Merge pull request #734 from lantanagroup/remove-imrs-from-context

Remove IMRs from report/measure context

api/src/main/java/com/lantanagroup/link/api/ReportGenerator.java

@@ -1,6 +1,7 @@
 package com.lantanagroup.link.api;
 
 import com.lantanagroup.link.Constants;
+import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.IReportAggregator;
 import com.lantanagroup.link.ReportIdHelper;
 import com.lantanagroup.link.config.api.ApiConfig;
@@ -73,15 +74,15 @@ public void generate(QueryPhase queryPhase) throws ExecutionException, Interrupt
                 }
                 try {
                   MeasureReport measureReport = generate(measureServiceWrapper, patient);
-                  synchronized (this) {
-                    measureContext.getPatientReportsByPatientId().put(patient.getId(), measureReport);
+                  if (queryPhase == QueryPhase.INITIAL && FhirHelper.hasNonzeroPopulationCount(measureReport)) {
+                    measureContext.getSupplementalPatientsOfInterest().add(patient);
                   }
                 } catch (Exception e) {
                   logger.error("Error generating measure report for patient {}", patient.getId(), e);
                 } finally {
                   int completed = progress.incrementAndGet();
-                  double percent = Math.round((completed * 100.0) / pois.size());
-                  logger.info("Progress ({}%) for report {} is {} of {}", String.format("%.2f", percent), reportContext.getMasterIdentifierValue(), completed, pois.size());
+                  double percent = (completed * 100.0) / pois.size();
+                  logger.info("Progress ({}%) for report {} is {} of {}", String.format("%.1f", percent), reportContext.getMasterIdentifierValue(), completed, pois.size());
                 }
               }))
               .get();
@@ -111,7 +112,7 @@ private MeasureReport generate(MeasureServiceWrapper measureServiceWrapper, Pati
   }
 
   public void aggregate() throws ParseException {
-    MeasureReport masterMeasureReport = this.reportAggregator.generate(this.criteria, this.measureContext);
+    MeasureReport masterMeasureReport = this.reportAggregator.generate(this.tenantService, this.criteria, this.measureContext);
     this.measureContext.setMeasureReport(masterMeasureReport);
 
     Aggregate aggregateReport = new Aggregate();

core/src/main/java/com/lantanagroup/link/GenericAggregator.java

@@ -1,6 +1,9 @@
 package com.lantanagroup.link;
 
 import com.lantanagroup.link.config.api.ApiConfig;
+import com.lantanagroup.link.db.TenantService;
+import com.lantanagroup.link.db.model.PatientMeasureReport;
+import com.lantanagroup.link.model.PatientOfInterestModel;
 import com.lantanagroup.link.model.ReportContext;
 import com.lantanagroup.link.model.ReportCriteria;
 import org.apache.commons.lang3.StringUtils;
@@ -11,7 +14,6 @@
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.text.ParseException;
-import java.util.Collection;
 import java.util.Optional;
 
 public abstract class GenericAggregator implements IReportAggregator {
@@ -20,10 +22,12 @@ public abstract class GenericAggregator implements IReportAggregator {
   @Autowired
   private ApiConfig config;
 
-  protected abstract void aggregatePatientReports(MeasureReport masterMeasureReport, Collection<MeasureReport> measureReports);
+  protected abstract void aggregatePatientReport(MeasureReport masterMeasureReport, MeasureReport measureReport);
+
+  protected abstract void finishAggregation(MeasureReport masterMeasureReport);
 
   @Override
-  public MeasureReport generate(ReportCriteria criteria, ReportContext.MeasureContext measureContext) throws ParseException {
+  public MeasureReport generate(TenantService tenantService, ReportCriteria criteria, ReportContext.MeasureContext measureContext) throws ParseException {
     // Create the master measure report
     MeasureReport masterMeasureReport = new MeasureReport();
     masterMeasureReport.setId(measureContext.getReportId());
@@ -39,8 +43,16 @@ public MeasureReport generate(ReportCriteria criteria, ReportContext.MeasureCont
       masterMeasureReport.setMeasure(measureContext.getMeasure().getUrl());
     }
 
-    // TODO: Swap the order of aggregatePatientReports and createGroupsFromMeasure?
-    this.aggregatePatientReports(masterMeasureReport, measureContext.getPatientReports());
+    for (PatientOfInterestModel poi : measureContext.getPatientsOfInterest()) {
+      String pmrId = ReportIdHelper.getPatientMeasureReportId(measureContext.getReportId(), poi.getId());
+      PatientMeasureReport pmr = tenantService.getPatientMeasureReport(pmrId);
+      if (pmr == null) {
+        logger.warn("Patient measure report not found in database: {}", pmrId);
+        continue;
+      }
+      this.aggregatePatientReport(masterMeasureReport, pmr.getMeasureReport());
+    }
+    this.finishAggregation(masterMeasureReport);
 
     this.createGroupsFromMeasure(masterMeasureReport, measureContext);
 

core/src/main/java/com/lantanagroup/link/IReportAggregator.java

@@ -1,11 +1,12 @@
 package com.lantanagroup.link;
 
+import com.lantanagroup.link.db.TenantService;
 import com.lantanagroup.link.model.ReportContext;
 import com.lantanagroup.link.model.ReportCriteria;
 import org.hl7.fhir.r4.model.MeasureReport;
 
 import java.text.ParseException;
 
 public interface IReportAggregator {
-  MeasureReport generate(ReportCriteria criteria, ReportContext.MeasureContext measureContext) throws ParseException;
+  MeasureReport generate(TenantService tenantService, ReportCriteria criteria, ReportContext.MeasureContext measureContext) throws ParseException;
 }

core/src/main/java/com/lantanagroup/link/model/ReportContext.java

@@ -1,7 +1,6 @@
 package com.lantanagroup.link.model;
 
 import ca.uhn.fhir.rest.client.api.IGenericClient;
-import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.auth.LinkCredentials;
 import com.lantanagroup.link.db.model.PatientList;
 import com.lantanagroup.link.db.model.tenant.QueryPlan;
@@ -19,15 +18,15 @@
 @Getter
 @Setter
 public class ReportContext {
-  private HttpServletRequest request;
-  private LinkCredentials user;
-  private String masterIdentifierValue;
-  private List<PatientList> patientLists = new ArrayList<>();
-  private List<PatientOfInterestModel> patientsOfInterest = new ArrayList<>();
-  private List<MeasureContext> measureContexts = new ArrayList<>();
-  private QueryPlan queryPlan;
-  private IGenericClient client;
-  private List<String> debugPatients = new ArrayList<>();
+  private volatile HttpServletRequest request;
+  private volatile LinkCredentials user;
+  private volatile String masterIdentifierValue;
+  private volatile List<PatientList> patientLists = new ArrayList<>();
+  private volatile List<PatientOfInterestModel> initialPatientsOfInterest = new ArrayList<>();
+  private volatile List<MeasureContext> measureContexts = new ArrayList<>();
+  private volatile QueryPlan queryPlan;
+  private volatile IGenericClient client;
+  private volatile List<String> debugPatients = new ArrayList<>();
 
   public ReportContext() {
   }
@@ -37,10 +36,14 @@ public ReportContext(HttpServletRequest request, LinkCredentials user) {
     this.user = user;
   }
 
+  public List<PatientOfInterestModel> getPatientsOfInterest() {
+    return initialPatientsOfInterest;
+  }
+
   public List<PatientOfInterestModel> getPatientsOfInterest(QueryPhase queryPhase) {
     switch (queryPhase) {
       case INITIAL:
-        return patientsOfInterest;
+        return initialPatientsOfInterest;
       case SUPPLEMENTAL:
         return measureContexts.stream()
                 .flatMap(measureContext -> measureContext.getPatientsOfInterest(queryPhase).stream())
@@ -54,33 +57,27 @@ public List<PatientOfInterestModel> getPatientsOfInterest(QueryPhase queryPhase)
   @Getter
   @Setter
   public static class MeasureContext {
-    private String bundleId;
-    private Bundle reportDefBundle;
-    private Measure measure;
-    private String reportId;
-    private List<PatientOfInterestModel> patientsOfInterest = new ArrayList<>();
-    private Map<String, MeasureReport> patientReportsByPatientId = new HashMap<>();
-    private MeasureReport measureReport;
+    private volatile String bundleId;
+    private volatile Bundle reportDefBundle;
+    private volatile Measure measure;
+    private volatile String reportId;
+    private volatile List<PatientOfInterestModel> initialPatientsOfInterest = new ArrayList<>();
+    private volatile List<PatientOfInterestModel> supplementalPatientsOfInterest = Collections.synchronizedList(new ArrayList<>());
+    private volatile MeasureReport measureReport;
+
+    public List<PatientOfInterestModel> getPatientsOfInterest() {
+      return initialPatientsOfInterest;
+    }
 
     public List<PatientOfInterestModel> getPatientsOfInterest(QueryPhase queryPhase) {
       switch (queryPhase) {
         case INITIAL:
-          return patientsOfInterest;
+          return initialPatientsOfInterest;
         case SUPPLEMENTAL:
-          Set<String> patientIds = patientReportsByPatientId.entrySet().stream()
-                  .filter(reportById -> FhirHelper.hasNonzeroPopulationCount(reportById.getValue()))
-                  .map(Map.Entry::getKey)
-                  .collect(Collectors.toSet());
-          return patientsOfInterest.stream()
-                  .filter(poi -> patientIds.contains(poi.getId()))
-                  .collect(Collectors.toList());
+          return supplementalPatientsOfInterest;
         default:
           throw new IllegalArgumentException(queryPhase.toString());
       }
     }
-
-    public Collection<MeasureReport> getPatientReports() {
-      return patientReportsByPatientId.values();
-    }
   }
 }

core/src/test/java/com/lantanagroup/link/nhsn/ApplyConceptMapsTest.java

@@ -95,7 +95,7 @@ public void testExecute() {
     model.setId("10000");
     patientOfInterestModel.add(model);
 
-    context.setPatientsOfInterest(patientOfInterestModel);
+    context.setInitialPatientsOfInterest(patientOfInterestModel);
 
     List<Coding> codes = new ArrayList<>();
     codes.add(getLocation().getType().get(0).getCoding().get(0));

nhsn/src/main/java/com/lantanagroup/link/nhsn/ReportAggregator.java

@@ -9,7 +9,6 @@
 import org.springframework.context.annotation.Primary;
 import org.springframework.stereotype.Component;
 
-import java.util.Collection;
 import java.util.Optional;
 
 @Component
@@ -38,23 +37,23 @@ protected void addSubjectResult(
             "MeasureReport/" + individualMeasureReport.getIdElement().getIdPart());
   }
 
-  public void aggregatePatientReports(MeasureReport masterMeasureReport, Collection<MeasureReport> measureReports) {
-    // aggregate all individual reports in ones
-    for (MeasureReport patientMeasureReportResource : measureReports) {
-      for (MeasureReport.MeasureReportGroupComponent group : patientMeasureReportResource.getGroup()) {
-        for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
-          // Check if group and population code exist in master, if not create
-          MeasureReport.MeasureReportGroupPopulationComponent measureGroupPopulation = getOrCreateGroupAndPopulation(masterMeasureReport, population, group);
-          // Add population.count to the master group/population count
-          measureGroupPopulation.setCount(measureGroupPopulation.getCount() + population.getCount());
-          // If this population incremented the master
-          if (population.getCount() > 0) {
-            // add subject results
-            addSubjectResult(patientMeasureReportResource, measureGroupPopulation);
-          }
+  public void aggregatePatientReport(MeasureReport masterMeasureReport, MeasureReport measureReport) {
+    for (MeasureReport.MeasureReportGroupComponent group : measureReport.getGroup()) {
+      for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
+        // Check if group and population code exist in master, if not create
+        MeasureReport.MeasureReportGroupPopulationComponent measureGroupPopulation = getOrCreateGroupAndPopulation(masterMeasureReport, population, group);
+        // Add population.count to the master group/population count
+        measureGroupPopulation.setCount(measureGroupPopulation.getCount() + population.getCount());
+        // If this population incremented the master
+        if (population.getCount() > 0) {
+          // add subject results
+          addSubjectResult(measureReport, measureGroupPopulation);
         }
       }
     }
+  }
+
+  public void finishAggregation(MeasureReport masterMeasureReport) {
     for (MeasureReport.MeasureReportGroupComponent group : masterMeasureReport.getGroup()) {
       for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
         logger.debug(

nhsn/src/main/java/com/lantanagroup/link/nhsn/StoredListProvider.java

@@ -54,9 +54,9 @@ public void loadPatientsOfInterest(TenantService tenantService, ReportCriteria c
     Collector<PatientOfInterestModel, ?, Map<String, PatientOfInterestModel>> deduplicator =
             Collectors.toMap(PatientOfInterestModel::toString, Function.identity(), (poi1, poi2) -> poi1);
     Map<String, PatientOfInterestModel> poiMap = context.getPatientsOfInterest().stream().collect(deduplicator);
-    context.setPatientsOfInterest(new ArrayList<>(poiMap.values()));
+    context.setInitialPatientsOfInterest(new ArrayList<>(poiMap.values()));
     for (ReportContext.MeasureContext measureContext : context.getMeasureContexts()) {
-      measureContext.setPatientsOfInterest(measureContext.getPatientsOfInterest().stream()
+      measureContext.setInitialPatientsOfInterest(measureContext.getPatientsOfInterest().stream()
               .collect(deduplicator)
               .values().stream()
               .map(poi -> poiMap.get(poi.toString()))

nhsn/src/test/java/com/lantanagroup/link/nhsn/EncounterStatusTransformerTest.java

@@ -58,7 +58,7 @@ public void execute() throws ParseException {
     patientOfInterest.setId(patientID);
     List<PatientOfInterestModel> patientsOfInterest = new ArrayList<>();
     patientsOfInterest.add(patientOfInterest);
-    context.setPatientsOfInterest(patientsOfInterest);
+    context.setInitialPatientsOfInterest(patientsOfInterest);
     context.setMasterIdentifierValue(reportID);
     String bundleId = ReportIdHelper.getPatientDataBundleId(context.getMasterIdentifierValue(), patientOfInterest.getId());
 

nhsn/src/test/java/com/lantanagroup/link/nhsn/ReportAggregatorTests.java

@@ -1,5 +1,9 @@
 package com.lantanagroup.link.nhsn;
 
+import com.lantanagroup.link.ReportIdHelper;
+import com.lantanagroup.link.db.TenantService;
+import com.lantanagroup.link.db.model.PatientMeasureReport;
+import com.lantanagroup.link.model.PatientOfInterestModel;
 import com.lantanagroup.link.model.ReportContext;
 import com.lantanagroup.link.model.ReportCriteria;
 import org.hl7.fhir.r4.model.*;
@@ -9,6 +13,9 @@
 
 import java.text.ParseException;
 
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
 public class ReportAggregatorTests {
   private Bundle getReportDefBundle() {
     Bundle measureDefBundle = new Bundle();
@@ -36,12 +43,21 @@ private ReportContext.MeasureContext getMeasureContext(String version) {
     context.getMeasure().setUrl("http://test.com/fhir/Measure/SomeMeasure");
     context.getMeasure().setVersion(version);
     context.setReportDefBundle(this.getReportDefBundle());
-    context.getPatientReportsByPatientId().put("test-patient1", this.getPatientMeasureReport("test-patient1", 1));
-    context.getPatientReportsByPatientId().put("test-patient2", this.getPatientMeasureReport("test-patient2", 2));
-    context.getPatientReportsByPatientId().put("test-patient3", this.getPatientMeasureReport("test-patient3", 0));
+    context.setReportId("abc123");
     return context;
   }
 
+  private void addPatientOfInterest(ReportContext.MeasureContext context, TenantService tenantService, String patientId, int populationCount) {
+    PatientOfInterestModel poi = new PatientOfInterestModel();
+    poi.setReference("Patient/" + patientId);
+    poi.setId(patientId);
+    context.getPatientsOfInterest().add(poi);
+    String pmrId = ReportIdHelper.getPatientMeasureReportId(context.getReportId(), patientId);
+    PatientMeasureReport pmr = new PatientMeasureReport();
+    pmr.setMeasureReport(this.getPatientMeasureReport(patientId, populationCount));
+    when(tenantService.getPatientMeasureReport(pmrId)).thenReturn(pmr);
+  }
+
   @Test
   public void aggregationWithoutMeasureVersionTest() throws ParseException {
     ReportContext.MeasureContext context = this.getMeasureContext(null);
@@ -50,7 +66,7 @@ public void aggregationWithoutMeasureVersionTest() throws ParseException {
             "2023-08-22T00:00:00Z",
             "2023-08-22T23:59:59Z");
     ReportAggregator aggregator = new ReportAggregator();
-    MeasureReport aggregate = aggregator.generate(criteria, context);
+    MeasureReport aggregate = aggregator.generate(mock(TenantService.class), criteria, context);
     Assert.assertEquals("http://test.com/fhir/Measure/SomeMeasure", aggregate.getMeasure());
   }
 
@@ -62,7 +78,7 @@ public void aggregationWithMeasureVersionTest() throws ParseException {
             "2023-08-22T00:00:00Z",
             "2023-08-22T23:59:59Z");
     ReportAggregator aggregator = new ReportAggregator();
-    MeasureReport aggregate = aggregator.generate(criteria, context);
+    MeasureReport aggregate = aggregator.generate(mock(TenantService.class), criteria, context);
     Assert.assertEquals("http://test.com/fhir/Measure/SomeMeasure|1.0.1", aggregate.getMeasure());
   }
 
@@ -74,7 +90,11 @@ public void aggregationCountTest() throws ParseException {
             "2023-08-22T00:00:00Z",
             "2023-08-22T23:59:59Z");
     ReportAggregator aggregator = new ReportAggregator();
-    MeasureReport aggregate = aggregator.generate(criteria, context);
+    TenantService tenantService = mock(TenantService.class);
+    addPatientOfInterest(context, tenantService, "test-patient1", 1);
+    addPatientOfInterest(context, tenantService, "test-patient2", 2);
+    addPatientOfInterest(context, tenantService, "test-patient3", 0);
+    MeasureReport aggregate = aggregator.generate(tenantService, criteria, context);
     Assert.assertEquals(MeasurePopulation.INITIALPOPULATION.toCode(), aggregate.getGroupFirstRep().getPopulationFirstRep().getCode().getCodingFirstRep().getCode());
     Assert.assertEquals(3, aggregate.getGroupFirstRep().getPopulationFirstRep().getCount());
   }