Lab Integration Workflow

Owned by Piotr Mankowski
Last updated: Jun 07, 2022 by Jan Flowers
8 min read

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The Lab Order workflow between OpenELIS and OpenMRS will use the FHIR Workflow Module and suggested Communication Patterns to implement the ordering of lab tests from OpenMRS to OpenELIS and the returning the results to OpenMRS.

The current communication workflow uses HL7 V2.5.1 messages as documented here: (https://github.com/openelisglobal/openelisglobal-core/wiki/Result-Reporting). This functionality is implemented in openmrs-module-labintegration, an OpenMRS module made for an implementation of OpenMRS deployed in Haiti called iSantePlus.  

Communication Overview

Implementation Guide

iSantéPlus

  1. Install iSantePlus using one of the following approaches:
    1. Docker: https://github.com/IsantePlus/isanteplus-docker
    2. Apache Tomcat WAR: SOP iSantePlus Installation.docx
  2. Install the OpenMRS FHIR module using the following omod file: openmrs-module-fhir2.omod

  3. Install the iSantePlus Lab on FHIR module using the following omod file: labonfhir-1.0.0-SNAPSHOT.omod

  4. Restart iSantePlus

  5. Start up the OpenELIS Update Task in `System Administration` → `Advanced Administration` → `Scheduler` → `Manage Scheduler`

OpenELIS Global 2.x

  1. Install OpenELIS Global 2.x using the instructions at: http://docs.openelis-global.org/en/latest/install/
  2. Navigate to the "results reporting" configuration: https://IPforyourserver:8443/OpenELIS-Global/ResultReportingConfiguration.do
  3. Move the radio button for Result Reporting to "Enable" and enter in the URL for the OpenMRS connection like in the example below. 
    1. Please note, the Test URL button may not respond to the FHIR module, so please disregard any errors if you click it.  
  4. Click Save at the bottom of the page. 

Required FHIR Resources

Task

> more info

The Task resource is created along with the corresponding ServiceRequest resource when a clinician creates a TestOrder and decides to send it to OpenELIS.

This resource is used to track the status of the lab order request from initiation to completion, and as a container for all other resources related to the given order.

Example Task:

{
    "resourceType": "Task",
    "id": "88ffa7fb-0419-4097-8b45-24f0d843c5ea",
    "identifier": [
        {
            "system": "http://isanteplus.org/ext/task/identifier",
            "value": "88ffa7fb-0419-4097-8b45-24f0d843c5ea"
        }
    ],
    "basedOn": [
        {
            "reference": "ServiceRequest/ebf83ba0-9d3c-497f-9aa0-d839ec506202",
            "type": "ServiceRequest"
        },
        {
            "reference": "ServiceRequest/73e96ecb-a78d-41c8-a55f-d9b90f759e5f",
            "type": "ServiceRequest"
        }
    ],
    "status": "requested",
    "intent": "order",
    "for": {
        "reference": "Patient/e14e9bda-d273-4c74-8509-5732a4ebaf19",
        "type": "Patient"
    },
    "encounter": {
        "reference": "Encounter/7f5aabd9-6375-47c8-a8d6-30f219b6e2f1",
        "type": "Encounter"
    },
    "authoredOn": "2020-04-28T17:33:19+00:00",
    "owner": {
        "reference": "Practitioner/f9badd80-ab76-11e2-9e96-0800200c9a66",
        "type": "Practitioner"
    }
}

ServiceRequest

> more info

The ServiceRequest resource represents the TestOrder placed in OpenMRS. It is referenced from the Task with the Task.basedOn element, and sent to OpenELIS with the Task to initiate the processing of the order. 

Example Service Request:

{
    "resourceType": "ServiceRequest",
    "id": "73e96ecb-a78d-41c8-a55f-d9b90f759e5f",
    "status": "active",
    "intent": "order",
    "code": {
        "coding": [
            {
                "code": "790AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
            },
            {
                "system": "http://loinc.org",
                "code": "14682-9"
            },
            {
                "system": "urn:oid:2.16.840.1.113883.3.7201",
                "code": "790"
            }
        ]
    },
    "subject": {
        "reference": "Patient/e14e9bda-d273-4c74-8509-5732a4ebaf19",
        "type": "Patient"
    },
    "encounter": {
        "reference": "Encounter/7f5aabd9-6375-47c8-a8d6-30f219b6e2f1",
        "type": "Encounter"
    }
}

DiagnosticReport

> more info

The DiagnosticReport resource  is the container for the results of an Order, and holds these results in the DiagnosticReport.result element as references to Observation resources. 

Example Diagnostic Report

{
  "resourceType": "DiagnosticReport",
  "id": "93",
  "meta": {
    "versionId": "1",
    "lastUpdated": "2020-04-28T17:33:36.163+00:00",
    "source": "#55t4lpDZF4q3TCZ0"
  },
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> Untitled Diagnostic Report </div><table class=\"hapiPropertyTable\"><tbody><tr><td>Status</td><td>FINAL</td></tr></tbody></table></div>"
  },
  "identifier": [
    {
      "system": "https://isanteplusdemo.com/openmrs/ws/fhir2/",
      "value": "ebf83ba0-9d3c-497f-9aa0-d839ec506202"
    }
  ],
  "status": "final",
  "code": {
    "coding": [
      {
        "code": "1008AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
      },
      {
        "system": "http://loinc.org",
        "code": "22748-8"
      },
      {
        "system": "urn:oid:2.16.840.1.113883.3.7201",
        "code": "1008"
      }
    ]
  },
  "subject": {
    "reference": "Patient/2"
  },
  "result": [
    {
      "reference": "Observation/92",
      "type": "Observation"
    }
  ]
}

Observation

> more info

The Observation resource contains the results of the Lab Order request.

Example Observation:

{
  "resourceType": "Observation",
  "id": "92",
  "meta": {
    "versionId": "1",
    "lastUpdated": "2020-04-28T17:33:36.124+00:00",
    "source": "#xAVz0uUE6c3l42Za"
  },
  "identifier": [
    {
      "system": "https://isanteplusdemo.com/openmrs/ws/fhir2/",
      "value": "ebf83ba0-9d3c-497f-9aa0-d839ec506202"
    }
  ],
  "status": "final",
  "code": {
    "coding": [
      {
        "code": "1008AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
      },
      {
        "system": "http://loinc.org",
        "code": "22748-8"
      },
      {
        "system": "urn:oid:2.16.840.1.113883.3.7201",
        "code": "1008"
      }
    ]
  },
  "subject": {
    "reference": "Patient/2"
  },
  "valueQuantity": {
    "value": 55,
    "unit": "UI/L"
  }
}

Patient

> more info

The Patient resource contains vital information for OpenELIS to fullfill the lab order request, and is referenced by the Task.

Example Patient:

{
    "resourceType": "Patient",
    "id": "e14e9bda-d273-4c74-8509-5732a4ebaf19",
    "identifier": [
        {
            "id": "5981a256-d60c-44b1-beae-9bdd2cf572f8",
            "use": "official",
            "system": "iSantePlus ID",
            "value": "10012R"
        },
        {
            "id": "75a67d54-6fff-44d1-9c3e-2116c967b475",
            "use": "usual",
            "system": "Code National",
            "value": "100000"
        },
        {
            "id": "29447d21-3cd6-42a9-9ab2-79ebfa710a01",
            "use": "usual",
            "system": "ECID",
            "value": "04d759e0-5d02-11e8-b899-0242ac12000b"
        }
    ],
    "active": true,
    "name": [
        {
            "id": "511275de-e301-44a3-95d2-28d0d3b35387",
            "family": "Mankowski",
            "given": [
                "Piotr"
            ]
        }
    ],
    "gender": "male",
    "birthDate": "1987-01-01",
    "deceasedBoolean": false,
    "address": [
        {
            "id": "d4f7c809-3d01-4032-b64d-4c22e8eccbbc",
            "use": "home",
            "country": "Haiti"
        }
    ]
}

Deliverables (Lab)

  1. Demo - continuity of care pilot - 
  2. Public Communication - OpenMRS Talk/Design Forum/
  3. Documentation - functional and technical reqs (HIE doc, implementation guide, Wiki page contents)
  4. Present at OpenMRS & OpenHIE   

Relevant FHIR Docs

Relevant Talk Posts

Demo Video iSantePlus to OpenMRS