Consider last stored ValueSet not necessarily current version anymore.

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.rest.api.SortOrderEnum;
 import ca.uhn.fhir.rest.api.SortSpec;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
@@ -41,6 +42,7 @@ import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.ImplementationGuide;
 import org.hl7.fhir.r4.model.Questionnaire;
 import org.hl7.fhir.r4.model.StructureDefinition;
+import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -51,6 +53,7 @@ import javax.annotation.PostConstruct;
 import javax.transaction.Transactional;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Optional;
 import java.util.concurrent.TimeUnit;
 import java.util.function.Supplier;
 
@@ -71,6 +74,10 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
 
 	@Autowired
 	private DaoRegistry myDaoRegistry;
+
+	@Autowired
+	private ITermReadSvc myITermReadSvc;
+
 	private Class<? extends IBaseResource> myCodeSystemType;
 	private Class<? extends IBaseResource> myStructureDefinitionType;
 	private Class<? extends IBaseResource> myValueSetType;
@@ -97,9 +104,23 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
 
 	@Override
 	public IBaseResource fetchValueSet(String theSystem) {
+		// if no version is present, we need to append the current version,
+		// if one exists, in case it is not the last loaded
+		theSystem = appendCurrentVersion(theSystem);
 		return fetchResource(myValueSetType, theSystem);
 	}
 
+
+	private String appendCurrentVersion(String theSystem) {
+		// if version is included there is nothing to add here
+		if (theSystem.contains("|"))  return theSystem;
+
+		Optional<String> currentVersionOpt = myITermReadSvc.getValueSetCurrentVersion(new UriType(theSystem));
+
+		return currentVersionOpt.map(ver -> theSystem + "|" + ver).orElse(theSystem);
+	}
+
+
 	@Override
 	public IBaseResource fetchStructureDefinition(String theUrl) {
 		return fetchResource(myStructureDefinitionType, theUrl);
@@ -174,6 +195,9 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
 						params.add(ValueSet.SP_VERSION, new TokenParam(theUri.substring(versionSeparator + 1)));
 						params.add(ValueSet.SP_URL, new UriParam(theUri.substring(0, versionSeparator)));
 					} else {
+						// last loaded ValueSet not necessarily is the current version anymore, so code should be executing
+						// this path only when there is no current version pointed for the ValueSet
+						ourLog.warn("Fetching ValueSet current version as last loaded");
 						params.add(ValueSet.SP_URL, new UriParam(theUri));
 					}
 					params.setSort(new SortSpec("_lastUpdated").setOrder(SortOrderEnum.DESC));

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

@@ -44,14 +44,28 @@ public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
 	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myExpansionStatus = :expansion_status")
 	Slice<TermValueSet> findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetPreExpansionStatusEnum theExpansionStatus);
 
-	@Query(value="SELECT vs FROM TermValueSet vs INNER JOIN ResourceTable r ON r.myId = vs.myResourcePid WHERE vs.myUrl = :url ORDER BY r.myUpdated DESC")
-	List<TermValueSet> findTermValueSetByUrl(Pageable thePage, @Param("url") String theUrl);
-
 	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url AND vs.myVersion IS NULL")
 	Optional<TermValueSet> findTermValueSetByUrlAndNullVersion(@Param("url") String theUrl);
 
 	@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url AND vs.myVersion = :version")
 	Optional<TermValueSet> findTermValueSetByUrlAndVersion(@Param("url") String theUrl, @Param("version") String theVersion);
 
+	/**
+	 * Obtain the only ValueSet for the url which myIsCurrentVersion is true if one exists
+	 * or the last loaded ValueSet for the url which version is null otherwise
+	 */
+	@Query("select vs FROM TermValueSet vs JOIN FETCH vs.myResource r WHERE vs.myUrl = :url AND (vs.myIsCurrentVersion is true or " +
+		"(vs.myIsCurrentVersion is false AND vs.myVersion is null AND not exists(" +
+		"FROM TermValueSet WHERE myUrl = :url AND myIsCurrentVersion is true )) ) order by r.myUpdated DESC")
+	List<TermValueSet> listTermValueSetsByUrlAndCurrentVersion(@Param("url") String theUrl, Pageable pageable);
 
+	/**
+	 * This method uses the previous one to get a possible list of ValueSets and return the first if any
+	 * because the query will obtain no more than one if one with the myCurrentVersion flag exists but
+	 * could obtain more if one with that flag doesn't exist. For that reason the query is Pageable and ordered
+	 */
+	default Optional<TermValueSet> findTermValueSetByUrlAndCurrentVersion(@Param("url") String theUrl) {
+		List<TermValueSet> termValueSets = listTermValueSetsByUrlAndCurrentVersion(theUrl, Pageable.ofSize(1));
+		return termValueSets.isEmpty()? Optional.empty() : Optional.of(termValueSets.get(0));
+	}
 }

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

@@ -26,6 +26,7 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.annotations.ColumnDefault;
+import org.hibernate.annotations.OptimisticLock;
 
 import javax.annotation.Nonnull;
 import javax.persistence.*;
@@ -85,6 +86,10 @@ public class TermValueSet implements Serializable {
 	@Column(name = "EXPANSION_STATUS", nullable = false, length = MAX_EXPANSION_STATUS_LENGTH)
 	private TermValueSetPreExpansionStatusEnum myExpansionStatus;
 
+	@OptimisticLock(excluded = true)
+	@Column(name = "CURRENT_VERSION")
+	private Boolean myIsCurrentVersion = false;
+
 	@Transient
 	private transient Integer myHashCode;
 
@@ -198,6 +203,14 @@ public class TermValueSet implements Serializable {
 		return this;
 	}
 
+	public Boolean getCurrentVersion() {
+		return myIsCurrentVersion;
+	}
+
+	public void setCurrentVersion(Boolean theCurrentVersion) {
+		myIsCurrentVersion = theCurrentVersion;
+	}
+
 	@Override
 	public boolean equals(Object theO) {
 		if (this == theO) return true;

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

@@ -68,6 +68,7 @@ import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
 import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
 import ca.uhn.fhir.jpa.util.LogicUtil;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -117,6 +118,7 @@ import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
 import org.quartz.JobExecutionContext;
@@ -231,6 +233,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 	@Autowired
 	private ITermConceptMappingSvc myTermConceptMappingSvc;
 
+	@Autowired
+	private ITermValueSetDao myTermValueSetDao;
+
 	private volatile IValidationSupport myJpaValidationSupport;
 	private volatile IValidationSupport myValidationSupport;
 
@@ -445,12 +450,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 			if (theValueSetToExpand.hasVersion()) {
 				optionalTermValueSet = myValueSetDao.findTermValueSetByUrlAndVersion(theValueSetToExpand.getUrl(), theValueSetToExpand.getVersion());
 			} else {
-				List<TermValueSet> termValueSets = myValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 1), theValueSetToExpand.getUrl());
+				optionalTermValueSet = myValueSetDao.findTermValueSetByUrlAndCurrentVersion(theValueSetToExpand.getUrl());
-				if (termValueSets.size() > 0) {
-					optionalTermValueSet = Optional.of(termValueSets.get(0));
-				} else {
-					optionalTermValueSet = Optional.empty();
-				}
 			}
 		} else {
 			optionalTermValueSet = Optional.empty();
@@ -1884,7 +1884,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 
 	@Override
 	@Transactional
-	public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
+	public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet , RequestDetails theRequestDetails) {
 
 		ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
 		if (isPlaceholder(theValueSet)) {
@@ -1904,6 +1904,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		termValueSet.setVersion(theValueSet.getVersion());
 		termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
 
+		// value sets must be marked as current only when version is present and flag indicates that
+		if (theValueSet.getVersion() != null) {
+			if (ITermCodeSystemStorageSvc.isMakeVersionCurrent(theRequestDetails)) {
+				makeVersionCurrent(theValueSet);
+			}
+		}
+
 		// Delete version being replaced
 		deleteValueSetForResource(theResourceTable);
 
@@ -1940,6 +1947,31 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		}
 	}
 
+
+	private void makeVersionCurrent(ValueSet theValueSet) {
+		resetCurrentValueSetVersion(theValueSet);
+
+		TermValueSet termValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(
+			theValueSet.getUrl(), theValueSet.getVersion())
+			.orElseThrow(() ->
+				new InternalErrorException("Couldn't retrieve TermValueSet with url: " +
+					theValueSet.getUrl() + " and version: " + theValueSet.getVersion() ) );
+
+		termValueSet.setCurrentVersion(true);
+		myTermValueSetDao.save(termValueSet);
+	}
+
+
+	private void resetCurrentValueSetVersion(ValueSet theValueSet) {
+		Optional<TermValueSet> termValueSetOpt = myTermValueSetDao.findTermValueSetByUrlAndCurrentVersion(theValueSet.getUrl());
+		if (! termValueSetOpt.isPresent())  return;
+
+		TermValueSet termValueSet = termValueSetOpt.get();
+		termValueSet.setCurrentVersion(false);
+		myTermValueSetDao.save(termValueSet);
+	}
+
+
 	@Override
 	@Transactional
 	public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB,
@@ -2481,4 +2513,18 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		return termConcept;
 	}
 
+
+	@Override
+	@Transactional
+	public Optional<String> getValueSetCurrentVersion(UriType theUrl) {
+		Optional<TermValueSet> termValueSetOpt =
+			myTermValueSetDao.findTermValueSetByUrlAndCurrentVersion(theUrl.getValueAsString());
+
+		if (! termValueSetOpt.isPresent() || StringUtils.isBlank(termValueSetOpt.get().getVersion())) {
+			return Optional.empty();
+		}
+
+		return termValueSetOpt.map(TermValueSet::getVersion);
+	}
+
 }

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

@@ -399,7 +399,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
 			theCodeSystemResource.getVersion(), theCodeSystemVersion, resource, theRequest);
 
 		myDeferredStorageSvc.addConceptMapsToStorageQueue(theConceptMaps);
-		myDeferredStorageSvc.addValueSetsToStorageQueue(theValueSets);
+		myDeferredStorageSvc.addValueSetsToStorageQueue(theValueSets, theRequest);
 
 		return csId;
 	}

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

@@ -37,6 +37,7 @@ import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
 import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
 import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.util.StopWatch;
 import com.google.common.annotations.VisibleForTesting;
 import org.apache.commons.lang3.Validate;
@@ -49,6 +50,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Slice;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.util.Pair;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
@@ -65,6 +67,7 @@ import java.util.UUID;
 import java.util.concurrent.ConcurrentLinkedQueue;
 import java.util.concurrent.TimeUnit;
 import java.util.function.Supplier;
+import java.util.stream.Collectors;
 
 public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 
@@ -72,7 +75,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	final private List<TermCodeSystem> myDeferredCodeSystemsDeletions = Collections.synchronizedList(new ArrayList<>());
 	final private Queue<TermCodeSystemVersion> myDeferredCodeSystemVersionsDeletions = new ConcurrentLinkedQueue<>();
 	final private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
-	final private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
+	final private List<Pair<ValueSet, RequestDetails>> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
 	final private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
 	final private List<TermConceptParentChildLink> myConceptLinksToSaveLater = Collections.synchronizedList(new ArrayList<>());
 	@Autowired
@@ -116,9 +119,9 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 	}
 
 	@Override
-	public void addValueSetsToStorageQueue(List<ValueSet> theValueSets) {
+	public void addValueSetsToStorageQueue(List<ValueSet> theValueSets, RequestDetails theRequestDetails) {
 		Validate.notNull(theValueSets);
-		myDeferredValueSets.addAll(theValueSets);
+		myDeferredValueSets.addAll(theValueSets.stream().map(vs -> Pair.of(vs, theRequestDetails)).collect(Collectors.toList()));
 	}
 
 	@Override
@@ -214,12 +217,15 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
 		}
 	}
 
+
 	private void processDeferredValueSets() {
 		int count = Math.min(myDeferredValueSets.size(), 200);
-		for (ValueSet nextValueSet : new ArrayList<>(myDeferredValueSets.subList(0, count))) {
+		for (Pair<ValueSet, RequestDetails> nextPair : new ArrayList<>(myDeferredValueSets.subList(0, count))) {
-			ourLog.info("Creating ValueSet: {}", nextValueSet.getId());
+			ValueSet valueSet = nextPair.getFirst();
-			myTerminologyVersionAdapterSvc.createOrUpdateValueSet(nextValueSet);
+			RequestDetails requestDetails = nextPair.getSecond();
-			myDeferredValueSets.remove(nextValueSet);
+			ourLog.info("Creating ValueSet: {}", valueSet.getId());
+			myTerminologyVersionAdapterSvc.createOrUpdateValueSet(valueSet, requestDetails);
+			myDeferredValueSets.remove(nextPair);
 		}
 		ourLog.info("Saved {} deferred ValueSet resources, have {} remaining", count, myDeferredValueSets.size());
 	}

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

@@ -40,7 +40,16 @@ import java.util.List;
  */
 public interface ITermCodeSystemStorageSvc {
 
-	static final String MAKE_LOADING_VERSION_CURRENT = "make.loading.version.current";
+	String MAKE_LOADING_VERSION_CURRENT = "make.loading.version.current";
+
+
+	/**
+	 * Defaults to true when parameter is null or entry is not present in requestDetails.myUserData
+	 */
+	static boolean isMakeVersionCurrent(RequestDetails theRequestDetails) {
+		return theRequestDetails == null ||
+			(boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
+	}
 
 	void deleteCodeSystem(TermCodeSystem theCodeSystem);
 

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
 
@@ -52,7 +53,7 @@ public interface ITermDeferredStorageSvc {
 
 	void addConceptMapsToStorageQueue(List<ConceptMap> theConceptMaps);
 
-	void addValueSetsToStorageQueue(List<ValueSet> theValueSets);
+	void addValueSetsToStorageQueue(List<ValueSet> theValueSets, RequestDetails theRequestDetails);
 
 	void deleteCodeSystem(TermCodeSystem theCodeSystem);
 

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

@@ -4,12 +4,10 @@ import ca.uhn.fhir.context.support.ConceptValidationOptions;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.api.model.TranslationRequest;
 import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
-import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.term.IValueSetConceptAccumulator;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.util.FhirVersionIndependentConcept;
 import org.hl7.fhir.instance.model.api.IBaseCoding;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
@@ -17,7 +15,7 @@ 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.CodeSystem;
-import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
 
 import javax.annotation.Nonnull;
@@ -91,7 +89,13 @@ public interface ITermReadSvc extends IValidationSupport {
 
 	void deleteValueSetAndChildren(ResourceTable theResourceTable);
 
-	void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet);
+
+	void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet, RequestDetails theRequestDetails);
+
+	default void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
+		storeTermValueSet(theResourceTable, theValueSet, null);
+	}
+
 
 	IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB);
 
@@ -119,4 +123,5 @@ public interface ITermReadSvc extends IValidationSupport {
 	 */
 	CodeValidationResult codeSystemValidateCode(IIdType theCodeSystemId, String theValueSetUrl, String theVersion, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
 
+	Optional<String> getValueSetCurrentVersion(UriType theUrl);
 }

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

@@ -41,6 +41,6 @@ public interface ITermVersionAdapterSvc {
 
 	void createOrUpdateConceptMap(ConceptMap theNextConceptMap);
 
-	void createOrUpdateValueSet(ValueSet theValueSet);
+	void createOrUpdateValueSet(ValueSet theValueSet, RequestDetails theRequestDetails);
 
 }