Package ca.uhn.fhir.jpa.term

Class TermReadSvcImpl

java.lang.Object

ca.uhn.fhir.jpa.term.TermReadSvcImpl

All Implemented Interfaces:

ca.uhn.fhir.context.support.IValidationSupport, ca.uhn.fhir.jpa.model.sched.IHasScheduledJobs, ITermReadSvc

public class TermReadSvcImpl
extends Object
implements ITermReadSvc, ca.uhn.fhir.jpa.model.sched.IHasScheduledJobs

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	TermReadSvcImpl.Job

Nested classes/interfaces inherited from interface ca.uhn.fhir.context.support.IValidationSupport

ca.uhn.fhir.context.support.IValidationSupport.BaseConceptProperty, ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult, ca.uhn.fhir.context.support.IValidationSupport.CodingConceptProperty, ca.uhn.fhir.context.support.IValidationSupport.ConceptDesignation, ca.uhn.fhir.context.support.IValidationSupport.IssueSeverity, ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult, ca.uhn.fhir.context.support.IValidationSupport.StringConceptProperty, ca.uhn.fhir.context.support.IValidationSupport.TranslateCodeRequest, ca.uhn.fhir.context.support.IValidationSupport.ValueSetExpansionOutcome

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_FETCH_SIZE
static final int	DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS
static final int	MAX_MASS_INDEXER_OBJECT_LOADING_THREADS
protected ITermCodeSystemDao	myCodeSystemDao
protected ITermConceptDao	myConceptDao
protected ITermConceptDesignationDao	myConceptDesignationDao
protected ITermConceptPropertyDao	myConceptPropertyDao
protected ca.uhn.fhir.context.FhirContext	myContext
protected DaoRegistry	myDaoRegistry
protected jakarta.persistence.EntityManager	myEntityManager
protected ITermValueSetDao	myTermValueSetDao
protected ITermValueSetConceptDao	myValueSetConceptDao
protected ITermValueSetConceptDesignationDao	myValueSetConceptDesignationDao

Fields inherited from interface ca.uhn.fhir.context.support.IValidationSupport

TYPE_CODING, TYPE_STRING, URL_PREFIX_VALUE_SET

Constructor Summary

Constructors

Constructor	Description
TermReadSvcImpl()

Method Summary

Modifier and Type	Method	Description
boolean	applyFilter(String theDisplay, String theFilterDisplay)
void	clearCaches()	This method is present only for unit tests, do not call from client code
void	deleteValueSetAndChildren(ResourceTable theResourceTable)
void	deleteValueSetForResource(ResourceTable theResourceTable)
ca.uhn.fhir.context.support.IValidationSupport.ValueSetExpansionOutcome	expandValueSet(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, org.hl7.fhir.instance.model.api.IBaseResource theValueSetToExpand)
org.hl7.fhir.r4.model.ValueSet	expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, String theValueSetCanonicalUrl)
org.hl7.fhir.instance.model.api.IBaseResource	expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, org.hl7.fhir.instance.model.api.IBaseResource theInput)	Version independent
void	expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, org.hl7.fhir.instance.model.api.IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator)
org.hl7.fhir.r4.model.ValueSet	expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, org.hl7.fhir.r4.model.ValueSet theValueSetToExpand)
void	expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, org.hl7.fhir.r4.model.ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator)
List<FhirVersionIndependentConcept>	expandValueSetIntoConceptList(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, String theValueSetCanonicalUrl)
org.hl7.fhir.r4.model.CodeSystem	fetchCanonicalCodeSystemFromCompleteContext(String theSystem)
org.hl7.fhir.r4.model.ValueSet	fetchCanonicalValueSetFromCompleteContext(String theSystem)
org.hl7.fhir.instance.model.api.IBaseResource	fetchValueSet(String theValueSetUrl)
Optional<TermConcept>	findCode(String theCodeSystem, String theCode)
List<TermConcept>	findCodes(String theCodeSystem, List<String> theCodeList)
Set<TermConcept>	findCodesAbove(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode)
List<FhirVersionIndependentConcept>	findCodesAbove(String theSystem, String theCode)
List<FhirVersionIndependentConcept>	findCodesAboveUsingBuiltInSystems(String theSystem, String theCode)
Set<TermConcept>	findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode)
List<FhirVersionIndependentConcept>	findCodesBelow(String theSystem, String theCode)
List<FhirVersionIndependentConcept>	findCodesBelowUsingBuiltInSystems(String theSystem, String theCode)
Optional<TermValueSet>	findCurrentTermValueSet(String theUrl)	When the search is for unversioned loinc system it uses the forcedId to obtain the current version, as it is not necessarily the last one anymore.
ca.uhn.fhir.context.FhirContext	getFhirContext()
String	invalidatePreCalculatedExpansion(org.hl7.fhir.instance.model.api.IIdType theValueSetId, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)
boolean	isCodeSystemSupported(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext, String theSystem)
boolean	isValueSetPreExpandedForCodeValidation(org.hl7.fhir.instance.model.api.IBaseResource theValueSet)	Version independent
boolean	isValueSetPreExpandedForCodeValidation(org.hl7.fhir.r4.model.ValueSet theValueSet)
boolean	isValueSetSupported(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext, String theValueSetUrl)
ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult	lookupCode(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.context.support.LookupCodeRequest theLookupCodeRequest)
void	preExpandDeferredValueSetsToTerminologyTables()
protected ca.uhn.fhir.context.support.IValidationSupport	provideValidationSupport()
Optional<org.hl7.fhir.instance.model.api.IBaseResource>	readCodeSystemByForcedId(String theForcedId)	Version independent
ReindexTerminologyResult	reindexTerminology()	Version independent Recreates freetext indexes for TermConcept and nested TermConceptProperty
void	scheduleJobs(ca.uhn.fhir.jpa.model.sched.ISchedulerService theSchedulerService)
static void	setForceDisableHibernateSearchForUnitTest(boolean theForceDisableHibernateSearchForUnitTest)
static void	setInvokeOnNextCallForUnitTest(Runnable theInvokeOnNextCallForUnitTest)
void	start()
void	storeTermValueSet(ResourceTable theResourceTable, org.hl7.fhir.r4.model.ValueSet theValueSet)
IFhirResourceDaoCodeSystem.SubsumesResult	subsumes(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeA, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeB, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem, org.hl7.fhir.instance.model.api.IBaseCoding theCodingA, org.hl7.fhir.instance.model.api.IBaseCoding theCodingB)
ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	validateCode(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.context.support.ConceptValidationOptions theOptions, String theCodeSystemUrl, String theCode, String theDisplay, String theValueSetUrl)
ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	validateCodeInValueSet(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.context.support.ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, org.hl7.fhir.instance.model.api.IBaseResource theValueSet)
ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	validateCodeIsInPreExpandedValueSet(ca.uhn.fhir.context.support.ConceptValidationOptions theOptions, org.hl7.fhir.instance.model.api.IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, org.hl7.fhir.instance.model.api.IBaseDatatype theCoding, org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConcept)	Version independent
protected ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	validateCodeIsInPreExpandedValueSet(ca.uhn.fhir.context.support.ConceptValidationOptions theValidationOptions, org.hl7.fhir.r4.model.ValueSet theValueSet, String theSystem, String theCode, String theDisplay, org.hl7.fhir.r4.model.Coding theCoding, org.hl7.fhir.r4.model.CodeableConcept theCodeableConcept)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ca.uhn.fhir.context.support.IValidationSupport

expandValueSet, fetchAllConformanceResources, fetchAllNonBaseStructureDefinitions, fetchAllSearchParameters, fetchAllStructureDefinitions, fetchBinary, fetchCodeSystem, fetchResource, fetchStructureDefinition, generateSnapshot, getName, invalidateCaches, isEnabledValidationForCodingsLogicalAnd, isRemoteTerminologyServiceConfigured, lookupCode, lookupCode, translateConcept

Field Details

DEFAULT_FETCH_SIZE

public static final int DEFAULT_FETCH_SIZE

See Also:

• Constant Field Values

DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS

public static final int DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS

See Also:

• Constant Field Values

MAX_MASS_INDEXER_OBJECT_LOADING_THREADS

public static final int MAX_MASS_INDEXER_OBJECT_LOADING_THREADS

See Also:

• Constant Field Values

myDaoRegistry

@Autowired
protected DaoRegistry myDaoRegistry

myCodeSystemDao

@Autowired
protected ITermCodeSystemDao myCodeSystemDao

myConceptDao

@Autowired
protected ITermConceptDao myConceptDao

myConceptPropertyDao

@Autowired
protected ITermConceptPropertyDao myConceptPropertyDao

myConceptDesignationDao

@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao

myTermValueSetDao

@Autowired
protected ITermValueSetDao myTermValueSetDao

myValueSetConceptDao

@Autowired
protected ITermValueSetConceptDao myValueSetConceptDao

myValueSetConceptDesignationDao

@Autowired
protected ITermValueSetConceptDesignationDao myValueSetConceptDesignationDao

myContext

@Autowired
protected ca.uhn.fhir.context.FhirContext myContext

myEntityManager

protected jakarta.persistence.EntityManager myEntityManager

Constructor Details

TermReadSvcImpl

public TermReadSvcImpl()

Method Details

isCodeSystemSupported

public boolean isCodeSystemSupported(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext,
 String theSystem)

Specified by:

isCodeSystemSupported in interface ca.uhn.fhir.context.support.IValidationSupport

isValueSetSupported

public boolean isValueSetSupported(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext,
 String theValueSetUrl)

Specified by:

isValueSetSupported in interface ca.uhn.fhir.context.support.IValidationSupport

clearCaches

public void clearCaches()

This method is present only for unit tests, do not call from client code

deleteValueSetForResource

public void deleteValueSetForResource(ResourceTable theResourceTable)

deleteValueSetAndChildren

@Transactional
public void deleteValueSetAndChildren(ResourceTable theResourceTable)

Specified by:

deleteValueSetAndChildren in interface ITermReadSvc

expandValueSetIntoConceptList

@Transactional
public List<FhirVersionIndependentConcept> expandValueSetIntoConceptList(@Nullable
 ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions,
 @Nonnull
 String theValueSetCanonicalUrl)

Specified by:

expandValueSetIntoConceptList in interface ITermReadSvc

expandValueSet

public org.hl7.fhir.r4.model.ValueSet expandValueSet(@Nullable
 ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions,
 @Nonnull
 String theValueSetCanonicalUrl)

Specified by:

expandValueSet in interface ITermReadSvc

expandValueSet

public org.hl7.fhir.r4.model.ValueSet expandValueSet(@Nullable
 ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions,
 @Nonnull
 org.hl7.fhir.r4.model.ValueSet theValueSetToExpand)

Specified by:

expandValueSet in interface ITermReadSvc

applyFilter

public boolean applyFilter(String theDisplay,
 String theFilterDisplay)

expandValueSet

public void expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions,
 org.hl7.fhir.r4.model.ValueSet theValueSetToExpand,
 IValueSetConceptAccumulator theValueSetCodeAccumulator)

Specified by:

expandValueSet in interface ITermReadSvc

invalidatePreCalculatedExpansion

@Transactional
public String invalidatePreCalculatedExpansion(org.hl7.fhir.instance.model.api.IIdType theValueSetId,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Specified by:

invalidatePreCalculatedExpansion in interface ITermReadSvc

isValueSetPreExpandedForCodeValidation

@Transactional
public boolean isValueSetPreExpandedForCodeValidation(org.hl7.fhir.r4.model.ValueSet theValueSet)

Specified by:

isValueSetPreExpandedForCodeValidation in interface ITermReadSvc

validateCodeIsInPreExpandedValueSet

protected ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(ca.uhn.fhir.context.support.ConceptValidationOptions theValidationOptions,
 org.hl7.fhir.r4.model.ValueSet theValueSet,
 String theSystem,
 String theCode,
 String theDisplay,
 org.hl7.fhir.r4.model.Coding theCoding,
 org.hl7.fhir.r4.model.CodeableConcept theCodeableConcept)

findCode

public Optional<TermConcept> findCode(String theCodeSystem,
 String theCode)

Specified by:

findCode in interface ITermReadSvc

findCodes

@Transactional(propagation=MANDATORY)
public List<TermConcept> findCodes(String theCodeSystem,
 List<String> theCodeList)

Specified by:

findCodes in interface ITermReadSvc

findCodesAbove

@Transactional(propagation=REQUIRED)
public Set<TermConcept> findCodesAbove(Long theCodeSystemResourcePid,
 Long theCodeSystemVersionPid,
 String theCode)

Specified by:

findCodesAbove in interface ITermReadSvc

findCodesAbove

@Transactional
public List<FhirVersionIndependentConcept> findCodesAbove(String theSystem,
 String theCode)

Specified by:

findCodesAbove in interface ITermReadSvc

findCodesBelow

@Transactional(propagation=REQUIRED)
public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid,
 Long theCodeSystemVersionPid,
 String theCode)

Specified by:

findCodesBelow in interface ITermReadSvc

findCodesBelow

@Transactional
public List<FhirVersionIndependentConcept> findCodesBelow(String theSystem,
 String theCode)

Specified by:

findCodesBelow in interface ITermReadSvc

start

@PostConstruct
public void start()

scheduleJobs

public void scheduleJobs(ca.uhn.fhir.jpa.model.sched.ISchedulerService theSchedulerService)

Specified by:

scheduleJobs in interface ca.uhn.fhir.jpa.model.sched.IHasScheduledJobs

preExpandDeferredValueSetsToTerminologyTables

public void preExpandDeferredValueSetsToTerminologyTables()

Specified by:

preExpandDeferredValueSetsToTerminologyTables in interface ITermReadSvc

storeTermValueSet

@Transactional
public void storeTermValueSet(ResourceTable theResourceTable,
 org.hl7.fhir.r4.model.ValueSet theValueSet)

Specified by:

storeTermValueSet in interface ITermReadSvc

subsumes

@Transactional
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeA,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeB,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem,
 org.hl7.fhir.instance.model.api.IBaseCoding theCodingA,
 org.hl7.fhir.instance.model.api.IBaseCoding theCodingB)

Specified by:

subsumes in interface ITermReadSvc

lookupCode

public ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult lookupCode(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext,
 @Nonnull
 ca.uhn.fhir.context.support.LookupCodeRequest theLookupCodeRequest)

Specified by:

lookupCode in interface ca.uhn.fhir.context.support.IValidationSupport

validateCodeInValueSet

@Transactional
public ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult validateCodeInValueSet(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext,
 ca.uhn.fhir.context.support.ConceptValidationOptions theOptions,
 String theCodeSystem,
 String theCode,
 String theDisplay,
 @Nonnull
 org.hl7.fhir.instance.model.api.IBaseResource theValueSet)

Specified by:

validateCodeInValueSet in interface ca.uhn.fhir.context.support.IValidationSupport

validateCode

public ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult validateCode(@Nonnull
 ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext,
 @Nonnull
 ca.uhn.fhir.context.support.ConceptValidationOptions theOptions,
 String theCodeSystemUrl,
 String theCode,
 String theDisplay,
 String theValueSetUrl)

Specified by:

validateCode in interface ca.uhn.fhir.context.support.IValidationSupport

fetchCanonicalCodeSystemFromCompleteContext

public org.hl7.fhir.r4.model.CodeSystem fetchCanonicalCodeSystemFromCompleteContext(String theSystem)

Specified by:

fetchCanonicalCodeSystemFromCompleteContext in interface ITermReadSvc

provideValidationSupport

@Nonnull
protected ca.uhn.fhir.context.support.IValidationSupport provideValidationSupport()

fetchCanonicalValueSetFromCompleteContext

public org.hl7.fhir.r4.model.ValueSet fetchCanonicalValueSetFromCompleteContext(String theSystem)

fetchValueSet

public org.hl7.fhir.instance.model.api.IBaseResource fetchValueSet(String theValueSetUrl)

Specified by:

fetchValueSet in interface ca.uhn.fhir.context.support.IValidationSupport

getFhirContext

public ca.uhn.fhir.context.FhirContext getFhirContext()

Specified by:

getFhirContext in interface ca.uhn.fhir.context.support.IValidationSupport

findCodesAboveUsingBuiltInSystems

public List<FhirVersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem,
 String theCode)

Specified by:

findCodesAboveUsingBuiltInSystems in interface ITermReadSvc

findCodesBelowUsingBuiltInSystems

public List<FhirVersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem,
 String theCode)

Specified by:

findCodesBelowUsingBuiltInSystems in interface ITermReadSvc

findCurrentTermValueSet

public Optional<TermValueSet> findCurrentTermValueSet(String theUrl)

When the search is for unversioned loinc system it uses the forcedId to obtain the current version, as it is not necessarily the last one anymore. For other cases it keeps on considering the last uploaded as the current

Specified by:

findCurrentTermValueSet in interface ITermReadSvc

readCodeSystemByForcedId

public Optional<org.hl7.fhir.instance.model.api.IBaseResource> readCodeSystemByForcedId(String theForcedId)

Description copied from interface: ITermReadSvc

Version independent

Specified by:

readCodeSystemByForcedId in interface ITermReadSvc

reindexTerminology

@Transactional
public ReindexTerminologyResult reindexTerminology()
                                            throws InterruptedException

Description copied from interface: ITermReadSvc

Version independent Recreates freetext indexes for TermConcept and nested TermConceptProperty

Specified by:

reindexTerminology in interface ITermReadSvc

Throws:

InterruptedException

expandValueSet

public ca.uhn.fhir.context.support.IValidationSupport.ValueSetExpansionOutcome expandValueSet(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext,
 ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions,
 @Nonnull
 org.hl7.fhir.instance.model.api.IBaseResource theValueSetToExpand)

Specified by:

expandValueSet in interface ca.uhn.fhir.context.support.IValidationSupport

expandValueSet

public org.hl7.fhir.instance.model.api.IBaseResource expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions,
 org.hl7.fhir.instance.model.api.IBaseResource theInput)

Description copied from interface: ITermReadSvc

Version independent

Specified by:

expandValueSet in interface ITermReadSvc

expandValueSet

public void expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions,
 org.hl7.fhir.instance.model.api.IBaseResource theValueSetToExpand,
 IValueSetConceptAccumulator theValueSetCodeAccumulator)

Specified by:

expandValueSet in interface ITermReadSvc

validateCodeIsInPreExpandedValueSet

public ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(ca.uhn.fhir.context.support.ConceptValidationOptions theOptions,
 org.hl7.fhir.instance.model.api.IBaseResource theValueSet,
 String theSystem,
 String theCode,
 String theDisplay,
 org.hl7.fhir.instance.model.api.IBaseDatatype theCoding,
 org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConcept)

Description copied from interface: ITermReadSvc

Version independent

Specified by:

validateCodeIsInPreExpandedValueSet in interface ITermReadSvc

isValueSetPreExpandedForCodeValidation

public boolean isValueSetPreExpandedForCodeValidation(org.hl7.fhir.instance.model.api.IBaseResource theValueSet)

Description copied from interface: ITermReadSvc

Version independent

Specified by:

isValueSetPreExpandedForCodeValidation in interface ITermReadSvc

setForceDisableHibernateSearchForUnitTest

public static void setForceDisableHibernateSearchForUnitTest(boolean theForceDisableHibernateSearchForUnitTest)

setInvokeOnNextCallForUnitTest

public static void setInvokeOnNextCallForUnitTest(Runnable theInvokeOnNextCallForUnitTest)