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Set Up the OpenMRS Hapi Fhir server Locally .
use the Docker Compose file below to easily spin up a fully configured Hapi FHIR server Instance that has Support for both the $collect-data and $evaluate-measure FHIR operationsCode Block language yml title docker-compose.yml version: "3" services: hapi-fhir-jpaserver-start: image: openmrsinfra/openmrs-hapi-fhir:openmrs-fhir-plir_cql container_name: hapi-fhir-cql restart: on-failure ports: - "8090:8080"Move to directory of the the above docker-compose.yml file and run
Code Block language bash docker-compose up
This will spin up an instance of the hapi fhir jpa server and should be accesible at http://localhost:8090/
In order to acces the server end points . use the Basic Credentials belowCode Block language groovy username : hapi password : hapi123
Load a sample Testing Dataset with Observations , Patients and Encounters.
For The purpose of this Testing , we will load/Post the sample Data set directly to the Hapi fhir Server. Create a sample Dataset with Observations linked to these Concepts .
Alternatively you can use an already created Sample Observation Fhir Data For Testing TX-PVLS Indicator Calculation or the one for TX-CURR when calculating for TX-CURR indicator . We can use a simple API client like Postman to Load the data into the hapi fhir server.
Load the sample dataset into the POST Body for Postman and make a Post request to the endpoint belowCode Block language xml POST : http://localhost:8090/fhir
Load the Required Libraries For the Calculation of TX_PVLS PVLS or TX-CURR .
See FHIR CQL Libraries for the Calculation of TX_PVLS. In or FHIR CQL Libraries for TX-CURR. In Order to persist the Library Resource IDs into the Hapi FHIR server , we shall use PUT instead of POST.
Note that we Load both the TX_PVLS LIbrary LIbrary or TX_CURR and FHIRHelpers Library into the HAPI Fhir server .
i) Load the FHIRHelpers Library Resource into the PUT Body for Postman and send the PUT request to this end point belowCode Block language bash PUT: http://localhost:8090/fhir/Library/library-FHIRHelpers-4.0.1
ii) Load TX_PVLS LIbrary Resource into the PUT Body for Postman and send the PUT request to this end point belowCode Block language bash PUT : http://localhost:8090/fhir/Library/TX-PVLS or http://localhost:8090/fhir/Library/TX-CURRLoad the TX-PVLS Measure resource .
see the FHIR Measure Resource For Calculation of TX_PVLS indicator or FHIR Measure Resource for calculating TX_CURR indicator . In order to persist the Resource ID , we shall use PUT instead of POST.
Load the TX-PVLS or TX-CURR resource into the PUT Body for Postman and send a PUT request to the endpoint belowCode Block language bash PUT : http://localhost:8090/fhir/Measure/TX-PVLS or http://localhost:8090/fhir/Measure/TX-CURRGenerating the Data set relevant for TX_PVLS./TX-CURR
In order to generate the relevant dateset for the TX_PVLS PVLS or TX_CURR Indicator , invoke the collect-data operation using the following request
This should return a sample result-Code Block language bash GET : http://localhost:8090/fhir/Measure/TX-PVLS/$collect-data?periodStart=2021-01-01&periodEnd=2021-12-31
or http://localhost:8090/fhir/Measure/TX-CURR/$collect-data?periodStart=2021-01-01&periodEnd=2021-12-31
This should return a sample result-set like belowExpand title Sample Result set Code Block language xml { "resourceType": "Parameters", "parameter": [ { "name": "measureReport", "resource": { "resourceType": "MeasureReport", "status": "complete", "type": "data-collection", "measure": "Measure/TX_PVLS", "evaluatedResource": [ { "reference": "http://localhost:8090/fhir/Observation/5" }, { "reference": "http://localhost:8090/fhir/Observation/7" }, { "reference": "http://localhost:8090/fhir/Observation/8" }, { "reference": "http://localhost:8090/fhir/Observation/9" }, { "reference": "http://localhost:8090/fhir/Patient/9c5162a4-1cbb-4239-8813-da2d10be1ff4" }, { "reference": "http://localhost:8090/fhir/Patient/337679e5-aae4-4d95-8583-758e6551b953" }, { "reference": "http://localhost:8090/fhir/Patient/337679e5-aae4-4d95-8583-758e6551b9xx" } ] } }, { "name": "resource", "resource": { "resourceType": "Observation", "id": "5", "meta": { "versionId": "1", "lastUpdated": "2021-03-08T07:45:52.968+00:00", "source": "#aoXNf2q7CgVTGdH3" }, "status": "final", "category": [ { "coding": [ { "system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory", "display": "Laboratory" } ] } ], "code": { "coding": [ { "code": "1305AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "display": "HIV VIRAL LOAD, QUALITATIVE" }, { "system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL", "code": "1305", "display": "HIV VIRAL LOAD, QUALITATIVE" } ] }, "subject": { "reference": "Patient/9c5162a4-1cbb-4239-8813-da2d10be1ff4", "type": "Patient", "display": "Obs_Test2 Obs_Test2 Obs_Test2 (OpenMRS ID: 10001V)" }, "encounter": { "reference": "Encounter/13cbf9b8-24fa-4806-8f2b-8e4f489b1f96", "type": "Encounter" }, "effectiveDateTime": "2021-01-26T08:12:28+00:00", "issued": "2021-01-26T08:12:28.000+00:00", "valueCodeableConcept": { "coding": [ { "code": "1306AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "display": "BEYOND DETECTABLE LIMIT" }, { "system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL", "code": "1306", "display": "BEYOND DETECTABLE LIMIT" } ] } } }, { "name": "resource", "resource": { "resourceType": "Observation", "id": "7", "meta": { "versionId": "1", "lastUpdated": "2021-03-08T07:45:52.968+00:00", "source": "#aoXNf2q7CgVTGdH3" }, "status": "final", "category": [ { "coding": [ { "system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory", "display": "Laboratory" } ] } ], "code": { "coding": [ { "code": "856AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "display": "HIV viral load" }, { "system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL", "code": "856", "display": "HIV viral load" } ] }, "subject": { "reference": "Patient/337679e5-aae4-4d95-8583-758e6551b953", "type": "Patient", "display": "Obs_Test1 Obs_Test1 Obs_Test1 (OpenMRS ID: 10000X)" }, "encounter": { "reference": "Encounter/4b91bc4f-9eef-4144-a88f-d8998ae932cf", "type": "Encounter" }, "effectiveDateTime": "2021-01-26T08:11:12+00:00", "issued": "2021-01-26T08:11:12.000+00:00", "valueQuantity": { "value": 23 } } }, { "name": "resource", "resource": { "resourceType": "Observation", "id": "8", "meta": { "versionId": "1", "lastUpdated": "2021-03-08T07:45:52.968+00:00", "source": "#aoXNf2q7CgVTGdH3" }, "status": "final", "category": [ { "coding": [ { "system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory", "display": "Laboratory" } ] } ], "code": { "coding": [ { "code": "856AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "display": "HIV viral load" }, { "system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL", "code": "856", "display": "HIV viral load" } ] }, "subject": { "reference": "Patient/337679e5-aae4-4d95-8583-758e6551b953", "type": "Patient", "display": "Obs_Test1 Obs_Test1 Obs_Test1 (OpenMRS ID: 10000X)" }, "encounter": { "reference": "Encounter/4b91bc4f-9eef-4144-a88f-d8998ae932cf", "type": "Encounter" }, "effectiveDateTime": "2021-01-26T08:11:12+00:00", "issued": "2021-01-26T08:11:12.000+00:00", "valueQuantity": { "value": 23 } } }, { "name": "resource", "resource": { "resourceType": "Observation", "id": "9", "meta": { "versionId": "1", "lastUpdated": "2021-03-08T07:45:52.968+00:00", "source": "#aoXNf2q7CgVTGdH3" }, "status": "final", "category": [ { "coding": [ { "system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory", "display": "Laboratory" } ] } ], "code": { "coding": [ { "code": "856AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "display": "HIV viral load" }, { "system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL", "code": "856", "display": "HIV viral load" } ] }, "subject": { "reference": "Patient/337679e5-aae4-4d95-8583-758e6551b9xx", "type": "Patient", "display": "Obs_Test1 Obs_Test1 Obs_Test1 (OpenMRS ID: 10000X)" }, "encounter": { "reference": "Encounter/4b91bc4f-9eef-4144-a88f-d8998ae932cf", "type": "Encounter" }, "effectiveDateTime": "2021-01-26T08:11:12+00:00", "issued": "2021-01-26T08:11:12.000+00:00", "valueQuantity": { "value": 2000 } } }, { "name": "resource", "resource": { "resourceType": "Patient", "id": "9c5162a4-1cbb-4239-8813-da2d10be1ff4", "meta": { "versionId": "1", "lastUpdated": "2021-03-08T07:45:53.514+00:00", "source": "#aoXNf2q7CgVTGdH3" }, "text": { "status": "generated", "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>" } } }, { "name": "resource", "resource": { "resourceType": "Patient", "id": "337679e5-aae4-4d95-8583-758e6551b953", "meta": { "versionId": "1", "lastUpdated": "2021-03-08T07:45:53.594+00:00", "source": "#aoXNf2q7CgVTGdH3" }, "text": { "status": "generated", "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>" } } }, { "name": "resource", "resource": { "resourceType": "Patient", "id": "337679e5-aae4-4d95-8583-758e6551b9xx", "meta": { "versionId": "1", "lastUpdated": "2021-03-08T07:45:53.699+00:00", "source": "#aoXNf2q7CgVTGdH3" }, "text": { "status": "generated", "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>" } } } ] }Calculating the TX-PVLS Indicator and Generating the Measure Report
In order to generate the Measure report as a result of the indicator calculation , invoke the evaluate-measure operation using the following requestCode Block language bash GET : http://localhost:8090/fhir/Measure/TX-PVLS/$evaluate-measure?periodStart=2019-01-01&periodEnd=2030-12-31This should generate and return a MesureReport result like below
Code Block language xml
, "periodOR collect-data operation for TX-CURR
| Code Block | ||
|---|---|---|
| ||
{ "resourceType": "Parameters", "parameter": [ { "name": "measureReport", "resource": { |
...
"resourceType": |
...
"MeasureReport",
"status": "complete",
"type": "data-collection",
"measure": "Measure/TX_CURR",
"evaluatedResource": [
{
"reference": "http://localhost:8090/fhir/Observation/3"
},
{
"reference": "http://localhost:8090/fhir/Observation/5"
},
{
"reference": "http://localhost:8090/fhir/Patient/9c5162a4-1cbb-4239-8813-da2d10be1ff4"
},
{
"reference": "http://localhost:8090/fhir/Patient/337679e5-aae4-4d95-8583-758e6551b953"
}
]
}
},
{
"name": "resource",
"resource": {
"resourceType": "Observation",
"id": "3",
"meta": {
"versionId": "1",
"lastUpdated": "2021-06-11T14:08:01.343+00:00",
"source": "#SWejcS1NYfNe3dbs"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory",
"display": "Laboratory"
}
]
}
],
"code": {
"coding": [
{
"code": "160119AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"display": "CURRENTLY TAKING ARV"
},
{
"system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL",
"code": "160119",
"display": "CURRENTLY TAKING ARV"
}
]
},
"subject": {
"reference": "Patient/9c5162a4-1cbb-4239-8813-da2d10be1ff4",
"type": "Patient",
"display": "Obs_Test2 Obs_Test2 Obs_Test2 (OpenMRS ID: 10001V)"
},
"encounter": {
"reference": "Encounter/13cbf9b8-24fa-4806-8f2b-8e4f489b1f96",
"type": "Encounter"
},
"effectiveDateTime": "2021-06-01T08:12:28+00:00",
"issued": "2021-06-01T08:12:28.000+00:00",
"valueCodeableConcept": {
"coding": [
{
"code": "1065AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"display": "YES"
},
{
"system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL",
"code": "1065",
"display": "YES"
}
]
}
}
},
{
"name": "resource",
"resource": {
"resourceType": "Observation",
"id": "5",
"meta": {
"versionId": "1",
"lastUpdated": "2021-06-11T14:08:01.343+00:00",
"source": "#SWejcS1NYfNe3dbs"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory",
"display": "Laboratory"
}
]
}
],
"code": {
"coding": [
{
"code": "160119AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"display": "CURRENTLY TAKING ARV"
},
{
"system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL",
"code": "160119",
"display": "CURRENTLY TAKING ARV"
}
]
},
"subject": {
"reference": "Patient/337679e5-aae4-4d95-8583-758e6551b953",
"type": "Patient",
"display": "Obs_Test1 Obs_Test1 Obs_Test1 (OpenMRS ID: 10000X)"
},
"encounter": {
"reference": "Encounter/4b91bc4f-9eef-4144-a88f-d8998ae932cf",
"type": "Encounter"
},
"effectiveDateTime": "2021-06-01T08:11:12+00:00",
"issued": "2021-06-01T08:11:12.000+00:00",
"valueCodeableConcept": {
"coding": [
{
"code": "1066AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"display": "NO"
},
{
"system": "https://openconceptlab.org/orgs/CIEL/sources/CIEL",
"code": "1066",
"display": "NO"
}
]
}
}
},
{
"name": "resource",
"resource": {
"resourceType": "Patient",
"id": "9c5162a4-1cbb-4239-8813-da2d10be1ff4",
"meta": {
"versionId": "1",
"lastUpdated": "2021-06-11T14:08:01.844+00:00",
"source": "#SWejcS1NYfNe3dbs"
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>"
}
}
},
{
"name": "resource",
"resource": {
"resourceType": "Patient",
"id": "337679e5-aae4-4d95-8583-758e6551b953",
"meta": {
"versionId": "1",
"lastUpdated": "2021-06-11T14:08:01.956+00:00",
"source": "#SWejcS1NYfNe3dbs"
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>"
}
}
}
]
} |
Calculating the TX-PVLS or TX-CURR Indicator and Generating the Measure Report
In order to generate the Measure report as a result of the indicator calculation , invoke the evaluate-measure operation using the following requestCode Block language bash GET : http://localhost:8090/fhir/Measure/TX-PVLS/$evaluate-measure?periodStart=2019-01-01&periodEnd=2030-12-31 or http://localhost:8090/fhir/Measure/TX-CURR/$evaluate-measure?periodStart=2019-01-01&periodEnd=2030-12-31This should generate and return a MesureReport for TX-PVLS result like below
Code Block language xml { "resourceType": "MeasureReport", "status": "complete", "type": "summary", "measure": "Measure/TX-PVLS", "period": { "start": "2019-01-01T00:00:00+00:00", "end": "2030-12-31T00:00:00+00:00" }, "group": [ { "id": "population", "population": [ { "code": { "coding": [ { "code": "initial-population" } ] }, "count": 3 }, { "code": { "coding": [ { "code": "numerator" } ] "end": "2030-12-31T00:00:00+00:00" }, "group": [ }, { "idcount": "population", 2 "population": [ }, { "code": { "coding": [ { "code": "initial-populationdenominator" } ] }, "count": 3 }, { ], "codemeasureScore": { "codingvalue": [0.6666666666666666 } { } ], "evaluatedResource": [ { "codereference": "numerator#Observation/9" }, { }"reference": "#Observation/8" }, { ] "reference": "#Observation/7" }, { "countreference": 2"#Observation/5" } },] }
OR TX-CURR result like below
| Code Block | ||
|---|---|---|
| ||
{ |
...
"resourceType": "MeasureReport", "status": "complete", "type": "summary", |
...
"measure": "Measure/TX-CURR", " |
...
period": { "start": "2021-01-01T00:00:00+00:00", "end": "2021-06-02T00:00:00+00:00" }, " |
...
group": [ { "id": "population", |
...
"population": [ { |
...
|
...
"code": { |
...
"coding": [ |
...
{ |
...
" |
...
code": |
...
"initial-population" |
...
|
...
} |
...
|
...
] |
...
|
...
}, |
...
...
" |
...
count": |
...
1 |
...
} |
...
|
...
] |
...
} |
...
], " |
...
evaluatedResource": |
...
[ |
...
{
"reference": "#Observation/ |
...
5" }, { "reference": "#Observation/ |
...
3" } ] } |
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