post-merge updates

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>
LinuxForHealth · Oct 18, 2021 · e34f78b · e34f78b
1 parent ff520bf
commit e34f78b
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Showing 20 changed files with 333 additions and 317 deletions.
diff --git a/...eration/fhir-operation-cpg/src/test/java/com/ibm/fhir/operation/cpg/CqlOperationTest.java b/...eration/fhir-operation-cpg/src/test/java/com/ibm/fhir/operation/cpg/CqlOperationTest.java
@@ -10,8 +10,6 @@
 import static com.ibm.fhir.cql.helpers.ModelHelper.concept;
 import static com.ibm.fhir.cql.helpers.ModelHelper.fhirboolean;
 import static com.ibm.fhir.cql.helpers.ModelHelper.fhirstring;
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.fail;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.anyBoolean;
 import static org.mockito.ArgumentMatchers.anyString;
@@ -20,12 +18,14 @@
 import static org.mockito.Mockito.mockStatic;
 import static org.mockito.Mockito.spy;
 import static org.mockito.Mockito.when;
+import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.fail;
 
 import javax.ws.rs.core.MultivaluedMap;
 
-import org.testng.annotations.Test;
 import org.mockito.MockedStatic;
+import org.testng.annotations.Test;
 
 import com.ibm.fhir.cql.Constants;
 import com.ibm.fhir.cql.helpers.LibraryHelper;
@@ -63,8 +63,15 @@ public void testInlineExpression() throws Exception {
         String encounterCode = "office-visit";
         Coding reason = coding(codesystem, encounterCode);
 
-        Encounter encounter =
-                Encounter.builder().reasonCode(concept(reason)).status(EncounterStatus.FINISHED).clazz(reason).period(Period.builder().start(DateTime.now()).end(DateTime.now()).build()).build();
+        Encounter encounter = Encounter.builder()
+                .reasonCode(concept(reason))
+                .status(EncounterStatus.FINISHED)
+                .clazz(reason)
+                .period(Period.builder()
+                    .start(DateTime.now())
+                    .end(DateTime.now())
+                    .build())
+                .build();
 
         String expression = "[Encounter] e where e.status = 'finished'";
 
@@ -85,7 +92,7 @@ public void testInlineExpression() throws Exception {
 
             // when(mockRegistry.getResource(javastring(fhirHelpers.getUrl()), Library.class)).thenReturn(fhirHelpers);
 
-            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
+            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext(null);
             Parameters result = getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);
             assertNotNull(result);
 
@@ -136,7 +143,7 @@ public void testInlineExpressionWithIncludes() throws Exception {
             canonical = ModelHelper.canonical(modelInfo.getUrl(), modelInfo.getVersion());
             when(mockRegistry.getResource(canonical.getValue(), Library.class)).thenReturn(modelInfo);
 
-            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
+            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext("cql");
             getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);
         }
     }
@@ -158,7 +165,7 @@ public void testInlineExpressionInvalid() throws Exception {
             FHIRRegistry mockRegistry = spy(FHIRRegistry.class);
             staticRegistry.when(FHIRRegistry::getInstance).thenReturn(mockRegistry);
 
-            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
+            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext("cql");
             getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);
             fail("Missing expected Exception");
         } catch (FHIROperationException fex) {
@@ -189,7 +196,7 @@ public void testInlineExpressionWithDebug() throws Exception {
             FHIRRegistry mockRegistry = spy(FHIRRegistry.class);
             staticRegistry.when(FHIRRegistry::getInstance).thenReturn(mockRegistry);
 
-            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext();
+            FHIROperationContext ctx = FHIROperationContext.createSystemOperationContext("cql");
             Parameters result = getOperation().doInvoke(ctx, null, null, null, parameters, resourceHelper);
 
             assertNotNull(result);

diff --git a/...on/fhir-operation-cqf/src/test/java/com/ibm/fhir/operation/cqf/CareGapsOperationTest.java b/...on/fhir-operation-cqf/src/test/java/com/ibm/fhir/operation/cqf/CareGapsOperationTest.java
@@ -11,8 +11,6 @@
 import static com.ibm.fhir.cql.helpers.ModelHelper.concept;
 import static com.ibm.fhir.cql.helpers.ModelHelper.fhirstring;
 import static com.ibm.fhir.cql.helpers.ModelHelper.valueset;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertSame;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.anyBoolean;
 import static org.mockito.ArgumentMatchers.anyString;
@@ -23,14 +21,16 @@
 import static org.mockito.Mockito.spy;
 import static org.mockito.Mockito.when;
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertSame;
 
 import java.time.LocalDate;
 import java.time.temporal.ChronoUnit;
 import java.util.List;
 
+import org.mockito.MockedStatic;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
-import org.mockito.MockedStatic;
 
 import com.ibm.fhir.cql.helpers.ParameterMap;
 import com.ibm.fhir.model.resource.Bundle;
@@ -70,8 +70,15 @@ public void testDoEvaluationEXM74() throws Exception {
         String codesystem = "http://snomed.ct/info";
         String encounterCode = "office-visit";
         Coding reason = coding(codesystem, encounterCode);
-        Encounter encounter =
-                Encounter.builder().reasonCode(concept(reason)).status(EncounterStatus.FINISHED).clazz(reason).period(Period.builder().start(DateTime.now()).end(DateTime.now()).build()).build();
+        Encounter encounter = Encounter.builder()
+                .reasonCode(concept(reason))
+                .status(EncounterStatus.FINISHED)
+                .clazz(reason)
+                .period(Period.builder()
+                    .start(DateTime.now())
+                    .end(DateTime.now())
+                    .build())
+                .build();
 
         String procedureCode = "fluoride-application";
         Coding type = coding(codesystem, procedureCode);
@@ -116,7 +123,7 @@ public void testDoEvaluationEXM74() throws Exception {
             fhirLibraries.stream().forEach(l -> when(mockRegistry.getResource(canonical(l.getUrl(), l.getVersion()).getValue(), Library.class)).thenReturn(l));
 
             Parameters result =
-                    operation.doInvoke(FHIROperationContext.createResourceTypeOperationContext(), Measure.class, null, null, parameters, resourceHelper);
+                    operation.doInvoke(FHIROperationContext.createResourceTypeOperationContext("care-gap"), Measure.class, null, null, parameters, resourceHelper);
             assertNotNull(result);
 
             ParameterMap resultMap = new ParameterMap(result);
@@ -127,7 +134,7 @@ public void testDoEvaluationEXM74() throws Exception {
 
     @SuppressWarnings("unchecked")
     protected SingleResourceResult<? extends Resource> asResult(Resource patient) {
-        SingleResourceResult<Resource> result = (SingleResourceResult<Resource>) mock(SingleResourceResult.class);
+        SingleResourceResult<Resource> result = mock(SingleResourceResult.class);
         when(result.isSuccess()).thenReturn(true);
         when(result.getResource()).thenReturn(patient);
         return result;

diff --git a/...-operation-cqf/src/test/java/com/ibm/fhir/operation/cqf/EvaluateMeasureOperationTest.java b/...-operation-cqf/src/test/java/com/ibm/fhir/operation/cqf/EvaluateMeasureOperationTest.java
@@ -11,8 +11,6 @@
 import static com.ibm.fhir.cql.helpers.ModelHelper.concept;
 import static com.ibm.fhir.cql.helpers.ModelHelper.fhirstring;
 import static com.ibm.fhir.cql.helpers.ModelHelper.valueset;
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.anyBoolean;
 import static org.mockito.ArgumentMatchers.anyString;
@@ -21,6 +19,8 @@
 import static org.mockito.Mockito.mockStatic;
 import static org.mockito.Mockito.spy;
 import static org.mockito.Mockito.when;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
 
 import java.time.LocalDate;
 import java.time.LocalTime;
@@ -31,9 +31,9 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
+import org.mockito.MockedStatic;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
-import org.mockito.MockedStatic;
 
 import com.ibm.fhir.cql.helpers.ParameterMap;
 import com.ibm.fhir.model.resource.Encounter;
@@ -57,86 +57,86 @@
 import com.ibm.fhir.server.operation.spi.FHIRResourceHelpers;
 
 public class EvaluateMeasureOperationTest {
-    
+
     private EvaluateMeasureOperation operation;
-    
+
     @BeforeMethod
     public void setup() {
         operation = new EvaluateMeasureOperation();
     }
-    
+
     @Test
     public void testDoEvaluationEXM74() throws Exception {
         Patient patient = (Patient) TestHelper.getTestResource("Patient.json");
 
         String codesystem = "http://snomed.ct/info";
         String encounterCode = "office-visit";
-        Coding reason = coding(codesystem, encounterCode); 
+        Coding reason = coding(codesystem, encounterCode);
         Encounter encounter = Encounter.builder()
                 .reasonCode(concept(reason))
                 .status(EncounterStatus.FINISHED)
                 .clazz(reason)
                 .period(Period.builder().start(DateTime.now()).end(DateTime.now()).build())
                 .build();
-        
+
         String procedureCode = "fluoride-application";
         Coding type = coding(codesystem, procedureCode);
         Procedure procedure = Procedure.builder().subject(Reference.builder().reference(fhirstring("Patient/"
                 + patient.getId())).build()).code(concept(type)).status(ProcedureStatus.COMPLETED).performed(DateTime.of("2019-03-14")).build();
-        
+
         List<Measure> measures = TestHelper.getBundleResources("EXM74-10.2.000-request.json", Measure.class);
         assertEquals( measures.size(), 1 );
         Measure measure = measures.get(0);
         String measureURL = canonical(measure.getUrl(), measure.getVersion()).getValue();
-        
+
         List<Library> fhirLibraries = TestHelper.getBundleResources("EXM74-10.2.000-request.json", Library.class);
-        
+
         List<String> names = fhirLibraries.stream().map( l -> l.getName().getValue()).collect(Collectors.toList());
         System.out.println(names);
-        
+
         LocalDate periodStart = LocalDate.of(2000, 1, 1);
         LocalDate periodEnd = periodStart.plus(1, ChronoUnit.YEARS);
-        
+
         Parameters.Parameter pPeriodStart = Parameters.Parameter.builder().name(fhirstring(EvaluateMeasureOperation.PARAM_IN_PERIOD_START)).value(Date.of(periodStart)).build();
         Parameters.Parameter pPeriodEnd = Parameters.Parameter.builder().name(fhirstring(EvaluateMeasureOperation.PARAM_IN_PERIOD_END)).value(Date.of(periodEnd)).build();
         Parameters.Parameter pReportType = Parameters.Parameter.builder().name(fhirstring(EvaluateMeasureOperation.PARAM_IN_REPORT_TYPE)).value(MeasureReportType.INDIVIDUAL).build();
         Parameters.Parameter pMeasure = Parameters.Parameter.builder().name(fhirstring(EvaluateMeasureOperation.PARAM_IN_MEASURE)).value(fhirstring(measureURL)).build();
         Parameters.Parameter pSubject = Parameters.Parameter.builder().name(fhirstring(EvaluateMeasureOperation.PARAM_IN_SUBJECT)).value(fhirstring("Patient/" + patient.getId())).build();
-        
+
         Parameters parameters = Parameters.builder().parameter(pPeriodStart, pPeriodEnd, pReportType, pMeasure, pSubject).build();
 
         FHIRResourceHelpers resourceHelper = mock(FHIRResourceHelpers.class);
         when(resourceHelper.doRead(eq("Patient"), eq(patient.getId()), anyBoolean(), anyBoolean(), any())).thenAnswer(x -> TestHelper.asResult(patient));
-      
+
         when(resourceHelper.doSearch(eq("Encounter"), anyString(), anyString(), any(), anyString(), any())).thenReturn( bundle(encounter) );
         when(resourceHelper.doSearch(eq("Procedure"), anyString(), anyString(), any(), anyString(), any())).thenReturn( bundle(procedure) );
-        
+
         try (MockedStatic<FHIRRegistry> staticRegistry = mockStatic(FHIRRegistry.class)) {
             FHIRRegistry mockRegistry = spy(FHIRRegistry.class);
             staticRegistry.when(FHIRRegistry::getInstance).thenReturn(mockRegistry);
 
-            
+
             when(mockRegistry.getResource("http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1001", ValueSet.class)).thenReturn( valueset(codesystem, encounterCode) );
             when(mockRegistry.getResource("http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.125.12.1002", ValueSet.class)).thenReturn( valueset(codesystem, procedureCode) );
-            
+
             when(mockRegistry.getResource(measureURL, Measure.class)).thenReturn( measure );
             fhirLibraries.stream().forEach( l -> when(mockRegistry.getResource( canonical(l.getUrl(), l.getVersion()).getValue(), Library.class )).thenReturn(l) );
-            
-            Parameters result = operation.doInvoke(FHIROperationContext.createResourceTypeOperationContext(),
+
+            Parameters result = operation.doInvoke(FHIROperationContext.createResourceTypeOperationContext("evaluate-measure"),
                 Measure.class, null, null, parameters, resourceHelper);
             assertNotNull(result);
-            
+
             ParameterMap resultMap = new ParameterMap(result);
             MeasureReport report = (MeasureReport) resultMap.getSingletonParameter(EvaluateMeasureOperation.PARAM_OUT_RETURN).getResource();
             assertEquals( report.getMeasure().getValue(), measureURL );
-            
+
             ZoneOffset zoneOffset = OffsetDateTime.now().getOffset();
             ZonedDateTime expectedStart = OffsetDateTime.of(periodStart, LocalTime.MIN, zoneOffset).toZonedDateTime();
             ZonedDateTime expectedEnd= OffsetDateTime.of(periodEnd, LocalTime.MAX, zoneOffset).toZonedDateTime();
 
             Period expectedPeriod = Period.builder().start(DateTime.of(expectedStart)).end(DateTime.of(expectedEnd)).build();
             assertEquals( report.getPeriod(), expectedPeriod );
-            
+
             assertEquals( report.getGroup().size(), 1 );
             MeasureReport.Group group = report.getGroup().get(0);
             assertEquals( group.getPopulation().size(), 3 );

diff --git a/...on-cqf/src/test/java/com/ibm/fhir/operation/cqf/LibraryDataRequirementsOperationTest.java b/...on-cqf/src/test/java/com/ibm/fhir/operation/cqf/LibraryDataRequirementsOperationTest.java
@@ -14,19 +14,20 @@
 import com.ibm.fhir.server.operation.spi.FHIROperationContext;
 
 public class LibraryDataRequirementsOperationTest extends BaseDataRequirementsOperationTest {
-    
+
     @Test
     public void testInstanceLibrary() throws Exception {
-        runTest( FHIROperationContext.createInstanceOperationContext(), Library.class, primaryLibrary -> primaryLibrary.getId(), primaryLibrary -> null );
+        runTest( FHIROperationContext.createInstanceOperationContext("data-requirements"), Library.class, primaryLibrary -> primaryLibrary.getId(), primaryLibrary -> null );
     }
-    
+
     @Test
     public void testSystemLibrary() throws Exception {
-        runTest( FHIROperationContext.createSystemOperationContext(), null, primaryLibrary -> null, primaryLibrary -> { 
+        runTest( FHIROperationContext.createSystemOperationContext("data-requirements"), null, primaryLibrary -> null, primaryLibrary -> {
             return Parameters.builder().parameter( Parameters.Parameter.builder().name(fhirstring("target")).value(fhirstring(primaryLibrary.getId())).build()).build();
         });
     }
-
+
+    @Override
     public AbstractDataRequirementsOperation getOperation() {
         return new LibraryDataRequirementsOperation();
     }