Make test observation lists thread safe (#1105)
* Initial refactoring to move database matcher out into its own class * MAJOR REFOACTOR: Pulled indexing code out of BaseHapiFhirDao into a new class ResourceIndexedSearchParams * made observations lists thread safe to stop intermittent test failures
This commit is contained in:
Ken Stevens
GitHub
parent
3b8629617b
commit
3d008aee5d
File diff suppressed because it is too large
Load Diff
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@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
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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.IResourceSearchViewDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
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import ca.uhn.fhir.jpa.dao.index.ResourceIndexedSearchParams;
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import ca.uhn.fhir.jpa.entity.*;
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import ca.uhn.fhir.jpa.entity.*;
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import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
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import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
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import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
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import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
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@ -1496,7 +1497,7 @@ public class SearchBuilder implements ISearchBuilder {
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}
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}
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}
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}
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Set<String> uniqueQueryStrings = BaseHapiFhirDao.extractCompositeStringUniquesValueChains(myResourceName, params);
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Set<String> uniqueQueryStrings = ResourceIndexedSearchParams.extractCompositeStringUniquesValueChains(myResourceName, params);
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if (ourTrackHandlersForUnitTest) {
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if (ourTrackHandlersForUnitTest) {
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ourLastHandlerParamsForUnitTest = theParams;
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ourLastHandlerParamsForUnitTest = theParams;
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ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.UNIQUE_INDEX;
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ourLastHandlerMechanismForUnitTest = HandlerTypeEnum.UNIQUE_INDEX;
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@ -0,0 +1,33 @@
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package ca.uhn.fhir.jpa.dao.index;
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import java.util.Map;
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import java.util.Set;
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import javax.persistence.EntityManager;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.ISearchParamExtractor;
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import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
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public interface IndexingSupport {
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public DaoConfig getConfig();
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public ISearchParamExtractor getSearchParamExtractor();
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public ISearchParamRegistry getSearchParamRegistry();
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public FhirContext getContext();
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public EntityManager getEntityManager();
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public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType);
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public Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> getResourceTypeToDao();
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public boolean isLogicalReference(IIdType nextId);
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public IForcedIdDao getForcedIdDao();
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public <R extends IBaseResource> Set<Long> processMatchUrl(String theMatchUrl, Class<R> theResourceType);
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public Long translateForcedIdToPid(String theResourceName, String theResourceId);
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public String toResourceName(Class<? extends IBaseResource> theResourceType);
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public IResourceIndexedCompositeStringUniqueDao getResourceIndexedCompositeStringUniqueDao();
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}
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@ -0,0 +1,852 @@
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package ca.uhn.fhir.jpa.dao.index;
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import static org.apache.commons.lang3.StringUtils.compare;
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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 java.util.ArrayList;
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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.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 javax.persistence.EntityManager;
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import org.apache.commons.lang3.StringUtils;
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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.IBaseExtension;
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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.IIdType;
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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 ca.uhn.fhir.context.ConfigurationException;
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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.BaseHapiFhirDao;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.PathAndRef;
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import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
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import ca.uhn.fhir.jpa.entity.ForcedId;
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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.ResourceTable;
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import ca.uhn.fhir.jpa.search.JpaRuntimeSearchParam;
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import ca.uhn.fhir.model.api.IQueryParameterType;
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import ca.uhn.fhir.parser.DataFormatException;
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import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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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.UnprocessableEntityException;
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import ca.uhn.fhir.util.FhirTerser;
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import ca.uhn.fhir.util.UrlUtil;
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public class ResourceIndexedSearchParams {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceIndexedSearchParams.class);
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// FIXME rename
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private final IndexingSupport myIndexingService;
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private final Collection<ResourceIndexedSearchParamString> stringParams;
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private final Collection<ResourceIndexedSearchParamToken> tokenParams;
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private final Collection<ResourceIndexedSearchParamNumber> numberParams;
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private final Collection<ResourceIndexedSearchParamQuantity> quantityParams;
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private final Collection<ResourceIndexedSearchParamDate> dateParams;
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private final Collection<ResourceIndexedSearchParamUri> uriParams;
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private final Collection<ResourceIndexedSearchParamCoords> coordsParams;
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private final Collection<ResourceIndexedCompositeStringUnique> compositeStringUniques;
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private final Collection<ResourceLink> links;
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private Set<String> populatedResourceLinkParameters = Collections.emptySet();
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public ResourceIndexedSearchParams(IndexingSupport indexingService, ResourceTable theEntity) {
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this.myIndexingService = indexingService;
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stringParams = new ArrayList<>();
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if (theEntity.isParamsStringPopulated()) {
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stringParams.addAll(theEntity.getParamsString());
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}
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tokenParams = new ArrayList<>();
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if (theEntity.isParamsTokenPopulated()) {
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tokenParams.addAll(theEntity.getParamsToken());
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}
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numberParams = new ArrayList<>();
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if (theEntity.isParamsNumberPopulated()) {
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numberParams.addAll(theEntity.getParamsNumber());
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}
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quantityParams = new ArrayList<>();
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if (theEntity.isParamsQuantityPopulated()) {
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quantityParams.addAll(theEntity.getParamsQuantity());
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}
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dateParams = new ArrayList<>();
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if (theEntity.isParamsDatePopulated()) {
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dateParams.addAll(theEntity.getParamsDate());
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}
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uriParams = new ArrayList<>();
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if (theEntity.isParamsUriPopulated()) {
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uriParams.addAll(theEntity.getParamsUri());
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}
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coordsParams = new ArrayList<>();
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if (theEntity.isParamsCoordsPopulated()) {
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coordsParams.addAll(theEntity.getParamsCoords());
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}
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links = new ArrayList<>();
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if (theEntity.isHasLinks()) {
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links.addAll(theEntity.getResourceLinks());
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}
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compositeStringUniques = new ArrayList<>();
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if (theEntity.isParamsCompositeStringUniquePresent()) {
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compositeStringUniques.addAll(theEntity.getParamsCompositeStringUnique());
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}
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}
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public ResourceIndexedSearchParams(IndexingSupport indexingService) {
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this.myIndexingService = indexingService;
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stringParams = Collections.emptySet();
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tokenParams = Collections.emptySet();
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numberParams = Collections.emptySet();
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quantityParams = Collections.emptySet();
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dateParams = Collections.emptySet();
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uriParams = Collections.emptySet();
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coordsParams = Collections.emptySet();
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links = Collections.emptySet();
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compositeStringUniques = Collections.emptySet();
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}
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public ResourceIndexedSearchParams(IndexingSupport indexingService, Date theUpdateTime, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams existingParams) {
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this.myIndexingService = indexingService;
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stringParams = extractSearchParamStrings(theEntity, theResource);
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numberParams = extractSearchParamNumber(theEntity, theResource);
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quantityParams = extractSearchParamQuantity(theEntity, theResource);
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dateParams = extractSearchParamDates(theEntity, theResource);
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uriParams = extractSearchParamUri(theEntity, theResource);
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coordsParams = extractSearchParamCoords(theEntity, theResource);
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ourLog.trace("Storing date indexes: {}", dateParams);
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tokenParams = new HashSet<>();
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for (BaseResourceIndexedSearchParam next : extractSearchParamTokens(theEntity, theResource)) {
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if (next instanceof ResourceIndexedSearchParamToken) {
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tokenParams.add((ResourceIndexedSearchParamToken) next);
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} else {
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stringParams.add((ResourceIndexedSearchParamString) next);
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}
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}
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Set<Entry<String, RuntimeSearchParam>> activeSearchParams = myIndexingService.getSearchParamRegistry().getActiveSearchParams(theEntity.getResourceType()).entrySet();
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DaoConfig myConfig = indexingService.getConfig();
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if (myConfig .getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
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findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.STRING, stringParams);
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findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.NUMBER, numberParams);
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findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.QUANTITY, quantityParams);
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findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.DATE, dateParams);
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findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.URI, uriParams);
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findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.TOKEN, tokenParams);
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}
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setUpdatedTime(stringParams, theUpdateTime);
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setUpdatedTime(numberParams, theUpdateTime);
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setUpdatedTime(quantityParams, theUpdateTime);
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setUpdatedTime(dateParams, theUpdateTime);
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setUpdatedTime(uriParams, theUpdateTime);
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setUpdatedTime(coordsParams, theUpdateTime);
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setUpdatedTime(tokenParams, theUpdateTime);
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/*
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* Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo". These match URLs are resolved and replaced with the ID of the
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* matching resource.
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*/
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if (myConfig.isAllowInlineMatchUrlReferences()) {
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FhirTerser terser = myIndexingService.getContext().newTerser();
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List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
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for (IBaseReference nextRef : allRefs) {
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IIdType nextId = nextRef.getReferenceElement();
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String nextIdText = nextId.getValue();
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if (nextIdText == null) {
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continue;
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}
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int qmIndex = nextIdText.indexOf('?');
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if (qmIndex != -1) {
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for (int i = qmIndex - 1; i >= 0; i--) {
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if (nextIdText.charAt(i) == '/') {
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if (i < nextIdText.length() - 1 && nextIdText.charAt(i + 1) == '?') {
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// Just in case the URL is in the form Patient/?foo=bar
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continue;
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}
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nextIdText = nextIdText.substring(i + 1);
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break;
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}
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}
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String resourceTypeString = nextIdText.substring(0, nextIdText.indexOf('?')).replace("/", "");
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RuntimeResourceDefinition matchResourceDef = myIndexingService.getContext().getResourceDefinition(resourceTypeString);
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if (matchResourceDef == null) {
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String msg = myIndexingService.getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlInvalidResourceType", nextId.getValue(), resourceTypeString);
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throw new InvalidRequestException(msg);
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}
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Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
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Set<Long> matches = myIndexingService.processMatchUrl(nextIdText, matchResourceType);
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if (matches.isEmpty()) {
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String msg = indexingService.getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
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throw new ResourceNotFoundException(msg);
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}
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if (matches.size() > 1) {
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String msg = indexingService.getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlMultipleMatches", nextId.getValue());
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throw new PreconditionFailedException(msg);
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}
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Long next = matches.iterator().next();
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String newId = translatePidIdToForcedId(resourceTypeString, next);
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ourLog.debug("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId);
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nextRef.setReference(newId);
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}
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}
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}
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links = new HashSet<>();
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populatedResourceLinkParameters = extractResourceLinks(theEntity, theResource, links, theUpdateTime);
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/*
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* If the existing resource already has links and those match links we still want, use them instead of removing them and re adding them
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*/
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for (Iterator<ResourceLink> existingLinkIter = existingParams.getResourceLinks().iterator(); existingLinkIter.hasNext(); ) {
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ResourceLink nextExisting = existingLinkIter.next();
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if (links.remove(nextExisting)) {
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existingLinkIter.remove();
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links.add(nextExisting);
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}
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}
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/*
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* Handle composites
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*/
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compositeStringUniques = extractCompositeStringUniques(theEntity, stringParams, tokenParams, numberParams, quantityParams, dateParams, uriParams, links);
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}
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public Collection<ResourceLink> getResourceLinks() {
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return links;
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}
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protected Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) {
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return myIndexingService.getSearchParamExtractor().extractSearchParamCoords(theEntity, theResource);
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}
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protected Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
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return myIndexingService.getSearchParamExtractor().extractSearchParamDates(theEntity, theResource);
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}
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protected Set<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource) {
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return myIndexingService.getSearchParamExtractor().extractSearchParamNumber(theEntity, theResource);
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}
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protected Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource) {
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return myIndexingService.getSearchParamExtractor().extractSearchParamQuantity(theEntity, theResource);
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}
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||||||
|
protected Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource) {
|
||||||
|
return myIndexingService.getSearchParamExtractor().extractSearchParamStrings(theEntity, theResource);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IBaseResource theResource) {
|
||||||
|
return myIndexingService.getSearchParamExtractor().extractSearchParamTokens(theEntity, theResource);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected Set<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IBaseResource theResource) {
|
||||||
|
return myIndexingService.getSearchParamExtractor().extractSearchParamUri(theEntity, theResource);
|
||||||
|
}
|
||||||
|
|
||||||
|
@SuppressWarnings("unchecked")
|
||||||
|
private <RT extends BaseResourceIndexedSearchParam> void findMissingSearchParams(ResourceTable theEntity, Set<Entry<String, RuntimeSearchParam>> activeSearchParams, RestSearchParameterTypeEnum type,
|
||||||
|
Collection<RT> paramCollection) {
|
||||||
|
for (Entry<String, RuntimeSearchParam> nextEntry : activeSearchParams) {
|
||||||
|
String nextParamName = nextEntry.getKey();
|
||||||
|
if (nextEntry.getValue().getParamType() == type) {
|
||||||
|
boolean haveParam = false;
|
||||||
|
for (BaseResourceIndexedSearchParam nextParam : paramCollection) {
|
||||||
|
if (nextParam.getParamName().equals(nextParamName)) {
|
||||||
|
haveParam = true;
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!haveParam) {
|
||||||
|
BaseResourceIndexedSearchParam param;
|
||||||
|
switch (type) {
|
||||||
|
case DATE:
|
||||||
|
param = new ResourceIndexedSearchParamDate();
|
||||||
|
break;
|
||||||
|
case NUMBER:
|
||||||
|
param = new ResourceIndexedSearchParamNumber();
|
||||||
|
break;
|
||||||
|
case QUANTITY:
|
||||||
|
param = new ResourceIndexedSearchParamQuantity();
|
||||||
|
break;
|
||||||
|
case STRING:
|
||||||
|
param = new ResourceIndexedSearchParamString()
|
||||||
|
.setDaoConfig(myIndexingService.getConfig());
|
||||||
|
break;
|
||||||
|
case TOKEN:
|
||||||
|
param = new ResourceIndexedSearchParamToken();
|
||||||
|
break;
|
||||||
|
case URI:
|
||||||
|
param = new ResourceIndexedSearchParamUri();
|
||||||
|
break;
|
||||||
|
case COMPOSITE:
|
||||||
|
case HAS:
|
||||||
|
case REFERENCE:
|
||||||
|
default:
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
param.setResource(theEntity);
|
||||||
|
param.setMissing(true);
|
||||||
|
param.setParamName(nextParamName);
|
||||||
|
paramCollection.add((RT) param);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setParams(ResourceTable theEntity) {
|
||||||
|
theEntity.setParamsString(stringParams);
|
||||||
|
theEntity.setParamsStringPopulated(stringParams.isEmpty() == false);
|
||||||
|
theEntity.setParamsToken(tokenParams);
|
||||||
|
theEntity.setParamsTokenPopulated(tokenParams.isEmpty() == false);
|
||||||
|
theEntity.setParamsNumber(numberParams);
|
||||||
|
theEntity.setParamsNumberPopulated(numberParams.isEmpty() == false);
|
||||||
|
theEntity.setParamsQuantity(quantityParams);
|
||||||
|
theEntity.setParamsQuantityPopulated(quantityParams.isEmpty() == false);
|
||||||
|
theEntity.setParamsDate(dateParams);
|
||||||
|
theEntity.setParamsDatePopulated(dateParams.isEmpty() == false);
|
||||||
|
theEntity.setParamsUri(uriParams);
|
||||||
|
theEntity.setParamsUriPopulated(uriParams.isEmpty() == false);
|
||||||
|
theEntity.setParamsCoords(coordsParams);
|
||||||
|
theEntity.setParamsCoordsPopulated(coordsParams.isEmpty() == false);
|
||||||
|
theEntity.setParamsCompositeStringUniquePresent(compositeStringUniques.isEmpty() == false);
|
||||||
|
theEntity.setResourceLinks(links);
|
||||||
|
theEntity.setHasLinks(links.isEmpty() == false);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
private Set<ResourceIndexedCompositeStringUnique> extractCompositeStringUniques(ResourceTable theEntity, Collection<ResourceIndexedSearchParamString> theStringParams, Collection<ResourceIndexedSearchParamToken> theTokenParams, Collection<ResourceIndexedSearchParamNumber> theNumberParams, Collection<ResourceIndexedSearchParamQuantity> theQuantityParams, Collection<ResourceIndexedSearchParamDate> theDateParams, Collection<ResourceIndexedSearchParamUri> theUriParams, Collection<ResourceLink> theLinks) {
|
||||||
|
Set<ResourceIndexedCompositeStringUnique> compositeStringUniques;
|
||||||
|
compositeStringUniques = new HashSet<>();
|
||||||
|
List<JpaRuntimeSearchParam> uniqueSearchParams = myIndexingService.getSearchParamRegistry().getActiveUniqueSearchParams(theEntity.getResourceType());
|
||||||
|
for (JpaRuntimeSearchParam next : uniqueSearchParams) {
|
||||||
|
|
||||||
|
List<List<String>> partsChoices = new ArrayList<>();
|
||||||
|
|
||||||
|
for (RuntimeSearchParam nextCompositeOf : next.getCompositeOf()) {
|
||||||
|
Collection<? extends BaseResourceIndexedSearchParam> paramsListForCompositePart = null;
|
||||||
|
Collection<ResourceLink> linksForCompositePart = null;
|
||||||
|
Collection<String> linksForCompositePartWantPaths = null;
|
||||||
|
switch (nextCompositeOf.getParamType()) {
|
||||||
|
case NUMBER:
|
||||||
|
paramsListForCompositePart = theNumberParams;
|
||||||
|
break;
|
||||||
|
case DATE:
|
||||||
|
paramsListForCompositePart = theDateParams;
|
||||||
|
break;
|
||||||
|
case STRING:
|
||||||
|
paramsListForCompositePart = theStringParams;
|
||||||
|
break;
|
||||||
|
case TOKEN:
|
||||||
|
paramsListForCompositePart = theTokenParams;
|
||||||
|
break;
|
||||||
|
case REFERENCE:
|
||||||
|
linksForCompositePart = theLinks;
|
||||||
|
linksForCompositePartWantPaths = new HashSet<>();
|
||||||
|
linksForCompositePartWantPaths.addAll(nextCompositeOf.getPathsSplit());
|
||||||
|
break;
|
||||||
|
case QUANTITY:
|
||||||
|
paramsListForCompositePart = theQuantityParams;
|
||||||
|
break;
|
||||||
|
case URI:
|
||||||
|
paramsListForCompositePart = theUriParams;
|
||||||
|
break;
|
||||||
|
case COMPOSITE:
|
||||||
|
case HAS:
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
|
||||||
|
ArrayList<String> nextChoicesList = new ArrayList<>();
|
||||||
|
partsChoices.add(nextChoicesList);
|
||||||
|
|
||||||
|
String key = UrlUtil.escapeUrlParam(nextCompositeOf.getName());
|
||||||
|
if (paramsListForCompositePart != null) {
|
||||||
|
for (BaseResourceIndexedSearchParam nextParam : paramsListForCompositePart) {
|
||||||
|
if (nextParam.getParamName().equals(nextCompositeOf.getName())) {
|
||||||
|
IQueryParameterType nextParamAsClientParam = nextParam.toQueryParameterType();
|
||||||
|
String value = nextParamAsClientParam.getValueAsQueryToken(myIndexingService.getContext());
|
||||||
|
if (isNotBlank(value)) {
|
||||||
|
value = UrlUtil.escapeUrlParam(value);
|
||||||
|
nextChoicesList.add(key + "=" + value);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (linksForCompositePart != null) {
|
||||||
|
for (ResourceLink nextLink : linksForCompositePart) {
|
||||||
|
if (linksForCompositePartWantPaths.contains(nextLink.getSourcePath())) {
|
||||||
|
String value = nextLink.getTargetResource().getIdDt().toUnqualifiedVersionless().getValue();
|
||||||
|
if (isNotBlank(value)) {
|
||||||
|
value = UrlUtil.escapeUrlParam(value);
|
||||||
|
nextChoicesList.add(key + "=" + value);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
Set<String> queryStringsToPopulate = extractCompositeStringUniquesValueChains(theEntity.getResourceType(), partsChoices);
|
||||||
|
|
||||||
|
for (String nextQueryString : queryStringsToPopulate) {
|
||||||
|
if (isNotBlank(nextQueryString)) {
|
||||||
|
compositeStringUniques.add(new ResourceIndexedCompositeStringUnique(theEntity, nextQueryString));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return compositeStringUniques;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* This method is used to create a set of all possible combinations of
|
||||||
|
* parameters across a set of search parameters. An example of why
|
||||||
|
* this is needed:
|
||||||
|
* <p>
|
||||||
|
* Let's say we have a unique index on (Patient:gender AND Patient:name).
|
||||||
|
* Then we pass in <code>SMITH, John</code> with a gender of <code>male</code>.
|
||||||
|
* </p>
|
||||||
|
* <p>
|
||||||
|
* In this case, because the name parameter matches both first and last name,
|
||||||
|
* we now need two unique indexes:
|
||||||
|
* <ul>
|
||||||
|
* <li>Patient?gender=male&name=SMITH</li>
|
||||||
|
* <li>Patient?gender=male&name=JOHN</li>
|
||||||
|
* </ul>
|
||||||
|
* </p>
|
||||||
|
* <p>
|
||||||
|
* So this recursive algorithm calculates those
|
||||||
|
* </p>
|
||||||
|
*
|
||||||
|
* @param theResourceType E.g. <code>Patient
|
||||||
|
* @param thePartsChoices E.g. <code>[[gender=male], [name=SMITH, name=JOHN]]</code>
|
||||||
|
*/
|
||||||
|
public static Set<String> extractCompositeStringUniquesValueChains(String
|
||||||
|
theResourceType, List<List<String>> thePartsChoices) {
|
||||||
|
|
||||||
|
for (List<String> next : thePartsChoices) {
|
||||||
|
next.removeIf(StringUtils::isBlank);
|
||||||
|
if (next.isEmpty()) {
|
||||||
|
return Collections.emptySet();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (thePartsChoices.isEmpty()) {
|
||||||
|
return Collections.emptySet();
|
||||||
|
}
|
||||||
|
|
||||||
|
thePartsChoices.sort((o1, o2) -> {
|
||||||
|
String str1 = null;
|
||||||
|
String str2 = null;
|
||||||
|
if (o1.size() > 0) {
|
||||||
|
str1 = o1.get(0);
|
||||||
|
}
|
||||||
|
if (o2.size() > 0) {
|
||||||
|
str2 = o2.get(0);
|
||||||
|
}
|
||||||
|
return compare(str1, str2);
|
||||||
|
});
|
||||||
|
|
||||||
|
List<String> values = new ArrayList<>();
|
||||||
|
Set<String> queryStringsToPopulate = new HashSet<>();
|
||||||
|
extractCompositeStringUniquesValueChains(theResourceType, thePartsChoices, values, queryStringsToPopulate);
|
||||||
|
return queryStringsToPopulate;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void extractCompositeStringUniquesValueChains(String
|
||||||
|
theResourceType, List<List<String>> thePartsChoices, List<String> theValues, Set<String> theQueryStringsToPopulate) {
|
||||||
|
if (thePartsChoices.size() > 0) {
|
||||||
|
List<String> nextList = thePartsChoices.get(0);
|
||||||
|
Collections.sort(nextList);
|
||||||
|
for (String nextChoice : nextList) {
|
||||||
|
theValues.add(nextChoice);
|
||||||
|
extractCompositeStringUniquesValueChains(theResourceType, thePartsChoices.subList(1, thePartsChoices.size()), theValues, theQueryStringsToPopulate);
|
||||||
|
theValues.remove(theValues.size() - 1);
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (theValues.size() > 0) {
|
||||||
|
StringBuilder uniqueString = new StringBuilder();
|
||||||
|
uniqueString.append(theResourceType);
|
||||||
|
|
||||||
|
for (int i = 0; i < theValues.size(); i++) {
|
||||||
|
uniqueString.append(i == 0 ? "?" : "&");
|
||||||
|
uniqueString.append(theValues.get(i));
|
||||||
|
}
|
||||||
|
|
||||||
|
theQueryStringsToPopulate.add(uniqueString.toString());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return Returns a set containing all of the parameter names that
|
||||||
|
* were found to have a value
|
||||||
|
*/
|
||||||
|
@SuppressWarnings("unchecked")
|
||||||
|
protected Set<String> extractResourceLinks(ResourceTable theEntity, IBaseResource theResource, Collection<ResourceLink> theLinks, Date theUpdateTime) {
|
||||||
|
HashSet<String> retVal = new HashSet<>();
|
||||||
|
String resourceType = theEntity.getResourceType();
|
||||||
|
|
||||||
|
/*
|
||||||
|
* For now we don't try to load any of the links in a bundle if it's the actual bundle we're storing..
|
||||||
|
*/
|
||||||
|
if (theResource instanceof IBaseBundle) {
|
||||||
|
return Collections.emptySet();
|
||||||
|
}
|
||||||
|
|
||||||
|
Map<String, RuntimeSearchParam> searchParams = myIndexingService.getSearchParamRegistry().getActiveSearchParams(myIndexingService.toResourceName(theResource.getClass()));
|
||||||
|
for (RuntimeSearchParam nextSpDef : searchParams.values()) {
|
||||||
|
|
||||||
|
if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
String nextPathsUnsplit = nextSpDef.getPath();
|
||||||
|
if (isBlank(nextPathsUnsplit)) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
boolean multiType = false;
|
||||||
|
if (nextPathsUnsplit.endsWith("[x]")) {
|
||||||
|
multiType = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
List<PathAndRef> refs = myIndexingService.getSearchParamExtractor().extractResourceLinks(theResource, nextSpDef);
|
||||||
|
for (PathAndRef nextPathAndRef : refs) {
|
||||||
|
Object nextObject = nextPathAndRef.getRef();
|
||||||
|
|
||||||
|
/*
|
||||||
|
* A search parameter on an extension field that contains
|
||||||
|
* references should index those references
|
||||||
|
*/
|
||||||
|
if (nextObject instanceof IBaseExtension<?, ?>) {
|
||||||
|
nextObject = ((IBaseExtension<?, ?>) nextObject).getValue();
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nextObject instanceof CanonicalType) {
|
||||||
|
nextObject = new Reference(((CanonicalType) nextObject).getValueAsString());
|
||||||
|
}
|
||||||
|
|
||||||
|
IIdType nextId;
|
||||||
|
if (nextObject instanceof IBaseReference) {
|
||||||
|
IBaseReference nextValue = (IBaseReference) nextObject;
|
||||||
|
if (nextValue.isEmpty()) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
nextId = nextValue.getReferenceElement();
|
||||||
|
|
||||||
|
/*
|
||||||
|
* This can only really happen if the DAO is being called
|
||||||
|
* programatically with a Bundle (not through the FHIR REST API)
|
||||||
|
* but Smile does this
|
||||||
|
*/
|
||||||
|
if (nextId.isEmpty() && nextValue.getResource() != null) {
|
||||||
|
nextId = nextValue.getResource().getIdElement();
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nextId.isEmpty() || nextId.getValue().startsWith("#")) {
|
||||||
|
// This is a blank or contained resource reference
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
} else if (nextObject instanceof IBaseResource) {
|
||||||
|
nextId = ((IBaseResource) nextObject).getIdElement();
|
||||||
|
if (nextId == null || nextId.hasIdPart() == false) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
} else if (myIndexingService.getContext().getElementDefinition((Class<? extends IBase>) nextObject.getClass()).getName().equals("uri")) {
|
||||||
|
continue;
|
||||||
|
} else if (resourceType.equals("Consent") && nextPathAndRef.getPath().equals("Consent.source")) {
|
||||||
|
// Consent#source-identifier has a path that isn't typed - This is a one-off to deal with that
|
||||||
|
continue;
|
||||||
|
} else {
|
||||||
|
if (!multiType) {
|
||||||
|
if (nextSpDef.getName().equals("sourceuri")) {
|
||||||
|
continue; // TODO: disable this eventually - ConceptMap:sourceuri is of type reference but points to a URI
|
||||||
|
}
|
||||||
|
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());
|
||||||
|
} else {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
retVal.add(nextSpDef.getName());
|
||||||
|
|
||||||
|
if (myIndexingService.isLogicalReference(nextId)) {
|
||||||
|
ResourceLink resourceLink = new ResourceLink(nextPathAndRef.getPath(), theEntity, nextId, theUpdateTime);
|
||||||
|
if (theLinks.add(resourceLink)) {
|
||||||
|
ourLog.debug("Indexing remote resource reference URL: {}", nextId);
|
||||||
|
}
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
String baseUrl = nextId.getBaseUrl();
|
||||||
|
String typeString = nextId.getResourceType();
|
||||||
|
if (isBlank(typeString)) {
|
||||||
|
throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Does not contain resource type - " + nextId.getValue());
|
||||||
|
}
|
||||||
|
RuntimeResourceDefinition resourceDefinition;
|
||||||
|
try {
|
||||||
|
resourceDefinition = myIndexingService.getContext().getResourceDefinition(typeString);
|
||||||
|
} catch (DataFormatException e) {
|
||||||
|
throw new InvalidRequestException(
|
||||||
|
"Invalid resource reference found at path[" + nextPathsUnsplit + "] - Resource type is unknown or not supported on this server - " + nextId.getValue());
|
||||||
|
}
|
||||||
|
|
||||||
|
if (isNotBlank(baseUrl)) {
|
||||||
|
if (!myIndexingService.getConfig().getTreatBaseUrlsAsLocal().contains(baseUrl) && !myIndexingService.getConfig().isAllowExternalReferences()) {
|
||||||
|
String msg = myIndexingService.getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "externalReferenceNotAllowed", nextId.getValue());
|
||||||
|
throw new InvalidRequestException(msg);
|
||||||
|
} else {
|
||||||
|
ResourceLink resourceLink = new ResourceLink(nextPathAndRef.getPath(), theEntity, nextId, theUpdateTime);
|
||||||
|
if (theLinks.add(resourceLink)) {
|
||||||
|
ourLog.debug("Indexing remote resource reference URL: {}", nextId);
|
||||||
|
}
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
Class<? extends IBaseResource> type = resourceDefinition.getImplementingClass();
|
||||||
|
String id = nextId.getIdPart();
|
||||||
|
if (StringUtils.isBlank(id)) {
|
||||||
|
throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Does not contain resource ID - " + nextId.getValue());
|
||||||
|
}
|
||||||
|
|
||||||
|
IFhirResourceDao<?> dao = myIndexingService.getDao(type);
|
||||||
|
if (dao == null) {
|
||||||
|
StringBuilder b = new StringBuilder();
|
||||||
|
b.append("This server (version ");
|
||||||
|
b.append(myIndexingService.getContext().getVersion().getVersion());
|
||||||
|
b.append(") is not able to handle resources of type[");
|
||||||
|
b.append(nextId.getResourceType());
|
||||||
|
b.append("] - Valid resource types for this server: ");
|
||||||
|
b.append(myIndexingService.getResourceTypeToDao().keySet().toString());
|
||||||
|
|
||||||
|
throw new InvalidRequestException(b.toString());
|
||||||
|
}
|
||||||
|
Long valueOf;
|
||||||
|
try {
|
||||||
|
valueOf = myIndexingService.translateForcedIdToPid(typeString, id);
|
||||||
|
} catch (ResourceNotFoundException e) {
|
||||||
|
if (myIndexingService.getConfig().isEnforceReferentialIntegrityOnWrite() == false) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
RuntimeResourceDefinition missingResourceDef = myIndexingService.getContext().getResourceDefinition(type);
|
||||||
|
String resName = missingResourceDef.getName();
|
||||||
|
|
||||||
|
if (myIndexingService.getConfig().isAutoCreatePlaceholderReferenceTargets()) {
|
||||||
|
IBaseResource newResource = missingResourceDef.newInstance();
|
||||||
|
newResource.setId(resName + "/" + id);
|
||||||
|
IFhirResourceDao<IBaseResource> placeholderResourceDao = (IFhirResourceDao<IBaseResource>) myIndexingService.getDao(newResource.getClass());
|
||||||
|
ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
|
||||||
|
valueOf = placeholderResourceDao.update(newResource).getEntity().getId();
|
||||||
|
} else {
|
||||||
|
throw new InvalidRequestException("Resource " + resName + "/" + id + " not found, specified in path: " + nextPathsUnsplit);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
ResourceTable target = myIndexingService.getEntityManager().find(ResourceTable.class, valueOf);
|
||||||
|
RuntimeResourceDefinition targetResourceDef = myIndexingService.getContext().getResourceDefinition(type);
|
||||||
|
if (target == null) {
|
||||||
|
String resName = targetResourceDef.getName();
|
||||||
|
throw new InvalidRequestException("Resource " + resName + "/" + id + " not found, specified in path: " + nextPathsUnsplit);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!typeString.equals(target.getResourceType())) {
|
||||||
|
throw new UnprocessableEntityException(
|
||||||
|
"Resource contains reference to " + nextId.getValue() + " but resource with ID " + nextId.getIdPart() + " is actually of type " + target.getResourceType());
|
||||||
|
}
|
||||||
|
|
||||||
|
if (target.getDeleted() != null) {
|
||||||
|
String resName = targetResourceDef.getName();
|
||||||
|
throw new InvalidRequestException("Resource " + resName + "/" + id + " is deleted, specified in path: " + nextPathsUnsplit);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nextSpDef.getTargets() != null && !nextSpDef.getTargets().contains(typeString)) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
ResourceLink resourceLink = new ResourceLink(nextPathAndRef.getPath(), theEntity, target, theUpdateTime);
|
||||||
|
theLinks.add(resourceLink);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
theEntity.setHasLinks(theLinks.size() > 0);
|
||||||
|
|
||||||
|
return retVal;
|
||||||
|
}
|
||||||
|
|
||||||
|
private void setUpdatedTime(Collection<? extends BaseResourceIndexedSearchParam> theParams, Date theUpdateTime) {
|
||||||
|
for (BaseResourceIndexedSearchParam nextSearchParam : theParams) {
|
||||||
|
nextSearchParam.setUpdated(theUpdateTime);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private String translatePidIdToForcedId(String theResourceType, Long theId) {
|
||||||
|
ForcedId forcedId = myIndexingService.getForcedIdDao().findByResourcePid(theId);
|
||||||
|
if (forcedId != null) {
|
||||||
|
return forcedId.getResourceType() + '/' + forcedId.getForcedId();
|
||||||
|
} else {
|
||||||
|
return theResourceType + '/' + theId.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void removeCommon(ResourceTable theEntity, ResourceIndexedSearchParams existingParams) {
|
||||||
|
EntityManager myEntityManager = myIndexingService.getEntityManager();
|
||||||
|
|
||||||
|
calculateHashes(stringParams);
|
||||||
|
for (ResourceIndexedSearchParamString next : removeCommon(existingParams.stringParams, stringParams)) {
|
||||||
|
next.setDaoConfig(myIndexingService.getConfig());
|
||||||
|
myEntityManager .remove(next);
|
||||||
|
theEntity.getParamsString().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedSearchParamString next : removeCommon(stringParams, existingParams.stringParams)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
calculateHashes(tokenParams);
|
||||||
|
for (ResourceIndexedSearchParamToken next : removeCommon(existingParams.tokenParams, tokenParams)) {
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getParamsToken().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedSearchParamToken next : removeCommon(tokenParams, existingParams.tokenParams)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
calculateHashes(numberParams);
|
||||||
|
for (ResourceIndexedSearchParamNumber next : removeCommon(existingParams.numberParams, numberParams)) {
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getParamsNumber().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedSearchParamNumber next : removeCommon(numberParams, existingParams.numberParams)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
calculateHashes(quantityParams);
|
||||||
|
for (ResourceIndexedSearchParamQuantity next : removeCommon(existingParams.quantityParams, quantityParams)) {
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getParamsQuantity().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedSearchParamQuantity next : removeCommon(quantityParams, existingParams.quantityParams)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Store date SP's
|
||||||
|
calculateHashes(dateParams);
|
||||||
|
for (ResourceIndexedSearchParamDate next : removeCommon(existingParams.dateParams, dateParams)) {
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getParamsDate().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedSearchParamDate next : removeCommon(dateParams, existingParams.dateParams)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Store URI SP's
|
||||||
|
calculateHashes(uriParams);
|
||||||
|
for (ResourceIndexedSearchParamUri next : removeCommon(existingParams.uriParams, uriParams)) {
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getParamsUri().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedSearchParamUri next : removeCommon(uriParams, existingParams.uriParams)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Store Coords SP's
|
||||||
|
calculateHashes(coordsParams);
|
||||||
|
for (ResourceIndexedSearchParamCoords next : removeCommon(existingParams.coordsParams, coordsParams)) {
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getParamsCoords().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedSearchParamCoords next : removeCommon(coordsParams, existingParams.coordsParams)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Store resource links
|
||||||
|
for (ResourceLink next : removeCommon(existingParams.links, links)) {
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getResourceLinks().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceLink next : removeCommon(links, existingParams.links)) {
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
|
||||||
|
// make sure links are indexed
|
||||||
|
theEntity.setResourceLinks(links);
|
||||||
|
|
||||||
|
// Store composite string uniques
|
||||||
|
if (myIndexingService.getConfig().isUniqueIndexesEnabled()) {
|
||||||
|
for (ResourceIndexedCompositeStringUnique next : removeCommon(existingParams.compositeStringUniques, compositeStringUniques)) {
|
||||||
|
ourLog.debug("Removing unique index: {}", next);
|
||||||
|
myEntityManager.remove(next);
|
||||||
|
theEntity.getParamsCompositeStringUnique().remove(next);
|
||||||
|
}
|
||||||
|
for (ResourceIndexedCompositeStringUnique next : removeCommon(compositeStringUniques, existingParams.compositeStringUniques)) {
|
||||||
|
if (myIndexingService.getConfig().isUniqueIndexesCheckedBeforeSave()) {
|
||||||
|
ResourceIndexedCompositeStringUnique existing = myIndexingService.getResourceIndexedCompositeStringUniqueDao().findByQueryString(next.getIndexString());
|
||||||
|
if (existing != null) {
|
||||||
|
String msg = myIndexingService.getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "uniqueIndexConflictFailure", theEntity.getResourceType(), next.getIndexString(), existing.getResource().getIdDt().toUnqualifiedVersionless().getValue());
|
||||||
|
throw new PreconditionFailedException(msg);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
ourLog.debug("Persisting unique index: {}", next);
|
||||||
|
myEntityManager.persist(next);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void calculateHashes(Collection<? extends BaseResourceIndexedSearchParam> theStringParams) {
|
||||||
|
for (BaseResourceIndexedSearchParam next : theStringParams) {
|
||||||
|
next.calculateHashes();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private <T> Collection<T> removeCommon(Collection<T> theInput, Collection<T> theToRemove) {
|
||||||
|
assert theInput != theToRemove;
|
||||||
|
|
||||||
|
if (theInput.isEmpty()) {
|
||||||
|
return theInput;
|
||||||
|
}
|
||||||
|
|
||||||
|
ArrayList<T> retVal = new ArrayList<>(theInput);
|
||||||
|
retVal.removeAll(theToRemove);
|
||||||
|
return retVal;
|
||||||
|
}
|
||||||
|
|
||||||
|
public Set<String> getPopulatedResourceLinkParameters() {
|
||||||
|
return populatedResourceLinkParameters;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -27,6 +27,8 @@ import ca.uhn.fhir.jpa.config.BaseConfig;
|
||||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||||
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
|
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
|
||||||
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
|
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
|
||||||
|
import ca.uhn.fhir.jpa.subscription.matcher.ISubscriptionMatcher;
|
||||||
|
import ca.uhn.fhir.jpa.subscription.matcher.SubscriptionMatcherDatabase;
|
||||||
import ca.uhn.fhir.jpa.util.JpaConstants;
|
import ca.uhn.fhir.jpa.util.JpaConstants;
|
||||||
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
|
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
|
||||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||||
|
|
@ -284,6 +286,7 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
|
||||||
|
|
||||||
public abstract Subscription.SubscriptionChannelType getChannelType();
|
public abstract Subscription.SubscriptionChannelType getChannelType();
|
||||||
|
|
||||||
|
// TODO KHS move out
|
||||||
@SuppressWarnings("unchecked")
|
@SuppressWarnings("unchecked")
|
||||||
public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
|
public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
|
||||||
if (myResourceTypeToDao == null) {
|
if (myResourceTypeToDao == null) {
|
||||||
|
|
@ -433,7 +436,8 @@ public abstract class BaseSubscriptionInterceptor<S extends IBaseResource> exten
|
||||||
|
|
||||||
protected void registerSubscriptionCheckingSubscriber() {
|
protected void registerSubscriptionCheckingSubscriber() {
|
||||||
if (mySubscriptionCheckingSubscriber == null) {
|
if (mySubscriptionCheckingSubscriber == null) {
|
||||||
mySubscriptionCheckingSubscriber = new SubscriptionCheckingSubscriber(getSubscriptionDao(), getChannelType(), this);
|
ISubscriptionMatcher subscriptionMatcher = new SubscriptionMatcherDatabase(getSubscriptionDao(), this);
|
||||||
|
mySubscriptionCheckingSubscriber = new SubscriptionCheckingSubscriber(getSubscriptionDao(), getChannelType(), this, subscriptionMatcher );
|
||||||
}
|
}
|
||||||
getProcessingChannel().subscribe(mySubscriptionCheckingSubscriber);
|
getProcessingChannel().subscribe(mySubscriptionCheckingSubscriber);
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,17 @@
|
||||||
package ca.uhn.fhir.jpa.subscription;
|
package ca.uhn.fhir.jpa.subscription;
|
||||||
|
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||||
|
import org.hl7.fhir.instance.model.api.IIdType;
|
||||||
|
import org.hl7.fhir.r4.model.Subscription;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
import org.springframework.messaging.Message;
|
||||||
|
import org.springframework.messaging.MessageChannel;
|
||||||
|
import org.springframework.messaging.MessagingException;
|
||||||
|
|
||||||
/*-
|
/*-
|
||||||
* #%L
|
* #%L
|
||||||
* HAPI FHIR JPA Server
|
* HAPI FHIR JPA Server
|
||||||
|
|
@ -25,27 +37,20 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
|
||||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||||
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
|
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
|
||||||
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
|
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
|
||||||
|
import ca.uhn.fhir.jpa.subscription.matcher.ISubscriptionMatcher;
|
||||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
|
||||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
|
||||||
import org.hl7.fhir.instance.model.api.IIdType;
|
|
||||||
import org.hl7.fhir.r4.model.Subscription;
|
|
||||||
import org.slf4j.Logger;
|
|
||||||
import org.slf4j.LoggerFactory;
|
|
||||||
import org.springframework.messaging.Message;
|
|
||||||
import org.springframework.messaging.MessageChannel;
|
|
||||||
import org.springframework.messaging.MessagingException;
|
|
||||||
|
|
||||||
import java.util.List;
|
|
||||||
|
|
||||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||||
|
|
||||||
public class SubscriptionCheckingSubscriber extends BaseSubscriptionSubscriber {
|
public class SubscriptionCheckingSubscriber extends BaseSubscriptionSubscriber {
|
||||||
private Logger ourLog = LoggerFactory.getLogger(SubscriptionCheckingSubscriber.class);
|
private Logger ourLog = LoggerFactory.getLogger(SubscriptionCheckingSubscriber.class);
|
||||||
|
|
||||||
public SubscriptionCheckingSubscriber(IFhirResourceDao theSubscriptionDao, Subscription.SubscriptionChannelType theChannelType, BaseSubscriptionInterceptor theSubscriptionInterceptor) {
|
private final ISubscriptionMatcher mySubscriptionMatcher;
|
||||||
|
|
||||||
|
public SubscriptionCheckingSubscriber(IFhirResourceDao theSubscriptionDao, Subscription.SubscriptionChannelType theChannelType, BaseSubscriptionInterceptor theSubscriptionInterceptor, ISubscriptionMatcher theSubscriptionMatcher) {
|
||||||
super(theSubscriptionDao, theChannelType, theSubscriptionInterceptor);
|
super(theSubscriptionDao, theChannelType, theSubscriptionInterceptor);
|
||||||
|
this.mySubscriptionMatcher = theSubscriptionMatcher;
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
|
|
@ -107,16 +112,7 @@ public class SubscriptionCheckingSubscriber extends BaseSubscriptionSubscriber {
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
|
|
||||||
// run the subscriptions query and look for matches, add the id as part of the criteria to avoid getting matches of previous resources rather than the recent resource
|
if (!mySubscriptionMatcher.match(nextCriteriaString, msg)) {
|
||||||
String criteria = nextCriteriaString;
|
|
||||||
criteria += "&_id=" + resourceType + "/" + resourceId;
|
|
||||||
criteria = massageCriteria(criteria);
|
|
||||||
|
|
||||||
IBundleProvider results = performSearch(criteria);
|
|
||||||
|
|
||||||
ourLog.debug("Subscription check found {} results for query: {}", results.size(), criteria);
|
|
||||||
|
|
||||||
if (results.size() == 0) {
|
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,7 @@
|
||||||
|
package ca.uhn.fhir.jpa.subscription.matcher;
|
||||||
|
|
||||||
|
import ca.uhn.fhir.jpa.subscription.ResourceModifiedMessage;
|
||||||
|
|
||||||
|
public interface ISubscriptionMatcher {
|
||||||
|
boolean match(String criteria, ResourceModifiedMessage msg);
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,67 @@
|
||||||
|
package ca.uhn.fhir.jpa.subscription.matcher;
|
||||||
|
|
||||||
|
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||||
|
import org.hl7.fhir.instance.model.api.IIdType;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import ca.uhn.fhir.context.FhirContext;
|
||||||
|
import ca.uhn.fhir.context.RuntimeResourceDefinition;
|
||||||
|
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
|
||||||
|
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||||
|
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
|
||||||
|
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
|
||||||
|
import ca.uhn.fhir.jpa.subscription.BaseSubscriptionInterceptor;
|
||||||
|
import ca.uhn.fhir.jpa.subscription.ResourceModifiedMessage;
|
||||||
|
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||||
|
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||||
|
|
||||||
|
public class SubscriptionMatcherDatabase implements ISubscriptionMatcher {
|
||||||
|
private Logger ourLog = LoggerFactory.getLogger(SubscriptionMatcherDatabase.class);
|
||||||
|
|
||||||
|
private final IFhirResourceDao<?> mySubscriptionDao;
|
||||||
|
|
||||||
|
private final BaseSubscriptionInterceptor mySubscriptionInterceptor;
|
||||||
|
|
||||||
|
public SubscriptionMatcherDatabase(IFhirResourceDao<?> theSubscriptionDao, BaseSubscriptionInterceptor theSubscriptionInterceptor) {
|
||||||
|
mySubscriptionDao = theSubscriptionDao;
|
||||||
|
mySubscriptionInterceptor = theSubscriptionInterceptor;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean match(String criteria, ResourceModifiedMessage msg) {
|
||||||
|
IIdType id = msg.getId(getContext());
|
||||||
|
String resourceType = id.getResourceType();
|
||||||
|
String resourceId = id.getIdPart();
|
||||||
|
|
||||||
|
// run the subscriptions query and look for matches, add the id as part of the criteria to avoid getting matches of previous resources rather than the recent resource
|
||||||
|
criteria += "&_id=" + resourceType + "/" + resourceId;
|
||||||
|
|
||||||
|
IBundleProvider results = performSearch(criteria);
|
||||||
|
|
||||||
|
ourLog.debug("Subscription check found {} results for query: {}", results.size(), criteria);
|
||||||
|
|
||||||
|
return results.size() > 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Search based on a query criteria
|
||||||
|
*/
|
||||||
|
protected IBundleProvider performSearch(String theCriteria) {
|
||||||
|
RuntimeResourceDefinition responseResourceDef = mySubscriptionDao.validateCriteriaAndReturnResourceDefinition(theCriteria);
|
||||||
|
SearchParameterMap responseCriteriaUrl = BaseHapiFhirDao.translateMatchUrl(mySubscriptionDao, getContext(), theCriteria, responseResourceDef);
|
||||||
|
|
||||||
|
RequestDetails req = new ServletSubRequestDetails();
|
||||||
|
req.setSubRequest(true);
|
||||||
|
|
||||||
|
IFhirResourceDao<? extends IBaseResource> responseDao = mySubscriptionInterceptor.getDao(responseResourceDef.getImplementingClass());
|
||||||
|
responseCriteriaUrl.setLoadSynchronousUpTo(1);
|
||||||
|
|
||||||
|
IBundleProvider responseResults = responseDao.search(responseCriteriaUrl, req);
|
||||||
|
return responseResults;
|
||||||
|
}
|
||||||
|
|
||||||
|
public FhirContext getContext() {
|
||||||
|
return mySubscriptionDao.getContext();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,12 @@
|
||||||
|
package ca.uhn.fhir.jpa.subscription.matcher;
|
||||||
|
|
||||||
|
import ca.uhn.fhir.jpa.subscription.ResourceModifiedMessage;
|
||||||
|
|
||||||
|
public class SubscriptionMatcherInMemory implements ISubscriptionMatcher {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean match(String criteria, ResourceModifiedMessage msg) {
|
||||||
|
// FIXME KHS implement
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -26,6 +26,7 @@ import org.junit.*;
|
||||||
|
|
||||||
import javax.servlet.http.HttpServletRequest;
|
import javax.servlet.http.HttpServletRequest;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
|
import java.util.Collections;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
import static org.hamcrest.CoreMatchers.containsString;
|
import static org.hamcrest.CoreMatchers.containsString;
|
||||||
|
|
@ -44,8 +45,8 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
|
||||||
private static RestfulServer ourListenerRestServer;
|
private static RestfulServer ourListenerRestServer;
|
||||||
private static Server ourListenerServer;
|
private static Server ourListenerServer;
|
||||||
private static String ourListenerServerBase;
|
private static String ourListenerServerBase;
|
||||||
private static List<Observation> ourCreatedObservations = Lists.newArrayList();
|
private static List<Observation> ourCreatedObservations = Collections.synchronizedList(Lists.newArrayList());
|
||||||
private static List<Observation> ourUpdatedObservations = Lists.newArrayList();
|
private static List<Observation> ourUpdatedObservations = Collections.synchronizedList(Lists.newArrayList());
|
||||||
private static List<Patient> ourCreatedPatients = Lists.newArrayList();
|
private static List<Patient> ourCreatedPatients = Lists.newArrayList();
|
||||||
private static List<Patient> ourUpdatedPatients = Lists.newArrayList();
|
private static List<Patient> ourUpdatedPatients = Lists.newArrayList();
|
||||||
private static List<String> ourContentTypes = new ArrayList<>();
|
private static List<String> ourContentTypes = new ArrayList<>();
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue