}
+
 export function getHapiPassthrough(): any {
   return async (req: Request, res: Response) => {
     const targetUri = config.get('fhirServer:baseURL') + req.url

src/lib/locationMap.ts

@@ -3,7 +3,8 @@ import * as Excel from 'exceljs'
 
 type FacilityMapping = {
   index: number
-  orderingFacility: string
+  orderingFacilityMflCode: string
+  orderingFacilityName: string
   receivingFacility: string
   provider: string
   patientType: string
@@ -33,11 +34,12 @@ async function getFacilityMappings() {
   const mappings = rows.map((row: Excel.Row): FacilityMapping => {
     return {
       index: parseInt(getCellValue(row, 1)),
-      orderingFacility: getCellValue(row, 4),
+      orderingFacilityMflCode: getCellValue(row, 4),
+      orderingFacilityName: getCellValue(row, 5),
       receivingFacility: getCellValue(row, 2),
-      provider: getCellValue(row, 6),
-      patientType: getCellValue(row, 8),
-      patientStatus: getCellValue(row, 7),
+      provider: getCellValue(row, 7),
+      patientType: getCellValue(row, 9),
+      patientStatus: getCellValue(row, 8),
       xLocation: getCellValue(row, 3),
     }
   })

src/workflows/botswana/IpmsWorkflows.ts

@@ -13,12 +13,11 @@ import {
   IDiagnosticReport,
   IObservation,
   IPatient,
-  IReference,
-  IServiceRequest,
   ITask,
   TaskStatusKind,
 } from '@ahryman40k/ts-fhir-types/lib/R4'
 import { saveBundle } from '../../hapi/lab'
+import { hapiGet } from '../../lib/helpers'
 
 // New Error Type for IPMS Workflow Errors
 export class IpmsWorkflowError extends Error {
@@ -327,9 +326,15 @@ export async function handleAdtFromIpms(adtMessage: string): Promise<any> {
   }
 }
 
+/**
+ * Handles ORU (Observation Result) messages received from IPMS (Integrated Patient Management System).
+ */
 export async function handleOruFromIpms(message: any): Promise<R4.IBundle> {
-  let translatedBundle, resultBundle: R4.IBundle = { resourceType: 'Bundle' }
-  let taskPatient, task;
+  let translatedBundle: R4.IBundle = { resourceType: 'Bundle' }
+  let resultBundle: R4.IBundle = { resourceType: 'Bundle' }
+  let serviceRequestBundle: R4.IBundle = { resourceType: 'Bundle' }
+
+  let taskPatient, task
 
   try {
     if (!message)
@@ -343,7 +348,7 @@ export async function handleOruFromIpms(message: any): Promise<R4.IBundle> {
     if (translatedBundle && translatedBundle.entry) {
 
       // Extract Patient, DiagnosticReport, and Observation
-      let patient: IPatient = <IPatient>(
+      const patient: IPatient = <IPatient>(
         translatedBundle.entry.find((e: any) => e.resource && e.resource.resourceType == 'Patient')!
           .resource!
       )
@@ -352,7 +357,7 @@ export async function handleOruFromIpms(message: any): Promise<R4.IBundle> {
         translatedBundle.entry.find((e: any) => e.resource && e.resource.resourceType == 'DiagnosticReport')!.resource!
       )
 
-      let obs: IObservation = <IObservation>(
+      const obs: IObservation = <IObservation>(
         translatedBundle.entry.find((e: any) => e.resource && e.resource.resourceType == 'Observation')!
           .resource!
       )
@@ -368,26 +373,24 @@ export async function handleOruFromIpms(message: any): Promise<R4.IBundle> {
       */
 
       // Extract Lab Order ID from Diagnostic Report
-      const labOrderId = dr.identifier && dr.identifier.length > 0 ? dr.identifier.find((i: any) => config.get('bwConfig:labOrderSystemUrl') && i.system == config.get('bwConfig:labOrderSystemUrl').value) : undefined
-      const labOrderMrn = dr.identifier && dr.identifier.length > 0 ? dr.identifier.find((i: any) => config.get('bwConfig:mrnSystemUrl') && i.system == config.get('bwConfig:mrnSystemUrl').value) : undefined
+      const labOrderId = dr.identifier && dr.identifier.length > 0 ? dr.identifier.find((i: any) => i.system == config.get('bwConfig:labOrderSystemUrl')) : undefined
+      const labOrderMrn = dr.identifier && dr.identifier.length > 0 ? dr.identifier.find((i: any) => i.system == config.get('bwConfig:mrnSystemUrl')) : undefined
 
-      let options = {
-        timeout: config.get('bwConfig:requestTimeout'),
-        searchParams: {},
-      }     
-
-      // Grab service request with Task:
-      options.searchParams = {
-        _revInclude: 'Task:basedOn',
-        _include: 'ServiceRequest.patient',
-        _id: labOrderId,
+      if(labOrderId && labOrderId.value) {
+        const options = {
+          timeout: config.get('bwConfig:requestTimeout'),
+          searchParams: new URLSearchParams(),
+        }     
+
+        options.searchParams.append('_include','Task:patient')
+        options.searchParams.append('_include','Task:based-on')
+        options.searchParams.append('based-on',labOrderId.value)
+
+        serviceRequestBundle = <R4.IBundle> (await hapiGet('Task', options))
       }
 
-      const serviceRequestBundle: IBundle = await got
-        .get(`${config.get('fhirServer:baseURL')}/ServiceRequest`, options)
-        .json()
-
       if(serviceRequestBundle && serviceRequestBundle.entry && serviceRequestBundle.entry.length > 0) {  
+
         // Extract Task and Patient Resources from ServiceRequest Bundle
         taskPatient = <IPatient>(
           serviceRequestBundle.entry.find((e: any) => e.resource && e.resource.resourceType == 'Patient')!
@@ -399,14 +402,19 @@ export async function handleOruFromIpms(message: any): Promise<R4.IBundle> {
         )
 
         // TODO: Validate Patient Match by Identifier/CR match
+        // taskPatient.identifier == patient.identifier (for omang/brn/ppn) or make sure the two are linked in CR
 
       } else {
-        logger.error('Could not find ServiceRequest with Lab Order ID ' + labOrderId + '!')
+        logger.error('Could not find ServiceRequest with Lab Order ID ' + JSON.stringify(labOrderId) + '!')
         return new IpmsErrorBundle('Could not find ServiceRequest with Lab Order ID ' + labOrderId + '!').bundle;
       }
 
+      // Update Obs and DR with Patient Reference
+      obs.subject = { reference: 'Patient/' + taskPatient.id }
+      dr.subject = { reference: 'Patient/' + taskPatient.id }
+
       // Generate SendBundle with Task, DiagnosticReport, Patient, and Observation
-      let entry = createSendBundleEntry(task, patient, dr, obs)
+      const entry = createSendBundleEntry(task, dr, obs)
 
       // TODO: Only send if valid details available
       const sendBundle: R4.IBundle = {
@@ -479,21 +487,15 @@ function processIpmsPatient(patient: R4.IPatient): any {
   return { omang: omang, bcn: bcn, ppn: ppn, options: options }
 }
 
-function createSendBundleEntry(task: R4.ITask | undefined, patient: R4.IPatient | undefined, dr: R4.IDiagnosticReport | undefined, obs: R4.IObservation | undefined): R4.IBundle_Entry[] {
-  let entry = []
+function createSendBundleEntry(task: R4.ITask | undefined, dr: R4.IDiagnosticReport | undefined, obs: R4.IObservation | undefined): R4.IBundle_Entry[] {
+  const entry = []
 
   if (task) {
     entry.push({
       resource: task,
       request: { method: Bundle_RequestMethodKind._put, url: 'Task/' + task.id }
     })
   }
-  if(patient) {
-    entry.push({
-      resource: patient,
-      request: { method: Bundle_RequestMethodKind._put, url: 'Patient/' + patient.id },
-    })
-  }
   if(dr) {
     entry.push({
       resource: dr,

src/workflows/botswana/terminologyWorkflows.ts

@@ -49,7 +49,8 @@ export async function translateCoding(r: R4.IServiceRequest | R4.IDiagnosticRepo
 
       logger.info(`PIMS Coding: ${JSON.stringify(pimsCoding)}`)
       logger.info(`CIEL Coding: ${JSON.stringify(cielCoding)}`)
-
+      logger.info(`IPMS Coding: ${JSON.stringify(ipmsCoding)}`)
+
       if(ipmsCoding && ipmsCoding.code) {
         // 1. IPMS Resulting Workflow: 
         //    Translation from IPMS --> PIMS and CIEL
@@ -128,19 +129,6 @@ export async function translateCoding(r: R4.IServiceRequest | R4.IDiagnosticRepo
         }
       }
 
-      // Get LOINC Coding for all Workflows
-      if (cielCoding && cielCoding.code) {
-        loincCoding = await getMappedCode(
-          `/orgs/CIEL/sources/CIEL/mappings/?toConceptSource=LOINC&fromConcept=${cielCoding.code}`,
-        )
-        if (loincCoding && loincCoding.code) {
-          r.code.coding.push({
-            system: config.get('bwConfig:loincSystemUrl'),
-            code: loincCoding.code,
-            display: loincCoding.display,
-          })
-        }
-      }
       return r
     } else {
       logger.error('Could not any codings to translate in:\n' + JSON.stringify(r))