Merge branch 'master' of github.com:jamesagnew/hapi-fhir
This commit is contained in:
jamesagnew
commit
cfdb3b222e
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@ -146,12 +146,12 @@ public class DaoConfig {
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private boolean myEnableInMemorySubscriptionMatching = true;
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private boolean myEnforceReferenceTargetTypes = true;
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private ClientIdStrategyEnum myResourceClientIdStrategy = ClientIdStrategyEnum.ALPHANUMERIC;
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private boolean myFilterParameterEnabled = false;
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private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
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/**
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* EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
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*/
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private boolean myPreExpandValueSetsExperimental = false;
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private boolean myFilterParameterEnabled = false;
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private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
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/**
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* EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
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*/
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@ -21,8 +21,6 @@ package ca.uhn.fhir.jpa.dao.data;
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*/
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import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
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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.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Modifying;
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import org.springframework.data.jpa.repository.Query;
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@ -33,17 +31,14 @@ import java.util.Optional;
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public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConcept, Long> {
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@Query("SELECT COUNT(*) FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
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@Query("SELECT COUNT(*) FROM TermValueSetConcept vsc WHERE vsc.myValueSetPid = :pid")
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Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
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@Query("DELETE FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
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@Query("DELETE FROM TermValueSetConcept vsc WHERE vsc.myValueSetPid = :pid")
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@Modifying
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void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
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@Query("SELECT vsc from TermValueSetConcept vsc LEFT OUTER JOIN FETCH vsc.myDesignations WHERE vsc.myValueSet.myId = :pid")
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Slice<TermValueSetConcept> findByTermValueSetIdAndPreFetchDesignations(Pageable thePage, @Param("pid") Long theValueSetId);
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@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
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@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSetPid = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
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Optional<TermValueSetConcept> findByTermValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
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@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.myCode = :codeval")
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@ -51,4 +46,11 @@ public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConce
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@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
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Optional<TermValueSetConcept> findByValueSetResourcePidSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
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@Query("SELECT vsc.myId FROM TermValueSetConcept vsc WHERE vsc.myValueSetPid = :pid ORDER BY vsc.myId")
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List<Long> findIdsByTermValueSetId(@Param("pid") Long theValueSetId);
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@Query("UPDATE TermValueSetConcept vsc SET vsc.myOrder = :order WHERE vsc.myId = :pid")
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@Modifying
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void updateOrderById(@Param("pid") Long theId, @Param("order") int theOrder);
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}
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@ -30,10 +30,10 @@ import org.springframework.data.repository.query.Param;
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public interface ITermValueSetConceptDesignationDao extends JpaRepository<TermValueSetConceptDesignation, Long> {
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@Query("SELECT COUNT(vscd) FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
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@Query("SELECT COUNT(vscd) FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSetPid = :pid")
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Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
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@Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
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@Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSetPid = :pid")
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@Modifying
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void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
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@ -0,0 +1,35 @@
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package ca.uhn.fhir.jpa.dao.data;
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import ca.uhn.fhir.jpa.entity.TermValueSetConceptView;
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import org.springframework.data.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Query;
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import org.springframework.data.repository.query.Param;
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import java.util.List;
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/*
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2019 University Health Network
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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public interface ITermValueSetConceptViewDao extends JpaRepository<TermValueSetConceptView, Long> {
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@Query("SELECT v FROM TermValueSetConceptView v WHERE v.myConceptValueSetPid = :pid AND v.myConceptOrder >= :from AND v.myConceptOrder < :to ORDER BY v.myConceptOrder")
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List<TermValueSetConceptView> findByTermValueSetId(@Param("from") int theFrom, @Param("to") int theTo, @Param("pid") Long theValueSetId);
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}
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@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
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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.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Modifying;
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import org.springframework.data.jpa.repository.Query;
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import org.springframework.data.repository.query.Param;
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@ -33,10 +32,6 @@ import java.util.Optional;
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public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
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@Query("DELETE FROM TermValueSet vs WHERE vs.myId = :pid")
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@Modifying
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void deleteByTermValueSetId(@Param("pid") Long theId);
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@Query("SELECT vs FROM TermValueSet vs WHERE vs.myResourcePid = :resource_pid")
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Optional<TermValueSet> findByResourcePid(@Param("resource_pid") Long theResourcePid);
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@ -93,12 +93,12 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
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boolean allSystemsAreSuppportedByTerminologyService = true;
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for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
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if (!myTerminologySvc.supportsSystem(next.getSystem())) {
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if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
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allSystemsAreSuppportedByTerminologyService = false;
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}
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}
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for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
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if (!myTerminologySvc.supportsSystem(next.getSystem())) {
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if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
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allSystemsAreSuppportedByTerminologyService = false;
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}
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}
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@ -125,12 +125,12 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
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boolean allSystemsAreSuppportedByTerminologyService = true;
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for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
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if (!myTerminologySvc.supportsSystem(next.getSystem())) {
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if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
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allSystemsAreSuppportedByTerminologyService = false;
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}
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}
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for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
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if (!myTerminologySvc.supportsSystem(next.getSystem())) {
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if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
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allSystemsAreSuppportedByTerminologyService = false;
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}
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}
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@ -160,6 +160,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
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}
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ValueSet source = new ValueSet();
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source.setUrl(theUri);
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source.getCompose().addInclude().addValueSet(theUri);
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@ -156,6 +156,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
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}
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ValueSet source = new ValueSet();
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source.setUrl(theUri);
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source.getCompose().addInclude().addValueSet(theUri);
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@ -162,6 +162,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
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}
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ValueSet source = new ValueSet();
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source.setUrl(theUri);
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source.getCompose().addInclude().addValueSet(theUri);
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@ -23,7 +23,6 @@ package ca.uhn.fhir.jpa.entity;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.util.ValidateUtil;
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import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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import org.apache.commons.lang3.builder.ToStringBuilder;
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import org.apache.commons.lang3.builder.ToStringStyle;
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import org.hibernate.annotations.ColumnDefault;
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@ -67,7 +66,7 @@ public class TermValueSet implements Serializable {
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@Column(name = "VSNAME", nullable = true, length = MAX_NAME_LENGTH)
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private String myName;
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@OneToMany(mappedBy = "myValueSet")
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@OneToMany(mappedBy = "myValueSet", fetch = FetchType.LAZY)
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private List<TermValueSetConcept> myConcepts;
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@Column(name = "TOTAL_CONCEPTS", nullable = false)
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@ -82,6 +81,9 @@ public class TermValueSet implements Serializable {
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@Column(name = "EXPANSION_STATUS", nullable = false, length = MAX_EXPANSION_STATUS_LENGTH)
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private TermValueSetPreExpansionStatusEnum myExpansionStatus;
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@Transient
|
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private transient Integer myHashCode;
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public TermValueSet() {
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super();
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myExpansionStatus = TermValueSetPreExpansionStatusEnum.NOT_EXPANDED;
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@ -196,9 +198,10 @@ public class TermValueSet implements Serializable {
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@Override
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public int hashCode() {
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return new HashCodeBuilder(17, 37)
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.append(getUrl())
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.toHashCode();
|
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if (myHashCode == null) {
|
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myHashCode = getUrl().hashCode();
|
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}
|
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return myHashCode;
|
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}
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|
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@Override
|
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|
|
|
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|
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@ -40,7 +40,8 @@ import static org.apache.commons.lang3.StringUtils.length;
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* bork up migration tasks.
|
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*/
|
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@Table(name = "TRM_VALUESET_CONCEPT", uniqueConstraints = {
|
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@UniqueConstraint(name = "IDX_VS_CONCEPT_CS_CD", columnNames = {"VALUESET_PID", "SYSTEM_URL", "CODEVAL"})
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@UniqueConstraint(name = "IDX_VS_CONCEPT_CS_CD", columnNames = {"VALUESET_PID", "SYSTEM_URL", "CODEVAL"}),
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@UniqueConstraint(name = "IDX_VS_CONCEPT_ORDER", columnNames = {"VALUESET_PID", "VALUESET_ORDER"})
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})
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@Entity()
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public class TermValueSetConcept implements Serializable {
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@ -52,10 +53,16 @@ public class TermValueSetConcept implements Serializable {
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@Column(name = "PID")
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private Long myId;
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@ManyToOne()
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@ManyToOne(fetch = FetchType.LAZY)
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@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_PID"))
|
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private TermValueSet myValueSet;
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@Column(name = "VALUESET_PID", insertable = false, updatable = false, nullable = false)
|
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private Long myValueSetPid;
|
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@Column(name = "VALUESET_ORDER", nullable = false)
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private int myOrder;
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|
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@Transient
|
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private String myValueSetUrl;
|
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|
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|
|
@ -71,9 +78,12 @@ public class TermValueSetConcept implements Serializable {
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@Column(name = "DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
|
||||
private String myDisplay;
|
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|
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@OneToMany(mappedBy = "myConcept")
|
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@OneToMany(mappedBy = "myConcept", fetch = FetchType.LAZY)
|
||||
private List<TermValueSetConceptDesignation> myDesignations;
|
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|
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@Transient
|
||||
private transient Integer myHashCode;
|
||||
|
||||
public Long getId() {
|
||||
return myId;
|
||||
}
|
||||
|
|
@ -87,6 +97,15 @@ public class TermValueSetConcept implements Serializable {
|
|||
return this;
|
||||
}
|
||||
|
||||
public int getOrder() {
|
||||
return myOrder;
|
||||
}
|
||||
|
||||
public TermValueSetConcept setOrder(int theOrder) {
|
||||
myOrder = theOrder;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getValueSetUrl() {
|
||||
if (myValueSetUrl == null) {
|
||||
myValueSetUrl = getValueSet().getUrl();
|
||||
|
|
@ -153,7 +172,7 @@ public class TermValueSetConcept implements Serializable {
|
|||
TermValueSetConcept that = (TermValueSetConcept) theO;
|
||||
|
||||
return new EqualsBuilder()
|
||||
.append(getValueSetUrl(), that.getValueSetUrl())
|
||||
.append(myValueSetPid, that.myValueSetPid)
|
||||
.append(getSystem(), that.getSystem())
|
||||
.append(getCode(), that.getCode())
|
||||
.isEquals();
|
||||
|
|
@ -161,11 +180,14 @@ public class TermValueSetConcept implements Serializable {
|
|||
|
||||
@Override
|
||||
public int hashCode() {
|
||||
return new HashCodeBuilder(17, 37)
|
||||
.append(getValueSetUrl())
|
||||
.append(getSystem())
|
||||
.append(getCode())
|
||||
.toHashCode();
|
||||
if (myHashCode == null) {
|
||||
myHashCode = new HashCodeBuilder(17, 37)
|
||||
.append(myValueSetPid)
|
||||
.append(getSystem())
|
||||
.append(getCode())
|
||||
.toHashCode();
|
||||
}
|
||||
return myHashCode;
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -173,6 +195,8 @@ public class TermValueSetConcept implements Serializable {
|
|||
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
|
||||
.append("myId", myId)
|
||||
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
|
||||
.append("myValueSetPid", myValueSetPid)
|
||||
.append("myOrder", myOrder)
|
||||
.append("myValueSetUrl", this.getValueSetUrl())
|
||||
.append("myValueSetName", this.getValueSetName())
|
||||
.append("mySystem", mySystem)
|
||||
|
|
|
|||
|
|
@ -48,14 +48,20 @@ public class TermValueSetConceptDesignation implements Serializable {
|
|||
@Column(name = "PID")
|
||||
private Long myId;
|
||||
|
||||
@ManyToOne()
|
||||
@ManyToOne(fetch = FetchType.LAZY)
|
||||
@JoinColumn(name = "VALUESET_CONCEPT_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_CONCEPT_PID"))
|
||||
private TermValueSetConcept myConcept;
|
||||
|
||||
@Column(name = "VALUESET_CONCEPT_PID", insertable = false, updatable = false, nullable = false)
|
||||
private Long myConceptPid;
|
||||
|
||||
@ManyToOne(fetch = FetchType.LAZY)
|
||||
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VSCD_VS_PID"))
|
||||
private TermValueSet myValueSet;
|
||||
|
||||
@Column(name = "VALUESET_PID", insertable = false, updatable = false, nullable = false)
|
||||
private Long myValueSetPid;
|
||||
|
||||
@Transient
|
||||
private String myValueSetUrl;
|
||||
|
||||
|
|
@ -77,6 +83,9 @@ public class TermValueSetConceptDesignation implements Serializable {
|
|||
@Column(name = "VAL", nullable = false, length = MAX_LENGTH)
|
||||
private String myValue;
|
||||
|
||||
@Transient
|
||||
private transient Integer myHashCode;
|
||||
|
||||
public Long getId() {
|
||||
return myId;
|
||||
}
|
||||
|
|
@ -188,13 +197,16 @@ public class TermValueSetConceptDesignation implements Serializable {
|
|||
|
||||
@Override
|
||||
public int hashCode() {
|
||||
return new HashCodeBuilder(17, 37)
|
||||
.append(getLanguage())
|
||||
.append(getUseSystem())
|
||||
.append(getUseCode())
|
||||
.append(getUseDisplay())
|
||||
.append(getValue())
|
||||
.toHashCode();
|
||||
if (myHashCode == null) {
|
||||
myHashCode = new HashCodeBuilder(17, 37)
|
||||
.append(getLanguage())
|
||||
.append(getUseSystem())
|
||||
.append(getUseCode())
|
||||
.append(getUseDisplay())
|
||||
.append(getValue())
|
||||
.toHashCode();
|
||||
}
|
||||
return myHashCode;
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -202,7 +214,9 @@ public class TermValueSetConceptDesignation implements Serializable {
|
|||
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
|
||||
.append("myId", myId)
|
||||
.append(myConcept != null ? ("myConcept - id=" + myConcept.getId()) : ("myConcept=(null)"))
|
||||
.append("myConceptPid", myConceptPid)
|
||||
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
|
||||
.append("myValueSetPid", myValueSetPid)
|
||||
.append("myValueSetUrl", this.getValueSetUrl())
|
||||
.append("myValueSetName", this.getValueSetName())
|
||||
.append("myLanguage", myLanguage)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,135 @@
|
|||
package ca.uhn.fhir.jpa.entity;
|
||||
|
||||
/*
|
||||
* #%L
|
||||
* HAPI FHIR JPA Server
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2019 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.hibernate.annotations.Immutable;
|
||||
import org.hibernate.annotations.Subselect;
|
||||
|
||||
import javax.persistence.Column;
|
||||
import javax.persistence.Entity;
|
||||
import javax.persistence.Id;
|
||||
import java.io.Serializable;
|
||||
|
||||
@Entity
|
||||
@Immutable
|
||||
@Subselect(
|
||||
"SELECT CONCAT(vsc.PID, ' ', vscd.PID) AS PID, " +
|
||||
" vsc.PID AS CONCEPT_PID, " +
|
||||
" vsc.VALUESET_PID AS CONCEPT_VALUESET_PID, " +
|
||||
" vsc.VALUESET_ORDER AS CONCEPT_VALUESET_ORDER, " +
|
||||
" vsc.SYSTEM_URL AS CONCEPT_SYSTEM_URL, " +
|
||||
" vsc.CODEVAL AS CONCEPT_CODEVAL, " +
|
||||
" vsc.DISPLAY AS CONCEPT_DISPLAY, " +
|
||||
" vscd.PID AS DESIGNATION_PID, " +
|
||||
" vscd.LANG AS DESIGNATION_LANG, " +
|
||||
" vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, " +
|
||||
" vscd.USE_CODE AS DESIGNATION_USE_CODE, " +
|
||||
" vscd.USE_DISPLAY AS DESIGNATION_USE_DISPLAY, " +
|
||||
" vscd.VAL AS DESIGNATION_VAL " +
|
||||
"FROM TRM_VALUESET_CONCEPT vsc " +
|
||||
" LEFT OUTER JOIN TRM_VALUESET_C_DESIGNATION vscd ON vsc.PID = vscd.VALUESET_CONCEPT_PID"
|
||||
)
|
||||
public class TermValueSetConceptView implements Serializable {
|
||||
private static final long serialVersionUID = 1L;
|
||||
|
||||
private static final int MAX_LENGTH = 500;
|
||||
|
||||
@Id
|
||||
@Column(name="PID", length = MAX_LENGTH)
|
||||
private String myPid;
|
||||
|
||||
@Column(name = "CONCEPT_PID")
|
||||
private Long myConceptPid;
|
||||
|
||||
@Column(name = "CONCEPT_VALUESET_PID")
|
||||
private Long myConceptValueSetPid;
|
||||
|
||||
@Column(name = "CONCEPT_VALUESET_ORDER")
|
||||
private int myConceptOrder;
|
||||
|
||||
@Column(name = "CONCEPT_SYSTEM_URL", length = TermCodeSystem.MAX_URL_LENGTH)
|
||||
private String myConceptSystemUrl;
|
||||
|
||||
@Column(name = "CONCEPT_CODEVAL", length = TermConcept.MAX_CODE_LENGTH)
|
||||
private String myConceptCode;
|
||||
|
||||
@Column(name = "CONCEPT_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
|
||||
private String myConceptDisplay;
|
||||
|
||||
@Column(name = "DESIGNATION_PID")
|
||||
private Long myDesignationPid;
|
||||
|
||||
@Column(name = "DESIGNATION_LANG", length = TermValueSetConceptDesignation.MAX_LENGTH)
|
||||
private String myDesignationLang;
|
||||
|
||||
@Column(name = "DESIGNATION_USE_SYSTEM", length = TermValueSetConceptDesignation.MAX_LENGTH)
|
||||
private String myDesignationUseSystem;
|
||||
|
||||
@Column(name = "DESIGNATION_USE_CODE", length = TermValueSetConceptDesignation.MAX_LENGTH)
|
||||
private String myDesignationUseCode;
|
||||
|
||||
@Column(name = "DESIGNATION_USE_DISPLAY", length = TermValueSetConceptDesignation.MAX_LENGTH)
|
||||
private String myDesignationUseDisplay;
|
||||
|
||||
@Column(name = "DESIGNATION_VAL", length = TermValueSetConceptDesignation.MAX_LENGTH)
|
||||
private String myDesignationVal;
|
||||
|
||||
|
||||
public Long getConceptPid() {
|
||||
return myConceptPid;
|
||||
}
|
||||
|
||||
public String getConceptSystemUrl() {
|
||||
return myConceptSystemUrl;
|
||||
}
|
||||
|
||||
public String getConceptCode() {
|
||||
return myConceptCode;
|
||||
}
|
||||
|
||||
public String getConceptDisplay() {
|
||||
return myConceptDisplay;
|
||||
}
|
||||
|
||||
public Long getDesignationPid() {
|
||||
return myDesignationPid;
|
||||
}
|
||||
|
||||
public String getDesignationLang() {
|
||||
return myDesignationLang;
|
||||
}
|
||||
|
||||
public String getDesignationUseSystem() {
|
||||
return myDesignationUseSystem;
|
||||
}
|
||||
|
||||
public String getDesignationUseCode() {
|
||||
return myDesignationUseCode;
|
||||
}
|
||||
|
||||
public String getDesignationUseDisplay() {
|
||||
return myDesignationUseDisplay;
|
||||
}
|
||||
|
||||
public String getDesignationVal() {
|
||||
return myDesignationVal;
|
||||
}
|
||||
}
|
||||
|
|
@ -28,14 +28,15 @@ import ca.uhn.fhir.jpa.dao.data.*;
|
|||
import ca.uhn.fhir.jpa.entity.*;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
|
||||
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
import ca.uhn.fhir.util.ObjectUtil;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import ca.uhn.fhir.util.ValidateUtil;
|
||||
import com.github.benmanes.caffeine.cache.Cache;
|
||||
import com.github.benmanes.caffeine.cache.Caffeine;
|
||||
|
|
@ -159,6 +160,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
private IFulltextSearchSvc myFulltextSearchSvc;
|
||||
@Autowired
|
||||
private PlatformTransactionManager myTxManager;
|
||||
@Autowired
|
||||
private ITermValueSetConceptViewDao myTermValueSetConceptViewDao;
|
||||
|
||||
private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
|
||||
String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
|
||||
|
|
@ -392,7 +395,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
ourLog.info("Deleting existing TermValueSet[{}] and its children...", existingTermValueSet.getId());
|
||||
myValueSetConceptDesignationDao.deleteByTermValueSetId(existingTermValueSet.getId());
|
||||
myValueSetConceptDao.deleteByTermValueSetId(existingTermValueSet.getId());
|
||||
myValueSetDao.deleteByTermValueSetId(existingTermValueSet.getId());
|
||||
myValueSetDao.deleteById(existingTermValueSet.getId());
|
||||
ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
|
||||
}
|
||||
}
|
||||
|
|
@ -485,8 +488,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
}
|
||||
|
||||
if (!optionalTermValueSet.isPresent()) {
|
||||
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory expansion without parameters. Will schedule this ValueSet for pre-expansion. {}", getValueSetInfo(theValueSetToExpand));
|
||||
myDeferredValueSets.add(theValueSetToExpand);
|
||||
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory expansion without parameters. {}", getValueSetInfo(theValueSetToExpand));
|
||||
return expandValueSet(theValueSetToExpand); // In-memory expansion.
|
||||
}
|
||||
|
||||
|
|
@ -518,7 +520,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
theExpansionComponent.addParameter().setName("offset").setValue(new IntegerType(theOffset));
|
||||
theExpansionComponent.addParameter().setName("count").setValue(new IntegerType(theCount));
|
||||
|
||||
if (theCount == 0 || total == 0) {
|
||||
if (theCount == 0) {
|
||||
return;
|
||||
}
|
||||
|
||||
|
|
@ -527,58 +529,64 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
|
||||
private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
|
||||
int conceptsExpanded = 0;
|
||||
int designationsExpanded = 0;
|
||||
int toIndex = theOffset + theCount;
|
||||
Slice<TermValueSetConcept> slice = myValueSetConceptDao.findByTermValueSetIdAndPreFetchDesignations(SearchCoordinatorSvcImpl.toPage(theOffset, toIndex), theTermValueSet.getId());
|
||||
if (!slice.hasContent()) {
|
||||
logConceptsExpanded(theTermValueSet, conceptsExpanded);
|
||||
Collection<TermValueSetConceptView> conceptViews = myTermValueSetConceptViewDao.findByTermValueSetId(theOffset, toIndex, theTermValueSet.getId());
|
||||
|
||||
if (conceptViews.isEmpty()) {
|
||||
logConceptsExpanded("No concepts to expand. ", theTermValueSet, conceptsExpanded);
|
||||
return;
|
||||
}
|
||||
|
||||
for (TermValueSetConcept concept : slice.getContent()) {
|
||||
ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
|
||||
containsComponent.setSystem(concept.getSystem());
|
||||
containsComponent.setCode(concept.getCode());
|
||||
containsComponent.setDisplay(concept.getDisplay());
|
||||
Map<Long, ValueSet.ValueSetExpansionContainsComponent> pidToConcept = new HashMap<>();
|
||||
for (TermValueSetConceptView conceptView : conceptViews) {
|
||||
|
||||
// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
|
||||
expandDesignations(theTermValueSet, concept, containsComponent);
|
||||
Long conceptPid = conceptView.getConceptPid();
|
||||
ValueSet.ValueSetExpansionContainsComponent containsComponent;
|
||||
|
||||
if (!pidToConcept.containsKey(conceptPid)) {
|
||||
containsComponent = theExpansionComponent.addContains();
|
||||
containsComponent.setSystem(conceptView.getConceptSystemUrl());
|
||||
containsComponent.setCode(conceptView.getConceptCode());
|
||||
containsComponent.setDisplay(conceptView.getConceptDisplay());
|
||||
pidToConcept.put(conceptPid, containsComponent);
|
||||
} else {
|
||||
containsComponent = pidToConcept.get(conceptPid);
|
||||
}
|
||||
|
||||
// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to designations optional.
|
||||
if (conceptView.getDesignationPid() != null) {
|
||||
ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.addDesignation();
|
||||
designationComponent.setLanguage(conceptView.getDesignationLang());
|
||||
designationComponent.setUse(new Coding(
|
||||
conceptView.getDesignationUseSystem(),
|
||||
conceptView.getDesignationUseCode(),
|
||||
conceptView.getDesignationUseDisplay()));
|
||||
designationComponent.setValue(conceptView.getDesignationVal());
|
||||
|
||||
if (++designationsExpanded % 250 == 0) {
|
||||
logDesignationsExpanded("Expansion of designations in progress. ", theTermValueSet, designationsExpanded);
|
||||
}
|
||||
}
|
||||
|
||||
if (++conceptsExpanded % 250 == 0) {
|
||||
logConceptsExpanded(theTermValueSet, conceptsExpanded);
|
||||
logConceptsExpanded("Expansion of concepts in progress. ", theTermValueSet, conceptsExpanded);
|
||||
}
|
||||
}
|
||||
|
||||
logConceptsExpanded(theTermValueSet, conceptsExpanded);
|
||||
logDesignationsExpanded("Finished expanding designations. ", theTermValueSet, designationsExpanded);
|
||||
logConceptsExpanded("Finished expanding concepts. ", theTermValueSet, conceptsExpanded);
|
||||
}
|
||||
|
||||
private void logConceptsExpanded(TermValueSet theTermValueSet, int theConceptsExpanded) {
|
||||
private void logConceptsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theConceptsExpanded) {
|
||||
if (theConceptsExpanded > 0) {
|
||||
ourLog.info("Have expanded {} concepts in ValueSet[{}]", theConceptsExpanded, theTermValueSet.getUrl());
|
||||
ourLog.info("{}Have expanded {} concepts in ValueSet[{}]", theLogDescriptionPrefix, theConceptsExpanded, theTermValueSet.getUrl());
|
||||
}
|
||||
}
|
||||
|
||||
private void expandDesignations(TermValueSet theValueSet, TermValueSetConcept theConcept, ValueSet.ValueSetExpansionContainsComponent theContainsComponent) {
|
||||
int designationsExpanded = 0;
|
||||
for (TermValueSetConceptDesignation designation : theConcept.getDesignations()) {
|
||||
ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
|
||||
designationComponent.setLanguage(designation.getLanguage());
|
||||
designationComponent.setUse(new Coding(
|
||||
designation.getUseSystem(),
|
||||
designation.getUseCode(),
|
||||
designation.getUseDisplay()));
|
||||
designationComponent.setValue(designation.getValue());
|
||||
|
||||
if (++designationsExpanded % 250 == 0) {
|
||||
logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
|
||||
}
|
||||
}
|
||||
|
||||
logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
|
||||
}
|
||||
|
||||
private void logDesignationsExpanded(TermValueSet theValueSet, TermValueSetConcept theConcept, int theDesignationsExpanded) {
|
||||
private void logDesignationsExpanded(String theLogDescriptionPrefix, TermValueSet theTermValueSet, int theDesignationsExpanded) {
|
||||
if (theDesignationsExpanded > 0) {
|
||||
ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", theDesignationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
|
||||
ourLog.info("{}Have expanded {} designations in ValueSet[{}]", theLogDescriptionPrefix, theDesignationsExpanded, theTermValueSet.getUrl());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -600,10 +608,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
ourLog.debug("Handling includes");
|
||||
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getInclude()) {
|
||||
for (int i = 0; ; i++) {
|
||||
int finalI = i;
|
||||
int queryIndex = i;
|
||||
Boolean shouldContinue = myTxTemplate.execute(t -> {
|
||||
boolean add = true;
|
||||
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter, finalI);
|
||||
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter, queryIndex);
|
||||
});
|
||||
if (!shouldContinue) {
|
||||
break;
|
||||
|
|
@ -615,10 +623,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
ourLog.debug("Handling excludes");
|
||||
for (ValueSet.ConceptSetComponent exclude : theValueSetToExpand.getCompose().getExclude()) {
|
||||
for (int i = 0; ; i++) {
|
||||
int finalI = i;
|
||||
int queryIndex = i;
|
||||
Boolean shouldContinue = myTxTemplate.execute(t -> {
|
||||
boolean add = false;
|
||||
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, exclude, add, theCodeCounter, finalI);
|
||||
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, exclude, add, theCodeCounter, queryIndex);
|
||||
});
|
||||
if (!shouldContinue) {
|
||||
break;
|
||||
|
|
@ -626,6 +634,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
}
|
||||
}
|
||||
|
||||
if (theValueSetCodeAccumulator instanceof ValueSetConceptAccumulator) {
|
||||
myTxTemplate.execute(t -> ((ValueSetConceptAccumulator) theValueSetCodeAccumulator).removeGapsFromConceptOrder());
|
||||
}
|
||||
|
||||
ourLog.info("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
|
||||
}
|
||||
|
||||
|
|
@ -935,8 +947,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
Optional<TermValueSet> optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid);
|
||||
|
||||
if (!optionalTermValueSet.isPresent()) {
|
||||
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory code validation. Will schedule this ValueSet for pre-expansion. {}", getValueSetInfo(theValueSet));
|
||||
myDeferredValueSets.add(theValueSet);
|
||||
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory code validation. {}", getValueSetInfo(theValueSet));
|
||||
return false;
|
||||
}
|
||||
|
||||
|
|
@ -968,7 +979,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
if (theCoding.hasSystem() && theCoding.hasCode()) {
|
||||
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theCoding.getSystem(), theCoding.getCode()));
|
||||
}
|
||||
} else if (theCodeableConcept != null){
|
||||
} else if (theCodeableConcept != null) {
|
||||
for (Coding coding : theCodeableConcept.getCoding()) {
|
||||
if (coding.hasSystem() && coding.hasCode()) {
|
||||
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, coding.getSystem(), coding.getCode()));
|
||||
|
|
@ -1750,7 +1761,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
} catch (FHIRException fe) {
|
||||
throw new InternalErrorException(fe);
|
||||
}
|
||||
myConceptMapDao.save(termConceptMap);
|
||||
termConceptMap = myConceptMapDao.save(termConceptMap);
|
||||
int codesSaved = 0;
|
||||
|
||||
if (theConceptMap.hasGroup()) {
|
||||
|
|
@ -1793,7 +1804,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
termConceptMapGroupElementTarget.setEquivalence(elementTarget.getEquivalence());
|
||||
myConceptMapGroupElementTargetDao.save(termConceptMapGroupElementTarget);
|
||||
|
||||
if (codesSaved++ % 250 == 0) {
|
||||
if (++codesSaved % 250 == 0) {
|
||||
ourLog.info("Have saved {} codes in ConceptMap", codesSaved);
|
||||
myConceptMapGroupElementTargetDao.flush();
|
||||
}
|
||||
|
|
@ -1815,7 +1826,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
throw new UnprocessableEntityException(msg);
|
||||
}
|
||||
|
||||
ourLog.info("Done storing TermConceptMap.");
|
||||
ourLog.info("Done storing TermConceptMap[{}]", termConceptMap.getId());
|
||||
}
|
||||
|
||||
@Scheduled(fixedDelay = 600000) // 10 minutes.
|
||||
|
|
@ -1932,7 +1943,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
Optional<TermValueSet> optionalExistingTermValueSetByUrl = myValueSetDao.findByUrl(url);
|
||||
if (!optionalExistingTermValueSetByUrl.isPresent()) {
|
||||
|
||||
myValueSetDao.save(termValueSet);
|
||||
termValueSet = myValueSetDao.save(termValueSet);
|
||||
|
||||
} else {
|
||||
TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
|
||||
|
|
@ -1946,7 +1957,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
throw new UnprocessableEntityException(msg);
|
||||
}
|
||||
|
||||
ourLog.info("Done storing TermValueSet.");
|
||||
ourLog.info("Done storing TermValueSet[{}]", termValueSet.getId());
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -2354,6 +2365,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
return retVal;
|
||||
}
|
||||
|
||||
protected void throwInvalidValueSet(String theValueSet) {
|
||||
throw new ResourceNotFoundException("Unknown ValueSet: " + UrlUtil.escapeUrlParam(theValueSet));
|
||||
}
|
||||
|
||||
private static void extractLinksFromConceptAndChildren(TermConcept theConcept, List<TermConceptParentChildLink> theLinks) {
|
||||
theLinks.addAll(theConcept.getParents());
|
||||
for (TermConceptParentChildLink child : theConcept.getChildren()) {
|
||||
|
|
|
|||
|
|
@ -210,9 +210,10 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
|
|||
|
||||
@Override
|
||||
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
|
||||
// TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may time-out.
|
||||
ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
|
||||
if (vs == null) {
|
||||
return Collections.emptyList();
|
||||
super.throwInvalidValueSet(theValueSet);
|
||||
}
|
||||
|
||||
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
|
||||
|
|
|
|||
|
|
@ -122,9 +122,10 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
|
|||
|
||||
@Override
|
||||
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
|
||||
// TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may time-out.
|
||||
ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
|
||||
if (vs == null) {
|
||||
return Collections.emptyList();
|
||||
super.throwInvalidValueSet(theValueSet);
|
||||
}
|
||||
|
||||
return expandValueSetAndReturnVersionIndependentConcepts(vs);
|
||||
|
|
|
|||
|
|
@ -131,9 +131,10 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
|
|||
|
||||
@Override
|
||||
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
|
||||
// TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may time-out.
|
||||
ValueSet valueSetR5 = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
|
||||
if (valueSetR5 == null) {
|
||||
return Collections.emptyList();
|
||||
super.throwInvalidValueSet(theValueSet);
|
||||
}
|
||||
|
||||
return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5));
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ import ca.uhn.fhir.util.ValidateUtil;
|
|||
|
||||
import javax.annotation.Nonnull;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.*;
|
||||
|
|
@ -44,6 +45,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
private ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao;
|
||||
private int myConceptsSaved;
|
||||
private int myDesignationsSaved;
|
||||
private int myConceptsExcluded;
|
||||
|
||||
public ValueSetConceptAccumulator(@Nonnull TermValueSet theTermValueSet, @Nonnull ITermValueSetDao theValueSetDao, @Nonnull ITermValueSetConceptDao theValueSetConceptDao, @Nonnull ITermValueSetConceptDesignationDao theValueSetConceptDesignationDao) {
|
||||
myTermValueSet = theTermValueSet;
|
||||
|
|
@ -52,6 +54,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
myValueSetConceptDesignationDao = theValueSetConceptDesignationDao;
|
||||
myConceptsSaved = 0;
|
||||
myDesignationsSaved = 0;
|
||||
myConceptsExcluded = 0;
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -88,6 +91,10 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
myTermValueSet.decrementTotalConcepts();
|
||||
myValueSetDao.save(myTermValueSet);
|
||||
ourLog.info("Done excluding [{}|{}] from ValueSet[{}]", concept.getSystem(), concept.getCode(), myTermValueSet.getUrl());
|
||||
|
||||
if (++myConceptsExcluded % 250 == 0) {
|
||||
ourLog.info("Have excluded {} concepts from ValueSet[{}]", myConceptsExcluded, myTermValueSet.getUrl());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -97,6 +104,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
|
||||
TermValueSetConcept concept = new TermValueSetConcept();
|
||||
concept.setValueSet(myTermValueSet);
|
||||
concept.setOrder(myConceptsSaved);
|
||||
concept.setSystem(theSystem);
|
||||
concept.setCode(theCode);
|
||||
if (isNotBlank(theDisplay)) {
|
||||
|
|
@ -105,7 +113,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
myValueSetConceptDao.save(concept);
|
||||
myValueSetDao.save(myTermValueSet.incrementTotalConcepts());
|
||||
|
||||
if (myConceptsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
|
||||
if (++myConceptsSaved % 250 == 0) {
|
||||
ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSet.getUrl());
|
||||
}
|
||||
|
||||
|
|
@ -130,14 +138,30 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
|
|||
myValueSetConceptDesignationDao.save(designation);
|
||||
myValueSetDao.save(myTermValueSet.incrementTotalConceptDesignations());
|
||||
|
||||
if (myDesignationsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
|
||||
ourLog.info("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSet.getUrl());
|
||||
if (++myDesignationsSaved % 250 == 0) {
|
||||
ourLog.debug("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSet.getUrl());
|
||||
}
|
||||
|
||||
return designation;
|
||||
}
|
||||
|
||||
// TODO: DM 2019-07-16 - We need TermValueSetConceptProperty, similar to TermConceptProperty.
|
||||
// TODO: DM 2019-07-16 - We should also populate TermValueSetConceptProperty entities here.
|
||||
// TODO: DM 2019-07-30 - Expansions don't include the properties themselves; they are needed to facilitate filters and parameterized expansions.
|
||||
public Boolean removeGapsFromConceptOrder() {
|
||||
if (myConceptsExcluded <= 0) {
|
||||
return false;
|
||||
}
|
||||
|
||||
ourLog.info("Removing gaps from concept order for ValueSet[{}]", myTermValueSet.getUrl());
|
||||
int order = 0;
|
||||
List<Long> conceptIds = myValueSetConceptDao.findIdsByTermValueSetId(myTermValueSet.getId());
|
||||
for (Long conceptId : conceptIds) {
|
||||
myValueSetConceptDao.updateOrderById(conceptId, order++);
|
||||
}
|
||||
ourLog.info("Have removed gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSet.getUrl());
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
// TODO: DM 2019-07-16 - We may need TermValueSetConceptProperty, similar to TermConceptProperty.
|
||||
// TODO: DM 2019-07-16 - If so, we should also populate TermValueSetConceptProperty entities here.
|
||||
// TODO: DM 2019-07-30 - Expansions don't include the properties themselves; they may be needed to facilitate filters and parameterized expansions.
|
||||
}
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ import ca.uhn.fhir.parser.IParser;
|
|||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
import ca.uhn.fhir.rest.param.TokenParamModifier;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.validation.FhirValidator;
|
||||
|
|
@ -801,8 +802,8 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
|||
try {
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Unable to find imported value set http://example.com/my_value_set", e.getMessage());
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals("Unknown ValueSet: http%3A%2F%2Fexample.com%2Fmy_value_set", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1117,10 +1118,13 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
|
|||
valueSet.setUrl(URL_MY_VALUE_SET);
|
||||
myValueSetDao.update(valueSet, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
params.add(Observation.SP_STATUS, new TokenParam(null, "final"));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
try {
|
||||
params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
params.add(Observation.SP_STATUS, new TokenParam(null, "final"));
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals("Unknown ValueSet: http%3A%2F%2Fexample.com%2Fmy_value_set", e.getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ import ca.uhn.fhir.parser.IParser;
|
|||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
import ca.uhn.fhir.rest.param.TokenParamModifier;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.validation.FhirValidator;
|
||||
|
|
@ -1168,9 +1169,12 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
params.add(AuditEvent.SP_TYPE, new TokenParam(null, "http://hl7.org/fhir/ValueSet/audit-event-type").setModifier(TokenParamModifier.IN));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myAuditEventDao.search(params)), containsInAnyOrder(idIn1.getValue(), idIn2.getValue()));
|
||||
|
||||
params = new SearchParameterMap();
|
||||
params.add(AuditEvent.SP_TYPE, new TokenParam(null, "http://hl7.org/fhir/ValueSet/v3-PurposeOfUse").setModifier(TokenParamModifier.IN));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myAuditEventDao.search(params)), empty());
|
||||
try {
|
||||
params = new SearchParameterMap();
|
||||
params.add(AuditEvent.SP_TYPE, new TokenParam(null, "http://hl7.org/fhir/ValueSet/v3-PurposeOfUse").setModifier(TokenParamModifier.IN));
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals("Unknown ValueSet: http%3A%2F%2Fhl7.org%2Ffhir%2FValueSet%2Fv3-PurposeOfUse", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -1203,8 +1207,8 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
try {
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Unable to find imported value set http://example.com/my_value_set", e.getMessage());
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals("Unknown ValueSet: http%3A%2F%2Fexample.com%2Fmy_value_set", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1234,10 +1238,13 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
valueSet.setUrl(URL_MY_VALUE_SET);
|
||||
myValueSetDao.update(valueSet, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
params.add(Observation.SP_STATUS, new TokenParam(null, "final"));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
try {
|
||||
params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
params.add(Observation.SP_STATUS, new TokenParam(null, "final"));
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals("Unknown ValueSet: http%3A%2F%2Fnon_existant_VS", e.getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,14 +1,16 @@
|
|||
package ca.uhn.fhir.jpa.provider.dstu3;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
|
||||
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
|
|
@ -25,11 +27,14 @@ import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
|
|||
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
|
||||
import org.hl7.fhir.dstu3.model.codesystems.HttpVerb;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.After;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
|
||||
import org.springframework.transaction.support.TransactionTemplate;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
|
@ -43,18 +48,76 @@ import static org.junit.Assert.*;
|
|||
public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3Test {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3ValueSetTest.class);
|
||||
private IIdType myExtensionalCsId;
|
||||
private IIdType myExtensionalVsId;
|
||||
private IIdType myLocalValueSetId;
|
||||
private Long myExtensionalCsIdOnResourceTable;
|
||||
private Long myExtensionalVsIdOnResourceTable;
|
||||
private ValueSet myLocalVs;
|
||||
|
||||
@Before
|
||||
@Transactional
|
||||
public void before02() throws IOException {
|
||||
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
|
||||
myCodeSystemDao.create(cs, mySrd);
|
||||
private void loadAndPersistCodeSystemAndValueSet(HttpVerb theVerb) throws IOException {
|
||||
loadAndPersistCodeSystem(theVerb);
|
||||
loadAndPersistValueSet(theVerb);
|
||||
}
|
||||
|
||||
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
|
||||
private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
|
||||
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
|
||||
codeSystem.setId("CodeSystem/cs");
|
||||
persistCodeSystem(codeSystem, theVerb);
|
||||
}
|
||||
|
||||
private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
|
||||
switch (theVerb) {
|
||||
case POST:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
case PUT:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalCsId = myCodeSystemDao.update(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
default:
|
||||
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
|
||||
}
|
||||
myExtensionalCsIdOnResourceTable = myCodeSystemDao.readEntity(myExtensionalCsId, null).getId();
|
||||
}
|
||||
|
||||
private void loadAndPersistValueSet(HttpVerb theVerb) throws IOException {
|
||||
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
valueSet.setId("ValueSet/vs");
|
||||
persistValueSet(valueSet, theVerb);
|
||||
}
|
||||
|
||||
private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
|
||||
switch (theVerb) {
|
||||
case POST:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
case PUT:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalVsId = myValueSetDao.update(theValueSet, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
default:
|
||||
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
|
||||
}
|
||||
myExtensionalVsIdOnResourceTable = myValueSetDao.readEntity(myExtensionalVsId, null).getId();
|
||||
}
|
||||
|
||||
private CodeSystem createExternalCs() {
|
||||
|
|
@ -78,7 +141,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
}
|
||||
|
||||
private void createLocalCsAndVs() {
|
||||
//@formatter:off
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
|
||||
|
|
@ -92,7 +154,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.addConcept().setCode("B").setDisplay("Code B")
|
||||
.addConcept(new ConceptDefinitionComponent().setCode("BA").setDisplay("Code BA"))
|
||||
.addConcept(new ConceptDefinitionComponent().setCode("BB").setDisplay("Code BB"));
|
||||
//@formatter:on
|
||||
myCodeSystemDao.create(codeSystem, mySrd);
|
||||
|
||||
createLocalVs(codeSystem);
|
||||
|
|
@ -169,7 +230,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
|
||||
|
||||
@Test
|
||||
public void testExpandValueSetPropertySearchWithRegexExcludeUsingOr() {
|
||||
public void testExpandValueSetPropertySearchWithRegexExcludeUsingOr() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
createLoincSystemWithSomeCodes();
|
||||
|
||||
List<String> codes;
|
||||
|
|
@ -207,7 +270,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
|
||||
|
||||
@Test
|
||||
public void testExpandValueSetPropertySearchWithRegexExcludeNoFilter() {
|
||||
public void testExpandValueSetPropertySearchWithRegexExcludeNoFilter() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
createLoincSystemWithSomeCodes();
|
||||
|
||||
List<String> codes;
|
||||
|
|
@ -233,8 +298,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
|
||||
|
||||
@Test
|
||||
public void testExpandById() {
|
||||
//@formatter:off
|
||||
public void testExpandById() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
|
@ -242,7 +308,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -263,9 +328,42 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByIdWithFilter() {
|
||||
public void testExpandByIdWithPreExpansion() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
.named("expand")
|
||||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, Matchers.containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
|
||||
assertThat(resp, Matchers.containsString("<expansion>"));
|
||||
assertThat(resp, Matchers.containsString("<contains>"));
|
||||
assertThat(resp, Matchers.containsString("<system value=\"http://acme.org\"/>"));
|
||||
assertThat(resp, Matchers.containsString("<code value=\"8450-9\"/>"));
|
||||
assertThat(resp, Matchers.containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
|
||||
assertThat(resp, Matchers.containsString("</contains>"));
|
||||
assertThat(resp, Matchers.containsString("<contains>"));
|
||||
assertThat(resp, Matchers.containsString("<system value=\"http://acme.org\"/>"));
|
||||
assertThat(resp, Matchers.containsString("<code value=\"11378-7\"/>"));
|
||||
assertThat(resp, Matchers.containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
assertThat(resp, Matchers.containsString("</contains>"));
|
||||
assertThat(resp, Matchers.containsString("</expansion>"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByIdWithFilter() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
|
@ -273,7 +371,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withParameter(Parameters.class, "filter", new StringType("first"))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -290,7 +387,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
* https://groups.google.com/d/msgid/hapi-fhir/CAN2Cfy8kW%2BAOkgC6VjPsU3gRCpExCNZBmJdi-k5R_TWeyWH4tA%40mail.gmail.com?utm_medium=email&utm_source=footer
|
||||
*/
|
||||
@Test
|
||||
public void testExpandByIdentifier() {
|
||||
public void testExpandByIdentifier() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -308,7 +407,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrl() {
|
||||
public void testExpandByUrl() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -325,11 +426,72 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrlWithBogusUrl() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
|
||||
.execute();
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals(404, e.getStatusCode());
|
||||
assertEquals("HTTP 404 Not Found: Unknown ValueSet: http%3A%2F%2Fwww.healthintersections.com.au%2Ffhir%2FValueSet%2Fbogus", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrlWithPreExpansion() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, Matchers.stringContainsInOrder(
|
||||
"<code value=\"11378-7\"/>",
|
||||
"<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrlWithPreExpansionAndBogusUrl() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
try {
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
|
||||
.execute();
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals(404, e.getStatusCode());
|
||||
assertEquals("HTTP 404 Not Found: Unknown ValueSet: http%3A%2F%2Fwww.healthintersections.com.au%2Ffhir%2FValueSet%2Fbogus", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByValueSet() throws IOException {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -337,15 +499,12 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withParameter(Parameters.class, "valueSet", toExpand)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
//@formatter:off
|
||||
assertThat(resp, Matchers.stringContainsInOrder(
|
||||
"<code value=\"11378-7\"/>",
|
||||
"<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
//@formatter:on
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -354,7 +513,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
createLocalVsPointingAtBuiltInCodeSystem();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -362,7 +520,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withParameter(Parameters.class, "valueSet", myLocalVs)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -376,7 +533,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
assertNotNull(myLocalVs);
|
||||
myLocalVs.setId("");
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -384,7 +540,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withParameter(Parameters.class, "valueSet", myLocalVs)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -397,6 +552,8 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
|
||||
@Test
|
||||
public void testExpandInvalidParams() throws IOException {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
|
|
@ -467,7 +624,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
createLocalVsPointingAtBuiltInCodeSystem();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myLocalValueSetId)
|
||||
|
|
@ -475,7 +631,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -488,7 +643,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
createExternalCsAndLocalVs();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myLocalValueSetId)
|
||||
|
|
@ -496,7 +650,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -512,7 +665,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
createExternalCsAndLocalVs();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -520,7 +672,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withParameter(Parameters.class, "identifier", new UriType(URL_MY_VALUE_SET))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -536,7 +687,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
createExternalCsAndLocalVsWithUnknownCode();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
|
|
@ -547,7 +697,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
}
|
||||
//@formatter:on
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -576,8 +725,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() {
|
||||
//@formatter:off
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
|
@ -585,7 +735,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.execute();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -595,6 +744,8 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
createLocalCsAndVs();
|
||||
createLocalVsWithIncludeConcept();
|
||||
|
||||
|
|
@ -617,8 +768,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemType() {
|
||||
//@formatter:off
|
||||
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -626,7 +778,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.execute();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -638,7 +789,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
* Technically this is the wrong param name
|
||||
*/
|
||||
@Test
|
||||
public void testValiedateCodeAgainstBuiltInSystem() {
|
||||
public void testValiedateCodeAgainstBuiltInSystem() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -666,7 +819,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
* Technically this is the right param name
|
||||
*/
|
||||
@Test
|
||||
public void testValiedateCodeAgainstBuiltInSystemByUrl() {
|
||||
public void testValiedateCodeAgainstBuiltInSystemByUrl() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -690,6 +845,11 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
assertEquals("Burn", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
|
||||
}
|
||||
|
||||
@After
|
||||
public void afterResetPreExpansionDefault() {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
|
|
|
|||
|
|
@ -347,22 +347,16 @@ public class ExpungeR4Test extends BaseResourceProviderR4Test {
|
|||
public void testExpungeEverythingWhereResourceInSearchResults() {
|
||||
createStandardPatients();
|
||||
|
||||
runInTransaction(() -> {
|
||||
await().until(()->mySearchEntityDao.count() == 0);
|
||||
await().until(()->mySearchResultDao.count() == 0);
|
||||
});
|
||||
await().until(()-> runInTransaction(() -> mySearchEntityDao.count() == 0));
|
||||
await().until(()-> runInTransaction(() -> mySearchResultDao.count() == 0));
|
||||
|
||||
PersistedJpaSearchFirstPageBundleProvider search = (PersistedJpaSearchFirstPageBundleProvider) myPatientDao.search(new SearchParameterMap());
|
||||
assertEquals(PersistedJpaSearchFirstPageBundleProvider.class, search.getClass());
|
||||
assertEquals(2, search.size().intValue());
|
||||
assertEquals(2, search.getResources(0, 2).size());
|
||||
|
||||
runInTransaction(() -> {
|
||||
await().until(()->mySearchEntityDao.count() == 1);
|
||||
await().until(()->mySearchResultDao.count() == 2);
|
||||
ourLog.info("Search results: {}", mySearchResultDao.findAll().toString());
|
||||
assertEquals(mySearchResultDao.findAll().toString(), 2, mySearchResultDao.count());
|
||||
});
|
||||
await().until(()-> runInTransaction(() -> mySearchEntityDao.count() == 1));
|
||||
await().until(()-> runInTransaction(() -> mySearchResultDao.count() == 2));
|
||||
|
||||
mySystemDao.expunge(new ExpungeOptions()
|
||||
.setExpungeEverything(true), null);
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
package ca.uhn.fhir.jpa.provider.r4;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
|
|
@ -8,6 +9,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
|
|||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
|
|
@ -24,10 +26,13 @@ import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
|
|||
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
|
||||
import org.hl7.fhir.r4.model.codesystems.HttpVerb;
|
||||
import org.junit.After;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
|
||||
import org.springframework.transaction.support.TransactionTemplate;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
|
@ -40,18 +45,76 @@ import static org.junit.Assert.*;
|
|||
public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4ValueSetTest.class);
|
||||
private IIdType myExtensionalCsId;
|
||||
private IIdType myExtensionalVsId;
|
||||
private IIdType myLocalValueSetId;
|
||||
private Long myExtensionalCsIdOnResourceTable;
|
||||
private Long myExtensionalVsIdOnResourceTable;
|
||||
private ValueSet myLocalVs;
|
||||
|
||||
@Before
|
||||
@Transactional
|
||||
public void before02() throws IOException {
|
||||
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
|
||||
myCodeSystemDao.create(cs, mySrd);
|
||||
private void loadAndPersistCodeSystemAndValueSet(HttpVerb theVerb) throws IOException {
|
||||
loadAndPersistCodeSystem(theVerb);
|
||||
loadAndPersistValueSet(theVerb);
|
||||
}
|
||||
|
||||
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
|
||||
private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
|
||||
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
|
||||
codeSystem.setId("CodeSystem/cs");
|
||||
persistCodeSystem(codeSystem, theVerb);
|
||||
}
|
||||
|
||||
private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
|
||||
switch (theVerb) {
|
||||
case POST:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
case PUT:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalCsId = myCodeSystemDao.update(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
default:
|
||||
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
|
||||
}
|
||||
myExtensionalCsIdOnResourceTable = myCodeSystemDao.readEntity(myExtensionalCsId, null).getId();
|
||||
}
|
||||
|
||||
private void loadAndPersistValueSet(HttpVerb theVerb) throws IOException {
|
||||
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
valueSet.setId("ValueSet/vs");
|
||||
persistValueSet(valueSet, theVerb);
|
||||
}
|
||||
|
||||
private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
|
||||
switch (theVerb) {
|
||||
case POST:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
case PUT:
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
myExtensionalVsId = myValueSetDao.update(theValueSet, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
});
|
||||
break;
|
||||
default:
|
||||
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
|
||||
}
|
||||
myExtensionalVsIdOnResourceTable = myValueSetDao.readEntity(myExtensionalVsId, null).getId();
|
||||
}
|
||||
|
||||
private CodeSystem createExternalCs() {
|
||||
|
|
@ -128,8 +191,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandById() {
|
||||
//@formatter:off
|
||||
public void testExpandById() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
|
@ -137,7 +201,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -158,9 +221,42 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByIdWithFilter() {
|
||||
public void testExpandByIdWithPreExpansion() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
.named("expand")
|
||||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
|
||||
assertThat(resp, containsString("<expansion>"));
|
||||
assertThat(resp, containsString("<contains>"));
|
||||
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
|
||||
assertThat(resp, containsString("<code value=\"8450-9\"/>"));
|
||||
assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
|
||||
assertThat(resp, containsString("</contains>"));
|
||||
assertThat(resp, containsString("<contains>"));
|
||||
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
|
||||
assertThat(resp, containsString("<code value=\"11378-7\"/>"));
|
||||
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
assertThat(resp, containsString("</contains>"));
|
||||
assertThat(resp, containsString("</expansion>"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByIdWithFilter() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
|
@ -168,7 +264,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withParameter(Parameters.class, "filter", new StringType("first"))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -178,7 +273,31 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrl() {
|
||||
public void testExpandByIdWithFilterWithPreExpansion() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "filter", new StringType("first"))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
assertThat(resp, not(containsString("<display value=\"Systolic blood pressure--expiration\"/>")));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrl() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -195,8 +314,70 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrlWithBogusUrl() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
|
||||
.execute();
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals(404, e.getStatusCode());
|
||||
assertEquals("HTTP 404 Not Found: Unknown ValueSet: http%3A%2F%2Fwww.healthintersections.com.au%2Ffhir%2FValueSet%2Fbogus", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrlWithPreExpansion() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, stringContainsInOrder(
|
||||
"<code value=\"11378-7\"/>",
|
||||
"<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByUrlWithPreExpansionAndBogusUrl() throws Exception {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
try {
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
|
||||
.execute();
|
||||
} catch (ResourceNotFoundException e) {
|
||||
assertEquals(404, e.getStatusCode());
|
||||
assertEquals("HTTP 404 Not Found: Unknown ValueSet: http%3A%2F%2Fwww.healthintersections.com.au%2Ffhir%2FValueSet%2Fbogus", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByValueSet() throws IOException {
|
||||
loadAndPersistCodeSystem(HttpVerb.POST);
|
||||
|
||||
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
|
||||
Parameters respParam = ourClient
|
||||
|
|
@ -215,13 +396,36 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByValueSetWithPreExpansion() throws IOException {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(true);
|
||||
|
||||
loadAndPersistCodeSystem(HttpVerb.POST);
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
.named("expand")
|
||||
.withParameter(Parameters.class, "valueSet", toExpand)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
assertThat(resp, stringContainsInOrder(
|
||||
"<code value=\"11378-7\"/>",
|
||||
"<display value=\"Systolic blood pressure at First encounter\"/>"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandInlineVsAgainstBuiltInCs() {
|
||||
createLocalVsPointingAtBuiltInCodeSystem();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -229,7 +433,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withParameter(Parameters.class, "valueSet", myLocalVs)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -243,7 +446,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
assertNotNull(myLocalVs);
|
||||
myLocalVs.setId("");
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -251,7 +453,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withParameter(Parameters.class, "valueSet", myLocalVs)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -263,7 +464,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandInvalidParams() throws IOException {
|
||||
public void testExpandInvalidParams() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
|
|
@ -334,7 +537,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
createLocalVsPointingAtBuiltInCodeSystem();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myLocalValueSetId)
|
||||
|
|
@ -342,7 +544,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -355,7 +556,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
createExternalCsAndLocalVs();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myLocalValueSetId)
|
||||
|
|
@ -363,7 +563,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
|
||||
ourLog.info(resp);
|
||||
|
|
@ -401,7 +600,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
createExternalCsAndLocalVsWithUnknownCode();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
//@formatter:off
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
|
|
@ -412,7 +610,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
}
|
||||
//@formatter:on
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -438,8 +635,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() {
|
||||
//@formatter:off
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
|
@ -498,8 +696,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemType() {
|
||||
//@formatter:off
|
||||
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
|
@ -585,6 +784,11 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
}
|
||||
|
||||
@After
|
||||
public void afterResetPreExpansionDefault() {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
|
|
|
|||
|
|
@ -658,7 +658,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals(0, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
|
||||
myTermValueSetConceptDao.deleteByTermValueSetId(termValueSetId);
|
||||
assertEquals(0, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
|
||||
myTermValueSetDao.deleteByTermValueSetId(termValueSetId);
|
||||
myTermValueSetDao.deleteById(termValueSetId);
|
||||
assertFalse(myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).isPresent());
|
||||
}
|
||||
});
|
||||
|
|
@ -695,7 +695,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals(0, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
|
||||
myTermValueSetConceptDao.deleteByTermValueSetId(termValueSetId);
|
||||
assertEquals(0, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
|
||||
myTermValueSetDao.deleteByTermValueSetId(termValueSetId);
|
||||
myTermValueSetDao.deleteById(termValueSetId);
|
||||
assertFalse(myTermValueSetDao.findByResourcePid(myExtensionalVsIdOnResourceTable).isPresent());
|
||||
}
|
||||
});
|
||||
|
|
@ -885,19 +885,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Systolic blood pressure 8 hour minimum", containsComponent.getDisplay());
|
||||
assertFalse(containsComponent.hasDesignation());
|
||||
|
||||
myTermSvc.saveDeferred();
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
|
||||
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
|
||||
|
||||
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
|
||||
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
|
||||
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
|
||||
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
|
||||
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
|
||||
assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
|
||||
assertEquals(1000, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
|
||||
assertEquals(0, expandedValueSet.getExpansion().getParameter().size());
|
||||
|
||||
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getContains().size());
|
||||
|
||||
|
|
@ -2097,11 +2090,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
|
||||
|
||||
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8450-9", concept.getCode());
|
||||
assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
|
||||
assertEquals(2, concept.getDesignations().size());
|
||||
assertEquals(0, concept.getOrder());
|
||||
|
||||
TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2118,20 +2112,22 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(1);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("11378-7", concept.getCode());
|
||||
assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(1, concept.getOrder());
|
||||
|
||||
// ...
|
||||
|
||||
concept = termValueSet.getConcepts().get(22);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8491-3", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
|
||||
assertEquals(1, concept.getDesignations().size());
|
||||
assertEquals(22, concept.getOrder());
|
||||
|
||||
designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2141,11 +2137,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(23);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8492-1", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(23, concept.getOrder());
|
||||
});
|
||||
}
|
||||
|
||||
|
|
@ -2195,11 +2192,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
|
||||
|
||||
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8450-9", concept.getCode());
|
||||
assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
|
||||
assertEquals(2, concept.getDesignations().size());
|
||||
assertEquals(0, concept.getOrder());
|
||||
|
||||
TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2216,20 +2214,22 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(1);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("11378-7", concept.getCode());
|
||||
assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(1, concept.getOrder());
|
||||
|
||||
// ...
|
||||
|
||||
concept = termValueSet.getConcepts().get(22);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8491-3", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
|
||||
assertEquals(1, concept.getDesignations().size());
|
||||
assertEquals(22, concept.getOrder());
|
||||
|
||||
designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2239,11 +2239,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(23);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8492-1", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(23, concept.getOrder());
|
||||
});
|
||||
}
|
||||
|
||||
|
|
@ -2293,11 +2294,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
|
||||
|
||||
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8450-9", concept.getCode());
|
||||
assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
|
||||
assertEquals(2, concept.getDesignations().size());
|
||||
assertEquals(0, concept.getOrder());
|
||||
|
||||
TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2314,20 +2316,22 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(1);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("11378-7", concept.getCode());
|
||||
assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(1, concept.getOrder());
|
||||
|
||||
// ...
|
||||
|
||||
concept = termValueSet.getConcepts().get(22 - 2);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
concept = termValueSet.getConcepts().get(20);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8491-3", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
|
||||
assertEquals(1, concept.getDesignations().size());
|
||||
assertEquals(20, concept.getOrder());
|
||||
|
||||
designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2336,12 +2340,13 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Synonym", designation.getUseDisplay());
|
||||
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(23 - 2);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
concept = termValueSet.getConcepts().get(21);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8492-1", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(21, concept.getOrder());
|
||||
});
|
||||
}
|
||||
|
||||
|
|
@ -2391,11 +2396,12 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
|
||||
|
||||
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8450-9", concept.getCode());
|
||||
assertEquals("Systolic blood pressure--expiration", concept.getDisplay());
|
||||
assertEquals(2, concept.getDesignations().size());
|
||||
assertEquals(0, concept.getOrder());
|
||||
|
||||
TermValueSetConceptDesignation designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2412,20 +2418,22 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Systoliskt blodtryck - utgång", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(1);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("11378-7", concept.getCode());
|
||||
assertEquals("Systolic blood pressure at First encounter", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(1, concept.getOrder());
|
||||
|
||||
// ...
|
||||
|
||||
concept = termValueSet.getConcepts().get(22 - 2);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
concept = termValueSet.getConcepts().get(20);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8491-3", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 1 hour minimum", concept.getDisplay());
|
||||
assertEquals(1, concept.getDesignations().size());
|
||||
assertEquals(20, concept.getOrder());
|
||||
|
||||
designation = concept.getDesignations().get(0);
|
||||
assertEquals("nl", designation.getLanguage());
|
||||
|
|
@ -2434,12 +2442,13 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Synonym", designation.getUseDisplay());
|
||||
assertEquals("Systolische bloeddruk minimaal 1 uur", designation.getValue());
|
||||
|
||||
concept = termValueSet.getConcepts().get(23 - 2);
|
||||
ourLog.info("Code:\n" + concept.toString());
|
||||
concept = termValueSet.getConcepts().get(21);
|
||||
ourLog.info("Concept:\n" + concept.toString());
|
||||
assertEquals("http://acme.org", concept.getSystem());
|
||||
assertEquals("8492-1", concept.getCode());
|
||||
assertEquals("Systolic blood pressure 8 hour minimum", concept.getDisplay());
|
||||
assertEquals(0, concept.getDesignations().size());
|
||||
assertEquals(21, concept.getOrder());
|
||||
});
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -100,6 +100,15 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
|
|||
.dropIndex("IDX_VALUESET_EXP_STATUS");
|
||||
|
||||
version.dropIdGenerator("SEQ_SEARCHPARM_ID");
|
||||
|
||||
// TermValueSetConcept
|
||||
version.startSectionWithMessage("Processing table: TRM_VALUESET_CONCEPT");
|
||||
Builder.BuilderWithTableName termValueSetConceptTable = version.onTable("TRM_VALUESET_CONCEPT");
|
||||
termValueSetConceptTable.addColumn("VALUESET_ORDER").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.INT);
|
||||
termValueSetConceptTable
|
||||
.addIndex("IDX_VS_CONCEPT_ORDER")
|
||||
.unique(true)
|
||||
.withColumns("VALUESET_PID", "VALUESET_ORDER");
|
||||
}
|
||||
|
||||
protected void init400() {
|
||||
|
|
|
|||
Loading…
Reference in New Issue