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

This commit is contained in:
James Agnew 2018-07-01 11:49:53 -04:00
parent faaac4a2e8 6ef34a8c5f
commit e158d88f50
8 changed files with 517 additions and 166 deletions
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307
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -1,5 +1,86 @@
package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.compare;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
import java.io.CharArrayWriter;
import java.io.UnsupportedEncodingException;
import java.text.Normalizer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.UUID;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.Tuple;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.apache.http.client.utils.URLEncodedUtils;
import org.hibernate.Session;
import org.hibernate.internal.SessionImpl;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.BaseResource;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.Reference;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.domain.SliceImpl;
import org.springframework.stereotype.Repository;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Sets;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
/*
* #%L
* HAPI FHIR JPA Server
@ -19,10 +100,70 @@ package ca.uhn.fhir.jpa.dao;
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamCoordsDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamDateDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamNumberDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamQuantityDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamTokenDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.entity.BaseTag;
import ca.uhn.fhir.jpa.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.IBaseResourceEntity;
import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
import ca.uhn.fhir.jpa.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.entity.ResourceLink;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.ResourceTag;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.entity.SearchInclude;
import ca.uhn.fhir.jpa.entity.SearchParam;
import ca.uhn.fhir.jpa.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.entity.SearchResult;
import ca.uhn.fhir.jpa.entity.SearchStatusEnum;
import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.entity.TagDefinition;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
@ -32,7 +173,12 @@ import ca.uhn.fhir.jpa.util.DeleteConflict;
import ca.uhn.fhir.jpa.util.ExpungeOptions;
import ca.uhn.fhir.jpa.util.ExpungeOutcome;
import ca.uhn.fhir.jpa.util.JpaConstants;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.primitive.IdDt;
@ -48,61 +194,31 @@ import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriAndListParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.*;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.apache.http.client.utils.URLEncodedUtils;
import org.hibernate.Session;
import org.hibernate.internal.SessionImpl;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.r4.model.BaseResource;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.Reference;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.domain.SliceImpl;
import org.springframework.stereotype.Repository;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import javax.persistence.*;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
import java.io.CharArrayWriter;
import java.io.UnsupportedEncodingException;
import java.text.Normalizer;
import java.util.*;
import java.util.Map.Entry;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.*;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.XmlUtil;
@SuppressWarnings("WeakerAccess")
@Repository
@ -186,6 +302,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
protected IResourceTableDao myResourceTableDao;
@Autowired
protected IResourceTagDao myResourceTagDao;
@Autowired
protected IResourceSearchViewDao myResourceViewDao;
@Autowired(required = true)
private DaoConfig myConfig;
private FhirContext myContext;
@ -199,8 +317,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
private ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
@Autowired
private ISearchResultDao mySearchResultDao;
//@Autowired
//private ISearchResultDao mySearchResultDao;
@Autowired
private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
private ApplicationContext myApplicationContext;
@ -1174,7 +1292,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
public SearchBuilder newSearchBuilder() {
SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myFulltextSearchSvc, this, myResourceIndexedSearchParamUriDao,
myForcedIdDao,
myTerminologySvc, mySerarchParamRegistry, myResourceHistoryTableDao, myResourceTagDao);
myTerminologySvc, mySerarchParamRegistry, myResourceTagDao, myResourceViewDao);
return builder;
}
@ -1223,7 +1341,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
}
private void populateResourceIdFromEntity(BaseHasResource theEntity, final IBaseResource theResource) {
private void populateResourceIdFromEntity(IBaseResourceEntity theEntity, final IBaseResource theResource) {
IIdType id = theEntity.getIdDt();
if (getContext().getVersion().getVersion().isRi()) {
id = getContext().getVersion().newIdType().setValue(id.getValue());
@ -1355,7 +1473,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
@SuppressWarnings("unchecked")
private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, BaseHasResource theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res) {
private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res) {
R retVal = (R) res;
if (theEntity.getDeleted() != null) {
res = (IResource) myContext.getResourceDefinition(theResourceType).newInstance();
@ -1421,7 +1539,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
@SuppressWarnings("unchecked")
private <R extends IBaseResource> R populateResourceMetadataRi(Class<R> theResourceType, BaseHasResource theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res) {
private <R extends IBaseResource> R populateResourceMetadataRi(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res) {
R retVal = (R) res;
if (theEntity.getDeleted() != null) {
res = (IAnyResource) myContext.getResourceDefinition(theResourceType).newInstance();
@ -1601,34 +1719,47 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
public IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation) {
RuntimeResourceDefinition type = myContext.getResourceDefinition(theEntity.getResourceType());
Class<? extends IBaseResource> resourceType = type.getImplementingClass();
return toResource(resourceType, theEntity, null, null, theForHistoryOperation);
return toResource(resourceType, theEntity, null, theForHistoryOperation);
}
@SuppressWarnings("unchecked")
@Override
public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, ResourceHistoryTable theHistory, Collection<ResourceTag> theTagList,
boolean theForHistoryOperation) {
public <R extends IBaseResource> R toResource(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<ResourceTag> theTagList, boolean theForHistoryOperation) {
// 1. get resource, it's encoding and the tags if any
byte[] resourceBytes = null;
ResourceEncodingEnum resourceEncoding = null;
Collection<? extends BaseTag> myTagList = null;
// May 28, 2018 - #936
// Could set historyList to null, if it's not called in the loop for the backward compatibility
ResourceHistoryTable history;
if (theEntity instanceof ResourceHistoryTable) {
history = (ResourceHistoryTable) theEntity;
} else {
if (theHistory == null) {
history = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
} else {
history = theHistory;
}
}
ResourceHistoryTable history = (ResourceHistoryTable) theEntity;
resourceBytes = history.getResource();
resourceEncoding = history.getEncoding();
myTagList = history.getTags();
} else if (theEntity instanceof ResourceTable) {
ResourceTable resource = (ResourceTable)theEntity;
ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
if (history == null) {
return null;
}
resourceBytes = history.getResource();
resourceEncoding = history.getEncoding();
myTagList = resource.getTags();
} else if (theEntity instanceof ResourceSearchView) {
// This is the search View
ResourceSearchView myView = (ResourceSearchView)theEntity;
resourceBytes = myView.getResource();
resourceEncoding = myView.getEncoding();
if (theTagList == null)
myTagList = new HashSet<>();
else
myTagList = theTagList;
} else {
// something wrong
return null;
}
byte[] resourceBytes = history.getResource();
ResourceEncodingEnum resourceEncoding = history.getEncoding();
// 2. get The text
String resourceText = null;
switch (resourceEncoding) {
case JSON:
@ -1645,18 +1776,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
break;
}
// get preload the tagList
Collection<? extends BaseTag> myTagList;
if (theTagList == null)
myTagList = theEntity.getTags();
else
myTagList = theTagList;
/*
* Use the appropriate custom type if one is specified in the context
*/
// 3. Use the appropriate custom type if one is specified in the context
Class<R> resourceType = theResourceType;
if (myContext.hasDefaultTypeForProfile()) {
for (BaseTag nextTag : myTagList) {
@ -1674,6 +1794,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
}
// 4. parse the text to FHIR
R retVal;
if (resourceEncoding != ResourceEncodingEnum.DEL) {
IParser parser = resourceEncoding.newParser(getContext(theEntity.getFhirVersion()));
@ -1704,6 +1825,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
// 5. fill MetaData
if (retVal instanceof IResource) {
IResource res = (IResource) retVal;
retVal = populateResourceMetadataHapi(resourceType, theEntity, myTagList, theForHistoryOperation, res);
@ -1712,7 +1834,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
retVal = populateResourceMetadataRi(resourceType, theEntity, myTagList, theForHistoryOperation, res);
}
return retVal;
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -207,7 +207,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
StopWatch w = new StopWatch();
T resourceToDelete = toResource(myResourceType, entity, null, null, false);
T resourceToDelete = toResource(myResourceType, entity, null, false);
// Notify IServerOperationInterceptors about pre-action call
if (theReques != null) {
@ -289,7 +289,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
ResourceTable entity = myEntityManager.find(ResourceTable.class, pid);
deletedResources.add(entity);
T resourceToDelete = toResource(myResourceType, entity, null, null, false);
T resourceToDelete = toResource(myResourceType, entity, null, false);
// Notify IServerOperationInterceptors about pre-action call
if (theRequest != null) {
@ -854,7 +854,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
BaseHasResource entity = readEntity(theId);
validateResourceType(entity);
T retVal = toResource(myResourceType, entity, null, null, false);
T retVal = toResource(myResourceType, entity, null, false);
IPrimitiveType<Date> deleted;
if (retVal instanceof IResource) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IDao.java
View File

@ -9,7 +9,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.IBaseResourceEntity;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.ResourceTag;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
@ -59,6 +59,6 @@ public interface IDao {
IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation);
<R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, ResourceHistoryTable theHistory, Collection<ResourceTag> theTagList, boolean theForHistoryOperation);
<R extends IBaseResource> R toResource(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<ResourceTag> theTagList, boolean theForHistoryOperation);
}

82
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -85,6 +85,7 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.entity.ForcedId;
@ -98,6 +99,7 @@ import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.entity.ResourceLink;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.ResourceTag;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.entity.SearchParam;
import ca.uhn.fhir.jpa.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.entity.TagDefinition;
@ -174,8 +176,8 @@ public class SearchBuilder implements ISearchBuilder {
private IHapiTerminologySvc myTerminologySvc;
private int myFetchSize;
protected IResourceHistoryTableDao myResourceHistoryTableDao;
protected IResourceTagDao myResourceTagDao;
protected IResourceSearchViewDao myResourceSearchViewDao;
/**
* Constructor
@ -184,7 +186,7 @@ public class SearchBuilder implements ISearchBuilder {
IFulltextSearchSvc theFulltextSearchSvc, BaseHapiFhirDao<?> theDao,
IResourceIndexedSearchParamUriDao theResourceIndexedSearchParamUriDao, IForcedIdDao theForcedIdDao,
IHapiTerminologySvc theTerminologySvc, ISearchParamRegistry theSearchParamRegistry,
IResourceHistoryTableDao theResourceHistoryTableDao, IResourceTagDao theResourceTagDao) {
IResourceTagDao theResourceTagDao, IResourceSearchViewDao theResourceViewDao) {
myContext = theFhirContext;
myEntityManager = theEntityManager;
myFulltextSearchSvc = theFulltextSearchSvc;
@ -193,8 +195,8 @@ public class SearchBuilder implements ISearchBuilder {
myForcedIdDao = theForcedIdDao;
myTerminologySvc = theTerminologySvc;
mySearchParamRegistry = theSearchParamRegistry;
myResourceHistoryTableDao = theResourceHistoryTableDao;
myResourceTagDao = theResourceTagDao;
myResourceSearchViewDao = theResourceViewDao;
}
private void addPredicateComposite(String theResourceName, RuntimeSearchParam theParamDef, List<? extends IQueryParameterType> theNextAnd) {
@ -1675,52 +1677,39 @@ public class SearchBuilder implements ISearchBuilder {
private void doLoadPids(List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation, EntityManager entityManager, FhirContext context, IDao theDao,
Map<Long, Integer> position, Collection<Long> pids) {
CriteriaBuilder builder = entityManager.getCriteriaBuilder();
CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
Root<ResourceTable> from = cq.from(ResourceTable.class);
cq.where(from.get("myId").in(pids));
TypedQuery<ResourceTable> q = entityManager.createQuery(cq);
List<ResourceTable> resultList = q.getResultList();
//-- Issue #963: Load resource histories based on pids once to improve the performance
Map<Long, ResourceHistoryTable> historyMap = getResourceHistoryMap(pids);
// -- get the resource from the searchView
Collection<ResourceSearchView> resourceSearchViewList = myResourceSearchViewDao.findByResourceIds(pids);
//-- preload all tags with tag definition if any
Map<Long, Collection<ResourceTag>> tagMap = getResourceTagMap(resultList);
Map<Long, Collection<ResourceTag>> tagMap = getResourceTagMap(resourceSearchViewList);
//-- pre-load all forcedId
Map<Long, ForcedId> forcedIdMap = getForcedIdMap(pids);
ForcedId forcedId = null;
Long resourceId = null;
for (ResourceTable next : resultList) {
for (ResourceSearchView next : resourceSearchViewList) {
Class<? extends IBaseResource> resourceType = context.getResourceDefinition(next.getResourceType()).getImplementingClass();
resourceId = next.getId();
forcedId = forcedIdMap.get(resourceId);
if (forcedId != null)
next.setForcedId(forcedId);
IBaseResource resource = theDao.toResource(resourceType, next, historyMap.get(next.getId()), tagMap.get(next.getId()), theForHistoryOperation);
IBaseResource resource = theDao.toResource(resourceType, next, tagMap.get(resourceId), theForHistoryOperation);
if (resource == null) {
ourLog.warn("Unable to find resource {}/{}/_history/{} in database", next.getResourceType(), next.getIdDt().getIdPart(), next.getVersion());
continue;
}
Integer index = position.get(next.getId());
Integer index = position.get(resourceId);
if (index == null) {
ourLog.warn("Got back unexpected resource PID {}", next.getId());
ourLog.warn("Got back unexpected resource PID {}", resourceId);
continue;
}
if (resource instanceof IResource) {
if (theRevIncludedPids.contains(next.getId())) {
if (theRevIncludedPids.contains(resourceId)) {
ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IResource) resource, BundleEntrySearchModeEnum.INCLUDE);
} else {
ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IResource) resource, BundleEntrySearchModeEnum.MATCH);
}
} else {
if (theRevIncludedPids.contains(next.getId())) {
if (theRevIncludedPids.contains(resourceId)) {
ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IAnyResource) resource, BundleEntrySearchModeEnum.INCLUDE.getCode());
} else {
ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put((IAnyResource) resource, BundleEntrySearchModeEnum.MATCH.getCode());
@ -1731,30 +1720,12 @@ public class SearchBuilder implements ISearchBuilder {
}
}
//-- load all history in to the map
private Map<Long, ResourceHistoryTable> getResourceHistoryMap(Collection<Long> pids) {
private Map<Long, Collection<ResourceTag>> getResourceTagMap(Collection<ResourceSearchView> theResourceSearchViewList) {
Map<Long, ResourceHistoryTable> historyMap = new HashMap<Long, ResourceHistoryTable>();
if (pids.size() == 0)
return historyMap;
Collection<ResourceHistoryTable> historyList = myResourceHistoryTableDao.findByResourceIds(pids);
for (ResourceHistoryTable history : historyList) {
historyMap.put(history.getResourceId(), history);
}
return historyMap;
}
private Map<Long, Collection<ResourceTag>> getResourceTagMap(List<ResourceTable> resourceList) {
List<Long> idList = new ArrayList<Long>(resourceList.size());
List<Long> idList = new ArrayList<Long>(theResourceSearchViewList.size());
//-- find all resource has tags
for (ResourceTable resource: resourceList) {
for (ResourceSearchView resource: theResourceSearchViewList) {
if (resource.isHasTags())
idList.add(resource.getId());
}
@ -1787,23 +1758,6 @@ public class SearchBuilder implements ISearchBuilder {
return tagMap;
}
//-- load all forcedId in to the map
private Map<Long, ForcedId> getForcedIdMap(Collection<Long> pids) {
Map<Long, ForcedId> forceIdMap = new HashMap<Long, ForcedId>();
if (pids.size() == 0)
return forceIdMap;
Collection<ForcedId> forceIdList = myForcedIdDao.findByResourcePids(pids);
for (ForcedId forcedId : forceIdList) {
forceIdMap.put(forcedId.getResourcePid(), forcedId);
}
return forceIdMap;
}
@Override
public void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation,
EntityManager entityManager, FhirContext context, IDao theDao) {

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceSearchViewDao.java Normal file
View File

@ -0,0 +1,35 @@
package ca.uhn.fhir.jpa.dao.data;
import java.util.Collection;
/*
* #%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 org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
public interface IResourceSearchViewDao extends JpaRepository<ResourceSearchView, Long> {
@Query("SELECT v FROM ResourceSearchView v WHERE v.myResourceId in (:pids)")
Collection<ResourceSearchView> findByResourceIds(@Param("pids") Collection<Long> pids);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseHasResource.java
View File

@ -30,7 +30,7 @@ import java.util.Collection;
import java.util.Date;
@MappedSuperclass
public abstract class BaseHasResource {
public abstract class BaseHasResource implements IBaseResourceEntity {
@Column(name = "RES_DELETED_AT", nullable = true)
@Temporal(TemporalType.TIMESTAMP)

41
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/IBaseResourceEntity.java Normal file
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@ -0,0 +1,41 @@
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 java.util.Date;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
public interface IBaseResourceEntity {
Date getDeleted();
FhirVersionEnum getFhirVersion();
Long getId();
IdDt getIdDt();
InstantDt getPublished();
Long getResourceId();
String getResourceType();
InstantDt getUpdated();
Date getUpdatedDate();
long getVersion();
boolean isHasTags();
}

200
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceSearchView.java Normal file
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@ -0,0 +1,200 @@
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 java.io.Serializable;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.Id;
import javax.persistence.Lob;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
import org.hibernate.annotations.Immutable;
import org.hibernate.annotations.Subselect;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.api.Constants;
//@formatter:off
@Entity
@Immutable
@Subselect("SELECT h.pid as pid " +
", h.res_id as res_id " +
", h.res_type as res_type " +
", h.res_version as res_version " + // FHIR version
", h.res_ver as res_ver " + // resource version
", h.has_tags as has_tags " +
", h.res_deleted_at as res_deleted_at " +
", h.res_published as res_published " +
", h.res_updated as res_updated " +
", h.res_text as res_text " +
", h.res_encoding as res_encoding " +
", f.forced_id as forced_pid " +
"FROM HFJ_RES_VER h "
+ " LEFT OUTER JOIN HFJ_FORCED_ID f ON f.resource_pid = h.res_id "
+ " INNER JOIN HFJ_RESOURCE r ON r.res_id = h.res_id and r.res_ver = h.res_ver")
// @formatter:on
public class ResourceSearchView implements IBaseResourceEntity, Serializable {
private static final long serialVersionUID = 1L;
@Id
@Column(name = "PID")
private Long myId;
@Column(name = "RES_ID")
private Long myResourceId;
@Column(name = "RES_TYPE")
private String myResourceType;
@Column(name = "RES_VERSION")
@Enumerated(EnumType.STRING)
private FhirVersionEnum myFhirVersion;
@Column(name = "RES_VER")
private Long myResourceVersion;
@Column(name = "HAS_TAGS")
private boolean myHasTags;
@Column(name = "RES_DELETED_AT")
@Temporal(TemporalType.TIMESTAMP)
private Date myDeleted;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "RES_PUBLISHED")
private Date myPublished;
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "RES_UPDATED")
private Date myUpdated;
@Column(name = "RES_TEXT")
@Lob()
private byte[] myResource;
@Column(name = "RES_ENCODING")
@Enumerated(EnumType.STRING)
private ResourceEncodingEnum myEncoding;
@Column(name = "forced_pid")
private String myForcedPid;
public ResourceSearchView() {
}
@Override
public Date getDeleted() {
return myDeleted;
}
public void setDeleted(Date theDate) {
myDeleted = theDate;
}
@Override
public FhirVersionEnum getFhirVersion() {
return myFhirVersion;
}
public void setFhirVersion(FhirVersionEnum theFhirVersion) {
myFhirVersion = theFhirVersion;
}
public String getForcedId() {
return myForcedPid;
}
@Override
public Long getId() {
return myResourceId;
}
@Override
public IdDt getIdDt() {
if (myForcedPid == null) {
Long id = myResourceId;
return new IdDt(myResourceType + '/' + id + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
} else {
return new IdDt(
getResourceType() + '/' + getForcedId() + '/' + Constants.PARAM_HISTORY + '/' + getVersion());
}
}
@Override
public InstantDt getPublished() {
if (myPublished != null) {
return new InstantDt(myPublished);
} else {
return null;
}
}
public void setPublished(Date thePublished) {
myPublished = thePublished;
}
@Override
public Long getResourceId() {
return myResourceId;
}
@Override
public String getResourceType() {
return myResourceType;
}
@Override
public InstantDt getUpdated() {
return new InstantDt(myUpdated);
}
@Override
public Date getUpdatedDate() {
return myUpdated;
}
@Override
public long getVersion() {
return myResourceVersion;
}
@Override
public boolean isHasTags() {
return myHasTags;
}
public byte[] getResource() {
return myResource;
}
public ResourceEncodingEnum getEncoding() {
return myEncoding;
}
}