Updated the Cql FhirDal to implement Translator FhirDal and introduce…

plugin/cql/src/main/java/org/opencds/cqf/ruler/cql/JpaFhirDal.java

@@ -1,13 +1,19 @@
 package org.opencds.cqf.ruler.cql;
 
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal;
-
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.UriParam;
+import org.cqframework.fhir.api.FhirDal;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import java.math.BigDecimal;
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
 
 @SuppressWarnings("unchecked")
 public class JpaFhirDal implements FhirDal {
@@ -45,16 +51,37 @@ public void delete(IIdType theId) {
 
 	}
 
-	// TODO: the search interfaces need some work
 	@Override
-	public Iterable<IBaseResource> search(String theResourceType) {
-		return this.daoRegistry.getResourceDao(theResourceType).search(SearchParameterMap.newSynchronous())
-				.getAllResources();
-	}
+	public IBaseBundle search(String theResourceType, Map<String, List<List<IQueryParameterType>>> theSearchParameters) {
+		SearchParameterMap searchParameterMap = new SearchParameterMap();
+		for(Map.Entry<String, List<List<IQueryParameterType>>> entry : theSearchParameters.entrySet()) {
+			String keyValue = entry.getKey();
 
-	@Override
-	public Iterable<IBaseResource> searchByUrl(String theResourceType, String theUrl) {
-		return this.daoRegistry.getResourceDao(theResourceType)
-				.search(SearchParameterMap.newSynchronous().add("url", new UriParam(theUrl))).getAllResources();
+			for(List<IQueryParameterType> value : entry.getValue()) {
+				for (IQueryParameterType query : value) {
+					searchParameterMap.add(keyValue, query);
+				}
+			}
+		}
+
+		List<IBaseResource> searchResults = this.daoRegistry.getResourceDao(theResourceType).search(searchParameterMap).getAllResources();
+
+		ca.uhn.fhir.util.BundleBuilder builder = new ca.uhn.fhir.util.BundleBuilder(daoRegistry.getSystemDao().getContext());
+		builder
+			.setBundleField("type", "searchset")
+			.setBundleField("id", UUID.randomUUID().toString())
+			.setMetaField("lastUpdated", builder.newPrimitive("instant", new java.util.Date()));
+
+		for (var resource : searchResults) {
+			IBase entry = builder.addEntry();
+			builder.addToEntry(entry, "resource", resource);
+
+			// Add search results
+			IBase search = builder.addSearch(entry);
+			builder.setSearchField(search, "mode", "match");
+			builder.setSearchField(search, "score", builder.newPrimitive("decimal", BigDecimal.ONE));
+		}
+
+		return builder.getBundle();
 	}
 }

plugin/cql/src/test/java/org/opencds/cqf/ruler/cql/JpaFhirDalIT.java

@@ -0,0 +1,50 @@
+package org.opencds.cqf.ruler.cql;
+
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.rest.param.UriParam;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Library;
+import org.junit.jupiter.api.Test;
+import org.opencds.cqf.cql.evaluator.fhir.util.Canonicals;
+import org.opencds.cqf.ruler.test.DaoIntegrationTest;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
+	classes = { JpaFhirDalIT.class, CqlConfig.class }, properties = { "hapi.fhir.fhir_version=r4" })
+public class JpaFhirDalIT extends DaoIntegrationTest {
+
+	@Autowired
+	private JpaFhirDalFactory fhirDalFactory;
+
+	@Test
+	void testFhirDalSearch() throws Exception {
+		JpaFhirDal fhirDal = new JpaFhirDal(this.getDaoRegistry());
+
+		String url = "http://somewhere.org/fhir/Library/SpecificationLibrary";
+		this.update(newResource(Library.class, "A123").setUrl(url));
+		this.update(newResource(Library.class, "A234").setUrl(url));
+
+		Map<String, List<List<IQueryParameterType>>> searchParams = new HashMap<>();
+
+		List<IQueryParameterType> urlList = new ArrayList<>();
+		urlList.add(new UriParam(Canonicals.getUrl(url)));
+		searchParams.put("url", List.of(urlList));
+
+		IBaseBundle searchResultsBundle = (IBaseBundle)fhirDal.search(Canonicals.getResourceType(url), searchParams);
+
+		assertNotNull(searchResultsBundle);
+		assertTrue(((Bundle)searchResultsBundle).getEntry().size() == 2);
+		assertTrue(((Bundle)searchResultsBundle).getType() == Bundle.BundleType.SEARCHSET);
+		assertTrue(((Library)((Bundle)searchResultsBundle).getEntryFirstRep().getResource()).getUrl().equals(url));
+	}
+}

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/CrConfig.java

@@ -2,6 +2,7 @@
 
 import java.util.function.Function;
 
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
 import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
 import org.opencds.cqf.external.annotations.OnDSTU3Condition;
@@ -36,6 +37,11 @@ SearchParameterResolver searchParameterResolver(FhirContext fhirContext) {
 		return new SearchParameterResolver(fhirContext);
 	}
 
+	@Bean
+	JpaCRFhirDalFactory jpaCRFhirDalFactory(DaoRegistry daoRegistry) {
+		return rd -> new JpaCRFhirDal(daoRegistry, rd);
+	}
+
 	@Bean
 	@Conditional(OnDSTU3Condition.class)
 	public org.opencds.cqf.ruler.cr.dstu3.provider.ActivityDefinitionApplyProvider dstu3ActivityDefinitionApplyProvider() {

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/JpaCRFhirDal.java

@@ -0,0 +1,60 @@
+package org.opencds.cqf.ruler.cr;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal;
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.UriParam;
+
+@SuppressWarnings("unchecked")
+public class JpaCRFhirDal implements FhirDal {
+
+	protected final DaoRegistry daoRegistry;
+	protected final RequestDetails requestDetails;
+
+	public JpaCRFhirDal(DaoRegistry daoRegistry) {
+		this(daoRegistry, null);
+	}
+
+	public JpaCRFhirDal(DaoRegistry daoRegistry, RequestDetails requestDetails) {
+		this.daoRegistry = daoRegistry;
+		this.requestDetails = requestDetails;
+	}
+
+	@Override
+	public void create(IBaseResource theResource) {
+		this.daoRegistry.getResourceDao(theResource.fhirType()).create(theResource, requestDetails);
+	}
+
+	@Override
+	public IBaseResource read(IIdType theId) {
+		return this.daoRegistry.getResourceDao(theId.getResourceType()).read(theId, requestDetails);
+	}
+
+	@Override
+	public void update(IBaseResource theResource) {
+		this.daoRegistry.getResourceDao(theResource.fhirType()).update(theResource, requestDetails);
+	}
+
+	@Override
+	public void delete(IIdType theId) {
+		this.daoRegistry.getResourceDao(theId.getResourceType()).delete(theId, requestDetails);
+
+	}
+
+	// TODO: the search interfaces need some work
+	@Override
+	public Iterable<IBaseResource> search(String theResourceType) {
+		return this.daoRegistry.getResourceDao(theResourceType).search(SearchParameterMap.newSynchronous())
+				.getAllResources();
+	}
+
+	@Override
+	public Iterable<IBaseResource> searchByUrl(String theResourceType, String theUrl) {
+		return this.daoRegistry.getResourceDao(theResourceType)
+				.search(SearchParameterMap.newSynchronous().add("url", new UriParam(theUrl))).getAllResources();
+	}
+}

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/JpaCRFhirDalFactory.java

@@ -0,0 +1,7 @@
+package org.opencds.cqf.ruler.cr;
+
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+
+public interface JpaCRFhirDalFactory {
+	JpaCRFhirDal create(RequestDetails requestDetails);
+}

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/dstu3/ExpressionEvaluation.java

@@ -25,8 +25,8 @@
 import org.opencds.cqf.cql.evaluator.cql2elm.content.InMemoryLibrarySourceProvider;
 import org.opencds.cqf.ruler.cql.CqlProperties;
 import org.opencds.cqf.ruler.cql.JpaDataProviderFactory;
-import org.opencds.cqf.ruler.cql.JpaFhirDal;
-import org.opencds.cqf.ruler.cql.JpaFhirDalFactory;
+import org.opencds.cqf.ruler.cr.JpaCRFhirDal;
+import org.opencds.cqf.ruler.cr.JpaCRFhirDalFactory;
 import org.opencds.cqf.ruler.cql.JpaLibrarySourceProviderFactory;
 import org.opencds.cqf.ruler.cql.JpaTerminologyProviderFactory;
 import org.opencds.cqf.ruler.cql.LibraryLoaderFactory;
@@ -47,7 +47,7 @@ public class ExpressionEvaluation {
 	@Autowired
 	private JpaTerminologyProviderFactory jpaTerminologyProviderFactory;
 	@Autowired
-	private JpaFhirDalFactory jpaFhirDalFactory;
+	private JpaCRFhirDalFactory jpaCRFhirDalFactory;
 	@Autowired
 	private CqlProperties cqlProperties;
 	@Autowired
@@ -60,8 +60,8 @@ public class ExpressionEvaluation {
 	 */
 	public Object evaluateInContext(DomainResource instance, String cql, Boolean aliasedExpression, String patientId,
 			RequestDetails theRequest) {
-		JpaFhirDal jpaFhirDal = jpaFhirDalFactory.create(theRequest);
-		List<Reference> libraries = getLibraryReferences(instance, jpaFhirDal, theRequest);
+		JpaCRFhirDal jpaCRFhirDal = jpaCRFhirDalFactory.create(theRequest);
+		List<Reference> libraries = getLibraryReferences(instance, jpaCRFhirDal, theRequest);
 		// String fhirVersion =
 		// this.context.getVersion().getVersion().getFhirVersionString();
 		String fhirVersion = "3.0.0";
@@ -90,7 +90,7 @@ public Object evaluateInContext(DomainResource instance, String cql, Boolean ali
 				// log error
 			}
 			if (executionLibrary == null) {
-				Library library = (Library) jpaFhirDal.read(new IdType("Library", vi.getId()));
+				Library library = (Library) jpaCRFhirDal.read(new IdType("Library", vi.getId()));
 				vi.setId(library.getName());
 				if (library.getVersion() != null) {
 					vi.setVersion(library.getVersion());
@@ -104,7 +104,7 @@ public Object evaluateInContext(DomainResource instance, String cql, Boolean ali
 					"library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '"
 							+ fhirVersion
 							+ "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s",
-					buildIncludes(tempLibraryLoader, jpaFhirDal, libraries), instance.fhirType(), instance.fhirType(),
+					buildIncludes(tempLibraryLoader, jpaCRFhirDal, libraries), instance.fhirType(), instance.fhirType(),
 					instance.fhirType(), vi.getId() + ".\"" + cql + "\"");
 			// String source = String.format("library LocalLibrary using FHIR version '1.8'
 			// include FHIRHelpers version '1.8' called FHIRHelpers %s parameter %s %s
@@ -120,7 +120,7 @@ public Object evaluateInContext(DomainResource instance, String cql, Boolean ali
 					"library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '"
 							+ fhirVersion
 							+ "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s",
-					buildIncludes(tempLibraryLoader, jpaFhirDal, libraries), instance.fhirType(), instance.fhirType(),
+					buildIncludes(tempLibraryLoader, jpaCRFhirDal, libraries), instance.fhirType(), instance.fhirType(),
 					instance.fhirType(), cql);
 		}
 
@@ -149,15 +149,15 @@ public Object evaluateInContext(DomainResource instance, String cql, Boolean ali
 		return context.resolveExpressionRef("Expression").evaluate(context);
 	}
 
-	private List<Reference> getLibraryReferences(DomainResource instance, JpaFhirDal jpaFhirDal,
+	private List<Reference> getLibraryReferences(DomainResource instance, JpaCRFhirDal jpaCRFhirDal,
 			RequestDetails theRequest) {
 		List<Reference> references = new ArrayList<>();
 
 		if (instance.hasContained()) {
 			for (Resource resource : instance.getContained()) {
 				if (resource instanceof Library) {
 					resource.setId(resource.getIdElement().getIdPart().replace("#", ""));
-					jpaFhirDal.update((Library) resource);
+					jpaCRFhirDal.update((Library) resource);
 					// getLibraryLoader().putLibrary(resource.getIdElement().getIdPart(),
 					// getLibraryLoader().toElmLibrary((Library) resource));
 				}
@@ -192,7 +192,7 @@ else if (instance instanceof Measure) {
 		return cleanReferences(references);
 	}
 
-	private String buildIncludes(LibraryLoader libraryLoader, JpaFhirDal jpaFhirDal, Iterable<Reference> references) {
+	private String buildIncludes(LibraryLoader libraryLoader, JpaCRFhirDal jpaCRFhirDal, Iterable<Reference> references) {
 		StringBuilder builder = new StringBuilder();
 		for (Reference reference : references) {
 			VersionedIdentifier vi = getVersionedIdentifierFromReference(reference);
@@ -212,7 +212,7 @@ private String buildIncludes(LibraryLoader libraryLoader, JpaFhirDal jpaFhirDal,
 			}
 			// else check local data for Library to get name and version from
 			else {
-				Library library = (Library) jpaFhirDal.read(reference.getReferenceElement());
+				Library library = (Library) jpaCRFhirDal.read(reference.getReferenceElement());
 				builder.append(buildLibraryIncludeString(reference, library.getName(), library.getVersion()));
 			}
 		}

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/dstu3/service/MeasureService.java

@@ -20,7 +20,7 @@
 import org.opencds.cqf.cql.evaluator.measure.MeasureEvaluationOptions;
 import org.opencds.cqf.ruler.behavior.DaoRegistryUser;
 import org.opencds.cqf.ruler.cql.JpaDataProviderFactory;
-import org.opencds.cqf.ruler.cql.JpaFhirDalFactory;
+import org.opencds.cqf.ruler.cr.JpaCRFhirDalFactory;
 import org.opencds.cqf.ruler.cql.JpaLibrarySourceProviderFactory;
 import org.opencds.cqf.ruler.cql.JpaTerminologyProviderFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -44,7 +44,7 @@ public class MeasureService implements DaoRegistryUser {
 	private JpaLibrarySourceProviderFactory libraryContentProviderFactory;
 
 	@Autowired
-	private JpaFhirDalFactory fhirDalFactory;
+	private JpaCRFhirDalFactory fhirDalFactory;
 
 	@Autowired
 	private Map<org.cqframework.cql.elm.execution.VersionedIdentifier, org.cqframework.cql.elm.execution.Library> globalLibraryCache;