DSTU3 submit-data, R4 and DSTU3 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",
@@ -38,6 +38,8 @@
 		"Codeable",
 		"contentgroup",
 		"DEQM",
+		"Eicrs",
+		"mgsc",
 		"drawio",
 		"FHIR",
 		"Gson",
@@ -56,4 +58,4 @@
 		"**/.settings": true,
 		"**/.factorypath": true
 	}
-}
+}

core/src/main/java/org/opencds/cqf/ruler/Application.java

@@ -1,6 +1,7 @@
 package org.opencds.cqf.ruler;
 
 import org.opencds.cqf.ruler.config.BeanFinderConfig;
+import org.opencds.cqf.ruler.config.ServerProperties;
 import org.opencds.cqf.ruler.config.TesterUIConfig;
 import org.opencds.cqf.ruler.external.FhirTesterConfig;
 import org.opencds.cqf.ruler.external.annotations.OnEitherVersion;
@@ -67,4 +68,9 @@ public ServletRegistrationBean<Server> hapiServletRegistration() {
 
 		return servletRegistrationBean;
 	}
+
+	@Bean
+	public ServerProperties serverProperties() {
+		return new ServerProperties();
+	}
 }

core/src/main/java/org/opencds/cqf/ruler/Server.java

@@ -1,5 +1,7 @@
 package org.opencds.cqf.ruler;
 
+import static com.google.common.base.MoreObjects.firstNonNull;
+
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -14,6 +16,7 @@
 import org.opencds.cqf.ruler.capability.ExtensibleJpaCapabilityStatementProvider;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaConformanceProviderDstu2;
 import org.opencds.cqf.ruler.capability.ExtensibleJpaConformanceProviderDstu3;
+import org.opencds.cqf.ruler.config.ServerProperties;
 import org.opencds.cqf.ruler.external.AppProperties;
 import org.opencds.cqf.ruler.external.BaseJpaRestfulServer;
 import org.slf4j.Logger;
@@ -29,6 +32,7 @@
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 
 public class Server extends BaseJpaRestfulServer {
+	private static final long serialVersionUID = 1L;
 
 	private static Logger log = LoggerFactory.getLogger(Server.class);
 
@@ -45,12 +49,13 @@ public class Server extends BaseJpaRestfulServer {
 	private IValidationSupport myValidationSupport;
 
 	@Autowired
-	AppProperties myAppProperties;
+	ApplicationContext myApplicationContext;
 
 	@Autowired
-	ApplicationContext myApplicationContext;
+	AppProperties myAppProperties;
 
-	private static final long serialVersionUID = 1L;
+	@Autowired
+	ServerProperties myServerProperties;
 
 	public Server() {
 		super();
@@ -68,35 +73,37 @@ protected void initialize() throws ServletException {
 		}
 
 		FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
+
+		String implementationDescription = myServerProperties.getImplementation_description();
 		if (fhirVersion == FhirVersionEnum.DSTU2) {
 			List<MetadataExtender<Conformance>> extenderList = extenders.values().stream()
 					.map(x -> (MetadataExtender<Conformance>) x).collect(Collectors.toList());
 			ExtensibleJpaConformanceProviderDstu2 confProvider = new ExtensibleJpaConformanceProviderDstu2(this,
 					fhirSystemDao,
 					daoConfig, extenderList);
-			confProvider.setImplementationDescription("CQF RULER DSTU2 Server");
+			confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER DSTU2 Server"));
 			setServerConformanceProvider(confProvider);
 		} else {
 			if (fhirVersion == FhirVersionEnum.DSTU3) {
 				List<MetadataExtender<CapabilityStatement>> extenderList = extenders.values().stream()
 						.map(x -> (MetadataExtender<CapabilityStatement>) x).collect(Collectors.toList());
 				ExtensibleJpaConformanceProviderDstu3 confProvider = new ExtensibleJpaConformanceProviderDstu3(this,
 						fhirSystemDao, daoConfig, searchParamRegistry, extenderList);
-				confProvider.setImplementationDescription("CQF RULER DSTU3 Server");
+				confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER DSTU3 Server"));
 				setServerConformanceProvider(confProvider);
 			} else if (fhirVersion == FhirVersionEnum.R4) {
 				List<MetadataExtender<IBaseConformance>> extenderList = extenders.values().stream()
 						.map(x -> (MetadataExtender<IBaseConformance>) x).collect(Collectors.toList());
 				ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(this,
 						fhirSystemDao, daoConfig, searchParamRegistry, myValidationSupport, extenderList);
-				confProvider.setImplementationDescription("CQF RULER R4 Server");
+				confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER R4 Server"));
 				setServerConformanceProvider(confProvider);
 			} else if (fhirVersion == FhirVersionEnum.R5) {
 				List<MetadataExtender<IBaseConformance>> extenderList = extenders.values().stream()
 						.map(x -> (MetadataExtender<IBaseConformance>) x).collect(Collectors.toList());
 				ExtensibleJpaCapabilityStatementProvider confProvider = new ExtensibleJpaCapabilityStatementProvider(this,
 						fhirSystemDao, daoConfig, searchParamRegistry, myValidationSupport, extenderList);
-				confProvider.setImplementationDescription("CQF RULER R5 Server");
+				confProvider.setImplementationDescription(firstNonNull(implementationDescription, "CQF RULER R5 Server"));
 				setServerConformanceProvider(confProvider);
 			} else {
 				throw new IllegalStateException();

core/src/main/java/org/opencds/cqf/ruler/behavior/ResourceCreator.java

@@ -5,7 +5,7 @@
 
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.opencds.cqf.ruler.utility.Resources;
+import org.opencds.cqf.ruler.utility.Ids;
 
 public interface ResourceCreator extends FhirContextUser {
 	@SuppressWarnings("unchecked")
@@ -19,6 +19,26 @@ default <T extends IBaseResource, I extends IIdType> T newResource(I theId) {
 	}
 
 	default <T extends IBaseResource> T newResource(Class<T> theResourceClass, String theIdPart) {
-		return Resources.newResource(theResourceClass, theIdPart);
+		checkNotNull(theResourceClass);
+		checkNotNull(theIdPart);
+
+		T newResource = newResource(theResourceClass);
+		newResource.setId((IIdType)Ids.newId(getFhirContext(), newResource.fhirType(), theIdPart));
+
+		return newResource;
+	}
+
+	@SuppressWarnings("unchecked")
+	default <T extends IBaseResource> T newResource(Class<T> theResourceClass) {
+		checkNotNull(theResourceClass);
+
+		return (T)this.getFhirContext().getResourceDefinition(theResourceClass).newInstance();
+	}
+
+	@SuppressWarnings("unchecked")
+	default <T extends IBaseResource> T newResource(String theResourceType) {
+		checkNotNull(theResourceType);
+
+		return (T)this.getFhirContext().getResourceDefinition(theResourceType).newInstance();
 	}
 }

core/src/main/java/org/opencds/cqf/ruler/config/ServerProperties.java

@@ -0,0 +1,22 @@
+package org.opencds.cqf.ruler.config;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@ConfigurationProperties(prefix = "hapi.fhir")
+@Configuration
+@EnableConfigurationProperties
+public class ServerProperties {
+	private String implementation_description = null;
+
+	public String getImplementation_description() {
+		return implementation_description;
+	 }
+
+	 public void setImplementation_description(String implementation_description) {
+		this.implementation_description = implementation_description;
+	 }
+
+
+}

core/src/main/java/org/opencds/cqf/ruler/utility/CanonicalParts.java

@@ -1,6 +1,6 @@
 package org.opencds.cqf.ruler.utility;
 
-public class CanonicalParts {
+public final class CanonicalParts {
 	private final String url;
 	private final String idPart;
 	private final String resourceType;

core/src/main/java/org/opencds/cqf/ruler/utility/Ids.java

@@ -1,5 +1,6 @@
 package org.opencds.cqf.ruler.utility;
 
+import static com.google.common.base.Preconditions.checkArgument;
 import static com.google.common.base.Preconditions.checkNotNull;
 
 import org.hl7.fhir.instance.model.api.IBase;
@@ -103,6 +104,33 @@ public static <IdType extends IIdType> IdType newId(FhirContext theFhirContext,
 		return newId(theFhirContext.getVersion().getVersion(), theId);
 	}
 
+	/**
+	 * The gets the "simple" Id for the Resource, without qualifiers or versions. For example, "Patient/123".
+	 * <p>This is shorthand for resource.getIdElement().toUnqualifiedVersionless().getValue()
+	 * @param resource the Resource to get the Id for
+	 * @return the simple Id
+	 */
+	public static String simple(IBaseResource resource) {
+		checkNotNull(resource);
+		checkArgument(resource.getIdElement() != null);
+
+		return simple(resource.getIdElement());
+	}
+
+		/**
+	 * The gets the "simple" Id for the Id, without qualifiers or versions. For example, "Patient/123".
+	 * <p>This is shorthand for id.toUnqualifiedVersionless().getValue()
+	 * @param id the IIdType to get the Id for
+	 * @return the simple Id
+	 */
+	public static String simple(IIdType id) {
+		checkNotNull(id);
+		checkArgument(id.hasResourceType());
+		checkArgument(id.hasIdPart());
+
+		return id.toUnqualifiedVersionless().getValue();
+	}
+
 	/**
 	 * Creates the appropriate IIdType for a given FhirVersionEnum
 	 * 

core/src/main/java/org/opencds/cqf/ruler/utility/Libraries.java

@@ -5,12 +5,13 @@
 
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.function.Function;
 
+import com.google.common.collect.ImmutableMap;
+
 import org.apache.commons.lang3.tuple.Triple;
 import org.cqframework.cql.elm.execution.Library;
 import org.cqframework.cql.elm.execution.UsingDef;
@@ -78,12 +79,9 @@ public static String getVersion(IBaseResource library) {
 		return libraryFunctions.getVersion().apply(library);
 	}
 
-	private static Map<String, String> urlsByModelName = new HashMap<String, String>() {
-		{
-			put("FHIR", "http://hl7.org/fhir");
-			put("QDM", "urn:healthit-gov:qdm:v5_4");
-		}
-	};
+	private static Map<String, String> urlsByModelName = ImmutableMap.of(
+		"FHIR", "http://hl7.org/fhir",
+		"QDM", "urn:healthit-gov:qdm:v5_4");
 
 	// Returns a list of (Model, Version, Url) for the usings in library. The
 	// "System" using is excluded.

core/src/main/java/org/opencds/cqf/ruler/utility/LibraryFunctions.java

@@ -5,7 +5,7 @@
 
 import org.hl7.fhir.instance.model.api.IBase;
 
-class LibraryFunctions {
+final class LibraryFunctions {
 
 	private final Function<IBase, List<IBase>> getAttachments;
 	private final Function<IBase, String> getContentType;

core/src/main/java/org/opencds/cqf/ruler/utility/Resources.java

@@ -15,6 +15,16 @@ public static <T extends IBaseResource, I extends IIdType> T newResource(Class<T
 		checkNotNull(theResourceClass);
 		checkNotNull(theIdPart);
 		checkArgument(!theIdPart.contains("/"), "theIdPart must be a simple id. Do not include resourceType or history");
+		T resource = newResource(theResourceClass);
+
+		@SuppressWarnings("unchecked")
+		I id = (I) Ids.newId(theResourceClass, theIdPart);
+		resource.setId(id);
+		return resource;
+	}
+
+	public static <T extends IBaseResource> T newResource(Class<T> theResourceClass) {
+		checkNotNull(theResourceClass);
 		T resource = null;
 		try {
 			resource = (T) theResourceClass.getConstructor().newInstance();
@@ -23,9 +33,6 @@ public static <T extends IBaseResource, I extends IIdType> T newResource(Class<T
 					"theResourceClass must be a type with an empty default constructor to use this function");
 		}
 
-		@SuppressWarnings("unchecked")
-		I id = (I) Ids.newId(theResourceClass, theIdPart);
-		resource.setId(id);
 		return resource;
 	}
 }

core/src/main/java/org/opencds/cqf/ruler/utility/Translators.java

@@ -16,6 +16,8 @@
 
 public class Translators {
 
+	private Translators() {}
+
 	public static String errorsToString(Iterable<CqlTranslatorException> exceptions) {
 		ArrayList<String> errors = new ArrayList<>();
 		for (CqlTranslatorException error : exceptions) {

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

@@ -0,0 +1,83 @@
+package org.opencds.cqf.ruler.utility.dstu3;
+
+import static com.google.common.base.Preconditions.checkNotNull;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+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) {
+		checkNotNull(theId);
+
+		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) {
+		checkNotNull(theIdPart);
+
+		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) {
+		checkNotNull(name);
+
+		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) {
+		checkNotNull(name);
+		checkNotNull(value);
+
+		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) {
+		checkNotNull(name);
+		checkNotNull(resource);
+
+		org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent c = newPart(name, parts);
+		c.setResource(resource);
+		return c;
+	}
+
+	public static List<org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent> getPartsByName(
+			org.hl7.fhir.dstu3.model.Parameters parameters, String name) {
+		checkNotNull(parameters);
+		checkNotNull(name);
+
+		return parameters.getParameter().stream().filter(x -> name.equals(x.getName())).collect(Collectors.toList());
+	}
+}