Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added Lab order FHIR for R5, Added Lab Result FHIR #1

Open
wants to merge 16 commits into
base: main
Choose a base branch
from
Open

Added Lab order FHIR for R5, Added Lab Result FHIR #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
16 commits
Select commit Hold shift + click to select a range
545cba3
Added Lab order FHIR for R5, Added Lab Result FHIR
sushantpatil1214 Aug 7, 2024
3892cb1
Added new values
sushantpatil1214 Aug 12, 2024
a6c01dd
Added env variables for orgnisations
sushantpatil1214 Aug 12, 2024
26e912f
Added logic for lab results mapping
sushantpatil1214 Aug 12, 2024
09eccf0
Results fix for R5
sushantpatil1214 Aug 13, 2024
d088765
Results fix for R5
sushantpatil1214 Aug 13, 2024
3a7bcdb
Results fix for variables
sushantpatil1214 Aug 13, 2024
32cfa71
Code clean
sushantpatil1214 Aug 13, 2024
6b89af8
Added Logic for Get Lab results from FHIR and mapp to normal JSON
sushantpatil1214 Aug 13, 2024
97ed939
Added routes
sushantpatil1214 Aug 14, 2024
d4a3ba9
Added routes
sushantpatil1214 Aug 14, 2024
733d33f
Added endpoint
sushantpatil1214 Aug 14, 2024
cf30a41
Fix Id's
sushantpatil1214 Aug 14, 2024
10e9de7
Added logic for patientArtNo
sushantpatil1214 Sep 16, 2024
38034f5
Handeled date
sushantpatil1214 Sep 18, 2024
0de3556
Merge pull request #2 from jembi/lab_result_mapping
sushantpatil1214 Sep 19, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions .idea/.gitignore
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

172 changes: 147 additions & 25 deletions importer/openhim-core/openhim-import.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
{
"name": "FHIR Server",
"description": "A FHIR server (HAPI FHIR)",
"urlPattern": "^/raw-fhir.*$",
"urlPattern": "^/hapi-fhir-jpaserver/fhir.*$",
"isAsynchronousProcess": false,
"methods": [
"GET",
Expand All @@ -53,10 +53,10 @@
"type": "http",
"status": "enabled",
"secured": false,
"host": "hapi-fhir",
"port": 8080,
"host": "197.243.18.12",
"port": 8085,
"path": "",
"pathTransform": "s/raw-//g",
"pathTransform": "",
"primary": true,
"username": "",
"password": "",
Expand All @@ -80,7 +80,7 @@
"autoRetryEnabled": false,
"autoRetryPeriodMinutes": 60,
"updatedBy": {
"id": "667d76cff305884a415ea9b1",
"id": "66bca8368e4b6e6029568565",
"name": "Super User"
}
},
Expand Down Expand Up @@ -133,21 +133,21 @@
"txViewAcl": [],
"txViewFullAcl": [],
"txRerunAcl": [],
"alerts": [],
"status": "enabled",
"rewriteUrls": false,
"addAutoRewriteRules": true,
"rewriteUrlsConfig": [],
"autoRetryEnabled": false,
"autoRetryPeriodMinutes": 60,
"updatedBy": {
"id": "667d76cff305884a415ea9b1",
"id": "66bca8368e4b6e6029568565",
"name": "Super User"
},
"alerts": []
}
},
{
"name": "EMR Lab Order",
"urlPattern": "^/emr-lab-order$",
"name": "Get Lab Results",
"urlPattern": "^^/get-lab-results.*$$",
"isAsynchronousProcess": false,
"methods": [
"GET",
Expand All @@ -171,13 +171,13 @@
"authType": "public",
"routes": [
{
"name": "Generate Lab Source ID",
"name": "Get Lab Results",
"type": "http",
"status": "enabled",
"secured": false,
"host": "rwanda-custom-mapping-mediator",
"port": 8084,
"path": "/lab-orders-source-id",
"path": "",
"pathTransform": "",
"primary": true,
"username": "",
Expand All @@ -194,21 +194,20 @@
"txViewAcl": [],
"txViewFullAcl": [],
"txRerunAcl": [],
"alerts": [],
"status": "enabled",
"rewriteUrls": false,
"addAutoRewriteRules": true,
"rewriteUrlsConfig": [],
"autoRetryEnabled": false,
"autoRetryPeriodMinutes": 60,
"updatedBy": {
"id": "667d76cff305884a415ea9b1",
"id": "66bca8368e4b6e6029568565",
"name": "Super User"
},
"alerts": [],
"priority": 2
}
},
{
"name": "VLSM And FHIR Lab Order",
"name": "FHIR Lab Order UUID Generation",
"urlPattern": "^/vlsm/order$",
"isAsynchronousProcess": false,
"methods": [
Expand All @@ -223,6 +222,7 @@
"PATCH"
],
"type": "http",
"priority": 2,
"tcpPort": null,
"tcpHost": null,
"pollingSchedule": null,
Expand Down Expand Up @@ -256,21 +256,20 @@
"txViewAcl": [],
"txViewFullAcl": [],
"txRerunAcl": [],
"alerts": [],
"status": "enabled",
"rewriteUrls": false,
"addAutoRewriteRules": true,
"rewriteUrlsConfig": [],
"autoRetryEnabled": false,
"autoRetryPeriodMinutes": 60,
"updatedBy": {
"id": "667d76cff305884a415ea9b1",
"id": "66bca8368e4b6e6029568565",
"name": "Super User"
},
"alerts": [],
"priority": 2
}
},
{
"name": "Smart FHIR",
"name": "Lab Order FHIR",
"urlPattern": "^/lab-order$",
"isAsynchronousProcess": false,
"methods": [
Expand All @@ -285,6 +284,7 @@
"PATCH"
],
"type": "http",
"priority": 3,
"tcpPort": null,
"tcpHost": null,
"pollingSchedule": null,
Expand Down Expand Up @@ -318,14 +318,136 @@
"txViewAcl": [],
"txViewFullAcl": [],
"txRerunAcl": [],
"alerts": [],
"status": "enabled",
"rewriteUrls": false,
"addAutoRewriteRules": true,
"rewriteUrlsConfig": [],
"autoRetryEnabled": false,
"autoRetryPeriodMinutes": 60,
"updatedBy": {
"id": "66bca8368e4b6e6029568565",
"name": "Super User"
}
},
{
"name": "Post VLSM Lab Results To FHIR",
"urlPattern": "^/lab-results$",
"isAsynchronousProcess": false,
"methods": [
"GET",
"POST",
"DELETE",
"PUT",
"OPTIONS",
"HEAD",
"TRACE",
"CONNECT",
"PATCH"
],
"type": "http",
"tcpPort": null,
"tcpHost": null,
"pollingSchedule": null,
"requestBody": true,
"responseBody": true,
"allow": [],
"whitelist": [],
"authType": "public",
"routes": [
{
"name": "Post Lab Result Mediator",
"type": "http",
"status": "enabled",
"secured": false,
"host": "rwanda-custom-mapping-mediator",
"port": 8084,
"path": "",
"pathTransform": "",
"primary": true,
"username": "",
"password": "",
"forwardAuthHeader": false
}
],
"matchContentTypes": [],
"matchContentRegex": null,
"matchContentXpath": null,
"matchContentJson": null,
"matchContentValue": null,
"properties": [],
"txViewAcl": [],
"txViewFullAcl": [],
"txRerunAcl": [],
"alerts": [],
"status": "enabled",
"rewriteUrls": false,
"addAutoRewriteRules": true,
"rewriteUrlsConfig": [],
"autoRetryEnabled": false,
"autoRetryPeriodMinutes": 60,
"updatedBy": {
"id": "66bca8368e4b6e6029568565",
"name": "Super User"
}
},
{
"name": "OpenHIM Mapping Mediator",
"urlPattern": "^/endpoints.*$",
"isAsynchronousProcess": false,
"methods": [
"GET",
"POST",
"DELETE",
"PUT",
"OPTIONS",
"HEAD",
"TRACE",
"CONNECT",
"PATCH"
],
"type": "http",
"tcpPort": null,
"tcpHost": null,
"pollingSchedule": null,
"requestBody": true,
"responseBody": true,
"allow": [],
"whitelist": [],
"authType": "public",
"routes": [
{
"name": "Mapping Mediator",
"type": "http",
"status": "enabled",
"secured": false,
"host": "openhim-mapping-mediator",
"port": 3003,
"path": "",
"pathTransform": "",
"primary": true,
"username": "",
"password": "",
"forwardAuthHeader": false
}
],
"matchContentTypes": [],
"matchContentRegex": null,
"matchContentXpath": null,
"matchContentJson": null,
"matchContentValue": null,
"properties": [],
"txViewAcl": [],
"txViewFullAcl": [],
"txRerunAcl": [],
"status": "enabled",
"rewriteUrls": false,
"addAutoRewriteRules": true,
"rewriteUrlsConfig": [],
"autoRetryEnabled": false,
"autoRetryPeriodMinutes": 60,
"updatedBy": {
"id": "667d76cff305884a415ea9b1",
"id": "66bca8368e4b6e6029568565",
"name": "Super User"
},
"alerts": []
Expand All @@ -349,8 +471,8 @@
],
"defaultChannelConfig": [],
"configDefs": [],
"_lastHeartbeat": "2024-06-28T06:12:25.042Z",
"_uptime": 20155.843693203
"_lastHeartbeat": "2024-08-14T13:18:59.080Z",
"_uptime": 1651.129535758
}
],
"ContactGroups": []
Expand Down
7 changes: 7 additions & 0 deletions importer/openhim-mapping-mediator/docker-compose.config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@ services:
target: /metadata.js
- source: mediator-config-jsonToFhirLabOrder.json
target: /jsonToFhirLabOrder.json
- source: mediator-config-jsonToFhirLabResult.json
target: /jsonToFhirLabResult.json
networks:
mapping-mediator:
# This command will only attempt to import the config when the uptime responds with a 2xx
Expand All @@ -28,6 +30,11 @@ configs:
name: mediator-config-jsonToFhirLabOrder.json-${mediator_config_jsonToFhirLabOrder_json_DIGEST:?err}
labels:
name: fhir
mediator-config-jsonToFhirLabResult.json:
file: ./jsonToFhirLabResult.json
name: mediator-config-jsonToFhirLabResult.json-${mediator_config_jsonToFhirLabResult_json_DIGEST:?err}
labels:
name: fhir

networks:
mapping-mediator:
Expand Down
16 changes: 9 additions & 7 deletions importer/openhim-mapping-mediator/jsonToFhirLabOrder.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,15 @@

"fullUrlPerfORG": "$exists(requestBody.performingOrganizationID) ? 'Organization/' & requestBody.performingOrganizationID : null",
"resourceIdPerfORG": "$exists(requestBody.performingOrganizationID) ? requestBody.performingOrganizationID : null",
"provinceId": "$exists(requestBody.provinceIds) ? requestBody.provinceIds : null",
"requestUrlPerfORG": "$exists(requestBody.performingOrganizationID) ? 'Organization/' & requestBody.performingOrganizationID : null",

"fullUrlServiceReq": "$exists(requestBody.serviceRequestID) ? 'ServiceRequest/' & requestBody.serviceRequestID : null",
"valueServiceReq": "$exists(requestBody.labsourceid) ? requestBody.labsourceid : null",
"valueServiceReq": "$exists(requestBody.upid) ? requestBody.upid : null",
"resourceIdServiceReq": "$exists(requestBody.serviceRequestID) ? requestBody.serviceRequestID : null",
"subjectReferenceServiceReq": "$exists(requestBody.patientId) ? 'Patient/' & requestBody.patientId : null",
"encounterReferenceServiceReq": "$exists(requestBody.encounterID) ? 'Encounter/' & requestBody.encounterID : null",
"occurrenceDateTimeServiceReq": "$exists(requestBody.requestDate) ? requestBody.requestDate : null",
"requesterReferenceServiceReq": "$exists(requestBody.requestingPractitionerID) ? 'Practitioner/' & requestBody.requestingPractitionerID : null",
"performerReferenceServiceReq": "$exists(requestBody.performingPractitionerID) ? 'Practitioner/' & requestBody.performingPractitionerID : null",
"reasonReferenceServiceReq": "$exists(requestBody.reasonForHIVTestingID) ? 'Observation/' & requestBody.reasonForHIVTestingID : null",
Expand Down Expand Up @@ -150,6 +152,7 @@
"subjectReferenceObsHivTestResult": "$exists(requestBody.patientId) ? 'Patient/' & requestBody.patientId : null",
"encounterReferenceObsHivTestResult": "$exists(requestBody.encounterID) ? 'Encounter/' & requestBody.encounterID : null",
"performerObsHivTestResult": "$exists(requestBody.organizationID) ? 'Organization/' & requestBody.organizationID : null",
"lastViralLoadResult": "$exists(requestBody.vlResult) ? requestBody.vlResult : 1001",
"notereferenceObsHivTestResult": "$exists(requestBody.organizationID) ? 'Organization/' & requestBody.organizationID : null",
"requestUrlObsHivTestResult": "$exists(requestBody.hivTestResultID) ? 'Observation/' & requestBody.hivTestResultID : null",

Expand All @@ -163,7 +166,7 @@
"fullUrlSpecimenDefspeciConserv":"$exists(requestBody.hivLabResultTaskID) ? 'Task/' & requestBody.hivLabResultTaskID : null",
"resourceIdSpecimenDefspeciConserv": "$exists(requestBody.hivLabResultTaskID) ? requestBody.hivLabResultTaskID : null",
"valueIntegerSpecimenDefspeciConserv": "$exists(requestBody.resultStatus) ? requestBody.resultStatus : null",
"identifiervalueSpecimenDefspeciConserv": "$exists(requestBody.labsourceid) ? requestBody.labsourceid : null",
"identifiervalueSpecimenDefspeciConserv": "$exists(requestBody.upid) ? requestBody.upid : null",
"basedOnrefoneSpecimenDefspeciConserv": "$exists(requestBody.serviceRequestID) ? 'ServiceRequest/' & requestBody.serviceRequestID : null",
"basedOnreftwoSpecimenDefspeciConserv": "$exists(requestBody.sampleDispatchedToLabID) ? 'Transport/' & requestBody.sampleDispatchedToLabID : null",
"basedOnrefthreeSpecimenDefspeciConserv": "$exists(requestBody.resultDispatchedToRequestingFacilityID) ? 'Transport/' & requestBody.resultDispatchedToRequestingFacilityID : null",
Expand Down Expand Up @@ -441,7 +444,7 @@
"transforms.resourceIdPerfORG":"entry[3].resource.id",
"constants.profilePerfORG":"entry[3].resource.meta.profile[0]",
"constants.urlPerfOrgProvince":"entry[3].resource.extension[0].url",
"requestBody.provinceId":"entry[3].resource.extension[0].valueInteger",
"transforms.provinceId":"entry[3].resource.extension[0].valueInteger",
"constants.urlPerfOrgDistrict":"entry[3].resource.extension[1].url",
"constants.valueIntegerPerfOrgDistrict":"entry[3].resource.extension[1].valueInteger",
"constants.codingSystemPerfORG":"entry[3].resource.identifier[0].type.coding[].system",
Expand Down Expand Up @@ -476,7 +479,7 @@
"constants.textCodeServiceReq":"entry[4].resource.code.concept.text",
"transforms.subjectReferenceServiceReq":"entry[4].resource.subject.reference",
"transforms.encounterReferenceServiceReq":"entry[4].resource.encounter.reference",
"constants.occurrenceDateTimeServiceReq":"entry[4].resource.occurrenceDateTime",
"transforms.occurrenceDateTimeServiceReq":"entry[4].resource.occurrenceDateTime",
"transforms.requesterReferenceServiceReq":"entry[4].resource.requester.reference",
"transforms.performerReferenceServiceReq":"entry[4].resource.performer[].reference",
"transforms.reasonReferenceServiceReq":"entry[4].resource.reason[].reference.reference",
Expand Down Expand Up @@ -757,7 +760,7 @@
"transforms.encounterReferenceObsHivTestResult":"entry[18].resource.encounter.reference",
"requestBody.lastViralLoadTestDate":"entry[18].resource.effectiveDateTime",
"transforms.performerObsHivTestResult":"entry[18].resource.performer[].reference",
"requestBody.lastViralLoadResult":"entry[18].resource.valueInteger",
"transforms.lastViralLoadResult":"entry[18].resource.valueInteger",
"constants.interpretationSystemCodeObsHivTestResult":"entry[18].resource.interpretation[].coding[].system",
"constants.interpretationCodeCodeObsHivTestResult":"entry[18].resource.interpretation[].coding[].code",
"constants.interpretationDisplayCodeObsHivTestResult":"entry[18].resource.interpretation[].coding[].display",
Expand Down Expand Up @@ -1143,7 +1146,6 @@
"codeCodeServiceReq": "25836-8",
"displayCodeServiceReq": "HIV 1 RNA [#/volume] (viral load) in Specimen by NAA with probe detection",
"textCodeServiceReq": "Test Type",
"occurrenceDateTimeServiceReq": "2012-01-05",
"timeServiceReq": "2015-02-07T13:28:17-05:00",
"textUrlServiceReq": "additional notes here",
"methodServiceReq": "PUT",
Expand Down Expand Up @@ -1526,7 +1528,7 @@
"headers": {
"contentType": "application/json"
},
"url": "http://openhim-core:5001/raw-fhir"
"url": "http://openhim-core:5001/hapi-fhir-jpaserver/fhir/"
},
"extract": {
"JeMPIResponse": "$.body"
Expand Down
Loading