idx int64 0 41.2k | question stringlengths 74 4.21k | target stringlengths 5 888 |
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32,800 | public void visit ( IBaseResource theResource , IModelVisitor theVisitor ) { BaseRuntimeElementCompositeDefinition < ? > def = myContext . getResourceDefinition ( theResource ) ; visit ( new IdentityHashMap < Object , Object > ( ) , theResource , theResource , null , null , def , theVisitor ) ; } | Visit all elements in a given resource |
32,801 | public SubscriptionMatchResult match ( String theCriteria , IBaseResource theResource , ResourceIndexedSearchParams theSearchParams ) { RuntimeResourceDefinition resourceDefinition ; if ( theResource == null ) { resourceDefinition = UrlUtil . parseUrlResourceType ( myFhirContext , theCriteria ) ; } else { resourceDefinition = myFhirContext . getResourceDefinition ( theResource ) ; } SearchParameterMap searchParameterMap ; try { searchParameterMap = myMatchUrlService . translateMatchUrl ( theCriteria , resourceDefinition ) ; } catch ( UnsupportedOperationException e ) { return SubscriptionMatchResult . unsupportedFromReason ( SubscriptionMatchResult . PARSE_FAIL ) ; } searchParameterMap . clean ( ) ; if ( searchParameterMap . getLastUpdated ( ) != null ) { return SubscriptionMatchResult . unsupportedFromParameterAndReason ( Constants . PARAM_LASTUPDATED , SubscriptionMatchResult . STANDARD_PARAMETER ) ; } for ( Map . Entry < String , List < List < IQueryParameterType > > > entry : searchParameterMap . entrySet ( ) ) { String theParamName = entry . getKey ( ) ; List < List < IQueryParameterType > > theAndOrParams = entry . getValue ( ) ; SubscriptionMatchResult result = matchIdsWithAndOr ( theParamName , theAndOrParams , resourceDefinition , theResource , theSearchParams ) ; if ( ! result . matched ( ) ) { return result ; } } return SubscriptionMatchResult . successfulMatch ( ) ; } | This method is called in two different scenarios . With a null theResource it determines whether database matching might be required . Otherwise it tries to perform the match in - memory returning UNSUPPORTED if it s not possible . |
32,802 | public void registerOsgiProvider ( Object provider ) throws FhirConfigurationException { if ( null == provider ) { throw new NullPointerException ( "FHIR Provider cannot be null" ) ; } try { super . registerProvider ( provider ) ; log . trace ( "registered provider. class [" + provider . getClass ( ) . getName ( ) + "]" ) ; this . serverProviders . add ( provider ) ; } catch ( Exception e ) { log . error ( "Error registering FHIR Provider" , e ) ; throw new FhirConfigurationException ( "Error registering FHIR Provider" , e ) ; } } | Dynamically registers a single provider with the RestfulServer |
32,803 | public void unregisterOsgiProvider ( Object provider ) throws FhirConfigurationException { if ( null == provider ) { throw new NullPointerException ( "FHIR Provider cannot be null" ) ; } try { this . serverProviders . remove ( provider ) ; log . trace ( "unregistered provider. class [" + provider . getClass ( ) . getName ( ) + "]" ) ; super . unregisterProvider ( provider ) ; } catch ( Exception e ) { log . error ( "Error unregistering FHIR Provider" , e ) ; throw new FhirConfigurationException ( "Error unregistering FHIR Provider" , e ) ; } } | Dynamically unregisters a single provider with the RestfulServer |
32,804 | public void registerOsgiProviders ( Collection < Object > providers ) throws FhirConfigurationException { if ( null == providers ) { throw new NullPointerException ( "FHIR Provider list cannot be null" ) ; } try { super . registerProviders ( providers ) ; for ( Object provider : providers ) { log . trace ( "registered provider. class [" + provider . getClass ( ) . getName ( ) + "]" ) ; this . serverProviders . add ( provider ) ; } } catch ( Exception e ) { log . error ( "Error registering FHIR Providers" , e ) ; throw new FhirConfigurationException ( "Error registering FHIR Providers" , e ) ; } } | Dynamically registers a list of providers with the RestfulServer |
32,805 | public void unregisterOsgiProviders ( Collection < Object > providers ) throws FhirConfigurationException { if ( null == providers ) { throw new NullPointerException ( "FHIR Provider list cannot be null" ) ; } try { for ( Object provider : providers ) { log . trace ( "unregistered provider. class [" + provider . getClass ( ) . getName ( ) + "]" ) ; this . serverProviders . remove ( provider ) ; } super . unregisterProvider ( providers ) ; } catch ( Exception e ) { log . error ( "Error unregistering FHIR Providers" , e ) ; throw new FhirConfigurationException ( "Error unregistering FHIR Providers" , e ) ; } } | Dynamically unregisters a list of providers with the RestfulServer |
32,806 | public void unregisterOsgiProviders ( ) throws FhirConfigurationException { Collection < Object > providers = new ArrayList < Object > ( ) ; providers . addAll ( this . serverProviders ) ; this . unregisterOsgiProviders ( providers ) ; } | Dynamically unregisters all of providers currently registered |
32,807 | public List < Patient > search ( @ RequiredParam ( name = "family" ) StringParam theParam ) { List < Patient > retVal = new ArrayList < Patient > ( ) ; for ( Patient next : myPatients . values ( ) ) { String familyName = next . getNameFirstRep ( ) . getFamilyAsSingleString ( ) . toLowerCase ( ) ; if ( familyName . contains ( theParam . getValue ( ) . toLowerCase ( ) ) == false ) { continue ; } retVal . add ( next ) ; } return retVal ; } | A search with a parameter |
32,808 | String extractPrefixAndReturnRest ( String theString ) { int offset = 0 ; while ( true ) { if ( theString . length ( ) == offset ) { break ; } else { char nextChar = theString . charAt ( offset ) ; if ( nextChar == '-' || Character . isDigit ( nextChar ) ) { break ; } } offset ++ ; } String prefix = theString . substring ( 0 , offset ) ; if ( ! isBlank ( prefix ) ) { myPrefix = ParamPrefixEnum . forValue ( prefix ) ; if ( myPrefix == null ) { switch ( prefix ) { case ">=" : myPrefix = ParamPrefixEnum . GREATERTHAN_OR_EQUALS ; break ; case ">" : myPrefix = ParamPrefixEnum . GREATERTHAN ; break ; case "<=" : myPrefix = ParamPrefixEnum . LESSTHAN_OR_EQUALS ; break ; case "<" : myPrefix = ParamPrefixEnum . LESSTHAN ; break ; case "~" : myPrefix = ParamPrefixEnum . APPROXIMATE ; break ; default : ourLog . warn ( "Invalid prefix being ignored: {}" , prefix ) ; break ; } if ( myPrefix != null ) { ourLog . warn ( "Date parameter has legacy prefix '{}' which has been removed from FHIR. This should be replaced with '{}'" , prefix , myPrefix ) ; } } } return theString . substring ( offset ) ; } | Eg . if this is invoked with gt2012 - 11 - 02 sets the prefix to GREATER_THAN and returns 2012 - 11 - 02 |
32,809 | protected void preProcessResourceForStorage ( T theResource ) { String type = getContext ( ) . getResourceDefinition ( theResource ) . getName ( ) ; if ( ! getResourceName ( ) . equals ( type ) ) { throw new InvalidRequestException ( getContext ( ) . getLocalizer ( ) . getMessage ( BaseHapiFhirResourceDao . class , "incorrectResourceType" , type , getResourceName ( ) ) ) ; } if ( theResource . getIdElement ( ) . hasIdPart ( ) ) { if ( ! theResource . getIdElement ( ) . isIdPartValid ( ) ) { throw new InvalidRequestException ( getContext ( ) . getLocalizer ( ) . getMessage ( BaseHapiFhirResourceDao . class , "failedToCreateWithInvalidId" , theResource . getIdElement ( ) . getIdPart ( ) ) ) ; } } if ( getConfig ( ) . getTreatBaseUrlsAsLocal ( ) . isEmpty ( ) == false ) { FhirTerser t = getContext ( ) . newTerser ( ) ; List < ResourceReferenceInfo > refs = t . getAllResourceReferences ( theResource ) ; for ( ResourceReferenceInfo nextRef : refs ) { IIdType refId = nextRef . getResourceReference ( ) . getReferenceElement ( ) ; if ( refId != null && refId . hasBaseUrl ( ) ) { if ( getConfig ( ) . getTreatBaseUrlsAsLocal ( ) . contains ( refId . getBaseUrl ( ) ) ) { IIdType newRefId = refId . toUnqualified ( ) ; nextRef . getResourceReference ( ) . setReference ( newRefId . getValue ( ) ) ; } } } } } | May be overridden by subclasses to validate resources prior to storage |
32,810 | public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition ( String criteria ) { String resourceName ; if ( criteria == null || criteria . trim ( ) . isEmpty ( ) ) { throw new IllegalArgumentException ( "Criteria cannot be empty" ) ; } if ( criteria . contains ( "?" ) ) { resourceName = criteria . substring ( 0 , criteria . indexOf ( "?" ) ) ; } else { resourceName = criteria ; } return getContext ( ) . getResourceDefinition ( resourceName ) ; } | Get the resource definition from the criteria which specifies the resource type |
32,811 | public DateTimeType makeDateTimeFromIVL ( Element ivl ) throws Exception { if ( ivl == null ) return null ; if ( ivl . hasAttribute ( "value" ) ) return makeDateTimeFromTS ( ivl ) ; Element high = cda . getChild ( ivl , "high" ) ; if ( high != null ) return makeDateTimeFromTS ( high ) ; Element low = cda . getChild ( ivl , "low" ) ; if ( low != null ) return makeDateTimeFromTS ( low ) ; return null ; } | this is a weird one - where CDA has an IVL and FHIR has a date |
32,812 | public String analyse ( String unit ) throws UcumException { if ( Utilities . noString ( unit ) ) return "(unity)" ; assert checkStringParam ( unit ) : paramError ( "analyse" , "unit" , "must not be null or empty" ) ; Term term = new ExpressionParser ( model ) . parse ( unit ) ; return new FormalStructureComposer ( ) . compose ( term ) ; } | given a unit return a formal description of what the units stand for using full names |
32,813 | public static String determineServletContextPath ( HttpServletRequest theRequest , RestfulServer server ) { String retVal ; if ( server . getServletContext ( ) != null ) { if ( server . getServletContext ( ) . getMajorVersion ( ) >= 3 || ( server . getServletContext ( ) . getMajorVersion ( ) > 2 && server . getServletContext ( ) . getMinorVersion ( ) >= 5 ) ) { retVal = server . getServletContext ( ) . getContextPath ( ) ; } else { retVal = theRequest . getContextPath ( ) ; } } else { retVal = theRequest . getContextPath ( ) ; } retVal = StringUtils . defaultString ( retVal ) ; return retVal ; } | Determines the servlet s context path . |
32,814 | public static List < String > getOtherChildren ( CodeSystem cs , ConceptDefinitionComponent c ) { List < String > res = new ArrayList < String > ( ) ; for ( ConceptPropertyComponent p : c . getProperty ( ) ) { if ( "parent" . equals ( p . getCode ( ) ) ) { res . add ( p . getValue ( ) . primitiveValue ( ) ) ; } } return res ; } | returns additional parents not in the heirarchy |
32,815 | public Boolean equalsUsingFhirPathRules ( BaseDateTimeType theOther ) { BaseDateTimeType me = this ; int lowestPrecision = Math . min ( me . getPrecision ( ) . ordinal ( ) , theOther . getPrecision ( ) . ordinal ( ) ) ; TemporalPrecisionEnum lowestPrecisionEnum = TemporalPrecisionEnum . values ( ) [ lowestPrecision ] ; if ( me . getPrecision ( ) != lowestPrecisionEnum ) { me = new DateTimeType ( me . getValueAsString ( ) ) ; me . setPrecision ( lowestPrecisionEnum ) ; } if ( theOther . getPrecision ( ) != lowestPrecisionEnum ) { theOther = new DateTimeType ( theOther . getValueAsString ( ) ) ; theOther . setPrecision ( lowestPrecisionEnum ) ; } if ( me . hasTimezoneIfRequired ( ) != theOther . hasTimezoneIfRequired ( ) ) { if ( me . getPrecision ( ) == theOther . getPrecision ( ) ) { if ( me . getPrecision ( ) . ordinal ( ) >= TemporalPrecisionEnum . MINUTE . ordinal ( ) && theOther . getPrecision ( ) . ordinal ( ) >= TemporalPrecisionEnum . MINUTE . ordinal ( ) ) { boolean couldBeTheSameTime = couldBeTheSameTime ( me , theOther ) || couldBeTheSameTime ( theOther , me ) ; if ( ! couldBeTheSameTime ) { return false ; } } } return null ; } if ( me . getPrecision ( ) == theOther . getPrecision ( ) ) { if ( me . getPrecision ( ) . ordinal ( ) >= TemporalPrecisionEnum . MINUTE . ordinal ( ) ) { long leftTime = me . getValue ( ) . getTime ( ) ; long rightTime = theOther . getValue ( ) . getTime ( ) ; return leftTime == rightTime ; } else { String leftTime = me . getValueAsString ( ) ; String rightTime = theOther . getValueAsString ( ) ; return leftTime . equals ( rightTime ) ; } } if ( ( ( Integer ) 0 ) . equals ( me . getMillis ( ) ) ) { if ( ( ( Integer ) 0 ) . equals ( theOther . getMillis ( ) ) ) { if ( me . getPrecision ( ) . ordinal ( ) >= TemporalPrecisionEnum . SECOND . ordinal ( ) ) { if ( theOther . getPrecision ( ) . ordinal ( ) >= TemporalPrecisionEnum . SECOND . ordinal ( ) ) { return me . getValue ( ) . getTime ( ) == theOther . getValue ( ) . getTime ( ) ; } } } } return false ; } | This method implements a datetime equality check using the rules as defined by FHIRPath . |
32,816 | public String getSubscriptionId ( FhirContext theFhirContext ) { String retVal = null ; if ( getSubscription ( ) != null ) { retVal = getSubscription ( ) . getIdElement ( theFhirContext ) . getValue ( ) ; } return retVal ; } | Helper method to fetch the subscription ID |
32,817 | public boolean ensureSearchEntityLoaded ( ) { if ( mySearchEntity == null ) { ensureDependenciesInjected ( ) ; TransactionTemplate txTemplate = new TransactionTemplate ( myPlatformTransactionManager ) ; txTemplate . setPropagationBehavior ( TransactionDefinition . PROPAGATION_REQUIRED ) ; txTemplate . setIsolationLevel ( TransactionDefinition . ISOLATION_READ_COMMITTED ) ; return txTemplate . execute ( s -> { try { setSearchEntity ( mySearchDao . findByUuid ( myUuid ) ) ; if ( mySearchEntity == null ) { return false ; } ourLog . trace ( "Retrieved search with version {} and total {}" , mySearchEntity . getVersion ( ) , mySearchEntity . getTotalCount ( ) ) ; mySearchEntity . getIncludes ( ) . size ( ) ; return true ; } catch ( NoResultException e ) { return false ; } } ) ; } return true ; } | Returns false if the entity can t be found |
32,818 | @ SuppressWarnings ( "deprecation" ) public boolean equalsIgnoreBase ( IdDt theId ) { if ( theId == null ) { return false ; } if ( theId . isEmpty ( ) ) { return isEmpty ( ) ; } return ObjectUtils . equals ( getResourceType ( ) , theId . getResourceType ( ) ) && ObjectUtils . equals ( getIdPart ( ) , theId . getIdPart ( ) ) && ObjectUtils . equals ( getVersionIdPart ( ) , theId . getVersionIdPart ( ) ) ; } | Returns true if this IdDt matches the given IdDt in terms of resource type and ID but ignores the URL base |
32,819 | public Object intercept ( final InvocationContext ctx ) throws JaxRsResponseException { try { return ctx . proceed ( ) ; } catch ( final Exception theException ) { final AbstractJaxRsProvider theServer = ( AbstractJaxRsProvider ) ctx . getTarget ( ) ; throw convertException ( theServer , theException ) ; } } | This interceptor will catch all exception and convert them using the exceptionhandler |
32,820 | public JaxRsResponseException convertException ( final AbstractJaxRsProvider theServer , final Throwable theException ) { if ( theServer . withStackTrace ( ) ) { exceptionHandler . setReturnStackTracesForExceptionTypes ( Throwable . class ) ; } final JaxRsRequest requestDetails = theServer . getRequest ( null , null ) . build ( ) ; final BaseServerResponseException convertedException = preprocessException ( theException , requestDetails ) ; return new JaxRsResponseException ( convertedException ) ; } | This method convert an exception to a JaxRsResponseException |
32,821 | public Response convertExceptionIntoResponse ( final JaxRsRequest theRequest , final JaxRsResponseException theException ) throws IOException { return handleExceptionWithoutServletError ( theRequest , theException ) ; } | This method converts an exception into a response |
32,822 | public static < T > T getTargetObject ( Object proxy , Class < T > clazz ) throws Exception { while ( ( AopUtils . isJdkDynamicProxy ( proxy ) ) ) { return clazz . cast ( getTargetObject ( ( ( Advised ) proxy ) . getTargetSource ( ) . getTarget ( ) , clazz ) ) ; } return clazz . cast ( proxy ) ; } | Retrieve the Spring proxy object s target object |
32,823 | public static IBundleProvider newEmptyList ( ) { final InstantDt published = InstantDt . withCurrentTime ( ) ; return new IBundleProvider ( ) { public List < IBaseResource > getResources ( int theFromIndex , int theToIndex ) { return Collections . emptyList ( ) ; } public Integer size ( ) { return 0 ; } public InstantDt getPublished ( ) { return published ; } public Integer preferredPageSize ( ) { return null ; } public String getUuid ( ) { return null ; } } ; } | Create a new unmodifiable empty resource list with the current time as the publish date . |
32,824 | private List < String > getHeaderValues ( String headerName ) { if ( additionalHttpHeaders . get ( headerName ) == null ) { additionalHttpHeaders . put ( headerName , new ArrayList < String > ( ) ) ; } return additionalHttpHeaders . get ( headerName ) ; } | Gets the header values list for a given header . If the header doesn t have any values an empty list will be returned . |
32,825 | public void interceptRequest ( IHttpRequest theRequest ) { for ( Map . Entry < String , List < String > > header : additionalHttpHeaders . entrySet ( ) ) { for ( String headerValue : header . getValue ( ) ) { if ( headerValue != null ) { theRequest . addHeader ( header . getKey ( ) , headerValue ) ; } } } } | Adds the additional header values to the HTTP request . |
32,826 | void sealAndInitialize ( FhirContext theContext , Map < Class < ? extends IBase > , BaseRuntimeElementDefinition < ? > > theClassToElementDefinitions ) { for ( BaseRuntimeChildDefinition next : myExtensions ) { next . sealAndInitialize ( theContext , theClassToElementDefinitions ) ; } for ( RuntimeChildDeclaredExtensionDefinition next : myExtensions ) { String extUrl = next . getExtensionUrl ( ) ; if ( myUrlToExtension . containsKey ( extUrl ) ) { throw new ConfigurationException ( "Duplicate extension URL[" + extUrl + "] in Element[" + getName ( ) + "]" ) ; } myUrlToExtension . put ( extUrl , next ) ; if ( next . isModifier ( ) ) { myExtensionsModifier . add ( next ) ; } else { myExtensionsNonModifier . add ( next ) ; } } myExtensions = Collections . unmodifiableList ( myExtensions ) ; } | Invoked prior to use to perform any initialization and make object mutable . |
32,827 | private String emitInnerTypes ( ) { StringBuilder itDefs = new StringBuilder ( ) ; while ( emittedInnerTypes . size ( ) < innerTypes . size ( ) ) { for ( Pair < StructureDefinition , ElementDefinition > it : new HashSet < Pair < StructureDefinition , ElementDefinition > > ( innerTypes ) ) { if ( ! emittedInnerTypes . contains ( it ) ) { itDefs . append ( "\n" ) . append ( genInnerTypeDef ( it . getLeft ( ) , it . getRight ( ) ) ) ; emittedInnerTypes . add ( it ) ; } } } return itDefs . toString ( ) ; } | Generate a flattened definition for the inner types |
32,828 | private String emitDataTypes ( ) { StringBuilder dtDefs = new StringBuilder ( ) ; while ( emittedDatatypes . size ( ) < datatypes . size ( ) ) { for ( String dt : new HashSet < String > ( datatypes ) ) { if ( ! emittedDatatypes . contains ( dt ) ) { StructureDefinition sd = context . fetchResource ( StructureDefinition . class , ProfileUtilities . sdNs ( dt , null ) ) ; if ( sd != null && ! uniq_structure_urls . contains ( sd . getUrl ( ) ) ) dtDefs . append ( "\n" ) . append ( genShapeDefinition ( sd , false ) ) ; emittedDatatypes . add ( dt ) ; } } } return dtDefs . toString ( ) ; } | Generate a shape definition for the current set of datatypes |
32,829 | private String simpleElement ( StructureDefinition sd , ElementDefinition ed , String typ ) { String addldef = "" ; ElementDefinition . ElementDefinitionBindingComponent binding = ed . getBinding ( ) ; if ( binding . hasStrength ( ) && binding . getStrength ( ) == Enumerations . BindingStrength . REQUIRED && "code" . equals ( typ ) ) { ValueSet vs = resolveBindingReference ( sd , binding . getValueSet ( ) ) ; if ( vs != null ) { addldef = tmplt ( VALUESET_DEFN_TEMPLATE ) . add ( "vsn" , vsprefix ( vs . getUrl ( ) ) ) . render ( ) ; required_value_sets . add ( vs ) ; } } if ( ed . hasFixed ( ) ) { addldef = tmplt ( FIXED_VALUE_TEMPLATE ) . add ( "val" , ed . getFixed ( ) . primitiveValue ( ) ) . render ( ) ; } return tmplt ( SIMPLE_ELEMENT_DEFN_TEMPLATE ) . add ( "typ" , typ ) . add ( "vsdef" , addldef ) . render ( ) ; } | Generate a type reference and optional value set definition |
32,830 | private String genTypeRef ( StructureDefinition sd , ElementDefinition ed , String id , ElementDefinition . TypeRefComponent typ ) { if ( typ . hasProfile ( ) ) { if ( typ . getCode ( ) . equals ( "Reference" ) ) return genReference ( "" , typ ) ; else if ( ProfileUtilities . getChildList ( sd , ed ) . size ( ) > 0 ) { innerTypes . add ( new ImmutablePair < StructureDefinition , ElementDefinition > ( sd , ed ) ) ; return simpleElement ( sd , ed , id ) ; } else { String ref = getTypeName ( typ ) ; datatypes . add ( ref ) ; return simpleElement ( sd , ed , ref ) ; } } else if ( typ . getCodeElement ( ) . getExtensionsByUrl ( ToolingExtensions . EXT_RDF_TYPE ) . size ( ) > 0 ) { String xt = null ; try { xt = typ . getCodeElement ( ) . getExtensionString ( ToolingExtensions . EXT_RDF_TYPE ) ; } catch ( FHIRException e ) { e . printStackTrace ( ) ; } ST td_entry = tmplt ( PRIMITIVE_ELEMENT_DEFN_TEMPLATE ) . add ( "typ" , xt . replace ( "xsd:token" , "xsd:string" ) . replace ( "xsd:int" , "xsd:integer" ) ) ; StringBuilder facets = new StringBuilder ( ) ; if ( ed . hasMinValue ( ) ) { Type mv = ed . getMinValue ( ) ; facets . append ( tmplt ( MINVALUE_TEMPLATE ) . add ( "val" , mv . primitiveValue ( ) ) . render ( ) ) ; } if ( ed . hasMaxValue ( ) ) { Type mv = ed . getMaxValue ( ) ; facets . append ( tmplt ( MAXVALUE_TEMPLATE ) . add ( "val" , mv . primitiveValue ( ) ) . render ( ) ) ; } if ( ed . hasMaxLength ( ) ) { int ml = ed . getMaxLength ( ) ; facets . append ( tmplt ( MAXLENGTH_TEMPLATE ) . add ( "val" , ml ) . render ( ) ) ; } if ( ed . hasPattern ( ) ) { Type pat = ed . getPattern ( ) ; facets . append ( tmplt ( PATTERN_TEMPLATE ) . add ( "val" , pat . primitiveValue ( ) ) . render ( ) ) ; } td_entry . add ( "facets" , facets . toString ( ) ) ; return td_entry . render ( ) ; } else if ( typ . getCode ( ) == null ) { ST primitive_entry = tmplt ( PRIMITIVE_ELEMENT_DEFN_TEMPLATE ) ; primitive_entry . add ( "typ" , "xsd:string" ) ; return primitive_entry . render ( ) ; } else if ( typ . getCode ( ) . equals ( "xhtml" ) ) { return tmplt ( XHTML_TYPE_TEMPLATE ) . render ( ) ; } else { datatypes . add ( typ . getCode ( ) ) ; return simpleElement ( sd , ed , typ . getCode ( ) ) ; } } | Generate a type reference |
32,831 | private ST genAlternativeTypes ( ElementDefinition ed , String id , String shortId ) { ST shex_alt = tmplt ( ALTERNATIVE_SHAPES_TEMPLATE ) ; List < String > altEntries = new ArrayList < String > ( ) ; for ( ElementDefinition . TypeRefComponent typ : ed . getType ( ) ) { altEntries . add ( genAltEntry ( id , typ ) ) ; } shex_alt . add ( "altEntries" , StringUtils . join ( altEntries , " OR\n " ) ) ; return shex_alt ; } | Generate a set of alternative shapes |
32,832 | private String genAltEntry ( String id , ElementDefinition . TypeRefComponent typ ) { if ( ! typ . getCode ( ) . equals ( "Reference" ) ) throw new AssertionError ( "We do not handle " + typ . getCode ( ) + " alternatives" ) ; return genReference ( id , typ ) ; } | Generate an alternative shape for a reference |
32,833 | private String genChoiceEntry ( StructureDefinition sd , ElementDefinition ed , String id , String base , ElementDefinition . TypeRefComponent typ ) { ST shex_choice_entry = tmplt ( ELEMENT_TEMPLATE ) ; String ext = typ . getCode ( ) ; shex_choice_entry . add ( "id" , "fhir:" + base + Character . toUpperCase ( ext . charAt ( 0 ) ) + ext . substring ( 1 ) + " " ) ; shex_choice_entry . add ( "card" , "" ) ; shex_choice_entry . add ( "defn" , genTypeRef ( sd , ed , id , typ ) ) ; shex_choice_entry . add ( "comment" , " " ) ; return shex_choice_entry . render ( ) ; } | Generate an entry in a choice list |
32,834 | private String genInnerTypeDef ( StructureDefinition sd , ElementDefinition ed ) { String path = ed . hasBase ( ) ? ed . getBase ( ) . getPath ( ) : ed . getPath ( ) ; ; ST element_reference = tmplt ( SHAPE_DEFINITION_TEMPLATE ) ; element_reference . add ( "resourceDecl" , "" ) ; element_reference . add ( "id" , path ) ; String comment = ed . getShort ( ) ; element_reference . add ( "comment" , comment == null ? " " : "# " + comment ) ; List < String > elements = new ArrayList < String > ( ) ; for ( ElementDefinition child : ProfileUtilities . getChildList ( sd , path , null ) ) elements . add ( genElementDefinition ( sd , child ) ) ; element_reference . add ( "elements" , StringUtils . join ( elements , "\n" ) ) ; return element_reference . render ( ) ; } | Generate a definition for a referenced element |
32,835 | private String genReference ( String id , ElementDefinition . TypeRefComponent typ ) { ST shex_ref = tmplt ( REFERENCE_DEFN_TEMPLATE ) ; String ref = getTypeName ( typ ) ; shex_ref . add ( "id" , id ) ; shex_ref . add ( "ref" , ref ) ; references . add ( ref ) ; return shex_ref . render ( ) ; } | Generate a reference to a resource |
32,836 | private String getTypeName ( ElementDefinition . TypeRefComponent typ ) { if ( typ . hasTargetProfile ( ) ) { String [ ] els = typ . getTargetProfile ( ) . get ( 0 ) . getValue ( ) . split ( "/" ) ; return els [ els . length - 1 ] ; } else if ( typ . hasProfile ( ) ) { String [ ] els = typ . getProfile ( ) . get ( 0 ) . getValue ( ) . split ( "/" ) ; return els [ els . length - 1 ] ; } else { return typ . getCode ( ) ; } } | Return the type name for typ |
32,837 | public IMatches < IAndUnits > withPrefix ( final ParamPrefixEnum thePrefix ) { return new NumberClientParam . IMatches < IAndUnits > ( ) { public IAndUnits number ( long theNumber ) { return new AndUnits ( thePrefix , Long . toString ( theNumber ) ) ; } public IAndUnits number ( String theNumber ) { return new AndUnits ( thePrefix , theNumber ) ; } } ; } | Use the given quantity prefix |
32,838 | public BaseMethodBinding < ? > determineResourceMethod ( RequestDetails requestDetails , String requestPath ) { RequestTypeEnum requestType = requestDetails . getRequestType ( ) ; ResourceBinding resourceBinding = null ; BaseMethodBinding < ? > resourceMethod = null ; String resourceName = requestDetails . getResourceName ( ) ; if ( myServerConformanceMethod . incomingServerRequestMatchesMethod ( requestDetails ) ) { resourceMethod = myServerConformanceMethod ; } else if ( resourceName == null ) { resourceBinding = myServerBinding ; } else { resourceBinding = myResourceNameToBinding . get ( resourceName ) ; if ( resourceBinding == null ) { throwUnknownResourceTypeException ( resourceName ) ; } } if ( resourceMethod == null ) { if ( resourceBinding != null ) { resourceMethod = resourceBinding . getMethod ( requestDetails ) ; } if ( resourceMethod == null ) { resourceMethod = myGlobalBinding . getMethod ( requestDetails ) ; } } if ( resourceMethod == null ) { if ( isBlank ( requestPath ) ) { throw new InvalidRequestException ( myFhirContext . getLocalizer ( ) . getMessage ( RestfulServer . class , "rootRequest" ) ) ; } throwUnknownFhirOperationException ( requestDetails , requestPath , requestType ) ; } return resourceMethod ; } | Figure out and return whichever method binding is appropriate for the given request |
32,839 | public List < IServerInterceptor > getInterceptors_ ( ) { List < IServerInterceptor > retVal = getInterceptorService ( ) . getAllRegisteredInterceptors ( ) . stream ( ) . filter ( t -> t instanceof IServerInterceptor ) . map ( t -> ( IServerInterceptor ) t ) . collect ( Collectors . toList ( ) ) ; return Collections . unmodifiableList ( retVal ) ; } | Returns a list of all registered server interceptors |
32,840 | public void setPlainProviders ( Collection < Object > theProviders ) { Validate . noNullElements ( theProviders , "theProviders must not contain any null elements" ) ; myPlainProviders . clear ( ) ; if ( theProviders != null ) { myPlainProviders . addAll ( theProviders ) ; } } | Sets the non - resource specific providers which implement method calls on this server . |
32,841 | public void registerProvider ( Object provider ) { if ( provider != null ) { Collection < Object > providerList = new ArrayList < > ( 1 ) ; providerList . add ( provider ) ; registerProviders ( providerList ) ; } } | Register a single provider . This could be a Resource Provider or a plain provider not associated with any resource . |
32,842 | public void registerProviders ( Collection < ? > theProviders ) { Validate . noNullElements ( theProviders , "theProviders must not contain any null elements" ) ; myProviderRegistrationMutex . lock ( ) ; try { if ( ! myStarted ) { for ( Object provider : theProviders ) { ourLog . info ( "Registration of provider [" + provider . getClass ( ) . getName ( ) + "] will be delayed until FHIR server startup" ) ; if ( provider instanceof IResourceProvider ) { myResourceProviders . add ( ( IResourceProvider ) provider ) ; } else { myPlainProviders . add ( provider ) ; } } return ; } } finally { myProviderRegistrationMutex . unlock ( ) ; } registerProviders ( theProviders , false ) ; } | Register a group of theProviders . These could be Resource Providers plain theProviders or a mixture of the two . |
32,843 | public void setProviders ( Object ... theProviders ) { Validate . noNullElements ( theProviders , "theProviders must not contain any null elements" ) ; myPlainProviders . clear ( ) ; if ( theProviders != null ) { myPlainProviders . addAll ( Arrays . asList ( theProviders ) ) ; } } | Sets the non - resource specific providers which implement method calls on this server |
32,844 | public void unregisterInterceptor ( Object theInterceptor ) { Validate . notNull ( theInterceptor , "Interceptor can not be null" ) ; getInterceptorService ( ) . unregisterInterceptor ( theInterceptor ) ; } | Unregisters an interceptor |
32,845 | public void submitResourceModified ( final ResourceModifiedMessage theMsg ) { if ( TransactionSynchronizationManager . isSynchronizationActive ( ) ) { TransactionSynchronizationManager . registerSynchronization ( new TransactionSynchronizationAdapter ( ) { public int getOrder ( ) { return 0 ; } public void afterCommit ( ) { sendToProcessingChannel ( theMsg ) ; } } ) ; } else { sendToProcessingChannel ( theMsg ) ; } } | This is an internal API - Use with caution! |
32,846 | public static Template parse ( String input ) { return new Template ( input , Tag . getTags ( ) , Filter . getFilters ( ) ) ; } | Returns a new Template instance from a given input string . |
32,847 | public String toStringAST ( ) { StringBuilder builder = new StringBuilder ( ) ; walk ( root , builder ) ; return builder . toString ( ) ; } | Returns a string representation of the AST of the parsed input source . |
32,848 | private < T extends BaseResourceIndex > void tryToReuseIndexEntities ( List < T > theIndexesToRemove , List < T > theIndexesToAdd ) { for ( int addIndex = 0 ; addIndex < theIndexesToAdd . size ( ) ; addIndex ++ ) { if ( theIndexesToRemove . isEmpty ( ) ) { break ; } T targetEntity = theIndexesToAdd . get ( addIndex ) ; if ( targetEntity . getId ( ) != null ) { continue ; } T entityToReuse = theIndexesToRemove . remove ( theIndexesToRemove . size ( ) - 1 ) ; targetEntity . setId ( entityToReuse . getId ( ) ) ; } } | The logic here is that often times when we update a resource we are dropping one index row and adding another . This method tries to reuse rows that would otherwise have been deleted by updating them with the contents of rows that would have otherwise been added . In other words we re trying to replace one delete + one insert with one update |
32,849 | private ConcurrentHashMap < String , BaseMethodBinding < ? > > getMapForOperation ( RestOperationTypeEnum operationType ) { ConcurrentHashMap < String , BaseMethodBinding < ? > > result = operationBindings . get ( operationType ) ; if ( result == null ) { operationBindings . putIfAbsent ( operationType , new ConcurrentHashMap < String , BaseMethodBinding < ? > > ( ) ) ; return getMapForOperation ( operationType ) ; } else { return result ; } } | Get the map for the given operation type . If no map exists for this operation type create a new hashmap for this operation type and add it to the operation bindings . |
32,850 | public BaseMethodBinding < ? > getBinding ( RestOperationTypeEnum operationType , String theBindingKey ) { String bindingKey = StringUtils . defaultIfBlank ( theBindingKey , DEFAULT_METHOD_KEY ) ; ConcurrentHashMap < String , BaseMethodBinding < ? > > map = getMapForOperation ( operationType ) ; if ( map == null || ! map . containsKey ( bindingKey ) ) { throw new NotImplementedOperationException ( "Operation not implemented" ) ; } else { return map . get ( bindingKey ) ; } } | Get the binding |
32,851 | public static JaxRsMethodBindings getMethodBindings ( AbstractJaxRsProvider theProvider , Class < ? extends AbstractJaxRsProvider > theProviderClass ) { if ( ! getClassBindings ( ) . containsKey ( theProviderClass ) ) { JaxRsMethodBindings foundBindings = new JaxRsMethodBindings ( theProvider , theProviderClass ) ; getClassBindings ( ) . putIfAbsent ( theProviderClass , foundBindings ) ; } return getClassBindings ( ) . get ( theProviderClass ) ; } | Get the method bindings for the given class . If this class is not yet contained in the classBindings they will be added for this class |
32,852 | public void addExecuteOnlyIfColumnExists ( String theTableName , String theColumnName ) { myConditionalOnExistenceOf . add ( new TableAndColumn ( theTableName , theColumnName ) ) ; } | This task will only execute if the following column exists |
32,853 | public String pluralize ( Object word ) { if ( word == null ) return null ; String wordStr = word . toString ( ) . trim ( ) ; if ( wordStr . length ( ) == 0 ) return wordStr ; if ( isUncountable ( wordStr ) ) return wordStr ; for ( Rule rule : this . plurals ) { String result = rule . apply ( wordStr ) ; if ( result != null ) return result ; } return wordStr ; } | Returns the plural form of the word in the string . |
32,854 | public String singularize ( Object word ) { if ( word == null ) return null ; String wordStr = word . toString ( ) . trim ( ) ; if ( wordStr . length ( ) == 0 ) return wordStr ; if ( isUncountable ( wordStr ) ) return wordStr ; for ( Rule rule : this . singulars ) { String result = rule . apply ( wordStr ) ; if ( result != null ) return result ; } return wordStr ; } | Returns the singular form of the word in the string . |
32,855 | public String capitalize ( String words ) { if ( words == null ) return null ; String result = words . trim ( ) ; if ( result . length ( ) == 0 ) return "" ; if ( result . length ( ) == 1 ) return result . toUpperCase ( ) ; return "" + Character . toUpperCase ( result . charAt ( 0 ) ) + result . substring ( 1 ) . toLowerCase ( ) ; } | Returns a copy of the input with the first character converted to uppercase and the remainder to lowercase . |
32,856 | public boolean outgoingResponse ( RequestDetails theRequestDetails , Bundle theResponseObject , HttpServletRequest theServletRequest , HttpServletResponse theServletResponse ) throws AuthenticationException { if ( myClientParamsOptional && myDataStore == null ) { log . debug ( "No auditing configured." ) ; return true ; } if ( theResponseObject == null || theResponseObject . isEmpty ( ) ) { log . debug ( "No bundle to audit" ) ; return true ; } try { log . info ( "Auditing bundle: " + theResponseObject + " from request " + theRequestDetails ) ; SecurityEvent auditEvent = new SecurityEvent ( ) ; auditEvent . setEvent ( getEventInfo ( theRequestDetails ) ) ; Participant participant = getParticipant ( theServletRequest ) ; if ( participant == null ) { log . debug ( "No participant to audit" ) ; return true ; } List < Participant > participants = new ArrayList < SecurityEvent . Participant > ( 1 ) ; participants . add ( participant ) ; auditEvent . setParticipant ( participants ) ; SecurityEventObjectLifecycleEnum lifecycle = mapResourceTypeToSecurityLifecycle ( theRequestDetails . getRestOperationType ( ) ) ; byte [ ] query = getQueryFromRequestDetails ( theRequestDetails ) ; List < ObjectElement > auditableObjects = new ArrayList < SecurityEvent . ObjectElement > ( ) ; for ( BundleEntry entry : theResponseObject . getEntries ( ) ) { IResource resource = entry . getResource ( ) ; ObjectElement auditableObject = getObjectElement ( resource , lifecycle , query ) ; if ( auditableObject != null ) auditableObjects . add ( auditableObject ) ; } if ( auditableObjects . isEmpty ( ) ) { log . debug ( "No auditable resources to audit." ) ; return true ; } else { log . debug ( "Auditing " + auditableObjects . size ( ) + " resources." ) ; } auditEvent . setObject ( auditableObjects ) ; auditEvent . setSource ( getSourceElement ( theServletRequest ) ) ; store ( auditEvent ) ; return true ; } catch ( Exception e ) { log . error ( "Unable to audit resource: " + theResponseObject + " from request: " + theRequestDetails , e ) ; throw new InternalErrorException ( "Auditing failed, unable to complete request" , e ) ; } } | Intercept the outgoing response to perform auditing of the request data if the bundle contains auditable resources . |
32,857 | protected Event getEventInfo ( RequestDetails theRequestDetails ) { Event event = new Event ( ) ; event . setAction ( mapResourceTypeToSecurityEventAction ( theRequestDetails . getRestOperationType ( ) ) ) ; event . setDateTimeWithMillisPrecision ( new Date ( ) ) ; event . setOutcome ( SecurityEventOutcomeEnum . SUCCESS ) ; return event ; } | Generates the Event segment of the SecurityEvent based on the incoming request details |
32,858 | protected byte [ ] getQueryFromRequestDetails ( RequestDetails theRequestDetails ) { byte [ ] query ; try { query = theRequestDetails . getCompleteUrl ( ) . getBytes ( "UTF-8" ) ; } catch ( UnsupportedEncodingException e1 ) { log . warn ( "Unable to encode URL to bytes in UTF-8, defaulting to platform default charset." , e1 ) ; query = theRequestDetails . getCompleteUrl ( ) . getBytes ( ) ; } return query ; } | Return the query URL encoded to bytes to be set as the Object . query on the Security Event |
32,859 | protected ObjectElement getObjectElement ( IResource resource , SecurityEventObjectLifecycleEnum lifecycle , byte [ ] query ) throws InstantiationException , IllegalAccessException { String resourceType = resource . getResourceName ( ) ; if ( myAuditableResources . containsKey ( resourceType ) ) { log . debug ( "Found auditable resource of type: " + resourceType ) ; @ SuppressWarnings ( "unchecked" ) IResourceAuditor < IResource > auditableResource = ( IResourceAuditor < IResource > ) myAuditableResources . get ( resourceType ) . newInstance ( ) ; auditableResource . setResource ( resource ) ; if ( auditableResource . isAuditable ( ) ) { ObjectElement object = new ObjectElement ( ) ; object . setReference ( new ResourceReferenceDt ( resource . getId ( ) ) ) ; object . setLifecycle ( lifecycle ) ; object . setQuery ( query ) ; object . setName ( auditableResource . getName ( ) ) ; object . setIdentifier ( ( IdentifierDt ) auditableResource . getIdentifier ( ) ) ; object . setType ( auditableResource . getType ( ) ) ; object . setDescription ( auditableResource . getDescription ( ) ) ; Map < String , String > detailMap = auditableResource . getDetail ( ) ; if ( detailMap != null && ! detailMap . isEmpty ( ) ) { List < ObjectDetail > details = new ArrayList < SecurityEvent . ObjectDetail > ( ) ; for ( Entry < String , String > entry : detailMap . entrySet ( ) ) { ObjectDetail detail = makeObjectDetail ( entry . getKey ( ) , entry . getValue ( ) ) ; details . add ( detail ) ; } object . setDetail ( details ) ; } if ( auditableResource . getSensitivity ( ) != null ) { CodingDt coding = object . getSensitivity ( ) . addCoding ( ) ; coding . setSystem ( auditableResource . getSensitivity ( ) . getSystemElement ( ) . getValue ( ) ) ; coding . setCode ( auditableResource . getSensitivity ( ) . getCodeElement ( ) . getValue ( ) ) ; coding . setDisplay ( auditableResource . getSensitivity ( ) . getDisplayElement ( ) . getValue ( ) ) ; } return object ; } else { log . debug ( "Resource is not auditable" ) ; } } else { log . debug ( "No auditor configured for resource type " + resourceType ) ; } return null ; } | If the resource is considered an auditable resource containing PHI create an ObjectElement otherwise return null |
32,860 | protected ObjectDetail makeObjectDetail ( String type , String value ) { ObjectDetail detail = new ObjectDetail ( ) ; if ( type != null ) detail . setType ( type ) ; if ( value != null ) detail . setValue ( value . getBytes ( ) ) ; return detail ; } | Helper method to create an ObjectDetail from a pair of Strings . |
32,861 | protected List < CodingDt > getAccessType ( HttpServletRequest theServletRequest ) { List < CodingDt > types = new ArrayList < CodingDt > ( ) ; if ( theServletRequest . getHeader ( Constants . HEADER_AUTHORIZATION ) != null && theServletRequest . getHeader ( Constants . HEADER_AUTHORIZATION ) . startsWith ( "OAuth" ) ) { types . add ( new CodingDt ( SecurityEventSourceTypeEnum . USER_DEVICE . getSystem ( ) , SecurityEventSourceTypeEnum . USER_DEVICE . getCode ( ) ) ) ; } else { String userId = theServletRequest . getHeader ( UserInfoInterceptor . HEADER_USER_ID ) ; String appId = theServletRequest . getHeader ( UserInfoInterceptor . HEADER_APPLICATION_NAME ) ; if ( userId == null && appId != null ) types . add ( new CodingDt ( SecurityEventSourceTypeEnum . APPLICATION_SERVER . getSystem ( ) , SecurityEventSourceTypeEnum . APPLICATION_SERVER . getCode ( ) ) ) ; else types . add ( new CodingDt ( SecurityEventSourceTypeEnum . USER_DEVICE . getSystem ( ) , SecurityEventSourceTypeEnum . USER_DEVICE . getCode ( ) ) ) ; } return types ; } | Return the access type for this request |
32,862 | protected SecurityEventActionEnum mapResourceTypeToSecurityEventAction ( ca . uhn . fhir . rest . api . RestOperationTypeEnum theRestfulOperationTypeEnum ) { if ( theRestfulOperationTypeEnum == null ) return null ; switch ( theRestfulOperationTypeEnum ) { case READ : return SecurityEventActionEnum . READ_VIEW_PRINT ; case CREATE : return SecurityEventActionEnum . CREATE ; case DELETE : return SecurityEventActionEnum . DELETE ; case HISTORY_INSTANCE : return SecurityEventActionEnum . READ_VIEW_PRINT ; case HISTORY_TYPE : return SecurityEventActionEnum . READ_VIEW_PRINT ; case SEARCH_TYPE : return SecurityEventActionEnum . READ_VIEW_PRINT ; case UPDATE : return SecurityEventActionEnum . UPDATE ; case VALIDATE : return SecurityEventActionEnum . READ_VIEW_PRINT ; case VREAD : return SecurityEventActionEnum . READ_VIEW_PRINT ; default : return SecurityEventActionEnum . READ_VIEW_PRINT ; } } | Returns the SecurityEventActionEnum corresponding to the specified RestfulOperationTypeEnum |
32,863 | protected SecurityEventObjectLifecycleEnum mapResourceTypeToSecurityLifecycle ( ca . uhn . fhir . rest . api . RestOperationTypeEnum theRestfulOperationTypeEnum ) { if ( theRestfulOperationTypeEnum == null ) return null ; switch ( theRestfulOperationTypeEnum ) { case READ : return SecurityEventObjectLifecycleEnum . ACCESS_OR_USE ; case CREATE : return SecurityEventObjectLifecycleEnum . ORIGINATION_OR_CREATION ; case DELETE : return SecurityEventObjectLifecycleEnum . LOGICAL_DELETION ; case HISTORY_INSTANCE : return SecurityEventObjectLifecycleEnum . ACCESS_OR_USE ; case HISTORY_TYPE : return SecurityEventObjectLifecycleEnum . ACCESS_OR_USE ; case SEARCH_TYPE : return SecurityEventObjectLifecycleEnum . ACCESS_OR_USE ; case UPDATE : return SecurityEventObjectLifecycleEnum . AMENDMENT ; case VALIDATE : return SecurityEventObjectLifecycleEnum . VERIFICATION ; case VREAD : return SecurityEventObjectLifecycleEnum . ACCESS_OR_USE ; default : return SecurityEventObjectLifecycleEnum . ACCESS_OR_USE ; } } | Returns the SecurityEventObjectLifecycleEnum corresponding to the specified RestfulOperationTypeEnum |
32,864 | public void addAuditableResource ( String resourceType , Class < ? extends IResourceAuditor < ? extends IResource > > auditableResource ) { if ( myAuditableResources == null ) myAuditableResources = new HashMap < String , Class < ? extends IResourceAuditor < ? extends IResource > > > ( ) ; myAuditableResources . put ( resourceType , auditableResource ) ; } | Add a type of auditable resource and its auditor to this AuditingInterceptor s resource map |
32,865 | public IBaseOperationOutcome toOperationOutcome ( ) { IBaseOperationOutcome oo = ( IBaseOperationOutcome ) myCtx . getResourceDefinition ( "OperationOutcome" ) . newInstance ( ) ; populateOperationOutcome ( oo ) ; return oo ; } | Create an OperationOutcome resource which contains all of the messages found as a result of this validation |
32,866 | public void populateOperationOutcome ( IBaseOperationOutcome theOperationOutcome ) { for ( SingleValidationMessage next : myMessages ) { String location ; if ( isNotBlank ( next . getLocationString ( ) ) ) { location = next . getLocationString ( ) ; } else if ( next . getLocationLine ( ) != null || next . getLocationCol ( ) != null ) { location = "Line[" + next . getLocationLine ( ) + "] Col[" + next . getLocationCol ( ) + "]" ; } else { location = null ; } String severity = next . getSeverity ( ) != null ? next . getSeverity ( ) . getCode ( ) : null ; OperationOutcomeUtil . addIssue ( myCtx , theOperationOutcome , severity , next . getMessage ( ) , location , Constants . OO_INFOSTATUS_PROCESSING ) ; } if ( myMessages . isEmpty ( ) ) { String message = myCtx . getLocalizer ( ) . getMessage ( ValidationResult . class , "noIssuesDetected" ) ; OperationOutcomeUtil . addIssue ( myCtx , theOperationOutcome , "information" , message , null , "informational" ) ; } } | Populate an operation outcome with the results of the validation |
32,867 | public void initialize ( ) { try { Class . forName ( "org.hl7.fhir.instance.model.QuestionnaireResponse" ) ; myValidateResponses = true ; } catch ( ClassNotFoundException e ) { myValidateResponses = Boolean . FALSE ; } } | Initialize the bean |
32,868 | public void compose ( JsonCreator writer , Resource resource ) throws IOException { json = writer ; composeResource ( resource ) ; } | Compose a resource using a pre - existing JsonWriter |
32,869 | public static String escapeXML ( String rawContent , String charset , boolean isNoLines ) { if ( rawContent == null ) return "" ; else { StringBuffer sb = new StringBuffer ( ) ; for ( int i = 0 ; i < rawContent . length ( ) ; i ++ ) { char ch = rawContent . charAt ( i ) ; if ( ch == '\'' ) sb . append ( "'" ) ; else if ( ch == '&' ) sb . append ( "&" ) ; else if ( ch == '"' ) sb . append ( """ ) ; else if ( ch == '<' ) sb . append ( "<" ) ; else if ( ch == '>' ) sb . append ( ">" ) ; else if ( ch > '~' && charset != null && charSetImpliesAscii ( charset ) ) sb . append ( "&#x" + Integer . toHexString ( ch ) . toUpperCase ( ) + ";" ) ; else if ( isNoLines ) { if ( ch == '\r' ) sb . append ( "
" ) ; else if ( ch != '\n' ) sb . append ( ch ) ; } else sb . append ( ch ) ; } return sb . toString ( ) ; } } | Converts the raw characters to XML escape characters . |
32,870 | public List < Property > children ( ) { List < Property > result = new ArrayList < Property > ( ) ; listChildren ( result ) ; return result ; } | Supports iterating the children elements in some generic processor or browser All defined children will be listed even if they have no value on this instance |
32,871 | public synchronized void registerValidatorModule ( IValidatorModule theValidator ) { Validate . notNull ( theValidator , "theValidator must not be null" ) ; ArrayList < IValidatorModule > newValidators = new ArrayList < IValidatorModule > ( myValidators . size ( ) + 1 ) ; newValidators . addAll ( myValidators ) ; newValidators . add ( theValidator ) ; myValidators = newValidators ; } | Add a new validator module to this validator . You may register as many modules as you like at any time . |
32,872 | public synchronized void unregisterValidatorModule ( IValidatorModule theValidator ) { Validate . notNull ( theValidator , "theValidator must not be null" ) ; ArrayList < IValidatorModule > newValidators = new ArrayList < IValidatorModule > ( myValidators . size ( ) + 1 ) ; newValidators . addAll ( myValidators ) ; newValidators . remove ( theValidator ) ; myValidators = newValidators ; } | Removes a validator module from this validator . You may register as many modules as you like and remove them at any time . |
32,873 | private IBundleProvider performSearch ( String theCriteria ) { IFhirResourceDao < ? > subscriptionDao = myDaoRegistry . getSubscriptionDao ( ) ; RuntimeResourceDefinition responseResourceDef = subscriptionDao . validateCriteriaAndReturnResourceDefinition ( theCriteria ) ; SearchParameterMap responseCriteriaUrl = myMatchUrlService . translateMatchUrl ( theCriteria , responseResourceDef ) ; IFhirResourceDao < ? extends IBaseResource > responseDao = myDaoRegistry . getResourceDao ( responseResourceDef . getImplementingClass ( ) ) ; responseCriteriaUrl . setLoadSynchronousUpTo ( 1 ) ; TransactionTemplate txTemplate = new TransactionTemplate ( myTxManager ) ; txTemplate . setPropagationBehavior ( TransactionDefinition . PROPAGATION_REQUIRES_NEW ) ; return txTemplate . execute ( t -> responseDao . search ( responseCriteriaUrl ) ) ; } | Search based on a query criteria |
32,874 | private ProfilingWrapper wrap ( Base object ) { ProfilingWrapper res = new ProfilingWrapper ( context , resource , object ) ; res . cache = cache ; res . engine = engine ; return res ; } | This is a convenient called for |
32,875 | private void start ( List < ValidationMessage > errors , WrapperElement resource , WrapperElement element , StructureDefinition profile , NodeStack stack ) throws FHIRException { if ( rule ( errors , IssueType . STRUCTURE , element . line ( ) , element . col ( ) , stack . getLiteralPath ( ) , profile . hasSnapshot ( ) , "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided" ) ) { validateElement ( errors , profile , profile . getSnapshot ( ) . getElement ( ) . get ( 0 ) , null , null , resource , element , element . getName ( ) , stack , false ) ; checkDeclaredProfiles ( errors , resource , element , stack ) ; if ( element . getResourceType ( ) . equals ( "Bundle" ) ) validateBundle ( errors , element , stack ) ; if ( element . getResourceType ( ) . equals ( "Observation" ) ) validateObservation ( errors , element , stack ) ; } } | the instance validator had no issues against the base resource profile |
32,876 | public Response create ( final String resource ) throws IOException { return execute ( getResourceRequest ( RequestTypeEnum . POST , RestOperationTypeEnum . CREATE ) . resource ( resource ) ) ; } | Create a new resource with a server assigned id |
32,877 | public Response conditionalUpdate ( final String resource ) throws IOException { return execute ( getResourceRequest ( RequestTypeEnum . PUT , RestOperationTypeEnum . UPDATE ) . resource ( resource ) ) ; } | Update an existing resource based on the given condition |
32,878 | public Response delete ( ) throws IOException { return execute ( getResourceRequest ( RequestTypeEnum . DELETE , RestOperationTypeEnum . DELETE ) ) ; } | Delete a resource based on the given condition |
32,879 | @ Path ( "/{id}" ) public Response delete ( @ PathParam ( "id" ) final String id ) throws IOException { return execute ( getResourceRequest ( RequestTypeEnum . DELETE , RestOperationTypeEnum . DELETE ) . id ( id ) ) ; } | Delete a resource |
32,880 | @ Path ( "/{id}" ) public Response find ( @ PathParam ( "id" ) final String id ) throws IOException { return execute ( getResourceRequest ( RequestTypeEnum . GET , RestOperationTypeEnum . READ ) . id ( id ) ) ; } | Read the current state of the resource |
32,881 | protected Response customOperation ( final String resource , final RequestTypeEnum requestType , final String id , final String operationName , final RestOperationTypeEnum operationType ) throws IOException { final Builder request = getResourceRequest ( requestType , operationType ) . resource ( resource ) . id ( id ) ; return execute ( request , operationName ) ; } | Execute a custom operation |
32,882 | @ Path ( "/{id}/_history/{version}" ) public Response findHistory ( @ PathParam ( "id" ) final String id , @ PathParam ( "version" ) final String version ) throws IOException { final Builder theRequest = getResourceRequest ( RequestTypeEnum . GET , RestOperationTypeEnum . VREAD ) . id ( id ) . version ( version ) ; return execute ( theRequest ) ; } | Retrieve the update history for a particular resource |
32,883 | @ Path ( "/{id}/{compartment}" ) public Response findCompartment ( @ PathParam ( "id" ) final String id , @ PathParam ( "compartment" ) final String compartment ) throws IOException { final Builder theRequest = getResourceRequest ( RequestTypeEnum . GET , RestOperationTypeEnum . SEARCH_TYPE ) . id ( id ) . compartment ( compartment ) ; return execute ( theRequest , compartment ) ; } | Compartment Based Access |
32,884 | private Response execute ( final Builder theRequestBuilder , final String methodKey ) throws IOException { final JaxRsRequest theRequest = theRequestBuilder . build ( ) ; final BaseMethodBinding < ? > method = getBinding ( theRequest . getRestOperationType ( ) , methodKey ) ; try { return ( Response ) method . invokeServer ( this , theRequest ) ; } catch ( final Throwable theException ) { return handleException ( theRequest , theException ) ; } } | Execute the method described by the requestBuilder and methodKey |
32,885 | protected BaseMethodBinding < ? > getBinding ( final RestOperationTypeEnum restOperation , final String theBindingKey ) { return getBindings ( ) . getBinding ( restOperation , theBindingKey ) ; } | Return the method binding for the given rest operation |
32,886 | private Builder getResourceRequest ( final RequestTypeEnum requestType , final RestOperationTypeEnum restOperation ) { return getRequest ( requestType , restOperation , getResourceType ( ) . getSimpleName ( ) ) ; } | Return the request builder based on the resource name for the server |
32,887 | public void reset ( ) { fieldDelimiter = DEFAULT_DELIMITER_FIELD ; componentDelimiter = DEFAULT_DELIMITER_COMPONENT ; subComponentDelimiter = DEFAULT_DELIMITER_SUBCOMPONENT ; repetitionDelimiter = DEFAULT_DELIMITER_REPETITION ; escapeCharacter = DEFAULT_CHARACTER_ESCAPE ; } | reset to default HL7 values |
32,888 | public void check ( ) throws FHIRException { rule ( componentDelimiter != fieldDelimiter , "Delimiter Error: \"" + componentDelimiter + "\" is used for both CPComponent and CPField" ) ; rule ( subComponentDelimiter != fieldDelimiter , "Delimiter Error: \"" + subComponentDelimiter + "\" is used for both CPSubComponent and CPField" ) ; rule ( subComponentDelimiter != componentDelimiter , "Delimiter Error: \"" + subComponentDelimiter + "\" is used for both CPSubComponent and CPComponent" ) ; rule ( repetitionDelimiter != fieldDelimiter , "Delimiter Error: \"" + repetitionDelimiter + "\" is used for both Repetition and CPField" ) ; rule ( repetitionDelimiter != componentDelimiter , "Delimiter Error: \"" + repetitionDelimiter + "\" is used for both Repetition and CPComponent" ) ; rule ( repetitionDelimiter != subComponentDelimiter , "Delimiter Error: \"" + repetitionDelimiter + "\" is used for both Repetition and CPSubComponent" ) ; rule ( escapeCharacter != fieldDelimiter , "Delimiter Error: \"" + escapeCharacter + "\" is used for both Escape and CPField" ) ; rule ( escapeCharacter != componentDelimiter , "Delimiter Error: \"" + escapeCharacter + "\" is used for both Escape and CPComponent" ) ; rule ( escapeCharacter != subComponentDelimiter , "Delimiter Error: \"" + escapeCharacter + "\" is used for both Escape and CPSubComponent" ) ; rule ( escapeCharacter != repetitionDelimiter , "Delimiter Error: \"" + escapeCharacter + "\" is used for both Escape and Repetition" ) ; } | check that the delimiters are valid |
32,889 | public String getEscape ( char ch ) { if ( ch == escapeCharacter ) return escapeCharacter + "E" + escapeCharacter ; else if ( ch == fieldDelimiter ) return escapeCharacter + "F" + escapeCharacter ; else if ( ch == componentDelimiter ) return escapeCharacter + "S" + escapeCharacter ; else if ( ch == subComponentDelimiter ) return escapeCharacter + "T" + escapeCharacter ; else if ( ch == repetitionDelimiter ) return escapeCharacter + "R" + escapeCharacter ; else return null ; } | get the escape for a character |
32,890 | public char getDelimiterEscapeChar ( char ch ) throws DefinitionException { if ( ch == 'E' ) return escapeCharacter ; else if ( ch == 'F' ) return fieldDelimiter ; else if ( ch == 'S' ) return componentDelimiter ; else if ( ch == 'T' ) return subComponentDelimiter ; else if ( ch == 'R' ) return repetitionDelimiter ; else throw new DefinitionException ( "internal error in getDelimiterEscapeChar" ) ; } | get escape for ch in an escape |
32,891 | public Response getPages ( @ QueryParam ( Constants . PARAM_PAGINGACTION ) String thePageId ) throws IOException { JaxRsRequest theRequest = getRequest ( RequestTypeEnum . GET , RestOperationTypeEnum . GET_PAGE ) . build ( ) ; try { return ( Response ) myBinding . invokeServer ( this , theRequest ) ; } catch ( JaxRsResponseException theException ) { return new JaxRsExceptionInterceptor ( ) . convertExceptionIntoResponse ( theRequest , theException ) ; } } | This method implements the getpages action |
32,892 | @ SuppressWarnings ( "unchecked" ) public static < T extends IBaseResource > List < T > toListOfResourcesOfType ( FhirContext theContext , IBaseBundle theBundle , Class < T > theTypeToInclude ) { Objects . requireNonNull ( theTypeToInclude , "ResourceType must not be null" ) ; List < T > retVal = new ArrayList < > ( ) ; RuntimeResourceDefinition def = theContext . getResourceDefinition ( theBundle ) ; BaseRuntimeChildDefinition entryChild = def . getChildByName ( "entry" ) ; List < IBase > entries = entryChild . getAccessor ( ) . getValues ( theBundle ) ; BaseRuntimeElementCompositeDefinition < ? > entryChildElem = ( BaseRuntimeElementCompositeDefinition < ? > ) entryChild . getChildByName ( "entry" ) ; BaseRuntimeChildDefinition resourceChild = entryChildElem . getChildByName ( "resource" ) ; for ( IBase nextEntry : entries ) { for ( IBase next : resourceChild . getAccessor ( ) . getValues ( nextEntry ) ) { if ( theTypeToInclude . isAssignableFrom ( next . getClass ( ) ) ) { retVal . add ( ( T ) next ) ; } } } return retVal ; } | Extract all of the resources of a given type from a given bundle |
32,893 | public boolean isAllParametersHaveNoModifier ( ) { for ( List < List < IQueryParameterType > > nextParamName : values ( ) ) { for ( List < IQueryParameterType > nextAnd : nextParamName ) { for ( IQueryParameterType nextOr : nextAnd ) { if ( isNotBlank ( nextOr . getQueryParameterQualifier ( ) ) ) { return false ; } } } } return true ; } | This will only return true if all parameters have no modifier of any kind |
32,894 | public DateRangeParam setLowerBoundInclusive ( Date theLowerBound ) { validateAndSet ( new DateParam ( ParamPrefixEnum . GREATERTHAN_OR_EQUALS , theLowerBound ) , myUpperBound ) ; return this ; } | Sets the lower bound to be greaterthan or equal to the given date |
32,895 | public DateRangeParam setUpperBoundInclusive ( Date theUpperBound ) { validateAndSet ( myLowerBound , new DateParam ( ParamPrefixEnum . LESSTHAN_OR_EQUALS , theUpperBound ) ) ; return this ; } | Sets the upper bound to be greaterthan or equal to the given date |
32,896 | public DateRangeParam setLowerBoundExclusive ( Date theLowerBound ) { validateAndSet ( new DateParam ( ParamPrefixEnum . GREATERTHAN , theLowerBound ) , myUpperBound ) ; return this ; } | Sets the lower bound to be greaterthan to the given date |
32,897 | public DateRangeParam setUpperBoundExclusive ( Date theUpperBound ) { validateAndSet ( myLowerBound , new DateParam ( ParamPrefixEnum . LESSTHAN , theUpperBound ) ) ; return this ; } | Sets the upper bound to be greaterthan to the given date |
32,898 | public void setRangeFromDatesInclusive ( IPrimitiveType < Date > theLowerBound , IPrimitiveType < Date > theUpperBound ) { IPrimitiveType < Date > lowerBound = theLowerBound ; IPrimitiveType < Date > upperBound = theUpperBound ; if ( lowerBound != null && lowerBound . getValue ( ) != null && upperBound != null && upperBound . getValue ( ) != null ) { if ( lowerBound . getValue ( ) . after ( upperBound . getValue ( ) ) ) { IPrimitiveType < Date > temp = lowerBound ; lowerBound = upperBound ; upperBound = temp ; } } validateAndSet ( lowerBound != null ? new DateParam ( GREATERTHAN_OR_EQUALS , lowerBound ) : null , upperBound != null ? new DateParam ( LESSTHAN_OR_EQUALS , upperBound ) : null ) ; } | Sets the range from a pair of dates inclusive on both ends . Note that if theLowerBound is after theUpperBound thie method will automatically reverse the order of the arguments in order to create an inclusive range . |
32,899 | public void setPropertyFile ( String ... thePropertyFile ) { Validate . notNull ( thePropertyFile , "Property file can not be null" ) ; myPropertyFile = Arrays . asList ( thePropertyFile ) ; } | Set the property file to use |
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