Pilot testing updates (#3)

* Fixes

* ORM messaging updates and fixes

* fix

* OCL path fix

* Location mapping updates

* IPMS pilot updates

* Resulting testing updates

* Pilot testing updates

* Fix

config.json

@@ -10,7 +10,7 @@
   "mediator": {
     "api": {
       "username": "[email protected]",
-      "password": "openhim",
+      "password": "instant101",
       "apiURL": "https://openhim-core:8080",
       "trustSelfSigned": true,
       "urn": "urn:mediator:hl7v2tofhir_translator"

data/templates/fhir/ADT_A04_TO_IPMS copy.hbs

@@ -0,0 +1,7 @@
+{{#with msg.fhir}}
+MSH|^~\&|DM||||{{date}}||ADT^A04|{{controlId}}|D|2.4|||AL|NE|
+EVN||{{date}}|||ZZHGGMMO^Healthpost^Mmopane|{{date}}|
+PID|1||NEW||{{patientFamilyName}}^{{patientFirstName.[0]}}^^^^^F||{{patientDob}}|{{patientSex}}||CT|{{patientStreetAddress}}^^{{patientCity}}^{{patientProvince}}^{{patientPostalCode}}||{{patientHomePhoneNumber}}^^^{{patientEmail}}|{{patientBusinessPhoneNumber}}||{{patientMaritalStatus}}|AC||{{patientOmang}}|
+PV1|1|O|{{targetFacility.ipmsXlocation}}||||{{targetFacility.provider}}^^^^^^^^^^^^XX|||||||||||{{targetFacility.patientType}}||U|||||||||||||||||||{{targetFacility.name}}||{{targetFacility.patientStatus}}|||{{date}}|
+ROL|1|AD|AT|{{providerId}}^{{providerLastName}}^{{providerFirstName.[0]}}|
+{{/with}}

data/templates/fhir/ADT_A04_TO_IPMS.hbs

@@ -2,6 +2,6 @@
 MSH|^~\&|DM||||{{date}}||ADT^A04|{{controlId}}|D|2.4|||AL|NE|
 EVN||{{date}}|||ZZHGGMMO^Healthpost^Mmopane|{{date}}|
 PID|1||NEW||{{patientFamilyName}}^{{patientFirstName.[0]}}^^^^^F||{{patientDob}}|{{patientSex}}||CT|{{patientStreetAddress}}^^{{patientCity}}^{{patientProvince}}^{{patientPostalCode}}||{{patientHomePhoneNumber}}^^^{{patientEmail}}|{{patientBusinessPhoneNumber}}||{{patientMaritalStatus}}|AC||{{patientOmang}}|
-PV1|1|O|HGGMMO||||ZZHGGMMO^Healthpost^Mmopane^^^^^^^^^^XX|||||||||||POV||U|||||||||||||||||||GGC||REG|||{{date}}|
+PV1|1|O|{{targetFacility.ipmsXlocation}}||||{{targetFacility.provider}}^^^^^^^^^^^^XX|||||||||||{{targetFacility.patientType}}||U|||||||||||||||||||{{targetFacility.name}}||{{targetFacility.patientStatus}}|||{{date}}|
 ROL|1|AD|AT|{{providerId}}^{{providerLastName}}^{{providerFirstName.[0]}}|
 {{/with}}

data/templates/fhir/ORM_O01_TO_IPMS.hbs

@@ -1,6 +1,6 @@
 {{#with msg.fhir}}
-MSH|^~\&|LAB||LAB||{{date}}||ORM^O01|{{controlId}}|D|2.4|||AL|NE|
+MSH|^~\&|{{orderTypeFlag}}||{{orderTypeFlag}}||{{date}}||ORM^O01|{{controlId}}|D|2.4|||AL|NE|
 PID|1||{{medicalRecordNumber}}^^^^MR^GGC~{{patientOmang}}^^^^SS^GGC~{{patientIdentifier}}^^^^PI^GGC~{{unknownIdentifier}}^^^^HUB^GGC||{{patientFamilyName}}^{{patientFirstName.[0]}}^^^^^L||{{patientDoB}}|{{sex}}||CT|{{patientStreetAddress}}^^{{patientCity}}^{{patientProvince}}^{{patientPostalCode}}||{{patientBusinessPhoneNumber}}|||{{maritalStatus}}||{{patientAccountNumber}}|
-ORC|NW|{{labOrderId}}^LAB|{{medicalRecordNumber}}||FINAL||^^^^^R^||{{labOrderDatetime}}|||
-OBR|1|{{labOrderId}}^LAB||{{labOrderMnemonic}}^{{labOrderName}}|R|{{labOrderDatetime}}|{{labOrderDatetime}}|||||||^^|{{providerId}}^{{providerLastName}}^{{providerFirstName.[0]}}^^^^^||
+ORC|NW|{{labOrderId}}^{{orderTypeFlag}}|{{medicalRecordNumber}}||FINAL||^^^^^R^||{{labOrderDatetime}}|||
+OBR|1|{{labOrderId}}^{{orderTypeFlag}}||{{labOrderMnemonic}}^{{labOrderName}}|R|{{labOrderDatetime}}|{{labOrderDatetime}}||||||||SPUTUM^^^SPUTUM|{{providerId}}^{{providerLastName}}^{{providerFirstName.[0]}}^^^^^||
 {{/with}}

data/templates/hl7v2/CodeSystem/IDType.hbs

@@ -163,6 +163,10 @@
         "code" : "IND",
         "display" : "Indigenous/Aboriginal",
         "system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
+    {{else if (eq inCode 'LAB')}},
+        "code" : "LAB",
+        "display" : "Laboratory Order ID",
+        "system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
     {{else if (eq inCode 'LACSN')}},
         "code" : "LACSN",
         "display" : "Laboratory Accession ID",

data/templates/hl7v2/DataType/CWECodeableConceptIpms.hbs

@@ -0,0 +1,49 @@
+"coding":
+[
+    {
+    	{{#if mapping}}
+			{{#with (evaluate mapping inCode=CWE-1)}}
+                "code":"{{code}}",
+                "display":"{{display}}",
+                "system":"{{system}}",
+                "version":"{{version}}",
+        	{{/with}}
+		{{else}}
+            "code":"{{CWE-1}}",
+            "display":"{{CWE-2}}",
+            "system":"https://api.openconceptlab.org/orgs/I-TECH-UW/sources/IPMSLAB/",
+            "version":"{{CWE-7}}",
+        {{/if}}
+    },
+    {
+        {{#if mapping}}
+            {{#with (evaluate mapping inCode=CWE-4)}}
+                "code":"{{code}}",
+                "display":"{{display}}",
+                "system":"{{system}}",
+                "version":"{{version}}",
+        	{{/with}}
+		{{else}}
+            "code":"{{CWE-4}}",
+            "display":"{{CWE-5}}",
+            "system":"https://api.openconceptlab.org/orgs/I-TECH-UW/sources/IPMSLAB/",
+            "version":"{{CWE-8}}",
+        {{/if}}
+    },
+    {
+        {{#if mapping}}
+            {{#with (evaluate mapping inCode=CWE-10)}}
+                "code":"{{code}}",
+                "display":"{{display}}",
+                "system":"{{system}}",
+                "version":"{{version}}",
+        	{{/with}}
+        {{else}}
+            "code":"{{CWE-10}}",
+            "display":"{{CWE-11}}",
+            "system":"https://api.openconceptlab.org/orgs/I-TECH-UW/sources/IPMSLAB/",
+            "version":"{{CWE-13}}",
+        {{/if}}
+    },
+],
+"text":"{{CWE-9}}",

data/templates/hl7v2/Resources/DiagnosticReport.hbs

@@ -68,16 +68,26 @@
                     ],
                 },
             },
-            { {{>DataType/EIIdentifier.hbs EI=OBR-2}} },
-            { {{>DataType/EIIdentifier.hbs EI=OBR-3}} },
+            {{#if OBR-2}},
+            {
+                "system":"http://moh.bw.org/ext/identifier/lab-order-id",
+                {{>DataType/EIIdentifier.hbs EI=OBR-2}},
+            },
+            {{/if}},
+            {{#if OBR-3}},
+            {
+                "system":"http://moh.bw.org/ext/identifier/pi",
+                {{>DataType/EIIdentifier.hbs EI=OBR-3}},
+            },
+            {{/if}},
         ],
         "effectiveDateTime":"{{formatAsDateTime ORC-9}}",
         {{#if (not OBR-8)}},
             "effectiveDateTime":"{{formatAsDateTime OBR-7}}",
         {{/if}},
         "code":
         {
-            {{>DataType/CWECodeableConcept.hbs CWE=OBR-4}},
+            {{>DataType/CWECodeableConceptIpms.hbs CWE=OBR-4}},
         },
         "effectivePeriod":
         {

debug.docker-compose.yml

@@ -14,7 +14,7 @@ services:
     container_name: built-fhir-converter
     hostname: fhir-converter
     restart: unless-stopped
-    image: ghcr.io/b-techbw/openhim-mediator-fhir-converter:local
+    image: itechuw/openhim-mediator-fhir-converter:debug
     build: ./
     ports:
       - 2019:2019
@@ -32,4 +32,4 @@ services:
 networks:
   hie:
     external: true
-    name: hie-botswana_hie
+    name: openhim_public

src/lib/fhir/fhir.js

@@ -56,21 +56,66 @@ module.exports = class fhir extends dataHandler {
             let entry = bundle.entry.find(e => e.resource.resourceType == resourceName)
             return (entry && entry.resource) ? entry.resource : null
         } catch (e) {
-            logger.error(`Can't get ${resourceName} from \n${JSON.stringify(bundle)}`)
+            console.log(`Can't get ${resourceName} from \n${JSON.stringify(bundle)}`)
             return null
         }
     }
 
+    getSourceLocation(bundle) {
+        try {
+            let task = this.getResource(bundle, "Task")
+            const sourceLocationId = task.requester ? task.requester.reference.split('/')[1] : null
+
+            let sourceLocation = bundle.entry.find(e => e.resource.resourceType == "Location" && e.resource.id == sourceLocationId)
+            if(sourceLocation && sourceLocation.resource) {
+                return sourceLocation.resource.name
+            }
+        } catch (error) {
+            console.log(`Can't get source location from \n${JSON.stringify(bundle)}`)
+        }
+        return null
+    }
+
+    /** Set IPMS-specific location mappings */
+    setIpmsLocationInformation(bundle, res) {
+        try {
+            let task = this.getResource(bundle, "Task")
+            const targetLocationId = task.location ? task.location.reference.split('/')[1] : null
+
+            let targetLocation = bundle.entry.find(e => e.resource.resourceType == "Location" && e.resource.id == targetLocationId)
+            if(targetLocation && targetLocation.resource) {
+                let target = targetLocation.resource
+                let provider = target.extension.find(e => e && e.url && e.url.includes("ipms-provider") && e.valueString)
+                let patientType = target.extension.find(e => e && e.url && e.url.includes("ipms-patient-type") && e.valueString)
+                let patientStatus = target.extension.find(e => e && e.url && e.url.includes("ipms-patient-status") && e.valueString)
+                let ipmsXlocation = target.extension.find(e => e && e.url && e.url.includes("ipms-xlocation") && e.valueString)
+
+                res.targetFacility = {
+                    name: target.name,
+                    provider: provider ? provider.valueString : "",
+                    patientType: patientType ? patientType.valueString : "",
+                    patientStatus: patientStatus ? patientStatus.valueString : "",
+                    ipmsXlocation: ipmsXlocation ? ipmsXlocation.valueString : ""
+                }
+            }
+        } catch (error) {
+            console.log(`Can't get target location information from \n${JSON.stringify(bundle)}`)
+        }
+            console.log(`Target facility: ${JSON.stringify(res.targetFacility)}`)
+        return res
+    }
+
     parseAdt(bundle) {
         let res = {};
         let patient = this.getResource(bundle, "Patient");
-        let sourceLocation = this.getResource(bundle, "Location");
-        let provider = this.getResource(bundle, "Practitioner");;
+        let sourceLocation = this.getSourceLocation(bundle);
+        let provider = this.getResource(bundle, "Practitioner");
 
         res = this.setPatientData(patient, res);
         res = this.setProviderData(provider, res);
+        res = this.setIpmsLocationInformation(bundle, res);
 
-        res.facilityId = sourceLocation ? sourceLocation.id : "";
+        res.facilityId = sourceLocation ? sourceLocation : "";
         res.kinFamilyName = "";
         res.kinFirstName = "";
         res.kinRelCode = "";
@@ -79,6 +124,7 @@ module.exports = class fhir extends dataHandler {
         res.kinCity = "";
         res.kinProvince = "";
         res.kinPostalCode = "";
+
         return res;
     }
     parseOrm(bundle) {
@@ -95,7 +141,8 @@ module.exports = class fhir extends dataHandler {
         res = this.setProviderData(provider, res);
 
         res.facilityId = sourceLocation ? sourceLocation.id : "";
-        res.labOrderId = task.identifier ? task.identifier[0].value : "";
+        res.labOrderId = serviceRequest ? serviceRequest.id : "";
+
         let orderDateTime = new Date()
         try {
             orderDateTime = serviceRequest.authoredOn ? new Date(serviceRequest.authoredOn) : (task.authoredOn ? new Date(task.authoredOn) : orderDateTime)
@@ -109,8 +156,13 @@ module.exports = class fhir extends dataHandler {
             let ipmsCode = serviceRequest.code.coding.find(e => e.system == "https://api.openconceptlab.org/orgs/I-TECH-UW/sources/IPMSLAB/")
             res.labOrderMnemonic = ipmsCode && ipmsCode.code ? ipmsCode.code : "";
             res.labOrderName = ipmsCode && ipmsCode.display ? ipmsCode.display : "";
+            if(ipmsCode && ipmsCode.extension && ipmsCode.extension.length > 0) {
+                let orderTypeFlag = ipmsCode.extension.find(e => e && e.url && e.url.includes("ipms-order-type") && e.valueString)
+                res.orderTypeFlag = orderTypeFlag ? orderTypeFlag.valueString : "LAB";
+            }
         }
 
+
         return res;
     }
 
@@ -119,12 +171,13 @@ module.exports = class fhir extends dataHandler {
         res.patientDob = patient.birthDate.split('-').join('');
         res.patientSex = patient.gender && patient.gender == 'male' ? "M" : "F";
 
-        if(patient.address){
-            res.patientStreetAddress = patient.address.length > 0 && patient.address[0].line.length > 0 ? patient.address[0].line[0] : "";
-            res.patientCity = patient.address.length > 0 ? patient.address[0].city : "";
-            res.patientProvince = patient.address.length > 0 ? patient.address[0].state : "";
-            res.patientPostalCode = patient.address.length > 0 ? patient.address[0].postalCode : "";
+        if(patient.address && patient.address.length > 0){
+            res.patientStreetAddress = patient.address[0].line && patient.address[0].line.length > 0 ? patient.address[0].line[0] : "";
+            res.patientCity = patient.address[0].city || "";
+            res.patientProvince = patient.address[0].state || "";
+            res.patientPostalCode = patient.address[0].postalCode || "";
         }
+
         res.patientMaritalStatus = patient.maritalStatus && patient.maritalStatus.coding.length > 0 ? patient.maritalStatus.coding[0].code : "";    
 
         let q;

tsconfig.json

@@ -71,6 +71,6 @@
     // "skipLibCheck": true,                     /* Skip type checking of declaration files. */
     // "forceConsistentCasingInFileNames": true  /* Disallow inconsistently-cased references to the same file. */
   },
-  "include": ["src/**/*"],
+  "include": ["src/**/*", "src/lib/**/*"],
   "exclude" : ["src/**/__tests__"]
 }