444 migrate collect data and data req operations (#448)

* operation migration collect-data, data-req wip

* data req tests

* expanding test coverage

* data req testing coverage expanded

* expanded coverage

cqf-fhir-cql/pom.xml

@@ -30,6 +30,10 @@
  <groupId>info.cqframework</groupId>
  <artifactId>cql-to-elm</artifactId>
  </dependency>
+ <dependency>
+ <groupId>info.cqframework</groupId>
+ <artifactId>elm-fhir</artifactId>
+ </dependency>
  <dependency>
  <groupId>info.cqframework</groupId>
  <artifactId>quick</artifactId>

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/helper/SubjectContext.java

@@ -0,0 +1,20 @@
+package org.opencds.cqf.fhir.cr.measure.helper;
+
+public class SubjectContext {
+ public SubjectContext(String contextType, Object contextValue) {
+ this.contextType = contextType;
+ this.contextValue = contextValue;
+ }
+
+ private String contextType;
+
+ public String getContextType() {
+ return contextType;
+ }
+
+ private Object contextValue;
+
+ public Object getContextValue() {
+ return contextValue;
+ }
+}

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4CollectDataService.java

@@ -0,0 +1,141 @@
+package org.opencds.cqf.fhir.cr.measure.r4;
+
+import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.stream.Collectors;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Resource;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
+import org.opencds.cqf.fhir.cr.measure.common.MeasureEvalType;
+import org.opencds.cqf.fhir.utility.Ids;
+import org.opencds.cqf.fhir.utility.monad.Eithers;
+
+public class R4CollectDataService {
+ private final Repository repository;
+ private final MeasureEvaluationOptions measureEvaluationOptions;
+
+ public R4CollectDataService(Repository repository, MeasureEvaluationOptions measureEvaluationOptions) {
+ this.repository = repository;
+ this.measureEvaluationOptions = measureEvaluationOptions;
+ }
+
+ /**
+ * Implements the <a href=
+ * "http:https://hl7.org/fhir/R4/measure-operation-collect-data.html">$collect-data</a>
+ * operation found in the
+ * <a href="http:https://hl7.org/fhir/R4/clinicalreasoning-module.html">FHIR Clinical
+ * Reasoning Module</a>.
+ *
+ * <p>
+ * Returns a set of parameters with the generated MeasureReport and the
+ * resources that were used during the Measure evaluation
+ *
+ * @param measureId the measureId of the Measure to sub data for
+ * @param periodStart The start of the reporting period
+ * @param periodEnd The end of the reporting period
+ * @param subject the subject to use for the evaluation
+ * @param practitioner the practitioner to use for the evaluation
+ * received.
+ * @return Parameters the parameters containing the MeasureReport and the
+ * evaluated Resources
+ */
+ public Parameters collectData(
+ IdType measureId, String periodStart, String periodEnd, String subject, String practitioner) {
+
+ Parameters parameters = new Parameters();
+ var subjectProvider = new R4RepositorySubjectProvider();
+ var processor = new R4MeasureProcessor(this.repository, this.measureEvaluationOptions, subjectProvider);
+
+ // getSubjects
+ List<String> subjectList = getSubjects(subject, practitioner, subjectProvider);
+ // if(subjectList.isEmpty() || subjectList == null){
+
+ // }
+ // loop over subjects
+ if (!subjectList.isEmpty()) {
+ for (String patient : subjectList) {
+ var subjects = Collections.singletonList(patient);
+ // add resources per subject to Parameters
+ addReports(processor, measureId, periodStart, periodEnd, subjects, parameters);
+ }
+ } else {
+ addReports(processor, measureId, periodStart, periodEnd, subjectList, parameters);
+ }
+ return parameters;
+ }
+
+ private void addReports(
+ R4MeasureProcessor processor,
+ IdType measureId,
+ String periodStart,
+ String periodEnd,
+ List<String> subjects,
+ Parameters parameters) {
+ MeasureReport report = processor.evaluateMeasure(
+ Eithers.forMiddle3(measureId),
+ periodStart,
+ periodEnd,
+ MeasureEvalType.SUBJECT.toCode(),
+ subjects,
+ null,
+ null,
+ null);
+
+ report.setType(MeasureReport.MeasureReportType.DATACOLLECTION);
+ report.setGroup(null);
+ String subjectId = null;
+ if (!subjects.isEmpty()) {
+ subjectId = subjects.get(0).replace("Patient/", "");
+ } else {
+ subjectId = "no-subjectId";
+ }
+ parameters.addParameter(part("measureReport-" + subjectId, report));
+ if (!report.getEvaluatedResource().isEmpty()) {
+ populateEvaluatedResources(report, parameters, subjectId);
+ }
+ }
+
+ private List<String> getSubjects(String subject, String practitioner, R4RepositorySubjectProvider subjectProvider) {
+ if (StringUtils.isNotBlank(practitioner)) {
+ if (!practitioner.contains("/")) {
+ practitioner = "Practitioner/".concat(practitioner);
+ }
+ subject = practitioner;
+ }
+
+ return subjectProvider
+ .getSubjects(repository, MeasureEvalType.SUBJECT, subject)
+ .collect(Collectors.toList());
+ }
+
+ protected void populateEvaluatedResources(MeasureReport measureReport, Parameters parameters, String subject) {
+ measureReport.getEvaluatedResource().forEach(evaluatedResource -> {
+ IIdType resourceId = evaluatedResource.getReferenceElement();
+ if (resourceId.getResourceType() == null) {
+ return;
+ } else {
+ Ids.simple(resourceId);
+ }
+
+ Class<? extends IBaseResource> resourceType = repository
+ .fhirContext()
+ .getResourceDefinition(resourceId.getResourceType())
+ .newInstance()
+ .getClass();
+ IBaseResource resource = repository.read(resourceType, resourceId);
+
+ if (resource instanceof Resource) {
+ Resource resourceBase = (Resource) resource;
+ parameters.addParameter(part("resource-" + subject, resourceBase));
+ }
+ });
+ }
+}