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Merge remote-tracking branch 'remotes/origin/master' into ja_20190822_1440_infinispan_query_cache 

# Conflicts:
#	hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
#	src/changes/changes.xml
This commit is contained in:
Ken Stevens 2019-08-28 10:37:17 -04:00
parent 17f58a61c3 5650bc9baa
commit 259426b0dd
51 changed files with 2375 additions and 446 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java
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@ -76,7 +76,7 @@ public class ValidateUtil {
}
public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage, Object... theValues) {
if (theSuccess == false) {
if (!theSuccess) {
throw new InvalidRequestException(String.format(theMessage, theValues));
}
}

6
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -127,5 +127,11 @@ ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemU
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.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.term.BaseHapiTerminologySvcImpl.valueSetNotReadyForExpand=ValueSet is not ready for operation $expand; current status: {0} | {1}
ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.notExpanded=The ValueSet is waiting to be picked up and pre-expanded by a scheduled task.
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.expansionInProgress=The ValueSet has been picked up by a scheduled task and pre-expansion is in progress.
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.expanded=The ValueSet has been picked up by a scheduled task and pre-expansion is complete.
ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum.failedToExpand=The ValueSet has been picked up by a scheduled task and pre-expansion has failed.

22
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -90,28 +90,12 @@
<artifactId>commons-cli</artifactId>
</dependency>
<!-- This example uses Derby embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
<!-- This example uses H2 embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
dependency for your database platform. -->
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<!--<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyshared</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
</dependency>-->
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<dependency>

15
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
View File

@ -1,17 +1,16 @@
package ca.uhn.fhir.jpa.demo;
import java.util.Properties;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.hibernate.dialect.H2Dialect;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import javax.sql.DataSource;
import java.util.Properties;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -38,20 +37,20 @@ public class CommonConfig {
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
* The following bean configures the database connection. The 'url' property value of "jdbc:h2:file:target./jpaserver_h2_files" indicates that the server should save resources in a
* directory called "jpaserver_h2_files".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@Bean(destroyMethod = "close")
public DataSource dataSource() {
String url = "jdbc:derby:directory:target/jpaserver_derby_files;create=true";
String url = "jdbc:h2:file:./target/jpaserver_h2_files";
if (isNotBlank(ContextHolder.getDatabaseUrl())) {
url = ContextHolder.getDatabaseUrl();
}
BasicDataSource retVal = new BasicDataSource();
retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
retVal.setDriver(new org.h2.Driver());
retVal.setUrl(url);
retVal.setUsername("");
retVal.setPassword("");
@ -61,7 +60,7 @@ public class CommonConfig {
@Bean
public Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
extraProperties.put("hibernate.dialect", H2Dialect.class.getName());
extraProperties.put("hibernate.format_sql", "true");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");

6
hapi-fhir-jpaserver-base/pom.xml
View File

@ -146,7 +146,11 @@
<artifactId>logback-classic</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>

92
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
View File

@ -152,6 +152,18 @@ public class DaoConfig {
private boolean myPreExpandValueSetsExperimental = false;
private boolean myFilterParameterEnabled = false;
private StoreMetaSourceInformation myStoreMetaSourceInformation = StoreMetaSourceInformation.SOURCE_URI_AND_REQUEST_ID;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
*/
private int myPreExpandValueSetsDefaultOffsetExperimental = 0;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
*/
private int myPreExpandValueSetsDefaultCountExperimental = 1000;
/**
* EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
*/
private int myPreExpandValueSetsMaxCountExperimental = 1000;
/**
* Constructor
@ -1707,6 +1719,86 @@ public class DaoConfig {
}
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the default value of {@code offset} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* </p>
* <p>
* The default value for this setting is {@code 0}.
* </p>
*/
public int getPreExpandValueSetsDefaultOffsetExperimental() {
return myPreExpandValueSetsDefaultOffsetExperimental;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*/
public int getPreExpandValueSetsDefaultCountExperimental() {
return myPreExpandValueSetsDefaultCountExperimental;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* </p>
* <p>
* If {@code thePreExpandValueSetsDefaultCountExperimental} is greater than
* {@link DaoConfig#getPreExpandValueSetsMaxCountExperimental()}, the lesser value is used.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*/
public void setPreExpandValueSetsDefaultCountExperimental(int thePreExpandValueSetsDefaultCountExperimental) {
myPreExpandValueSetsDefaultCountExperimental = Math.min(thePreExpandValueSetsDefaultCountExperimental, getPreExpandValueSetsMaxCountExperimental());
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*/
public int getPreExpandValueSetsMaxCountExperimental() {
return myPreExpandValueSetsMaxCountExperimental;
}
/**
* EXPERIMENTAL - Do not use in production!
* <p>
* This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
* {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
* </p>
* <p>
* If {@code thePreExpandValueSetsMaxCountExperimental} is lesser than
* {@link DaoConfig#getPreExpandValueSetsDefaultCountExperimental()}, the default {@code count} is lowered to the
* new max {@code count}.
* </p>
* <p>
* The default value for this setting is {@code 1000}.
* </p>
*/
public void setPreExpandValueSetsMaxCountExperimental(int thePreExpandValueSetsMaxCountExperimental) {
myPreExpandValueSetsMaxCountExperimental = thePreExpandValueSetsMaxCountExperimental;
setPreExpandValueSetsDefaultCountExperimental(Math.min(getPreExpandValueSetsDefaultCountExperimental(), getPreExpandValueSetsMaxCountExperimental()));
}
public enum IndexEnabledEnum {
ENABLED,
DISABLED

59
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
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@ -20,15 +20,25 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.*;
import javax.annotation.PostConstruct;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.ComposeInclude;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.ComposeIncludeConcept;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.ExpansionContains;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.instance.hapi.validation.CachingValidationSupport;
import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
@ -38,20 +48,14 @@ 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.context.FhirContext;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.model.dstu2.resource.ValueSet.*;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import javax.annotation.PostConstruct;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
implements IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>, IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt> {
@ -95,7 +99,11 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequest) {
ValueSet source = loadValueSetForExpansion(theId, theRequest);
return expand(source, theFilter);
}
@Override
public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequest) {
throw new UnsupportedOperationException();
}
@Override
@ -131,6 +139,11 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
return retVal;
}
@Override
public ValueSet expand(ValueSet source, String theFilter, int theOffset, int theCount) {
throw new UnsupportedOperationException();
}
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter) {
if (isBlank(theUri)) {
@ -153,7 +166,11 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
}
return expand(source, theFilter);
}
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
throw new UnsupportedOperationException();
}
@Override

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoValueSet.java
View File

@ -27,15 +27,21 @@ public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> exten
T expand(IIdType theId, String theFilter, RequestDetails theRequestDetails);
T expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails);
T expand(T theSource, String theFilter);
T expand(T theSource, String theFilter, int theOffset, int theCount);
T expandByIdentifier(String theUri, String theFilter);
T expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount);
void purgeCaches();
ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
public class ValidateCodeResult {
class ValidateCodeResult {
private String myDisplay;
private String myMessage;
private boolean myResult;

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
View File

@ -21,20 +21,34 @@ package ca.uhn.fhir.jpa.dao.data;
*/
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
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.List;
import java.util.Optional;
public interface ITermValueSetConceptDao extends JpaRepository<TermValueSetConcept, Long> {
@Query("SELECT COUNT(*) FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("DELETE FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
@Modifying
void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
Optional<TermValueSetConcept> findByValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
@Query("SELECT vsc from TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
Slice<TermValueSetConcept> findByTermValueSetId(Pageable thePage, @Param("pid") Long theValueSetId);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
Optional<TermValueSetConcept> findByTermValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.myCode = :codeval")
List<TermValueSetConcept> findOneByValueSetIdAndCode(@Param("resource_pid") Long theValueSetId, @Param("codeval") String theCode);
@Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
List<TermValueSetConcept> findOneByValueSetIdSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDesignationDao.java
View File

@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.dao.data;
*/
import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
@ -28,8 +30,13 @@ import org.springframework.data.repository.query.Param;
public interface ITermValueSetConceptDesignationDao extends JpaRepository<TermValueSetConceptDesignation, Long> {
@Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myValueSet.myId = :pid")
@Query("SELECT COUNT(vscd) FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
@Modifying
void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
@Query("SELECT vscd FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myId = :pid")
Slice<TermValueSetConceptDesignation> findByTermValueSetConceptId(Pageable thePage, @Param("pid") Long theValueSetConceptId);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
View File

@ -21,9 +21,9 @@ package ca.uhn.fhir.jpa.dao.data;
*/
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetExpansionStatusEnum;
import org.springframework.data.domain.Page;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
@ -44,6 +44,6 @@ public interface ITermValueSetDao extends JpaRepository<TermValueSet, Long> {
Optional<TermValueSet> findByUrl(@Param("url") String theUrl);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myExpansionStatus = :expansion_status")
Page<TermValueSet> findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetExpansionStatusEnum theExpansionStatus);
Slice<TermValueSet> findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetPreExpansionStatusEnum theExpansionStatus);
}

102
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -75,6 +75,12 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
return expand(source, theFilter);
}
@Override
public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
ValueSet source = read(theId, theRequestDetails);
return expand(source, theFilter, theOffset, theCount);
}
private ValueSet doExpand(ValueSet theSource) {
validateIncludes("include", theSource.getCompose().getInclude());
@ -105,7 +111,38 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
ValueSet retVal = outcome.getValueset();
retVal.setStatus(PublicationStatus.ACTIVE);
return retVal;
}
private ValueSet doExpand(ValueSet theSource, int theOffset, int theCount) {
validateIncludes("include", theSource.getCompose().getInclude());
validateIncludes("exclude", theSource.getCompose().getExclude());
/*
* If all of the code systems are supported by the HAPI FHIR terminology service, let's
* use that as it's more efficient.
*/
boolean allSystemsAreSuppportedByTerminologyService = true;
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
if (allSystemsAreSuppportedByTerminologyService) {
return (ValueSet) myTerminologySvc.expandValueSet(theSource, theOffset, theCount);
}
HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
ValueSet retVal = outcome.getValueset();
retVal.setStatus(PublicationStatus.ACTIVE);
return retVal;
}
private void validateIncludes(String name, List<ConceptSetComponent> listToValidate) {
@ -148,20 +185,42 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
// }
//
// return expand(defaultValueSet, theFilter);
}
@Override
public ValueSet expand(ValueSet source, String theFilter) {
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
}
ValueSet retVal = doExpand(source, theOffset, theCount);
return retVal;
}
@Override
public ValueSet expand(ValueSet theSource, String theFilter) {
ValueSet toExpand = new ValueSet();
// for (UriType next : source.getCompose().getInclude()) {
// for (UriType next : theSource.getCompose().getInclude()) {
// ConceptSetComponent include = toExpand.getCompose().addInclude();
// include.setSystem(next.getValue());
// addFilterIfPresent(theFilter, include);
// }
for (ConceptSetComponent next : source.getCompose().getInclude()) {
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
@ -170,7 +229,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
toExpand.getCompose().getExclude().addAll(source.getCompose().getExclude());
toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand);
@ -179,7 +238,32 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
return retVal;
}
@Override
public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
ValueSet toExpand = new ValueSet();
toExpand.setId(theSource.getId());
toExpand.setUrl(theSource.getUrl());
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
if (toExpand.getCompose().isEmpty()) {
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand, theOffset, theCount);
if (isNotBlank(theFilter)) {
applyFilter(retVal.getExpansion().getTotalElement(), retVal.getExpansion().getContains(), theFilter);
}
return retVal;
}
private void applyFilter(IntegerType theTotalElement, List<ValueSetExpansionContainsComponent> theContains, String theFilter) {
@ -246,10 +330,14 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
}
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/TransactionProcessorVersionAdapterDstu3.java
View File

@ -21,19 +21,24 @@ package ca.uhn.fhir.jpa.dao.dstu3;
*/
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.codesystems.IssueType;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.Date;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class TransactionProcessorVersionAdapterDstu3 implements TransactionProcessor.ITransactionProcessorVersionAdapter<Bundle, Bundle.BundleEntryComponent> {
@Override
public void setResponseStatus(Bundle.BundleEntryComponent theBundleEntry, String theStatus) {
@ -106,6 +111,22 @@ public class TransactionProcessorVersionAdapterDstu3 implements TransactionProce
if (value != null) {
retVal = value.toCode();
}
/*
* This is a workaround for the fact that PATCH isn't a valid constant for
* DSTU3 Bundle.entry.request.method (it was added in R4)
*/
if (isBlank(retVal)) {
if (theEntry.getResource() instanceof IBaseBinary) {
String contentType = ((IBaseBinary) theEntry.getResource()).getContentType();
try {
PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(contentType);
retVal = "PATCH";
} catch (InvalidRequestException e) {
// ignore
}
}
}
return retVal;
}

110
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -70,6 +70,12 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
return expand(source, theFilter);
}
@Override
public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
ValueSet source = read(theId, theRequestDetails);
return expand(source, theFilter, theOffset, theCount);
}
private ValueSet doExpand(ValueSet theSource) {
/*
@ -109,6 +115,32 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
// return retVal;
}
private ValueSet doExpand(ValueSet theSource, int theOffset, int theCount) {
boolean allSystemsAreSuppportedByTerminologyService = true;
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
if (allSystemsAreSuppportedByTerminologyService) {
return myTerminologySvc.expandValueSet(theSource, theOffset, theCount);
}
HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
ValueSet retVal = outcome.getValueset();
retVal.setStatus(PublicationStatus.ACTIVE);
return retVal;
}
private void validateIncludes(String name, List<ConceptSetComponent> listToValidate) {
for (ConceptSetComponent nextExclude : listToValidate) {
if (isBlank(nextExclude.getSystem()) && !ElementUtil.isEmpty(nextExclude.getConcept(), nextExclude.getFilter())) {
@ -149,20 +181,42 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
// }
//
// return expand(defaultValueSet, theFilter);
}
@Override
public ValueSet expand(ValueSet source, String theFilter) {
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
}
ValueSet retVal = doExpand(source, theOffset, theCount);
return retVal;
}
@Override
public ValueSet expand(ValueSet theSource, String theFilter) {
ValueSet toExpand = new ValueSet();
// for (UriType next : source.getCompose().getInclude()) {
// for (UriType next : theSource.getCompose().getInclude()) {
// ConceptSetComponent include = toExpand.getCompose().addInclude();
// include.setSystem(next.getValue());
// addFilterIfPresent(theFilter, include);
// }
for (ConceptSetComponent next : source.getCompose().getInclude()) {
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
@ -171,7 +225,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
toExpand.getCompose().getExclude().addAll(source.getCompose().getExclude());
toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand);
@ -180,7 +234,32 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
}
return retVal;
}
@Override
public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
ValueSet toExpand = new ValueSet();
toExpand.setId(theSource.getId());
toExpand.setUrl(theSource.getUrl());
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
if (toExpand.getCompose().isEmpty()) {
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand, theOffset, theCount);
if (isNotBlank(theFilter)) {
applyFilter(retVal.getExpansion().getTotalElement(), retVal.getExpansion().getContains(), theFilter);
}
return retVal;
}
private void applyFilter(IntegerType theTotalElement, List<ValueSetExpansionContainsComponent> theContains, String theFilter) {
@ -207,15 +286,15 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
}
@Override
public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
public ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
List<IIdType> valueSetIds = Collections.emptyList();
boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
boolean haveCoding = theCoding != null && theCoding.isEmpty() == false;
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveCoding = theCoding != null && !theCoding.isEmpty();
boolean haveCode = theCode != null && !theCode.isEmpty();
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
@ -224,7 +303,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam = theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
boolean haveIdentifierParam = theValueSetIdentifier != null && !theValueSetIdentifier.isEmpty();
ValueSet vs = null;
if (theId != null) {
vs = read(theId, theRequestDetails);
@ -241,15 +320,20 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
// String system = toStringOrNull(theSystem);
IContextValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
if (result.isFound()) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
return retVal;
}
}
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
}
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
@ -268,10 +352,10 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
return thePrimitive != null ? thePrimitive.getValue() : null;
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(List<ValueSetExpansionContainsComponent> contains, String theSystem, String theCode,
private ValidateCodeResult validateCodeIsInContains(List<ValueSetExpansionContainsComponent> contains, String theSystem, String theCode,
Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
return result;
}

102
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -70,6 +70,12 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
return expand(source, theFilter);
}
@Override
public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
ValueSet source = read(theId, theRequestDetails);
return expand(source, theFilter, theOffset, theCount);
}
private ValueSet doExpand(ValueSet theSource) {
/*
@ -109,6 +115,38 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
// return retVal;
}
private ValueSet doExpand(ValueSet theSource, int theOffset, int theCount) {
/*
* If all of the code systems are supported by the HAPI FHIR terminology service, let's
* use that as it's more efficient.
*/
boolean allSystemsAreSuppportedByTerminologyService = true;
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
if (allSystemsAreSuppportedByTerminologyService) {
return (ValueSet) myTerminologySvc.expandValueSet(theSource, theOffset, theCount);
}
HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
ValueSet retVal = outcome.getValueset();
retVal.setStatus(PublicationStatus.ACTIVE);
return retVal;
}
private void validateIncludes(String name, List<ConceptSetComponent> listToValidate) {
for (ConceptSetComponent nextExclude : listToValidate) {
if (isBlank(nextExclude.getSystem()) && !ElementUtil.isEmpty(nextExclude.getConcept(), nextExclude.getFilter())) {
@ -149,20 +187,42 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
// }
//
// return expand(defaultValueSet, theFilter);
}
@Override
public ValueSet expand(ValueSet source, String theFilter) {
public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
}
ValueSet retVal = doExpand(source, theOffset, theCount);
return retVal;
}
@Override
public ValueSet expand(ValueSet theSource, String theFilter) {
ValueSet toExpand = new ValueSet();
// for (UriType next : source.getCompose().getInclude()) {
// for (UriType next : theSource.getCompose().getInclude()) {
// ConceptSetComponent include = toExpand.getCompose().addInclude();
// include.setSystem(next.getValue());
// addFilterIfPresent(theFilter, include);
// }
for (ConceptSetComponent next : source.getCompose().getInclude()) {
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
@ -171,7 +231,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
toExpand.getCompose().getExclude().addAll(source.getCompose().getExclude());
toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand);
@ -180,7 +240,32 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
}
return retVal;
}
@Override
public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
ValueSet toExpand = new ValueSet();
toExpand.setId(theSource.getId());
toExpand.setUrl(theSource.getUrl());
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
if (toExpand.getCompose().isEmpty()) {
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand, theOffset, theCount);
if (isNotBlank(theFilter)) {
applyFilter(retVal.getExpansion().getTotalElement(), retVal.getExpansion().getContains(), theFilter);
}
return retVal;
}
private void applyFilter(IntegerType theTotalElement, List<ValueSetExpansionContainsComponent> theContains, String theFilter) {
@ -247,9 +332,14 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
}
if (vs != null) {
ValidateCodeResult result;
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
} else {
ValueSet expansion = doExpand(vs);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
}
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
View File

@ -71,11 +71,11 @@ public class TermValueSet implements Serializable {
@Enumerated(EnumType.STRING)
@Column(name = "EXPANSION_STATUS", nullable = false, length = MAX_EXPANSION_STATUS_LENGTH)
private TermValueSetExpansionStatusEnum myExpansionStatus;
private TermValueSetPreExpansionStatusEnum myExpansionStatus;
public TermValueSet() {
super();
myExpansionStatus = TermValueSetExpansionStatusEnum.NOT_EXPANDED;
myExpansionStatus = TermValueSetPreExpansionStatusEnum.NOT_EXPANDED;
}
public Long getId() {
@ -120,11 +120,11 @@ public class TermValueSet implements Serializable {
return myConcepts;
}
public TermValueSetExpansionStatusEnum getExpansionStatus() {
public TermValueSetPreExpansionStatusEnum getExpansionStatus() {
return myExpansionStatus;
}
public void setExpansionStatus(TermValueSetExpansionStatusEnum theExpansionStatus) {
public void setExpansionStatus(TermValueSetPreExpansionStatusEnum theExpansionStatus) {
myExpansionStatus = theExpansionStatus;
}

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
View File

@ -52,6 +52,16 @@ public class TermValueSetConceptDesignation implements Serializable {
@JoinColumn(name = "VALUESET_CONCEPT_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_CONCEPT_PID"))
private TermValueSetConcept myConcept;
@ManyToOne()
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VSCD_VS_PID"))
private TermValueSet myValueSet;
@Transient
private String myValueSetUrl;
@Transient
private String myValueSetName;
@Column(name = "LANG", nullable = true, length = MAX_LENGTH)
private String myLanguage;
@ -80,6 +90,31 @@ public class TermValueSetConceptDesignation implements Serializable {
return this;
}
public TermValueSet getValueSet() {
return myValueSet;
}
public TermValueSetConceptDesignation 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 getLanguage() {
return myLanguage;
}
@ -167,6 +202,9 @@ public class TermValueSetConceptDesignation implements Serializable {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConcept != null ? ("myConcept - id=" + myConcept.getId()) : ("myConcept=(null)"))
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
.append("myValueSetUrl", this.getValueSetUrl())
.append("myValueSetName", this.getValueSetName())
.append("myLanguage", myLanguage)
.append("myUseSystem", myUseSystem)
.append("myUseCode", myUseCode)

42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetExpansionStatusEnum.java
View File

@ -1,42 +0,0 @@
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%
*/
/**
* This enum is used to indicate the expansion status of a given ValueSet in the terminology tables. In this context,
* an expanded ValueSet has its included concepts stored in the terminology tables as well.
*/
public enum TermValueSetExpansionStatusEnum {
/**
* This status indicates the ValueSet is waiting to be picked up and expanded by a scheduled task.
*/
NOT_EXPANDED,
/**
* This status indicates the ValueSet has been picked up by a scheduled task and is mid-expansion.
*/
EXPANSION_IN_PROGRESS,
/**
* This status indicates the ValueSet has been picked up by a scheduled task and expansion is complete.
*/
EXPANDED
}

71
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnum.java Normal file
View File

@ -0,0 +1,71 @@
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 java.util.Collections;
import java.util.HashMap;
import java.util.Map;
/**
* This enum is used to indicate the pre-expansion status of a given ValueSet in the terminology tables. In this context,
* an expanded ValueSet has its included concepts stored in the terminology tables as well.
*/
public enum TermValueSetPreExpansionStatusEnum {
/**
* Sorting agnostic.
*/
NOT_EXPANDED("notExpanded"),
EXPANSION_IN_PROGRESS("expansionInProgress"),
EXPANDED("expanded"),
FAILED_TO_EXPAND("failedToExpand");
private static Map<String, TermValueSetPreExpansionStatusEnum> ourValues;
private String myCode;
TermValueSetPreExpansionStatusEnum(String theCode) {
myCode = theCode;
}
public String getCode() {
return myCode;
}
public static TermValueSetPreExpansionStatusEnum fromCode(String theCode) {
if (ourValues == null) {
HashMap<String, TermValueSetPreExpansionStatusEnum> values = new HashMap<String, TermValueSetPreExpansionStatusEnum>();
for (TermValueSetPreExpansionStatusEnum next : values()) {
values.put(next.getCode(), next);
}
ourValues = Collections.unmodifiableMap(values);
}
return ourValues.get(theCode);
}
/**
* Convert from Enum ordinal to Enum type.
*
* Usage:
*
* <code>TermValueSetExpansionStatusEnum termValueSetExpansionStatusEnum = TermValueSetExpansionStatusEnum.values[ordinal];</code>
*/
public static final TermValueSetPreExpansionStatusEnum values[] = values();
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java
View File

@ -1,9 +1,10 @@
package ca.uhn.fhir.jpa.provider;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.util.ExpungeOptions;
import ca.uhn.fhir.jpa.util.ExpungeOutcome;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -12,6 +13,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.jboss.logging.MDC;
import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest;
import java.util.Date;
@ -42,6 +44,10 @@ import java.util.TreeSet;
public class BaseJpaProvider {
public static final String REMOTE_ADDR = "req.remoteAddr";
public static final String REMOTE_UA = "req.userAgent";
@Autowired
protected DaoConfig myDaoConfig;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaProvider.class);
private FhirContext myContext;

41
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
View File

@ -35,6 +35,7 @@ import javax.servlet.http.HttpServletRequest;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDstu3<ValueSet> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetDstu3.class);
@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
public ValueSet expand(
@ -46,6 +47,8 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "identifier", min = 0, max = 1) UriType theIdentifier,
@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
RequestDetails theRequestDetails) {
boolean haveId = theId != null && theId.hasIdPart();
@ -55,19 +58,51 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
}
boolean haveIdentifier = url != null && isNotBlank(url.getValue());
boolean haveValueSet = theValueSet != null && theValueSet.isEmpty() == false;
boolean haveValueSet = theValueSet != null && !theValueSet.isEmpty();
if (!haveId && !haveIdentifier && !haveValueSet) {
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request");
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request.");
}
if (moreThanOneTrue(haveId, haveIdentifier, haveValueSet)) {
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
}
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental();
if (theOffset != null && theOffset.hasValue()) {
if (theOffset.getValue() >= 0) {
offset = theOffset.getValue();
} else {
throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
}
}
int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
if (theCount != null && theCount.hasValue()) {
if (theCount.getValue() >= 0) {
count = theCount.getValue();
} else {
throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
}
}
int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
if (count > countMax) {
ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
count = countMax;
}
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter), offset, count);
} else {
return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
}
} else {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
@ -75,7 +110,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
} else {
return dao.expand(theValueSet, toFilterString(theFilter));
}
}
} finally {
endRequest(theServletRequest);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderConceptMapR4.java
View File

@ -62,7 +62,7 @@ public class BaseJpaResourceProviderConceptMapR4 extends JpaResourceProviderR4<C
&& theSourceValueSet.hasValue();
boolean haveSourceCoding = theSourceCoding != null
&& theSourceCoding.hasCode();
boolean haveSourceCodeableConcept= theSourceCodeableConcept != null
boolean haveSourceCodeableConcept = theSourceCodeableConcept != null
&& theSourceCodeableConcept.hasCoding()
&& theSourceCodeableConcept.getCodingFirstRep().hasCode();
boolean haveTargetValueSet = theTargetValueSet != null

41
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderValueSetR4.java
View File

@ -35,6 +35,7 @@ import javax.servlet.http.HttpServletRequest;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<ValueSet> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetR4.class);
@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
public ValueSet expand(
@ -43,23 +44,57 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
@OperationParam(name = "valueSet", min = 0, max = 1) ValueSet theValueSet,
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
RequestDetails theRequestDetails) {
boolean haveId = theId != null && theId.hasIdPart();
boolean haveIdentifier = theUrl != null && isNotBlank(theUrl.getValue());
boolean haveValueSet = theValueSet != null && theValueSet.isEmpty() == false;
boolean haveValueSet = theValueSet != null && !theValueSet.isEmpty();
if (!haveId && !haveIdentifier && !haveValueSet) {
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request");
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request.");
}
if (moreThanOneTrue(haveId, haveIdentifier, haveValueSet)) {
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.");
}
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental();
if (theOffset != null && theOffset.hasValue()) {
if (theOffset.getValue() >= 0) {
offset = theOffset.getValue();
} else {
throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
}
}
int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
if (theCount != null && theCount.hasValue()) {
if (theCount.getValue() >= 0) {
count = theCount.getValue();
} else {
throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
}
}
int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
if (count > countMax) {
ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
count = countMax;
}
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
} else {
return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
}
} else {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
@ -67,7 +102,7 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4<Val
} else {
return dao.expand(theValueSet, toFilterString(theFilter));
}
}
} finally {
endRequest(theServletRequest);
}

41
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java
View File

@ -35,6 +35,7 @@ import javax.servlet.http.HttpServletRequest;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<ValueSet> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetR5.class);
@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
public ValueSet expand(
@ -43,23 +44,57 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
@OperationParam(name = "valueSet", min = 0, max = 1) ValueSet theValueSet,
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
@OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
@OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
RequestDetails theRequestDetails) {
boolean haveId = theId != null && theId.hasIdPart();
boolean haveIdentifier = theUrl != null && isNotBlank(theUrl.getValue());
boolean haveValueSet = theValueSet != null && theValueSet.isEmpty() == false;
boolean haveValueSet = theValueSet != null && !theValueSet.isEmpty();
if (!haveId && !haveIdentifier && !haveValueSet) {
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request");
throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request.");
}
if (moreThanOneTrue(haveId, haveIdentifier, haveValueSet)) {
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.");
}
int offset = myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental();
if (theOffset != null && theOffset.hasValue()) {
if (theOffset.getValue() >= 0) {
offset = theOffset.getValue();
} else {
throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
}
}
int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
if (theCount != null && theCount.hasValue()) {
if (theCount.getValue() >= 0) {
count = theCount.getValue();
} else {
throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
}
}
int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
if (count > countMax) {
ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
count = countMax;
}
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
if (myDaoConfig.isPreExpandValueSetsExperimental()) {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
} else {
return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
}
} else {
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
@ -67,7 +102,7 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5<Val
} else {
return dao.expand(theValueSet, toFilterString(theFilter));
}
}
} finally {
endRequest(theServletRequest);
}

453
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
@ -351,7 +352,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (optionalExistingTermConceptMapById.isPresent()) {
TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapById.get();
ourLog.info("Deleting existing TermConceptMap {} and its children...", existingTermConceptMap.getId());
ourLog.info("Deleting existing TermConceptMap[{}] and its children...", existingTermConceptMap.getId());
for (TermConceptMapGroup group : existingTermConceptMap.getConceptMapGroups()) {
for (TermConceptMapGroupElement element : group.getConceptMapGroupElements()) {
@ -368,7 +369,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
ourLog.info("Done deleting existing TermConceptMap {} and its children.", existingTermConceptMap.getId());
ourLog.info("Done deleting existing TermConceptMap[{}] and its children.", existingTermConceptMap.getId());
ourLog.info("Flushing...");
myConceptMapGroupElementTargetDao.flush();
@ -392,11 +393,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (optionalExistingTermValueSetById.isPresent()) {
TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();
ourLog.info("Deleting existing TermValueSet {} and its children...", existingTermValueSet.getId());
ourLog.info("Deleting existing TermValueSet[{}] and its children...", existingTermValueSet.getId());
myValueSetConceptDesignationDao.deleteByTermValueSetId(existingTermValueSet.getId());
myValueSetConceptDao.deleteByTermValueSetId(existingTermValueSet.getId());
myValueSetDao.deleteByTermValueSetId(existingTermValueSet.getId());
ourLog.info("Done deleting existing TermValueSet {} and its children.", existingTermValueSet.getId());
ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
ourLog.info("Flushing...");
myValueSetConceptDesignationDao.flush();
@ -420,7 +421,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
count = 0;
while (true) {
Slice<T> link = theLoader.get();
if (link.hasContent() == false) {
if (!link.hasContent()) {
break;
}
@ -478,29 +479,222 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return valueSet;
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public ValueSet expandValueSet(ValueSet theValueSetToExpand, int theOffset, int theCount) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSetToExpand, "ValueSet to expand can not be null");
Optional<TermValueSet> optionalTermValueSet;
if (theValueSetToExpand.hasId()) {
optionalTermValueSet = myValueSetDao.findByResourcePid(theValueSetToExpand.getIdElement().getIdPartAsLong());
} else if (theValueSetToExpand.hasUrl()) {
optionalTermValueSet = myValueSetDao.findByUrl(theValueSetToExpand.getUrl());
} else {
throw new UnprocessableEntityException("ValueSet to be expanded must provide either ValueSet.id or ValueSet.url");
}
if (!optionalTermValueSet.isPresent()) {
throw new InvalidRequestException("ValueSet is not present in terminology tables: " + theValueSetToExpand.getUrl());
}
TermValueSet termValueSet = optionalTermValueSet.get();
validatePreExpansionStatusOfValueSetOrThrowException(termValueSet.getExpansionStatus());
ValueSet.ValueSetExpansionComponent expansionComponent = new ValueSet.ValueSetExpansionComponent();
expansionComponent.setIdentifier(UUID.randomUUID().toString());
expansionComponent.setTimestamp(new Date());
populateExpansionComponent(expansionComponent, termValueSet, theOffset, theCount);
ValueSet valueSet = new ValueSet();
valueSet.setStatus(Enumerations.PublicationStatus.ACTIVE);
valueSet.setCompose(theValueSetToExpand.getCompose());
valueSet.setExpansion(expansionComponent);
return valueSet;
}
private void validatePreExpansionStatusOfValueSetOrThrowException(TermValueSetPreExpansionStatusEnum thePreExpansionStatus) {
if (TermValueSetPreExpansionStatusEnum.EXPANDED != thePreExpansionStatus) {
String statusMsg = myContext.getLocalizer().getMessage(
TermValueSetPreExpansionStatusEnum.class,
thePreExpansionStatus.getCode());
String msg = myContext.getLocalizer().getMessage(
BaseHapiTerminologySvcImpl.class,
"valueSetNotReadyForExpand",
thePreExpansionStatus.name(),
statusMsg);
throw new UnprocessableEntityException(msg);
}
}
private void populateExpansionComponent(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
int total = myValueSetConceptDao.countByTermValueSetId(theTermValueSet.getId());
theExpansionComponent.setTotal(total);
theExpansionComponent.setOffset(theOffset);
theExpansionComponent.addParameter().setName("offset").setValue(new IntegerType(theOffset));
theExpansionComponent.addParameter().setName("count").setValue(new IntegerType(theCount));
if (theCount == 0 || total == 0) {
return;
}
expandConcepts(theExpansionComponent, theTermValueSet, theOffset, theCount);
}
private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
int conceptsExpanded = 0;
for (int i = theOffset; i < (theOffset + theCount); i++) {
final int page = i;
Supplier<Slice<TermValueSetConcept>> loader = () -> myValueSetConceptDao.findByTermValueSetId(PageRequest.of(page, 1), theTermValueSet.getId());
Slice<TermValueSetConcept> slice = loader.get();
if (!slice.hasContent()) {
break;
}
for (TermValueSetConcept concept : slice.getContent()) {
ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
containsComponent.setSystem(concept.getSystem());
containsComponent.setCode(concept.getCode());
containsComponent.setDisplay(concept.getDisplay());
// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
expandDesignations(theTermValueSet, concept, containsComponent);
if (++conceptsExpanded % 250 == 0) {
ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
}
}
if (!slice.hasNext()) {
break;
}
}
if (conceptsExpanded > 0) {
ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
}
}
private void expandDesignations(TermValueSet theValueSet, TermValueSetConcept theConcept, ValueSet.ValueSetExpansionContainsComponent theContainsComponent) {
int designationsExpanded = 0;
int index = 0;
while (true) {
final int page = index++;
Supplier<Slice<TermValueSetConceptDesignation>> loader = () -> myValueSetConceptDesignationDao.findByTermValueSetConceptId(PageRequest.of(page, 1000), theConcept.getId());
Slice<TermValueSetConceptDesignation> slice = loader.get();
if (!slice.hasContent()) {
break;
}
for (TermValueSetConceptDesignation designation : slice.getContent()) {
ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
designationComponent.setLanguage(designation.getLanguage());
designationComponent.setUse(new Coding(
designation.getUseSystem(),
designation.getUseCode(),
designation.getUseDisplay()));
designationComponent.setValue(designation.getValue());
if (++designationsExpanded % 250 == 0) {
ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
}
}
if (!slice.hasNext()) {
break;
}
}
if (designationsExpanded > 0) {
ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
}
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
expandValueSet(theValueSetToExpand, theValueSetCodeAccumulator, new AtomicInteger(0));
}
@SuppressWarnings("ConstantConditions")
private void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator, AtomicInteger theCodeCounter) {
Set<String> addedCodes = new HashSet<>();
StopWatch sw = new StopWatch();
String valueSetInfo = getValueSetInfo(theValueSetToExpand);
ourLog.info("Working with {}", valueSetInfo);
// Handle includes
ourLog.debug("Handling includes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getInclude()) {
for (int i = 0; ; i++) {
int finalI = i;
Boolean shouldContinue = myTxTemplate.execute(t -> {
boolean add = true;
expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter);
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter, finalI);
});
if (!shouldContinue) {
break;
}
}
}
// Handle excludes
ourLog.debug("Handling excludes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getExclude()) {
for (ValueSet.ConceptSetComponent exclude : theValueSetToExpand.getCompose().getExclude()) {
for (int i = 0; ; i++) {
int finalI = i;
Boolean shouldContinue = myTxTemplate.execute(t -> {
boolean add = false;
expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter);
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, exclude, add, theCodeCounter, finalI);
});
if (!shouldContinue) {
break;
}
}
}
ourLog.info("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
}
private String getValueSetInfo(ValueSet theValueSet) {
StringBuilder sb = new StringBuilder();
boolean isIdentified = false;
sb
.append("ValueSet:");
if (theValueSet.hasId()) {
isIdentified = true;
sb
.append(" ValueSet.id[")
.append(theValueSet.getId())
.append("]");
}
if (theValueSet.hasUrl()) {
isIdentified = true;
sb
.append(" ValueSet.url[")
.append(theValueSet.getUrl())
.append("]");
}
if (theValueSet.hasIdentifier()) {
isIdentified = true;
sb
.append(" ValueSet.identifier[")
.append(theValueSet.getIdentifierFirstRep().getSystem())
.append("|")
.append(theValueSet.getIdentifierFirstRep().getValue())
.append("]");
}
if (!isIdentified) {
sb.append(" None of ValueSet.id, ValueSet.url, and ValueSet.identifier are provided.");
}
return sb.toString();
}
protected List<VersionIndependentConcept> expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.r4.model.ValueSet theValueSetToExpandR4) {
org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = expandValueSet(theValueSetToExpandR4).getExpansion();
@ -513,16 +707,21 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return retVal;
}
private void expandValueSetHandleIncludeOrExclude(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, boolean theAdd, AtomicInteger theCodeCounter) {
/**
* @return Returns true if there are potentially more results to process.
*/
private Boolean expandValueSetHandleIncludeOrExclude(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex) {
String system = theInclude.getSystem();
boolean hasSystem = isNotBlank(system);
boolean hasValueSet = theInclude.getValueSet().size() > 0;
if (hasSystem) {
ourLog.info("Starting {} expansion around code system: {}", (theAdd ? "inclusion" : "exclusion"), system);
ourLog.info("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
if (cs != null) {
TermCodeSystemVersion csv = cs.getCurrentVersion();
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
@ -532,7 +731,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
if (myFulltextSearchSvc == null) {
expandWithoutHibernateSearch(theValueSetCodeAccumulator, theAddedCodes, theInclude, system, theAdd, theCodeCounter);
return;
return false;
}
/*
@ -592,10 +791,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
String value = nextFilter.getValue();
if (value.endsWith("$")) {
value = value.substring(0, value.length() - 1);
} else if (value.endsWith(".*") == false) {
} else if (!value.endsWith(".*")) {
value = value + ".*";
}
if (value.startsWith("^") == false && value.startsWith(".*") == false) {
if (!value.startsWith("^") && !value.startsWith(".*")) {
value = ".*" + value;
} else if (value.startsWith("^")) {
value = value.substring(1);
@ -646,24 +845,42 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
int maxResult = 50000;
jpaQuery.setMaxResults(maxResult);
/*
* DM 2019-08-21 - Processing slows after any ValueSets with many codes explicitly identified. This might
* be due to the dark arts that is memory management. Will monitor but not do anything about this right now.
*/
BooleanQuery.setMaxClauseCount(10000);
StopWatch sw = new StopWatch();
AtomicInteger count = new AtomicInteger(0);
for (Object next : jpaQuery.getResultList()) {
int maxResultsPerBatch = 10000;
jpaQuery.setMaxResults(maxResultsPerBatch);
jpaQuery.setFirstResult(theQueryIndex * maxResultsPerBatch);
ourLog.info("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
StopWatch swForBatch = new StopWatch();
AtomicInteger countForBatch = new AtomicInteger(0);
List resultList = jpaQuery.getResultList();
int resultsInBatch = resultList.size();
int firstResult = jpaQuery.getFirstResult();
for (Object next : resultList) {
count.incrementAndGet();
countForBatch.incrementAndGet();
TermConcept concept = (TermConcept) next;
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, concept, theAdd, theCodeCounter);
}
ourLog.info("Batch expansion for {} with starting index of {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), firstResult, countForBatch, swForBatch.getMillis());
if (maxResult == count.get()) {
throw new InternalErrorException("Expansion fragment produced too many (>= " + maxResult + ") results");
}
if (resultsInBatch < maxResultsPerBatch) {
ourLog.info("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
return false;
} else {
return true;
}
} else {
// No codesystem matching the URL found in the database
@ -673,7 +890,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
throw new InvalidRequestException("Unknown code system: " + system);
}
if (theInclude.getConcept().isEmpty() == false) {
if (!theInclude.getConcept().isEmpty()) {
for (ValueSet.ConceptReferenceComponent next : theInclude.getConcept()) {
String nextCode = next.getCode();
if (isNoneBlank(system, nextCode) && !theAddedCodes.contains(system + "|" + nextCode)) {
@ -693,10 +910,12 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
addConceptsToList(theValueSetCodeAccumulator, theAddedCodes, system, concept, theAdd);
}
return false;
}
} else if (hasValueSet) {
for (CanonicalType nextValueSet : theInclude.getValueSet()) {
ourLog.info("Starting {} expansion around ValueSet URI: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
ourLog.info("Starting {} expansion around ValueSet: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
List<VersionIndependentConcept> expanded = expandValueSet(nextValueSet.getValueAsString());
for (VersionIndependentConcept nextConcept : expanded) {
@ -715,9 +934,14 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
return false;
} else {
throw new InvalidRequestException("ValueSet contains " + (theAdd ? "include" : "exclude") + " criteria with no system defined");
}
}
private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
@ -736,6 +960,48 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
protected ValidateCodeResult validateCodeIsInPreExpandedValueSet(
ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
Long valueSetId = theValueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong();
List<TermValueSetConcept> concepts = new ArrayList<>();
if (isNotBlank(theCode)) {
if (isNotBlank(theSystem)) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theSystem, theCode);
} else {
concepts = myValueSetConceptDao.findOneByValueSetIdAndCode(valueSetId, theCode);
}
} else if (theCoding != null) {
if (theCoding.hasSystem() && theCoding.hasCode()) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theCoding.getSystem(), theCoding.getCode());
}
} else if (theCodeableConcept != null){
for (Coding coding : theCodeableConcept.getCoding()) {
if (coding.hasSystem() && coding.hasCode()) {
concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, coding.getSystem(), coding.getCode());
if (!concepts.isEmpty()) {
break;
}
}
}
}
for (TermValueSetConcept concept : concepts) {
if (isNotBlank(theDisplay) && theDisplay.equals(concept.getDisplay())) {
return new ValidateCodeResult(true, "Validation succeeded", concept.getDisplay());
}
}
if (!concepts.isEmpty()) {
return new ValidateCodeResult(true, "Validation succeeded", concepts.get(0).getDisplay());
}
return null;
}
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild();
@ -781,7 +1047,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_MANDATORY);
return txTemplate.execute(t->{
return txTemplate.execute(t -> {
TermCodeSystemVersion csv = findCurrentCodeSystemVersionForSystem(theCodeSystem);
return myConceptDao.findByCodeSystemAndCode(csv, theCode);
});
@ -798,7 +1064,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
StopWatch stopwatch = new StopWatch();
Optional<TermConcept> concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
if (concept.isPresent() == false) {
if (!concept.isPresent()) {
return Collections.emptySet();
}
@ -829,7 +1095,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
Stopwatch stopwatch = Stopwatch.createStarted();
Optional<TermConcept> concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
if (concept.isPresent() == false) {
if (!concept.isPresent()) {
return Collections.emptySet();
}
@ -1014,8 +1280,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (concepts.hasContent() == false) {
Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(PageRequest.of(0, maxResult));
if (!concepts.hasContent()) {
if (myChildToParentPidCache != null) {
ourLog.info("Clearing parent concept cache");
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
@ -1122,28 +1388,28 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Transactional(propagation = Propagation.NEVER)
@Override
public synchronized void saveDeferred() {
if (!myProcessDeferred) {
if (isProcessDeferredPaused()) {
return;
} else if (myDeferredConcepts.isEmpty() && myConceptLinksToSaveLater.isEmpty()) {
} else if (isNoDeferredConceptsAndNoConceptLinksToSaveLater()) {
processReindexing();
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
if (!myDeferredConcepts.isEmpty() || !myConceptLinksToSaveLater.isEmpty()) {
if (isDeferredConceptsOrConceptLinksToSaveLater()) {
tt.execute(t -> {
processDeferredConcepts();
return null;
});
}
if (myDeferredValueSets.size() > 0) {
if (isDeferredValueSets()) {
tt.execute(t -> {
processDeferredValueSets();
return null;
});
}
if (myDeferredConceptMaps.size() > 0) {
if (isDeferredConceptMaps()) {
tt.execute(t -> {
processDeferredConceptMaps();
return null;
@ -1152,6 +1418,42 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
private boolean isProcessDeferredPaused() {
return !myProcessDeferred;
}
private boolean isNoDeferredConceptsAndNoConceptLinksToSaveLater() {
return isNoDeferredConcepts() && isNoConceptLinksToSaveLater();
}
private boolean isDeferredConceptsOrConceptLinksToSaveLater() {
return isDeferredConcepts() || isConceptLinksToSaveLater();
}
private boolean isDeferredConcepts() {
return !myDeferredConcepts.isEmpty();
}
private boolean isNoDeferredConcepts() {
return myDeferredConcepts.isEmpty();
}
private boolean isConceptLinksToSaveLater() {
return !myConceptLinksToSaveLater.isEmpty();
}
private boolean isNoConceptLinksToSaveLater() {
return myConceptLinksToSaveLater.isEmpty();
}
private boolean isDeferredValueSets() {
return !myDeferredValueSets.isEmpty();
}
private boolean isDeferredConceptMaps() {
return !myDeferredConceptMaps.isEmpty();
}
@Override
public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
myApplicationContext = theApplicationContext;
@ -1498,31 +1800,86 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Scheduled(fixedDelay = 600000) // 10 minutes.
@Override
public synchronized void preExpandValueSetToTerminologyTables() {
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
if (isNotSafeToPreExpandValueSets()) {
ourLog.info("Skipping scheduled pre-expansion of ValueSets while deferred entities are being loaded.");
return;
}
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
while (true) {
TermValueSet valueSetToExpand = txTemplate.execute(t -> {
Optional<TermValueSet> optionalTermValueSet = getNextTermValueSetNotExpanded();
if (optionalTermValueSet.isPresent()) {
if (!optionalTermValueSet.isPresent()) {
return null;
}
TermValueSet termValueSet = optionalTermValueSet.get();
termValueSet.setExpansionStatus(TermValueSetExpansionStatusEnum.EXPANSION_IN_PROGRESS);
myValueSetDao.saveAndFlush(termValueSet);
ValueSet valueSet = getValueSetFromResourceTable(termValueSet.getResource());
expandValueSet(valueSet, new ValueSetConceptAccumulator(termValueSet, myValueSetConceptDao, myValueSetConceptDesignationDao));
termValueSet.setExpansionStatus(TermValueSetExpansionStatusEnum.EXPANDED);
myValueSetDao.saveAndFlush(termValueSet);
}
}
termValueSet.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
return myValueSetDao.saveAndFlush(termValueSet);
});
if (valueSetToExpand == null) {
return;
}
// We have a ValueSet to pre-expand.
try {
ValueSet valueSet = txTemplate.execute(t -> {
TermValueSet refreshedValueSetToExpand = myValueSetDao.findById(valueSetToExpand.getId()).get();
return getValueSetFromResourceTable(refreshedValueSetToExpand.getResource());
});
expandValueSet(valueSet, new ValueSetConceptAccumulator(valueSetToExpand, myValueSetConceptDao, myValueSetConceptDesignationDao));
// We are done with this ValueSet.
txTemplate.execute(t -> {
valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANDED);
myValueSetDao.saveAndFlush(valueSetToExpand);
return null;
});
} catch (Exception e) {
ourLog.error("Failed to pre-expand ValueSet: " + e.getMessage(), e);
txTemplate.execute(t -> {
valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.FAILED_TO_EXPAND);
myValueSetDao.saveAndFlush(valueSetToExpand);
return null;
});
}
}
}
private boolean isNotSafeToPreExpandValueSets() {
return !isSafeToPreExpandValueSets();
}
private boolean isSafeToPreExpandValueSets() {
if (isProcessDeferredPaused()) {
return false;
}
if (isDeferredConcepts()) {
return false;
}
if (isConceptLinksToSaveLater()) {
return false;
}
if (isDeferredValueSets()) {
return false;
}
if (isDeferredConceptMaps()) {
return false;
}
return true;
}
protected abstract ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable);
private Optional<TermValueSet> getNextTermValueSetNotExpanded() {
Optional<TermValueSet> retVal = Optional.empty();
Page<TermValueSet> page = myValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetExpansionStatusEnum.NOT_EXPANDED);
Slice<TermValueSet> page = myValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);
if (!page.getContent().isEmpty()) {
retVal = Optional.of(page.getContent().get(0));

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
View File

@ -20,13 +20,13 @@ package ca.uhn.fhir.jpa.term;
* #L%
*/
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.*;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
@ -92,6 +92,11 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
throw new UnsupportedOperationException();
}
@Override
public IBaseResource expandValueSet(IBaseResource theValueSetToExpand, int theOffset, int theCount) {
throw new UnsupportedOperationException();
}
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
throw new UnsupportedOperationException();
@ -144,4 +149,8 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
return retVal;
}
@Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
throw new UnsupportedOperationException();
}
}

40
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -15,6 +16,7 @@ import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -29,7 +31,8 @@ import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
@ -177,6 +180,20 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
}
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
ValueSet valueSetToExpand = (ValueSet) theInput;
try {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = VersionConvertor_30_40.convertValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(valueSetToExpandR4, theOffset, theCount);
return VersionConvertor_30_40.convertValueSet(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
@ -345,5 +362,26 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
return null;
}
@Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValueSet valueSet = (ValueSet) theValueSet;
Coding coding = (Coding) theCoding;
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
try {
org.hl7.fhir.r4.model.ValueSet valueSetR4;
valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
for (Coding nestedCoding : codeableConcept.getCoding()) {
codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
}
return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
View File

@ -2,18 +2,17 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.terminologies.ValueSetExpander;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -137,6 +136,12 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
return super.expandValueSet(valueSetToExpand);
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
ValueSet valueSetToExpand = (ValueSet) theInput;
return super.expandValueSet(valueSetToExpand, theOffset, theCount);
}
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
@ -272,4 +277,11 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
return super.lookupCode(theContext, theSystem, theCode);
}
@Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValueSet valueSet = (ValueSet) theValueSet;
Coding coding = (Coding) theCoding;
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
return super.validateCodeIsInPreExpandedValueSet(valueSet, theSystem, theCode, theDisplay, coding, codeableConcept);
}
}

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
View File

@ -2,14 +2,16 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
@ -143,6 +145,13 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(valueSetToExpand, theOffset, theCount);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
}
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSetToExpand);
@ -280,4 +289,19 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
return super.lookupCode(theContext, theSystem, theCode);
}
@Override
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
org.hl7.fhir.r4.model.ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSet);
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
for (Coding nestedCoding : codeableConcept.getCoding()) {
codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
}
return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
}
}

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
View File

@ -1,16 +1,12 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseCoding;
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.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.r4.model.*;
import javax.annotation.Nullable;
import java.util.List;
@ -44,6 +40,8 @@ public interface IHapiTerminologySvc {
ValueSet expandValueSet(ValueSet theValueSetToExpand);
ValueSet expandValueSet(ValueSet theValueSetToExpand, int theOffset, int theCount);
void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
/**
@ -51,6 +49,11 @@ public interface IHapiTerminologySvc {
*/
IBaseResource expandValueSet(IBaseResource theValueSetToExpand);
/**
* Version independent
*/
IBaseResource expandValueSet(IBaseResource theValueSetToExpand, int theOffset, int theCount);
void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
List<VersionIndependentConcept> expandValueSet(String theValueSet);
@ -109,4 +112,9 @@ public interface IHapiTerminologySvc {
AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theDelta);
void preExpandValueSetToTerminologyTables();
/**
* Version independent
*/
ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
}

207
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
View File

@ -32,7 +32,9 @@ import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.*;
@ -41,6 +43,7 @@ import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -67,26 +70,10 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
public static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
public static final String IMGTHLA_HLA_XML = "hla.xml";
public static final String LOINC_ANSWERLIST_FILE = "AnswerList.csv";
public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink.csv";
public static final String LOINC_DOCUMENT_ONTOLOGY_FILE = "DocumentOntology.csv";
public static final String LOINC_UPLOAD_PROPERTIES_FILE = "loincupload.properties";
public static final String LOINC_FILE = "LoincTable/Loinc.csv";
public static final String LOINC_HIERARCHY_FILE = "MultiAxialHierarchy.csv";
public static final String LOINC_PART_FILE = "Part.csv";
public static final String LOINC_PART_LINK_FILE = "LoincPartLink.csv";
public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping.csv";
public static final String LOINC_RSNA_PLAYBOOK_FILE = "LoincRsnaRadiologyPlaybook.csv";
public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE = "Top2000CommonLabResultsUs.csv";
public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE = "Top2000CommonLabResultsSi.csv";
public static final String LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE = "LoincUniversalLabOrdersValueSet.csv";
public static final String LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV = "LoincIeeeMedicalDeviceCodeMappingTable.csv";
public static final String LOINC_IMAGING_DOCUMENT_CODES_FILE = "ImagingDocumentCodes.csv";
public static final String LOINC_GROUP_FILE = "Group.csv";
public static final String LOINC_GROUP_TERMS_FILE = "GroupLoincTerms.csv";
public static final String LOINC_PARENT_GROUP_FILE = "ParentGroup.csv";
public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
@ -219,35 +206,61 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
@Override
public UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
List<String> loincUploadPropertiesFragment = Arrays.asList(
LOINC_UPLOAD_PROPERTIES_FILE.getCode()
);
descriptors.verifyMandatoryFilesExist(loincUploadPropertiesFragment);
Properties uploadProperties = getProperties(descriptors, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
List<String> mandatoryFilenameFragments = Arrays.asList(
LOINC_FILE,
LOINC_HIERARCHY_FILE,
LOINC_UPLOAD_PROPERTIES_FILE,
LOINC_ANSWERLIST_FILE,
LOINC_ANSWERLIST_LINK_FILE,
LOINC_PART_FILE,
LOINC_PART_LINK_FILE,
LOINC_PART_RELATED_CODE_MAPPING_FILE,
LOINC_DOCUMENT_ONTOLOGY_FILE,
LOINC_RSNA_PLAYBOOK_FILE,
LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE,
LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE,
LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE,
LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV,
LOINC_IMAGING_DOCUMENT_CODES_FILE
uploadProperties.getProperty(LOINC_ANSWERLIST_FILE.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_ANSWERLIST_LINK_FILE.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_DOCUMENT_ONTOLOGY_FILE.getCode(), LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_HIERARCHY_FILE.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE.getCode(), LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode())
);
descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
List<String> optionalFilenameFragments = Arrays.asList(
uploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()),
uploadProperties.getProperty(LOINC_PARENT_GROUP_FILE.getCode(), LOINC_PARENT_GROUP_FILE_DEFAULT.getCode())
);
descriptors.verifyOptionalFilesExist(optionalFilenameFragments);
ourLog.info("Beginning LOINC processing");
return processLoincFiles(descriptors, theRequestDetails);
return processLoincFiles(descriptors, theRequestDetails, uploadProperties);
}
}
@NotNull
private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
Properties retVal = new Properties();
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
if (next.getFilename().endsWith(thePropertiesFile)) {
try {
try (InputStream inputStream = next.getInputStream()) {
retVal.load(inputStream);
}
} catch (IOException e) {
throw new InternalErrorException("Failed to read " + thePropertiesFile, e);
}
}
}
return retVal;
}
@Override
public UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
@ -444,7 +457,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
// return new UploadStatistics(conceptCount, target);
}
UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails, Properties theUploadProperties) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = new HashMap<>();
final List<ValueSet> valueSets = new ArrayList<>();
@ -469,93 +482,82 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
IRecordHandler handler;
Properties uploadProperties = new Properties();
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
if (next.getFilename().endsWith("loincupload.properties")) {
try {
try (InputStream inputStream = next.getInputStream()) {
uploadProperties.load(inputStream);
}
} catch (IOException e) {
throw new InternalErrorException("Failed to read loincupload.properties", e);
}
}
}
// Part file
// Part
handler = new LoincPartHandler(codeSystemVersion, code2concept);
iterateOverZipFile(theDescriptors, LOINC_PART_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
Map<PartTypeAndPartName, String> partTypeAndPartNameToPartNumber = ((LoincPartHandler) handler).getPartTypeAndPartNameToPartNumber();
// Loinc Codes
// LOINC codes
handler = new LoincHandler(codeSystemVersion, code2concept, propertyNamesToTypes, partTypeAndPartNameToPartNumber);
iterateOverZipFile(theDescriptors, LOINC_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Loinc Hierarchy
// LOINC hierarchy
handler = new LoincHierarchyHandler(codeSystemVersion, code2concept);
iterateOverZipFile(theDescriptors, LOINC_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_HIERARCHY_FILE.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Answer lists (ValueSets of potential answers/values for loinc "questions")
handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Answer lists (ValueSets of potential answers/values for LOINC "questions")
handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_ANSWERLIST_FILE.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Answer list links (connects loinc observation codes to answerlist codes)
// Answer list links (connects LOINC observation codes to answer list codes)
handler = new LoincAnswerListLinkHandler(code2concept, valueSets);
iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_ANSWERLIST_LINK_FILE.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// RSNA Playbook file
// RSNA playbook
// Note that this should come before the "Part Related Code Mapping"
// file because there are some duplicate mappings between these
// two files, and the RSNA Playbook file has more metadata
handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_RSNA_PLAYBOOK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Part link file
// Part link
handler = new LoincPartLinkHandler(codeSystemVersion, code2concept);
iterateOverZipFile(theDescriptors, LOINC_PART_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Part related code mapping
handler = new LoincPartRelatedCodeMappingHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_PART_RELATED_CODE_MAPPING_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
handler = new LoincPartRelatedCodeMappingHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Document Ontology File
handler = new LoincDocumentOntologyHandler(code2concept, propertyNamesToTypes, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_DOCUMENT_ONTOLOGY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Document ontology
handler = new LoincDocumentOntologyHandler(code2concept, propertyNamesToTypes, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_DOCUMENT_ONTOLOGY_FILE.getCode(), LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Top 2000 Codes - US
handler = new LoincTop2000LabResultsUsHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Top 2000 codes - US
handler = new LoincTop2000LabResultsUsHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Top 2000 Codes - SI
handler = new LoincTop2000LabResultsSiHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Top 2000 codes - SI
handler = new LoincTop2000LabResultsSiHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Universal Lab Order ValueSet
handler = new LoincUniversalOrderSetHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Universal lab order ValueSet
handler = new LoincUniversalOrderSetHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE.getCode(), LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// IEEE Medical Device Codes
handler = new LoincIeeeMedicalDeviceCodeHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV, handler, ',', QuoteMode.NON_NUMERIC, false);
// IEEE medical device codes
handler = new LoincIeeeMedicalDeviceCodeHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Imaging Document Codes
handler = new LoincImagingDocumentCodeHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_IMAGING_DOCUMENT_CODES_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Imaging document codes
handler = new LoincImagingDocumentCodeHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Group File
handler = new LoincGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Group
handler = new LoincGroupFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Group Terms File
handler = new LoincGroupTermsFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_GROUP_TERMS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Group terms
handler = new LoincGroupTermsFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Parent Group File
handler = new LoincParentGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
iterateOverZipFile(theDescriptors, LOINC_PARENT_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Parent group
handler = new LoincParentGroupFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PARENT_GROUP_FILE.getCode(), LOINC_PARENT_GROUP_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
IOUtils.closeQuietly(theDescriptors);
valueSets.add(getValueSetLoincAll());
for (Entry<String, TermConcept> next : code2concept.entrySet()) {
TermConcept nextConcept = next.getValue();
if (nextConcept.getParents().isEmpty()) {
@ -573,6 +575,23 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
return new UploadStatistics(conceptCount, target);
}
private ValueSet getValueSetLoincAll() {
ValueSet retVal = new ValueSet();
retVal.setId("loinc-all");
retVal.setUrl("http://loinc.org/vs");
retVal.setVersion("1.0.0");
retVal.setName("All LOINC codes");
retVal.setStatus(Enumerations.PublicationStatus.ACTIVE);
retVal.setDate(new Date());
retVal.setPublisher("Regenstrief Institute, Inc.");
retVal.setDescription("A value set that includes all LOINC codes");
retVal.setCopyright("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/");
retVal.getCompose().addInclude().setSystem(IHapiTerminologyLoaderSvc.LOINC_URI);
return retVal;
}
private UploadStatistics processSnomedCtFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> id2concept = new HashMap<>();
@ -732,7 +751,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
private void verifyOptionalFilesExist(List<String> theExpectedFilenameFragments) {
List<String> notFound = notFound(theExpectedFilenameFragments);
if (!notFound.isEmpty()) {
ourLog.warn("Could not find the following optional file: " + notFound);
ourLog.warn("Could not find the following optional files: " + notFound);
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -71,7 +71,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
// Get existing entity so it can be deleted.
Optional<TermValueSetConcept> optionalConcept = myValueSetConceptDao.findByValueSetIdSystemAndCode(myTermValueSet.getId(), theSystem, theCode);
Optional<TermValueSetConcept> optionalConcept = myValueSetConceptDao.findByTermValueSetIdSystemAndCode(myTermValueSet.getId(), theSystem, theCode);
if (optionalConcept.isPresent()) {
TermValueSetConcept concept = optionalConcept.get();
@ -103,9 +103,8 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
myValueSetConceptDao.save(concept);
if (myConceptsSaved++ % 250 == 0) {
if (myConceptsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSet.getUrl());
myValueSetConceptDao.flush();
}
return concept;
@ -116,6 +115,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
TermValueSetConceptDesignation designation = new TermValueSetConceptDesignation();
designation.setConcept(theConcept);
designation.setValueSet(myTermValueSet);
designation.setLanguage(theDesignation.getLanguage());
if (isNoneBlank(theDesignation.getUseSystem(), theDesignation.getUseCode())) {
designation.setUseSystem(theDesignation.getUseSystem());
@ -127,9 +127,8 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
designation.setValue(theDesignation.getValue());
myValueSetConceptDesignationDao.save(designation);
if (myDesignationsSaved++ % 250 == 0) {
ourLog.info("Have pre-expanded {} designations in ValueSet[{}]", myDesignationsSaved, myTermValueSet.getUrl());
myValueSetConceptDesignationDao.flush();
if (myDesignationsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
ourLog.info("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSet.getUrl());
}
return designation;

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java
View File

@ -22,15 +22,23 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.model.api.annotation.Block;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.Collection;
@Block()
public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.ValueSetExpansionComponent implements IValueSetConceptAccumulator {
private final int myMaxResults = 50000;
private int myConceptsCount;
public ValueSetExpansionComponentWithConceptAccumulator() {
myConceptsCount = 0;
}
@Override
public void includeConcept(String theSystem, String theCode, String theDisplay) {
incrementConceptsCount();
ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
contains.setSystem(theSystem);
contains.setCode(theCode);
@ -39,6 +47,7 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
@Override
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
incrementConceptsCount();
ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
contains.setSystem(theSystem);
contains.setCode(theCode);
@ -65,4 +74,10 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
theSystem.equals(t.getSystem()) &&
theCode.equals(t.getCode()));
}
private void incrementConceptsCount() {
if (++myConceptsCount > myMaxResults) {
throw new InternalErrorException("Expansion produced too many (>= " + myMaxResults + ") results");
}
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
View File

@ -34,6 +34,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.*;
public abstract class BaseLoincHandler implements IRecordHandler {
@ -114,7 +115,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
conceptMap.setId(theMapping.getConceptMapId());
conceptMap.setUrl(theMapping.getConceptMapUri());
conceptMap.setName(theMapping.getConceptMapName());
conceptMap.setVersion(myUploadProperties.getProperty("conceptmap.version"));
conceptMap.setVersion(myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()));
conceptMap.setPublisher(REGENSTRIEF_INSTITUTE_INC);
conceptMap.addContact()
.setName(REGENSTRIEF_INSTITUTE_INC)

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
View File

@ -31,7 +31,9 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import static org.apache.commons.lang3.StringUtils.*;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincAnswerListHandler extends BaseLoincHandler {
@ -72,7 +74,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
}
// Answer list ValueSet
ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, "answerlist.version");
ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, LOINC_ANSWERLIST_VERSION.getCode());
if (vs.getIdentifier().isEmpty()) {
vs.addIdentifier()
.setSystem("urn:ietf:rfc:3986")

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.term.loinc;
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.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
@ -52,6 +53,18 @@ public class LoincHierarchyHandler implements IRecordHandler {
TermConcept child = getOrCreate(childCode, childCodeText);
parent.addChild(child, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
parent.addPropertyCoding(
"child",
IHapiTerminologyLoaderSvc.LOINC_URI,
child.getCode(),
child.getDisplay());
child.addPropertyCoding(
"parent",
IHapiTerminologyLoaderSvc.LOINC_URI,
parent.getCode(),
parent.getDisplay());
}
}

142
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java Normal file
View File

@ -0,0 +1,142 @@
package ca.uhn.fhir.jpa.term.loinc;
/*
* #%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 java.util.Collections;
import java.util.HashMap;
import java.util.Map;
/**
* This enum is used to facilitate configurable filenames when uploading LOINC.
*/
public enum LoincUploadPropertiesEnum {
/**
* Sorting agnostic.
*/
LOINC_UPLOAD_PROPERTIES_FILE("loincupload.properties"),
/*
* MANDATORY
*/
// Answer lists (ValueSets of potential answers/values for LOINC "questions")
LOINC_ANSWERLIST_FILE("loinc.answerlist.file"),
LOINC_ANSWERLIST_FILE_DEFAULT("AnswerList.csv"),
// Answer list links (connects LOINC observation codes to answer list codes)
LOINC_ANSWERLIST_LINK_FILE("loinc.answerlist.link.file"),
LOINC_ANSWERLIST_LINK_FILE_DEFAULT("LoincAnswerListLink.csv"),
// Document ontology
LOINC_DOCUMENT_ONTOLOGY_FILE("loinc.document.ontology.file"),
LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT("DocumentOntology.csv"),
// LOINC codes
LOINC_FILE("loinc.file"),
LOINC_FILE_DEFAULT("LoincTable/Loinc.csv"),
// LOINC hierarchy
LOINC_HIERARCHY_FILE("loinc.hierarchy.file"),
LOINC_HIERARCHY_FILE_DEFAULT("MultiAxialHierarchy.csv"),
// IEEE medical device codes
LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE("loinc.ieee.medical.device.code.mapping.table.file"),
LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT("LoincIeeeMedicalDeviceCodeMappingTable.csv"),
// Imaging document codes
LOINC_IMAGING_DOCUMENT_CODES_FILE("loinc.imaging.document.codes.file"),
LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT("ImagingDocumentCodes.csv"),
// Part
LOINC_PART_FILE("loinc.part.file"),
LOINC_PART_FILE_DEFAULT("Part.csv"),
// Part link
LOINC_PART_LINK_FILE("loinc.part.link.file"),
LOINC_PART_LINK_FILE_DEFAULT("LoincPartLink.csv"),
// Part related code mapping
LOINC_PART_RELATED_CODE_MAPPING_FILE("loinc.part.related.code.mapping.file"),
LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT("PartRelatedCodeMapping.csv"),
// RSNA playbook
LOINC_RSNA_PLAYBOOK_FILE("loinc.rsna.playbook.file"),
LOINC_RSNA_PLAYBOOK_FILE_DEFAULT("LoincRsnaRadiologyPlaybook.csv"),
// Top 2000 codes - SI
LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE("loinc.top2000.common.lab.results.si.file"),
LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT("Top2000CommonLabResultsSi.csv"),
// Top 2000 codes - US
LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE("loinc.top2000.common.lab.results.us.file"),
LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT("Top2000CommonLabResultsUs.csv"),
// Universal lab order ValueSet
LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE("loinc.universal.lab.order.valueset.file"),
LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT("LoincUniversalLabOrdersValueSet.csv"),
/*
* OPTIONAL
*/
// This is the version identifier for the answer list file
LOINC_ANSWERLIST_VERSION("loinc.answerlist.version"),
// This is the version identifier for uploaded ConceptMap resources
LOINC_CONCEPTMAP_VERSION("loinc.conceptmap.version"),
// Group
LOINC_GROUP_FILE("loinc.group.file"),
LOINC_GROUP_FILE_DEFAULT("Group.csv"),
// Group terms
LOINC_GROUP_TERMS_FILE("loinc.group.terms.file"),
LOINC_GROUP_TERMS_FILE_DEFAULT("GroupLoincTerms.csv"),
// Parent group
LOINC_PARENT_GROUP_FILE("loinc.parent.group.file"),
LOINC_PARENT_GROUP_FILE_DEFAULT("ParentGroup.csv");
private static Map<String, LoincUploadPropertiesEnum> ourValues;
private String myCode;
LoincUploadPropertiesEnum(String theCode) {
myCode = theCode;
}
public String getCode() {
return myCode;
}
public static LoincUploadPropertiesEnum fromCode(String theCode) {
if (ourValues == null) {
HashMap<String, LoincUploadPropertiesEnum> values = new HashMap<String, LoincUploadPropertiesEnum>();
for (LoincUploadPropertiesEnum next : values()) {
values.put(next.getCode(), next);
}
ourValues = Collections.unmodifiableMap(values);
}
return ourValues.get(theCode);
}
/**
* Convert from Enum ordinal to Enum type.
*
* Usage:
*
* <code>LoincUploadPropertiesEnum loincUploadPropertiesEnum = LoincUploadPropertiesEnum.values[ordinal];</code>
*/
public static final LoincUploadPropertiesEnum values[] = values();
}

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnumTest.java Normal file
View File

@ -0,0 +1,21 @@
package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.i18n.HapiLocalizer;
import org.junit.Test;
import static org.junit.Assert.fail;
public class TermValueSetPreExpansionStatusEnumTest {
@Test
public void testHaveDescriptions() {
HapiLocalizer localizer = new HapiLocalizer();
for (TermValueSetPreExpansionStatusEnum next : TermValueSetPreExpansionStatusEnum.values()) {
String key = "ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum." + next.getCode();
String msg = localizer.getMessage(key);
if (msg.equals(HapiLocalizer.UNKNOWN_I18N_KEY_MESSAGE)) {
fail("No value for key: " + key);
}
}
}
}

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -397,7 +397,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandInvalidParams() throws IOException {
//@formatter:off
try {
ourClient
.operation()
@ -407,11 +406,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request", e.getMessage());
assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request.", e.getMessage());
}
//@formatter:on
//@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-dstu3.xml");
ourClient
@ -425,9 +422,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
//@formatter:on
//@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-dstu3.xml");
ourClient
@ -441,8 +436,30 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
//@formatter:on
try {
ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "offset", new IntegerType(-1))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: offset parameter for $expand operation must be >= 0 when specified. offset: -1", e.getMessage());
}
try {
ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "count", new IntegerType(-1))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: count parameter for $expand operation must be >= 0 when specified. count: -1", e.getMessage());
}
}
@Test

52
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java
View File

@ -4,11 +4,19 @@ import static org.hamcrest.Matchers.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.concurrent.TimeUnit;
import ca.uhn.fhir.rest.api.Constants;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
@ -180,6 +188,50 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
}
@Test
public void testPatchUsingJsonPatch_Transaction() throws Exception {
String methodName = "testPatchUsingJsonPatch_Transaction";
IIdType pid1;
{
Patient patient = new Patient();
patient.setActive(true);
patient.addIdentifier().setSystem("urn:system").setValue("0");
patient.addName().setFamily(methodName).addGiven("Joe");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
String patchString = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
Binary patch = new Binary();
patch.setContentType(ca.uhn.fhir.rest.api.Constants.CT_JSON_PATCH);
patch.setContent(patchString.getBytes(Charsets.UTF_8));
// Note that we don't set the type
Bundle input = new Bundle();
input.setType(Bundle.BundleType.TRANSACTION);
input.addEntry()
.setFullUrl(pid1.getValue())
.setResource(patch)
.getRequest().setUrl(pid1.getValue());
HttpPost post = new HttpPost(ourServerBase);
String encodedRequest = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
ourLog.info("Requet:\n{}", encodedRequest);
post.setEntity(new StringEntity(encodedRequest, ContentType.parse(ca.uhn.fhir.rest.api.Constants.CT_FHIR_JSON_NEW+ Constants.CHARSET_UTF8_CTSUFFIX)));
try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseString);
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(responseString, containsString("\"resourceType\":\"Bundle\""));
}
Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
assertEquals("2", newPt.getIdElement().getVersionIdPart());
assertEquals(false, newPt.getActive());
}
@Test
public void testTransactionWithGetHardLimitLargeSynchronous() {
List<String> ids = create20Patients();

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
View File

@ -1,8 +1,6 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
@ -20,6 +18,7 @@ import java.util.List;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.*;
@ -37,24 +36,24 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
addFile(zos, "loincupload.properties");
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_DOCUMENT_ONTOLOGY_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_RSNA_PLAYBOOK_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
addFile(zos, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
addFile(zos, LOINC_PART_FILE_DEFAULT.getCode());
addFile(zos, LOINC_FILE_DEFAULT.getCode());
addFile(zos, LOINC_HIERARCHY_FILE_DEFAULT.getCode());
addFile(zos, LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
addFile(zos, LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
addFile(zos, LOINC_GROUP_FILE_DEFAULT.getCode());
addFile(zos, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
addFile(zos, LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
addFile(zos, LOINC_PART_LINK_FILE_DEFAULT.getCode());
addFile(zos, LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
addFile(zos, LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
addFile(zos, LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
addFile(zos, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
addFile(zos, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
addFile(zos, LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
addFile(zos, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
addFile(zos, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
zos.close();

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -264,7 +264,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandInvalidParams() throws IOException {
//@formatter:off
try {
ourClient
.operation()
@ -274,11 +273,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request", e.getMessage());
assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request.", e.getMessage());
}
//@formatter:on
//@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/r4/extensional-case-r4.xml");
ourClient
@ -292,9 +289,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
//@formatter:on
//@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/r4/extensional-case.xml");
ourClient
@ -308,8 +303,30 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
//@formatter:on
try {
ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "offset", new IntegerType(-1))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: offset parameter for $expand operation must be >= 0 when specified. offset: -1", e.getMessage());
}
try {
ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withParameter(Parameters.class, "count", new IntegerType(-1))
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: count parameter for $expand operation must be >= 0 when specified. count: -1", e.getMessage());
}
}
@Test

165
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@ -19,8 +20,11 @@ import org.mockito.Captor;
import org.mockito.Mock;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
@ -252,6 +256,22 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
assertEquals("42176-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
assertEquals("1,3 beta glucan [Mass/volume] in Serum", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
// All LOINC codes
assertTrue(valueSets.containsKey("loinc-all"));
vs = valueSets.get("loinc-all");
assertEquals("http://loinc.org/vs", vs.getUrl());
assertEquals("1.0.0", vs.getVersion());
assertEquals("All LOINC codes", vs.getName());
assertEquals(Enumerations.PublicationStatus.ACTIVE, vs.getStatus());
assertTrue(vs.hasDate());
assertEquals("Regenstrief Institute, Inc.", vs.getPublisher());
assertEquals("A value set that includes all LOINC codes", vs.getDescription());
assertEquals("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/", vs.getCopyright());
assertTrue(vs.hasCompose());
assertTrue(vs.getCompose().hasInclude());
assertEquals(1, vs.getCompose().getInclude().size());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
// IEEE Medical Device Codes
conceptMap = conceptMaps.get(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_ID);
ourLog.debug(FhirContext.forR4().newXmlParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
@ -322,8 +342,8 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
@Test
public void testLoadLoincMissingMandatoryFiles() throws IOException {
myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE);
myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
myFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
myFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
// Actually do the load
try {
@ -336,26 +356,129 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
}
}
public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_FILE, TerminologyLoaderSvcImpl.LOINC_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_FILE, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_DOCUMENT_ONTOLOGY_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_RSNA_PLAYBOOK_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
theFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
theFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_FILE_DEFAULT.getCode(), LOINC_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_HIERARCHY_FILE_DEFAULT.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_FILE_DEFAULT.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_PART_FILE_DEFAULT.getCode(), LOINC_PART_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_DEFAULT.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
theFiles.addFileZip("/loinc/", LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
}
@Test
public void testLoadLoincMultiaxialHierarchySupport() throws Exception {
addLoincMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
Map<String, ValueSet> valueSets = extractValueSets();
Map<String, ConceptMap> conceptMaps = extractConceptMaps();
ConceptMap conceptMap;
TermConcept code;
ValueSet vs;
ConceptMap.ConceptMapGroupComponent group;
// Normal loinc code
code = concepts.get("10013-1");
assertEquals("10013-1", code.getCode());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, code.getCodingProperties("PROPERTY").get(0).getSystem());
assertEquals("LP6802-5", code.getCodingProperties("PROPERTY").get(0).getCode());
assertEquals("Elpot", code.getCodingProperties("PROPERTY").get(0).getDisplay());
assertEquals("EKG.MEAS", code.getStringProperty("CLASS"));
assertEquals("R' wave amplitude in lead I", code.getDisplay());
// Codes with parent and child properties
code = concepts.get("LP31755-9");
assertEquals("LP31755-9", code.getCode());
List<TermConceptProperty> properties = new ArrayList<>(code.getProperties());
assertEquals(1, properties.size());
assertEquals("child", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals("LP14559-6", properties.get(0).getValue());
assertEquals("Microorganism", properties.get(0).getDisplay());
assertEquals(0, code.getParents().size());
assertEquals(1, code.getChildren().size());
TermConcept childCode = code.getChildren().get(0).getChild();
assertEquals("LP14559-6", childCode.getCode());
assertEquals("Microorganism", childCode.getDisplay());
properties = new ArrayList<>(childCode.getProperties());
assertEquals(2, properties.size());
assertEquals("parent", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals(code.getCode(), properties.get(0).getValue());
assertEquals(code.getDisplay(), properties.get(0).getDisplay());
assertEquals("child", properties.get(1).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
assertEquals("LP98185-9", properties.get(1).getValue());
assertEquals("Bacteria", properties.get(1).getDisplay());
assertEquals(1, childCode.getParents().size());
assertEquals(1, childCode.getChildren().size());
assertEquals(code.getCode(), new ArrayList<>(childCode.getParents()).get(0).getParent().getCode());
TermConcept nestedChildCode = childCode.getChildren().get(0).getChild();
assertEquals("LP98185-9", nestedChildCode.getCode());
assertEquals("Bacteria", nestedChildCode.getDisplay());
properties = new ArrayList<>(nestedChildCode.getProperties());
assertEquals(2, properties.size());
assertEquals("parent", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals(childCode.getCode(), properties.get(0).getValue());
assertEquals(childCode.getDisplay(), properties.get(0).getDisplay());
assertEquals("child", properties.get(1).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
assertEquals("LP14082-9", properties.get(1).getValue());
assertEquals("Bacteria", properties.get(1).getDisplay());
assertEquals(1, nestedChildCode.getParents().size());
assertEquals(1, nestedChildCode.getChildren().size());
assertEquals(childCode.getCode(), new ArrayList<>(nestedChildCode.getParents()).get(0).getParent().getCode());
TermConcept doublyNestedChildCode = nestedChildCode.getChildren().get(0).getChild();
assertEquals("LP14082-9", doublyNestedChildCode.getCode());
assertEquals("Bacteria", doublyNestedChildCode.getDisplay());
properties = new ArrayList<>(doublyNestedChildCode.getProperties());
assertEquals(4, properties.size());
assertEquals("parent", properties.get(0).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
assertEquals(nestedChildCode.getCode(), properties.get(0).getValue());
assertEquals(nestedChildCode.getDisplay(), properties.get(0).getDisplay());
assertEquals("child", properties.get(1).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
assertEquals("LP52258-8", properties.get(1).getValue());
assertEquals("Bacteria | Body Fluid", properties.get(1).getDisplay());
assertEquals("child", properties.get(2).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(2).getCodeSystem());
assertEquals("LP52260-4", properties.get(2).getValue());
assertEquals("Bacteria | Cerebral spinal fluid", properties.get(2).getDisplay());
assertEquals("child", properties.get(3).getKey());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(3).getCodeSystem());
assertEquals("LP52960-9", properties.get(3).getValue());
assertEquals("Bacteria | Cervix", properties.get(3).getDisplay());
assertEquals(1, doublyNestedChildCode.getParents().size());
assertEquals(3, doublyNestedChildCode.getChildren().size());
assertEquals(nestedChildCode.getCode(), new ArrayList<>(doublyNestedChildCode.getParents()).get(0).getParent().getCode());
assertEquals("LP52258-8", doublyNestedChildCode.getChildren().get(0).getChild().getCode());
assertEquals("LP52260-4", doublyNestedChildCode.getChildren().get(1).getChild().getCode());
assertEquals("LP52960-9", doublyNestedChildCode.getChildren().get(2).getChild().getCode());
}
@AfterClass

405
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -13,7 +14,7 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport.CodeValidationResult;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
@ -562,6 +563,40 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
}
@Test
public void testDeleteValueSet() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
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));
myTermSvc.preExpandValueSetToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
Long termValueSetId = myTermValueSetDao.findByResourcePid(valueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong()).get().getId();
assertEquals(3, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
assertEquals(24, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myTermValueSetConceptDesignationDao.deleteByTermValueSetId(termValueSetId);
assertEquals(0, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
myTermValueSetConceptDao.deleteByTermValueSetId(termValueSetId);
assertEquals(0, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
myTermValueSetDao.deleteByTermValueSetId(termValueSetId);
assertFalse(myTermValueSetDao.findByResourcePid(valueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong()).isPresent());
}
});
}
@Test
public void testDuplicateCodeSystemUrls() throws Exception {
loadAndPersistCodeSystem();
@ -595,6 +630,294 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
loadAndPersistValueSet();
}
@Test
public void testExpandTermValueSetAndChildren() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
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));
myTermSvc.preExpandValueSetToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
assertEquals(1000, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getContains().size());
ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8450-9", containsComponent.getCode());
assertEquals("Systolic blood pressure--expiration", containsComponent.getDisplay());
assertEquals(2, containsComponent.getDesignation().size());
ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
assertEquals("nl", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systolische bloeddruk - expiratie", designationComponent.getValue());
designationComponent = containsComponent.getDesignation().get(1);
assertEquals("sv", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systoliskt blodtryck - utgång", designationComponent.getValue());
containsComponent = expandedValueSet.getExpansion().getContains().get(1);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("11378-7", containsComponent.getCode());
assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
// ...
containsComponent = expandedValueSet.getExpansion().getContains().get(22);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8491-3", containsComponent.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
assertEquals(1, containsComponent.getDesignation().size());
designationComponent = containsComponent.getDesignation().get(0);
assertEquals("nl", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
containsComponent = expandedValueSet.getExpansion().getContains().get(23);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8492-1", containsComponent.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
}
@Test
public void testExpandTermValueSetAndChildrenWithCount() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
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));
myTermSvc.preExpandValueSetToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 23);
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
assertEquals(23, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(23, expandedValueSet.getExpansion().getContains().size());
ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8450-9", containsComponent.getCode());
assertEquals("Systolic blood pressure--expiration", containsComponent.getDisplay());
assertEquals(2, containsComponent.getDesignation().size());
ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
assertEquals("nl", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systolische bloeddruk - expiratie", designationComponent.getValue());
designationComponent = containsComponent.getDesignation().get(1);
assertEquals("sv", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systoliskt blodtryck - utgång", designationComponent.getValue());
containsComponent = expandedValueSet.getExpansion().getContains().get(1);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("11378-7", containsComponent.getCode());
assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
// ...
containsComponent = expandedValueSet.getExpansion().getContains().get(22);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8491-3", containsComponent.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
assertEquals(1, containsComponent.getDesignation().size());
designationComponent = containsComponent.getDesignation().get(0);
assertEquals("nl", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
}
@Test
public void testExpandTermValueSetAndChildrenWithCountOfZero() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
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));
myTermSvc.preExpandValueSetToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 0);
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
assertEquals(0, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertFalse(expandedValueSet.getExpansion().hasContains());
}
@Test
public void testExpandTermValueSetAndChildrenWithOffset() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
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));
myTermSvc.preExpandValueSetToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(1, expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(1, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
assertEquals(1000, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(codeSystem.getConcept().size() - expandedValueSet.getExpansion().getOffset(), expandedValueSet.getExpansion().getContains().size());
ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("11378-7", containsComponent.getCode());
assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
containsComponent = expandedValueSet.getExpansion().getContains().get(1);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8493-9", containsComponent.getCode());
assertEquals("Systolic blood pressure 10 hour minimum", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
// ...
containsComponent = expandedValueSet.getExpansion().getContains().get(21);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8491-3", containsComponent.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
assertEquals(1, containsComponent.getDesignation().size());
ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
assertEquals("nl", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
containsComponent = expandedValueSet.getExpansion().getContains().get(22);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8492-1", containsComponent.getCode());
assertEquals("Systolic blood pressure 8 hour minimum", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
}
@Test
public void testExpandTermValueSetAndChildrenWithOffsetAndCount() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
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));
myTermSvc.preExpandValueSetToTerminologyTables();
ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, 22);
ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
assertEquals(1, expandedValueSet.getExpansion().getOffset());
assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
assertEquals(1, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
assertEquals(22, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
assertEquals(22, expandedValueSet.getExpansion().getContains().size());
ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("11378-7", containsComponent.getCode());
assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
containsComponent = expandedValueSet.getExpansion().getContains().get(1);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8493-9", containsComponent.getCode());
assertEquals("Systolic blood pressure 10 hour minimum", containsComponent.getDisplay());
assertFalse(containsComponent.hasDesignation());
// ...
containsComponent = expandedValueSet.getExpansion().getContains().get(21);
assertEquals("http://acme.org", containsComponent.getSystem());
assertEquals("8491-3", containsComponent.getCode());
assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
assertEquals(1, containsComponent.getDesignation().size());
ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
assertEquals("nl", designationComponent.getLanguage());
assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
assertEquals("900000000000013009", designationComponent.getUse().getCode());
assertEquals("Synonym", designationComponent.getUse().getDisplay());
assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
}
@Test
public void testExpandValueSetWithValueSetCodeAccumulator() {
createCodeSystem();
@ -607,17 +930,6 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
}
@Test
public void testValidateCode() {
createCodeSystem();
IValidationSupport.CodeValidationResult validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ParentWithNoChildrenA", null);
assertEquals(true, validation.isOk());
validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ZZZZZZZ", null);
assertEquals(false, validation.isOk());
}
@Test
public void testStoreTermCodeSystemAndChildren() throws Exception {
loadAndPersistCodeSystemWithDesignations();
@ -985,7 +1297,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(0, termValueSet.getConcepts().size());
assertEquals(TermValueSetExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
assertEquals(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
});
myTermSvc.preExpandValueSetToTerminologyTables();
@ -1003,7 +1315,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(codeSystem.getConcept().size(), termValueSet.getConcepts().size());
assertEquals(TermValueSetExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
ourLog.info("Code:\n" + concept.toString());
@ -1083,7 +1395,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(0, termValueSet.getConcepts().size());
assertEquals(TermValueSetExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
assertEquals(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
});
myTermSvc.preExpandValueSetToTerminologyTables();
@ -1101,7 +1413,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(codeSystem.getConcept().size() - 2, termValueSet.getConcepts().size());
assertEquals(TermValueSetExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
ourLog.info("Code:\n" + concept.toString());
@ -2291,6 +2603,67 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
@Test
public void testValidateCode() {
createCodeSystem();
CodeValidationResult validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ParentWithNoChildrenA", null);
assertEquals(true, validation.isOk());
validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ZZZZZZZ", null);
assertEquals(false, validation.isOk());
}
@Test
public void testValidateCodeIsInPreExpandedValueSet() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSetWithDesignations();
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));
myTermSvc.preExpandValueSetToTerminologyTables();
ValidateCodeResult result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, null, null, null, null);
assertNull(result);
result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, "BOGUS", null, null, null);
assertNull(result);
result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, "11378-7", null, null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, "11378-7", "Systolic blood pressure at First encounter", null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, "http://acme.org", "11378-7", null, null, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
Coding coding = new Coding("http://acme.org", "11378-7", "Systolic blood pressure at First encounter");
result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, null, null, coding, null);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding(new Coding("BOGUS", "BOGUS", "BOGUS"));
codeableConcept.addCoding(coding);
result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, null, null, null, codeableConcept);
assertTrue(result.isResult());
assertEquals("Validation succeeded", result.getMessage());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

94
hapi-fhir-jpaserver-base/src/test/resources/loinc/loincupload.properties
View File

@ -1,7 +1,95 @@
#################
### MANDATORY ###
#################
# This is the version identifier for the AnswerList file
answerlist.version=Beta.1
# Answer lists (ValueSets of potential answers/values for LOINC "questions")
## Default value if key not provided: AnswerList.csv
## File must be present
loinc.answerlist.file=AnswerList.csv
# Answer list links (connects LOINC observation codes to answer list codes)
## Default value if key not provided: LoincAnswerListLink.csv
## File must be present
loinc.answerlist.link.file=LoincAnswerListLink.csv
# Document ontology
## Default value if key not provided: DocumentOntology.csv
## File must be present
loinc.document.ontology.file=DocumentOntology.csv
# LOINC codes
## Default value if key not provided: LoincTable/Loinc.csv
## File must be present
loinc.file=LoincTable/Loinc.csv
# LOINC hierarchy
## Default value if key not provided: MultiAxialHierarchy.csv
## File must be present
loinc.hierarchy.file=MultiAxialHierarchy.csv
# IEEE medical device codes
## Default value if key not provided: LoincIeeeMedicalDeviceCodeMappingTable.csv
## File must be present
loinc.ieee.medical.device.code.mapping.table.file=LoincIeeeMedicalDeviceCodeMappingTable.csv
# Imaging document codes
## Default value if key not provided: ImagingDocumentCodes.csv
## File must be present
loinc.imaging.document.codes.file=ImagingDocumentCodes.csv
# Part
## Default value if key not provided: Part.csv
## File must be present
loinc.part.file=Part.csv
# Part link
## Default value if key not provided: LoincPartLink.csv
## File must be present
loinc.part.link.file=LoincPartLink.csv
# Part related code mapping
## Default value if key not provided: PartRelatedCodeMapping.csv
## File must be present
loinc.part.related.code.mapping.file=PartRelatedCodeMapping.csv
# RSNA playbook
## Default value if key not provided: LoincRsnaRadiologyPlaybook.csv
## File must be present
loinc.rsna.playbook.file=LoincRsnaRadiologyPlaybook.csv
# Top 2000 codes - SI
## Default value if key not provided: Top2000CommonLabResultsSi.csv
## File must be present
loinc.top2000.common.lab.results.si.file=Top2000CommonLabResultsSi.csv
# Top 2000 codes - US
## Default value if key not provided: Top2000CommonLabResultsUs.csv
## File must be present
loinc.top2000.common.lab.results.us.file=Top2000CommonLabResultsUs.csv
# Universal lab order ValueSet
## Default value if key not provided: LoincUniversalLabOrdersValueSet.csv
## File must be present
loinc.universal.lab.order.valueset.file=LoincUniversalLabOrdersValueSet.csv
################
### OPTIONAL ###
################
# This is the version identifier for the answer list file
## Key may be omitted
loinc.answerlist.version=Beta.1
# This is the version identifier for uploaded ConceptMap resources
conceptmap.version=Beta.1
## Key may be omitted
loinc.conceptmap.version=Beta.1
# Group
## Default value if key not provided: Group.csv
## File may be omitted
loinc.group.file=Group.csv
# Group terms
## Default value if key not provided: GroupLoincTerms.csv
## File may be omitted
loinc.group.terms.file=GroupLoincTerms.csv
# Parent group
## Default value if key not provided: ParentGroup.csv
## File may be omitted
loinc.parent.group.file=ParentGroup.csv

8
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -79,6 +79,14 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
resVerProv.addIndex("IDX_RESVERPROV_SOURCEURI").unique(false).withColumns("SOURCE_URI");
resVerProv.addIndex("IDX_RESVERPROV_REQUESTID").unique(false).withColumns("REQUEST_ID");
// TermValueSetConceptDesignation
version.startSectionWithMessage("Processing table: TRM_VALUESET_C_DESIGNATION");
Builder.BuilderWithTableName termValueSetConceptDesignationTable = version.onTable("TRM_VALUESET_C_DESIGNATION");
termValueSetConceptDesignationTable.addColumn("VALUESET_PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
termValueSetConceptDesignationTable
.addForeignKey("FK_TRM_VSCD_VS_PID")
.toColumn("VALUESET_PID")
.references("TRM_VALUESET", "PID");
// Drop HFJ_SEARCH_RESULT foreign keys
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_RES");
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_SEARCH");

5
hapi-fhir-structures-dstu2/pom.xml
View File

@ -216,6 +216,11 @@
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>

4
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java
View File

@ -802,7 +802,6 @@ public class XmlParserDstu2Test {
//@formatter:off
assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
"<meta>",
"<meta>",
"<profile value=\"http://foo/Profile1\"/>",
"<profile value=\"http://foo/Profile2\"/>",
@ -817,7 +816,6 @@ public class XmlParserDstu2Test {
"<display value=\"label2\"/>",
"</tag>",
"</meta>",
"</meta>",
"<name>",
"<family value=\"FAMILY\"/>",
"</name>",
@ -856,7 +854,6 @@ public class XmlParserDstu2Test {
//@formatter:off
assertThat(enc, stringContainsInOrder("<Patient xmlns=\"http://hl7.org/fhir\">",
"<meta>",
"<meta>",
"<tag>",
"<system value=\"scheme1\"/>",
@ -869,7 +866,6 @@ public class XmlParserDstu2Test {
"<display value=\"label2\"/>",
"</tag>",
"</meta>",
"</meta>",
"<name>",
"<family value=\"FAMILY\"/>",
"</name>",

5
hapi-fhir-test-utilities/pom.xml
View File

@ -46,11 +46,6 @@
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
</dependency>
</dependencies>
<build>

16
pom.xml
View File

@ -1062,21 +1062,7 @@
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<version>3.1.6</version>
<exclusions>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>java-hamcrest</artifactId>
</exclusion>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
</exclusion>
<exclusion>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-library</artifactId>
</exclusion>
</exclusions>
<version>4.0.0-rc1</version>
</dependency>
<dependency>
<groupId>org.codehaus.plexus</groupId>

20
src/changes/changes.xml
View File

@ -77,6 +77,26 @@
Two foreign keys have been dropped from the HFJ_SEARCH_RESULT table used by the FHIR search query cache. These
constraints did not add value and caused unneccessary contention when used under high load.
</action>
<action type="add">
It is now possible to submit a PATCH request as a part of a FHIR transaction in DSTU3 (previously this
was only supported in R4+). This is not officially part of the DSTU3 spec, but it can now be performed by
leaving the Bundle.entry.request.method blank in DSTU3 transactions and setting the request payload
as a Binary resource containing a valid patch.
</action>
<action type="change" issue="1366">
The HAPI FHIR CLI server now uses H2 as its database platform instead of Derby.
Note that this means that data in any existing installations will need to be
re-uploaded to the new database platform.
</action>
<action type="add" issue="1443">
LOINC concepts now include multiaxial hierarchical properties (e.g. <![CDATA[<code>parent</code>]]> and
<![CDATA[<code>child</code>]]>, which identify parent and child concepts.
</action>
<action type="add" issue="1445">
When loading LOINC terminology, a new ValueSet is automatically created with a single include element that
identifies the LOINC CodeSystem in <![CDATA[<code>ValueSet.compose.include.system</code>]]>. This ValueSet
includes all LOINC codes.
</action>
</release>
<release version="4.0.0" date="2019-08-14" description="Igloo">
<action type="add">