WIP collect data

.vscode/settings.json

@@ -13,7 +13,7 @@
 	],
 	"java.test.defaultConfig": "test-config",
 	"java.checkstyle.configuration": "${workspaceFolder}/config/checkstyle/checkstyle.xml",
-	"java.checkstyle.version": "9.21",
+	"java.checkstyle.version": "9.2.1",
 	"cSpell.enabledLanguageIds": [
 		"java",
 		"json",

core/src/main/java/org/opencds/cqf/ruler/utility/dstu3/Parameters.java

@@ -0,0 +1,58 @@
+package org.opencds.cqf.ruler.utility.dstu3;
+
+import org.hl7.fhir.dstu3.model.IdType;
+import org.opencds.cqf.ruler.utility.Ids;
+
+public class Parameters {
+
+	private Parameters() {
+	}
+
+	public static org.hl7.fhir.dstu3.model.Parameters newParameters(IdType theId,
+			org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.dstu3.model.Parameters p = newParameters(parts);
+		p.setId(theId);
+		return p;
+	}
+
+	public static org.hl7.fhir.dstu3.model.Parameters newParameters(String theIdPart,
+			org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent... parts) {
+		return newParameters((IdType) Ids.newId(org.hl7.fhir.dstu3.model.Parameters.class, theIdPart), parts);
+	}
+
+	public static org.hl7.fhir.dstu3.model.Parameters newParameters(
+			org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.dstu3.model.Parameters p = new org.hl7.fhir.dstu3.model.Parameters();
+		for (org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent c : parts) {
+			p.addParameter(c);
+		}
+
+		return p;
+	}
+
+	public static org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent c = new org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent();
+		c.setName(name);
+		for (org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent p : parts) {
+			c.addPart(p);
+		}
+
+		return c;
+	}
+
+	public static org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.dstu3.model.Type value, org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent c = newPart(name, parts);
+		c.setValue(value);
+		return c;
+	}
+
+	public static org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.dstu3.model.Resource resource,
+			org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent c = newPart(name, parts);
+		c.setResource(resource);
+		return c;
+	}
+}

core/src/main/java/org/opencds/cqf/ruler/utility/r4/Parameters.java

@@ -0,0 +1,58 @@
+package org.opencds.cqf.ruler.utility.r4;
+
+import org.hl7.fhir.r4.model.IdType;
+import org.opencds.cqf.ruler.utility.Ids;
+
+public class Parameters {
+
+	private Parameters() {
+	}
+
+	public static org.hl7.fhir.r4.model.Parameters newParameters(IdType theId,
+			org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r4.model.Parameters p = newParameters(parts);
+		p.setId(theId);
+		return p;
+	}
+
+	public static org.hl7.fhir.r4.model.Parameters newParameters(String theIdPart,
+			org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent... parts) {
+		return newParameters((IdType) Ids.newId(org.hl7.fhir.r4.model.Parameters.class, theIdPart), parts);
+	}
+
+	public static org.hl7.fhir.r4.model.Parameters newParameters(
+			org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r4.model.Parameters p = new org.hl7.fhir.r4.model.Parameters();
+		for (org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent c : parts) {
+			p.addParameter(c);
+		}
+
+		return p;
+	}
+
+	public static org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent c = new org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent();
+		c.setName(name);
+		for (org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent p : parts) {
+			c.addPart(p);
+		}
+
+		return c;
+	}
+
+	public static org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.r4.model.Type value, org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent c = newPart(name, parts);
+		c.setValue(value);
+		return c;
+	}
+
+	public static org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.r4.model.Resource resource,
+			org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent c = newPart(name, parts);
+		c.setResource(resource);
+		return c;
+	}
+}

core/src/main/java/org/opencds/cqf/ruler/utility/r5/Parameters.java

@@ -0,0 +1,58 @@
+package org.opencds.cqf.ruler.utility.r5;
+
+import org.hl7.fhir.r5.model.IdType;
+import org.opencds.cqf.ruler.utility.Ids;
+
+public class Parameters {
+
+	private Parameters() {
+	}
+
+	public static org.hl7.fhir.r5.model.Parameters newParameters(IdType theId,
+			org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r5.model.Parameters p = newParameters(parts);
+		p.setId(theId);
+		return p;
+	}
+
+	public static org.hl7.fhir.r5.model.Parameters newParameters(String theIdPart,
+			org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent... parts) {
+		return newParameters((IdType) Ids.newId(org.hl7.fhir.r5.model.Parameters.class, theIdPart), parts);
+	}
+
+	public static org.hl7.fhir.r5.model.Parameters newParameters(
+			org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r5.model.Parameters p = new org.hl7.fhir.r5.model.Parameters();
+		for (org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent c : parts) {
+			p.addParameter(c);
+		}
+
+		return p;
+	}
+
+	public static org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent c = new org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent();
+		c.setName(name);
+		for (org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent p : parts) {
+			c.addPart(p);
+		}
+
+		return c;
+	}
+
+	public static org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.r5.model.DataType value, org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent c = newPart(name, parts);
+		c.setValue(value);
+		return c;
+	}
+
+	public static org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent newPart(String name,
+			org.hl7.fhir.r5.model.Resource resource,
+			org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent... parts) {
+		org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent c = newPart(name, parts);
+		c.setResource(resource);
+		return c;
+	}
+}

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/r4/builder/ReferenceBuilder.java

@@ -12,7 +12,7 @@ public ReferenceBuilder() {
     public ReferenceBuilder buildReference(String reference) {
         complexProperty.setReference(reference);
         return this;
-    }
+	 }
 
     public ReferenceBuilder buildIdentifier(Identifier identifier) {
         complexProperty.setIdentifier(identifier);

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/r4/provider/CollectDataProvider.java

@@ -1,12 +1,11 @@
 package org.opencds.cqf.ruler.cr.r4.provider;
 
+import static org.opencds.cqf.ruler.utility.r4.Parameters.newParameters;
+import static org.opencds.cqf.ruler.utility.r4.Parameters.newPart;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.instance.model.api.IAnyResource;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Measure;
 import org.hl7.fhir.r4.model.MeasureReport;
@@ -27,45 +26,38 @@ public class CollectDataProvider extends DaoRegistryOperationProvider {
 	private MeasureEvaluateProvider measureEvaluateProvider;
 
 	@Operation(name = "$collect-data", idempotent = true, type = Measure.class)
-	public Parameters collectData(RequestDetails theRequestDetails, @IdParam IdType theId, @OperationParam(name = "periodStart") String periodStart,
-			  @OperationParam(name = "periodEnd") String periodEnd, @OperationParam(name = "patient") String patientRef,
-			  @OperationParam(name = "practitioner") String practitionerRef,
-			  @OperationParam(name = "lastReceivedOn") String lastReceivedOn) throws FHIRException {
+	public Parameters collectData(RequestDetails theRequestDetails, @IdParam IdType theId,
+			@OperationParam(name = "periodStart") String periodStart,
+			@OperationParam(name = "periodEnd") String periodEnd, @OperationParam(name = "patient") String patientRef,
+			@OperationParam(name = "practitioner") String practitionerRef,
+			@OperationParam(name = "lastReceivedOn") String lastReceivedOn) {
 
-		 MeasureReport report = measureEvaluateProvider.evaluateMeasure(theRequestDetails, theId, periodStart, periodEnd, null, patientRef, practitionerRef, lastReceivedOn, null);
-		 report.setType(MeasureReport.MeasureReportType.DATACOLLECTION);
-		 report.setGroup(null);
+		MeasureReport report = measureEvaluateProvider.evaluateMeasure(theRequestDetails, theId, periodStart, periodEnd,
+				null, patientRef, practitionerRef, lastReceivedOn, null);
+		report.setType(MeasureReport.MeasureReportType.DATACOLLECTION);
+		report.setGroup(null);
 
-		 Parameters parameters = new Parameters();
-		 parameters.addParameter(new Parameters.ParametersParameterComponent().setName("measureReport").setResource(report));
+		Parameters parameters = newParameters(newPart("measureReport", report));
 
-		 addEvaluatedResourcesToParameters(report, parameters);
+		addEvaluatedResourcesToParameters(report, parameters);
 
-		 return parameters;
+		return parameters;
 	}
 
-	private List<IAnyResource> addEvaluatedResources(MeasureReport report){
-		 List<IAnyResource> resources = new ArrayList<>();
-		 for (Reference evaluatedResource : report.getEvaluatedResource()) {
-			  IIdType theEvaluatedId = evaluatedResource.getReferenceElement();
-			  String resourceType = theEvaluatedId.getResourceType();
-			  if (resourceType != null) {
-					IBaseResource resourceBase = getDaoRegistry().getResourceDao(resourceType).read(theEvaluatedId);
-					if (resourceBase instanceof Resource) {
-						 Resource resource = (Resource) resourceBase;
-						 resources.add(resource);
-					}
-			  }
-		 }
-		 return resources;
+	private List<Resource> readEvaluatedResources(MeasureReport report) {
+		List<Resource> resources = new ArrayList<>();
+		for (Reference reference : report.getEvaluatedResource()) {
+			Resource resource = read(reference.getReferenceElement());
+			if (resource != null) {
+				resources.add(resource);
+			}
+		}
+
+		return resources;
 	}
 
 	private void addEvaluatedResourcesToParameters(MeasureReport report, Parameters parameters) {
-		 List<IAnyResource> resources;
-		 resources = addEvaluatedResources(report);
-		 resources.forEach(resource -> {
-			  parameters.addParameter(new Parameters.ParametersParameterComponent().setName("resource").setResource((Resource) resource));
-			  }
-		 );
+		readEvaluatedResources(report)
+			.forEach(resource -> parameters.addParameter(newPart("resource", resource)));
 	}
 }

plugin/ra/src/test/java/org/opencds/cqf/ruler/ra/r4/ReportProviderIT.java

@@ -17,7 +17,7 @@
 import org.opencds.cqf.ruler.ra.RAConfig;
 import org.opencds.cqf.ruler.ra.RAProperties;
 import org.opencds.cqf.ruler.test.RestIntegrationTest;
-import org.opencds.cqf.ruler.test.Urls;
+import org.opencds.cqf.ruler.test.utility.Urls;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 

test/src/main/java/org/opencds/cqf/ruler/test/DaoIntegrationTest.java

@@ -5,6 +5,7 @@
 import org.junit.jupiter.api.TestInstance.Lifecycle;
 import org.opencds.cqf.ruler.behavior.IdCreator;
 import org.opencds.cqf.ruler.behavior.ResourceCreator;
+import org.opencds.cqf.ruler.test.behavior.ResourceLoader;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
 import org.springframework.boot.autoconfigure.quartz.QuartzAutoConfiguration;

test/src/main/java/org/opencds/cqf/ruler/test/RestIntegrationTest.java

@@ -7,6 +7,7 @@
 import org.opencds.cqf.ruler.Application;
 import org.opencds.cqf.ruler.behavior.IdCreator;
 import org.opencds.cqf.ruler.behavior.ResourceCreator;
+import org.opencds.cqf.ruler.test.behavior.ResourceLoader;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.web.server.LocalServerPort;
 import org.springframework.context.annotation.Import;

test/src/main/java/org/opencds/cqf/ruler/test/ResourceLoader.java → test/src/main/java/org/opencds/cqf/ruler/test/behavior/ResourceLoader.java

@@ -1,4 +1,4 @@
-package org.opencds.cqf.ruler.test;
+package org.opencds.cqf.ruler.test.behavior;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -56,7 +56,7 @@ public default IBaseResource parseResource(String encoding, String resourceStrin
 				throw new IllegalArgumentException(
 						String.format("Expected encoding xml, or json.  %s is not a valid encoding", encoding));
 		}
-		
+
 		return parser.parseResource(resourceString);
 	}
 

test/src/main/java/org/opencds/cqf/ruler/test/Urls.java → test/src/main/java/org/opencds/cqf/ruler/test/utility/Urls.java

@@ -1,4 +1,4 @@
-package org.opencds.cqf.ruler.test;
+package org.opencds.cqf.ruler.test.utility;
 
 /**
  * This interface provides test utility functions for creating IGenericClients

test/src/test/java/org/opencds/cqf/ruler/test/UrlsTest.java

@@ -5,6 +5,7 @@
 
 import org.apache.commons.validator.routines.UrlValidator;
 import org.junit.jupiter.api.Test;
+import org.opencds.cqf.ruler.test.utility.Urls;
 
 public class UrlsTest  {
     @Test