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Resolve "experimental implementation for storing expanded ValueSets in terminology tables" (#1369) 

* Added experimental implementation for storing expanded ValueSets in terminology tables.

* Minor tweak to log message for consistency.

* Another minor tweak to log message for consistency.

* Renamed test.

* Addressing review comments.

* Added migration tasks.
This commit is contained in:
Diederik Muylwyk 2019-07-11 16:52:19 -04:00 committed by GitHub
parent 9b938262e6
commit 0729e38e6e
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GPG Key ID: 4AEE18F83AFDEB23
30 changed files with 1080 additions and 218 deletions
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16
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java
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@ -23,7 +23,7 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.*;
public class ValidateUtil {
@ -37,7 +37,7 @@ public class ValidateUtil {
}
/**
* Throws {@link IllegalArgumentException} if theValue is <= theMinimum
* Throws {@link IllegalArgumentException} if theValue is < theMinimum
*/
public static void isGreaterThanOrEqualTo(long theValue, long theMinimum, String theMessage) {
if (theValue < theMinimum) {
@ -45,6 +45,12 @@ public class ValidateUtil {
}
}
public static void isNotBlankOrThrowIllegalArgument(String theString, String theMessage) {
if (isBlank(theString)) {
throw new IllegalArgumentException(theMessage);
}
}
public static void isNotBlankOrThrowInvalidRequest(String theString, String theMessage) {
if (isBlank(theString)) {
throw new InvalidRequestException(theMessage);
@ -57,6 +63,12 @@ public class ValidateUtil {
}
}
public static void isNotTooLongOrThrowIllegalArgument(String theString, int theMaxLength, String theMessage) {
if (length(theString) > theMaxLength) {
throw new IllegalArgumentException(theMessage);
}
}
public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage) {
if (theSuccess == false) {
throw new InvalidRequestException(theMessage);

3
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -115,8 +115,9 @@ ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor.noParam=Note that cascadi
ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
View File

@ -145,6 +145,10 @@ public class DaoConfig {
private boolean myEnableInMemorySubscriptionMatching = true;
private boolean myEnforceReferenceTargetTypes = true;
private ClientIdStrategyEnum myResourceClientIdStrategy = ClientIdStrategyEnum.ALPHANUMERIC;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
*/
private boolean myPreExpandValueSetsExperimental = false;
/**
* Constructor
@ -1600,6 +1604,34 @@ public class DaoConfig {
myModelConfig.setWebsocketContextPath(theWebsocketContextPath);
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* future optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code false}.
* </p>
*/
public boolean isPreExpandValueSetsExperimental() {
return myPreExpandValueSetsExperimental;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* If set to {@code true}, ValueSets and expansions are stored in terminology tables. This is to facilitate
* future optimization of the $expand operation on large ValueSets.
* </p>
* <p>
* The default value for this setting is {@code false}.
* </p>
*/
public void setPreExpandValueSetsExperimental(boolean thePreExpandValueSetsExperimental) {
myPreExpandValueSetsExperimental = thePreExpandValueSetsExperimental;
}
public enum IndexEnabledEnum {
ENABLED,
DISABLED

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermCodeSystemDao.java
View File

@ -34,7 +34,7 @@ public interface ITermCodeSystemDao extends JpaRepository<TermCodeSystem, Long>
TermCodeSystem findByCodeSystemUri(@Param("code_system_uri") String theCodeSystemUri);
@Query("SELECT cs FROM TermCodeSystem cs WHERE cs.myResourcePid = :resource_pid")
TermCodeSystem findByResourcePid(@Param("resource_pid") Long theReourcePid);
TermCodeSystem findByResourcePid(@Param("resource_pid") Long theResourcePid);
@Query("SELECT cs FROM TermCodeSystem cs WHERE cs.myCurrentVersion.myId = :csv_pid")
Optional<TermCodeSystem> findWithCodeSystemVersionAsCurrentVersion(@Param("csv_pid") Long theCodeSystemVersionPid);

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetCodeDao.java Normal file
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@ -0,0 +1,35 @@
package ca.uhn.fhir.jpa.dao.data;
/*
* #%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 ca.uhn.fhir.jpa.entity.TermValueSetCode;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
public interface ITermValueSetCodeDao extends JpaRepository<TermValueSetCode, Long> {
@Query("DELETE FROM TermValueSetCode vsc WHERE vsc.myValueSet.myId = :pid")
@Modifying
void deleteTermValueSetCodesByValueSetId(@Param("pid") Long theValueSetId);
}

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java Normal file
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@ -0,0 +1,43 @@
package ca.uhn.fhir.jpa.dao.data;
/*
* #%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 ca.uhn.fhir.jpa.entity.TermValueSet;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.Optional;
public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
@Query("DELETE FROM TermValueSet vs WHERE vs.myId = :pid")
@Modifying
void deleteTermValueSetById(@Param("pid") Long theId);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myResourcePid = :resource_pid")
Optional<TermValueSet> findByResourcePid(@Param("resource_pid") Long theResourcePid);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url")
Optional<TermValueSet> findByUrl(@Param("url") String theUrl);
}

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -23,11 +23,15 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
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.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
@ -37,6 +41,8 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
@ -45,14 +51,18 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
private IValidationSupport myValidationSupport;
@ -295,4 +305,26 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
// nothing
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;
org.hl7.fhir.r4.model.ValueSet converted = VersionConvertor_30_40.convertValueSet(valueSet);
myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
}
}
return retVal;
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
View File

@ -74,6 +74,8 @@ public class ExpungeEverythingService {
counter.addAndGet(doExpungeEverythingQuery(txTemplate, ResourceLink.class));
counter.addAndGet(doExpungeEverythingQuery(txTemplate, SearchResult.class));
counter.addAndGet(doExpungeEverythingQuery(txTemplate, SearchInclude.class));
counter.addAndGet(doExpungeEverythingQuery(txTemplate, TermValueSetCode.class));
counter.addAndGet(doExpungeEverythingQuery(txTemplate, TermValueSet.class));
counter.addAndGet(doExpungeEverythingQuery(txTemplate, TermConceptParentChildLink.class));
counter.addAndGet(doExpungeEverythingQuery(txTemplate, TermConceptMapGroupElementTarget.class));
counter.addAndGet(doExpungeEverythingQuery(txTemplate, TermConceptMapGroupElement.class));

62
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -20,34 +20,43 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.Collections;
import java.util.List;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.ValueSet.*;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
@Autowired
@Qualifier("myJpaValidationSupportChainR4")
private IValidationSupport myValidationSupport;
@ -296,4 +305,21 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
// nothing
}
@Override
protected ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSetAndChildren(retVal, valueSet);
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
}
}
return retVal;
}
}

28
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
View File

@ -21,13 +21,16 @@ package ca.uhn.fhir.jpa.entity;
*/
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
//@formatter:off
@Table(name = "TRM_CODESYSTEM", uniqueConstraints = {
@ -37,9 +40,11 @@ import static org.apache.commons.lang3.StringUtils.left;
//@formatter:on
public class TermCodeSystem implements Serializable {
private static final long serialVersionUID = 1L;
public static final int CS_NAME_LENGTH = 200;
@Column(name = "CODE_SYSTEM_URI", nullable = false)
private static final int MAX_NAME_LENGTH = 200;
static final int MAX_URL_LENGTH = 200;
@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
private String myCodeSystemUri;
@OneToOne()
@ -55,7 +60,7 @@ public class TermCodeSystem implements Serializable {
private ResourceTable myResource;
@Column(name = "RES_ID", insertable = false, updatable = false)
private Long myResourcePid;
@Column(name = "CS_NAME", nullable = true)
@Column(name = "CS_NAME", nullable = true, length = MAX_NAME_LENGTH)
private String myName;
public String getCodeSystemUri() {
@ -66,16 +71,21 @@ public class TermCodeSystem implements Serializable {
return myName;
}
public void setCodeSystemUri(String theCodeSystemUri) {
public TermCodeSystem setCodeSystemUri(@Nonnull String theCodeSystemUri) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCodeSystemUri, "theCodeSystemUri must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCodeSystemUri, MAX_URL_LENGTH,
"URI exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theCodeSystemUri));
myCodeSystemUri = theCodeSystemUri;
return this;
}
public TermCodeSystemVersion getCurrentVersion() {
return myCurrentVersion;
}
public void setCurrentVersion(TermCodeSystemVersion theCurrentVersion) {
public TermCodeSystem setCurrentVersion(TermCodeSystemVersion theCurrentVersion) {
myCurrentVersion = theCurrentVersion;
return this;
}
public Long getPid() {
@ -86,12 +96,14 @@ public class TermCodeSystem implements Serializable {
return myResource;
}
public void setName(String theName) {
myName = left(theName, CS_NAME_LENGTH);
public TermCodeSystem setName(String theName) {
myName = left(theName, MAX_NAME_LENGTH);
return this;
}
public void setResource(ResourceTable theResource) {
public TermCodeSystem setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
@Override

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
View File

@ -22,12 +22,15 @@ package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ValidateUtil;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import static org.apache.commons.lang3.StringUtils.length;
//@formatter:off
@Table(name = "TRM_CODESYSTEM_VER"
// Note, we used to have a constraint named IDX_CSV_RESOURCEPID_AND_VER (don't reuse this)
@ -37,6 +40,8 @@ import java.util.Collection;
public class TermCodeSystemVersion implements Serializable {
private static final long serialVersionUID = 1L;
static final int MAX_VERSION_LENGTH = 200;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCodeSystem")
private Collection<TermConcept> myConcepts;
@ -50,7 +55,7 @@ public class TermCodeSystemVersion implements Serializable {
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
private ResourceTable myResource;
@Column(name = "CS_VERSION_ID", nullable = true, updatable = false)
@Column(name = "CS_VERSION_ID", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
private String myCodeSystemVersionId;
/**
* This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
@ -104,16 +109,21 @@ public class TermCodeSystemVersion implements Serializable {
return myCodeSystem;
}
public void setCodeSystem(TermCodeSystem theCodeSystem) {
public TermCodeSystemVersion setCodeSystem(TermCodeSystem theCodeSystem) {
myCodeSystem = theCodeSystem;
return this;
}
public String getCodeSystemVersionId() {
return myCodeSystemVersionId;
}
public void setCodeSystemVersionId(String theCodeSystemVersionId) {
public TermCodeSystemVersion setCodeSystemVersionId(String theCodeSystemVersionId) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(
theCodeSystemVersionId, MAX_VERSION_LENGTH,
"Version ID exceeds maximum length (" + MAX_VERSION_LENGTH + "): " + length(theCodeSystemVersionId));
myCodeSystemVersionId = theCodeSystemVersionId;
return this;
}
public Collection<TermConcept> getConcepts() {
@ -131,8 +141,9 @@ public class TermCodeSystemVersion implements Serializable {
return myResource;
}
public void setResource(ResourceTable theResource) {
public TermCodeSystemVersion setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
@Override

77
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -1,25 +1,5 @@
package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.search.annotations.*;
import org.hl7.fhir.r4.model.Coding;
import javax.annotation.Nonnull;
import javax.persistence.*;
import javax.persistence.Index;
import java.io.Serializable;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
* HAPI FHIR JPA Server
@ -40,6 +20,27 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.search.annotations.*;
import org.hl7.fhir.r4.model.Coding;
import javax.annotation.Nonnull;
import javax.persistence.Index;
import javax.persistence.*;
import java.io.Serializable;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Indexed(interceptor = DeferConceptIndexingInterceptor.class)
@Table(name = "TRM_CONCEPT", uniqueConstraints = {
@ -49,16 +50,17 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
})
public class TermConcept implements Serializable {
public static final int CODE_LENGTH = 500;
protected static final int MAX_DESC_LENGTH = 400;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
private static final long serialVersionUID = 1L;
static final int MAX_CODE_LENGTH = 500;
static final int MAX_DESC_LENGTH = 400;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
private Collection<TermConceptParentChildLink> myChildren;
@Column(name = "CODE", length = CODE_LENGTH, nullable = false)
@Column(name = "CODE", nullable = false, length = MAX_CODE_LENGTH)
@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
private String myCode;
@Temporal(TemporalType.TIMESTAMP)
@ -70,7 +72,7 @@ public class TermConcept implements Serializable {
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
@Fields({@Field(name = "myCodeSystemVersionPid")})
private long myCodeSystemVersionPid;
@Column(name = "DISPLAY", length = MAX_DESC_LENGTH, nullable = true)
@Column(name = "DISPLAY", nullable = true, length = MAX_DESC_LENGTH)
@Fields({
@Field(name = "myDisplay", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
@Field(name = "myDisplayEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
@ -187,20 +189,24 @@ public class TermConcept implements Serializable {
return myCode;
}
public void setCode(String theCode) {
ValidateUtil.isNotBlankOrThrowInvalidRequest(theCode, "Code must not be null or empty");
public TermConcept setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, MAX_CODE_LENGTH,
"Code exceeds maximum length (" + MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public TermCodeSystemVersion getCodeSystemVersion() {
return myCodeSystem;
}
public void setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
public TermConcept setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
myCodeSystem = theCodeSystemVersion;
if (theCodeSystemVersion.getPid() != null) {
myCodeSystemVersionPid = theCodeSystemVersion.getPid();
}
return this;
}
public List<Coding> getCodingProperties(String thePropertyName) {
@ -231,10 +237,7 @@ public class TermConcept implements Serializable {
}
public TermConcept setDisplay(String theDisplay) {
myDisplay = theDisplay;
if (isNotBlank(theDisplay) && theDisplay.length() > MAX_DESC_LENGTH) {
myDisplay = myDisplay.substring(0, MAX_DESC_LENGTH);
}
myDisplay = left(theDisplay, MAX_DESC_LENGTH);
return this;
}
@ -246,8 +249,9 @@ public class TermConcept implements Serializable {
return myIndexStatus;
}
public void setIndexStatus(Long theIndexStatus) {
public TermConcept setIndexStatus(Long theIndexStatus) {
myIndexStatus = theIndexStatus;
return this;
}
public String getParentPidsAsString() {
@ -272,8 +276,9 @@ public class TermConcept implements Serializable {
return mySequence;
}
public void setSequence(Integer theSequence) {
public TermConcept setSequence(Integer theSequence) {
mySequence = theSequence;
return this;
}
public List<String> getStringProperties(String thePropertyName) {
@ -300,8 +305,9 @@ public class TermConcept implements Serializable {
return myUpdated;
}
public void setUpdated(Date theUpdated) {
public TermConcept setUpdated(Date theUpdated) {
myUpdated = theUpdated;
return this;
}
@Override
@ -355,8 +361,9 @@ public class TermConcept implements Serializable {
myParentPids = b.toString();
}
public void setParentPids(String theParentPids) {
public TermConcept setParentPids(String theParentPids) {
myParentPids = theParentPids;
return this;
}
@Override

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java
View File

@ -20,16 +20,24 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_DESIG", uniqueConstraints = {
}, indexes = {
})
public class TermConceptDesignation implements Serializable {
private static final long serialVersionUID = 1L;
private static final int MAX_LENGTH = 500;
@ManyToOne
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CONCEPT"))
private TermConcept myConcept;
@ -38,15 +46,15 @@ public class TermConceptDesignation implements Serializable {
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_DESIG_PID")
@Column(name = "PID")
private Long myId;
@Column(name = "LANG", length = 500, nullable = true)
@Column(name = "LANG", nullable = true, length = MAX_LENGTH)
private String myLanguage;
@Column(name = "USE_SYSTEM", length = 500, nullable = true)
@Column(name = "USE_SYSTEM", nullable = true, length = MAX_LENGTH)
private String myUseSystem;
@Column(name = "USE_CODE", length = 500, nullable = true)
@Column(name = "USE_CODE", nullable = true, length = MAX_LENGTH)
private String myUseCode;
@Column(name = "USE_DISPLAY", length = 500, nullable = true)
@Column(name = "USE_DISPLAY", nullable = true, length = MAX_LENGTH)
private String myUseDisplay;
@Column(name = "VAL", length = 500, nullable = false)
@Column(name = "VAL", nullable = false, length = MAX_LENGTH)
private String myValue;
/**
* TODO: Make this non-null
@ -62,6 +70,8 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setLanguage(String theLanguage) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theLanguage, MAX_LENGTH,
"Language exceeds maximum length (" + MAX_LENGTH + "): " + length(theLanguage));
myLanguage = theLanguage;
return this;
}
@ -71,6 +81,8 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setUseCode(String theUseCode) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUseCode, MAX_LENGTH,
"Use code exceeds maximum length (" + MAX_LENGTH + "): " + length(theUseCode));
myUseCode = theUseCode;
return this;
}
@ -80,7 +92,7 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setUseDisplay(String theUseDisplay) {
myUseDisplay = theUseDisplay;
myUseDisplay = left(theUseDisplay, MAX_LENGTH);
return this;
}
@ -89,6 +101,9 @@ public class TermConceptDesignation implements Serializable {
}
public TermConceptDesignation setUseSystem(String theUseSystem) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUseSystem, MAX_LENGTH,
"Use system exceeds maximum length (" + MAX_LENGTH + "): " + length(theUseSystem));
myUseSystem = theUseSystem;
return this;
}
@ -97,7 +112,10 @@ public class TermConceptDesignation implements Serializable {
return myValue;
}
public TermConceptDesignation setValue(String theValue) {
public TermConceptDesignation setValue(@Nonnull String theValue) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theValue, "theValue must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theValue, MAX_LENGTH,
"Value exceeds maximum length (" + MAX_LENGTH + "): " + length(theValue));
myValue = theValue;
return this;
}

47
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMap.java
View File

@ -21,19 +21,27 @@ package ca.uhn.fhir.jpa.entity;
*/
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP", uniqueConstraints = {
@UniqueConstraint(name = "IDX_CONCEPT_MAP_URL", columnNames = {"URL"})
})
public class TermConceptMap implements Serializable {
private static final long serialVersionUID = 1L;
static final int MAX_URL_LENGTH = 200;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_MAP_PID", sequenceName = "SEQ_CONCEPT_MAP_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_PID")
@ -47,13 +55,13 @@ public class TermConceptMap implements Serializable {
@Column(name = "RES_ID", insertable = false, updatable = false)
private Long myResourcePid;
@Column(name = "SOURCE_URL", nullable = true, length = 200)
@Column(name = "SOURCE_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String mySource;
@Column(name = "TARGET_URL", nullable = true, length = 200)
@Column(name = "TARGET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myTarget;
@Column(name = "URL", length = 200, nullable = false)
@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
private String myUrl;
@OneToMany(mappedBy = "myConceptMap")
@ -75,47 +83,58 @@ public class TermConceptMap implements Serializable {
return myResource;
}
public void setResource(ResourceTable resource) {
myResource = resource;
public TermConceptMap setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
public Long getResourcePid() {
return myResourcePid;
}
public void setResourcePid(Long resourcePid) {
myResourcePid = resourcePid;
public TermConceptMap setResourcePid(Long theResourcePid) {
myResourcePid = theResourcePid;
return this;
}
public String getSource() {
return mySource;
}
public void setSource(String source) {
mySource = source;
public TermConceptMap setSource(String theSource) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSource, TermValueSet.MAX_URL_LENGTH,
"Source exceeds maximum length (" + TermValueSet.MAX_URL_LENGTH + "): " + length(theSource));
mySource = theSource;
return this;
}
public String getTarget() {
return myTarget;
}
public void setTarget(String target) {
myTarget = target;
public TermConceptMap setTarget(String theTarget) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTarget, TermValueSet.MAX_URL_LENGTH,
"Target exceeds maximum length (" + TermValueSet.MAX_URL_LENGTH + "): " + length(theTarget));
myTarget = theTarget;
return this;
}
public String getUrl() {
return myUrl;
}
public void setUrl(String theUrl) {
public TermConceptMap setUrl(@Nonnull String theUrl) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theUrl, "theUrl must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUrl, MAX_URL_LENGTH,
"URL exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theUrl));
myUrl = theUrl;
return this;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append("myResource", myResource.toString())
.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
.append("myResourcePid", myResourcePid)
.append("mySource", mySource)

47
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroup.java
View File

@ -20,17 +20,23 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP_GROUP")
public class TermConceptMapGroup implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_MAP_GROUP_PID", sequenceName = "SEQ_CONCEPT_MAP_GROUP_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_GROUP_PID")
@ -41,36 +47,37 @@ public class TermConceptMapGroup implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGROUP_CONCEPTMAP"))
private TermConceptMap myConceptMap;
@Column(name = "SOURCE_URL", nullable = false, length = 200)
@Column(name = "SOURCE_URL", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySource;
@Column(name = "SOURCE_VERSION", length = 100)
@Column(name = "SOURCE_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String mySourceVersion;
@Column(name = "TARGET_URL", nullable = false, length = 200)
@Column(name = "TARGET_URL", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
private String myTarget;
@Column(name = "TARGET_VERSION", length = 100)
@Column(name = "TARGET_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String myTargetVersion;
@OneToMany(mappedBy = "myConceptMapGroup")
private List<TermConceptMapGroupElement> myConceptMapGroupElements;
@Column(name= "CONCEPT_MAP_URL", length = 200, nullable = true)
@Column(name= "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
private String myConceptMapUrl;
@Column(name= "SOURCE_VS", length = 200, nullable = true)
@Column(name= "SOURCE_VS", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String mySourceValueSet;
@Column(name= "TARGET_VS", length = 200, nullable = true)
@Column(name= "TARGET_VS", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myTargetValueSet;
public TermConceptMap getConceptMap() {
return myConceptMap;
}
public void setConceptMap(TermConceptMap theTermConceptMap) {
public TermConceptMapGroup setConceptMap(TermConceptMap theTermConceptMap) {
myConceptMap = theTermConceptMap;
return this;
}
public List<TermConceptMapGroupElement> getConceptMapGroupElements() {
@ -96,8 +103,12 @@ public class TermConceptMapGroup implements Serializable {
return mySource;
}
public void setSource(String theSource) {
public TermConceptMapGroup setSource(@Nonnull String theSource) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theSource, "theSource must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSource, TermCodeSystem.MAX_URL_LENGTH,
"Source exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theSource));
this.mySource = theSource;
return this;
}
public String getSourceValueSet() {
@ -111,16 +122,23 @@ public class TermConceptMapGroup implements Serializable {
return mySourceVersion;
}
public void setSourceVersion(String theSourceVersion) {
public TermConceptMapGroup setSourceVersion(String theSourceVersion) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSourceVersion, TermCodeSystemVersion.MAX_VERSION_LENGTH,
"Source version ID exceeds maximum length (" + TermCodeSystemVersion.MAX_VERSION_LENGTH + "): " + length(theSourceVersion));
mySourceVersion = theSourceVersion;
return this;
}
public String getTarget() {
return myTarget;
}
public void setTarget(String theTarget) {
public TermConceptMapGroup setTarget(@Nonnull String theTarget) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theTarget, "theTarget must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTarget, TermCodeSystem.MAX_URL_LENGTH,
"Target exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theTarget));
this.myTarget = theTarget;
return this;
}
public String getTargetValueSet() {
@ -134,13 +152,16 @@ public class TermConceptMapGroup implements Serializable {
return myTargetVersion;
}
public void setTargetVersion(String theTargetVersion) {
public TermConceptMapGroup setTargetVersion(String theTargetVersion) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theTargetVersion, TermCodeSystemVersion.MAX_VERSION_LENGTH,
"Target version ID exceeds maximum length (" + TermCodeSystemVersion.MAX_VERSION_LENGTH + "): " + length(theTargetVersion));
myTargetVersion = theTargetVersion;
return this;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConceptMap != null ? ("myConceptMap - id=" + myConceptMap.getId()) : ("myConceptMap=(null)"))
.append("mySource", mySource)

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElement.java
View File

@ -20,22 +20,28 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import org.apache.commons.lang3.Validate;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP_GRP_ELEMENT", indexes = {
@Index(name = "IDX_CNCPT_MAP_GRP_CD", columnList = "SOURCE_CODE")
})
public class TermConceptMapGroupElement implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_MAP_GRP_ELM_PID", sequenceName = "SEQ_CONCEPT_MAP_GRP_ELM_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_MAP_GRP_ELM_PID")
@ -46,7 +52,7 @@ public class TermConceptMapGroupElement implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_GROUP_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGELEMENT_GROUP"))
private TermConceptMapGroup myConceptMapGroup;
@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
@Column(name = "SOURCE_CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
private String myCode;
@Column(name = "SOURCE_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
@ -55,33 +61,37 @@ public class TermConceptMapGroupElement implements Serializable {
@OneToMany(mappedBy = "myConceptMapGroupElement")
private List<TermConceptMapGroupElementTarget> myConceptMapGroupElementTargets;
@Column(name = "CONCEPT_MAP_URL", length = 200)
@Column(name = "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
private String myConceptMapUrl;
@Column(name = "SYSTEM_URL", length = 200)
@Column(name = "SYSTEM_URL", nullable = true, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySystem;
@Column(name = "SYSTEM_VERSION", length = 200)
@Column(name = "SYSTEM_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String mySystemVersion;
@Column(name = "VALUESET_URL", length = 200)
@Column(name = "VALUESET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myValueSet;
public String getCode() {
return myCode;
}
public void setCode(String theCode) {
Validate.notBlank(theCode, "theCode must not be blank");
public TermConceptMapGroupElement setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public TermConceptMapGroup getConceptMapGroup() {
return myConceptMapGroup;
}
public void setConceptMapGroup(TermConceptMapGroup theTermConceptMapGroup) {
public TermConceptMapGroupElement setConceptMapGroup(TermConceptMapGroup theTermConceptMapGroup) {
myConceptMapGroup = theTermConceptMapGroup;
return this;
}
public List<TermConceptMapGroupElementTarget> getConceptMapGroupElementTargets() {
@ -103,8 +113,9 @@ public class TermConceptMapGroupElement implements Serializable {
return myDisplay;
}
public void setDisplay(String theDisplay) {
myDisplay = theDisplay;
public TermConceptMapGroupElement setDisplay(String theDisplay) {
myDisplay = left(theDisplay, TermConcept.MAX_DESC_LENGTH);
return this;
}
public Long getId() {
@ -158,7 +169,7 @@ public class TermConceptMapGroupElement implements Serializable {
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConceptMapGroup != null ? ("myConceptMapGroup - id=" + myConceptMapGroup.getId()) : ("myConceptMapGroup=(null)"))
.append("myCode", myCode)

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElementTarget.java
View File

@ -20,20 +20,28 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_MAP_GRP_ELM_TGT", indexes = {
@Index(name = "IDX_CNCPT_MP_GRP_ELM_TGT_CD", columnList = "TARGET_CODE")
})
public class TermConceptMapGroupElementTarget implements Serializable {
private static final long serialVersionUID = 1L;
static final int MAX_EQUIVALENCE_LENGTH = 50;
@Id()
@SequenceGenerator(name = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID", sequenceName = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CNCPT_MAP_GRP_ELM_TGT_PID")
@ -44,31 +52,38 @@ public class TermConceptMapGroupElementTarget implements Serializable {
@JoinColumn(name = "CONCEPT_MAP_GRP_ELM_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TCMGETARGET_ELEMENT"))
private TermConceptMapGroupElement myConceptMapGroupElement;
@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.CODE_LENGTH)
@Column(name = "TARGET_CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
private String myCode;
@Column(name = "TARGET_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
@Column(name = "TARGET_DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
private String myDisplay;
@Enumerated(EnumType.STRING)
@Column(name = "TARGET_EQUIVALENCE", length = 50)
@Column(name = "TARGET_EQUIVALENCE", nullable = true, length = MAX_EQUIVALENCE_LENGTH)
private ConceptMapEquivalence myEquivalence;
@Column(name = "CONCEPT_MAP_URL", length = 200)
@Column(name = "CONCEPT_MAP_URL", nullable = true, length = TermConceptMap.MAX_URL_LENGTH)
private String myConceptMapUrl;
@Column(name = "SYSTEM_URL", length = 200)
@Column(name = "SYSTEM_URL", nullable = true, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySystem;
@Column(name = "SYSTEM_VERSION", length = 200)
@Column(name = "SYSTEM_VERSION", nullable = true, length = TermCodeSystemVersion.MAX_VERSION_LENGTH)
private String mySystemVersion;
@Column(name = "VALUESET_URL", length = 200)
@Column(name = "VALUESET_URL", nullable = true, length = TermValueSet.MAX_URL_LENGTH)
private String myValueSet;
public String getCode() {
return myCode;
}
public void setCode(String theCode) {
public TermConceptMapGroupElementTarget setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public TermConceptMapGroupElement getConceptMapGroupElement() {
@ -90,16 +105,18 @@ public class TermConceptMapGroupElementTarget implements Serializable {
return myDisplay;
}
public void setDisplay(String theDisplay) {
public TermConceptMapGroupElementTarget setDisplay(String theDisplay) {
myDisplay = theDisplay;
return this;
}
public ConceptMapEquivalence getEquivalence() {
return myEquivalence;
}
public void setEquivalence(ConceptMapEquivalence theEquivalence) {
public TermConceptMapGroupElementTarget setEquivalence(ConceptMapEquivalence theEquivalence) {
myEquivalence = theEquivalence;
return this;
}
public Long getId() {
@ -155,7 +172,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConceptMapGroupElement != null ? ("myConceptMapGroupElement - id=" + myConceptMapGroupElement.getId()) : ("myConceptMapGroupElement=(null)"))
.append("myCode", myCode)

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -20,21 +20,9 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import javax.persistence.*;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
@Entity
@Table(name = "TRM_CONCEPT_PC_LINK")
public class TermConceptParentChildLink implements Serializable {
@ -136,20 +124,24 @@ public class TermConceptParentChildLink implements Serializable {
return result;
}
public void setChild(TermConcept theChild) {
public TermConceptParentChildLink setChild(TermConcept theChild) {
myChild = theChild;
return this;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
public TermConceptParentChildLink setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
return this;
}
public void setParent(TermConcept theParent) {
public TermConceptParentChildLink setParent(TermConcept theParent) {
myParent = theParent;
return this;
}
public void setRelationshipType(RelationshipTypeEnum theRelationshipType) {
public TermConceptParentChildLink setRelationshipType(RelationshipTypeEnum theRelationshipType) {
myRelationshipType = theRelationshipType;
return this;
}
public enum RelationshipTypeEnum {

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
View File

@ -20,21 +20,29 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.validator.constraints.NotBlank;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_PROPERTY", uniqueConstraints = {
}, indexes = {
})
public class TermConceptProperty implements Serializable {
static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
private static final long serialVersionUID = 1L;
private static final int MAX_LENGTH = 500;
static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
@ManyToOne
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
private TermConcept myConcept;
@ -51,22 +59,22 @@ public class TermConceptProperty implements Serializable {
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PROP_PID")
@Column(name = "PID")
private Long myId;
@Column(name = "PROP_KEY", length = 500, nullable = false)
@Column(name = "PROP_KEY", nullable = false, length = MAX_LENGTH)
@NotBlank
private String myKey;
@Column(name = "PROP_VAL", length = 500, nullable = true)
@Column(name = "PROP_VAL", nullable = true, length = MAX_LENGTH)
private String myValue;
@Column(name = "PROP_TYPE", length = MAX_PROPTYPE_ENUM_LENGTH, nullable = false)
@Column(name = "PROP_TYPE", nullable = false, length = MAX_PROPTYPE_ENUM_LENGTH)
private TermConceptPropertyTypeEnum myType;
/**
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
@Column(name = "PROP_CODESYSTEM", length = 500, nullable = true)
@Column(name = "PROP_CODESYSTEM", length = MAX_LENGTH, nullable = true)
private String myCodeSystem;
/**
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
@Column(name = "PROP_DISPLAY", length = 500, nullable = true)
@Column(name = "PROP_DISPLAY", length = MAX_LENGTH, nullable = true)
private String myDisplay;
/**
@ -80,6 +88,8 @@ public class TermConceptProperty implements Serializable {
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
public TermConceptProperty setCodeSystem(String theCodeSystem) {
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCodeSystem, MAX_LENGTH,
"Property code system exceeds maximum length (" + MAX_LENGTH + "): " + length(theCodeSystem));
myCodeSystem = theCodeSystem;
return this;
}
@ -95,7 +105,7 @@ public class TermConceptProperty implements Serializable {
* Relevant only for properties of type {@link TermConceptPropertyTypeEnum#CODING}
*/
public TermConceptProperty setDisplay(String theDisplay) {
myDisplay = theDisplay;
myDisplay = left(theDisplay, MAX_LENGTH);
return this;
}
@ -103,15 +113,20 @@ public class TermConceptProperty implements Serializable {
return myKey;
}
public void setKey(String theKey) {
public TermConceptProperty setKey(@Nonnull String theKey) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theKey, "theKey must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theKey, MAX_LENGTH,
"Code exceeds maximum length (" + MAX_LENGTH + "): " + length(theKey));
myKey = theKey;
return this;
}
public TermConceptPropertyTypeEnum getType() {
return myType;
}
public TermConceptProperty setType(TermConceptPropertyTypeEnum theType) {
public TermConceptProperty setType(@Nonnull TermConceptPropertyTypeEnum theType) {
Validate.notNull(theType);
myType = theType;
return this;
}
@ -128,8 +143,9 @@ public class TermConceptProperty implements Serializable {
* This will contain the value for a {@link TermConceptPropertyTypeEnum#STRING string}
* property, and the code for a {@link TermConceptPropertyTypeEnum#CODING coding} property.
*/
public void setValue(String theValue) {
myValue = theValue;
public TermConceptProperty setValue(String theValue) {
myValue = left(theValue, MAX_LENGTH);
return this;
}
public TermConceptProperty setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
@ -137,8 +153,9 @@ public class TermConceptProperty implements Serializable {
return this;
}
public void setConcept(TermConcept theConcept) {
public TermConceptProperty setConcept(TermConcept theConcept) {
myConcept = theConcept;
return this;
}
@Override

144
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java Normal file
View File

@ -0,0 +1,144 @@
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 ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Table(name = "TRM_VALUESET", uniqueConstraints = {
@UniqueConstraint(name = "IDX_VALUESET_URL", columnNames = {"URL"})
})
@Entity()
public class TermValueSet implements Serializable {
private static final long serialVersionUID = 1L;
private static final int MAX_NAME_LENGTH = 200;
static final int MAX_URL_LENGTH = 200;
@Id()
@SequenceGenerator(name = "SEQ_VALUESET_PID", sequenceName = "SEQ_VALUESET_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_VALUESET_PID")
@Column(name = "PID")
private Long myId;
@Column(name = "URL", nullable = false, length = MAX_URL_LENGTH)
private String myUrl;
@OneToOne()
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMVALUESET_RES"))
private ResourceTable myResource;
@Column(name = "RES_ID", insertable = false, updatable = false)
private Long myResourcePid;
@Column(name = "NAME", nullable = true, length = MAX_NAME_LENGTH)
private String myName;
@OneToMany(mappedBy = "myValueSet")
private List<TermValueSetCode> myCodes;
public Long getId() {
return myId;
}
public String getUrl() {
return myUrl;
}
public TermValueSet setUrl(@Nonnull String theUrl) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theUrl, "theUrl must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theUrl, MAX_URL_LENGTH,
"URL exceeds maximum length (" + MAX_URL_LENGTH + "): " + length(theUrl));
myUrl = theUrl;
return this;
}
public ResourceTable getResource() {
return myResource;
}
public TermValueSet setResource(ResourceTable theResource) {
myResource = theResource;
return this;
}
public String getName() {
return myName;
}
public TermValueSet setName(String theName) {
myName = left(theName, MAX_NAME_LENGTH);
return this;
}
public List<TermValueSetCode> getCodes() {
if (myCodes == null) {
myCodes = new ArrayList<>();
}
return myCodes;
}
@Override
public boolean equals(Object theO) {
if (this == theO) return true;
if (!(theO instanceof TermValueSet)) return false;
TermValueSet that = (TermValueSet) theO;
return new EqualsBuilder()
.append(getUrl(), that.getUrl())
.isEquals();
}
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(getUrl())
.toHashCode();
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append("myUrl", myUrl)
.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
.append("myResourcePid", myResourcePid)
.append("myName", myName)
.append(myCodes != null ? ("myCodes - size=" + myCodes.size()) : ("myCodes=(null)"))
.toString();
}
}

172
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetCode.java Normal file
View File

@ -0,0 +1,172 @@
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 ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.annotation.Nonnull;
import javax.persistence.*;
import java.io.Serializable;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Table(name = "TRM_VALUESET_CODE", indexes = {
@Index(name = "IDX_VALUESET_CODE_CS_CD", columnList = "SYSTEM, CODE")
})
@Entity()
public class TermValueSetCode implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name = "SEQ_VALUESET_CODE_PID", sequenceName = "SEQ_VALUESET_CODE_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_VALUESET_CODE_PID")
@Column(name = "PID")
private Long myId;
@ManyToOne()
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_PID"))
private TermValueSet myValueSet;
@Transient
private String myValueSetUrl;
@Transient
private String myValueSetName;
@Column(name = "SYSTEM", nullable = false, length = TermCodeSystem.MAX_URL_LENGTH)
private String mySystem;
@Column(name = "CODE", nullable = false, length = TermConcept.MAX_CODE_LENGTH)
private String myCode;
@Column(name = "DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
private String myDisplay;
public Long getId() {
return myId;
}
public TermValueSet getValueSet() {
return myValueSet;
}
public TermValueSetCode setValueSet(TermValueSet theValueSet) {
myValueSet = theValueSet;
return this;
}
public String getValueSetUrl() {
if (myValueSetUrl == null) {
myValueSetUrl = getValueSet().getUrl();
}
return myValueSetUrl;
}
public String getValueSetName() {
if (myValueSetName == null) {
myValueSetName = getValueSet().getName();
}
return myValueSetName;
}
public String getSystem() {
return mySystem;
}
public TermValueSetCode setSystem(@Nonnull String theSystem) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theSystem, "theSystem must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theSystem, TermCodeSystem.MAX_URL_LENGTH,
"System exceeds maximum length (" + TermCodeSystem.MAX_URL_LENGTH + "): " + length(theSystem));
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "theSystem must not be null or empty");
if (theSystem.length() > TermCodeSystem.MAX_URL_LENGTH) {
throw new IllegalArgumentException();
}
mySystem = theSystem;
return this;
}
public String getCode() {
return myCode;
}
public TermValueSetCode setCode(@Nonnull String theCode) {
ValidateUtil.isNotBlankOrThrowIllegalArgument(theCode, "theCode must not be null or empty");
ValidateUtil.isNotTooLongOrThrowIllegalArgument(theCode, TermConcept.MAX_CODE_LENGTH,
"Code exceeds maximum length (" + TermConcept.MAX_CODE_LENGTH + "): " + length(theCode));
myCode = theCode;
return this;
}
public String getDisplay() {
return myDisplay;
}
public TermValueSetCode setDisplay(String theDisplay) {
myDisplay = left(theDisplay, TermConcept.MAX_DESC_LENGTH);
return this;
}
@Override
public boolean equals(Object theO) {
if (this == theO) return true;
if (!(theO instanceof TermValueSetCode)) return false;
TermValueSetCode that = (TermValueSetCode) theO;
return new EqualsBuilder()
.append(getValueSetUrl(), that.getValueSetUrl())
.append(getSystem(), that.getSystem())
.append(getCode(), that.getCode())
.isEquals();
}
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(getValueSetUrl())
.append(getSystem())
.append(getCode())
.toHashCode();
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
.append("myValueSetUrl", this.getValueSetUrl())
.append("myValueSetName", this.getValueSetName())
.append("mySystem", mySystem)
.append("myCode", myCode)
.append("myDisplay", myDisplay)
.toString();
}
}

102
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -119,6 +119,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao;
@Autowired
protected ITermValueSetDao myValueSetDao;
@Autowired
protected ITermValueSetCodeDao myValueSetCodeDao;
@Autowired
protected FhirContext myContext;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@ -388,6 +392,31 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
deleteConceptMap(theResourceTable);
}
public void deleteValueSet(ResourceTable theResourceTable) {
// Get existing entity so it can be deleted.
Optional<TermValueSet> optionalExistingTermValueSetById = myValueSetDao.findByResourcePid(theResourceTable.getId());
if (optionalExistingTermValueSetById.isPresent()) {
TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();
ourLog.info("Deleting existing TermValueSet {} and its children...", existingTermValueSet.getId());
myValueSetCodeDao.deleteTermValueSetCodesByValueSetId(existingTermValueSet.getId());
myValueSetDao.deleteTermValueSetById(existingTermValueSet.getId());
ourLog.info("Done deleting existing TermValueSet {} and its children.", existingTermValueSet.getId());
ourLog.info("Flushing...");
myValueSetCodeDao.flush();
myValueSetDao.flush();
ourLog.info("Done flushing.");
}
}
@Override
@Transactional
public void deleteValueSetAndChildren(ResourceTable theResourceTable) {
deleteValueSet(theResourceTable);
}
private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
int count;
ourLog.info(" * Deleting {}", theDescriptor);
@ -690,7 +719,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private void expandWithoutHibernateSearch(ValueSet.ValueSetExpansionComponent theExpansionComponent, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
ourLog.trace("Hibernate search is not enabled");
Validate.isTrue(theExpansionComponent.getParameter().isEmpty(), "Can not exapnd ValueSet with parameters - Hibernate Search is not enabled on this server.");
Validate.isTrue(theExpansionComponent.getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
@ -1144,7 +1173,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
myCodeSystemDao.save(codeSystem);
} else {
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri,
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
@ -1310,7 +1339,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
myConceptMapGroupElementTargetDao.save(termConceptMapGroupElementTarget);
if (codesSaved++ % 250 == 0) {
ourLog.info("Have saved {} codes in conceptmap", codesSaved);
ourLog.info("Have saved {} codes in ConceptMap", codesSaved);
myConceptMapGroupElementTargetDao.flush();
}
}
@ -1334,6 +1363,69 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
ourLog.info("Done storing TermConceptMap.");
}
@Override
@Transactional
public void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet) {
ourLog.info("Storing TermValueSet {}", theValueSet.getIdElement().getValue());
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theValueSet.getUrl(), "ValueSet has no value for ValueSet.url");
TermValueSet termValueSet = new TermValueSet();
termValueSet.setResource(theResourceTable);
termValueSet.setUrl(theValueSet.getUrl());
termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
// We delete old versions; we don't support versioned ValueSets.
deleteValueSet(theResourceTable);
/*
* Do the upload.
*/
String url = termValueSet.getUrl();
Optional<TermValueSet> optionalExistingTermValueSetByUrl = myValueSetDao.findByUrl(url);
if (!optionalExistingTermValueSetByUrl.isPresent()) {
myValueSetDao.save(termValueSet);
int codesSaved = 0;
ValueSet expandedValueSet = expandValueSet(theValueSet);
if (expandedValueSet.hasExpansion()) {
if (expandedValueSet.getExpansion().hasTotal() && expandedValueSet.getExpansion().getTotal() > 0) {
TermValueSetCode code;
for (ValueSet.ValueSetExpansionContainsComponent contains : expandedValueSet.getExpansion().getContains()) {
ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getSystem(), "ValueSet contains a code with no system value");
ValidateUtil.isNotBlankOrThrowInvalidRequest(contains.getCode(), "ValueSet contains a code with no code value");
code = new TermValueSetCode();
code.setValueSet(termValueSet);
code.setSystem(contains.getSystem());
code.setCode(contains.getCode());
code.setDisplay(contains.hasDisplay() ? contains.getDisplay() : null);
myValueSetCodeDao.save(code);
if (codesSaved++ % 250 == 0) {
ourLog.info("Have pre-expanded {} codes in ValueSet", codesSaved);
myValueSetCodeDao.flush();
}
}
}
}
} else {
TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
String msg = myContext.getLocalizer().getMessage(
BaseHapiTerminologySvcImpl.class,
"cannotCreateDuplicateValueSetUrl",
url,
existingTermValueSet.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
ourLog.info("Done storing TermValueSet.");
}
@Override
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB) {
VersionIndependentConcept conceptA = toConcept(theCodeA, theSystem, theCodingA);
@ -1581,9 +1673,9 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private int validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, ArrayList<String> theConceptsStack,
IdentityHashMap<TermConcept, Object> theAllConcepts) {
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodesystemValue is null");
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodeSystemVersion is null");
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() == theCodeSystem, "CodeSystems are not equal");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code with no code value");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "CodeSystem contains a code with no code value");
if (theConceptsStack.contains(theConcept.getCode())) {
throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());

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

@ -81,8 +81,12 @@ public interface IHapiTerminologySvc {
void deleteConceptMapAndChildren(ResourceTable theResourceTable);
void deleteValueSetAndChildren(ResourceTable theResourceTable);
void storeTermConceptMapAndChildren(ResourceTable theResourceTable, ConceptMap theConceptMap);
void storeTermValueSetAndChildren(ResourceTable theResourceTable, ValueSet theValueSet);
boolean supportsSystem(String theCodeSystem);
List<TermConceptMapGroupElementTarget> translate(TranslationRequest theTranslationRequest);

49
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -1,31 +1,13 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.util.*;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.entity.*;
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.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
@ -35,6 +17,25 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
@ -226,7 +227,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
myCodeSystemDao.create(codeSystem, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
}
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -118,6 +118,10 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myCodeSystemDaoR4")
protected IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemDao;
@Autowired
protected ITermCodeSystemDao myTermCodeSystemDao;
@Autowired
protected ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
@Autowired
@Qualifier("myCompartmentDefinitionDaoR4")
protected IFhirResourceDao<CompartmentDefinition> myCompartmentDefinitionDao;
@Autowired
@ -287,6 +291,10 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myValueSetDaoR4")
protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
@Autowired
protected ITermValueSetDao myTermValueSetDao;
@Autowired
protected ITermValueSetCodeDao myTermValueSetCodeDao;
@Autowired
protected ITermConceptMapDao myTermConceptMapDao;
@Autowired
protected ITermConceptMapGroupElementTargetDao myTermConceptMapGroupElementTargetDao;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
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@ -222,7 +222,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
myCodeSystemDao.create(codeSystem, mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertEquals("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
assertEquals("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/" + id.getIdPart(), e.getMessage());
}
}

30
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValueSetTest.java
View File

@ -1,34 +1,20 @@
package ca.uhn.fhir.jpa.dao.r4;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import java.io.IOException;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.util.TestUtil;
import java.io.IOException;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
@ -224,7 +210,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
@Test
public void testValiedateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
public void testValidateCodeAgainstBuiltInValueSetAndCodeSystemWithValidCode() {
IPrimitiveType<String> display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -177,7 +177,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Can not create multiple code systems with URI \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
assertThat(e.getMessage(), containsString("Can not create multiple CodeSystem resources with CodeSystem.url \"http://example.com/my_code_system\", already have one with resource ID: CodeSystem/"));
}
}

126
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
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@ -2,17 +2,12 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroup;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.UriType;
import org.junit.*;
import org.junit.rules.ExpectedException;
import org.slf4j.Logger;
@ -21,6 +16,7 @@ import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
@ -31,6 +27,8 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@Rule
public final ExpectedException expectedException = ExpectedException.none();
private IIdType myConceptMapId;
private IIdType myExtensionalCsId;
private IIdType myExtensionalVsId;
@Before
public void before() {
@ -40,6 +38,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
@After
public void after() {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
}
private void createAndPersistConceptMap() {
@ -56,6 +55,39 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
private void loadAndPersistCodeSystemAndValueSet() throws IOException {
loadAndPersistCodeSystem();
loadAndPersistValueSet();
}
private void loadAndPersistCodeSystem() throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
persistCodeSystem(codeSystem);
}
private void persistCodeSystem(CodeSystem theCodeSystem) {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
}
private void loadAndPersistValueSet() throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
persistValueSet(valueSet);
}
private void persistValueSet(ValueSet theValueSet) {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
}
});
}
@Test
public void testCreateConceptMapWithMissingSourceSystem() {
ConceptMap conceptMap = new ConceptMap();
@ -137,6 +169,16 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
}
@Test
public void testDuplicateCodeSystemUrls() throws Exception {
loadAndPersistCodeSystem();
expectedException.expect(UnprocessableEntityException.class);
expectedException.expectMessage("Can not create multiple CodeSystem resources with CodeSystem.url \"http://acme.org\", already have one with resource ID: CodeSystem/" + myExtensionalCsId.getIdPart());
loadAndPersistCodeSystem();
}
@Test
public void testDuplicateConceptMapUrls() {
createAndPersistConceptMap();
@ -147,6 +189,19 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
createAndPersistConceptMap();
}
@Test
public void testDuplicateValueSetUrls() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
// DM 2019-03-05 - We pre-load our custom CodeSystem otherwise pre-expansion of the ValueSet will fail.
loadAndPersistCodeSystemAndValueSet();
expectedException.expect(UnprocessableEntityException.class);
expectedException.expectMessage("Can not create multiple ValueSet resources with ValueSet.url \"http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2\", already have one with resource ID: ValueSet/" + myExtensionalVsId.getIdPart());
loadAndPersistValueSet();
}
@Test
public void testStoreTermConceptMapAndChildren() {
createAndPersistConceptMap();
@ -325,6 +380,63 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
@Test
public void testStoreTermValueSetAndChildren() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSet();
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
Optional<TermValueSet> optionalValueSetByResourcePid = myTermValueSetDao.findByResourcePid(myExtensionalVsId.getIdPartAsLong());
assertTrue(optionalValueSetByResourcePid.isPresent());
Optional<TermValueSet> optionalValueSetByUrl = myTermValueSetDao.findByUrl("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2");
assertTrue(optionalValueSetByUrl.isPresent());
TermValueSet valueSet = optionalValueSetByUrl.get();
assertSame(optionalValueSetByResourcePid.get(), valueSet);
ourLog.info("ValueSet:\n" + valueSet.toString());
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", valueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", valueSet.getName());
assertEquals(codeSystem.getConcept().size(), valueSet.getCodes().size());
TermValueSetCode code = valueSet.getCodes().get(0);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("8450-9", code.getCode());
assertEquals("Systolic blood pressure--expiration", code.getDisplay());
code = valueSet.getCodes().get(1);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("11378-7", code.getCode());
assertEquals("Systolic blood pressure at First encounter", code.getDisplay());
// ...
code = valueSet.getCodes().get(22);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("8491-3", code.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", code.getDisplay());
code = valueSet.getCodes().get(23);
ourLog.info("Code:\n" + code.toString());
assertEquals("http://acme.org", code.getSystem());
assertEquals("8492-1", code.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", code.getDisplay());
}
});
}
@Test
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
createAndPersistConceptMap();

35
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -75,6 +75,41 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
.renameColumn("mySystem", "SYSTEM_URL")
.renameColumn("mySystemVersion", "SYSTEM_VERSION")
.renameColumn("myValueSet", "VALUESET_URL");
// TermValueSet
version.startSectionWithMessage("Processing table: TRM_VALUESET");
version.addIdGenerator("SEQ_VALUESET_PID");
Builder.BuilderAddTableByColumns termValueSetTable = version.addTableByColumns("TRM_VALUESET", "PID");
termValueSetTable.addColumn("PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetTable.addColumn("URL").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING);
termValueSetTable
.addIndex("IDX_VALUESET_URL")
.unique(true)
.withColumns("URL");
termValueSetTable.addColumn("RES_ID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetTable
.addForeignKey("FK_TRMVALUESET_RES")
.toColumn("RES_ID")
.references("HFJ_RESOURCE", "RES_ID");
termValueSetTable.addColumn("NAME").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING);
// TermValueSetCode
version.startSectionWithMessage("Processing table: TRM_VALUESET_CODE");
version.addIdGenerator("SEQ_VALUESET_CODE_PID");
Builder.BuilderAddTableByColumns termValueSetCodeTable = version.addTableByColumns("TRM_VALUESET_CODE", "PID");
termValueSetCodeTable.addColumn("PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetCodeTable.addColumn("VALUESET_PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetCodeTable
.addForeignKey("FK_TRM_VALUESET_PID")
.toColumn("VALUESET_PID")
.references("TRM_VALUESET", "PID");
termValueSetCodeTable.addColumn("SYSTEM").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING);
termValueSetCodeTable.addColumn("CODE").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING);
termValueSetCodeTable
.addIndex("IDX_VALUESET_CODE_CS_CD")
.unique(false)
.withColumns("SYSTEM", "CODE");
termValueSetCodeTable.addColumn("DISPLAY").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.STRING);
}