impl ResourceSearchView, reduce sql to db
This commit is contained in:
frankjtao
parent
27c92e8178
commit
ccf3c17f59
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@ -1,5 +1,86 @@
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package ca.uhn.fhir.jpa.dao;
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import static org.apache.commons.lang3.StringUtils.compare;
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import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.apache.commons.lang3.StringUtils.trim;
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import java.io.CharArrayWriter;
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import java.io.UnsupportedEncodingException;
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import java.text.Normalizer;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.StringTokenizer;
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import java.util.UUID;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.stream.Collectors;
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import javax.annotation.PostConstruct;
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import javax.persistence.EntityManager;
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import javax.persistence.NoResultException;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import javax.persistence.Tuple;
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import javax.persistence.TypedQuery;
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import javax.persistence.criteria.CriteriaBuilder;
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import javax.persistence.criteria.CriteriaQuery;
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import javax.persistence.criteria.Predicate;
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import javax.persistence.criteria.Root;
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import javax.xml.stream.events.Characters;
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import javax.xml.stream.events.XMLEvent;
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import org.apache.commons.lang3.NotImplementedException;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.apache.http.NameValuePair;
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import org.apache.http.client.utils.URLEncodedUtils;
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import org.hibernate.Session;
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import org.hibernate.internal.SessionImpl;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseCoding;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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import org.hl7.fhir.instance.model.api.IBaseReference;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IDomainResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.hl7.fhir.r4.model.BaseResource;
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import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
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import org.hl7.fhir.r4.model.CanonicalType;
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import org.hl7.fhir.r4.model.Reference;
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import org.springframework.beans.BeansException;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.context.ApplicationContext;
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import org.springframework.context.ApplicationContextAware;
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import org.springframework.data.domain.PageRequest;
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import org.springframework.data.domain.Pageable;
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import org.springframework.data.domain.Slice;
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import org.springframework.data.domain.SliceImpl;
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import org.springframework.stereotype.Repository;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.support.TransactionTemplate;
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import com.google.common.annotations.VisibleForTesting;
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import com.google.common.base.Charsets;
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import com.google.common.collect.ArrayListMultimap;
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import com.google.common.collect.Sets;
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import com.google.common.hash.HashFunction;
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import com.google.common.hash.Hashing;
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/*
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* #%L
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* HAPI FHIR JPA Server
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@ -19,10 +100,70 @@ package ca.uhn.fhir.jpa.dao;
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.context.*;
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import ca.uhn.fhir.jpa.dao.data.*;
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import ca.uhn.fhir.jpa.entity.*;
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.context.RuntimeSearchParam;
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import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamCoordsDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamDateDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamNumberDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamQuantityDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamStringDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamTokenDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
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import ca.uhn.fhir.jpa.dao.data.ISearchDao;
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import ca.uhn.fhir.jpa.entity.BaseHasResource;
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import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
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import ca.uhn.fhir.jpa.entity.BaseTag;
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import ca.uhn.fhir.jpa.entity.ForcedId;
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import ca.uhn.fhir.jpa.entity.IBaseResourceEntity;
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import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
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import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
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import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedCompositeStringUnique;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
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import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
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import ca.uhn.fhir.jpa.entity.ResourceLink;
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import ca.uhn.fhir.jpa.entity.ResourceSearchView;
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import ca.uhn.fhir.jpa.entity.ResourceTable;
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import ca.uhn.fhir.jpa.entity.ResourceTag;
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import ca.uhn.fhir.jpa.entity.Search;
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import ca.uhn.fhir.jpa.entity.SearchInclude;
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import ca.uhn.fhir.jpa.entity.SearchParam;
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import ca.uhn.fhir.jpa.entity.SearchParamPresent;
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import ca.uhn.fhir.jpa.entity.SearchResult;
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import ca.uhn.fhir.jpa.entity.SearchStatusEnum;
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import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
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import ca.uhn.fhir.jpa.entity.SubscriptionTable;
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import ca.uhn.fhir.jpa.entity.TagDefinition;
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import ca.uhn.fhir.jpa.entity.TagTypeEnum;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
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import ca.uhn.fhir.jpa.entity.TermConceptMap;
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import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
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import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
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import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.jpa.entity.TermConceptProperty;
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import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
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import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
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import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
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@ -32,7 +173,12 @@ import ca.uhn.fhir.jpa.util.DeleteConflict;
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import ca.uhn.fhir.jpa.util.ExpungeOptions;
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import ca.uhn.fhir.jpa.util.ExpungeOutcome;
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import ca.uhn.fhir.jpa.util.JpaConstants;
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import ca.uhn.fhir.model.api.*;
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import ca.uhn.fhir.model.api.IQueryParameterAnd;
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import ca.uhn.fhir.model.api.IQueryParameterType;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.api.Tag;
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import ca.uhn.fhir.model.api.TagList;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
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import ca.uhn.fhir.model.primitive.IdDt;
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@ -48,61 +194,31 @@ import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.param.*;
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import ca.uhn.fhir.rest.server.exceptions.*;
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import ca.uhn.fhir.rest.param.DateRangeParam;
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import ca.uhn.fhir.rest.param.ParameterUtil;
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import ca.uhn.fhir.rest.param.StringAndListParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenAndListParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.param.UriAndListParam;
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import ca.uhn.fhir.rest.param.UriParam;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
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import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
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import ca.uhn.fhir.rest.server.interceptor.IServerOperationInterceptor;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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import ca.uhn.fhir.util.*;
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import com.google.common.annotations.VisibleForTesting;
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import com.google.common.base.Charsets;
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import com.google.common.collect.ArrayListMultimap;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import com.google.common.hash.HashFunction;
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import com.google.common.hash.Hashing;
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import org.apache.commons.lang3.NotImplementedException;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.apache.http.NameValuePair;
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import org.apache.http.client.utils.URLEncodedUtils;
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import org.hibernate.Session;
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import org.hibernate.internal.SessionImpl;
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import org.hl7.fhir.instance.model.api.*;
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import org.hl7.fhir.r4.model.BaseResource;
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import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
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import org.hl7.fhir.r4.model.CanonicalType;
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import org.hl7.fhir.r4.model.Reference;
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import org.springframework.beans.BeansException;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.context.ApplicationContext;
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import org.springframework.context.ApplicationContextAware;
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import org.springframework.data.domain.PageRequest;
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import org.springframework.data.domain.Pageable;
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import org.springframework.data.domain.Slice;
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import org.springframework.data.domain.SliceImpl;
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import org.springframework.stereotype.Repository;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.support.TransactionTemplate;
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import javax.annotation.PostConstruct;
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import javax.persistence.*;
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import javax.persistence.criteria.CriteriaBuilder;
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import javax.persistence.criteria.CriteriaQuery;
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import javax.persistence.criteria.Predicate;
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import javax.persistence.criteria.Root;
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import javax.xml.stream.events.Characters;
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import javax.xml.stream.events.XMLEvent;
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import java.io.CharArrayWriter;
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import java.io.UnsupportedEncodingException;
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import java.text.Normalizer;
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import java.util.*;
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import java.util.Map.Entry;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.stream.Collectors;
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import static org.apache.commons.lang3.StringUtils.*;
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import ca.uhn.fhir.util.CoverageIgnore;
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import ca.uhn.fhir.util.FhirTerser;
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import ca.uhn.fhir.util.OperationOutcomeUtil;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.util.UrlUtil;
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import ca.uhn.fhir.util.XmlUtil;
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@SuppressWarnings("WeakerAccess")
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@Repository
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@ -186,6 +302,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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protected IResourceTableDao myResourceTableDao;
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@Autowired
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protected IResourceTagDao myResourceTagDao;
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@Autowired
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protected IResourceSearchViewDao myResourceViewDao;
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@Autowired(required = true)
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private DaoConfig myConfig;
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private FhirContext myContext;
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@ -199,8 +317,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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private ISearchParamPresenceSvc mySearchParamPresenceSvc;
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@Autowired
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private ISearchParamRegistry mySearchParamRegistry;
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@Autowired
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private ISearchResultDao mySearchResultDao;
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//@Autowired
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//private ISearchResultDao mySearchResultDao;
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@Autowired
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private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
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private ApplicationContext myApplicationContext;
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@ -1174,7 +1292,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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public SearchBuilder newSearchBuilder() {
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SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myFulltextSearchSvc, this, myResourceIndexedSearchParamUriDao,
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myForcedIdDao,
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myTerminologySvc, mySerarchParamRegistry, myResourceHistoryTableDao, myResourceTagDao);
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myTerminologySvc, mySerarchParamRegistry, myResourceTagDao, myResourceViewDao);
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return builder;
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}
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@ -1223,7 +1341,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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}
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}
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private void populateResourceIdFromEntity(BaseHasResource theEntity, final IBaseResource theResource) {
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private void populateResourceIdFromEntity(IBaseResourceEntity theEntity, final IBaseResource theResource) {
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IIdType id = theEntity.getIdDt();
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if (getContext().getVersion().getVersion().isRi()) {
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id = getContext().getVersion().newIdType().setValue(id.getValue());
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@ -1355,7 +1473,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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}
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@SuppressWarnings("unchecked")
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private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, BaseHasResource theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res) {
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private <R extends IBaseResource> R populateResourceMetadataHapi(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IResource res) {
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R retVal = (R) res;
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if (theEntity.getDeleted() != null) {
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res = (IResource) myContext.getResourceDefinition(theResourceType).newInstance();
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@ -1421,7 +1539,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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}
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@SuppressWarnings("unchecked")
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private <R extends IBaseResource> R populateResourceMetadataRi(Class<R> theResourceType, BaseHasResource theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res) {
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private <R extends IBaseResource> R populateResourceMetadataRi(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<? extends BaseTag> theTagList, boolean theForHistoryOperation, IAnyResource res) {
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R retVal = (R) res;
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if (theEntity.getDeleted() != null) {
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res = (IAnyResource) myContext.getResourceDefinition(theResourceType).newInstance();
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@ -1601,37 +1719,50 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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public IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation) {
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RuntimeResourceDefinition type = myContext.getResourceDefinition(theEntity.getResourceType());
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Class<? extends IBaseResource> resourceType = type.getImplementingClass();
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return toResource(resourceType, theEntity, null, null, theForHistoryOperation);
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return toResource(resourceType, theEntity, null, theForHistoryOperation);
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}
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@SuppressWarnings("unchecked")
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@Override
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public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, ResourceHistoryTable theHistory, Collection<ResourceTag> theTagList,
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boolean theForHistoryOperation) {
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// May 28, 2018 - #936
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// Could set historyList to null, if it's not called in the loop for the backward compatibility
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ResourceHistoryTable history;
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public <R extends IBaseResource> R toResource(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<ResourceTag> theTagList, boolean theForHistoryOperation) {
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// 1. get resource, it's encoding and the tags if any
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byte[] resourceBytes = null;
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ResourceEncodingEnum resourceEncoding = null;
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Collection<? extends BaseTag> myTagList = null;
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if (theEntity instanceof ResourceHistoryTable) {
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history = (ResourceHistoryTable) theEntity;
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} else {
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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;
|
||||
}
|
||||
}
|
||||
|
||||
if (history == 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:
|
||||
case JSON:
|
||||
try {
|
||||
resourceText = new String(resourceBytes, "UTF-8");
|
||||
} catch (UnsupportedEncodingException e) {
|
||||
|
|
@ -1644,19 +1775,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
|
|||
case DEL:
|
||||
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;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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) {
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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) {
|
||||
|
||||
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) {
|
||||
private Map<Long, Collection<ResourceTag>> getResourceTagMap(Collection<ResourceSearchView> theResourceSearchViewList) {
|
||||
|
||||
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) {
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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();
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -2908,8 +2908,10 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
|
|||
myPatientDao.addTag(patientId, TagTypeEnum.TAG, "http://foo", "Cat", "Kittens");
|
||||
myPatientDao.addTag(patientId, TagTypeEnum.TAG, "http://foo", "Cow", "Calves");
|
||||
|
||||
System.out.println("patientId = " + patientId);
|
||||
retrieved = myPatientDao.read(patientId, mySrd);
|
||||
published = (TagList) retrieved.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
|
||||
System.out.println("published = " + published);
|
||||
sort(published);
|
||||
assertEquals(3, published.size());
|
||||
assertEquals(published.toString(), "Dog", published.get(0).getTerm());
|
||||
|
|
|
|||
Loading…
Reference in New Issue