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Work on terminology service

This commit is contained in:
jamesagnew 2016-02-16 21:29:00 -05:00
parent 1f875c1ca6
commit 9b304748ad
21 changed files with 820 additions and 41 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java
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@ -588,7 +588,10 @@ class ModelScanner {
*/
List<Class<? extends IBaseResource>> refTypesList = new ArrayList<Class<? extends IBaseResource>>();
for (Class<? extends IElement> nextType : childAnnotation.type()) {
if (IBaseResource.class.isAssignableFrom(nextType) == false) {
if (IBaseReference.class.isAssignableFrom(nextType)) {
refTypesList.add(myVersion.isRi() ? IAnyResource.class : IResource.class);
continue;
} else if (IBaseResource.class.isAssignableFrom(nextType) == false) {
throw new ConfigurationException("Field '" + next.getName() + "' in class '" + next.getDeclaringClass().getCanonicalName() + "' is of type " + BaseResourceReferenceDt.class + " but contains a non-resource type: " + nextType.getCanonicalName());
}
refTypesList.add((Class<? extends IBaseResource>) nextType);

21
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java Normal file
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@ -0,0 +1,21 @@
package ca.uhn.fhir.util;
import static org.apache.commons.lang3.StringUtils.isBlank;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class ValidateUtil {
public static void isNotNullOrThrowInvalidRequest(boolean theSuccess, String theMessage) {
if (theSuccess == false) {
throw new InvalidRequestException(theMessage);
}
}
public static void isNotBlankOrThrowInvalidRequest(String theString, String theMessage) {
if (isBlank(theString)) {
throw new InvalidRequestException(theMessage);
}
}
}

4
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
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@ -65,4 +65,6 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulCreate=Successfully create
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulUpdate=Successfully updated resource "{0}" in {1}ms
ca.uhn.fhir.jpa.dao.SearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}
ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}
ca.uhn.fhir.jpa.term.TerminologySvcImpl.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}

50
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/ValidateUtilTest.java Normal file
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@ -0,0 +1,50 @@
package ca.uhn.fhir.util;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import org.junit.Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class ValidateUtilTest {
@Test
public void testValidate() {
ValidateUtil.isNotNullOrThrowInvalidRequest(true, "");
try {
ValidateUtil.isNotNullOrThrowInvalidRequest(false, "The message");
fail();
} catch (InvalidRequestException e) {
assertEquals("The message", e.getMessage());
}
}
@Test
public void testIsNotBlank() {
ValidateUtil.isNotBlankOrThrowInvalidRequest("aa", "");
try {
ValidateUtil.isNotBlankOrThrowInvalidRequest("", "The message");
fail();
} catch (InvalidRequestException e) {
assertEquals("The message", e.getMessage());
}
try {
ValidateUtil.isNotBlankOrThrowInvalidRequest(null, "The message");
fail();
} catch (InvalidRequestException e) {
assertEquals("The message", e.getMessage());
}
try {
ValidateUtil.isNotBlankOrThrowInvalidRequest(" ", "The message");
fail();
} catch (InvalidRequestException e) {
assertEquals("The message", e.getMessage());
}
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
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@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.config;
import javax.annotation.Resource;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.annotation.Bean;
@ -37,6 +38,8 @@ import org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler;
import org.springframework.scheduling.config.ScheduledTaskRegistrar;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.term.ITerminologySvc;
import ca.uhn.fhir.jpa.term.TerminologySvcImpl;
@Configuration
@EnableScheduling
@ -95,6 +98,11 @@ public class BaseConfig implements SchedulingConfigurer {
return ourFhirContextDstu3;
}
@Bean(autowire=Autowire.BY_TYPE)
public ITerminologySvc terminologyService() {
return new TerminologySvcImpl();
}
@Bean
public TaskScheduler taskScheduler() {
ThreadPoolTaskScheduler retVal = new ThreadPoolTaskScheduler();

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
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@ -571,9 +571,14 @@ public class FhirSystemDaoDstu2 extends BaseHapiFhirSystemDao<Bundle, MetaDt> {
}
}
ourLog.info("Flushing context after {}", theActionName);
myEntityManager.flush();
long delay = System.currentTimeMillis() - start;
ourLog.info(theActionName + " completed in {}ms", new Object[] { delay });
int numEntries = theRequest.getEntry().size();
long delayPer = delay / numEntries;
ourLog.info("{} completed in {}ms ({} entries at {}ms per entry)", new Object[] { theActionName , delay, numEntries, delayPer });
response.setType(BundleTypeEnum.TRANSACTION_RESPONSE);
return response;

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermCodeSystemDao.java Normal file
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@ -0,0 +1,34 @@
package ca.uhn.fhir.jpa.dao.data;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
public interface ITermCodeSystemDao extends JpaRepository<TermCodeSystem, Long> {
@Query("SELECT cs FROM TermCodeSystem cs WHERE cs.myCodeSystemUri = :code_system_uri")
TermCodeSystem findByCodeSystemUri(@Param("code_system_uri") String theCodeSystemUri);
}

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermCodeSystemVersionDao.java Normal file
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@ -0,0 +1,34 @@
package ca.uhn.fhir.jpa.dao.data;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemVersion, Long> {
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResource.myId = :resource_id AND cs.myResourceVersionId = :version_id")
TermCodeSystemVersion findByCodeSystemResourceAndVersion(@Param("resource_id") Long theCodeSystemResourcePid, @Param("version_id") Long theCodeSystemVersionPid);
}

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDao.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 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
public interface ITermConceptDao extends JpaRepository<TermConcept, Long> {
@Query("SELECT c FROM TermConcept c WHERE c.myCodeSystem = :code_system AND c.myCode = :code")
TermConcept findByCodeSystemAndCode(@Param("code_system") TermCodeSystemVersion theCodeSystem, @Param("code") String theCode);
}

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java Normal file
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@ -0,0 +1,29 @@
package ca.uhn.fhir.jpa.dao.data;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.data.jpa.repository.JpaRepository;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConceptParentChildLink, Long> {
// nothing
}

42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
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@ -25,6 +25,7 @@ import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.OneToOne;
@ -34,24 +35,39 @@ import javax.persistence.UniqueConstraint;
//@formatter:off
@Table(name="TRM_CODESYSTEM", uniqueConstraints= {
@UniqueConstraint(name="IDX_CS_RESOURCEPID", columnNames= {"RES_ID"})
@UniqueConstraint(name="IDX_CS_CODESYSTEM", columnNames= {"CODE_SYSTEM_URI"})
})
@Entity()
//@formatter:on
public class TermCodeSystem implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name="SEQ_CODESYSTEM_PID", sequenceName="SEQ_CODESYSTEM_PID")
@GeneratedValue()
@Column(name="PID")
private Long myPid;
@OneToOne()
@JoinColumn(name="RES_ID", referencedColumnName="RES_ID", nullable=false, updatable=false)
private ResourceTable myResource;
@Column(name="RES_VERSION_ID", nullable=false, updatable=false)
private Long myResourceVersionId;
@Column(name="CODE_SYSTEM_URI", nullable=false)
private String myCodeSystemUri;
@Id()
@SequenceGenerator(name = "SEQ_CODESYSTEM_PID", sequenceName = "SEQ_CODESYSTEM_PID")
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CODESYSTEM_PID")
@Column(name = "PID")
private Long myPid;
@OneToOne()
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false)
private ResourceTable myResource;
public String getCodeSystemUri() {
return myCodeSystemUri;
}
public ResourceTable getResource() {
return myResource;
}
public void setCodeSystemUri(String theCodeSystemUri) {
myCodeSystemUri = theCodeSystemUri;
}
public void setResource(ResourceTable theResource) {
myResource = theResource;
}
}

88
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java Normal file
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@ -0,0 +1,88 @@
package ca.uhn.fhir.jpa.entity;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.OneToMany;
import javax.persistence.OneToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.UniqueConstraint;
//@formatter:off
@Table(name="TRM_CODESYSTEM_VER", uniqueConstraints= {
@UniqueConstraint(name="IDX_CSV_RESOURCEPID_AND_VER", columnNames= {"RES_ID", "RES_VERSION_ID"})
})
@Entity()
//@formatter:on
public class TermCodeSystemVersion implements Serializable {
private static final long serialVersionUID = 1L;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCodeSystem")
private Collection<TermConcept> myConcepts;
@Id()
@SequenceGenerator(name = "SEQ_CODESYSTEMVER_PID", sequenceName = "SEQ_CODESYSTEMVER_PID")
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CODESYSTEMVER_PID")
@Column(name = "PID")
private Long myPid;
@OneToOne()
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false)
private ResourceTable myResource;
@Column(name = "RES_VERSION_ID", nullable = false, updatable = false)
private Long myResourceVersionId;
public Collection<TermConcept> getConcepts() {
if (myConcepts == null) {
myConcepts = new ArrayList<TermConcept>();
}
return myConcepts;
}
public ResourceTable getResource() {
return myResource;
}
public Long getResourceVersionId() {
return myResourceVersionId;
}
public void setResource(ResourceTable theResource) {
myResource = theResource;
}
public void setResourceVersionId(Long theResourceVersionId) {
myResourceVersionId = theResourceVersionId;
}
}

122
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
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@ -21,36 +21,138 @@ package ca.uhn.fhir.jpa.entity;
*/
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import javax.persistence.CascadeType;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
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.OneToMany;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.UniqueConstraint;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
@Entity
@Table(name="TRM_CONCEPT")
@Table(name="TRM_CONCEPT", uniqueConstraints= {
@UniqueConstraint(name="IDX_CONCEPT_CS_CODE", columnNames= {"CODESYSTEM_PID", "CODE"})
})
public class TermConcept implements Serializable {
private static final long serialVersionUID = 1L;
@Id()
@SequenceGenerator(name="SEQ_CONCEPT_PID", sequenceName="SEQ_CONCEPT_PID")
@GeneratedValue()
@Column(name="PID")
private Long myPid;
@OneToMany(fetch=FetchType.LAZY, mappedBy="myParent")
private Collection<TermConceptParentChildLink> myChildren;
@ManyToOne()
@JoinColumn(name="CODESYSTEM_PID", referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_CONCEPT_PID_CS_PID"))
private TermCodeSystem myCodeSystem;
@Column(name="CODE", length=100, nullable=false)
private String myCode;
@ManyToOne()
@JoinColumn(name="CODESYSTEM_PID", referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_CONCEPT_PID_CS_PID"))
private TermCodeSystemVersion myCodeSystem;
@Column(name="DISPLAY", length=200, nullable=true)
private String myDisplay;
@OneToMany(cascade=CascadeType.ALL, fetch=FetchType.LAZY, mappedBy="myChild")
private Collection<TermConceptParentChildLink> myParents;
@Id()
@SequenceGenerator(name="SEQ_CONCEPT_PID", sequenceName="SEQ_CONCEPT_PID")
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CONCEPT_PID")
@Column(name="PID")
private Long myPid;
public TermConcept() {
super();
}
public TermConcept(TermCodeSystemVersion theCs, String theCode) {
setCodeSystem(theCs);
setCode(theCode);
}
public TermConcept addChild(TermConcept theChild) {
Validate.notNull(theChild.getCodeSystem(), "theChild.getCodeSystem() must not return null");
TermConceptParentChildLink link = new TermConceptParentChildLink();
link.setParent(this);
link.setCodeSystem(theChild.getCodeSystem());
link.setChild(theChild);
getChildren().add(link);
return this;
}
@Override
public boolean equals(Object theObj) {
if (!(theObj instanceof TermConcept)) {
return false;
}
if (theObj == this) {
return true;
}
TermConcept obj = (TermConcept)theObj;
if (obj.myPid == null) {
return false;
}
EqualsBuilder b = new EqualsBuilder();
b.append(myPid, obj.myPid);
return b.isEquals();
}
public Collection<TermConceptParentChildLink> getChildren() {
if (myChildren == null) {
myChildren = new ArrayList<TermConceptParentChildLink>();
}
return myChildren;
}
public String getCode() {
return myCode;
}
public TermCodeSystemVersion getCodeSystem() {
return myCodeSystem;
}
public String getDisplay() {
return myDisplay;
}
public Collection<TermConceptParentChildLink> getParents() {
if (myParents == null) {
myParents = new ArrayList<TermConceptParentChildLink>();
}
return myParents;
}
@Override
public int hashCode() {
HashCodeBuilder b = new HashCodeBuilder();
b.append(myPid);
return b.toHashCode();
}
public void setCode(String theCode) {
myCode = theCode;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
}
public void setDisplay(String theDisplay) {
myDisplay = theDisplay;
}
}

52
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -24,7 +24,9 @@ import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
@ -32,26 +34,50 @@ import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
@Entity
@Table(name="TRM_CONCEPT")
@Table(name="TRM_CONCEPT_PC_LINK")
public class TermConceptParentChildLink implements Serializable {
private static final long serialVersionUID = 1L;
@ManyToOne()
@JoinColumn(name="CHILD_PID", nullable=false, referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_TERM_CONCEPTPC_CHILD"))
private TermConcept myChild;
@ManyToOne()
@JoinColumn(name="CODESYSTEM_PID", nullable=false, foreignKey=@ForeignKey(name="FK_TERM_CONCEPTPC_CS"))
private TermCodeSystemVersion myCodeSystem;
@ManyToOne()
@JoinColumn(name="PARENT_PID", nullable=false, referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_TERM_CONCEPTPC_PARENT"))
private TermConcept myParent;
@Id()
@SequenceGenerator(name="SEQ_CONCEPT_PC_PID", sequenceName="SEQ_CONCEPT_PC_PID")
@GeneratedValue()
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CONCEPT_PC_PID")
@Column(name="PID")
private Long myPid;
@ManyToOne
@JoinColumn(name="PARENT_PID", nullable=false)
private TermConcept myParent;
@ManyToOne
@JoinColumn(name="CHILD_PID", nullable=false)
private TermConcept myChild;
public TermConcept getChild() {
return myChild;
}
@ManyToOne
@JoinColumn(name="CODESYSTEM_PID", nullable=false)
private TermCodeSystem myCodeSystem;
public TermCodeSystemVersion getCodeSystem() {
return myCodeSystem;
}
public TermConcept getParent() {
return myParent;
}
public void setChild(TermConcept theChild) {
myChild = theChild;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
}
public void setParent(TermConcept theParent) {
myParent = theParent;
}
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ITerminologySvc.java
View File

@ -1,5 +1,14 @@
package ca.uhn.fhir.jpa.term;
import java.util.Set;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
public interface ITerminologySvc {
void storeNewCodeSystemVersion(String theSystemUri, TermCodeSystemVersion theCodeSytem);
Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemResourceVersion, String theCode);
}

130
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologySvcImpl.java
View File

@ -1,6 +1,136 @@
package ca.uhn.fhir.jpa.term;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.Set;
import javax.transaction.Transactional;
import javax.transaction.Transactional.TxType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.validation.ValidationUtils;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.ValidateUtil;
public class TerminologySvcImpl implements ITerminologySvc {
private static final Object PLACEHOLDER_OBJECT = new Object();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologySvcImpl.class);
@Autowired
private ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@Autowired
private ITermConceptDao myConceptDao;
@Autowired
private ITermCodeSystemDao myCodeSystemDao;
@Autowired
private FhirContext myContext;
@Override
@Transactional(value=TxType.REQUIRED)
public void storeNewCodeSystemVersion(String theSystemUri, TermCodeSystemVersion theCodeSystem) {
ourLog.info("Storing code system");
ValidateUtil.isNotNullOrThrowInvalidRequest(theCodeSystem.getResource() != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
if (codeSystem == null) {
TermCodeSystem newCodeSystem = new TermCodeSystem();
newCodeSystem.setResource(theCodeSystem.getResource());
newCodeSystem.setCodeSystemUri(theSystemUri);
myCodeSystemDao.save(newCodeSystem);
} else {
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystem.getResource().getId())) {
throw new InvalidRequestException(myContext.getLocalizer().getMessage(TerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri, codeSystem.getResource().getIdDt().getValue()));
}
}
// Validate the code system
IdentityHashMap<TermConcept, Object> conceptsStack = new IdentityHashMap<TermConcept, Object>();
for (TermConcept next : theCodeSystem.getConcepts()) {
validateConceptForStorage(next, theCodeSystem, conceptsStack);
}
myCodeSystemVersionDao.save(theCodeSystem);
conceptsStack = new IdentityHashMap<TermConcept, Object>();
for (TermConcept next : theCodeSystem.getConcepts()) {
persistChildren(next, theCodeSystem, conceptsStack);
}
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack) {
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
return;
}
for (TermConceptParentChildLink next : theConcept.getChildren()) {
persistChildren(next.getChild(), theCodeSystem, theConceptsStack);
}
myConceptDao.save(theConcept);
for (TermConceptParentChildLink next : theConcept.getChildren()) {
myConceptParentChildLinkDao.save(next);
}
}
private void validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack) {
ValidateUtil.isNotNullOrThrowInvalidRequest(theConcept.getCodeSystem() == theCodeSystem, "Codesystem contains a code which does not reference the codesystem");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code which does not reference the codesystem");
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());
}
for (TermConceptParentChildLink next : theConcept.getChildren()) {
validateConceptForStorage(next.getChild(), theCodeSystem, theConceptsStack);
}
theConceptsStack.remove(theConcept);
}
@Transactional(value=TxType.REQUIRED)
@Override
public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
TermCodeSystemVersion codeSystem = myCodeSystemVersionDao.findByCodeSystemResourceAndVersion(theCodeSystemResourcePid, theCodeSystemVersionPid);
TermConcept concept = myConceptDao.findByCodeSystemAndCode(codeSystem, theCode);
Set<TermConcept> retVal = new HashSet<TermConcept>();
retVal.add(concept);
fetchChildren(concept, retVal);
return retVal;
}
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild();
if (theSetToPopulate.add(nextChild)) {
fetchChildren(nextChild, theSetToPopulate);
}
}
}

24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -13,6 +13,7 @@ import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.Search;
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.ConceptMap;
@ -61,6 +62,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
import ca.uhn.fhir.jpa.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
@ -78,7 +80,12 @@ import ca.uhn.fhir.jpa.entity.ResourceTag;
import ca.uhn.fhir.jpa.entity.SubscriptionFlaggedResource;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.entity.TagDefinition;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.term.ITerminologySvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.method.MethodUtil;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@ -88,6 +95,10 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@ContextConfiguration(classes= {TestDstu3Config.class})
//@formatter:on
public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
protected IResourceTableDao myResourceTableDao;
@Autowired
protected ITerminologySvc myTermSvc;
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
protected IValidationSupport myValidationSupport;
@ -99,6 +110,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myConceptMapDaoDstu3")
protected IFhirResourceDao<ConceptMap> myConceptMapDao;
@Autowired
@Qualifier("myCodeSystemDaoDstu3")
protected IFhirResourceDao<CodeSystem> myCodeSystemDao;
@Autowired
@Qualifier("myMedicationDaoDstu3")
protected IFhirResourceDao<Medication> myMedicationDao;
@Autowired
@ -241,6 +255,16 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
return null;
}
});
txTemplate.execute(new TransactionCallback<Void>() {
@Override
public Void doInTransaction(TransactionStatus theStatus) {
entityManager.createQuery("DELETE from " + TermConceptParentChildLink.class.getSimpleName() + " d").executeUpdate();
entityManager.createQuery("DELETE from " + TermConcept.class.getSimpleName() + " d").executeUpdate();
entityManager.createQuery("DELETE from " + TermCodeSystemVersion.class.getSimpleName() + " d").executeUpdate();
entityManager.createQuery("DELETE from " + TermCodeSystem.class.getSimpleName() + " d").executeUpdate();
return null;
}
});
txTemplate.execute(new TransactionCallback<Void>() {
@Override
public Void doInTransaction(TransactionStatus theStatus) {

151
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplTest.java Normal file
View File

@ -0,0 +1,151 @@
package ca.uhn.fhir.jpa.term;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.*;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class TerminologySvcImplTest extends BaseJpaDstu3Test {
@Test
public void testStoreCodeSystemInvalidCyclicLoop() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl("http://example.com/my_code_system");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parent = new TermConcept();
parent.setCodeSystem(cs);
parent.setCode("parent");
cs.getConcepts().add(parent);
TermConcept child = new TermConcept();
child.setCodeSystem(cs);
child.setCode("child");
parent.addChild(child);
child.addChild(parent);
try {
myTermSvc.storeNewCodeSystemVersion("http://foo", cs);
fail();
} catch (InvalidRequestException e) {
assertEquals("CodeSystem contains circular reference around code parent", e.getMessage());
}
}
@Test
public void testFetchIsA() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl("http://example.com/my_code_system");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA");
cs.getConcepts().add(parentA);
TermConcept childAA = new TermConcept(cs, "childAA");
parentA.addChild(childAA);
TermConcept childAAA = new TermConcept(cs, "childAAA");
childAA.addChild(childAAA);
TermConcept childAAB = new TermConcept(cs, "childAAB");
childAA.addChild(childAAB);
TermConcept childAB = new TermConcept(cs, "childAB");
parentA.addChild(childAB);
TermConcept parentB = new TermConcept(cs, "ParentB");
cs.getConcepts().add(parentB);
myTermSvc.storeNewCodeSystemVersion("http://foo", cs);
Set<TermConcept> concepts;
Set<String> codes;
concepts = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "ParentA");
codes = toCodes(concepts);
assertThat(codes, containsInAnyOrder("ParentA", "childAA", "childAAA", "childAAB", "childAB"));
concepts = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "childAA");
codes = toCodes(concepts);
assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
}
@Test
public void testCreateDuplicateCodeSystemUri() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl("http://example.com/my_code_system");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
myTermSvc.storeNewCodeSystemVersion("http://example.com/my_code_system", cs);
// Update
cs = new TermCodeSystemVersion();
TermConcept parentA = new TermConcept(cs, "ParentA");
cs.getConcepts().add(parentA);
id = myCodeSystemDao.update(codeSystem).getId().toUnqualified();
table = myResourceTableDao.findOne(id.getIdPartAsLong());
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
myTermSvc.storeNewCodeSystemVersion("http://example.com/my_code_system", cs);
// Try to update to a different resource
codeSystem = new CodeSystem();
codeSystem.setUrl("http://example.com/my_code_system");
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
id = myCodeSystemDao.create(codeSystem).getId().toUnqualified();
table = myResourceTableDao.findOne(id.getIdPartAsLong());
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
try {
myTermSvc.storeNewCodeSystemVersion("http://example.com/my_code_system", cs);
fail();
} catch (InvalidRequestException 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/"));
}
}
private Set<String> toCodes(Set<TermConcept> theConcepts) {
HashSet<String> retVal = new HashSet<String>();
for (TermConcept next : theConcepts) {
retVal.add(next.getCode());
}
return retVal;
}
}

3
hapi-fhir-structures-dstu3/src/main/resources/org/hl7/fhir/dstu3/model/fhirversion.properties
View File

@ -13,6 +13,7 @@ resource.CarePlan=org.hl7.fhir.dstu3.model.CarePlan
resource.Claim=org.hl7.fhir.dstu3.model.Claim
resource.ClaimResponse=org.hl7.fhir.dstu3.model.ClaimResponse
resource.ClinicalImpression=org.hl7.fhir.dstu3.model.ClinicalImpression
resource.CodeSystem=org.hl7.fhir.dstu3.model.CodeSystem
resource.Communication=org.hl7.fhir.dstu3.model.Communication
resource.CommunicationRequest=org.hl7.fhir.dstu3.model.CommunicationRequest
resource.Composition=org.hl7.fhir.dstu3.model.Composition
@ -54,6 +55,7 @@ resource.Immunization=org.hl7.fhir.dstu3.model.Immunization
resource.ImmunizationRecommendation=org.hl7.fhir.dstu3.model.ImmunizationRecommendation
resource.ImplementationGuide=org.hl7.fhir.dstu3.model.ImplementationGuide
resource.Library=org.hl7.fhir.dstu3.model.Library
resource.Linkage=org.hl7.fhir.dstu3.model.Linkage
resource.List=org.hl7.fhir.dstu3.model.ListResource
resource.Location=org.hl7.fhir.dstu3.model.Location
resource.Measure=org.hl7.fhir.dstu3.model.Measure
@ -85,6 +87,7 @@ resource.Procedure=org.hl7.fhir.dstu3.model.Procedure
resource.ProcedureRequest=org.hl7.fhir.dstu3.model.ProcedureRequest
resource.ProcessRequest=org.hl7.fhir.dstu3.model.ProcessRequest
resource.ProcessResponse=org.hl7.fhir.dstu3.model.ProcessResponse
resource.Protocol=org.hl7.fhir.dstu3.model.Protocol
resource.Provenance=org.hl7.fhir.dstu3.model.Provenance
resource.Questionnaire=org.hl7.fhir.dstu3.model.Questionnaire
resource.QuestionnaireResponse=org.hl7.fhir.dstu3.model.QuestionnaireResponse

12
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -18,7 +18,6 @@ import java.util.List;
import java.util.UUID;
import org.apache.commons.io.IOUtils;
import org.eclipse.jetty.util.IO;
import org.hamcrest.Matchers;
import org.hl7.fhir.dstu3.model.Binary;
import org.hl7.fhir.dstu3.model.Bundle;
@ -37,6 +36,7 @@ import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.HumanName;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
import org.hl7.fhir.dstu3.model.Linkage;
import org.hl7.fhir.dstu3.model.Medication;
import org.hl7.fhir.dstu3.model.MedicationOrder;
import org.hl7.fhir.dstu3.model.Observation;
@ -46,7 +46,6 @@ import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Quantity;
import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.Specimen;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@ -71,6 +70,15 @@ public class JsonParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
@Test
public void testLinkage() {
Linkage l = new Linkage();
l.addItem().getResource().setDisplay("FOO");
String out = ourCtx.newXmlParser().encodeResourceToString(l);
ourLog.info(out);
assertEquals("<Linkage xmlns=\"http://hl7.org/fhir\"><item><resource><display value=\"FOO\"/></resource></item></Linkage>", out);
}
@Test
public void testEncodeAndParseExtensions() throws Exception {

1
hapi-tinder-plugin/.classpath
View File

@ -22,6 +22,7 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry combineaccessrules="false" kind="src" path="/hapi-fhir-structures-dstu3"/>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>