Merge branch 'master' of github.com:jamesagnew/hapi-fhir

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/BaseClient.java

@@ -323,13 +323,24 @@ public abstract class BaseClient implements IRestfulClient {
 			}
 
 		} catch (DataFormatException e) {
-			//FIXME potential null access on httpResquest
+			String msg;
-			String msg = getFhirContext().getLocalizer().getMessage(BaseClient.class, "failedToParseResponse", httpRequest.getHttpVerbName(), httpRequest.getUri(), e.toString());
+			if ( httpRequest != null ) {
+				msg = getFhirContext().getLocalizer().getMessage(BaseClient.class, "failedToParseResponse", httpRequest.getHttpVerbName(), httpRequest.getUri(), e.toString());
+			}
+			else {
+				msg = getFhirContext().getLocalizer().getMessage(BaseClient.class, "failedToParseResponse", "UNKNOWN", "UNKNOWN", e.toString());
+			}
 			throw new FhirClientConnectionException(msg, e);
 		} catch (IllegalStateException e) {
 			throw new FhirClientConnectionException(e);
 		} catch (IOException e) {
-			String msg = getFhirContext().getLocalizer().getMessage(BaseClient.class, "ioExceptionDuringOperation", httpRequest.getHttpVerbName(), httpRequest.getUri(), e.toString());
+			String msg;
+			if ( httpRequest != null ) {
+				msg = getFhirContext().getLocalizer().getMessage(BaseClient.class, "failedToParseResponse", httpRequest.getHttpVerbName(), httpRequest.getUri(), e.toString());
+			}
+			else {
+				msg = getFhirContext().getLocalizer().getMessage(BaseClient.class, "failedToParseResponse", "UNKNOWN", "UNKNOWN", e.toString());
+			}
 			throw new FhirClientConnectionException(msg, e);
 		} catch (RuntimeException e) {
 			throw e;

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

@@ -479,30 +479,36 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(theResource);
 		if (tagList != null) {
 			for (Tag next : tagList) {
-				TagDefinition tag = getTag(TagTypeEnum.TAG, next.getScheme(), next.getTerm(), next.getLabel());
+				TagDefinition tag = getTagOrNull(TagTypeEnum.TAG, next.getScheme(), next.getTerm(), next.getLabel());
-				allDefs.add(tag);
+				if (tag != null) {
-				theEntity.addTag(tag);
+					allDefs.add(tag);
-				theEntity.setHasTags(true);
+					theEntity.addTag(tag);
+					theEntity.setHasTags(true);
+				}
 			}
 		}
 
 		List<BaseCodingDt> securityLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(theResource);
 		if (securityLabels != null) {
 			for (BaseCodingDt next : securityLabels) {
-				TagDefinition tag = getTag(TagTypeEnum.SECURITY_LABEL, next.getSystemElement().getValue(), next.getCodeElement().getValue(), next.getDisplayElement().getValue());
+				TagDefinition tag = getTagOrNull(TagTypeEnum.SECURITY_LABEL, next.getSystemElement().getValue(), next.getCodeElement().getValue(), next.getDisplayElement().getValue());
-				allDefs.add(tag);
+				if (tag != null) {
-				theEntity.addTag(tag);
+					allDefs.add(tag);
-				theEntity.setHasTags(true);
+					theEntity.addTag(tag);
+					theEntity.setHasTags(true);
+				}
 			}
 		}
 
 		List<IdDt> profiles = ResourceMetadataKeyEnum.PROFILES.get(theResource);
 		if (profiles != null) {
 			for (IIdType next : profiles) {
-				TagDefinition tag = getTag(TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null);
+				TagDefinition tag = getTagOrNull(TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null);
-				allDefs.add(tag);
+				if (tag != null) {
-				theEntity.addTag(tag);
+					allDefs.add(tag);
-				theEntity.setHasTags(true);
+					theEntity.addTag(tag);
+					theEntity.setHasTags(true);
+				}
 			}
 		}
 	}
@@ -511,30 +517,36 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		List<? extends IBaseCoding> tagList = theResource.getMeta().getTag();
 		if (tagList != null) {
 			for (IBaseCoding next : tagList) {
-				TagDefinition tag = getTag(TagTypeEnum.TAG, next.getSystem(), next.getCode(), next.getDisplay());
+				TagDefinition tag = getTagOrNull(TagTypeEnum.TAG, next.getSystem(), next.getCode(), next.getDisplay());
-				allDefs.add(tag);
+				if (tag != null) {
-				theEntity.addTag(tag);
+					allDefs.add(tag);
-				theEntity.setHasTags(true);
+					theEntity.addTag(tag);
+					theEntity.setHasTags(true);
+				}
 			}
 		}
 
 		List<? extends IBaseCoding> securityLabels = theResource.getMeta().getSecurity();
 		if (securityLabels != null) {
 			for (IBaseCoding next : securityLabels) {
-				TagDefinition tag = getTag(TagTypeEnum.SECURITY_LABEL, next.getSystem(), next.getCode(), next.getDisplay());
+				TagDefinition tag = getTagOrNull(TagTypeEnum.SECURITY_LABEL, next.getSystem(), next.getCode(), next.getDisplay());
-				allDefs.add(tag);
+				if (tag != null) {
-				theEntity.addTag(tag);
+					allDefs.add(tag);
-				theEntity.setHasTags(true);
+					theEntity.addTag(tag);
+					theEntity.setHasTags(true);
+				}
 			}
 		}
 
 		List<? extends IPrimitiveType<String>> profiles = theResource.getMeta().getProfile();
 		if (profiles != null) {
 			for (IPrimitiveType<String> next : profiles) {
-				TagDefinition tag = getTag(TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null);
+				TagDefinition tag = getTagOrNull(TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null);
-				allDefs.add(tag);
+				if (tag != null) {
-				theEntity.addTag(tag);
+					allDefs.add(tag);
-				theEntity.setHasTags(true);
+					theEntity.addTag(tag);
+					theEntity.setHasTags(true);
+				}
 			}
 		}
 	}
@@ -662,28 +674,28 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return mySearchParamRegistry.getActiveSearchParams(theResourceDef.getName()).values();
 	}
 
-	protected TagDefinition getTag(TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {
+	protected TagDefinition getTagOrNull(TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {
+		if (isBlank(theScheme) && isBlank(theTerm) && isBlank(theLabel)) {
+			return null;
+		}
+		
 		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
 		CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
 		Root<TagDefinition> from = cq.from(TagDefinition.class);
 
-		//@formatter:off
 		if (isNotBlank(theScheme)) {
 			cq.where(
-				builder.and(
+					builder.and(
-					builder.equal(from.get("myTagType"), theTagType), 
+							builder.equal(from.get("myTagType"), theTagType),
-					builder.equal(from.get("mySystem"), theScheme), 
+							builder.equal(from.get("mySystem"), theScheme),
-					builder.equal(from.get("myCode"), theTerm))
+							builder.equal(from.get("myCode"), theTerm)));
-				);
 		} else {
 			cq.where(
-				builder.and(
+					builder.and(
-					builder.equal(from.get("myTagType"), theTagType), 
+							builder.equal(from.get("myTagType"), theTagType),
-					builder.isNull(from.get("mySystem")), 
+							builder.isNull(from.get("mySystem")),
-					builder.equal(from.get("myCode"), theTerm))
+							builder.equal(from.get("myCode"), theTerm)));
-				);
 		}
-		//@formatter:on
 
 		TypedQuery<TagDefinition> q = myEntityManager.createQuery(cq);
 		try {
@@ -938,10 +950,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		if (def.isStandardType() == false) {
 			String profile = def.getResourceProfile("");
 			if (isNotBlank(profile)) {
-				TagDefinition tag = getTag(TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
+				TagDefinition tag = getTagOrNull(TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
-				allDefs.add(tag);
+				if (tag != null) {
-				theEntity.addTag(tag);
+					allDefs.add(tag);
-				theEntity.setHasTags(true);
+					theEntity.addTag(tag);
+					theEntity.setHasTags(true);
+				}
 			}
 		}
 
@@ -1151,7 +1165,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		if (dao == null) {
 			throw new InternalErrorException("No DAO for resource type: " + theResourceType.getName());
 		}
-		
+
 		Set<Long> ids = dao.searchForIds(paramMap);
 
 		return ids;

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

@@ -114,12 +114,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		entity.setHasTags(true);
 
-		TagDefinition def = getTag(TagTypeEnum.TAG, theScheme, theTerm, theLabel);
+		TagDefinition def = getTagOrNull(TagTypeEnum.TAG, theScheme, theTerm, theLabel);
-		BaseTag newEntity = entity.addTag(def);
+		if (def != null) {
-
+			BaseTag newEntity = entity.addTag(def);
-		myEntityManager.persist(newEntity);
+	
-		myEntityManager.merge(entity);
+			myEntityManager.persist(newEntity);
-
+			myEntityManager.merge(entity);
+		}
+		
 		ourLog.info("Processed addTag {}/{} on {} in {}ms", new Object[] { theScheme, theTerm, theId, w.getMillisAndRestart() });
 	}
 	
@@ -439,9 +441,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 			if (!hasTag) {
 				entity.setHasTags(true);
 				
-				TagDefinition def = getTag(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay());
+				TagDefinition def = getTagOrNull(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay());
-				BaseTag newEntity = entity.addTag(def);
+				if (def != null) {
-				myEntityManager.persist(newEntity);
+					BaseTag newEntity = entity.addTag(def);
+					myEntityManager.persist(newEntity);
+				}
 			}
 		}
 		//@formatter:on

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

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2017 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.springframework.data.jpa.repository.JpaRepository;
+
+import ca.uhn.fhir.jpa.entity.ResourceTag;
+
+public interface IResourceTagDao extends JpaRepository<ResourceTag, Long> {
+	// nothing
+}

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

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2017 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.springframework.data.jpa.repository.JpaRepository;
+
+import ca.uhn.fhir.jpa.entity.TagDefinition;
+
+public interface ITagDefinitionDao extends JpaRepository<TagDefinition, Long> {
+	// nothing
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -77,8 +77,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
 import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
-import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.dao.data.*;
-import ca.uhn.fhir.jpa.dao.data.ISearchDao;
 import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
@@ -105,6 +104,10 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
+	@Autowired
+	protected ITagDefinitionDao myTagDefinitionDao;
+	@Autowired
+	protected IResourceTagDao myResourceTagDao;	
 	@Autowired
 	protected ISearchDao mySearchEntityDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -8,6 +8,7 @@ import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.endsWith;
 import static org.hamcrest.Matchers.greaterThan;
 import static org.hamcrest.Matchers.hasItem;
+import static org.hamcrest.Matchers.hasSize;
 import static org.hamcrest.Matchers.matchesPattern;
 import static org.hamcrest.Matchers.not;
 import static org.junit.Assert.assertEquals;
@@ -154,6 +155,56 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		}
 	}
 
+	@Test
+	public void testCreateDuplicateTagsDoesNotCauseDuplicates() {
+		Patient p = new Patient();
+		p.setActive(true);
+		
+		p.getMeta().addTag().setSystem("FOO").setCode("BAR");
+		p.getMeta().addTag().setSystem("FOO").setCode("BAR");
+		p.getMeta().addTag().setSystem("FOO").setCode("BAR");
+		p.getMeta().addTag().setSystem("FOO").setCode("BAR");
+		p.getMeta().addTag().setSystem("FOO").setCode("BAR");
+		p.getMeta().addTag().setSystem("FOO").setCode("BAR");
+		p.getMeta().addTag().setSystem("FOO").setCode("BAR");
+		
+		myPatientDao.create(p);
+		
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+				assertThat(myResourceTagDao.findAll(), hasSize(1));
+				assertThat(myTagDefinitionDao.findAll(), hasSize(1));
+			}
+		});
+		
+	}
+	
+	@Test
+	public void testCreateEmptyTagsIsIgnored() {
+		Patient p = new Patient();
+		p.setActive(true);
+		
+		// Add an empty tag
+		p.getMeta().addTag();
+		
+		// Add another empty tag
+		p.getMeta().addTag().setSystem("");
+		p.getMeta().addTag().setCode("");
+		p.getMeta().addTag().setDisplay("");
+		
+		myPatientDao.create(p);
+		
+		new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+			@Override
+			protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+				assertThat(myResourceTagDao.findAll(), empty());
+				assertThat(myTagDefinitionDao.findAll(), empty());
+			}
+		});
+		
+	}
+
 	/**
 	 * This gets called from assertGone too! Careful about exceptions...
 	 */

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/DefaultProfileValidationSupport.java

@@ -22,243 +22,245 @@ import ca.uhn.fhir.context.FhirContext;
 
 public class DefaultProfileValidationSupport implements IValidationSupport {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DefaultProfileValidationSupport.class);
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DefaultProfileValidationSupport.class);
 
-	private Map<String, CodeSystem> myCodeSystems;
+  private Map<String, CodeSystem> myCodeSystems;
-	private Map<String, StructureDefinition> myStructureDefinitions;
+  private Map<String, StructureDefinition> myStructureDefinitions;
-	private Map<String, ValueSet> myValueSets;
+  private Map<String, ValueSet> myValueSets;
 
-	@Override
+  @Override
-	public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
+  public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
-		ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
+    ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
 
-		Set<String> wantCodes = new HashSet<String>();
+    Set<String> wantCodes = new HashSet<String>();
-		for (ConceptReferenceComponent next : theInclude.getConcept()) {
+    for (ConceptReferenceComponent next : theInclude.getConcept()) {
-			wantCodes.add(next.getCode());
+      wantCodes.add(next.getCode());
-		}
+    }
 
-		CodeSystem system = fetchCodeSystem(theContext, theInclude.getSystem());
+    CodeSystem system = fetchCodeSystem(theContext, theInclude.getSystem());
-		for (ConceptDefinitionComponent next : system.getConcept()) {
+    for (ConceptDefinitionComponent next : system.getConcept()) {
-			if (wantCodes.isEmpty() || wantCodes.contains(next.getCode())) {
+      if (wantCodes.isEmpty() || wantCodes.contains(next.getCode())) {
-				retVal.addContains().setSystem(theInclude.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
+        retVal.addContains().setSystem(theInclude.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
-			}
+      }
-		}
+    }
 
-		return retVal;
+    return retVal;
-	}
+  }
 
-	@Override
+  @Override
-	public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
+  public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
-		return new ArrayList<StructureDefinition>(provideStructureDefinitionMap(theContext).values());
+    return new ArrayList<StructureDefinition>(provideStructureDefinitionMap(theContext).values());
-	}
+  }
 
-	@Override
+  @Override
-	public CodeSystem fetchCodeSystem(FhirContext theContext, String theSystem) {
+  public CodeSystem fetchCodeSystem(FhirContext theContext, String theSystem) {
-		return (CodeSystem) fetchCodeSystemOrValueSet(theContext, theSystem, true);
+    return (CodeSystem) fetchCodeSystemOrValueSet(theContext, theSystem, true);
-	}
+  }
 
-	private DomainResource fetchCodeSystemOrValueSet(FhirContext theContext, String theSystem, boolean codeSystem) {
+  private DomainResource fetchCodeSystemOrValueSet(FhirContext theContext, String theSystem, boolean codeSystem) {
-		Map<String, CodeSystem> codeSystems = myCodeSystems;
+    synchronized (this) {
-		Map<String, ValueSet> valueSets = myValueSets;
+      Map<String, CodeSystem> codeSystems = myCodeSystems;
-		if (codeSystems == null) {
+      Map<String, ValueSet> valueSets = myValueSets;
-			codeSystems = new HashMap<String, CodeSystem>();
+      if (codeSystems == null || valueSets == null) {
-			valueSets = new HashMap<String, ValueSet>();
+        codeSystems = new HashMap<String, CodeSystem>();
+        valueSets = new HashMap<String, ValueSet>();
 
-			loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/instance/model/dstu3/valueset/valuesets.xml");
+        loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/instance/model/dstu3/valueset/valuesets.xml");
-			loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/instance/model/dstu3/valueset/v2-tables.xml");
+        loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/instance/model/dstu3/valueset/v2-tables.xml");
-			loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/instance/model/dstu3/valueset/v3-codesystems.xml");
+        loadCodeSystems(theContext, codeSystems, valueSets, "/org/hl7/fhir/instance/model/dstu3/valueset/v3-codesystems.xml");
 
-			myCodeSystems = codeSystems;
+        myCodeSystems = codeSystems;
-			myValueSets = valueSets;
+        myValueSets = valueSets;
-		}
+      }
 
-		if (codeSystem) {
+      if (codeSystem) {
-			return codeSystems.get(theSystem);
+        return codeSystems.get(theSystem);
-		} else {
+      } else {
-			return valueSets.get(theSystem);
+        return valueSets.get(theSystem);
-		}
+      }
-	}
+    }
+  }
 
-	@SuppressWarnings("unchecked")
+  @SuppressWarnings("unchecked")
-	@Override
+  @Override
-	public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
+  public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
-		Validate.notBlank(theUri, "theUri must not be null or blank");
+    Validate.notBlank(theUri, "theUri must not be null or blank");
-		
-		if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
-			return (T) fetchStructureDefinition(theContext, theUri);
-		}
-		if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
-			return (T) fetchValueSet(theContext, theUri);
-		}
-		//		if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
-		//			Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
-		//			if (defaultValueSets == null) {
-		//				String path = theContext.getVersion().getPathToSchemaDefinitions().replace("/schema", "/valueset") + "/valuesets.xml";
-		//				InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(path);
-		//				if (valuesetText == null) {
-		//					return null;
-		//				}
-		//				InputStreamReader reader;
-		//				try {
-		//					reader = new InputStreamReader(valuesetText, "UTF-8");
-		//				} catch (UnsupportedEncodingException e) {
-		//					// Shouldn't happen!
-		//					throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
-		//				}
-		//
-		//				defaultValueSets = new HashMap<String, ValueSet>();
-		//
-		//				Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
-		//				for (BundleEntryComponent next : bundle.getEntry()) {
-		//					IdType nextId = new IdType(next.getFullUrl());
-		//					if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
-		//						continue;
-		//					}
-		//					defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
-		//				}
-		//
-		//				myDefaultValueSets = defaultValueSets;
-		//			}
-		//
-		//			return (T) defaultValueSets.get(theUri);
-		//		}
 
-		return null;
+    if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
-	}
+      return (T) fetchStructureDefinition(theContext, theUri);
+    }
+    if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
+      return (T) fetchValueSet(theContext, theUri);
+    }
+    // if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
+    // Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
+    // if (defaultValueSets == null) {
+    // String path = theContext.getVersion().getPathToSchemaDefinitions().replace("/schema", "/valueset") + "/valuesets.xml";
+    // InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(path);
+    // if (valuesetText == null) {
+    // return null;
+    // }
+    // InputStreamReader reader;
+    // try {
+    // reader = new InputStreamReader(valuesetText, "UTF-8");
+    // } catch (UnsupportedEncodingException e) {
+    // // Shouldn't happen!
+    // throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
+    // }
+    //
+    // defaultValueSets = new HashMap<String, ValueSet>();
+    //
+    // Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
+    // for (BundleEntryComponent next : bundle.getEntry()) {
+    // IdType nextId = new IdType(next.getFullUrl());
+    // if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
+    // continue;
+    // }
+    // defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
+    // }
+    //
+    // myDefaultValueSets = defaultValueSets;
+    // }
+    //
+    // return (T) defaultValueSets.get(theUri);
+    // }
 
-	@Override
+    return null;
-	public StructureDefinition fetchStructureDefinition(FhirContext theContext, String theUrl) {
+  }
-		return provideStructureDefinitionMap(theContext).get(theUrl);
-	}
 
-	ValueSet fetchValueSet(FhirContext theContext, String theSystem) {
+  @Override
-		return (ValueSet) fetchCodeSystemOrValueSet(theContext, theSystem, false);
+  public StructureDefinition fetchStructureDefinition(FhirContext theContext, String theUrl) {
-	}
+    return provideStructureDefinitionMap(theContext).get(theUrl);
+  }
 
-	public void flush() {
+  ValueSet fetchValueSet(FhirContext theContext, String theSystem) {
-		myCodeSystems = null;
+    return (ValueSet) fetchCodeSystemOrValueSet(theContext, theSystem, false);
-		myStructureDefinitions = null;
+  }
-	}
 
-	@Override
+  public void flush() {
-	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
+    myCodeSystems = null;
-		CodeSystem cs = fetchCodeSystem(theContext, theSystem);
+    myStructureDefinitions = null;
-		return cs != null && cs.getContent() != CodeSystemContentMode.NOTPRESENT;
+  }
-	}
 
-	private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {
+  @Override
-		ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
+  public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
-		InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
+    CodeSystem cs = fetchCodeSystem(theContext, theSystem);
-		if (valuesetText != null) {
+    return cs != null && cs.getContent() != CodeSystemContentMode.NOTPRESENT;
-			InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
+  }
 
-			Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
+  private void loadCodeSystems(FhirContext theContext, Map<String, CodeSystem> theCodeSystems, Map<String, ValueSet> theValueSets, String theClasspath) {
-			for (BundleEntryComponent next : bundle.getEntry()) {
+    ourLog.info("Loading CodeSystem/ValueSet from classpath: {}", theClasspath);
-				if (next.getResource() instanceof CodeSystem) {
+    InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
-					CodeSystem nextValueSet = (CodeSystem) next.getResource();
+    if (valuesetText != null) {
-					nextValueSet.getText().setDivAsString("");
+      InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
-					String system = nextValueSet.getUrl();
-					if (isNotBlank(system)) {
-						theCodeSystems.put(system, nextValueSet);
-					}
-				} else if (next.getResource() instanceof ValueSet) {
-					ValueSet nextValueSet = (ValueSet) next.getResource();
-					nextValueSet.getText().setDivAsString("");
-					String system = nextValueSet.getUrl();
-					if (isNotBlank(system)) {
-						theValueSets.put(system, nextValueSet);
-					}
-				}
-			}
-		} else {
-			ourLog.warn("Unable to load resource: {}", theClasspath);
-		}
-	}
 
-	private void loadStructureDefinitions(FhirContext theContext, Map<String, StructureDefinition> theCodeSystems, String theClasspath) {
+      Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
-		ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
+      for (BundleEntryComponent next : bundle.getEntry()) {
-		InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
+        if (next.getResource() instanceof CodeSystem) {
-		if (valuesetText != null) {
+          CodeSystem nextValueSet = (CodeSystem) next.getResource();
-			InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
+          nextValueSet.getText().setDivAsString("");
+          String system = nextValueSet.getUrl();
+          if (isNotBlank(system)) {
+            theCodeSystems.put(system, nextValueSet);
+          }
+        } else if (next.getResource() instanceof ValueSet) {
+          ValueSet nextValueSet = (ValueSet) next.getResource();
+          nextValueSet.getText().setDivAsString("");
+          String system = nextValueSet.getUrl();
+          if (isNotBlank(system)) {
+            theValueSets.put(system, nextValueSet);
+          }
+        }
+      }
+    } else {
+      ourLog.warn("Unable to load resource: {}", theClasspath);
+    }
+  }
 
-			Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
+  private void loadStructureDefinitions(FhirContext theContext, Map<String, StructureDefinition> theCodeSystems, String theClasspath) {
-			for (BundleEntryComponent next : bundle.getEntry()) {
+    ourLog.info("Loading structure definitions from classpath: {}", theClasspath);
-				if (next.getResource() instanceof StructureDefinition) {
+    InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(theClasspath);
-					StructureDefinition nextSd = (StructureDefinition) next.getResource();
+    if (valuesetText != null) {
-					nextSd.getText().setDivAsString("");
+      InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);
-					String system = nextSd.getUrl();
-					if (isNotBlank(system)) {
-						theCodeSystems.put(system, nextSd);
-					}
-				}
-			}
-		} else {
-			ourLog.warn("Unable to load resource: {}", theClasspath);
-		}
-	}
 
-	private Map<String, StructureDefinition> provideStructureDefinitionMap(FhirContext theContext) {
+      Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
-		Map<String, StructureDefinition> structureDefinitions = myStructureDefinitions;
+      for (BundleEntryComponent next : bundle.getEntry()) {
-		if (structureDefinitions == null) {
+        if (next.getResource() instanceof StructureDefinition) {
-			structureDefinitions = new HashMap<String, StructureDefinition>();
+          StructureDefinition nextSd = (StructureDefinition) next.getResource();
+          nextSd.getText().setDivAsString("");
+          String system = nextSd.getUrl();
+          if (isNotBlank(system)) {
+            theCodeSystems.put(system, nextSd);
+          }
+        }
+      }
+    } else {
+      ourLog.warn("Unable to load resource: {}", theClasspath);
+    }
+  }
 
-			loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/instance/model/dstu3/profile/profiles-resources.xml");
+  private Map<String, StructureDefinition> provideStructureDefinitionMap(FhirContext theContext) {
-			loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/instance/model/dstu3/profile/profiles-types.xml");
+    Map<String, StructureDefinition> structureDefinitions = myStructureDefinitions;
-			loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/instance/model/dstu3/profile/profiles-others.xml");
+    if (structureDefinitions == null) {
+      structureDefinitions = new HashMap<String, StructureDefinition>();
 
-			myStructureDefinitions = structureDefinitions;
+      loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/instance/model/dstu3/profile/profiles-resources.xml");
-		}
+      loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/instance/model/dstu3/profile/profiles-types.xml");
-		return structureDefinitions;
+      loadStructureDefinitions(theContext, structureDefinitions, "/org/hl7/fhir/instance/model/dstu3/profile/profiles-others.xml");
-	}
 
-	@Override
+      myStructureDefinitions = structureDefinitions;
-	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+    }
-		CodeSystem cs = fetchCodeSystem(theContext, theCodeSystem);
+    return structureDefinitions;
-		if (cs != null) {
+  }
-			boolean caseSensitive = true;
-			if (cs.hasCaseSensitive()) {
-				caseSensitive = cs.getCaseSensitive();
-			}
-			
-			CodeValidationResult retVal = testIfConceptIsInList(theCode, cs.getConcept(), caseSensitive);
-			
-			if (retVal != null) {
-				return retVal;
-			}
-		}
 
-		return new CodeValidationResult(IssueSeverity.WARNING, "Unknown code: " + theCodeSystem + " / " + theCode);
+  @Override
-	}
+  public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
+    CodeSystem cs = fetchCodeSystem(theContext, theCodeSystem);
+    if (cs != null) {
+      boolean caseSensitive = true;
+      if (cs.hasCaseSensitive()) {
+        caseSensitive = cs.getCaseSensitive();
+      }
 
-	private CodeValidationResult testIfConceptIsInList(String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
+      CodeValidationResult retVal = testIfConceptIsInList(theCode, cs.getConcept(), caseSensitive);
-		String code = theCode;
-		if (theCaseSensitive == false) {
-			code = code.toUpperCase();
-		}
-		
-		return testIfConceptIsInListInner(conceptList, theCaseSensitive, code);
-	}
 
-	private CodeValidationResult testIfConceptIsInListInner(List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
+      if (retVal != null) {
-		CodeValidationResult retVal = null;
+        return retVal;
-		for (ConceptDefinitionComponent next : conceptList) {
+      }
-			String nextCandidate = next.getCode();
+    }
-			if (theCaseSensitive == false) {
-				nextCandidate = nextCandidate.toUpperCase();
-			}
-			if (nextCandidate.equals(code)) {
-				retVal = new CodeValidationResult(next);
-				break;
-			}
 
-			// recurse
+    return new CodeValidationResult(IssueSeverity.WARNING, "Unknown code: " + theCodeSystem + " / " + theCode);
-			retVal = testIfConceptIsInList(code, next.getConcept(), theCaseSensitive);
+  }
-			if (retVal != null) {
+
-				break;
+  private CodeValidationResult testIfConceptIsInList(String theCode, List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive) {
-			}
+    String code = theCode;
-		}
+    if (theCaseSensitive == false) {
-		
+      code = code.toUpperCase();
-		return retVal;
+    }
-	}
+
+    return testIfConceptIsInListInner(conceptList, theCaseSensitive, code);
+  }
+
+  private CodeValidationResult testIfConceptIsInListInner(List<ConceptDefinitionComponent> conceptList, boolean theCaseSensitive, String code) {
+    CodeValidationResult retVal = null;
+    for (ConceptDefinitionComponent next : conceptList) {
+      String nextCandidate = next.getCode();
+      if (theCaseSensitive == false) {
+        nextCandidate = nextCandidate.toUpperCase();
+      }
+      if (nextCandidate.equals(code)) {
+        retVal = new CodeValidationResult(next);
+        break;
+      }
+
+      // recurse
+      retVal = testIfConceptIsInList(code, next.getConcept(), theCaseSensitive);
+      if (retVal != null) {
+        break;
+      }
+    }
+
+    return retVal;
+  }
 
 }

hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/hapi/validation/DefaultProfileValidationSupport.java

@@ -29,19 +29,18 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
   public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
     return false;
   }
-  
+
   /**
    * Constructor
    */
   public DefaultProfileValidationSupport() {
     super();
   }
-  
+
   public void flush() {
     myDefaultValueSets = null;
     myCodeSystems = null;
   }
-  
 
   @SuppressWarnings("unchecked")
   @Override
@@ -93,18 +92,20 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
 
   @Override
   public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
-    Map<String, ValueSet> codeSystems = myCodeSystems;
+    synchronized (this) {
-    if (codeSystems == null) {
+      Map<String, ValueSet> valueSets = myCodeSystems;
-      codeSystems = new HashMap<String, ValueSet>();
+      if (valueSets == null) {
+        valueSets = new HashMap<String, ValueSet>();
 
-      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
+        loadCodeSystems(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
-      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
+        loadCodeSystems(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
-      loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
+        loadCodeSystems(theContext, valueSets, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
 
-      myCodeSystems = codeSystems;
+        myCodeSystems = valueSets;
+      }
+
+      return valueSets.get(theSystem);
     }
-
-    return codeSystems.get(theSystem);
   }
 
   private void loadCodeSystems(FhirContext theContext, Map<String, ValueSet> codeSystems, String file) {

src/changes/changes.xml

@@ -154,6 +154,19 @@
 				been received by the client when the error happens. Thanks to GitHub
 				user maclema for the pull request!
 			</action>
+			<action type="add">
+				Add a check in JPA server that prevents completely blank tags, profiles, and security labels
+				from being saved to the database. These were filtered out anyhow when the
+				result was returned back to the client but they were persisted which
+				just wasted space.
+			</action>
+			<action type="fix" issue="664">
+				Loading the build-in profile structures (StructureDefinition, ValueSet, etc) is now done in 
+				a synchronized block in order to prevent multiple loads happening if the server processes
+				multiple validations in parallel threads right after startup. Previously a heavy load could
+				cause the server to run out of memory and lock up. Thanks to Karl M Davis
+				for analysis and help fixing this!
+			</action>
 		</release>
 		<release version="2.4" date="2017-04-19">
 			<action type="add">