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Merge pull request #1432 from jamesagnew/1366-expand-operation-needs-to-be-optimized-for-large-valuesets-4 

Resolve "1366 expand operation needs to be optimized for large valuesets 4"
This commit is contained in:
Diederik Muylwyk 2019-08-26 09:55:05 -04:00 committed by GitHub
parent 7d008b2ee0 3f14a7a68b
commit 5071c62cb9
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
36 changed files with 1556 additions and 247 deletions
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2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java
View File

@ -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));
}
}

36
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -17,8 +17,8 @@ ca.uhn.fhir.rest.client.impl.GenericClient.noPagingLinkFoundInBundle=Can not per
ca.uhn.fhir.rest.client.impl.GenericClient.noVersionIdForVread=No version specified in URL for 'vread' operation: {0}
ca.uhn.fhir.rest.client.impl.GenericClient.incompleteUriForRead=The given URI is not an absolute URL and is not usable for this operation: {0}
ca.uhn.fhir.rest.client.impl.GenericClient.cannotDetermineResourceTypeFromUri=Unable to determine the resource type from the given URI: {0}
ca.uhn.fhir.rest.client.impl.RestfulClientFactory.failedToRetrieveConformance=Failed to retrieve the server metadata statement during client initialization. URL used was {0}
ca.uhn.fhir.rest.client.impl.RestfulClientFactory.wrongVersionInConformance=The server at base URL "{0}" returned a conformance statement indicating that it supports FHIR version "{1}" which corresponds to {2}, but this client is configured to use {3} (via the FhirContext).
ca.uhn.fhir.rest.client.impl.RestfulClientFactory.failedToRetrieveConformance=Failed to retrieve the server metadata statement during client initialization. URL used was {0}
ca.uhn.fhir.rest.client.impl.RestfulClientFactory.wrongVersionInConformance=The server at base URL "{0}" returned a conformance statement indicating that it supports FHIR version "{1}" which corresponds to {2}, but this client is configured to use {3} (via the FhirContext).
ca.uhn.fhir.rest.server.interceptor.auth.RuleImplOp.invalidRequestBundleTypeForTransaction=Invalid request Bundle.type value for transaction: {0}
@ -46,14 +46,14 @@ ca.uhn.fhir.rest.param.BaseParam.chainNotSupported=Invalid search parameter "{0}
ca.uhn.fhir.rest.server.method.ResourceParameter.invalidContentTypeInRequest=Incorrect Content-Type header value of "{0}" was provided in the request. A FHIR Content-Type is required for "{1}" operation
ca.uhn.fhir.rest.server.method.ResourceParameter.noContentTypeInRequest=No Content-Type header was provided in the request. This is required for "{0}" operation
ca.uhn.fhir.rest.server.method.ResourceParameter.failedToParseRequest=Failed to parse request body as {0} resource. Error was: {1}
ca.uhn.fhir.rest.server.method.ResourceParameter.failedToParseRequest=Failed to parse request body as {0} resource. Error was: {1}
ca.uhn.fhir.parser.ParserState.wrongResourceTypeFound=Incorrect resource type found, expected "{0}" but found "{1}"
ca.uhn.fhir.rest.server.RestfulServer.getPagesNonHttpGet=Requests for _getpages must use HTTP GET
ca.uhn.fhir.rest.server.RestfulServer.unknownMethod=Invalid request: The FHIR endpoint on this server does not know how to handle {0} operation[{1}] with parameters [{2}]
ca.uhn.fhir.rest.server.RestfulServer.rootRequest=This is the base URL of FHIR server. Unable to handle this request, as it does not contain a resource type or operation name.
ca.uhn.fhir.rest.server.RestfulServer.rootRequest.multitenant=This is the base URL of a multitenant FHIR server. Unable to handle this request, as it does not contain a tenant ID.
ca.uhn.fhir.validation.ValidationContext.unableToDetermineEncoding=Unable to determine encoding (e.g. XML / JSON) on validation input. Is this a valid FHIR resource body?
ca.uhn.fhir.validation.ValidationContext.unableToDetermineEncoding=Unable to determine encoding (e.g. XML / JSON) on validation input. Is this a valid FHIR resource body?
ca.uhn.fhir.validation.FhirValidator.noPhWarningOnStartup=Ph-schematron library not found on classpath, will not attempt to perform schematron validation
ca.uhn.fhir.validation.FhirValidator.noPhError=Ph-schematron library not found on classpath, can not enable perform schematron validation
ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected during validation
@ -62,22 +62,22 @@ ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected duri
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFailure=The operation has failed with a version constraint failure. This generally means that two clients/threads were trying to update the same resource at the same time, and this request was chosen as the failing request.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceIndexedCompositeStringUniqueConstraintFailure=The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.forcedIdConstraintFailure=The operation has failed with a client-assigned ID constraint failure. This typically means that multiple client threads are trying to create a new resource with the same client-assigned ID at the same time, and this thread was chosen to be rejected.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceIndexedCompositeStringUniqueConstraintFailure=The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.forcedIdConstraintFailure=The operation has failed with a client-assigned ID constraint failure. This typically means that multiple client threads are trying to create a new resource with the same client-assigned ID at the same time, and this thread was chosen to be rejected.
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlMultipleMatches=Invalid match URL "{0}" - Multiple resources match this search
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1}
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1}
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.uniqueIndexConflictFailure=Can not create resource of type {0} as it would create a duplicate index matching query: {1} (existing index belongs to {2})
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionContainsMultipleWithDuplicateId=Transaction bundle contains multiple resources with ID: {0}
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionEntryHasInvalidVerb=Transaction bundle entry has missing or invalid HTTP Verb specified in Bundle.entry({1}).request.method. Found value: "{0}"
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionMissingUrl=Unable to perform {0}, no URL provided.
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionInvalidUrl=Unable to perform {0}, URL provided is invalid: {1}
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionEntryHasInvalidVerb=Transaction bundle entry has missing or invalid HTTP Verb specified in Bundle.entry({1}).request.method. Found value: "{0}"
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionMissingUrl=Unable to perform {0}, no URL provided.
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionInvalidUrl=Unable to perform {0}, URL provided is invalid: {1}
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.cantValidateWithNoResource=No resource supplied for $validate operation (resource is required unless mode is \"delete\")
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.duplicateCreateForcedId=Can not create entity with ID[{0}], a resource with this ID already exists
@ -97,8 +97,8 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulDeletes=Successfully delet
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidSearchParameter=Unknown search parameter "{0}". Value search parameters for this search are: {1}
ca.uhn.fhir.jpa.dao.TransactionProcessor.missingMandatoryResource=Missing required resource in Bundle.entry[{1}].resource for operation {0}
ca.uhn.fhir.jpa.dao.TransactionProcessor.missingPatchContentType=Missing or invalid content type for PATCH operation
ca.uhn.fhir.jpa.dao.TransactionProcessor.missingPatchBody=Unable to determine PATCH body from request
ca.uhn.fhir.jpa.dao.TransactionProcessor.missingPatchContentType=Missing or invalid content type for PATCH operation
ca.uhn.fhir.jpa.dao.TransactionProcessor.missingPatchBody=Unable to determine PATCH body from request
ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.externalReferenceNotAllowed=Resource contains external reference to URL "{0}" but this server is not configured to allow external references
ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamExtractor.failedToExtractPaths=Failed to extract values from resource using FHIRPath "{0}": {1}
@ -118,8 +118,8 @@ ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor.noParam=Note that cascadi
ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.noAttachmentDataPresent=The resource with ID {0} has no data at path: {1}
ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownBlobId=Can not find the requested binary content. It may have been deleted.
ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownPath=Unable to find content in resource of type {0} at path: {1}
ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownBlobId=Can not find the requested binary content. It may have been deleted.
ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownPath=Unable to find content in resource of type {0} at path: {1}
ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of type {0} at path {1} is not appropriate for binary storage: {2}
@ -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
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@ -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
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@ -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");

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
View File

@ -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

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

@ -27,10 +27,16 @@ 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);

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
View File

@ -21,6 +21,8 @@ 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;
@ -30,11 +32,17 @@ 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")
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> findByValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
Optional<TermValueSetConcept> findByTermValueSetIdSystemAndCode(@Param("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);
}

99
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) {
@ -246,9 +330,8 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
if (vs != null) {
ValueSet expansion = doExpand(vs);
ValueSet expansion = doExpand(vs); // TODO: DM 2019-08-17 - Need to account for concepts in terminology tables. See #1431
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
@ -269,7 +352,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(List<ValueSetExpansionContainsComponent> contains, String theSystem, String theCode,
Coding theCoding, CodeableConcept theCodeableConcept) {
Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {

91
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) {
@ -247,7 +326,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
}
if (vs != null) {
ValueSet expansion = doExpand(vs);
ValueSet expansion = doExpand(vs); // TODO: DM 2019-08-17 - Need to account for concepts in terminology tables. See #1431
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
if (result != null) {

97
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) {
@ -247,7 +332,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
}
if (vs != null) {
ValueSet expansion = doExpand(vs);
ValueSet expansion = doExpand(vs); // TODO: DM 2019-08-17 - Need to account for concepts in terminology tables. See #1431
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
if (result != null) {

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;

51
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();
@ -55,27 +58,59 @@ 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 (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
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 {
return dao.expand(theValueSet, toFilterString(theFilter));
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
} 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

51
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(
@ -43,31 +44,65 @@ 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 (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
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 {
return dao.expand(theValueSet, toFilterString(theFilter));
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
} else {
return dao.expand(theValueSet, toFilterString(theFilter));
}
}
} finally {
endRequest(theServletRequest);
}

51
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(
@ -43,31 +44,65 @@ 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 (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
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 {
return dao.expand(theValueSet, toFilterString(theFilter));
if (haveId) {
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
} else {
return dao.expand(theValueSet, toFilterString(theFilter));
}
}
} finally {
endRequest(theServletRequest);
}

416
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -351,7 +351,7 @@ 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 +368,7 @@ 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 +392,11 @@ 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 +420,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
count = 0;
while (true) {
Slice<T> link = theLoader.get();
if (link.hasContent() == false) {
if (!link.hasContent()) {
break;
}
@ -478,28 +478,221 @@ 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()) {
boolean add = true;
expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter);
for (int i = 0; ; i++) {
int finalI = i;
Boolean shouldContinue = myTxTemplate.execute(t -> {
boolean add = true;
return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter, finalI);
});
if (!shouldContinue) {
break;
}
}
}
// Handle excludes
ourLog.debug("Handling excludes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getExclude()) {
boolean add = false;
expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter);
for (ValueSet.ConceptSetComponent exclude : theValueSetToExpand.getCompose().getExclude()) {
for (int i = 0; ; i++) {
int finalI = i;
Boolean shouldContinue = myTxTemplate.execute(t -> {
boolean add = false;
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) {
@ -513,16 +706,21 @@ 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 +730,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
if (myFulltextSearchSvc == null) {
expandWithoutHibernateSearch(theValueSetCodeAccumulator, theAddedCodes, theInclude, system, theAdd, theCodeCounter);
return;
return false;
}
/*
@ -592,10 +790,10 @@ 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);
@ -646,25 +844,43 @@ 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;
}
ourLog.info("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
} else {
// No codesystem matching the URL found in the database
@ -673,7 +889,7 @@ 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 +909,12 @@ 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 +933,14 @@ 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) {
@ -781,7 +1004,7 @@ 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 +1021,7 @@ 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 +1052,7 @@ 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 +1237,8 @@ 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;
@ -1076,7 +1299,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
} else {
return saveConcept(theConcept);
}
}
/**
@ -1122,28 +1345,28 @@ 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 +1375,42 @@ 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 +1757,86 @@ 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()) {
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);
if (!optionalTermValueSet.isPresent()) {
return null;
}
TermValueSet termValueSet = optionalTermValueSet.get();
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));

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
View File

@ -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();

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -177,6 +177,20 @@ 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;

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
View File

@ -137,6 +137,12 @@ 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;

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
View File

@ -143,6 +143,13 @@ 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);

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
View File

@ -44,6 +44,8 @@ public interface IHapiTerminologySvc {
ValueSet expandValueSet(ValueSet theValueSetToExpand);
ValueSet expandValueSet(ValueSet theValueSetToExpand, int theOffset, int theCount);
void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
/**
@ -51,6 +53,11 @@ 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);

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");
}
}
}

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

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

360
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -562,6 +562,40 @@ 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();
@ -572,6 +606,14 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
loadAndPersistCodeSystem();
}
@Test
public void testTest() {
ourLog.info("as is: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
ourLog.info("toString: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS.toString());
ourLog.info("name: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS.name());
ourLog.info("getCode: {}", TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS.getCode());
}
@Test
public void testDuplicateConceptMapUrls() {
createAndPersistConceptMap();
@ -595,6 +637,294 @@ 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 +937,6 @@ 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 +1304,7 @@ 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 +1322,7 @@ 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 +1402,7 @@ 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 +1420,7 @@ 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 +2610,17 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
@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());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

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");
}
protected void init400() {

5
src/changes/changes.xml
View File

@ -73,6 +73,11 @@
The informational message returned in an OperationOutcome when a delete failed due to cascades not being enabled
contained an incorrect example. This has been corrected.
</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>
</release>
<release version="4.0.0" date="2019-08-14" description="Igloo">
<action type="add">