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

D

daemonThread - Variable in class info.sswap.ontologies.exec.impl.HotboxPollerImpl
 
Data - Interface in info.sswap.ontologies.data.api
The data package standardizes a simple interface to arbitrary data for semantic Web services.
Data(SSWAPIndividual) - Static method in class info.sswap.ontologies.data.api.DataFactory
Open with automatic support for literal or resource data, including automatic support for base64 encoded attachments.
Data(SSWAPIndividual, DataFactory.Open) - Static method in class info.sswap.ontologies.data.api.DataFactory
Open with automatic support for base64 encoded attachments.
Data(SSWAPIndividual, DataFactory.Open, String, String) - Static method in class info.sswap.ontologies.data.api.DataFactory
Open with automatic support for base64 encoded attachments or HTTP Basic Authentication.
data_DataFormat - Variable in class info.sswap.ontologies.data.impl.DirectoryImpl
 
data_hasData - Variable in class info.sswap.ontologies.data.impl.DirectoryImpl
 
DataAccessException - Exception in info.sswap.api.model
A generic, unchecked exception thrown when a problem with accessing the underlying data should occur (e.g., because the data source is unavailable or the data cannot be parsed).
DataAccessException() - Constructor for exception info.sswap.api.model.DataAccessException
Creates a new exception
DataAccessException(String) - Constructor for exception info.sswap.api.model.DataAccessException
Creates a new exception with the specified message
DataAccessException(Throwable) - Constructor for exception info.sswap.api.model.DataAccessException
Creates a new exception with the specified underlying cause
DataAccessException(String, Throwable) - Constructor for exception info.sswap.api.model.DataAccessException
Creates a new exception with the specified message and the underlying cause
DataException - Exception in info.sswap.ontologies.data.api
Root class for all Data-specific exceptions.
DataException() - Constructor for exception info.sswap.ontologies.data.api.DataException
Creates a new exception
DataException(String) - Constructor for exception info.sswap.ontologies.data.api.DataException
Creates a new exception with the specified message
DataException(Throwable) - Constructor for exception info.sswap.ontologies.data.api.DataException
Creates a new exception with the specified underlying cause
DataException(String, Throwable) - Constructor for exception info.sswap.ontologies.data.api.DataException
Creates a new exception with the specified message and the underlying cause
DataFactory - Class in info.sswap.ontologies.data.api
Main entry point for support for the data ontology.
DataFactory() - Constructor for class info.sswap.ontologies.data.api.DataFactory
 
DataFactory.Open - Enum in info.sswap.ontologies.data.api
Directives on how to open data elements for reading and writing.
DataFactory.Open() - Constructor for enum info.sswap.ontologies.data.api.DataFactory.Open
 
DataFormatType - Variable in class info.sswap.ontologies.data.impl.AbstractData
 
dataSet - Variable in class info.sswap.ontologies.data.impl.DirectoryImpl
 
datatype - Variable in class info.sswap.api.input.impl.LiteralValueImpl
 
DATATYPE - Static variable in class info.sswap.api.input.io.JSONConstants
 
DatatypeImpl - Class in info.sswap.impl.empire.model
Implementation of SSWAPDatatype
DatatypeImpl(SourceModel, URI) - Constructor for class info.sswap.impl.empire.model.DatatypeImpl
Creates a datatype
datatypeImpls - Variable in class info.sswap.impl.empire.model.SourceModelImpl
 
datatypeURI - Variable in class info.sswap.impl.empire.model.Literal
 
date - Static variable in interface info.sswap.api.model.SSWAPDatatype.XSD
xsd:date
dateTime - Static variable in interface info.sswap.api.model.SSWAPDatatype.XSD
xsd:dateTime
decimal - Static variable in interface info.sswap.api.model.SSWAPDatatype.XSD
xsd:decimal
decIndent() - Method in class info.sswap.api.input.io.StringSerializer
 
declaredTypeIntersection - Variable in class info.sswap.impl.empire.model.IndividualImpl
Contains a type that is intersection of all declared types.
decreaseDepth() - Method in class info.sswap.api.input.io.SSWAPDeserializer.VisitedTerms
 
deepCopyElement(SourceModel, SSWAPElement, Set<URI>) - Method in class info.sswap.impl.empire.model.ImplFactory
Performs a deep copy of a SSWAPElement from one source model to another
deepCopyIndividual(SourceModel, SSWAPIndividual, Set<URI>) - Method in class info.sswap.impl.empire.model.ImplFactory
Perform a deep copy of a SSWAPIndividual into another source model
deepCopyIndividual(SourceModel, SSWAPIndividual, IndividualImpl, Set<URI>) - Method in class info.sswap.impl.empire.model.ImplFactory
 
deepCopyList(SourceModel, SSWAPList, Set<URI>) - Method in class info.sswap.impl.empire.model.ImplFactory
Perform a deep copy of a SSWAPList into another source model
DEFAULT_DISCOVERY_SERVER - Static variable in class info.sswap.impl.empire.model.RQGImpl
The default URL of the discovery server that is used when the system property did not specify one.
DEFAULT_MAX - Static variable in interface info.sswap.api.input.PropertyInput
 
DEFAULT_MIN - Static variable in interface info.sswap.api.input.PropertyInput
 
DEFAULT_SUGGESTED_POLLING_INTERVAL - Static variable in class info.sswap.api.servlet.RRGCache
Default suggested polling interval (in milliseconds)
defaultEntryTTL - Static variable in class info.sswap.impl.empire.io.ModelCache
Default time-to-live (TTL).
defaultMessage - Static variable in exception info.sswap.api.servlet.ClientException
 
defaultMessage - Static variable in exception info.sswap.api.servlet.RequestEntityTooLargeException
 
defaultSleepMilliSeconds - Variable in class info.sswap.ontologies.exec.impl.HotboxPollerImpl
 
degree - Variable in class info.sswap.impl.empire.io.Closure
 
DELIMITER_ENC - Variable in class info.sswap.impl.empire.model.RDFCSVWriter
Deprecated.  
DELIMITER_ENC - Variable in class info.sswap.impl.empire.model.RDFTSVWriter
 
DELIMITER_STR - Variable in class info.sswap.impl.empire.model.RDFCSVWriter
Deprecated. Default field delimiter
DELIMITER_STR - Variable in class info.sswap.impl.empire.model.RDFTSVWriter
Default field delimiter
dependentModels - Variable in class info.sswap.impl.empire.model.SourceModelImpl
All other SSWAPModels that are based on the information from the Jena model.
dependentModelsMap - Variable in class info.sswap.impl.empire.model.SourceModelImpl
Mapping of URIs of dependent models to actual models.
depth() - Method in class info.sswap.api.input.io.SSWAPDeserializer.VisitedTerms
 
dereference() - Method in interface info.sswap.api.model.SSWAPModel
If the object is not dereferenced, it dereferences it.
dereference(InputStream) - Method in interface info.sswap.api.model.SSWAPModel
Dereferences the object (if it is not yet dereferenced) but it reads the data from the given stream, rather than trying to to retrieve the URI of this object.
dereference() - Method in class info.sswap.impl.empire.model.ModelImpl
 
dereference(InputStream) - Method in class info.sswap.impl.empire.model.ModelImpl
 
dereference() - Method in class info.sswap.impl.empire.model.NodeImpl
Dereferences this node, by first calling dereference() on the source model (if there is one; in case there is no source model, this method immediately returns).
dereference(ProtocolImpl) - Method in class info.sswap.impl.empire.model.ProtocolImpl
Populates this graph (must not be dereferenced yet) with the contents of another graph.
dereference() - Method in class info.sswap.impl.empire.model.ProviderImpl
 
dereference() - Method in class info.sswap.impl.empire.model.ResourceImpl
Dereferences this SSWAPResource.
dereference() - Method in interface info.sswap.impl.empire.model.SourceModel
Attempts to populate the model with data by retrieving it from the URI of the model.
dereference(InputStream) - Method in interface info.sswap.impl.empire.model.SourceModel
Attempts to populate the model with data by retrieving it from the given stream.
dereference(Model) - Method in interface info.sswap.impl.empire.model.SourceModel
Attempts to populate the model with data retrieved from the given Jena model.
dereference() - Method in class info.sswap.impl.empire.model.SourceModelImpl
 
dereference(InputStream) - Method in class info.sswap.impl.empire.model.SourceModelImpl
 
dereference(Model) - Method in class info.sswap.impl.empire.model.SourceModelImpl
 
dereferenced - Variable in class info.sswap.impl.empire.model.ModelImpl
Flag indicating whether the object has been dereferenced (true).
DEREFERENCED_TYPES - Static variable in class info.sswap.impl.empire.io.ClosureBuilder
A set of types of that are dereferenced during the closure computation.
dereferenceQueue - Variable in class info.sswap.impl.empire.io.ClosureBuilder
The current list of URIs to be dereferenced for the current depth.
dereferenceURL(String) - Method in class info.sswap.impl.empire.io.ClosureBuilder
Retrieves a document at the specified URL and parses it into the Jena model.
description - Variable in class info.sswap.api.input.impl.AbstractInput
 
DESCRIPTION - Static variable in class info.sswap.api.input.io.JSONConstants
 
deserialize(T) - Method in interface info.sswap.api.input.io.InputDeserializer
Deserializes an Input instance from the given object.
deserialize(JSONObject) - Method in class info.sswap.api.input.io.JSONDeserializer
 
deserialize(SSWAPType) - Method in class info.sswap.api.input.io.SSWAPDeserializer
 
deserialize(SSWAPIndividual) - Method in class info.sswap.api.input.io.SSWAPIndividualDeserializer
 
deserialize(SSWAPProperty) - Method in class info.sswap.api.input.io.SSWAPIndividualDeserializer
 
deserializeValue(JSONObject) - Method in class info.sswap.api.input.io.JSONDeserializer
 
detachExistingGraphs() - Method in class info.sswap.impl.empire.model.ResourceImpl
 
detachExistingObjects() - Method in class info.sswap.impl.empire.model.SubjectImpl
 
detachExistingSubjects() - Method in class info.sswap.impl.empire.model.GraphImpl
 
detachProperties(Collection<SSWAPProperty>) - Method in class info.sswap.impl.empire.model.IndividualImpl
Detaches SSWAPProperties from this individual and source model.
Directory(SSWAPIndividual) - Static method in class info.sswap.ontologies.data.api.DataFactory
Create a new Directory from the subject individual.
Directory - Interface in info.sswap.ontologies.data.api
A data:DataBundle from the data ontology is an individual with one or more data:hasData statements.
DirectoryImpl - Class in info.sswap.ontologies.data.impl
Directory implementation.
DirectoryImpl(SSWAPIndividual) - Constructor for class info.sswap.ontologies.data.impl.DirectoryImpl
Create a Directory from the subject individual.
DISABLE_UNA_WHEN_CLOSING_WORLD - Static variable in class info.sswap.api.model.Config
We are not disabling UNA by default when closing the world during service invocations.
DISABLE_UNA_WHEN_CLOSING_WORLD_KEY - Static variable in class info.sswap.api.model.Config
Property name for controlling Unique Name Assumption (UNA) when closing the world during service invocations.
disableUNA(Collection<SSWAPElement>) - Method in class info.sswap.impl.empire.model.IndividualImpl
 
DISCOVERY_SERVER_PROPERTY_NAME - Static variable in class info.sswap.impl.empire.model.RQGImpl
The name of the system property that is used to retrieve the URI of the discovery server.
DISCOVERY_SERVER_URI_DEFAULT - Static variable in class info.sswap.api.model.Config
The default URI of the discovery server, if not otherwise specified.
DISCOVERY_SERVER_URI_KEY - Static variable in class info.sswap.api.model.Config
The URI of the discovery server (used to answer RQGs)
DISK_CACHE_ENABLED_DEFAULT - Static variable in class info.sswap.api.model.Config
The default value for enabling (or disabling) the disk cache (value is 'true' or 'false').
DISK_CACHE_ENABLED_KEY - Static variable in class info.sswap.api.model.Config
Key for enabling the disk cache (vs.
diskCacheEnabled - Variable in class info.sswap.impl.empire.io.ModelCache
Flag whether persistent cache is enabled or disabled.
doAddProperty(SSWAPProperty) - Method in class info.sswap.impl.empire.model.IndividualImpl
 
doAddType(SSWAPType) - Method in class info.sswap.impl.empire.model.IndividualImpl
 
doClosure() - Method in interface info.sswap.api.model.SSWAPModel
For every URI in the model, do successive HTTP GETs and read in the model.
doClosure(Model, boolean) - Method in class info.sswap.impl.empire.io.ClosureBuilder
Computes one degree of closure on the passed model
doClosure() - Method in class info.sswap.impl.empire.model.ModelImpl
 
doClosure() - Method in class info.sswap.impl.empire.model.ProtocolImpl
 
doClosure() - Method in interface info.sswap.impl.empire.model.SourceModel
For every URI in the model, do an HTTP GET and read in the model.
doClosure() - Method in class info.sswap.impl.empire.model.SourceModelImpl
Computes closure for this model.
doDereference(Object) - Method in class info.sswap.impl.empire.model.SourceModelImpl
Performs actual dereferencing
doGet(HttpServletRequest, HttpServletResponse) - Method in class info.sswap.api.servlet.AbstractSSWAPServlet
An HTTP GET equates to returning an RDG or creating a just-in-time RIG from the query string and invoking this service.
doInvoke(Long) - Method in class info.sswap.impl.empire.model.RIGImpl
Invokes the service with this RIG and the specified connect/read timeout (if provided).
doPost(HttpServletRequest, HttpServletResponse) - Method in class info.sswap.api.servlet.AbstractSSWAPServlet
An HTTP POST equates to a request service invocation.
doRemoveProperty(SSWAPProperty) - Method in class info.sswap.impl.empire.model.IndividualImpl
 
doRemoveType(SSWAPType) - Method in class info.sswap.impl.empire.model.IndividualImpl
 
doTypeRetrievingStep(Model, Model) - Method in class info.sswap.impl.empire.io.ClosureBuilder
 
duration - Static variable in interface info.sswap.api.model.SSWAPDatatype.XSD
xsd:duration

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