First checkin.

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

@@ -14,30 +14,43 @@ public static MeasureEvaluationOptions defaultOptions() {
 
     private boolean isValidationEnabled = false;
     private Map<String, ValidationProfile> validationProfiles = new HashMap<>();
+    private SubjectProviderOptions subjectProviderOptions;
 
     private EvaluationSettings evaluationSettings = null;
 
     public boolean isValidationEnabled() {
         return this.isValidationEnabled;
     }
 
-    public void setValidationEnabled(boolean enableValidation) {
+    public MeasureEvaluationOptions setValidationEnabled(boolean enableValidation) {
         this.isValidationEnabled = enableValidation;
+        return this;
     }
 
     public Map<String, ValidationProfile> getValidationProfiles() {
         return validationProfiles;
     }
 
-    public void setValidationProfiles(Map<String, ValidationProfile> validationProfiles) {
+    public MeasureEvaluationOptions setValidationProfiles(Map<String, ValidationProfile> validationProfiles) {
         this.validationProfiles = validationProfiles;
+        return this;
     }
 
-    public void setEvaluationSettings(EvaluationSettings evaluationSettings) {
+    public MeasureEvaluationOptions setEvaluationSettings(EvaluationSettings evaluationSettings) {
         this.evaluationSettings = evaluationSettings;
+        return this;
     }
 
     public EvaluationSettings getEvaluationSettings() {
         return this.evaluationSettings;
     }
+
+    public SubjectProviderOptions getSubjectProviderOptions() {
+        return subjectProviderOptions;
+    }
+
+    public MeasureEvaluationOptions setSubjectProviderOptions(SubjectProviderOptions theSubjectProviderOptions) {
+        this.subjectProviderOptions = theSubjectProviderOptions;
+        return this;
+    }
 }

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

@@ -0,0 +1,16 @@
+package org.opencds.cqf.fhir.cr.measure;
+
+// LUKETODO:  javadoc
+public class SubjectProviderOptions {
+
+    private boolean isPartOfEnabled;
+
+    public boolean isPartOfEnabled() {
+        return isPartOfEnabled;
+    }
+
+    public SubjectProviderOptions setPartOfEnabled(boolean thePartOfEnabled) {
+        isPartOfEnabled = thePartOfEnabled;
+        return this;
+    }
+}

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/common/SubjectProvider.java

@@ -8,4 +8,9 @@ public interface SubjectProvider {
     Stream<String> getSubjects(Repository repository, MeasureEvalType measureEvalType, String subjectId);
 
     Stream<String> getSubjects(Repository repository, MeasureEvalType measureEvalType, List<String> subjectIds);
+
+    // LUKETODO:  consider these contracts carefully
+    Stream<String> getSubjectsWithPartOf(Repository repository, MeasureEvalType measureEvalType, String subjectId);
+
+    Stream<String> getSubjectsWithPartOf(Repository repository, MeasureEvalType measureEvalType, List<String> subjectIds);
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/dstu3/Dstu3RepositorySubjectProvider.java

@@ -72,4 +72,16 @@ public Stream<String> getSubjects(Repository repository, MeasureEvalType measure
 
         return subjects.stream();
     }
+
+    @Override
+    public Stream<String> getSubjectsWithPartOf(Repository repository,
+            MeasureEvalType measureEvalType, String subjectId) {
+        throw new UnsupportedOperationException("Not implemented yet");
+    }
+
+    @Override
+    public Stream<String> getSubjectsWithPartOf(Repository repository,
+            MeasureEvalType measureEvalType, List<String> subjectIds) {
+        throw new UnsupportedOperationException("Not implemented yet");
+    }
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4CareGapsProcessor.java

@@ -41,6 +41,7 @@ public class R4CareGapsProcessor {
     private final Map<String, Resource> configuredResources = new HashMap<>();
     private final R4MeasureServiceUtils r4MeasureServiceUtils;
     private final R4CareGapsBundleBuilder r4CareGapsBundleBuilder;
+    private final R4RepositorySubjectProvider subjectProvider;
 
     public R4CareGapsProcessor(
             CareGapsProperties careGapsProperties,
@@ -59,6 +60,7 @@ public R4CareGapsProcessor(
                 serverBase,
                 configuredResources,
                 measurePeriodValidator);
+        subjectProvider = new R4RepositorySubjectProvider(measureEvaluationOptions.getSubjectProviderOptions());
     }
 
     public Parameters getCareGapsReport(
@@ -125,7 +127,6 @@ protected List<Measure> resolveMeasure(List<Either3<IdType, String, CanonicalTyp
     }
 
     protected List<String> getSubjects(String subject) {
-        R4RepositorySubjectProvider subjectProvider = new R4RepositorySubjectProvider();
         var subjects = subjectProvider.getSubjects(repository, null, subject).collect(Collectors.toList());
         if (!subjects.isEmpty()) {
             ourLog.info(String.format("care-gaps report requested for: %s subjects.", subjects.size()));

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

@@ -23,10 +23,13 @@
 public class R4CollectDataService {
     private final Repository repository;
     private final MeasureEvaluationOptions measureEvaluationOptions;
+    private final R4RepositorySubjectProvider subjectProvider;
 
     public R4CollectDataService(Repository repository, MeasureEvaluationOptions measureEvaluationOptions) {
         this.repository = repository;
         this.measureEvaluationOptions = measureEvaluationOptions;
+        subjectProvider = new R4RepositorySubjectProvider(
+            measureEvaluationOptions.getSubjectProviderOptions());
     }
 
     /**
@@ -57,7 +60,6 @@ public Parameters collectData(
             String practitioner) {
 
         Parameters parameters = new Parameters();
-        var subjectProvider = new R4RepositorySubjectProvider();
         var processor = new R4MeasureProcessor(this.repository, this.measureEvaluationOptions, subjectProvider);
 
         // getSubjects

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4MeasureService.java

@@ -22,6 +22,7 @@ public class R4MeasureService implements R4MeasureEvaluatorSingle {
     private final Repository repository;
     private final MeasureEvaluationOptions measureEvaluationOptions;
     private final MeasurePeriodValidator measurePeriodValidator;
+    private R4RepositorySubjectProvider subjectProvider;
 
     public R4MeasureService(
             Repository repository,
@@ -30,6 +31,8 @@ public R4MeasureService(
         this.repository = repository;
         this.measureEvaluationOptions = measureEvaluationOptions;
         this.measurePeriodValidator = measurePeriodValidator;
+        this.subjectProvider = new R4RepositorySubjectProvider(
+            measureEvaluationOptions.getSubjectProviderOptions());
     }
 
     @Override
@@ -51,7 +54,7 @@ public MeasureReport evaluate(
         measurePeriodValidator.validatePeriodStartAndEnd(periodStart, periodEnd);
 
         var repo = Repositories.proxy(repository, true, dataEndpoint, contentEndpoint, terminologyEndpoint);
-        var processor = new R4MeasureProcessor(repo, this.measureEvaluationOptions, new R4RepositorySubjectProvider());
+        var processor = new R4MeasureProcessor(repo, this.measureEvaluationOptions, subjectProvider);
 
         R4MeasureServiceUtils r4MeasureServiceUtils = new R4MeasureServiceUtils(repository);
         r4MeasureServiceUtils.ensureSupplementalDataElementSearchParameter();

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4MultiMeasureService.java

@@ -54,7 +54,7 @@ public R4MultiMeasureService(
         this.measurePeriodValidator = measurePeriodValidator;
         this.serverBase = serverBase;
 
-        subjectProvider = new R4RepositorySubjectProvider();
+        subjectProvider = new R4RepositorySubjectProvider(measureEvaluationOptions.getSubjectProviderOptions());
 
         r4Processor = new R4MeasureProcessor(repository, this.measureEvaluationOptions, subjectProvider);
 

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4RepositorySubjectProvider.java

@@ -8,25 +8,42 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
+import jakarta.annotation.Nullable;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Group;
 import org.hl7.fhir.r4.model.Group.GroupMemberComponent;
 import org.hl7.fhir.r4.model.Group.GroupType;
 import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.ResourceType;
 import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cr.measure.SubjectProviderOptions;
 import org.opencds.cqf.fhir.cr.measure.common.MeasureEvalType;
+import org.opencds.cqf.fhir.cr.measure.common.MeasureEvaluator;
 import org.opencds.cqf.fhir.cr.measure.common.SubjectProvider;
 import org.opencds.cqf.fhir.utility.iterable.BundleIterator;
 import org.opencds.cqf.fhir.utility.iterable.BundleMappingIterable;
 import org.opencds.cqf.fhir.utility.search.Searches;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class R4RepositorySubjectProvider implements SubjectProvider {
 
+    private static final Logger logger = LoggerFactory.getLogger(MeasureEvaluator.class);
+
+    private final SubjectProviderOptions subjectProviderOptions;
+
+    public R4RepositorySubjectProvider(SubjectProviderOptions subjectProviderOptions) {
+        this.subjectProviderOptions = subjectProviderOptions;
+    }
+
     @Override
-    public Stream<String> getSubjects(Repository repository, MeasureEvalType measureEvalType, String subjectId) {
+    public Stream<String> getSubjects(Repository repository, MeasureEvalType measureEvalType, @Nullable String subjectId) {
         return getSubjects(repository, measureEvalType, Collections.singletonList(subjectId));
     }
 
@@ -48,7 +65,7 @@ public Stream<String> getSubjects(Repository repository, MeasureEvalType measure
         List<String> subjects = new ArrayList<>();
         subjectIds.forEach(subjectId -> {
             // add resource reference if missing
-            if (subjectId.indexOf("/") == -1) {
+            if (!subjectId.contains("/")) {
                 subjectId = "Patient/".concat(subjectId);
             }
             // Single Patient
@@ -91,7 +108,9 @@ else if (r.getType().equals(GroupType.PRACTITIONER)) {
                         addPractitionerSubjectIds(practitioner, repository, subjects);
                     }
                 }
-
+                // LUKETODO: can we have a Group with Organizations?
+            } else if (subjectId.startsWith("Organization")) {
+                subjects.addAll(getOrganizationSubjectIds(subjectId, repository));
             } else {
                 throw new IllegalArgumentException(String.format("Unsupported subjectId: %s", subjectIds));
             }
@@ -100,6 +119,21 @@ else if (r.getType().equals(GroupType.PRACTITIONER)) {
         return subjects.stream();
     }
 
+
+    @Override
+    public Stream<String> getSubjectsWithPartOf(Repository repository,
+            MeasureEvalType measureEvalType, String subjectId) {
+        // LUKETODO:
+        throw new UnsupportedOperationException("Not implemented yet");
+    }
+
+    @Override
+    public Stream<String> getSubjectsWithPartOf(Repository repository,
+            MeasureEvalType measureEvalType, List<String> subjectIds) {
+        // LUKETODO:
+        throw new UnsupportedOperationException("Not implemented yet");
+    }
+
     private List<String> getMembersInGroup(Group group) {
         List<String> members = new ArrayList<>();
 
@@ -115,7 +149,7 @@ public void addPractitionerSubjectIds(String practitioner, Repository repository
 
         map.put(
                 "general-practitioner",
-                Collections.singletonList(new ReferenceParam(
+                List.of(new ReferenceParam(
                         practitioner.startsWith("Practitioner/") ? practitioner : "Practitioner/" + practitioner)));
 
         var bundle = repository.search(Bundle.class, Patient.class, map);
@@ -128,4 +162,64 @@ public void addPractitionerSubjectIds(String practitioner, Repository repository
             patients.add(refString);
         }
     }
+
+    private List<String> getOrganizationSubjectIds(
+            String organization,
+            Repository repository ) {
+
+        final List<String> managingOrganizationSubjectIds = getManagingOrganizationSubjectIds(
+            organization, repository).collect(Collectors.toList());
+        final List<String> partOfSubjectIds = getPartOfSubjectIds(organization, repository).collect(
+            Collectors.toList());
+        return Stream.concat(
+            managingOrganizationSubjectIds.stream(),
+            partOfSubjectIds.stream()
+            ).collect(Collectors.toUnmodifiableList());
+    }
+
+    private Stream<String> getManagingOrganizationSubjectIds(String organization, Repository repository) {
+        final Map<String, List<IQueryParameterType>> searchParams = new HashMap<>();
+
+        searchParams.put("organization", Collections.singletonList(new ReferenceParam(organization)));
+
+        var bundle = repository.search(Bundle.class, Patient.class, searchParams);
+
+        var bundleEntries = bundle.getEntry();
+
+        if (bundleEntries == null || bundleEntries.isEmpty()) {
+            return Stream.empty();
+        }
+
+        return bundleEntries
+            .stream()
+            .map(BundleEntryComponent::getResource)
+            .map(idElement -> idElement.getResourceType() + "/" + idElement.getIdPart());
+    }
+
+    private Stream<String> getPartOfSubjectIds(String organization, Repository repository) {
+
+        if (! subjectProviderOptions.isPartOfEnabled()) {
+            return Stream.empty();
+        }
+
+        final Map<String, List<IQueryParameterType>> searchParam = new HashMap<>();
+
+        searchParam.put(
+            "organization",
+            Collections.singletonList(new ReferenceParam("organization", organization)
+                .setChain("partof"))
+        );
+
+        return repository.search(Bundle.class, Patient.class, searchParam)
+            .getEntry()
+            .stream()
+            .map(BundleEntryComponent::getResource)
+            .filter(Patient.class::isInstance)
+            .map(Patient.class::cast)
+            // LUKETODO: do we keep this limitation or not?  if so, test for it
+            // TODO: JM, address next link if populated in future interation of feature.
+            // if results expand beyond paging limit of a bundle, a warning will pop to the user.
+            // This is unlikely to ever be an issue in a real deployment, but should be addressed at some point.
+            .map(idElement -> String.format("%s/%s", ResourceType.Patient, idElement.getIdPart()));
+    }
 }

cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/r4/Measure.java

@@ -104,6 +104,7 @@ public static class Given {
         private Repository repository;
         private MeasureEvaluationOptions evaluationOptions;
         private MeasurePeriodValidator measurePeriodValidator;
+        private R4RepositorySubjectProvider subjectProvider;
 
         public Given() {
             this.evaluationOptions = MeasureEvaluationOptions.defaultOptions();
@@ -119,6 +120,9 @@ public Given() {
                     .setValuesetExpansionMode(VALUESET_EXPANSION_MODE.PERFORM_NAIVE_EXPANSION);
 
             this.measurePeriodValidator = new MeasurePeriodValidator();
+
+            this.subjectProvider = new R4RepositorySubjectProvider(
+                evaluationOptions.getSubjectProviderOptions());
         }
 
         public Given repository(Repository repository) {
@@ -140,7 +144,7 @@ public Given evaluationOptions(MeasureEvaluationOptions evaluationOptions) {
         }
 
         private R4MeasureProcessor buildProcessor() {
-            return new R4MeasureProcessor(repository, evaluationOptions, new R4RepositorySubjectProvider());
+            return new R4MeasureProcessor(repository, evaluationOptions, subjectProvider);
         }
 
         private R4MeasureService buildMeasureService() {

cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/r4/MultiMeasure.java

@@ -92,6 +92,7 @@ public static class Given {
         private MeasureEvaluationOptions evaluationOptions;
         private String serverBase;
         private MeasurePeriodValidator measurePeriodValidator;
+        private R4RepositorySubjectProvider subjectProvider;
 
         public Given() {
             this.evaluationOptions = MeasureEvaluationOptions.defaultOptions();
@@ -109,6 +110,9 @@ public Given() {
             this.serverBase = "http://localhost";
 
             this.measurePeriodValidator = new MeasurePeriodValidator();
+
+            this.subjectProvider = new R4RepositorySubjectProvider(
+                evaluationOptions.getSubjectProviderOptions());
         }
 
         public MultiMeasure.Given repository(Repository repository) {
@@ -134,7 +138,7 @@ public MultiMeasure.Given serverBase(String serverBase) {
         }
 
         private R4MeasureProcessor buildProcessor() {
-            return new R4MeasureProcessor(repository, evaluationOptions, new R4RepositorySubjectProvider());
+            return new R4MeasureProcessor(repository, evaluationOptions, subjectProvider);
         }
 
         private R4MultiMeasureService buildMeasureService() {