More loinc work

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java

@@ -36,32 +36,39 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.primitive.StringDt;
 
 /**
- * Utilities for dealing with parameters resources
+ * Utilities for dealing with parameters resources in a version indepenedent way
  */
 public class ParametersUtil {
 
-	public static void addParameterToParameters(FhirContext theContext, IBaseResource theTargetResource, Object sourceClientArgument, String theName) {
+	/**
-		RuntimeResourceDefinition def = theContext.getResourceDefinition(theTargetResource);
+	 * Add a paratemer value to a Parameters resource
+	 * @param theContext The FhirContext
+	 * @param theParameters The Parameters resource
+	 * @param theName The parametr name
+	 * @param theValue The parameter value (can be a {@link IBaseResource resource} or a {@link IBaseDatatype datatype})
+	 */
+	public static void addParameterToParameters(FhirContext theContext, IBaseParameters theParameters, String theName, Object theValue) {
+		RuntimeResourceDefinition def = theContext.getResourceDefinition(theParameters);
 		BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
 		BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
 
-		addClientParameter(theContext, sourceClientArgument, theTargetResource, paramChild, paramChildElem, theName);
+		addClientParameter(theContext, theValue, theParameters, paramChild, paramChildElem, theName);
 	}
 
-	private static void addClientParameter(FhirContext theContext, Object theSourceClientArgument, IBaseResource theTargetResource, BaseRuntimeChildDefinition paramChild, BaseRuntimeElementCompositeDefinition<?> paramChildElem, String theName) {
+	private static void addClientParameter(FhirContext theContext, Object theValue, IBaseResource theTargetResource, BaseRuntimeChildDefinition paramChild, BaseRuntimeElementCompositeDefinition<?> paramChildElem, String theName) {
-		if (theSourceClientArgument instanceof IBaseResource) {
+		if (theValue instanceof IBaseResource) {
 			IBase parameter = createParameterRepetition(theContext, theTargetResource, paramChild, paramChildElem, theName);
-			paramChildElem.getChildByName("resource").getMutator().addValue(parameter, (IBaseResource) theSourceClientArgument);
+			paramChildElem.getChildByName("resource").getMutator().addValue(parameter, (IBaseResource) theValue);
-		} else if (theSourceClientArgument instanceof IBaseDatatype) {
+		} else if (theValue instanceof IBaseDatatype) {
 			IBase parameter = createParameterRepetition(theContext, theTargetResource, paramChild, paramChildElem, theName);
-			paramChildElem.getChildByName("value[x]").getMutator().addValue(parameter, (IBaseDatatype) theSourceClientArgument);
+			paramChildElem.getChildByName("value[x]").getMutator().addValue(parameter, (IBaseDatatype) theValue);
-		} else if (theSourceClientArgument instanceof Collection) {
+		} else if (theValue instanceof Collection) {
-			Collection<?> collection = (Collection<?>) theSourceClientArgument;
+			Collection<?> collection = (Collection<?>) theValue;
 			for (Object next : collection) {
 				addClientParameter(theContext, next, theTargetResource, paramChild, paramChildElem, theName);
 			}
 		} else {
-			throw new IllegalArgumentException("Don't know how to handle value of type " + theSourceClientArgument.getClass() + " for paramater " + theName);
+			throw new IllegalArgumentException("Don't know how to handle value of type " + theValue.getClass() + " for paramater " + theName);
 		}
 	}
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/GenericClient.java

@@ -914,11 +914,11 @@ public class GenericClient extends BaseClient implements IGenericClient {
 			IBaseParameters parameters = ParametersUtil.newInstance(myContext);
 			switch (myOperation) {
 			case ADD:
-				ParametersUtil.addParameterToParameters(myContext, parameters, myMeta, "meta");
+				ParametersUtil.addParameterToParameters(myContext, parameters, "meta", myMeta);
 				invocation = OperationMethodBinding.createOperationInvocation(myContext, myId.getResourceType(), myId.getIdPart(), "$meta-add", parameters, false);
 				break;
 			case DELETE:
-				ParametersUtil.addParameterToParameters(myContext, parameters, myMeta, "meta");
+				ParametersUtil.addParameterToParameters(myContext, parameters, "meta", myMeta);
 				invocation = OperationMethodBinding.createOperationInvocation(myContext, myId.getResourceType(), myId.getIdPart(), "$meta-delete", parameters, false);
 				break;
 			case GET:

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/OperationParameter.java

@@ -29,6 +29,7 @@ import java.util.Map;
 
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
@@ -179,7 +180,7 @@ public class OperationParameter implements IParameter {
 			sourceClientArgument = myConverter.outgoingClient(sourceClientArgument);
 		}
 
-		ParametersUtil.addParameterToParameters(theContext, theTargetResource, sourceClientArgument, myName);
+		ParametersUtil.addParameterToParameters(theContext, (IBaseParameters) theTargetResource, myName, sourceClientArgument);
 	}
 
 

hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/ValidateMethodBindingDstu2Plus.java

@@ -70,7 +70,7 @@ public class ValidateMethodBindingDstu2Plus extends OperationMethodBinding {
 	
 	public static BaseHttpClientInvocation createValidateInvocation(FhirContext theContext, IBaseResource theResource) {
 		IBaseParameters parameters = (IBaseParameters) theContext.getResourceDefinition("Parameters").newInstance();
-		ParametersUtil.addParameterToParameters(theContext, parameters, theResource, "resource");
+		ParametersUtil.addParameterToParameters(theContext, parameters, "resource", theResource);
 		
 		String resourceName = theContext.getResourceDefinition(theResource).getName();
 		String resourceId = theResource.getIdElement().getIdPart();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoCodeSystem.java

@@ -1,7 +1,18 @@
 package ca.uhn.fhir.jpa.dao;
 
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.StringType;
+
 import java.util.List;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -21,9 +32,6 @@ import java.util.List;
  * limitations under the License.
  * #L%
  */
-import org.hl7.fhir.instance.model.api.*;
-
-import ca.uhn.fhir.rest.api.server.RequestDetails;
 
 public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> extends IFhirResourceDao<T> {
 
@@ -31,7 +39,8 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
 
 	LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CD theCoding, RequestDetails theRequestDetails);
 
-	public class LookupCodeResult {
+	class LookupCodeResult {
+
 		private String myCodeDisplay;
 		private boolean myCodeIsAbstract;
 		private String myCodeSystemDisplayName;
@@ -39,62 +48,87 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
 		private boolean myFound;
 		private String mySearchedForCode;
 		private String mySearchedForSystem;
+		/**
+		 * Constructor
+		 */
+		public LookupCodeResult() {
+			super();
+		}
 
 		public String getCodeDisplay() {
 			return myCodeDisplay;
 		}
 
-		public String getCodeSystemDisplayName() {
-			return myCodeSystemDisplayName;
-		}
-
-		public String getCodeSystemVersion() {
-			return myCodeSystemVersion;
-		}
-
-		public String getSearchedForCode() {
-			return mySearchedForCode;
-		}
-
-		public String getSearchedForSystem() {
-			return mySearchedForSystem;
-		}
-
-		public boolean isCodeIsAbstract() {
-			return myCodeIsAbstract;
-		}
-
-		public boolean isFound() {
-			return myFound;
-		}
-
 		public void setCodeDisplay(String theCodeDisplay) {
 			myCodeDisplay = theCodeDisplay;
 		}
 
-		public void setCodeIsAbstract(boolean theCodeIsAbstract) {
+		public String getCodeSystemDisplayName() {
-			myCodeIsAbstract = theCodeIsAbstract;
+			return myCodeSystemDisplayName;
 		}
 
 		public void setCodeSystemDisplayName(String theCodeSystemDisplayName) {
 			myCodeSystemDisplayName = theCodeSystemDisplayName;
 		}
 
+		public String getCodeSystemVersion() {
+			return myCodeSystemVersion;
+		}
+
 		public void setCodeSystemVersion(String theCodeSystemVersion) {
 			myCodeSystemVersion = theCodeSystemVersion;
 		}
 
-		public void setFound(boolean theFound) {
+		public String getSearchedForCode() {
-			myFound = theFound;
+			return mySearchedForCode;
 		}
 
 		public void setSearchedForCode(String theSearchedForCode) {
 			mySearchedForCode = theSearchedForCode;
 		}
 
+		public String getSearchedForSystem() {
+			return mySearchedForSystem;
+		}
+
 		public void setSearchedForSystem(String theSearchedForSystem) {
 			mySearchedForSystem = theSearchedForSystem;
 		}
+
+		public boolean isCodeIsAbstract() {
+			return myCodeIsAbstract;
+		}
+
+		public void setCodeIsAbstract(boolean theCodeIsAbstract) {
+			myCodeIsAbstract = theCodeIsAbstract;
+		}
+
+		public boolean isFound() {
+			return myFound;
+		}
+
+		public void setFound(boolean theFound) {
+			myFound = theFound;
+		}
+
+		public void throwNotFoundIfAppropriate() {
+			if (isFound() == false) {
+				throw new ResourceNotFoundException("Unable to find code[" + getSearchedForCode() + "] in system[" + getSearchedForSystem() + "]");
+			}
+		}
+
+		public Parameters toParameters() {
+			Parameters retVal = new Parameters();
+
+			retVal.addParameter().setName("name").setValue(new StringType(getCodeSystemDisplayName()));
+			if (isNotBlank(getCodeSystemVersion())) {
+				retVal.addParameter().setName("version").setValue(new StringType(getCodeSystemVersion()));
+			}
+			retVal.addParameter().setName("display").setValue(new StringType(getCodeDisplay()));
+			retVal.addParameter().setName("abstract").setValue(new BooleanType(isCodeIsAbstract()));
+
+			return retVal;
+		}
 	}
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java

@@ -225,20 +225,13 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
 			} else if (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == null) {
 				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", retVal.getIdDt().getValue(), cs.getContentElement().getValueAsString());
 
-				TermCodeSystemVersion persCs = myCsvDao.findByCodeSystemResourceAndVersion(codeSystemResourcePid, retVal.getVersion());
+				TermCodeSystemVersion persCs = new TermCodeSystemVersion();
-				if (persCs != null) {
-					ourLog.info("Code system version already exists in database");
-				} else {
-
-					persCs = new TermCodeSystemVersion();
 				persCs.setResource(retVal);
 				persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
 				ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
 				myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, persCs);
 
 			}
-
-			}
 		}
 
 		return retVal;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java

@@ -219,7 +219,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
 				ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", retVal.getIdDt().getValue(), cs.getContentElement().getValueAsString());
 
 				Long codeSystemResourcePid = retVal.getId();
-				TermCodeSystemVersion persCs = myCsvDao.findByCodeSystemResourceAndVersion(codeSystemResourcePid, retVal.getVersion());
+				TermCodeSystemVersion persCs = myCsvDao.findCurrentVersionForCodeSystemResourcePid(codeSystemResourcePid);
 				if (persCs != null) {
 					ourLog.info("Code system version already exists in database");
 				} else {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProviderDstu2Plus.java

@@ -39,7 +39,7 @@ public abstract class BaseJpaSystemProviderDstu2Plus<T, MT> extends BaseJpaSyste
 		IBaseParameters retVal = ParametersUtil.newInstance(getContext());
 		
 		IPrimitiveType<?> string = ParametersUtil.createString(getContext(), "Marked " + count + " resources");
-		ParametersUtil.addParameterToParameters(getContext(), retVal, string, "status");
+		ParametersUtil.addParameterToParameters(getContext(), retVal, "status", string);
 
 		return retVal;
 	}
@@ -58,7 +58,7 @@ public abstract class BaseJpaSystemProviderDstu2Plus<T, MT> extends BaseJpaSyste
 		} else {
 			string = ParametersUtil.createString(getContext(), "Indexed " + count + " resources");
 		}
-		ParametersUtil.addParameterToParameters(getContext(), retVal, string, "status");
+		ParametersUtil.addParameterToParameters(getContext(), retVal, "status", string);
 
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCodeSystemDstu3.java

@@ -24,6 +24,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
 import org.hl7.fhir.dstu3.model.*;
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
@@ -32,6 +34,7 @@ import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import org.hl7.fhir.exceptions.FHIRException;
 
 public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderDstu3<CodeSystem> {
 
@@ -56,17 +59,11 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
 			LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
-			if (result.isFound()==false) {
+			result.throwNotFoundIfAppropriate();
-				throw new ResourceNotFoundException("Unable to find code[" + result.getSearchedForCode() + "] in system[" + result.getSearchedForSystem() + "]");
+			org.hl7.fhir.r4.model.Parameters parametersR4 = result.toParameters();
-			}
+			return VersionConvertor_30_40.convertParameters(parametersR4);
-			Parameters retVal = new Parameters();
+		} catch (FHIRException e) {
-			retVal.addParameter().setName("name").setValue(new StringType(result.getCodeSystemDisplayName()));
+			throw new InternalErrorException(e);
-			if (isNotBlank(result.getCodeSystemVersion())) {
-				retVal.addParameter().setName("version").setValue(new StringType(result.getCodeSystemVersion()));
-			}
-			retVal.addParameter().setName("display").setValue(new StringType(result.getCodeDisplay()));
-			retVal.addParameter().setName("abstract").setValue(new BooleanType(result.isCodeIsAbstract()));			
-			return retVal;
 		} finally {
 			endRequest(theServletRequest);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java

@@ -56,17 +56,8 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
 		try {
 			IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
 			LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
-			if (result.isFound()==false) {
+			result.throwNotFoundIfAppropriate();
-				throw new ResourceNotFoundException("Unable to find code[" + result.getSearchedForCode() + "] in system[" + result.getSearchedForSystem() + "]");
+			return result.toParameters();
-			}
-			Parameters retVal = new Parameters();
-			retVal.addParameter().setName("name").setValue(new StringType(result.getCodeSystemDisplayName()));
-			if (isNotBlank(result.getCodeSystemVersion())) {
-				retVal.addParameter().setName("version").setValue(new StringType(result.getCodeSystemVersion()));
-			}
-			retVal.addParameter().setName("display").setValue(new StringType(result.getCodeDisplay()));
-			retVal.addParameter().setName("abstract").setValue(new BooleanType(result.isCodeIsAbstract()));			
-			return retVal;
 		} finally {
 			endRequest(theServletRequest);
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java

@@ -299,8 +299,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		}
 	}
 
-	private TermConcept fetchLoadedCode(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
+	private TermConcept fetchLoadedCode(Long theCodeSystemResourcePid, String theCode) {
-		TermCodeSystemVersion codeSystem = myCodeSystemVersionDao.findByCodeSystemResourceAndVersion(theCodeSystemResourcePid, theCodeSystemVersionPid);
+		TermCodeSystemVersion codeSystem = myCodeSystemVersionDao.findCurrentVersionForCodeSystemResourcePid(theCodeSystemResourcePid);
 		return myConceptDao.findByCodeSystemAndCode(codeSystem, theCode);
 	}
 
@@ -330,7 +330,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	public Set<TermConcept> findCodesAbove(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
 		StopWatch stopwatch = new StopWatch();
 
-		TermConcept concept = fetchLoadedCode(theCodeSystemResourcePid, theCodeSystemVersionPid, theCode);
+		TermConcept concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
 		if (concept == null) {
 			return Collections.emptySet();
 		}
@@ -361,7 +361,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
 		Stopwatch stopwatch = Stopwatch.createStarted();
 
-		TermConcept concept = fetchLoadedCode(theCodeSystemResourcePid, theCodeSystemVersionPid, theCode);
+		TermConcept concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
 		if (concept == null) {
 			return Collections.emptySet();
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincDocumentOntologyHandler.java

@@ -15,7 +15,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
 
 public class LoincDocumentOntologyHandler extends BaseHandler implements IRecordHandler {
 
-	public static final String DOCUMENT_ONTOLOGY_CODES_VS_ID = "DOCUMENT_ONTOLOGY_CODES_VS";
+	public static final String DOCUMENT_ONTOLOGY_CODES_VS_ID = "DOCUMENT-ONTOLOGY-CODES-VS";
 	public static final String DOCUMENT_ONTOLOGY_CODES_VS_URI = "http://loinc.org/document-ontology-codes";
 	public static final String DOCUMENT_ONTOLOGY_CODES_VS_NAME = "LOINC Document Ontology Codes";
 	private final Map<String, TermConcept> myCode2Concept;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincPartRelatedCodeMappingHandler.java

@@ -20,7 +20,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
 
 public class LoincPartRelatedCodeMappingHandler implements IRecordHandler {
 
-	public static final String LOINC_TO_SNOMED_CM_ID = "LOINC_TO_SNOMED_CM";
+	public static final String LOINC_TO_SNOMED_CM_ID = "LOINC-TO-SNOMED-CM";
 	private static final Logger ourLog = LoggerFactory.getLogger(LoincPartRelatedCodeMappingHandler.class);
 	private final Map<String, TermConcept> myCode2Concept;
 	private final TermCodeSystemVersion myCodeSystemVersion;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java

@@ -18,14 +18,14 @@ import static org.apache.commons.lang3.StringUtils.trim;
 
 public class LoincRsnaPlaybookHandler implements IRecordHandler {
 
-	public static final String RSNA_CODES_VS_ID = "RSNA_LOINC_CODES_VS";
+	public static final String RSNA_CODES_VS_ID = "RSNA-LOINC-CODES-VS";
 	public static final String RSNA_CODES_VS_URI = "http://loinc.org/rsna-codes";
 	public static final String RSNA_CODES_VS_NAME = "RSNA Playbook";
-	public static final String RID_MAPPING_CM_ID = "LOINC_TO_RID_CODES_CM";
+	public static final String RID_MAPPING_CM_ID = "LOINC-TO-RID-CODES-CM";
 	public static final String RID_MAPPING_CM_URI = "http://loinc.org/rid-codes";
 	public static final String RID_MAPPING_CM_NAME = "RSNA Playbook RID Codes Mapping";
 	public static final String RID_CS_URI = "http://rid";
-	public static final String RPID_MAPPING_CM_ID = "LOINC_TO_RPID_CODES_CM";
+	public static final String RPID_MAPPING_CM_ID = "LOINC-TO-RPID-CODES-CM";
 	public static final String RPID_MAPPING_CM_URI = "http://loinc.org/rpid-codes";
 	public static final String RPID_MAPPING_CM_NAME = "RSNA Playbook RPID Codes Mapping";
 	public static final String RPID_CS_URI = "http://rpid";

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincTop2000LabResultsSiHandler.java

@@ -8,7 +8,7 @@ import java.util.Map;
 
 public class LoincTop2000LabResultsSiHandler extends BaseLoincTop2000LabResultsHandler {
 
-	public static final String TOP_2000_SI_VS_ID = "TOP_2000_SI_VS_ID";
+	public static final String TOP_2000_SI_VS_ID = "TOP-2000-LABRESULTS-SI";
 	public static final String TOP_2000_SI_VS_URI = "http://loinc.org/top-2000-lab-results-si";
 	public static final String TOP_2000_SI_VS_NAME = "Top 2000 Lab Results SI";
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincTop2000LabResultsUsHandler.java

@@ -8,7 +8,7 @@ import java.util.Map;
 
 public class LoincTop2000LabResultsUsHandler extends BaseLoincTop2000LabResultsHandler {
 
-	public static final String TOP_2000_US_VS_ID = "TOP_2000_LABRESULTS_US";
+	public static final String TOP_2000_US_VS_ID = "TOP-2000-LABRESULTS-US";
 	public static final String TOP_2000_US_VS_URI = "http://loinc.org/top-2000-lab-results-us";
 	public static final String TOP_2000_US_VS_NAME = "Top 2000 Lab Results US";
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationDstu3Test.java

@@ -1,34 +1,92 @@
 package ca.uhn.fhir.jpa.term;
 
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
 import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
 import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.convertors.VersionConvertor_30_40;
+import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.dstu3.model.ValueSet;
+import org.hl7.fhir.dstu3.model.Parameters;
+import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import java.io.IOException;
+import java.util.ArrayList;
-import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.assertThat;
 
 public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
 
+	private static final Logger ourLog = LoggerFactory.getLogger(TerminologyLoaderSvcIntegrationDstu3Test.class);
+
 	@Autowired
-	private TerminologyLoaderSvcImpl myLoader;
+	private IHapiTerminologyLoaderSvc myLoader;
+
+	@After
+	public void after() {
+		myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
+	}
+
+	@Before
+	public void before() {
+		myDaoConfig.setDeferIndexingForCodesystemsOfSize(20000);
+	}
+
+	@Test
+	public void testExpandWithProperty() throws Exception {
+		ZipCollectionBuilder files = new ZipCollectionBuilder();
+		TerminologyLoaderSvcLoincTest.createLoincBundle(files);
+		myLoader.loadLoinc(files.getFiles(), mySrd);
+
+		ValueSet input = new ValueSet();
+		input
+			.getCompose()
+			.addInclude()
+			.setSystem(IHapiTerminologyLoaderSvc.LOINC_URL)
+			.addFilter()
+			.setProperty("SCALE_TYP")
+			.setOp(ValueSet.FilterOperator.EQUAL)
+			.setValue("Ord");
+		ValueSet expanded = myValueSetDao.expand(input, null);
+		Set<String> codes = toExpandedCodes(expanded);
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded));
+		assertThat(codes, containsInAnyOrder("1001-7", "61438-8"));
+	}
+
+	@Test
+	public void testLookupWithProperties() throws Exception {
+		ZipCollectionBuilder files = new ZipCollectionBuilder();
+		TerminologyLoaderSvcLoincTest.createLoincBundle(files);
+		myLoader.loadLoinc(files.getFiles(), mySrd);
+
+		IFhirResourceDaoCodeSystem.LookupCodeResult result = myCodeSystemDao.lookupCode(new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URL), null, mySrd);
+		org.hl7.fhir.r4.model.Parameters parametersR4 = result.toParameters();
+		Parameters parameters = VersionConvertor_30_40.convertParameters(parametersR4);
+
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parameters));
+	}
+
+	private Set<String> toExpandedCodes(ValueSet theExpanded) {
+		return theExpanded
+			.getExpansion()
+			.getContains()
+			.stream()
+			.map(ValueSet.ValueSetExpansionContainsComponent::getCode)
+			.collect(Collectors.toSet());
+	}
 
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();
 	}
 
-	@Test
-	public void testLoadAndStoreLoinc() throws Exception {
-		ZipCollectionBuilder files = new ZipCollectionBuilder();
-		TerminologyLoaderSvcLoincTest.createLoincBundle(files);
-
-		myLoader.loadLoinc(files.getFiles(), mySrd);
-
-		Thread.sleep(120000);
-	}
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java

@@ -70,6 +70,15 @@ public class TerminologyLoaderSvcLoincTest {
 		mySvc.loadLoinc(myFiles.getFiles(), details);
 
 		verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		ValueSet input = new ValueSet();
+		input
+			.getCompose()
+			.addInclude()
+			.setSystem(IHapiTerminologyLoaderSvc.LOINC_URL)
+			.addFilter()
+			.setProperty("SCALE_TYP")
+			.setOp(ValueSet.FilterOperator.EQUAL)
+			.setValue("Ord");
 
 		TermCodeSystemVersion ver = myCsvCaptor.getValue();
 

pom.xml

@@ -1114,18 +1114,10 @@
 					<artifactId>maven-compiler-plugin</artifactId>
 					<version>3.7.0</version>
 					<configuration>
-						<source>1.7</source>
+						<source>1.8</source>
-						<target>1.7</target>
+						<target>1.8</target>
-						<!-- 
-						We compile the unit tests at Java 8. Might as well since they
-						need Java 8 in order to run (Jetty needs 8) so this way we can
-						use nice java 8 features in tests at least
-						-->
-						<testSource>1.8</testSource>
-						<testTarget>1.8</testTarget>
 						<forceJavacCompilerUse>true</forceJavacCompilerUse>
 						<encoding>UTF-8</encoding>
-
 						<fork>true</fork>
 						<meminitial>500m</meminitial>
 						<maxmem>2000m</maxmem>