Package ca.uhn.fhir.jpa.term

Class BaseTermReadSvcImpl

java.lang.Object

ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl

All Implemented Interfaces:

ca.uhn.fhir.context.support.IValidationSupport, ITermReadSvc

Direct Known Subclasses:

TermReadSvcDstu2, TermReadSvcDstu3, TermReadSvcR4, TermReadSvcR5

public abstract class BaseTermReadSvcImpl
extends Object
implements ITermReadSvc

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BaseTermReadSvcImpl.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
protected ITermCodeSystemDao	myCodeSystemDao
protected ITermConceptDao	myConceptDao
protected ITermConceptDesignationDao	myConceptDesignationDao
protected ITermConceptPropertyDao	myConceptPropertyDao
protected ca.uhn.fhir.context.FhirContext	myContext
protected ca.uhn.fhir.jpa.api.dao.DaoRegistry	myDaoRegistry
protected javax.persistence.EntityManager	myEntityManager
protected ITermValueSetDao	myTermValueSetDao
protected ITermValueSetConceptDao	myValueSetConceptDao
protected ITermValueSetConceptDesignationDao	myValueSetConceptDesignationDao

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

URL_PREFIX_VALUE_SET

Constructor Summary

Constructors

Constructor	Description
BaseTermReadSvcImpl()

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
ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	codeSystemValidateCode(org.hl7.fhir.instance.model.api.IIdType theCodeSystemId, String theCodeSystemUrl, String theVersion, String theCode, String theDisplay, org.hl7.fhir.instance.model.api.IBaseDatatype theCoding, org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConcept)	Version independent
void	deleteValueSetAndChildren(ResourceTable theResourceTable)
void	deleteValueSetForResource(ResourceTable theResourceTable)
org.hl7.fhir.r4.model.ValueSet	expandValueSet(ca.uhn.fhir.context.support.ValueSetExpansionOptions theExpansionOptions, String theValueSetCanonicalUrl)
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<ca.uhn.fhir.util.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	fetchCodeSystem(String theSystem)
org.hl7.fhir.instance.model.api.IBaseResource	fetchValueSet(String theValueSetUrl)
Optional<TermConcept>	findCode(String theCodeSystem, String theCode)
Set<TermConcept>	findCodesAbove(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode)
List<ca.uhn.fhir.util.FhirVersionIndependentConcept>	findCodesAbove(String theSystem, String theCode)
List<ca.uhn.fhir.util.FhirVersionIndependentConcept>	findCodesAboveUsingBuiltInSystems(String theSystem, String theCode)
Set<TermConcept>	findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode)
List<ca.uhn.fhir.util.FhirVersionIndependentConcept>	findCodesBelow(String theSystem, String theCode)
List<ca.uhn.fhir.util.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()
protected abstract org.hl7.fhir.r4.model.ValueSet	getValueSetFromResourceTable(ResourceTable theResourceTable)
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.r4.model.ValueSet theValueSet)
protected ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult	lookupCode(String theSystem, String theCode, String theDisplayLanguage)
void	preExpandDeferredValueSetsToTerminologyTables()
Optional<org.hl7.fhir.instance.model.api.IBaseResource>	readCodeSystemByForcedId(String theForcedId)	Version independent
void	scheduleJob()
static void	setInvokeOnNextCallForUnitTest(Runnable theInvokeOnNextCallForUnitTest)
void	start()
void	storeTermValueSet(ResourceTable theResourceTable, org.hl7.fhir.r4.model.ValueSet theValueSet)
ca.uhn.fhir.jpa.api.dao.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)
protected abstract org.hl7.fhir.r4.model.CodeableConcept	toCanonicalCodeableConcept(org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConcept)
protected abstract org.hl7.fhir.r4.model.CodeSystem	toCanonicalCodeSystem(org.hl7.fhir.instance.model.api.IBaseResource theCodeSystem)
protected abstract org.hl7.fhir.r4.model.Coding	toCanonicalCoding(org.hl7.fhir.instance.model.api.IBaseCoding theCoding)
protected abstract org.hl7.fhir.r4.model.Coding	toCanonicalCoding(org.hl7.fhir.instance.model.api.IBaseDatatype theCoding)
protected abstract org.hl7.fhir.r4.model.ValueSet	toCanonicalValueSet(org.hl7.fhir.instance.model.api.IBaseResource theValueSet)
ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	validateCode(ca.uhn.fhir.context.support.ConceptValidationOptions theOptions, org.hl7.fhir.instance.model.api.IIdType theValueSetId, String theValueSetIdentifier, String theCodeSystemIdentifierToValidate, String theCodeToValidate, String theDisplayToValidate, org.hl7.fhir.instance.model.api.IBaseDatatype theCodingToValidate, org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConceptToValidate)	Version independent
ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	validateCode(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext, ca.uhn.fhir.context.support.ConceptValidationOptions theOptions, String theCodeSystem, 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)
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.jpa.term.api.ITermReadSvc

expandValueSet, expandValueSet, isValueSetPreExpandedForCodeValidation, validateCodeIsInPreExpandedValueSet

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

expandValueSet, fetchAllConformanceResources, fetchAllNonBaseStructureDefinitions, fetchAllStructureDefinitions, fetchResource, fetchStructureDefinition, generateSnapshot, invalidateCaches, isRemoteTerminologyServiceConfigured, isValueSetSupported, lookupCode, lookupCode, translateConcept

Field Details

DEFAULT_FETCH_SIZE

public static final int DEFAULT_FETCH_SIZE

See Also:

• Constant Field Values

myDaoRegistry

@Autowired
protected ca.uhn.fhir.jpa.api.dao.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 javax.persistence.EntityManager myEntityManager

Constructor Details

BaseTermReadSvcImpl

public BaseTermReadSvcImpl()

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

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

Specified by:

expandValueSetIntoConceptList in interface ITermReadSvc

expandValueSet

@Transactional
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

@Transactional(propagation=REQUIRED)
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

@Transactional(propagation=REQUIRED)
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

findCodesAbove

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

Specified by:

findCodesAbove in interface ITermReadSvc

findCodesAbove

@Transactional
public List<ca.uhn.fhir.util.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<ca.uhn.fhir.util.FhirVersionIndependentConcept> findCodesBelow(String theSystem,
 String theCode)

Specified by:

findCodesBelow in interface ITermReadSvc

start

@PostConstruct
public void start()

scheduleJob

public void scheduleJob()

preExpandDeferredValueSetsToTerminologyTables

public void preExpandDeferredValueSetsToTerminologyTables()

Specified by:

preExpandDeferredValueSetsToTerminologyTables in interface ITermReadSvc

validateCode

@Transactional
public ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult validateCode(ca.uhn.fhir.context.support.ConceptValidationOptions theOptions,
 org.hl7.fhir.instance.model.api.IIdType theValueSetId,
 String theValueSetIdentifier,
 String theCodeSystemIdentifierToValidate,
 String theCodeToValidate,
 String theDisplayToValidate,
 org.hl7.fhir.instance.model.api.IBaseDatatype theCodingToValidate,
 org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConceptToValidate)

Description copied from interface: ITermReadSvc

Version independent

Specified by:

validateCode in interface ITermReadSvc

getValueSetFromResourceTable

protected abstract org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable)

storeTermValueSet

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

Specified by:

storeTermValueSet in interface ITermReadSvc

subsumes

@Transactional
public ca.uhn.fhir.jpa.api.dao.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

toCanonicalValueSet

protected abstract org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(org.hl7.fhir.instance.model.api.IBaseResource theValueSet)

lookupCode

protected ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult lookupCode(String theSystem,
 String theCode,
 String theDisplayLanguage)

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(ca.uhn.fhir.context.support.ValidationSupportContext theValidationSupportContext,
 ca.uhn.fhir.context.support.ConceptValidationOptions theOptions,
 String theCodeSystem,
 String theCode,
 String theDisplay,
 String theValueSetUrl)

Specified by:

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

fetchCodeSystem

public org.hl7.fhir.instance.model.api.IBaseResource fetchCodeSystem(String theSystem)

Specified by:

fetchCodeSystem 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

fetchCanonicalValueSetFromCompleteContext

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

toCanonicalCodeSystem

protected abstract org.hl7.fhir.r4.model.CodeSystem toCanonicalCodeSystem(org.hl7.fhir.instance.model.api.IBaseResource theCodeSystem)

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<ca.uhn.fhir.util.FhirVersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem,
 String theCode)

Specified by:

findCodesAboveUsingBuiltInSystems in interface ITermReadSvc

findCodesBelowUsingBuiltInSystems

public List<ca.uhn.fhir.util.FhirVersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem,
 String theCode)

Specified by:

findCodesBelowUsingBuiltInSystems in interface ITermReadSvc

toCanonicalCoding

@Nullable
protected abstract org.hl7.fhir.r4.model.Coding toCanonicalCoding(@Nullable
 org.hl7.fhir.instance.model.api.IBaseDatatype theCoding)

toCanonicalCoding

@Nullable
protected abstract org.hl7.fhir.r4.model.Coding toCanonicalCoding(@Nullable
 org.hl7.fhir.instance.model.api.IBaseCoding theCoding)

toCanonicalCodeableConcept

@Nullable
protected abstract org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(@Nullable
 org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConcept)

codeSystemValidateCode

@Transactional
public ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult codeSystemValidateCode(org.hl7.fhir.instance.model.api.IIdType theCodeSystemId,
 String theCodeSystemUrl,
 String theVersion,
 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:

codeSystemValidateCode 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

setInvokeOnNextCallForUnitTest

public static void setInvokeOnNextCallForUnitTest(Runnable theInvokeOnNextCallForUnitTest)