Sync with master

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

@@ -0,0 +1,28 @@
+package ca.uhn.fhir.jpa.dao.data;
+
+import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2018 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%
+ */
+
+public interface ITermConceptDesignationDao extends JpaRepository<TermConceptDesignation, Long> {
+	// nothing
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseResourceIndexedSearchParam.java

@@ -53,7 +53,7 @@ public abstract class BaseResourceIndexedSearchParam implements Serializable {
 	private Long myResourcePid;
 
 	@Field()
-	@Column(name = "RES_TYPE", nullable = false)
+	@Column(name = "RES_TYPE", nullable = false, length = 30)
 	private String myResourceType;
 
 	@Field()

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java

@@ -81,6 +81,9 @@ public class TermConcept implements Serializable {
 	@FieldBridge(impl = TermConceptPropertyFieldBridge.class)
 	private Collection<TermConceptProperty> myProperties;
 
+	@OneToMany(mappedBy = "myConcept", orphanRemoval = true)
+	private Collection<TermConceptDesignation> myDesignations;
+
 	@Id()
 	@SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")
 	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PID")
@@ -123,6 +126,13 @@ public class TermConcept implements Serializable {
 		}
 	}
 
+	public TermConceptDesignation addDesignation() {
+		TermConceptDesignation designation = new TermConceptDesignation();
+		designation.setConcept(this);
+		getDesignations().add(designation);
+		return designation;
+	}
+
 	private TermConceptProperty addProperty(@Nonnull TermConceptPropertyTypeEnum thePropertyType, @Nonnull String thePropertyName, @Nonnull String thePropertyValue) {
 		Validate.notBlank(thePropertyName);
 
@@ -189,6 +199,29 @@ public class TermConcept implements Serializable {
 		}
 	}
 
+	public List<Coding> getCodingProperties(String thePropertyName) {
+		List<Coding> retVal = new ArrayList<>();
+		for (TermConceptProperty next : getProperties()) {
+			if (thePropertyName.equals(next.getKey())) {
+				if (next.getType() == TermConceptPropertyTypeEnum.CODING) {
+					Coding coding = new Coding();
+					coding.setSystem(next.getCodeSystem());
+					coding.setCode(next.getValue());
+					coding.setDisplay(next.getDisplay());
+					retVal.add(coding);
+				}
+			}
+		}
+		return retVal;
+	}
+
+	public Collection<TermConceptDesignation> getDesignations() {
+		if (myDesignations == null) {
+			myDesignations = new ArrayList<>();
+		}
+		return myDesignations;
+	}
+
 	public String getDisplay() {
 		return myDisplay;
 	}
@@ -231,6 +264,14 @@ public class TermConcept implements Serializable {
 		return myProperties;
 	}
 
+	public Integer getSequence() {
+		return mySequence;
+	}
+
+	public void setSequence(Integer theSequence) {
+		mySequence = theSequence;
+	}
+
 	public List<String> getStringProperties(String thePropertyName) {
 		List<String> retVal = new ArrayList<>();
 		for (TermConceptProperty next : getProperties()) {
@@ -243,30 +284,6 @@ public class TermConcept implements Serializable {
 		return retVal;
 	}
 
-	public List<Coding> getCodingProperties(String thePropertyName) {
-		List<Coding> retVal = new ArrayList<>();
-		for (TermConceptProperty next : getProperties()) {
-			if (thePropertyName.equals(next.getKey())) {
-				if (next.getType() == TermConceptPropertyTypeEnum.CODING) {
-					Coding coding = new Coding();
-					coding.setSystem(next.getCodeSystem());
-					coding.setCode(next.getValue());
-					coding.setDisplay(next.getDisplay());
-					retVal.add(coding);
-				}
-			}
-		}
-		return retVal;
-	}
-
-	public Integer getSequence() {
-		return mySequence;
-	}
-
-	public void setSequence(Integer theSequence) {
-		mySequence = theSequence;
-	}
-
 	public String getStringProperty(String thePropertyName) {
 		List<String> properties = getStringProperties(thePropertyName);
 		if (properties.size() > 0) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java

@@ -0,0 +1,103 @@
+package ca.uhn.fhir.jpa.entity;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2018 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 javax.persistence.*;
+import java.io.Serializable;
+
+@Entity
+@Table(name = "TRM_CONCEPT_DESIG", uniqueConstraints = {
+}, indexes = {
+})
+public class TermConceptDesignation implements Serializable {
+
+	private static final long serialVersionUID = 1L;
+	@ManyToOne
+	@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
+	private TermConcept myConcept;
+	@Id()
+	@SequenceGenerator(name = "SEQ_CONCEPT_DESIG_PID", sequenceName = "SEQ_CONCEPT_DESIG_PID")
+	@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_DESIG_PID")
+	@Column(name = "PID")
+	private Long myId;
+	@Column(name = "LANG", length = 50, nullable = true)
+	private String myLanguage;
+	@Column(name = "USE_SYSTEM", length = 50, nullable = true)
+	private String myUseSystem;
+	@Column(name = "USE_CODE", length = 50, nullable = true)
+	private String myUseCode;
+	@Column(name = "USE_DISPLAY", length = 50, nullable = true)
+	private String myUseDisplay;
+	@Column(name = "VAL", length = 50, nullable = false)
+	private String myValue;
+
+	public String getLanguage() {
+		return myLanguage;
+	}
+
+	public TermConceptDesignation setLanguage(String theLanguage) {
+		myLanguage = theLanguage;
+		return this;
+	}
+
+	public String getUseCode() {
+		return myUseCode;
+	}
+
+	public TermConceptDesignation setUseCode(String theUseCode) {
+		myUseCode = theUseCode;
+		return this;
+	}
+
+	public String getUseDisplay() {
+		return myUseDisplay;
+	}
+
+	public TermConceptDesignation setUseDisplay(String theUseDisplay) {
+		myUseDisplay = theUseDisplay;
+		return this;
+	}
+
+	public String getUseSystem() {
+		return myUseSystem;
+	}
+
+	public TermConceptDesignation setUseSystem(String theUseSystem) {
+		myUseSystem = theUseSystem;
+		return this;
+	}
+
+	public String getValue() {
+		return myValue;
+	}
+
+	public TermConceptDesignation setValue(String theValue) {
+		myValue = theValue;
+		return this;
+	}
+
+	public TermConceptDesignation setConcept(TermConcept theConcept) {
+		myConcept = theConcept;
+		return this;
+	}
+
+
+}

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

@@ -78,6 +78,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	@Autowired
 	protected ITermConceptPropertyDao myConceptPropertyDao;
 	@Autowired
+	protected ITermConceptDesignationDao myConceptDesignationDao;
+	@Autowired
 	protected FhirContext myContext;
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	protected EntityManager myEntityManager;
@@ -94,7 +96,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	private boolean myProcessDeferred = true;
 	@Autowired
 	private PlatformTransactionManager myTransactionMgr;
-	@Autowired
+	@Autowired(required = false)
 	private IFhirResourceDaoCodeSystem<?, ?, ?> myCodeSystemResourceDao;
 
 	private void addCodeIfNotAlreadyAdded(String theCodeSystem, ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, TermConcept theConcept) {
@@ -106,6 +108,19 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		}
 	}
 
+	private void addConceptsToList(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, String theSystem, List<CodeSystem.ConceptDefinitionComponent> theConcept) {
+		for (CodeSystem.ConceptDefinitionComponent next : theConcept) {
+			if (!theAddedCodes.contains(next.getCode())) {
+				theAddedCodes.add(next.getCode());
+				ValueSet.ValueSetExpansionContainsComponent contains = theExpansionComponent.addContains();
+				contains.setCode(next.getCode());
+				contains.setSystem(theSystem);
+				contains.setDisplay(next.getDisplay());
+			}
+			addConceptsToList(theExpansionComponent, theAddedCodes, theSystem, next.getConcept());
+		}
+	}
+
 	private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
 		bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
 	}
@@ -142,11 +157,35 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	@Override
 	public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
 		ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
+
+		myEntityManager.flush();
+		TermCodeSystem cs = myCodeSystemDao.findOne(theCodeSystem.getPid());
+		cs.setCurrentVersion(null);
+		myCodeSystemDao.save(cs);
+		myCodeSystemDao.flush();
+
+		int i = 0;
 		for (TermCodeSystemVersion next : myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystem.getPid())) {
 			myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
-			myConceptDao.deleteByCodeSystemVersion(next.getPid());
+			for (TermConcept nextConcept : myConceptDao.findByCodeSystemVersion(next.getPid())) {
+				myConceptPropertyDao.delete(nextConcept.getProperties());
+				myConceptDesignationDao.delete(nextConcept.getDesignations());
+				myConceptDao.delete(nextConcept);
+			}
+			if (next.getCodeSystem().getCurrentVersion() == next) {
+				next.getCodeSystem().setCurrentVersion(null);
+				myCodeSystemDao.save(next.getCodeSystem());
+			}
+			myCodeSystemVersionDao.delete(next);
+
+			if (i % 1000 == 0) {
+				myEntityManager.flush();
+			}
 		}
-		myCodeSystemDao.delete(theCodeSystem.getPid());
+		myCodeSystemVersionDao.deleteForCodeSystem(theCodeSystem);
+		myCodeSystemDao.delete(theCodeSystem);
+
+		myEntityManager.flush();
 	}
 
 	private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
@@ -171,112 +210,140 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 	@Override
 	@Transactional(propagation = Propagation.REQUIRED)
 	public ValueSet expandValueSet(ValueSet theValueSetToExpand) {
-
-		ValueSet.ConceptSetComponent include = theValueSetToExpand.getCompose().getIncludeFirstRep();
-		String system = include.getSystem();
-		ourLog.info("Starting expansion around code system: {}", system);
-
-		TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
-		if (cs == null) {
-			throw new InvalidRequestException("Unknown code system: " + system);
-		}
-
-		TermCodeSystemVersion csv = cs.getCurrentVersion();
-
 		ValueSet.ValueSetExpansionComponent expansionComponent = new ValueSet.ValueSetExpansionComponent();
 		Set<String> addedCodes = new HashSet<>();
 		boolean haveIncludeCriteria = false;
 
-		/*
+		for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getInclude()) {
-		 * Include Concepts
+			String system = include.getSystem();
-		 */
+			if (isNotBlank(system)) {
-		for (ValueSet.ConceptReferenceComponent next : include.getConcept()) {
+				ourLog.info("Starting expansion around code system: {}", system);
-			String nextCode = next.getCode();
-			if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
-				haveIncludeCriteria = true;
-				TermConcept code = findCode(system, nextCode);
-				if (code != null) {
-					addedCodes.add(nextCode);
-					ValueSet.ValueSetExpansionContainsComponent contains = expansionComponent.addContains();
-					contains.setCode(nextCode);
-					contains.setSystem(system);
-					contains.setDisplay(code.getDisplay());
-				}
-			}
-		}
 
-		/*
+				TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
-		 * Filters
+				if (cs != null) {
-		 */
+					TermCodeSystemVersion csv = cs.getCurrentVersion();
 
-		if (include.getFilter().size() > 0) {
+					/*
-			haveIncludeCriteria = true;
+					 * Include Concepts
-
+					 */
-			FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
+					for (ValueSet.ConceptReferenceComponent next : include.getConcept()) {
-			QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
+						String nextCode = next.getCode();
-			BooleanJunction<?> bool = qb.bool();
+						if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
-
+							haveIncludeCriteria = true;
-			bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
+							TermConcept code = findCode(system, nextCode);
-
+							if (code != null) {
-			for (ValueSet.ConceptSetFilterComponent nextFilter : include.getFilter()) {
+								addedCodes.add(nextCode);
-				if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
+								ValueSet.ValueSetExpansionContainsComponent contains = expansionComponent.addContains();
-					continue;
+								contains.setCode(nextCode);
-				}
+								contains.setSystem(system);
-
+								contains.setDisplay(code.getDisplay());
-				if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
+							}
-					throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
+						}
-				}
-
-
-				if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
-					addDisplayFilterExact(qb, bool, nextFilter);
-				} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
-					if (nextFilter.getValue().trim().contains(" ")) {
-						addDisplayFilterExact(qb, bool, nextFilter);
-					} else {
-						addDisplayFilterInexact(qb, bool, nextFilter);
-					}
-				} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
-
-					TermConcept code = findCode(system, nextFilter.getValue());
-					if (code == null) {
-						throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
 					}
 
-					ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
+					/*
-					bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
+					 * Filters
+					 */
 
-				} else {
+					if (include.getFilter().size() > 0) {
+						haveIncludeCriteria = true;
+
+						FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
+						QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
+						BooleanJunction<?> bool = qb.bool();
+
+						bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
+
+						for (ValueSet.ConceptSetFilterComponent nextFilter : include.getFilter()) {
+							if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
+								continue;
+							}
+
+							if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
+								throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
+							}
+
+
+							if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
+								addDisplayFilterExact(qb, bool, nextFilter);
+							} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
+								if (nextFilter.getValue().trim().contains(" ")) {
+									addDisplayFilterExact(qb, bool, nextFilter);
+								} else {
+									addDisplayFilterInexact(qb, bool, nextFilter);
+								}
+							} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
+
+								TermConcept code = findCode(system, nextFilter.getValue());
+								if (code == null) {
+									throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
+								}
+
+								ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
+								bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
+
+							} else {
 
 //					bool.must(qb.keyword().onField("myProperties").matching(nextFilter.getStringProperty()+"="+nextFilter.getValue()).createQuery());
-					bool.must(qb.phrase().onField("myProperties").sentence(nextFilter.getProperty() + "=" + nextFilter.getValue()).createQuery());
+								bool.must(qb.phrase().onField("myProperties").sentence(nextFilter.getProperty() + "=" + nextFilter.getValue()).createQuery());
+
+							}
+						}
+
+						Query luceneQuery = bool.createQuery();
+						FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
+						jpaQuery.setMaxResults(1000);
+
+						StopWatch sw = new StopWatch();
+
+						@SuppressWarnings("unchecked")
+						List<TermConcept> result = jpaQuery.getResultList();
+
+						ourLog.info("Expansion completed in {}ms", sw.getMillis());
+
+						for (TermConcept nextConcept : result) {
+							addCodeIfNotAlreadyAdded(system, expansionComponent, addedCodes, nextConcept);
+						}
+
+						expansionComponent.setTotal(jpaQuery.getResultSize());
+					}
+
+					if (!haveIncludeCriteria) {
+						List<TermConcept> allCodes = findCodes(system);
+						for (TermConcept nextConcept : allCodes) {
+							addCodeIfNotAlreadyAdded(system, expansionComponent, addedCodes, nextConcept);
+						}
+					}
+
+				} else {
+					// No codesystem matching the URL found in the database
+
+					CodeSystem codeSystemFromContext = getCodeSystemFromContext(system);
+					if (codeSystemFromContext == null) {
+						throw new InvalidRequestException("Unknown code system: " + system);
+					}
+
+					if (include.getConcept().isEmpty() == false) {
+						for (ValueSet.ConceptReferenceComponent next : include.getConcept()) {
+							String nextCode = next.getCode();
+							if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
+								CodeSystem.ConceptDefinitionComponent code = findCode(codeSystemFromContext.getConcept(), nextCode);
+								if (code != null) {
+									addedCodes.add(nextCode);
+									ValueSet.ValueSetExpansionContainsComponent contains = expansionComponent.addContains();
+									contains.setCode(nextCode);
+									contains.setSystem(system);
+									contains.setDisplay(code.getDisplay());
+								}
+							}
+						}
+					} else {
+						List<CodeSystem.ConceptDefinitionComponent> concept = codeSystemFromContext.getConcept();
+						addConceptsToList(expansionComponent, addedCodes, system, concept);
+					}
 
 				}
 			}
-
-			Query luceneQuery = bool.createQuery();
-			FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
-			jpaQuery.setMaxResults(1000);
-
-			StopWatch sw = new StopWatch();
-
-			@SuppressWarnings("unchecked")
-			List<TermConcept> result = jpaQuery.getResultList();
-
-			ourLog.info("Expansion completed in {}ms", sw.getMillis());
-
-			for (TermConcept nextConcept : result) {
-				addCodeIfNotAlreadyAdded(system, expansionComponent, addedCodes, nextConcept);
-			}
-
-			expansionComponent.setTotal(jpaQuery.getResultSize());
-		}
-
-		if (!haveIncludeCriteria) {
-			List<TermConcept> allCodes = findCodes(system);
-			for (TermConcept nextConcept : allCodes) {
-				addCodeIfNotAlreadyAdded(system, expansionComponent, addedCodes, nextConcept);
-			}
 		}
 
 		ValueSet valueSet = new ValueSet();
@@ -284,9 +351,17 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		return valueSet;
 	}
 
-	@Override
+	protected List<VersionIndependentConcept> expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.r4.model.ValueSet theValueSetToExpandR4) {
-	public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
+		org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = expandValueSet(theValueSetToExpandR4).getExpansion();
-		throw new UnsupportedOperationException(); // FIXME implement
+
+		ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
+		for (org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent nextContains : expandedR4.getContains()) {
+			retVal.add(
+				new VersionIndependentConcept()
+					.setSystem(nextContains.getSystem())
+					.setCode(nextContains.getCode()));
+		}
+		return retVal;
 	}
 
 	private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
@@ -312,6 +387,16 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		}
 	}
 
+	private CodeSystem.ConceptDefinitionComponent findCode(List<CodeSystem.ConceptDefinitionComponent> theConcepts, String theCode) {
+		for (CodeSystem.ConceptDefinitionComponent next : theConcepts) {
+			if (theCode.equals(next.getCode())) {
+				return next;
+			}
+			findCode(next.getConcept(), theCode);
+		}
+		return null;
+	}
+
 	@Override
 	public TermConcept findCode(String theCodeSystem, String theCode) {
 		TermCodeSystemVersion csv = findCurrentCodeSystemVersionForSystem(theCodeSystem);
@@ -398,6 +483,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		return myCodeSystemDao.findByCodeSystemUri(theSystem);
 	}
 
+	protected abstract CodeSystem getCodeSystemFromContext(String theSystem);
+
 	private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
 		if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
 			return;
@@ -429,10 +516,14 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 			}
 		}
 
-		for (TermConceptProperty next : theConcept.getProperties()){
+		for (TermConceptProperty next : theConcept.getProperties()) {
 			myConceptPropertyDao.save(next);
 		}
 
+		for (TermConceptDesignation next : theConcept.getDesignations()) {
+			myConceptDesignationDao.save(next);
+		}
+
 	}
 
 	private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
@@ -636,12 +727,16 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc
 		for (TermCodeSystemVersion next : existing) {
 			ourLog.info(" * Deleting code system version {}", next.getPid());
 			myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
-			myConceptDao.deleteByCodeSystemVersion(next.getPid());
+			for (TermConcept nextConcept : myConceptDao.findByCodeSystemVersion(next.getPid())) {
+				myConceptPropertyDao.delete(nextConcept.getProperties());
+				myConceptDao.delete(nextConcept);
+			}
 		}
 
 		ourLog.info("Flushing...");
 
 		myConceptParentChildLinkDao.flush();
+		myConceptPropertyDao.flush();
 		myConceptDao.flush();
 
 		ourLog.info("Done flushing");

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

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.term.loinc;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
 import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ContactPoint;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.ValueSet;
 
@@ -79,6 +80,12 @@ abstract class BaseHandler implements IRecordHandler {
 			conceptMap.setId(theMapping.getConceptMapId());
 			conceptMap.setUrl(theMapping.getConceptMapUri());
 			conceptMap.setName(theMapping.getConceptMapName());
+			conceptMap.setPublisher("Regentrief Institute, Inc.");
+			conceptMap.addContact()
+				.setName("Regentrief Institute, Inc.")
+				.addTelecom()
+				.setSystem(ContactPoint.ContactPointSystem.URL)
+				.setValue("https://loinc.org");
 			myIdToConceptMaps.put(theMapping.getConceptMapId(), conceptMap);
 			myConceptMaps.add(conceptMap);
 		} else {
@@ -144,6 +151,12 @@ abstract class BaseHandler implements IRecordHandler {
 			vs.setId(theValueSetId);
 			vs.setName(theValueSetName);
 			vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
+			vs.setPublisher("Regentrief Institute, Inc.");
+			vs.addContact()
+				.setName("Regentrief Institute, Inc.")
+				.addTelecom()
+				.setSystem(ContactPoint.ContactPointSystem.URL)
+				.setValue("https://loinc.org");
 			myIdToValueSet.put(theValueSetId, vs);
 			myValueSets.add(vs);
 		} else {

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

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.term.loinc;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2018 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 ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.IRecordHandler;
@@ -9,6 +29,7 @@ import org.hl7.fhir.r4.model.ValueSet;
 import java.util.HashMap;
 import java.util.Map;
 
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 import static org.apache.commons.lang3.StringUtils.trim;
 
 public class LoincPartHandler implements IRecordHandler {
@@ -30,15 +51,23 @@ public class LoincPartHandler implements IRecordHandler {
 		String partTypeName = trim(theRecord.get("PartTypeName"));
 		String partName = trim(theRecord.get("PartName"));
 		String partDisplayName = trim(theRecord.get("PartDisplayName"));
-		String status = trim(theRecord.get("Status"));
 
-		if (!"ACTIVE".equals(status)) {
+		// Per Dan's note, we include deprecated parts
-			return;
+//		String status = trim(theRecord.get("Status"));
-		}
+//		if (!"ACTIVE".equals(status)) {
+//			return;
+//		}
 
 		TermConcept concept = new TermConcept(myCodeSystemVersion, partNumber);
 		concept.setDisplay(partName);
 
+		if (isNotBlank(partDisplayName)) {
+			concept.addDesignation()
+				.setConcept(concept)
+				.setUseDisplay("PartDisplayName")
+				.setValue(partDisplayName);
+		}
+
 		myCode2Concept.put(partDisplayName, concept);
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java

@@ -181,6 +181,11 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
 		TermConcept childAAA = new TermConcept(cs, "childAAA");
 		childAAA.addPropertyString("propA", "valueAAA");
 		childAAA.addPropertyString("propB", "foo");
+		childAAA.addDesignation()
+			.setUseSystem("http://designationsystem")
+			.setUseCode("somedesig")
+			.setUseDisplay("Designation Use")
+			.setValue("Bananas");
 		childAA.addChild(childAAA, RelationshipTypeEnum.ISA);
 
 		TermConcept childAAB = new TermConcept(cs, "childAAB");

src/changes/changes.xml

@@ -6,7 +6,37 @@
 		<title>HAPI FHIR Changelog</title>
 	</properties>
 	<body>
-		<release version="3.3.0" date="TBD">
+		<release version="3.4.0" date="TBD">
+			<action type="fix">
+				When performing a FHIR resource update in the JPA server
+				where the update happens within a transaction, and the
+				resource being updated contains placeholder IDs, and
+				the resource has not actually changed, a new version was
+				created even though there was not actually any change.
+				This particular combination of circumstances seems very
+				specific and improbable, but it is quite common for some
+				types of solutions (e.g. mapping HL7v2 data) so this
+				fix can prevent significant wasted space in some cases.
+			</action>
+			<action type="fix">
+				JPA server index tables did not have a column length specified
+				on the resource type column. This caused the default of 255 to
+				be used, which wasted a lot of space since resource names are all
+				less than 30 chars long and a single resource can have 10-100+
+				index rows depending on configuration. This has now been set
+				to a much more sensible 30.
+			</action>
+			<action type="fix">
+				The LOINC uploader for the JPA Terminology Server has been
+				significantly beefed up so that it now takes in the full
+				set of LOINC distribution artifacts, and creates not only
+				the LOINC CodeSystem but a complete set of concept properties,
+				a number of LOINC ValueSets, and a number of LOINC ConceptMaps.
+				This work was sponsored by the Regenstrief Institute. Thanks
+				to Regenstrief for their support!
+			</action>
+		</release>
+		<release version="3.3.0" date="2018-03-29">
 			<action type="add">
 				This release corrects an inefficiency in the JPA Server, but requires a schema
 				change in order to update. Prior to this version of HAPI FHIR, a CLOB column
@@ -14,12 +44,29 @@
 				tables: HFJ_RESOURCE and HFJ_RES_VER. Because the same content was stored in two
 				places, the database consumed more space than is needed to.
 				<![CDATA[<br/><br/>]]>
-				In order to reduce this duplication, two columns have been removed from the
+				In order to reduce this duplication, the
-				HFJ_RESOURCE table. This means that on any database that is being upgraded
+				<![CDATA[<code>RES_TEXT</code> and <code>RES_ENCODING</code>]]>
-				to HAPI FHIR 3.3.0+, you will need to remove the columns
+				columns have been
-				<![CDATA[<code>RES_TEXT</code> and <code>RES_ENCODING</code>]]> (or
+				<![CDATA[<b>dropped</b>]]>
-				set them to nullable if you want an easy means of rolling back). Naturally
+				from the
-				you should back your database up prior to making this change.
+				<![CDATA[<code>HFJ_RESOURCE]]>
+				table, and the
+				<![CDATA[<code>RES_TEXT</code> and <code>RES_ENCODING</code>]]>
+				columns have been
+				<![CDATA[<b>made NULLABLE</b>]]>
+				on the
+				<![CDATA[<code>HFJ_RES_VER]]>
+				table.
+				<![CDATA[<br/><br/>]]>
+				The following migration script may be used to apply these changes to
+				your database. Naturally you should back your database up prior to
+				making this change.
+				<![CDATA[
+				<pre>ALTER TABLE hfj_resource DROP COLUMN res_text;
+ALTER TABLE hfj_resource DROP COLUMN res_encoding;
+ALTER TABLE hfj_res_ver ALTER COLUMN res_encoding DROP NOT NULL;
+ALTER TABLE hfj_res_ver ALTER COLUMN res_text DROP NOT NULL;</pre>
+				]]>
 			</action>
 			<action type="fix">
 				The validation module has been refactored to use the R4 (currently maintained)
@@ -41,6 +88,28 @@
 					</ul>
 				]]>
 			</action>
+			<action type="add" issue="871">
+				A number of HAPI FHIR modules have been converted so that they now work
+				as OSGi modules. Unlike the previous OSGi module, which was a mega-JAR
+				with all of HAPI FHIR in it, this is simply the appropriate
+				OSGi manifest inside the existing JARs. Thanks to John Poth
+				for the Pull Request!
+				<![CDATA[
+				<br/><br/>
+				Note that this does not cover all modules in the project. Current support includes:
+				<ul>
+					<li>HAPI-FHIR structures DSTU2, HL7ORGDSTU2, DSTU2.1, DSTU3, R4</li>
+					<li>HAPI-FHIR Resource validation DSTU2, HL7ORGDSTU2, DSTU2.1, DSTU3, R4</li>
+					<li>Apache Karaf features for all the above</li>
+					<li> Integration Tests</li>
+				</ul>
+				Remaining work includes:
+				<ul>
+					<li>HAPI-FHIR Server support</li>
+					<li> HAPI-FHIR narrative support. This might be tricky as Thymeleaf doesn't support OSGi.</li>
+				</ul>
+				]]>
+			</action>
 			<action type="fix">
 				Fix a crash in the JSON parser when parsing extensions on repeatable
 				elements (e.g. Patient.address.line) where there is an extension on the
@@ -240,6 +309,48 @@
 				is supported according to the FHIR specification. Thanks
 				to Jeff Chung for the pull request!
 			</action>
+			<action type="fix">
+				JPA Server Operation Interceptor create/update methods will now no
+				longer be fired if the create/update operation being performed
+				is a no-op (e.g. a conditional create that did not need to perform
+				any action, or an update where the contents didn't actually change)
+			</action>
+			<action type="fix" issue="879">
+				JPA server sometimes updated resources even though the client
+				supplied an update with no actual changes in it, due to 
+				changes in the metadata section being considered content
+				changes. Thanks to Kyle Meadows for the pull request!
+			</action>
+			<action type="add" issue="817">
+				A new example project has been added called hapi-fhir-jpaserver-dynamic,
+				which uses application/environment properties to configure which version
+				of FHIR the server supports and other configuration. Thanks to
+				Anoush Mouradian for the pull request!
+			</action>
+			<action type="add" issue="581">
+				A new example project showing the use of JAX-RS Server Side Events has
+				been added. Thanks to Jens Kristian Villadsen for the pull request!
+			</action>
+			<action type="remove" issue="864">
+				An unneccesary reference to the Javassist library has been
+				removed from the build. Thanks to Łukasz Dywicki for the 
+				pull request!
+			</action>
+			<action type="add" issue="819">
+				Support has been added to the JPA server for the :not modifier. Thanks 
+				to Łukasz Dywicki for the pull request!
+			</action>
+			<action type="add" issue="877">
+				Suport for the :contains string search parameter modifier has been added to
+				the JPA server. Thanks to Anthony Sute for the pull request!
+			</action>
+			<action type="fix">
+				All instances of DefaultProfileValidationSupport (i.e. one for
+				each version of FHIR) have been fixed so that they explicitly
+				close any InputStreams they open in order to read the built-in
+				profile resources. Leaving these open caused resource starvation
+				in some cases under heavy load.
+			</action>
 		</release>
 		<release version="3.2.0" date="2018-01-13">
 			<action type="add">