Java tutorial
package ca.uhn.fhir.jpa.dao; import static org.apache.commons.lang3.StringUtils.isBlank; /* * #%L * HAPI FHIR JPA Server * %% * Copyright (C) 2014 - 2016 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 java.util.Date; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Set; import javax.persistence.Query; import javax.persistence.Tuple; import javax.persistence.TypedQuery; import javax.persistence.criteria.CriteriaBuilder; import javax.persistence.criteria.CriteriaQuery; import javax.persistence.criteria.Root; import org.hl7.fhir.instance.model.api.IBaseResource; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.transaction.PlatformTransactionManager; import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; import org.springframework.transaction.support.TransactionCallback; import org.springframework.transaction.support.TransactionTemplate; import ca.uhn.fhir.jpa.dao.data.IForcedIdDao; import ca.uhn.fhir.jpa.dao.data.ITermConceptDao; import ca.uhn.fhir.jpa.entity.ForcedId; import ca.uhn.fhir.jpa.entity.ResourceTable; import ca.uhn.fhir.jpa.util.ReindexFailureException; import ca.uhn.fhir.jpa.util.StopWatch; import ca.uhn.fhir.model.api.TagList; import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.model.primitive.InstantDt; import ca.uhn.fhir.rest.api.RestOperationTypeEnum; import ca.uhn.fhir.rest.method.RequestDetails; import ca.uhn.fhir.rest.server.IBundleProvider; import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException; import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails; public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBaseResource> implements IFhirSystemDao<T, MT> { private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirSystemDao.class); @Autowired private PlatformTransactionManager myTxManager; @Autowired private IForcedIdDao myForcedIdDao; @Autowired private ITermConceptDao myTermConceptDao; @Transactional(propagation = Propagation.REQUIRED) @Override public void deleteAllTagsOnServer(RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails); notifyInterceptors(RestOperationTypeEnum.DELETE_TAGS, requestDetails); myEntityManager.createQuery("DELETE from ResourceTag t").executeUpdate(); } private int doPerformReindexingPass(final Integer theCount) { TransactionTemplate txTemplate = new TransactionTemplate(myTxManager); txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED); int retVal = doPerformReindexingPassForResources(theCount, txTemplate); return retVal; } private int doPerformReindexingPassForResources(final Integer theCount, TransactionTemplate txTemplate) { return txTemplate.execute(new TransactionCallback<Integer>() { @SuppressWarnings("unchecked") @Override public Integer doInTransaction(TransactionStatus theStatus) { TypedQuery<ResourceTable> q = myEntityManager.createQuery( "SELECT t FROM " + ResourceTable.class.getSimpleName() + " t WHERE t.myIndexStatus IS null", ResourceTable.class); int maxResult = 500; if (theCount != null) { maxResult = Math.min(theCount, 2000); } q.setMaxResults(maxResult); List<ResourceTable> resources = q.getResultList(); if (resources.isEmpty()) { return 0; } ourLog.info("Indexing {} resources", resources.size()); int count = 0; long start = System.currentTimeMillis(); for (ResourceTable resourceTable : resources) { try { /* * This part is because from HAPI 1.5 - 1.6 we changed the format of forced ID to be "type/id" instead of just "id" */ ForcedId forcedId = resourceTable.getForcedId(); if (forcedId != null) { if (isBlank(forcedId.getResourceType())) { ourLog.info("Updating resource {} forcedId type to {}", forcedId.getForcedId(), resourceTable.getResourceType()); forcedId.setResourceType(resourceTable.getResourceType()); myForcedIdDao.save(forcedId); } } final IBaseResource resource = toResource(resourceTable, false); @SuppressWarnings("rawtypes") final IFhirResourceDao dao = getDao(resource.getClass()); dao.reindex(resource, resourceTable); } catch (Exception e) { ourLog.error("Failed to index resource {}: {}", new Object[] { resourceTable.getIdDt(), e.toString(), e }); throw new ReindexFailureException(resourceTable.getId()); } count++; } long delay = System.currentTimeMillis() - start; long avg = (delay / resources.size()); ourLog.info("Indexed {} / {} resources in {}ms - Avg {}ms / resource", new Object[] { count, resources.size(), delay, avg }); return resources.size(); } }); } @Override public TagList getAllTags(RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails); notifyInterceptors(RestOperationTypeEnum.GET_TAGS, requestDetails); StopWatch w = new StopWatch(); TagList retVal = super.getTags(null, null); ourLog.info("Processed getAllTags in {}ms", w.getMillisAndRestart()); return retVal; } @Override public Map<String, Long> getResourceCounts() { CriteriaBuilder builder = myEntityManager.getCriteriaBuilder(); CriteriaQuery<Tuple> cq = builder.createTupleQuery(); Root<?> from = cq.from(ResourceTable.class); cq.multiselect(from.get("myResourceType").as(String.class), builder.count(from.get("myResourceType")).as(Long.class)); cq.groupBy(from.get("myResourceType")); TypedQuery<Tuple> q = myEntityManager.createQuery(cq); Map<String, Long> retVal = new HashMap<String, Long>(); for (Tuple next : q.getResultList()) { String resourceName = next.get(0, String.class); Long count = next.get(1, Long.class); retVal.put(resourceName, count); } return retVal; } protected boolean hasValue(InstantDt theInstantDt) { return theInstantDt != null && theInstantDt.isEmpty() == false; } @Override public IBundleProvider history(Date theSince, Date theUntil, RequestDetails theRequestDetails) { if (theRequestDetails != null) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails); notifyInterceptors(RestOperationTypeEnum.HISTORY_SYSTEM, requestDetails); } StopWatch w = new StopWatch(); IBundleProvider retVal = super.history(null, null, theSince, theUntil); ourLog.info("Processed global history in {}ms", w.getMillisAndRestart()); return retVal; } protected ResourceTable loadFirstEntityFromCandidateMatches(Set<Long> candidateMatches) { return myEntityManager.find(ResourceTable.class, candidateMatches.iterator().next()); } @Transactional() @Override public int markAllResourcesForReindexing() { int retVal = myEntityManager .createQuery("UPDATE " + ResourceTable.class.getSimpleName() + " t SET t.myIndexStatus = null") .executeUpdate(); retVal += myTermConceptDao.markAllForReindexing(); return retVal; } private void markResourceAsIndexingFailed(final long theId) { TransactionTemplate txTemplate = new TransactionTemplate(myTxManager); txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW); txTemplate.execute(new TransactionCallback<Void>() { @Override public Void doInTransaction(TransactionStatus theStatus) { ourLog.info("Marking resource with PID {} as indexing_failed", new Object[] { theId }); Query q = myEntityManager .createQuery("UPDATE ResourceTable t SET t.myIndexStatus = :status WHERE t.myId = :id"); q.setParameter("status", INDEX_STATUS_INDEXING_FAILED); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager.createQuery("DELETE FROM ResourceTag t WHERE t.myResourceId = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager .createQuery("DELETE FROM ResourceIndexedSearchParamCoords t WHERE t.myResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager .createQuery("DELETE FROM ResourceIndexedSearchParamDate t WHERE t.myResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager .createQuery("DELETE FROM ResourceIndexedSearchParamNumber t WHERE t.myResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager.createQuery( "DELETE FROM ResourceIndexedSearchParamQuantity t WHERE t.myResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager .createQuery("DELETE FROM ResourceIndexedSearchParamString t WHERE t.myResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager .createQuery("DELETE FROM ResourceIndexedSearchParamToken t WHERE t.myResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager .createQuery("DELETE FROM ResourceIndexedSearchParamUri t WHERE t.myResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.mySourceResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); q = myEntityManager.createQuery("DELETE FROM ResourceLink t WHERE t.myTargetResourcePid = :id"); q.setParameter("id", theId); q.executeUpdate(); return null; } }); } @Override @Transactional(propagation = Propagation.NOT_SUPPORTED) public int performReindexingPass(final Integer theCount) { try { return doPerformReindexingPass(theCount); } catch (ReindexFailureException e) { ourLog.warn("Reindexing failed for resource {}", e.getResourceId()); markResourceAsIndexingFailed(e.getResourceId()); return -1; } } public void setTxManager(PlatformTransactionManager theTxManager) { myTxManager = theTxManager; } protected ResourceTable tryToLoadEntity(IdDt nextId) { ResourceTable entity; try { Long pid = translateForcedIdToPid(nextId.getResourceType(), nextId.getIdPart()); entity = myEntityManager.find(ResourceTable.class, pid); } catch (ResourceNotFoundException e) { entity = null; } return entity; } }