#48 - Added -measure-with-source operation and test

cqframework · May 16, 2018 · 37a27fa · 37a27fa
1 parent 255757a
commit 37a27fa
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Showing 6 changed files with 574 additions and 146 deletions.
diff --git a/src/main/java/org/opencds/cqf/evaluation/MeasureEvaluation.java b/src/main/java/org/opencds/cqf/evaluation/MeasureEvaluation.java
@@ -0,0 +1,159 @@
+package org.opencds.cqf.evaluation;
+
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.ReferenceParam;
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.builders.MeasureReportBuilder;
+import org.opencds.cqf.cql.data.DataProvider;
+import org.opencds.cqf.cql.execution.Context;
+import org.opencds.cqf.cql.runtime.Interval;
+import org.opencds.cqf.helpers.FhirMeasureBundler;
+import org.opencds.cqf.providers.JpaDataProvider;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.*;
+
+public class MeasureEvaluation {
+
+    private static final Logger logger = LoggerFactory.getLogger(MeasureEvaluation.class);
+
+    private DataProvider provider;
+    private Interval measurementPeriod;
+
+    public MeasureEvaluation(DataProvider provider, Interval measurementPeriod) {
+        this.provider = provider;
+        this.measurementPeriod = measurementPeriod;
+    }
+
+    public MeasureReport evaluatePatientMeasure(Measure measure, Context context, String patientId) {
+        logger.info("Generating individual report");
+
+        if (patientId == null) {
+            return evaluatePopulationMeasure(measure, context);
+        }
+
+        Iterable<Object> patientRetrieve = provider.retrieve("Patient", patientId, "Patient", null, null, null, null, null, null, null, null);
+        Patient patient = null;
+        if (patientRetrieve.iterator().hasNext()) {
+            patient = (Patient) patientRetrieve.iterator().next();
+        }
+
+        return evaluate(measure, context, patient == null ? Collections.emptyList() : Collections.singletonList(patient), MeasureReport.MeasureReportType.INDIVIDUAL);
+    }
+
+    public MeasureReport evaluatePatientListMeasure(Measure measure, Context context, String practitionerRef)
+    {
+        logger.info("Generating patient-list report");
+
+        List<Patient> patients = new ArrayList<>();
+        if (practitionerRef != null) {
+            SearchParameterMap map = new SearchParameterMap();
+            map.add(
+                    "general-practitioner",
+                    new ReferenceParam(
+                            practitionerRef.startsWith("Practitioner/")
+                                    ? practitionerRef
+                                    : "Practitioner/" + practitionerRef
+                    )
+            );
+
+            if (provider instanceof JpaDataProvider) {
+                IBundleProvider patientProvider = ((JpaDataProvider) provider).resolveResourceProvider("Patient").getDao().search(map);
+                List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
+                patientList.forEach(x -> patients.add((Patient) x));
+            }
+        }
+        return evaluate(measure, context, patients, MeasureReport.MeasureReportType.PATIENTLIST);
+    }
+
+    public MeasureReport evaluatePopulationMeasure(Measure measure, Context context) {
+        logger.info("Generating summary report");
+
+        List<Patient> patients = new ArrayList<>();
+        if (provider instanceof JpaDataProvider) {
+            IBundleProvider patientProvider = ((JpaDataProvider) provider).resolveResourceProvider("Patient").getDao().search(new SearchParameterMap());
+            List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
+            patientList.forEach(x -> patients.add((Patient) x));
+        }
+        return evaluate(measure, context, patients, MeasureReport.MeasureReportType.SUMMARY);
+    }
+
+    private MeasureReport evaluate(Measure measure, Context context, List<Patient> patients, MeasureReport.MeasureReportType type)
+    {
+        MeasureReportBuilder reportBuilder = new MeasureReportBuilder();
+        reportBuilder.buildStatus("complete");
+        reportBuilder.buildType(type);
+        reportBuilder.buildMeasureReference(measure.getIdElement().getValue());
+        if (type == MeasureReport.MeasureReportType.INDIVIDUAL && !patients.isEmpty()) {
+            reportBuilder.buildPatientReference(patients.get(0).getIdElement().getValue());
+        }
+        reportBuilder.buildPeriod(measurementPeriod);
+
+        MeasureReport report = reportBuilder.build();
+
+        List<Patient> initialPopulation = getInitalPopulation(measure, patients, context);
+        HashMap<String,Resource> resources = new HashMap<>();
+
+        for (Measure.MeasureGroupComponent group : measure.getGroup()) {
+            MeasureReport.MeasureReportGroupComponent reportGroup = new MeasureReport.MeasureReportGroupComponent();
+            reportGroup.setIdentifier(group.getIdentifier());
+            report.getGroup().add(reportGroup);
+
+            for (Measure.MeasureGroupPopulationComponent pop : group.getPopulation()) {
+                int count = 0;
+                // Worried about performance here with big populations...
+                for (Patient patient : initialPopulation) {
+                    context.setContextValue("Patient", patient.getIdElement().getIdPart());
+                    Object result = context.resolveExpressionRef(pop.getCriteria()).evaluate(context);
+                    if (result instanceof Boolean) {
+                        count += (Boolean) result ? 1 : 0;
+                    }
+                    else if (result instanceof Iterable) {
+                        for (Object item : (Iterable) result) {
+                            count++;
+                            if (item instanceof Resource) {
+                                resources.put(((Resource) item).getId(), (Resource) item);
+                            }
+                        }
+                    }
+                }
+                MeasureReport.MeasureReportGroupPopulationComponent populationReport = new MeasureReport.MeasureReportGroupPopulationComponent();
+                populationReport.setCount(count);
+                populationReport.setCode(pop.getCode());
+                populationReport.setIdentifier(pop.getIdentifier());
+                reportGroup.getPopulation().add(populationReport);
+            }
+        }
+
+        FhirMeasureBundler bundler = new FhirMeasureBundler();
+        org.hl7.fhir.dstu3.model.Bundle evaluatedResources = bundler.bundle(resources.values());
+        evaluatedResources.setId(UUID.randomUUID().toString());
+        report.setEvaluatedResources(new Reference('#' + evaluatedResources.getId()));
+        report.addContained(evaluatedResources);
+        return report;
+    }
+
+    private List<Patient> getInitalPopulation(Measure measure, List<Patient> population, Context context) {
+        List<Patient> initalPop = new ArrayList<>();
+        for (Measure.MeasureGroupComponent group : measure.getGroup()) {
+            for (Measure.MeasureGroupPopulationComponent pop : group.getPopulation()) {
+                if (pop.getCode().getCodingFirstRep().getCode().equals("initial-population")) {
+                    for (Patient patient : population) {
+                        context.setContextValue("Patient", patient.getIdElement().getIdPart());
+                        Object result = context.resolveExpressionRef(pop.getCriteria()).evaluate(context);
+                        if (result == null) {
+                            continue;
+                        }
+                        if ((Boolean) result) {
+                            initalPop.add(patient);
+                        }
+                    }
+                }
+            }
+        }
+        return initalPop;
+    }
+}
diff --git a/src/main/java/org/opencds/cqf/providers/BundleDataProviderStu3.java b/src/main/java/org/opencds/cqf/providers/BundleDataProviderStu3.java
@@ -21,17 +21,18 @@ public BundleDataProviderStu3(Bundle sourceData) {
         resourceMap = new HashMap<>();
 
         // populate map
-        if (sourceData.hasEntry()) {
-            for (Bundle.BundleEntryComponent entry : sourceData.getEntry()) {
-                if (entry.hasResource()) {
-                    Resource resource = entry.getResource();
-                    if (resourceMap.containsKey(resource.fhirType())) {
-                        resourceMap.get(resource.fhirType()).add(resource);
-                    }
-                    else {
-                        List<Object> resources = new ArrayList<>();
-                        resources.add(resource);
-                        resourceMap.put(resource.fhirType(), resources);
+        if (sourceData != null) {
+            if (sourceData.hasEntry()) {
+                for (Bundle.BundleEntryComponent entry : sourceData.getEntry()) {
+                    if (entry.hasResource()) {
+                        Resource resource = entry.getResource();
+                        if (resourceMap.containsKey(resource.fhirType())) {
+                            resourceMap.get(resource.fhirType()).add(resource);
+                        } else {
+                            List<Object> resources = new ArrayList<>();
+                            resources.add(resource);
+                            resourceMap.put(resource.fhirType(), resources);
+                        }
                     }
                 }
             }