A B C D E F G H I J K L M N O P Q R S T U V W X

R

range - Variable in class info.sswap.api.input.impl.PropertyInputImpl
 
RANGE - Static variable in class info.sswap.api.input.io.JSONConstants
 
range - Variable in class info.sswap.impl.empire.model.ReasoningServiceImpl.PropertyInformation
A string containing URI of a range of the property (if known), or null
RawData(SSWAPIndividual, DataFactory.Open) - Static method in class info.sswap.ontologies.data.api.DataFactory
Raw data (no base64 encoding or decoding).
RawData(SSWAPIndividual, DataFactory.Open, String, String) - Static method in class info.sswap.ontologies.data.api.DataFactory
Raw data (no base64 encoding or decoding) with HTTP Basic Authentication.
RDF_NS - Static variable in class info.sswap.impl.empire.Namespaces
The RDF namespace http://www.w3.org/1999/02/22-rdf-syntax-ns#
RDF_TYPE_URI - Static variable in class info.sswap.impl.empire.model.IndividualImpl
Constant for rdf:type property
RDF_TYPE_URI - Static variable in class info.sswap.impl.empire.model.SourceModelImpl
The URI for "rdf:type" property
RDFCSVWriter - Class in info.sswap.impl.empire.model
Deprecated. 
RDFCSVWriter() - Constructor for class info.sswap.impl.empire.model.RDFCSVWriter
Deprecated.  
RDFCSVWriter.DataStructure - Class in info.sswap.impl.empire.model
Deprecated.  
RDFCSVWriter.DataStructure() - Constructor for class info.sswap.impl.empire.model.RDFCSVWriter.DataStructure
Deprecated.  
RDFCSVWriter.MaxPropertyInstances - Class in info.sswap.impl.empire.model
Deprecated. The maximum number of instances of predicate (a subject with a property instance and a value) across all subjects.
RDFCSVWriter.MaxPropertyInstances() - Constructor for class info.sswap.impl.empire.model.RDFCSVWriter.MaxPropertyInstances
Deprecated.  
RDFCSVWriter.NameMapper - Class in info.sswap.impl.empire.model
Deprecated. Map names via re-writing rules: * blank nodes get mapped to simpler names; e.g., _:b1, _:b2, etc.
RDFCSVWriter.NameMapper(PrefixMapping) - Constructor for class info.sswap.impl.empire.model.RDFCSVWriter.NameMapper
Deprecated.  
RDFCSVWriter.SortedPredicates - Class in info.sswap.impl.empire.model
Deprecated. Key: predicate URI as a string Value: array of values for each property instance of the predicate (for a subject) TreeMap sort order must agree with MaxPropertyInstances
RDFCSVWriter.SortedPredicates() - Constructor for class info.sswap.impl.empire.model.RDFCSVWriter.SortedPredicates
Deprecated.  
RDFCSVWriter.SortedRows - Class in info.sswap.impl.empire.model
Deprecated. Key: subject URI or blank node id as a string Value: data structure of predicates for that subject
RDFCSVWriter.SortedRows() - Constructor for class info.sswap.impl.empire.model.RDFCSVWriter.SortedRows
Deprecated.  
RDFCSVWriter.Values - Class in info.sswap.impl.empire.model
Deprecated. An array of values (for a predicate)
RDFCSVWriter.Values() - Constructor for class info.sswap.impl.empire.model.RDFCSVWriter.Values
Deprecated.  
rdfErrorHandler - Variable in class info.sswap.impl.empire.model.RDFCSVWriter
Deprecated.  
rdfErrorHandler - Variable in class info.sswap.impl.empire.model.RDFTSVWriter
 
rdfIdEquals(ModelImpl) - Method in class info.sswap.impl.empire.model.ModelImpl
 
rdfIdHashCode() - Method in class info.sswap.impl.empire.model.ModelImpl
 
rdfKey - Variable in class info.sswap.impl.empire.model.DatatypeImpl
The RDF identifier of this data type.
rdfKey - Variable in class info.sswap.impl.empire.model.PredicateImpl
The RDF identifier of this type.
rdfKey - Variable in class info.sswap.impl.empire.model.TypeImpl
The RDF identifier of this type.
RDFRepresentation - Enum in info.sswap.api.model
Enumeration of different representations of RDF data.
RDFRepresentation(String) - Constructor for enum info.sswap.api.model.RDFRepresentation
 
RDFS_LITERAL - Static variable in class info.sswap.api.input.Vocabulary
 
RDFS_NS - Static variable in class info.sswap.impl.empire.Namespaces
The RDFS namespace http://www.w3.org/2000/01/rdf-schema#
RDFTSVWriter - Class in info.sswap.impl.empire.model
Write the model to the output stream in Tab Separated Value (TSV) according to the fundamental RDF truism: subject, predicate, object -> row, col, value The output is (possibly multiple) rows per subject, and one column per predicate.
RDFTSVWriter() - Constructor for class info.sswap.impl.empire.model.RDFTSVWriter
 
RDFTSVWriter.DataStructure - Class in info.sswap.impl.empire.model
 
RDFTSVWriter.DataStructure() - Constructor for class info.sswap.impl.empire.model.RDFTSVWriter.DataStructure
 
RDFTSVWriter.NameMapper - Class in info.sswap.impl.empire.model
 
RDFTSVWriter.NameMapper() - Constructor for class info.sswap.impl.empire.model.RDFTSVWriter.NameMapper
 
RDFTSVWriter.NameMapper(PrefixMapping) - Constructor for class info.sswap.impl.empire.model.RDFTSVWriter.NameMapper
 
RDG - Interface in info.sswap.api.model
A Resource Description Graph (RDG) describes a SSWAP semantic web service.
rdg - Variable in class info.sswap.api.servlet.AsyncRIGInvocation
The RIG of the service being invoked.
rdg - Variable in class info.sswap.impl.empire.model.RIGImpl
 
rdgFile - Variable in class info.sswap.api.servlet.AbstractSSWAPServlet
Absolute, fully resolved path and file name of the RDG on the file system
RDGImpl - Class in info.sswap.impl.empire.model
 
RDGImpl() - Constructor for class info.sswap.impl.empire.model.RDGImpl
 
rdgPath - Variable in class info.sswap.api.servlet.AbstractSSWAPServlet
Real path to the RDG on the file system as specified in web.xml (may be a directory)
rdgPath - Variable in class info.sswap.ontologies.exec.impl.ExecImpl
"RDGPath" as defined in web.xml.
read() - Method in class info.sswap.impl.empire.io.ByteLimitInputStream
Reads a single byte from the underlying stream.
read(byte[], int, int) - Method in class info.sswap.impl.empire.io.ByteLimitInputStream
Reads multiple bytes from the underlying stream
readData() - Method in interface info.sswap.ontologies.data.api.Data
Read the current data element (either a literal or by dereferencing the individual itself).
readData() - Method in class info.sswap.ontologies.data.impl.AttachmentImpl
 
readData() - Method in class info.sswap.ontologies.data.impl.LiteralData
Read the data, reading nothing (but no error) if there is no data to read.
readData() - Method in class info.sswap.ontologies.data.impl.ResourceData
Accesses, parses, and validates the data from the URL of the data individual.
readDescription(JSONObject, Input) - Method in class info.sswap.api.input.io.JSONDeserializer
 
readKnownURISchemes() - Static method in class info.sswap.impl.empire.model.ModelUtils
 
readLabel(JSONObject, Input) - Method in class info.sswap.api.input.io.JSONDeserializer
 
readProperties() - Method in class info.sswap.impl.empire.model.IndividualImpl
Scans the source model to find all the properties of this object, and initializes properties map.
readSSWAPDataObject(EntityManager, Class<T>) - Method in class info.sswap.impl.empire.model.ImplFactory
Reads a single Empire-annotated object from the data source managed by the specified entity manager.
readSSWAPDataObject(EntityManager, Class<T>, URI) - Method in class info.sswap.impl.empire.model.ImplFactory
 
readSSWAPDataObject(Object, String, Class<T>) - Method in class info.sswap.impl.empire.model.ImplFactory
Reads a single Empire-annotated object from a data source (usually a stream).
readTimeout - Variable in class info.sswap.impl.empire.io.ClosureBuilder
 
readTypes(Model, Resource) - Method in class info.sswap.impl.empire.model.IndividualImpl
Reads the declared type information about an individual
readValue(JSONObject, Input) - Method in class info.sswap.api.input.io.JSONDeserializer
 
reasoningService - Variable in class info.sswap.api.input.io.SSWAPDeserializer
 
ReasoningService - Interface in info.sswap.api.model
Interface to reasoning services about data types.
ReasoningServiceImpl - Class in info.sswap.impl.empire.model
Implementation of the reasoning service for a Jena model.
ReasoningServiceImpl(SourceModel) - Constructor for class info.sswap.impl.empire.model.ReasoningServiceImpl
Creates a reasoning service based on Pellet reasoner.
reasoningServiceImpl - Variable in class info.sswap.impl.empire.model.SourceModelImpl
The reasoning service (wrapping a PelletReasoner) for this Jena model.
ReasoningServiceImpl.ExplanationSyntax - Enum in info.sswap.impl.empire.model
 
ReasoningServiceImpl.ExplanationSyntax() - Constructor for enum info.sswap.impl.empire.model.ReasoningServiceImpl.ExplanationSyntax
 
ReasoningServiceImpl.IndividualTranslator - Class in info.sswap.impl.empire.model
Translates an individual into using the vocabulary used by the specified class.
ReasoningServiceImpl.IndividualTranslator() - Constructor for class info.sswap.impl.empire.model.ReasoningServiceImpl.IndividualTranslator
 
ReasoningServiceImpl.IndividualTranslator.TranslationCache - Class in info.sswap.impl.empire.model
Contains cache of translation results.
ReasoningServiceImpl.IndividualTranslator.TranslationCache() - Constructor for class info.sswap.impl.empire.model.ReasoningServiceImpl.IndividualTranslator.TranslationCache
 
ReasoningServiceImpl.PropertyInformation - Class in info.sswap.impl.empire.model
An entry for caching information about a property so that we do not have to query the reasoner repeatedly about properties.
ReasoningServiceImpl.PropertyInformation(ReasoningServiceImpl.PropertyType, boolean, String) - Constructor for class info.sswap.impl.empire.model.ReasoningServiceImpl.PropertyInformation
Creates a new property information entry
ReasoningServiceImpl.PropertyType - Enum in info.sswap.impl.empire.model
An enum for storing a type of a property (datatype vs object or undefined)
ReasoningServiceImpl.PropertyType() - Constructor for enum info.sswap.impl.empire.model.ReasoningServiceImpl.PropertyType
 
ReasoningServiceImpl.ReasoningTaskBase - Class in info.sswap.impl.empire.model
 
ReasoningServiceImpl.ReasoningTaskBase() - Constructor for class info.sswap.impl.empire.model.ReasoningServiceImpl.ReasoningTaskBase
 
ReasoningServiceImpl.ReasoningTaskBase.ClassIndividualMapping - Class in info.sswap.impl.empire.model
Represents a pair that consists of a class and an individual belonging to this class.
ReasoningServiceImpl.ReasoningTaskBase.ClassIndividualMapping(ATermAppl, ATermAppl) - Constructor for class info.sswap.impl.empire.model.ReasoningServiceImpl.ReasoningTaskBase.ClassIndividualMapping
Creates a pair that contains the mapping between the class and the individual.
refresh() - Method in class info.sswap.impl.empire.model.EmpireGeneratedNodeImpl
 
refresh() - Method in class info.sswap.impl.empire.model.IndividualImpl
Refreshes the information stored in this individual by rescanning the underlying data source.
refresh() - Method in class info.sswap.impl.empire.model.ModelImpl
Refreshes the data of this object (should be called, if the underlying RDF graph changed).
refresh() - Method in class info.sswap.impl.empire.model.SourceModelImpl
Refreshes the information encoded in this SSWAP model (and all dependent models) with the information stored in the underlying Jena model.
refreshSiblings() - Method in class info.sswap.impl.empire.model.ModelImpl
Refreshes SSWAPModels that are considered siblings of this one (i.e., models that have the same URI).
RELEASE_DATE_PROPERTY - Static variable in class info.sswap.api.model.VersionInformation
Name of the property that contains the release date.
releaseCrossModelTerms(SSWAPModel...) - Method in class info.sswap.impl.empire.model.ReasoningServiceImpl
Releases all the terms that were temporarily imported by assertCrossModelTerms() for each model.
remoteServiceURI - Variable in class info.sswap.api.servlet.AbstractSSWAPServlet
URI to be called to pass on service invocation to a remote service.
remove(Object) - Method in class info.sswap.impl.empire.model.ListImpl
 
remove(int) - Method in class info.sswap.impl.empire.model.ListImpl
 
removeAll(Collection<?>) - Method in class info.sswap.impl.empire.model.ListImpl
 
removeBNodes(Model) - Static method in class info.sswap.impl.empire.model.ModelUtils
Removes BNodes from a model by converting them into a resource with a URI (which belongs to a reserved namespace).
removeBNodes(Model, Iterator<? extends RDFNode>) - Static method in class info.sswap.impl.empire.model.ModelUtils
Removes BNodes from a Node iterator by converting them into a resource with a URI (which belongs to a reserved namespace).
removeDependentModel(ModelImpl) - Method in interface info.sswap.impl.empire.model.SourceModel
Removes a dependent SSWAP model from this source model
removeDependentModel(ModelImpl) - Method in class info.sswap.impl.empire.model.SourceModelImpl
 
removeExpiredData() - Method in class info.sswap.impl.empire.io.ModelCache
Removes all entries that are expired
removeExpiredData(boolean) - Method in class info.sswap.impl.empire.io.ModelCache
 
removeGraph(SSWAPGraph) - Method in class info.sswap.impl.empire.model.SubjectImpl
 
removeImport(URI) - Method in interface info.sswap.api.model.SSWAPModel
Removes an import from the list of imports
removeImport(URI) - Method in class info.sswap.impl.empire.model.ModelImpl
Removes an import from the list of imports
removeImport(URI) - Method in interface info.sswap.impl.empire.model.SourceModel
Removes an import from the list of imports
removeImport(URI) - Method in class info.sswap.impl.empire.model.SourceModelImpl
 
removeModel(SSWAPModel) - Method in interface info.sswap.api.model.ReasoningService
Removes a previously added submodel (via addModel(Model)).
removeModel(SSWAPModel) - Method in class info.sswap.impl.empire.model.ReasoningServiceImpl
 
removeNsPrefix(String) - Method in interface info.sswap.api.model.SSWAPModel
Removes a namespace prefix.
removeNsPrefix(String) - Method in class info.sswap.impl.empire.model.ModelImpl
 
removeNsPrefix(String) - Method in interface info.sswap.impl.empire.model.SourceModel
Removes a namespace prefix.
removeNsPrefix(String) - Method in class info.sswap.impl.empire.model.SourceModelImpl
 
removeProperties() - Method in class info.sswap.impl.empire.model.IndividualImpl
Removes all statements about this object that correspond to non-ignored properties.
removeProperty(SSWAPProperty) - Method in interface info.sswap.api.model.SSWAPIndividual
Removes a single property instance from this individual (identified by the specified SSWAPProperty instance).
removeProperty(SSWAPPredicate, SSWAPElement) - Method in interface info.sswap.api.model.SSWAPIndividual
Removes a single property from this individual (property is identified by the predicate and the value)
removeProperty() - Method in interface info.sswap.api.model.SSWAPProperty
Removes the property from the individual.
removeProperty(SSWAPProperty) - Method in class info.sswap.impl.empire.model.IndividualImpl
Removes a property from this individual.
removeProperty(SSWAPPredicate, SSWAPElement) - Method in class info.sswap.impl.empire.model.IndividualImpl
 
removeProperty() - Method in class info.sswap.impl.empire.model.PropertyImpl
 
removeSourceModel(SourceModel) - Method in class info.sswap.impl.empire.model.ReasoningServiceImpl
 
removeSubject(SSWAPSubject) - Method in class info.sswap.impl.empire.model.ObjectImpl
 
removeToken(RRG) - Method in class info.sswap.api.servlet.AsyncRIGInvocation
 
removeType(SSWAPType) - Method in interface info.sswap.api.model.SSWAPIndividual
Removes a type from the individual.
removeType(SSWAPType) - Method in class info.sswap.impl.empire.model.IndividualImpl
 
removeTypes() - Method in class info.sswap.impl.empire.model.IndividualImpl
 
renderInconsistencyExplanation() - Method in class info.sswap.impl.empire.model.ReasoningServiceImpl
 
replaceObject(SSWAPSubject, URI, SSWAPObject) - Method in class info.sswap.api.servlet.MapsTo
Deprecated. Use MapsTo.replaceObject(SSWAPSubject,SSWAPObject,URI) instead
replaceObject(SSWAPSubject, SSWAPObject, URI) - Method in class info.sswap.api.servlet.MapsTo
If the argument URI is different from the sswapObject URI, then schedule to MapsTo.assignObject(SSWAPSubject,URI) and MapsTo.unassignObject(SSWAPSubject,SSWAPObject).
RequestEntityTooLargeException - Exception in info.sswap.api.servlet
Exception class for HTTP response code 413 Request Entity Too Large.
RequestEntityTooLargeException() - Constructor for exception info.sswap.api.servlet.RequestEntityTooLargeException
 
requiredMapping(T, Collection<T>, Collection<T>, ProtocolImpl.MappingValidator<T>) - Method in class info.sswap.impl.empire.model.ProtocolImpl
Finds a mapping for a selected RDG individual.
requiredMappings(Collection<T>, Collection<T>, ProtocolImpl.MappingValidator<T>) - Method in class info.sswap.impl.empire.model.ProtocolImpl
Computes required mappings from RDG individuals to individuals in this protocol graph.
reservedQnames - Variable in class info.sswap.impl.empire.model.RDFTSVWriter.NameMapper
 
resetKB() - Method in class info.sswap.impl.empire.model.ReasoningServiceImpl
 
resetReasoningService() - Method in class info.sswap.impl.empire.model.SourceModelImpl
 
resolveParameters(RIG, Map<String, String[]>) - Method in class info.sswap.api.servlet.AbstractSSWAPServlet
Resolves query string parameters against name spaces to get absolute URIs.
resolveProperties(RIG, SSWAPNode, ParameterList) - Method in class info.sswap.api.servlet.AbstractSSWAPServlet
Removes all properties from sswapNode and adds back only those properties (parameters) from resolvedQNameMap that are ObjectProperties or DatatypeProperties
resolveProtocolModel(SSWAPProtocol) - Method in interface info.sswap.api.model.ModelResolver
Resolves a graph by performing a more specific resolution than for a generic source model
resolveProtocolModel(SSWAPProtocol) - Method in class info.sswap.impl.empire.io.ClosureModelResolver
 
resolveQueryString(RIG, Map<String, String[]>) - Method in class info.sswap.api.servlet.AbstractSSWAPServlet
Map query string parameters into fully qualified URLs or URNs.
resolveSourceModel(SourceModel) - Method in interface info.sswap.api.model.ModelResolver
 
resolveSourceModel(SourceModel) - Method in class info.sswap.impl.empire.io.ClosureModelResolver
 
resolveTerm(URI) - Method in interface info.sswap.api.model.ModelResolver
Resolves a specific term
resolveTerm(URI) - Method in class info.sswap.impl.empire.io.ClosureModelResolver
 
resource - Variable in class info.sswap.impl.empire.model.DatatypeImpl
The Jena resource that defines this data type (important for fast access to type information).
resource - Variable in class info.sswap.impl.empire.model.GraphImpl
 
resource - Variable in class info.sswap.impl.empire.model.PredicateImpl
The Jena resource that defines this type (important for fast access to type information).
resource - Variable in class info.sswap.impl.empire.model.TypeImpl
The Jena resource that defines this type (important for fast access to type information).
ResourceData - Class in info.sswap.ontologies.data.impl
Support for reading and writing resource data (data at the URL of an individual; usually a SSWAPSubject or SSWAPObject).
ResourceData(SSWAPIndividual) - Constructor for class info.sswap.ontologies.data.impl.ResourceData
Constructs an individual suitable for reading/writing data
resourceFlag - Static variable in class info.sswap.api.servlet.AbstractSSWAPServlet
Flag string appended to terms in the GET query string to identify them as pertaining to the SSWAPResouce
ResourceImpl - Class in info.sswap.impl.empire.model
Implementation of SSWAPResource.
ResourceImpl() - Constructor for class info.sswap.impl.empire.model.ResourceImpl
 
resources - Variable in class info.sswap.impl.empire.model.ProtocolImpl
 
resources - Variable in class info.sswap.impl.empire.model.RDFTSVWriter.DataStructure
 
resourceValidationEnabled - Variable in class info.sswap.impl.empire.model.RQGImpl
 
response - Variable in class info.sswap.impl.http.AbstractHTTPResponse
 
response - Variable in class info.sswap.impl.http.HTTPAPIImpl
 
result - Variable in class info.sswap.api.input.io.SSWAPIndividualDeserializer.PropertyInputVisitor
 
retainAll(Collection<?>) - Method in class info.sswap.impl.empire.model.ListImpl
 
retrieveAdditionalTerm(URI) - Method in class info.sswap.impl.empire.model.ReasoningServiceImpl
Retrieves additional term (by dereferencing it).
RIG - Interface in info.sswap.api.model
A Resource Invocation Graph (RIG) is for invocation of a SSWAP semantic web service.
rig - Variable in class info.sswap.api.servlet.MapsTo
 
RIG_INVOCATION_TIMEOUT_DEFAULT - Static variable in class info.sswap.api.model.Config
The default connect timeout (in milliseconds) during RIG invocation.
RIG_INVOCATION_TIMEOUT_KEY - Static variable in class info.sswap.api.model.Config
Property name for setting the connect timeout (in milliseconds) during RIG invocation.
RIGImpl - Class in info.sswap.impl.empire.model
Implementation of RIG.
RIGImpl() - Constructor for class info.sswap.impl.empire.model.RIGImpl
 
RQG - Interface in info.sswap.api.model
A Resource Query Graph (RQG) is a specialized query sent to a Discovery Server in request of all SSWAP semantic web services (RDGs) that satisfy the query.
RQGImpl - Class in info.sswap.impl.empire.model
Implementation of RQG interface
RQGImpl() - Constructor for class info.sswap.impl.empire.model.RQGImpl
 
RRG - Interface in info.sswap.api.model
A Resource Response Graph (RRG) is the return result of a SSWAP semantic web service.
RRG_EHCACHE_CACHE_NAME_DEFAULT - Static variable in class info.sswap.api.model.Config
Default value of the EHCache cache that stores RRGs (produced by the SSWAP service and available for asynchronous retrieval)
RRG_EHCACHE_CACHE_NAME_KEY - Static variable in class info.sswap.api.model.Config
Property name for the name of the EHCache cache for storing RRGs (produced by the SSWAP service and available for asynchronous retrieval)
RRG_EHCACHE_FILE_KEY - Static variable in class info.sswap.api.model.Config
Property name for the path to EHCache configuration file for storing RRGs.
RRG_RETRIEVAL_SUFFIX - Static variable in class info.sswap.api.servlet.AbstractSSWAPServlet
The suffix to the request string for RRG retrieval; that is, if a request ends with this suffix (attached to the regular service's URL), it indicates that the request is for retrieving a cached RRG, and not invoking the service.
RRGCache - Class in info.sswap.api.servlet
Manages cached RRGs and information about them (including information about RRGs that have not yet been computed, but they already have a token (identifier) so that the clients can query/poll for them).
RRGCache() - Constructor for class info.sswap.api.servlet.RRGCache
Private constructor (to be accessed only when creating the singleton instance)
RRGCache.Entry - Class in info.sswap.api.servlet
An entry of the cache.
RRGCache.Entry() - Constructor for class info.sswap.api.servlet.RRGCache.Entry
 
RRGImpl - Class in info.sswap.impl.empire.model
Implementation of RRG interface
RRGImpl() - Constructor for class info.sswap.impl.empire.model.RRGImpl
 
rrgSerialization - Variable in class info.sswap.api.servlet.RRGCache.Entry
The serialization of RRG as RDF/XML (we cannot have RRG object there because it is not Serializable) It may be null, if RRG has not yet been computed
rrgToken - Variable in class info.sswap.api.servlet.AsyncRIGInvocation
The token that will allow the caller to retrieve the resulting RRG.
run() - Method in class info.sswap.api.servlet.AsyncRIGInvocation
Main method of the asynchronous thread.
run() - Method in class info.sswap.ontologies.exec.impl.HotboxPollerImpl.DaemonThread
 

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Copyright (c) 2011, iPlant Collaborative, University of Arizona, Cold Spring Harbor Laboratories, University of Texas at Austin.