542 care gaps non document mode

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4CareGapsBundleBuilder.java

@@ -98,7 +98,8 @@ public List<Parameters.ParametersParameterComponent> makePatientBundles(
             @Nullable ZonedDateTime periodEnd,
             List<String> subjects,
             List<String> statuses,
-            List<IdType> measureIds) {
+            List<IdType> measureIds,
+            boolean isDocumentMode) {
 
         // retrieve reporter from configuration
         String reporter = RESOURCE_TYPE_ORGANIZATION.concat("/" + careGapsProperties.getCareGapsReporter());
@@ -126,8 +127,9 @@ public List<Parameters.ParametersParameterComponent> makePatientBundles(
             // Patient, subject comes in as format "ResourceType/[id]", no resourceType required to be specified.
             var patient = repository.read(Patient.class, new IdType(subject));
 
+            Bundle bundle;
             // finalize patient Bundle results
-            var bundle = makePatientBundle(result, statuses, patient);
+            bundle = makePatientBundle(result, statuses, patient, isDocumentMode);
 
             // add parameter with results
             if (bundle != null && bundle.hasEntry()) {
@@ -136,14 +138,18 @@ public List<Parameters.ParametersParameterComponent> makePatientBundles(
         }
         return paramResults;
     }
-
+    /**
+     * method to use for creating Care-Gaps Bundle per Patient. IsDocumentMode will control which
+     * resources are added or excluded from the final bundle
+     */
     @Nullable
-    public Bundle makePatientBundle(Bundle bundle, List<String> statuses, Patient patient) {
+    public Bundle makePatientBundle(Bundle bundle, List<String> statuses, Patient patient, boolean isDocumentMode) {
         Map<String, Resource> evalPlusSDE = new HashMap<>();
         List<DetectedIssue> detectedIssues = new ArrayList<>();
         List<MeasureReport> measureReports = new ArrayList<>();
         var gapEvaluator = new R4CareGapStatusEvaluator();
-        Composition composition = getComposition(patient);
+        var composition = getComposition(patient, isDocumentMode);
+
         // get Evaluation Bundle Results
         for (BundleEntryComponent entry : bundle.getEntry()) {
             MeasureReport mr = (MeasureReport) entry.getResource();
@@ -154,28 +160,33 @@ public Bundle makePatientBundle(Bundle bundle, List<String> statuses, Patient pa
             var gapStatus = gapEvaluator.getGroupGapStatus(measure, mr);
             var filteredGapStatus = filteredGapStatus(gapStatus, statuses);
             if (!filteredGapStatus.isEmpty()) {
-                // add Report to final Care-gap report
-                measureReports.add(mr);
+                if (isDocumentMode) {
+                    // add document mode required elements to final Care-gap report
+                    measureReports.add(mr);
+                    populateEvaluatedResources(mr, evalPlusSDE);
+                    populateSDEResources(mr, evalPlusSDE);
+                }
                 // Issue(s) Detected from MeasureReport
                 for (Map.Entry<String, CareGapsStatusCode> item : filteredGapStatus.entrySet()) {
                     String groupId = item.getKey();
                     CareGapsStatusCode careGapsStatusCode = item.getValue();
                     // create DetectedIssue per gap-status and MeasureReport.groupId
-                    DetectedIssue issue = getDetectedIssue(patient, mr, groupId, careGapsStatusCode);
+                    DetectedIssue issue =
+                            getDetectedIssue(patient, mr, groupId, careGapsStatusCode, measure, isDocumentMode);
                     // add DetectedIssue list to set on Bundle
                     detectedIssues.add(issue);
                     // add sections for DetectedIssues created
-                    composition.addSection(getSection(measure, mr, issue, careGapsStatusCode));
+                    if (isDocumentMode) {
+                        composition.addSection(getSection(measure, mr, issue, careGapsStatusCode));
+                    }
                 }
-                // Track evaluated Resources
-                populateEvaluatedResources(mr, evalPlusSDE);
-                populateSDEResources(mr, evalPlusSDE);
             }
         }
 
-        if (!measureReports.isEmpty()) {
+        if (!detectedIssues.isEmpty()) {
             // only add if a DetectedIssue is found and has MeasureReports
-            return addBundleEntries(serverBase, composition, detectedIssues, measureReports, evalPlusSDE);
+            return addBundleEntries(
+                    serverBase, composition, detectedIssues, measureReports, evalPlusSDE, isDocumentMode);
         } else {
             // return nothing if not-applicable
             return null;
@@ -215,18 +226,19 @@ private Composition.SectionComponent getSection(
                 .build();
     }
 
-    private Composition getComposition(Patient patient) {
-        return new CompositionBuilder<>(Composition.class)
-                .withProfile(CARE_GAPS_COMPOSITION_PROFILE)
-                .withType(CARE_GAPS_CODES.get("http://loinc.org/96315-7"))
-                .withStatus(Composition.CompositionStatus.FINAL.toString())
-                .withTitle("Care Gap Report for " + Ids.simplePart(patient))
-                .withSubject(Ids.simple(patient))
-                .withAuthor(Ids.simple(configuredResources.get("care_gaps_composition_section_author")))
-                // .withCustodian(organization) // TODO: Optional: identifies the organization
-                // who is responsible for ongoing maintenance of and accessing to this gaps in
-                // care report. Add as a setting and optionally read if it's there.
-                .build();
+    private Composition getComposition(Patient patient, boolean isDocumentMode) {
+        Composition composition = null;
+        if (isDocumentMode) {
+            composition = new CompositionBuilder<>(Composition.class)
+                    .withProfile(CARE_GAPS_COMPOSITION_PROFILE)
+                    .withType(CARE_GAPS_CODES.get("http://loinc.org/96315-7"))
+                    .withStatus(Composition.CompositionStatus.FINAL.toString())
+                    .withTitle("Care Gap Report for " + Ids.simplePart(patient))
+                    .withSubject(Ids.simple(patient))
+                    .withAuthor(Ids.simple(configuredResources.get("care_gaps_composition_section_author")))
+                    .build();
+        }
+        return composition;
     }
 
     private boolean isMultiRateMeasure(MeasureReport measureReport) {
@@ -237,7 +249,9 @@ private DetectedIssue getDetectedIssue(
             Patient patient,
             MeasureReport measureReport,
             String measureReportGroupId,
-            CareGapsStatusCode careGapsStatusCode) {
+            CareGapsStatusCode careGapsStatusCode,
+            Measure measure,
+            boolean isDocumentMode) {
 
         var detectedIssue = new DetectedIssueBuilder<>(DetectedIssue.class)
                 .withProfile(CARE_GAPS_DETECTED_ISSUE_PROFILE)
@@ -254,6 +268,11 @@ private DetectedIssue getDetectedIssue(
                                         careGapsStatusCode.toDisplayString())))
                 .build();
 
+        // add period from MeasureReport for Identified period of Issue
+        detectedIssue.setIdentified(measureReport.getPeriod());
+        // add Measure reference as Implicated reference for Issue
+        detectedIssue.setImplicated(Collections.singletonList(new Reference(Ids.simple(measure))));
+
         if (measureReportGroupId != null && isMultiRateMeasure(measureReport)) {
             // MeasureReportGroupComponent.id value set here to differentiate between DetectedIssue resources for the
             // same MeasureReport
@@ -262,6 +281,14 @@ private DetectedIssue getDetectedIssue(
             groupIdExt.setValue(new StringType(measureReportGroupId));
             detectedIssue.setExtension(Collections.singletonList(groupIdExt));
         }
+        if (!isDocumentMode) {
+            // add Report as contained resource
+            detectedIssue.setContained(Collections.singletonList(measureReport));
+            // update evidence reference to '#' prefixed reference to indicate it is contained.
+            detectedIssue
+                    .getEvidenceFirstRep()
+                    .setDetail(Collections.singletonList(new Reference("#" + measureReport.getId())));
+        }
         return detectedIssue;
     }
 
@@ -326,13 +353,20 @@ private Bundle addBundleEntries(
             Composition composition,
             List<DetectedIssue> detectedIssues,
             List<MeasureReport> measureReports,
-            Map<String, Resource> evalPlusSDEs) {
+            Map<String, Resource> evalPlusSDEs,
+            boolean isDocumentMode) {
         Bundle reportBundle = makeNewBundle();
-        reportBundle.addEntry(getBundleEntry(serverBase, composition));
-        measureReports.forEach(report -> reportBundle.addEntry(getBundleEntry(serverBase, report)));
-        detectedIssues.forEach(detectedIssue -> reportBundle.addEntry(getBundleEntry(serverBase, detectedIssue)));
-        configuredResources.values().forEach(resource -> reportBundle.addEntry(getBundleEntry(serverBase, resource)));
-        evalPlusSDEs.values().forEach(resource -> reportBundle.addEntry(getBundleEntry(serverBase, resource)));
+        if (isDocumentMode) {
+            reportBundle.addEntry(getBundleEntry(serverBase, composition));
+            measureReports.forEach(report -> reportBundle.addEntry(getBundleEntry(serverBase, report)));
+            detectedIssues.forEach(detectedIssue -> reportBundle.addEntry(getBundleEntry(serverBase, detectedIssue)));
+            configuredResources
+                    .values()
+                    .forEach(resource -> reportBundle.addEntry(getBundleEntry(serverBase, resource)));
+            evalPlusSDEs.values().forEach(resource -> reportBundle.addEntry(getBundleEntry(serverBase, resource)));
+        } else {
+            detectedIssues.forEach(detectedIssue -> reportBundle.addEntry(getBundleEntry(serverBase, detectedIssue)));
+        }
         return reportBundle;
     }
 

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

@@ -42,6 +42,8 @@ public class R4CareGapsProcessor {
     private final R4MeasureServiceUtils r4MeasureServiceUtils;
     private final R4CareGapsBundleBuilder r4CareGapsBundleBuilder;
 
+    private static final Boolean defaultDocumentMode = true;
+
     public R4CareGapsProcessor(
             CareGapsProperties careGapsProperties,
             Repository repository,
@@ -68,7 +70,8 @@ public Parameters getCareGapsReport(
             List<String> statuses,
             List<IdType> measureIds,
             List<String> measureIdentifiers,
-            List<CanonicalType> measureUrls) {
+            List<CanonicalType> measureUrls,
+            Boolean isDocumentMode) {
 
         // validate and set required configuration resources for care-gaps
         checkConfigurationReferences();
@@ -83,6 +86,11 @@ public Parameters getCareGapsReport(
         checkValidStatusCode(statuses);
         measureCompatibilityCheck(measures);
 
+        // Set default for optional parameter value
+        if (isDocumentMode == null) {
+            isDocumentMode = defaultDocumentMode;
+        }
+
         // Subject Population for Report
         List<String> subjects = getSubjects(subject);
 
@@ -92,7 +100,7 @@ public Parameters getCareGapsReport(
         // Build Patient Bundles
 
         List<Parameters.ParametersParameterComponent> components = r4CareGapsBundleBuilder.makePatientBundles(
-                periodStart, periodEnd, subjects, statuses, collectedMeasureIds);
+                periodStart, periodEnd, subjects, statuses, collectedMeasureIds, isDocumentMode);
 
         // Return Results with Bundles
         return result.setParameter(components);

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4CareGapsService.java

@@ -31,26 +31,32 @@ public R4CareGapsService(
     /**
      * Calculate measures describing gaps in care
      *
-     * @param periodStart
-     * @param periodEnd
-     * @param subject
-     * @param statuses
-     * @param measureIds
-     * @param measureIdentifiers
-     * @param measureUrls
+     * @param periodStart measurement period starting interval.
+     * @param periodEnd measurement period ending interval.
+     * @param subject subject population to use for care-gap results. Accepted values [empty=all Patients, Patient/{id}, Group/{id} type {person, practitioner}, Practitioner/{id}]
+     * @param statuses determines what care-gap statuses will be returned by the service if found. [prospective-gap, closed-gap, open-gap, not-applicable].
+     *                 If Result is 'not-applicable' for Measure, but status requested was 'open-gap', then no result will be returned.
+     * @param measureIds Measures to check care-gap for by resolving by fhir resource id
+     * @param measureIdentifiers Measures to check care-gap for by resolving identifier value or systemUrl|value
+     * @param measureUrls Measures to check care-gap for by resolving canonical url reference
+     * @param isDocumentMode optional, default is 'true'. This parameter determines if standard care-gaps
+     *                       formatted 'document' bundle is returned with [composition, Detected Issue,
+     *                       configured resources, evaluated resources, measure reports]. Or non-document mode,
+     *                       which just returns a bundle with [Detected Issue(s)], with contained Measure Report.
      * @return Parameters that includes zero to many document bundles that include Care Gap Measure
      *         Reports will be returned.
      */
     public Parameters getCareGapsReport(
             @Nullable ZonedDateTime periodStart,
             @Nullable ZonedDateTime periodEnd,
-            String subject,
+            @Nullable String subject,
             List<String> statuses,
             List<IdType> measureIds,
             List<String> measureIdentifiers,
-            List<CanonicalType> measureUrls) {
+            List<CanonicalType> measureUrls,
+            @Nullable Boolean isDocumentMode) {
 
         return r4CareGapsProcessor.getCareGapsReport(
-                periodStart, periodEnd, subject, statuses, measureIds, measureIdentifiers, measureUrls);
+                periodStart, periodEnd, subject, statuses, measureIds, measureIdentifiers, measureUrls, isDocumentMode);
     }
 }

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

@@ -161,6 +161,8 @@ public static class When {
         private List<CanonicalType> measureUrls = new ArrayList<>();
         private Supplier<Parameters> operation;
 
+        private Boolean isDocumentMode;
+
         public CareGaps.When periodEnd(ZonedDateTime periodEnd) {
             this.periodEnd = periodEnd;
             return this;
@@ -196,9 +198,21 @@ public CareGaps.When measureIdentifiers(String measureIdentifiers) {
             return this;
         }
 
+        public CareGaps.When isDocumentMode(Boolean isDocumentMode) {
+            this.isDocumentMode = isDocumentMode;
+            return this;
+        }
+
         public CareGaps.When getCareGapsReport() {
             this.operation = () -> service.getCareGapsReport(
-                    periodStart, periodEnd, subject, statuses, measureIds, measureIdentifiers, measureUrls);
+                    periodStart,
+                    periodEnd,
+                    subject,
+                    statuses,
+                    measureIds,
+                    measureIdentifiers,
+                    measureUrls,
+                    isDocumentMode);
             return this;
         }
 
@@ -283,7 +297,11 @@ public SelectedBundle detectedIssueCount(int detectedIssueCount) {
                             .size());
             return this;
         }
-        ;
+
+        public SelectedBundle bundleEntryCount(int count) {
+            assertEquals(count, bundleReport().getEntry().size());
+            return this;
+        }
 
         public DetectedIssue resourceToDetectedIssue(Resource theResource) {
             IParser parser = FhirContext.forR4Cached().newJsonParser();
@@ -407,6 +425,32 @@ public SelectedDetectedIssue hasCareGapStatus(String gapStatus) {
             return this;
         }
 
+        public SelectedDetectedIssue hasIdentifiedPeriod() {
+            assertTrue(detectedIssueReport().hasIdentifiedPeriod());
+            return this;
+        }
+
+        public SelectedDetectedIssue hasImplicatedMeasureReference() {
+            assertTrue(
+                    detectedIssueReport().getImplicatedFirstRep().getReference().startsWith("Measure"));
+            return this;
+        }
+
+        public SelectedDetectedIssue hasContainedMeasureReport() {
+            var containedResource = detectedIssueReport().getContained().get(0);
+            assertTrue(containedResource instanceof MeasureReport);
+            return this;
+        }
+
+        public SelectedDetectedIssue hasContainedEvidenceReference() {
+            assertTrue(detectedIssueReport()
+                    .getEvidenceFirstRep()
+                    .getDetailFirstRep()
+                    .getReference()
+                    .startsWith("#"));
+            return this;
+        }
+
         public SelectedDetectedIssue hasPatientReference(String patientRef) {
             assertEquals(
                     patientRef,