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

P

parseProvenanceQuery(String) - Method in class net.sf.taverna.t2.provenance.api.ProvenanceQueryParser

part_of - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

patchTopLevelnputs() - Method in class net.sf.taverna.t2.provenance.lineageservice.EventProcessor

fills in the VBs for the global inputs -- this removes the need for explicit events that account for these value bindings...

pathway - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

port - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

port_pathway - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

A canonical instance of class pathway to associate a semantic type with an instance of a port - the specific pathway with which the workflow will be run is not at this stage of workflow design.

port_value - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

PortsSequenceType - Class in net.sf.taverna.t2.provenance.lineageservice.types

PortsSequenceType() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.PortsSequenceType

PortsSequenceType(PortType[]) - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.PortsSequenceType

PortType - Class in net.sf.taverna.t2.provenance.lineageservice.types

PortType() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.PortType

PortType(DataDocumentType, LiteralType, String) - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.PortType

pq - Variable in class net.sf.taverna.t2.provenance.lineageservice.Provenance

pq - Variable in class net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter

preceded_by - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

ProcBinding - Class in net.sf.taverna.t2.provenance.lineageservice.utils

ProcBinding() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.utils.ProcBinding

process - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

processDataflowStructure(Dataflow, String, String) - Method in class net.sf.taverna.t2.provenance.lineageservice.EventProcessor

note: this method can be called as part of a recursion on sub-workflows

processEvent(ProvenanceItem, SharedVocabulary) - Method in class net.sf.taverna.t2.provenance.lineageservice.Provenance

parse d and generate SQL insert calls into the provenance DB

processor_exec - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

processor_spec - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

ProcessorType - Class in net.sf.taverna.t2.provenance.lineageservice.types

ProcessorType() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.ProcessorType

ProcessorType(ActivityType[], String) - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.ProcessorType

processProcessEvent(ProvenanceItem, String) - Method in class net.sf.taverna.t2.provenance.lineageservice.EventProcessor

processes an elementary process execution event from T2.

processTrees(String, String) - Method in class net.sf.taverna.t2.provenance.lineageservice.WorkflowDataProcessor

writes records to VarBinding or Collection by traversing the trees
expect this to be invoked after workflow completion

ProcessType - Class in net.sf.taverna.t2.provenance.lineageservice.types

ProcessType() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.ProcessType

ProcessType(ProcessorType[], String, String) - Constructor for class net.sf.taverna.t2.provenance.lineageservice.types.ProcessType

processWorkflowStructure(ProvenanceItem) - Method in class net.sf.taverna.t2.provenance.lineageservice.EventProcessor

this is the new version that makes use of the T2 deserializer populate static portion of the DB
the static structure may already be in the DB -- this is detected as a duplicate top-level workflow ID.

processWorkflowStructure(Dataflow) - Method in class net.sf.taverna.t2.provenance.lineageservice.EventProcessor

propagateANL(String) - Method in class net.sf.taverna.t2.provenance.lineageservice.EventProcessor

Provenance - Class in net.sf.taverna.t2.provenance.lineageservice

Implemented by the database class that a ProvenanceConnector implementation uses for storage purposes

Provenance() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.Provenance

Provenance(EventProcessor) - Constructor for class net.sf.taverna.t2.provenance.lineageservice.Provenance

ProvenanceAccess - Class in net.sf.taverna.t2.provenance.api

ProvenanceAccess(String) - Constructor for class net.sf.taverna.t2.provenance.api.ProvenanceAccess

ProvenanceAnalysis - Class in net.sf.taverna.t2.provenance.lineageservice

ProvenanceAnalysis() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis

ProvenanceAnalysis(ProvenanceQuery) - Constructor for class net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis

ProvenanceConnector - Class in net.sf.taverna.t2.provenance.connector

Collects ProvenanceItems as it travels up and down the dispatch stack inside the InvocationContext

ProvenanceConnector() - Constructor for class net.sf.taverna.t2.provenance.connector.ProvenanceConnector

ProvenanceConnectorFactory - Interface in net.sf.taverna.t2.provenance

ProvenanceConnectorFactoryRegistry - Class in net.sf.taverna.t2.provenance

Get all the instances of ProvenanceConnectorFactory that are available using this SPI Registry.

ProvenanceConnectorFactoryRegistry() - Constructor for class net.sf.taverna.t2.provenance.ProvenanceConnectorFactoryRegistry

ProvenanceConnectorRegistry - Class in net.sf.taverna.t2.provenance

Get all the instances of ProvenanceConnector that are available using this SPI Registry.

ProvenanceConnectorRegistry() - Constructor for class net.sf.taverna.t2.provenance.ProvenanceConnectorRegistry

ProvenanceConnectorType - Class in net.sf.taverna.t2.provenance.api

Defines names for the common Provenance Connector types

ProvenanceConnectorType() - Constructor for class net.sf.taverna.t2.provenance.api.ProvenanceConnectorType

ProvenanceEventType - Interface in net.sf.taverna.t2.provenance.lineageservice.types

Used by an implementation of Provenance to identify the item type

ProvenanceProcessor - Class in net.sf.taverna.t2.provenance.lineageservice.utils

a Var that has no pName is either a WF input or output, depending on isInput

ProvenanceProcessor() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceProcessor

ProvenanceQuery - Class in net.sf.taverna.t2.provenance.lineageservice

Handles all the querying of provenance items in the database layer.

ProvenanceQuery() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.ProvenanceQuery

ProvenanceQueryParser - Class in net.sf.taverna.t2.provenance.api

ProvenanceQueryParser() - Constructor for class net.sf.taverna.t2.provenance.api.ProvenanceQueryParser

ProvenanceSQL - Class in net.sf.taverna.t2.provenance.connector

ProvenanceSQL() - Constructor for class net.sf.taverna.t2.provenance.connector.ProvenanceSQL

ProvenanceUtils - Class in net.sf.taverna.t2.provenance.lineageservice.utils

ProvenanceUtils() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.utils.ProvenanceUtils

ProvenanceWriter - Class in net.sf.taverna.t2.provenance.lineageservice

Handles all the writing out of provenance items to the database layer.

ProvenanceWriter() - Constructor for class net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter

pubmed - Static variable in class net.sf.taverna.t2.provenance.lineageservice.rdf.JanusOntology

pw - Variable in class net.sf.taverna.t2.provenance.lineageservice.Provenance