Java tutorial
package ca.uhn.fhir.jpa.dao; /* * #%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 static org.apache.commons.lang3.StringUtils.isNotBlank; import java.util.*; import java.util.Map.Entry; import javax.annotation.PostConstruct; import javax.persistence.NoResultException; import javax.persistence.TypedQuery; import org.hl7.fhir.dstu3.model.IdType; import org.hl7.fhir.instance.model.api.*; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Required; import org.springframework.transaction.PlatformTransactionManager; import org.springframework.transaction.annotation.Propagation; import org.springframework.transaction.annotation.Transactional; import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.context.FhirVersionEnum; import ca.uhn.fhir.context.RuntimeResourceDefinition; import ca.uhn.fhir.context.RuntimeSearchParam; import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao; import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao; import ca.uhn.fhir.jpa.dao.data.ISearchResultDao; import ca.uhn.fhir.jpa.entity.*; import ca.uhn.fhir.jpa.interceptor.IJpaServerInterceptor; import ca.uhn.fhir.jpa.term.IHapiTerminologySvc; import ca.uhn.fhir.jpa.util.DeleteConflict; import ca.uhn.fhir.jpa.util.StopWatch; import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils; import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils; import ca.uhn.fhir.model.api.*; import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.rest.api.PatchTypeEnum; import ca.uhn.fhir.rest.api.RestOperationTypeEnum; import ca.uhn.fhir.rest.method.RequestDetails; import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum; import ca.uhn.fhir.rest.server.IBundleProvider; import ca.uhn.fhir.rest.server.exceptions.*; import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor; import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails; import ca.uhn.fhir.util.FhirTerser; import ca.uhn.fhir.util.ObjectUtil; import ca.uhn.fhir.util.OperationOutcomeUtil; import ca.uhn.fhir.util.ResourceReferenceInfo; @Transactional(propagation = Propagation.REQUIRED) public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends BaseHapiFhirDao<T> implements IFhirResourceDao<T> { private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class); @Autowired private DaoConfig myDaoConfig; @Autowired protected PlatformTransactionManager myPlatformTransactionManager; @Autowired private IResourceHistoryTableDao myResourceHistoryTableDao; @Autowired() protected IResourceIndexedSearchParamUriDao myResourceIndexedSearchParamUriDao; private String myResourceName; private Class<T> myResourceType; @Autowired(required = false) protected IFulltextSearchSvc mySearchDao; @Autowired() protected ISearchResultDao mySearchResultDao; private String mySecondaryPrimaryKeyParamName; @Autowired() protected IHapiTerminologySvc myTerminologySvc; @Override public void addTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) { StopWatch w = new StopWatch(); BaseHasResource entity = readEntity(theId); if (entity == null) { throw new ResourceNotFoundException(theId); } //@formatter:off for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) { if (ObjectUtil.equals(next.getTag().getTagType(), theTagType) && ObjectUtil.equals(next.getTag().getSystem(), theScheme) && ObjectUtil.equals(next.getTag().getCode(), theTerm)) { return; } } //@formatter:on entity.setHasTags(true); TagDefinition def = getTag(TagTypeEnum.TAG, theScheme, theTerm, theLabel); BaseTag newEntity = entity.addTag(def); myEntityManager.persist(newEntity); myEntityManager.merge(entity); ourLog.info("Processed addTag {}/{} on {} in {}ms", new Object[] { theScheme, theTerm, theId, w.getMillisAndRestart() }); } @Override public DaoMethodOutcome create(final T theResource) { return create(theResource, null, true, null); } @Override public DaoMethodOutcome create(final T theResource, RequestDetails theRequestDetails) { return create(theResource, null, true, theRequestDetails); } @Override public DaoMethodOutcome create(final T theResource, String theIfNoneExist) { return create(theResource, theIfNoneExist, null); } @Override public DaoMethodOutcome create(T theResource, String theIfNoneExist, boolean thePerformIndexing, RequestDetails theRequestDetails) { if (isNotBlank(theResource.getIdElement().getIdPart())) { if (getContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU1)) { if (theResource.getIdElement().isIdPartValidLong()) { String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "failedToCreateWithClientAssignedNumericId", theResource.getIdElement().getIdPart()); throw new InvalidRequestException(message, createErrorOperationOutcome(message, "processing")); } } else if (getContext().getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) { String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "failedToCreateWithClientAssignedId", theResource.getIdElement().getIdPart()); throw new InvalidRequestException(message, createErrorOperationOutcome(message, "processing")); } else { // As of DSTU3, ID and version in the body should be ignored for a create/update theResource.setId(""); } } return doCreate(theResource, theIfNoneExist, thePerformIndexing, new Date(), theRequestDetails); } @Override public DaoMethodOutcome create(final T theResource, String theIfNoneExist, RequestDetails theRequestDetails) { return create(theResource, theIfNoneExist, true, theRequestDetails); } public IBaseOperationOutcome createErrorOperationOutcome(String theMessage, String theCode) { return createOperationOutcome(OO_SEVERITY_ERROR, theMessage, theCode); } public IBaseOperationOutcome createInfoOperationOutcome(String theMessage) { return createOperationOutcome(OO_SEVERITY_INFO, theMessage, "informational"); } protected abstract IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode); @Override public DaoMethodOutcome delete(IIdType theId) { return delete(theId, null); } @Override public ResourceTable delete(IIdType theId, List<DeleteConflict> deleteConflicts, RequestDetails theRequestDetails) { if (theId == null || !theId.hasIdPart()) { throw new InvalidRequestException("Can not perform delete, no ID provided"); } final ResourceTable entity = readEntityLatestVersion(theId); if (theId.hasVersionIdPart() && Long.parseLong(theId.getVersionIdPart()) != entity.getVersion()) { throw new ResourceVersionConflictException( "Trying to delete " + theId + " but this is not the current version"); } validateOkToDelete(deleteConflicts, entity); // Notify interceptors if (theRequestDetails != null) { ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), theId.getResourceType(), theId); notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails); } Date updateTime = new Date(); ResourceTable savedEntity = updateEntity(null, entity, updateTime, updateTime); // Notify JPA interceptors if (theRequestDetails != null) { ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), theId.getResourceType(), theId); T resourceToDelete = toResource(myResourceType, entity, false); theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete); for (IServerInterceptor next : getConfig().getInterceptors()) { if (next instanceof IJpaServerInterceptor) { ((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity); } } } return savedEntity; } @Override public DaoMethodOutcome delete(IIdType theId, RequestDetails theRequestDetails) { List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>(); StopWatch w = new StopWatch(); ResourceTable savedEntity = delete(theId, deleteConflicts, theRequestDetails); validateDeleteConflictsEmptyOrThrowException(deleteConflicts); ourLog.info("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart()); return toMethodOutcome(savedEntity, null); } @Override public List<ResourceTable> deleteByUrl(String theUrl, List<DeleteConflict> deleteConflicts, RequestDetails theRequestDetails) { Set<Long> resource = processMatchUrl(theUrl, myResourceType); if (resource.size() > 1) { if (myDaoConfig.isAllowMultipleDelete() == false) { throw new PreconditionFailedException(getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "DELETE", theUrl, resource.size())); } } List<ResourceTable> retVal = new ArrayList<ResourceTable>(); for (Long pid : resource) { ResourceTable entity = myEntityManager.find(ResourceTable.class, pid); retVal.add(entity); validateOkToDelete(deleteConflicts, entity); // Notify interceptors IdDt idToDelete = entity.getIdDt(); ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, idToDelete.getResourceType(), idToDelete); notifyInterceptors(RestOperationTypeEnum.DELETE, requestDetails); // Perform delete Date updateTime = new Date(); updateEntity(null, entity, updateTime, updateTime); // Notify JPA interceptors T resourceToDelete = toResource(myResourceType, entity, false); theRequestDetails.getRequestOperationCallback().resourceDeleted(resourceToDelete); for (IServerInterceptor next : getConfig().getInterceptors()) { if (next instanceof IJpaServerInterceptor) { ((IJpaServerInterceptor) next).resourceDeleted(requestDetails, entity); } } } return retVal; } @Override public DaoMethodOutcome deleteByUrl(String theUrl, RequestDetails theRequestDetails) { StopWatch w = new StopWatch(); List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>(); List<ResourceTable> deletedResources = deleteByUrl(theUrl, deleteConflicts, theRequestDetails); validateDeleteConflictsEmptyOrThrowException(deleteConflicts); IBaseOperationOutcome oo; if (deletedResources.isEmpty()) { oo = OperationOutcomeUtil.newInstance(getContext()); String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "unableToDeleteNotFound", theUrl); String severity = "warning"; String code = "not-found"; OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code); } else { oo = OperationOutcomeUtil.newInstance(getContext()); String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", theUrl, deletedResources.size(), w.getMillis()); String severity = "information"; String code = "informational"; OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code); } ourLog.info("Processed delete on {} (matched {} resource(s)) in {}ms", new Object[] { theUrl, deletedResources.size(), w.getMillis() }); DaoMethodOutcome retVal = new DaoMethodOutcome(); retVal.setOperationOutcome(oo); return retVal; } @PostConstruct public void detectSearchDaoDisabled() { if (mySearchDao != null && mySearchDao.isDisabled()) { mySearchDao = null; } } private DaoMethodOutcome doCreate(T theResource, String theIfNoneExist, boolean thePerformIndexing, Date theUpdateTime, RequestDetails theRequestDetails) { StopWatch w = new StopWatch(); preProcessResourceForStorage(theResource); ResourceTable entity = new ResourceTable(); entity.setResourceType(toResourceName(theResource)); if (isNotBlank(theIfNoneExist)) { Set<Long> match = processMatchUrl(theIfNoneExist, myResourceType); if (match.size() > 1) { String msg = getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size()); throw new PreconditionFailedException(msg); } else if (match.size() == 1) { Long pid = match.iterator().next(); entity = myEntityManager.find(ResourceTable.class, pid); return toMethodOutcome(entity, theResource).setCreated(false); } } if (isNotBlank(theResource.getIdElement().getIdPart())) { if (isValidPid(theResource.getIdElement())) { throw new UnprocessableEntityException( "This server cannot create an entity with a user-specified numeric ID - Client should not specify an ID when creating a new resource, or should include at least one letter in the ID to force a client-defined ID"); } createForcedIdIfNeeded(entity, theResource.getIdElement()); if (entity.getForcedId() != null) { try { translateForcedIdToPid(getResourceName(), theResource.getIdElement().getIdPart()); throw new UnprocessableEntityException( getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "duplicateCreateForcedId", theResource.getIdElement().getIdPart())); } catch (ResourceNotFoundException e) { // good, this ID doesn't exist so we can create it } } } // Notify interceptors if (theRequestDetails != null) { ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), theResource); notifyInterceptors(RestOperationTypeEnum.CREATE, requestDetails); } // Perform actual DB update updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, theUpdateTime); theResource.setId(entity.getIdDt()); // Notify JPA interceptors if (theRequestDetails != null) { ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), theResource); theRequestDetails.getRequestOperationCallback().resourceCreated(theResource); for (IServerInterceptor next : getConfig().getInterceptors()) { if (next instanceof IJpaServerInterceptor) { ((IJpaServerInterceptor) next).resourceCreated(requestDetails, entity); } } } DaoMethodOutcome outcome = toMethodOutcome(entity, theResource).setCreated(true); String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulCreate", outcome.getId(), w.getMillisAndRestart()); outcome.setOperationOutcome(createInfoOperationOutcome(msg)); ourLog.info(msg); return outcome; } private <MT extends IBaseMetaType> void doMetaAdd(MT theMetaAdd, BaseHasResource entity) { List<TagDefinition> tags = toTagList(theMetaAdd); //@formatter:off for (TagDefinition nextDef : tags) { boolean hasTag = false; for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) { if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) { hasTag = true; break; } } if (!hasTag) { entity.setHasTags(true); TagDefinition def = getTag(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay()); BaseTag newEntity = entity.addTag(def); myEntityManager.persist(newEntity); } } //@formatter:on myEntityManager.merge(entity); } private <MT extends IBaseMetaType> void doMetaDelete(MT theMetaDel, BaseHasResource entity) { List<TagDefinition> tags = toTagList(theMetaDel); //@formatter:off for (TagDefinition nextDef : tags) { for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) { if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) { myEntityManager.remove(next); entity.getTags().remove(next); } } } //@formatter:on if (entity.getTags().isEmpty()) { entity.setHasTags(false); } myEntityManager.merge(entity); } @Override public TagList getAllResourceTags(RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails); notifyInterceptors(RestOperationTypeEnum.GET_TAGS, requestDetails); StopWatch w = new StopWatch(); TagList tags = super.getTags(myResourceType, null); ourLog.info("Processed getTags on {} in {}ms", myResourceName, w.getMillisAndRestart()); return tags; } protected abstract List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IBaseResource theResource, RuntimeResourceDefinition theResourceDef); public String getResourceName() { return myResourceName; } @Override public Class<T> getResourceType() { return myResourceType; } @Override public TagList getTags(IIdType theResourceId, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, null, theResourceId); notifyInterceptors(RestOperationTypeEnum.GET_TAGS, requestDetails); StopWatch w = new StopWatch(); TagList retVal = super.getTags(myResourceType, theResourceId); ourLog.info("Processed getTags on {} in {}ms", theResourceId, w.getMillisAndRestart()); return retVal; } @Override public IBundleProvider history(Date theSince, Date theUntil, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails); notifyInterceptors(RestOperationTypeEnum.HISTORY_TYPE, requestDetails); StopWatch w = new StopWatch(); IBundleProvider retVal = super.history(myResourceName, null, theSince, theUntil); ourLog.info("Processed history on {} in {}ms", myResourceName, w.getMillisAndRestart()); return retVal; } @Override public IBundleProvider history(final IIdType theId, final Date theSince, Date theUntil, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theId); notifyInterceptors(RestOperationTypeEnum.HISTORY_INSTANCE, requestDetails); StopWatch w = new StopWatch(); IIdType id = theId.withResourceType(myResourceName).toUnqualifiedVersionless(); BaseHasResource entity = readEntity(id); IBundleProvider retVal = super.history(myResourceName, entity.getId(), theSince, theUntil); ourLog.info("Processed history on {} in {}ms", id, w.getMillisAndRestart()); return retVal; } @Override public <MT extends IBaseMetaType> MT metaAddOperation(IIdType theResourceId, MT theMetaAdd, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theResourceId); notifyInterceptors(RestOperationTypeEnum.META_ADD, requestDetails); StopWatch w = new StopWatch(); BaseHasResource entity = readEntity(theResourceId); if (entity == null) { throw new ResourceNotFoundException(theResourceId); } ResourceTable latestVersion = readEntityLatestVersion(theResourceId); if (latestVersion.getVersion() != entity.getVersion()) { doMetaAdd(theMetaAdd, entity); } else { doMetaAdd(theMetaAdd, latestVersion); // Also update history entry ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(entity.getId(), entity.getVersion()); doMetaAdd(theMetaAdd, history); } ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[] { theResourceId, w.getMillisAndRestart() }); @SuppressWarnings("unchecked") MT retVal = (MT) metaGetOperation(theMetaAdd.getClass(), theResourceId, theRequestDetails); return retVal; } // @Override // public IBundleProvider everything(IIdType theId) { // Search search = new Search(); // search.setUuid(UUID.randomUUID().toString()); // search.setCreated(new Date()); // myEntityManager.persist(search); // // List<SearchResult> results = new ArrayList<SearchResult>(); // if (theId != null) { // Long pid = translateForcedIdToPid(theId); // ResourceTable entity = myEntityManager.find(ResourceTable.class, pid); // validateGivenIdIsAppropriateToRetrieveResource(theId, entity); // SearchResult res = new SearchResult(search); // res.setResourcePid(pid); // results.add(res); // } else { // TypedQuery<Tuple> query = createSearchAllByTypeQuery(); // for (Tuple next : query.getResultList()) { // SearchResult res = new SearchResult(search); // res.setResourcePid(next.get(0, Long.class)); // results.add(res); // } // } // // int totalCount = results.size(); // mySearchResultDao.save(results); // mySearchResultDao.flush(); // // CriteriaBuilder builder = myEntityManager.getCriteriaBuilder(); // // // Load _revincludes // CriteriaQuery<Long> cq = builder.createQuery(Long.class); // Root<ResourceLink> from = cq.from(ResourceLink.class); // cq.select(from.get("mySourceResourcePid").as(Long.class)); // // Subquery<Long> pidsSubquery = cq.subquery(Long.class); // Root<SearchResult> pidsSubqueryFrom = pidsSubquery.from(SearchResult.class); // pidsSubquery.select(pidsSubqueryFrom.get("myResourcePid").as(Long.class)); // pidsSubquery.where(pidsSubqueryFrom.get("mySearch").in(search)); // // cq.where(from.get("myTargetResourceId").in(pidsSubquery)); // TypedQuery<Long> query = myEntityManager.createQuery(cq); // // results = new ArrayList<SearchResult>(); // for (Long next : query.getResultList()) { // SearchResult res = new SearchResult(search); // res.setResourcePid(next); // results.add(res); // } // // // Save _revincludes // totalCount += results.size(); // mySearchResultDao.save(results); // mySearchResultDao.flush(); // // final int finalTotalCount = totalCount; // return new IBundleProvider() { // // @Override // public int size() { // return finalTotalCount; // } // // @Override // public Integer preferredPageSize() { // return null; // } // // @Override // public List<IBaseResource> getResources(int theFromIndex, int theToIndex) { // // TODO Auto-generated method stub // return null; // } // // @Override // public InstantDt getPublished() { // // TODO Auto-generated method stub // return null; // } // }; // } @Override public <MT extends IBaseMetaType> MT metaDeleteOperation(IIdType theResourceId, MT theMetaDel, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theResourceId); notifyInterceptors(RestOperationTypeEnum.META_DELETE, requestDetails); StopWatch w = new StopWatch(); BaseHasResource entity = readEntity(theResourceId); if (entity == null) { throw new ResourceNotFoundException(theResourceId); } ResourceTable latestVersion = readEntityLatestVersion(theResourceId); if (latestVersion.getVersion() != entity.getVersion()) { doMetaDelete(theMetaDel, entity); } else { doMetaDelete(theMetaDel, latestVersion); // Also update history entry ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(entity.getId(), entity.getVersion()); doMetaDelete(theMetaDel, history); } myEntityManager.flush(); ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() }); @SuppressWarnings("unchecked") MT retVal = (MT) metaGetOperation(theMetaDel.getClass(), theResourceId, theRequestDetails); return retVal; } @Override public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, IIdType theId, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theId); notifyInterceptors(RestOperationTypeEnum.META, requestDetails); Set<TagDefinition> tagDefs = new HashSet<TagDefinition>(); BaseHasResource entity = readEntity(theId); for (BaseTag next : entity.getTags()) { tagDefs.add(next.getTag()); } MT retVal = toMetaDt(theType, tagDefs); retVal.setLastUpdated(entity.getUpdatedDate()); retVal.setVersionId(Long.toString(entity.getVersion())); return retVal; } @Override public <MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), null); notifyInterceptors(RestOperationTypeEnum.META, requestDetails); String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t WHERE t.myResourceType = :res_type)"; TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class); q.setParameter("res_type", myResourceName); List<TagDefinition> tagDefinitions = q.getResultList(); MT retVal = toMetaDt(theType, tagDefinitions); return retVal; } @PostConstruct public void postConstruct() { RuntimeResourceDefinition def = getContext().getResourceDefinition(myResourceType); myResourceName = def.getName(); if (mySecondaryPrimaryKeyParamName != null) { RuntimeSearchParam sp = def.getSearchParam(mySecondaryPrimaryKeyParamName); if (sp == null) { throw new ConfigurationException("Unknown search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName + "]"); } if (sp.getParamType() != RestSearchParameterTypeEnum.TOKEN) { throw new ConfigurationException("Search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName + "] is not a token type, only token is supported"); } } } /** * May be overridden by subclasses to validate resources prior to storage * * @param theResource * The resource that is about to be stored */ protected void preProcessResourceForStorage(T theResource) { String type = getContext().getResourceDefinition(theResource).getName(); if (!getResourceName().equals(type)) { throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "incorrectResourceType", type, getResourceName())); } if (theResource.getIdElement().hasIdPart()) { if (!theResource.getIdElement().isIdPartValid()) { throw new InvalidRequestException( getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "failedToCreateWithInvalidId", theResource.getIdElement().getIdPart())); } } /* * Replace absolute references with relative ones if configured to do so */ if (getConfig().getTreatBaseUrlsAsLocal().isEmpty() == false) { FhirTerser t = getContext().newTerser(); List<ResourceReferenceInfo> refs = t.getAllResourceReferences(theResource); for (ResourceReferenceInfo nextRef : refs) { IIdType refId = nextRef.getResourceReference().getReferenceElement(); if (refId != null && refId.hasBaseUrl()) { if (getConfig().getTreatBaseUrlsAsLocal().contains(refId.getBaseUrl())) { IIdType newRefId = refId.toUnqualified(); nextRef.getResourceReference().setReference(newRefId.getValue()); } } } } } @Override public Set<Long> processMatchUrl(String theMatchUrl) { return processMatchUrl(theMatchUrl, getResourceType()); } @Override public T read(IIdType theId) { return read(theId, null); } @Override public T read(IIdType theId, RequestDetails theRequestDetails) { validateResourceTypeAndThrowIllegalArgumentException(theId); // Notify interceptors if (theRequestDetails != null) { ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theId); RestOperationTypeEnum operationType = theId.hasVersionIdPart() ? RestOperationTypeEnum.VREAD : RestOperationTypeEnum.READ; notifyInterceptors(operationType, requestDetails); } StopWatch w = new StopWatch(); BaseHasResource entity = readEntity(theId); validateResourceType(entity); T retVal = toResource(myResourceType, entity, false); IPrimitiveType<Date> deleted; if (retVal instanceof IResource) { deleted = ResourceMetadataKeyEnum.DELETED_AT.get((IResource) retVal); } else { deleted = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) retVal); } if (deleted != null && !deleted.isEmpty()) { throw new ResourceGoneException("Resource was deleted at " + deleted.getValueAsString()); } ourLog.info("Processed read on {} in {}ms", theId.getValue(), w.getMillisAndRestart()); return retVal; } @Override public BaseHasResource readEntity(IIdType theId) { boolean checkForForcedId = true; BaseHasResource entity = readEntity(theId, checkForForcedId); return entity; } @Override public BaseHasResource readEntity(IIdType theId, boolean theCheckForForcedId) { validateResourceTypeAndThrowIllegalArgumentException(theId); Long pid = translateForcedIdToPid(getResourceName(), theId.getIdPart()); BaseHasResource entity = myEntityManager.find(ResourceTable.class, pid); if (entity == null) { throw new ResourceNotFoundException(theId); } if (theId.hasVersionIdPart()) { if (theId.isVersionIdPartValidLong() == false) { throw new ResourceNotFoundException( getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidVersion", theId.getVersionIdPart(), theId.toUnqualifiedVersionless())); } if (entity.getVersion() != theId.getVersionIdPartAsLong().longValue()) { entity = null; } } if (entity == null) { if (theId.hasVersionIdPart()) { TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery( "SELECT t from ResourceHistoryTable t WHERE t.myResourceId = :RID AND t.myResourceType = :RTYP AND t.myResourceVersion = :RVER", ResourceHistoryTable.class); q.setParameter("RID", pid); q.setParameter("RTYP", myResourceName); q.setParameter("RVER", theId.getVersionIdPartAsLong()); try { entity = q.getSingleResult(); } catch (NoResultException e) { throw new ResourceNotFoundException( getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidVersion", theId.getVersionIdPart(), theId.toUnqualifiedVersionless())); } } } validateResourceType(entity); if (theCheckForForcedId) { validateGivenIdIsAppropriateToRetrieveResource(theId, entity); } return entity; } protected ResourceTable readEntityLatestVersion(IIdType theId) { ResourceTable entity = myEntityManager.find(ResourceTable.class, translateForcedIdToPid(getResourceName(), theId.getIdPart())); if (entity == null) { throw new ResourceNotFoundException(theId); } validateGivenIdIsAppropriateToRetrieveResource(theId, entity); return entity; } @Override public void reindex(T theResource, ResourceTable theEntity) { updateEntity(theResource, theEntity, null, true, false, theEntity.getUpdatedDate()); } @Override public void removeTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, RequestDetails theRequestDetails) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getResourceName(), theId); notifyInterceptors(RestOperationTypeEnum.DELETE_TAGS, requestDetails); StopWatch w = new StopWatch(); BaseHasResource entity = readEntity(theId); if (entity == null) { throw new ResourceNotFoundException(theId); } //@formatter:off for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) { if (ObjectUtil.equals(next.getTag().getTagType(), theTagType) && ObjectUtil.equals(next.getTag().getSystem(), theScheme) && ObjectUtil.equals(next.getTag().getCode(), theTerm)) { myEntityManager.remove(next); entity.getTags().remove(next); } } //@formatter:on if (entity.getTags().isEmpty()) { entity.setHasTags(false); } myEntityManager.merge(entity); ourLog.info("Processed remove tag {}/{} on {} in {}ms", new Object[] { theScheme, theTerm, theId.getValue(), w.getMillisAndRestart() }); } @Override public IBundleProvider search(Map<String, IQueryParameterType> theParams) { SearchParameterMap map = new SearchParameterMap(); for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) { map.add(nextEntry.getKey(), (nextEntry.getValue())); } return search(map); } @Override public IBundleProvider search(final SearchParameterMap theParams) { // Notify interceptors ActionRequestDetails requestDetails = new ActionRequestDetails(theParams.getRequestDetails(), getContext(), getResourceName(), null); notifyInterceptors(RestOperationTypeEnum.SEARCH_TYPE, requestDetails); SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao, myTerminologySvc); builder.setType(getResourceType(), getResourceName()); return builder.search(theParams); } @Override public IBundleProvider search(String theParameterName, IQueryParameterType theValue) { return search(Collections.singletonMap(theParameterName, theValue)); } @Override public Set<Long> searchForIds(Map<String, IQueryParameterType> theParams) { SearchParameterMap map = new SearchParameterMap(); for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) { map.add(nextEntry.getKey(), (nextEntry.getValue())); } return searchForIdsWithAndOr(map); } @Override public Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue) { return searchForIds(Collections.singletonMap(theParameterName, theValue)); } @Override public Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams) { theParams.setPersistResults(false); SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao, myTerminologySvc); builder.setType(getResourceType(), getResourceName()); builder.search(theParams); return builder.doGetPids(); } @SuppressWarnings("unchecked") @Required public void setResourceType(Class<? extends IBaseResource> theTableType) { myResourceType = (Class<T>) theTableType; } /** * If set, the given param will be treated as a secondary primary key, and multiple resources will not be able to share the same value. */ public void setSecondaryPrimaryKeyParamName(String theSecondaryPrimaryKeyParamName) { mySecondaryPrimaryKeyParamName = theSecondaryPrimaryKeyParamName; } protected <MT extends IBaseMetaType> MT toMetaDt(Class<MT> theType, Collection<TagDefinition> tagDefinitions) { MT retVal; try { retVal = theType.newInstance(); } catch (Exception e) { throw new InternalErrorException("Failed to instantiate " + theType.getName(), e); } for (TagDefinition next : tagDefinitions) { switch (next.getTagType()) { case PROFILE: retVal.addProfile(next.getCode()); break; case SECURITY_LABEL: retVal.addSecurity().setSystem(next.getSystem()).setCode(next.getCode()) .setDisplay(next.getDisplay()); break; case TAG: retVal.addTag().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay()); break; } } return retVal; } private DaoMethodOutcome toMethodOutcome(final BaseHasResource theEntity, IBaseResource theResource) { DaoMethodOutcome outcome = new DaoMethodOutcome(); IIdType id = theEntity.getIdDt(); if (getContext().getVersion().getVersion().isRi()) { id = new IdType(id.getValue()); } outcome.setId(id); outcome.setResource(theResource); if (theResource != null) { theResource.setId(id); if (theResource instanceof IResource) { ResourceMetadataKeyEnum.UPDATED.put((IResource) theResource, theEntity.getUpdated()); } else { IBaseMetaType meta = ((IAnyResource) theResource).getMeta(); meta.setLastUpdated(theEntity.getUpdatedDate()); } } return outcome; } private DaoMethodOutcome toMethodOutcome(final ResourceTable theEntity, IBaseResource theResource) { DaoMethodOutcome retVal = toMethodOutcome((BaseHasResource) theEntity, theResource); retVal.setEntity(theEntity); return retVal; } private ArrayList<TagDefinition> toTagList(IBaseMetaType theMeta) { ArrayList<TagDefinition> retVal = new ArrayList<TagDefinition>(); for (IBaseCoding next : theMeta.getTag()) { retVal.add(new TagDefinition(TagTypeEnum.TAG, next.getSystem(), next.getCode(), next.getDisplay())); } for (IBaseCoding next : theMeta.getSecurity()) { retVal.add(new TagDefinition(TagTypeEnum.SECURITY_LABEL, next.getSystem(), next.getCode(), next.getDisplay())); } for (IPrimitiveType<String> next : theMeta.getProfile()) { retVal.add( new TagDefinition(TagTypeEnum.PROFILE, BaseHapiFhirDao.NS_JPA_PROFILE, next.getValue(), null)); } return retVal; } @Override public DaoMethodOutcome update(T theResource) { return update(theResource, null, null); } @Override public DaoMethodOutcome update(T theResource, RequestDetails theRequestDetails) { return update(theResource, null, theRequestDetails); } @Override public DaoMethodOutcome update(T theResource, String theMatchUrl) { return update(theResource, theMatchUrl, null); } @Override public DaoMethodOutcome update(T theResource, String theMatchUrl, boolean thePerformIndexing, RequestDetails theRequestDetails) { StopWatch w = new StopWatch(); preProcessResourceForStorage(theResource); final ResourceTable entity; IIdType resourceId; if (isNotBlank(theMatchUrl)) { Set<Long> match = processMatchUrl(theMatchUrl, myResourceType); if (match.size() > 1) { String msg = getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "UPDATE", theMatchUrl, match.size()); throw new PreconditionFailedException(msg); } else if (match.size() == 1) { Long pid = match.iterator().next(); entity = myEntityManager.find(ResourceTable.class, pid); resourceId = entity.getIdDt(); } else { return create(theResource, null, thePerformIndexing, theRequestDetails); } } else { /* * Note: resourcdeId will not be null or empty here, because we check it and reject requests in BaseOutcomeReturningMethodBindingWithResourceParam */ resourceId = theResource.getIdElement(); try { entity = readEntityLatestVersion(resourceId); } catch (ResourceNotFoundException e) { if (resourceId.isIdPartValidLong()) { throw new InvalidRequestException(getContext().getLocalizer().getMessage( BaseHapiFhirResourceDao.class, "failedToCreateWithClientAssignedNumericId", theResource.getIdElement().getIdPart())); } return doCreate(theResource, null, thePerformIndexing, new Date(), theRequestDetails); } } if (resourceId.hasVersionIdPart() && Long.parseLong(resourceId.getVersionIdPart()) != entity.getVersion()) { throw new ResourceVersionConflictException( "Trying to update " + resourceId + " but this is not the current version"); } if (resourceId.hasResourceType() && !resourceId.getResourceType().equals(getResourceName())) { throw new UnprocessableEntityException( "Invalid resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] of type[" + entity.getResourceType() + "] - Does not match expected [" + getResourceName() + "]"); } // Notify interceptors ActionRequestDetails requestDetails = null; if (theRequestDetails != null) { requestDetails = new ActionRequestDetails(theRequestDetails, theResource, getResourceName(), resourceId); notifyInterceptors(RestOperationTypeEnum.UPDATE, requestDetails); } // Perform update ResourceTable savedEntity = updateEntity(theResource, entity, null, thePerformIndexing, thePerformIndexing, new Date()); // Notify interceptors if (theRequestDetails != null) { theRequestDetails.getRequestOperationCallback().resourceUpdated(theResource); for (IServerInterceptor next : getConfig().getInterceptors()) { if (next instanceof IJpaServerInterceptor) { ((IJpaServerInterceptor) next).resourceUpdated(requestDetails, entity); } } } DaoMethodOutcome outcome = toMethodOutcome(savedEntity, theResource).setCreated(false); String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulCreate", outcome.getId(), w.getMillisAndRestart()); outcome.setOperationOutcome(createInfoOperationOutcome(msg)); ourLog.info(msg); return outcome; } @Override public DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails) { ResourceTable entityToUpdate = readEntityLatestVersion(theId); if (theId.hasVersionIdPart()) { if (theId.getVersionIdPartAsLong() != entityToUpdate.getVersion()) { throw new ResourceVersionConflictException("Version " + theId.getVersionIdPart() + " is not the most recent version of this resource, unable to apply patch"); } } validateResourceType(entityToUpdate); IBaseResource resourceToUpdate = toResource(entityToUpdate, false); IBaseResource destination; if (thePatchType == PatchTypeEnum.JSON_PATCH) { destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody); } else { destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody); } @SuppressWarnings("unchecked") T destinationCasted = (T) destination; return update(destinationCasted, null, true, theRequestDetails); } @Override public DaoMethodOutcome update(T theResource, String theMatchUrl, RequestDetails theRequestDetails) { return update(theResource, theMatchUrl, true, theRequestDetails); } private void validateGivenIdIsAppropriateToRetrieveResource(IIdType theId, BaseHasResource entity) { if (entity.getForcedId() != null) { if (theId.isIdPartValidLong()) { // This means that the resource with the given numeric ID exists, but it has a "forced ID", meaning that // as far as the outside world is concerned, the given ID doesn't exist (it's just an internal pointer // to the // forced ID) throw new ResourceNotFoundException(theId); } } } protected void validateOkToDelete(List<DeleteConflict> theDeleteConflicts, ResourceTable theEntity) { TypedQuery<ResourceLink> query = myEntityManager.createQuery( "SELECT l FROM ResourceLink l WHERE l.myTargetResourcePid = :target_pid", ResourceLink.class); query.setParameter("target_pid", theEntity.getId()); query.setMaxResults(1); List<ResourceLink> resultList = query.getResultList(); if (resultList.isEmpty()) { return; } ResourceLink link = resultList.get(0); IdDt targetId = theEntity.getIdDt(); IdDt sourceId = link.getSourceResource().getIdDt(); String sourcePath = link.getSourcePath(); theDeleteConflicts.add(new DeleteConflict(sourceId, sourcePath, targetId)); } private void validateResourceType(BaseHasResource entity) { validateResourceType(entity, myResourceName); } private void validateResourceTypeAndThrowIllegalArgumentException(IIdType theId) { if (theId.hasResourceType() && !theId.getResourceType().equals(myResourceName)) { throw new IllegalArgumentException("Incorrect resource type (" + theId.getResourceType() + ") for this DAO, wanted: " + myResourceName); } } }