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Add support for the SDC Observation Extract Category extension (#475)
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* Add support for the SDC Observation Extract Category extension

* Fix test

---------

Co-authored-by: JP <jonathan.percival@smilecdr.com>
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@barhodes @JPercival
barhodes and JPercival authored Jul 3, 2024
1 parent bbc8295 commit 84880fe
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Showing 12 changed files with 299 additions and 39 deletions.
14 changes: 9 additions & 5 deletions ...r-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaireresponse/extract/ProcessItem.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,10 @@
import java.util.Map;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.fhir.utility.Constants;

public class ProcessItem {
public void processItem(
Expand All @@ -18,6 +20,7 @@ public void processItem(
throw new IllegalArgumentException(
"Unable to retrieve Questionnaire code map for Observation based extraction");
}
var categoryExt = request.getExtensionByUrl(item, Constants.SDC_QUESTIONNAIRE_OBSERVATION_EXTRACT_CATEGORY);
var answers = request.resolvePathList(item, "answer", IBaseBackboneElement.class);
if (!answers.isEmpty()) {
answers.forEach(answer -> {
Expand All @@ -30,7 +33,7 @@ public void processItem(
if (questionnaireCodeMap.get(linkId) != null
&& !questionnaireCodeMap.get(linkId).isEmpty()) {
resources.add(createObservationFromItemAnswer(
request, answer, linkId, subject, questionnaireCodeMap));
request, answer, linkId, subject, questionnaireCodeMap, categoryExt));
}
}
});
Expand All @@ -42,19 +45,20 @@ private IBaseResource createObservationFromItemAnswer(
IBaseBackboneElement answer,
String linkId,
IBaseReference subject,
Map<String, List<IBaseCoding>> questionnaireCodeMap) {
Map<String, List<IBaseCoding>> questionnaireCodeMap,
IBaseExtension<?, ?> categoryExt) {
// Observation-based extraction -
// http://build.fhir.org/ig/HL7/sdc/extraction.html#observation-based-extraction
switch (request.getFhirVersion()) {
case DSTU3:
return new org.opencds.cqf.fhir.cr.questionnaireresponse.extract.dstu3.ObservationResolver()
.resolve(request, answer, linkId, subject, questionnaireCodeMap);
.resolve(request, answer, linkId, subject, questionnaireCodeMap, categoryExt);
case R4:
return new org.opencds.cqf.fhir.cr.questionnaireresponse.extract.r4.ObservationResolver()
.resolve(request, answer, linkId, subject, questionnaireCodeMap);
.resolve(request, answer, linkId, subject, questionnaireCodeMap, categoryExt);
case R5:
return new org.opencds.cqf.fhir.cr.questionnaireresponse.extract.r5.ObservationResolver()
.resolve(request, answer, linkId, subject, questionnaireCodeMap);
.resolve(request, answer, linkId, subject, questionnaireCodeMap, categoryExt);

default:
return null;
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16 changes: 11 additions & 5 deletions ...java/org/opencds/cqf/fhir/cr/questionnaireresponse/extract/dstu3/ObservationResolver.java
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Expand Up @@ -18,17 +18,20 @@
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.fhir.cr.questionnaireresponse.extract.ExtractRequest;
import org.opencds.cqf.fhir.utility.Constants;

public class ObservationResolver {
public IBaseResource resolve(
ExtractRequest request,
IBaseBackboneElement baseAnswer,
String linkId,
IBaseReference subject,
Map<String, List<IBaseCoding>> questionnaireCodeMap) {
Map<String, List<IBaseCoding>> questionnaireCodeMap,
IBaseExtension<?, ?> categoryExt) {
var questionnaireResponse = (QuestionnaireResponse) request.getQuestionnaireResponse();
var answer = (QuestionnaireResponseItemAnswerComponent) baseAnswer;
var obs = new Observation();
Expand All @@ -37,10 +40,13 @@ public IBaseResource resolve(
// obs.setPartOf(questionnaireResponse.getPartOf());
obs.setStatus(Observation.ObservationStatus.FINAL);

var qrCategoryCoding = new Coding();
qrCategoryCoding.setCode("survey");
qrCategoryCoding.setSystem("http://hl7.org/fhir/observation-category");
obs.setCategory(Collections.singletonList(new CodeableConcept().addCoding(qrCategoryCoding)));
var qrCategoryCode = categoryExt == null
? new CodeableConcept()
.addCoding(new Coding()
.setSystem(Constants.SDC_OBSERVATION_CATEGORY)
.setCode(Constants.SDC_CATEGORY_SURVEY))
: (CodeableConcept) categoryExt.getValue();
obs.setCategory(Collections.singletonList(qrCategoryCode));

obs.setCode(new CodeableConcept()
.setCoding(questionnaireCodeMap.get(linkId).stream()
Expand Down
16 changes: 11 additions & 5 deletions ...in/java/org/opencds/cqf/fhir/cr/questionnaireresponse/extract/r4/ObservationResolver.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import java.util.stream.Collectors;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeableConcept;
Expand All @@ -21,14 +22,16 @@
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.StringType;
import org.opencds.cqf.fhir.cr.questionnaireresponse.extract.ExtractRequest;
import org.opencds.cqf.fhir.utility.Constants;

public class ObservationResolver {
public IBaseResource resolve(
ExtractRequest request,
IBaseBackboneElement baseAnswer,
String linkId,
IBaseReference subject,
Map<String, List<IBaseCoding>> questionnaireCodeMap) {
Map<String, List<IBaseCoding>> questionnaireCodeMap,
IBaseExtension<?, ?> categoryExt) {
var questionnaireResponse = (QuestionnaireResponse) request.getQuestionnaireResponse();
var answer = (QuestionnaireResponseItemAnswerComponent) baseAnswer;
var obs = new Observation();
Expand All @@ -37,10 +40,13 @@ public IBaseResource resolve(
obs.setPartOf(questionnaireResponse.getPartOf());
obs.setStatus(Observation.ObservationStatus.FINAL);

var qrCategoryCoding = new Coding();
qrCategoryCoding.setCode("survey");
qrCategoryCoding.setSystem("http://hl7.org/fhir/observation-category");
obs.setCategory(Collections.singletonList(new CodeableConcept().addCoding(qrCategoryCoding)));
var qrCategoryCode = categoryExt == null
? new CodeableConcept()
.addCoding(new Coding()
.setSystem(Constants.SDC_OBSERVATION_CATEGORY)
.setCode(Constants.SDC_CATEGORY_SURVEY))
: (CodeableConcept) categoryExt.getValue();
obs.setCategory(Collections.singletonList(qrCategoryCode));

obs.setCode(new CodeableConcept()
.setCoding(questionnaireCodeMap.get(linkId).stream()
Expand Down
16 changes: 11 additions & 5 deletions ...in/java/org/opencds/cqf/fhir/cr/questionnaireresponse/extract/r5/ObservationResolver.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import java.util.stream.Collectors;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.CodeableConcept;
Expand All @@ -22,14 +23,16 @@
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.StringType;
import org.opencds.cqf.fhir.cr.questionnaireresponse.extract.ExtractRequest;
import org.opencds.cqf.fhir.utility.Constants;

public class ObservationResolver {
public IBaseResource resolve(
ExtractRequest request,
IBaseBackboneElement baseAnswer,
String linkId,
IBaseReference subject,
Map<String, List<IBaseCoding>> questionnaireCodeMap) {
Map<String, List<IBaseCoding>> questionnaireCodeMap,
IBaseExtension<?, ?> categoryExt) {
var questionnaireResponse = (QuestionnaireResponse) request.getQuestionnaireResponse();
var answer = (QuestionnaireResponseItemAnswerComponent) baseAnswer;
var obs = new Observation();
Expand All @@ -38,10 +41,13 @@ public IBaseResource resolve(
obs.setPartOf(questionnaireResponse.getPartOf());
obs.setStatus(ObservationStatus.FINAL);

var qrCategoryCoding = new Coding();
qrCategoryCoding.setCode("survey");
qrCategoryCoding.setSystem("http://hl7.org/fhir/observation-category");
obs.setCategory(Collections.singletonList(new CodeableConcept().addCoding(qrCategoryCoding)));
var qrCategoryCode = categoryExt == null
? new CodeableConcept()
.addCoding(new Coding()
.setSystem(Constants.SDC_OBSERVATION_CATEGORY)
.setCode(Constants.SDC_CATEGORY_SURVEY))
: (CodeableConcept) categoryExt.getValue();
obs.setCategory(Collections.singletonList(qrCategoryCode));

obs.setCode(new CodeableConcept()
.setCoding(questionnaireCodeMap.get(linkId).stream()
Expand Down
2 changes: 1 addition & 1 deletion ...va/org/opencds/cqf/fhir/cr/questionnaireresponse/QuestionnaireResponseProcessorTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ private void testExtract(FhirContext fhirContext, String path, String questionna
void test() {
testExtract(fhirContextDstu3, "dstu3", "QRSharonDecision");
testExtract(fhirContextR4, "r4", "QRSharonDecision");
testExtract(fhirContextR4, "r5", "QRSharonDecision");
testExtract(fhirContextR5, "r5", "QRSharonDecision");
}

@Test
Expand Down
12 changes: 6 additions & 6 deletions ...r/questionnaireresponse/dstu3/tests/Bundle-extract-sdc-profile-example-multi-subject.json
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "survey"
"code": "exam"
}
]
}
Expand Down Expand Up @@ -82,7 +82,7 @@
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "survey"
"code": "exam"
}
]
}
Expand Down Expand Up @@ -140,7 +140,7 @@
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "survey"
"code": "exam"
}
]
}
Expand Down Expand Up @@ -198,7 +198,7 @@
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "survey"
"code": "exam"
}
]
}
Expand Down Expand Up @@ -256,7 +256,7 @@
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "survey"
"code": "exam"
}
]
}
Expand Down Expand Up @@ -314,7 +314,7 @@
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "survey"
"code": "exam"
}
]
}
Expand Down
78 changes: 78 additions & 0 deletions ...ionnaireresponse/dstu3/tests/QuestionnaireResponse-sdc-profile-example-multi-subject.json
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,19 @@
]
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "exam"
}
]
}
}
],
"linkId": "3",
"code": [
{
Expand All @@ -56,6 +69,19 @@
]
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "exam"
}
]
}
}
],
"linkId": "4",
"code": [
{
Expand Down Expand Up @@ -115,6 +141,19 @@
]
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "exam"
}
]
}
}
],
"linkId": "5.4",
"text": "Height",
"answer": [
Expand All @@ -128,6 +167,19 @@
]
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "exam"
}
]
}
}
],
"linkId": "5.5",
"text": "Weight",
"answer": [
Expand Down Expand Up @@ -182,6 +234,19 @@
]
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "exam"
}
]
}
}
],
"linkId": "5.4",
"text": "Height",
"answer": [
Expand All @@ -195,6 +260,19 @@
]
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/observation-category",
"code": "exam"
}
]
}
}
],
"linkId": "5.5",
"text": "Weight",
"answer": [
Expand Down
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