A B C D E G H I M O R S T U V

A

ArgumentsParsingException - Exception in org.apache.taverna.commandline.exceptions

ArgumentsParsingException(String) - Constructor for exception org.apache.taverna.commandline.exceptions.ArgumentsParsingException

ArgumentsParsingException(String, Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.ArgumentsParsingException

askedForHelp() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

askedForHelp() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

B

buildErrorValueString(ErrorDocument) - Static method in class org.apache.taverna.commandline.data.ErrorValueHandler

Creates a string representation of the ErrorValue.

C

checkForInvalid() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

checkProvidedInputs(Map<String, InputWorkflowPort>, CommandLineOptions) - Method in class org.apache.taverna.commandline.data.InputsHandler

CommandLineMasterPasswordException - Exception in org.apache.taverna.commandline.exceptions

CommandLineMasterPasswordException(String) - Constructor for exception org.apache.taverna.commandline.exceptions.CommandLineMasterPasswordException

CommandLineMasterPasswordException(String, Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.CommandLineMasterPasswordException

CommandLineMasterPasswordProvider - Class in org.apache.taverna.commandline

An implementation of MasterPasswordProvider that reads Credential Manager's master password from stdin (pipe or terminal) is -cmpassword option is present in command line arguments.

CommandLineMasterPasswordProvider(CommandLineOptions) - Constructor for class org.apache.taverna.commandline.CommandLineMasterPasswordProvider

CommandLineOptions - Interface in org.apache.taverna.commandline.options

CommandLineOptionsImpl - Class in org.apache.taverna.commandline

Handles the processing of command line arguments for enacting a workflow.

CommandLineOptionsImpl(String[]) - Constructor for class org.apache.taverna.commandline.CommandLineOptionsImpl

CommandLineTool - Class in org.apache.taverna.commandline

A utility class that wraps the process of executing a workflow, allowing workflows to be easily executed independently of the GUI.

CommandLineTool() - Constructor for class org.apache.taverna.commandline.CommandLineTool

CommandLineUtils - Class in org.apache.taverna.commandline

CommandLineUtils() - Constructor for class org.apache.taverna.commandline.CommandLineUtils

configureDatabase() - Method in class org.apache.taverna.commandline.data.DatabaseConfigurationHandler

CREDENTIAL_MANAGER_DIR_OPTION - Static variable in interface org.apache.taverna.commandline.options.CommandLineOptions

CREDENTIAL_MANAGER_PASSWORD_OPTION - Static variable in interface org.apache.taverna.commandline.options.CommandLineOptions

D

DatabaseConfigurationException - Exception in org.apache.taverna.commandline.exceptions

DatabaseConfigurationException() - Constructor for exception org.apache.taverna.commandline.exceptions.DatabaseConfigurationException

DatabaseConfigurationException(String) - Constructor for exception org.apache.taverna.commandline.exceptions.DatabaseConfigurationException

DatabaseConfigurationException(Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.DatabaseConfigurationException

DatabaseConfigurationException(String, Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.DatabaseConfigurationException

DatabaseConfigurationHandler - Class in org.apache.taverna.commandline.data

Handles the initialisation and configuration of the data source according to the command line arguments, or a properties file.

DatabaseConfigurationHandler(CommandLineOptions, DatabaseConfiguration, DatabaseManager) - Constructor for class org.apache.taverna.commandline.data.DatabaseConfigurationHandler

displayHelp() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

displayHelp(boolean) - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

displayHelp() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

displayHelp(boolean) - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

E

error(String) - Method in class org.apache.taverna.commandline.CommandLineTool

error(String, Throwable) - Method in class org.apache.taverna.commandline.CommandLineTool

error(Throwable) - Method in class org.apache.taverna.commandline.CommandLineTool

ErrorValueHandler - Class in org.apache.taverna.commandline.data

Handles ErrorValues and transforming them into String representations that can be stored as a file, or within a Baclava document.

ErrorValueHandler() - Constructor for class org.apache.taverna.commandline.data.ErrorValueHandler

G

getArgs() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getArgs() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getCredentialManagerDir() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getCredentialManagerDir() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getDatabasePort() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getDatabasePort() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getDatabaseProperties() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getDatabaseProperties() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getDBConfig() - Method in class org.apache.taverna.commandline.data.DatabaseConfigurationHandler

getInputBundle() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getInputBundle() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

Return the path for a data bundle which should be used for input values.

getInputFiles() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

Returns an array that alternates between a portname and path to a file containing the input values.

getInputFiles() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

Returns an array that alternates between a portname and path to a file containing the input values.

getInputValues() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getInputValues() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

Returns an array that alternates between a portname and an input values.

getLogFile() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getLogFile() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getMasterPassword(boolean) - Method in class org.apache.taverna.commandline.CommandLineMasterPasswordProvider

getMessage() - Method in exception org.apache.taverna.commandline.exceptions.InputMismatchException

getOptions() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getOutputDirectory() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getOutputDirectory() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getProviderPriority() - Method in class org.apache.taverna.commandline.CommandLineMasterPasswordProvider

getSaveResultsToBundle() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getSaveResultsToBundle() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getStartDatabase() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getStartDatabase() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getStartDatabaseOnly() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getStartDatabaseOnly() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

getWorkflow() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

getWorkflow() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

H

hasDelimiterFor(String) - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

hasDelimiterFor(String) - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

hasInputBundle() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

hasInputBundle() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

hasInputFiles() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

hasInputFiles() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

hasInputValues() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

hasInputValues() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

hasLogFile() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

hasLogFile() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

hasOption(String) - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

hasOption(String) - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

hasSaveResultsToBundle() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

hasSaveResultsToBundle() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

I

inputDelimiter(String) - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

inputDelimiter(String) - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

InputMismatchException - Exception in org.apache.taverna.commandline.exceptions

InputMismatchException(String, Set<String>, Set<String>) - Constructor for exception org.apache.taverna.commandline.exceptions.InputMismatchException

InputsHandler - Class in org.apache.taverna.commandline.data

Handles the reading, or processing, or input values according to arguments provided to the commandline.

InputsHandler() - Constructor for class org.apache.taverna.commandline.data.InputsHandler

InvalidOptionException - Exception in org.apache.taverna.commandline.exceptions

InvalidOptionException(String) - Constructor for exception org.apache.taverna.commandline.exceptions.InvalidOptionException

isClientServer() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

isClientServer() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

isEmbedded() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

isEmbedded() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

isInMemory() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

isInMemory() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

isProvenanceEnabled() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

isProvenanceEnabled() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

M

main(String[]) - Static method in class org.apache.taverna.commandline.TavernaCommandLine

Starts the Taverna Command-line Tool.

O

OpenDataflowException - Exception in org.apache.taverna.commandline.exceptions

OpenDataflowException() - Constructor for exception org.apache.taverna.commandline.exceptions.OpenDataflowException

OpenDataflowException(String) - Constructor for exception org.apache.taverna.commandline.exceptions.OpenDataflowException

OpenDataflowException(Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.OpenDataflowException

OpenDataflowException(String, Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.OpenDataflowException

org.apache.taverna.commandline - package org.apache.taverna.commandline

org.apache.taverna.commandline.data - package org.apache.taverna.commandline.data

org.apache.taverna.commandline.exceptions - package org.apache.taverna.commandline.exceptions

org.apache.taverna.commandline.options - package org.apache.taverna.commandline.options

overrideDefaults() - Method in class org.apache.taverna.commandline.data.DatabaseConfigurationHandler

R

readConfigirationFromFile(String) - Method in class org.apache.taverna.commandline.data.DatabaseConfigurationHandler

ReadInputException - Exception in org.apache.taverna.commandline.exceptions

ReadInputException(String) - Constructor for exception org.apache.taverna.commandline.exceptions.ReadInputException

ReadInputException(String, Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.ReadInputException

registerInputs(Map<String, InputWorkflowPort>, CommandLineOptions) - Method in class org.apache.taverna.commandline.data.InputsHandler

run() - Method in class org.apache.taverna.commandline.CommandLineTool

S

safeIsSameFile(Path, Path) - Static method in class org.apache.taverna.commandline.CommandLineUtils

SaveResultsException - Exception in org.apache.taverna.commandline.exceptions

SaveResultsException(String) - Constructor for exception org.apache.taverna.commandline.exceptions.SaveResultsException

SaveResultsException(String, Throwable) - Constructor for exception org.apache.taverna.commandline.exceptions.SaveResultsException

saveResultsForPort(String, Path) - Method in class org.apache.taverna.commandline.data.SaveResultsHandler

Given the Data on an output port, saves the data on a disk in the output directory.

SaveResultsHandler - Class in org.apache.taverna.commandline.data

Handles all recording of results as they are received by the CommandLineResultListener or when the workflow enactment has completed.

SaveResultsHandler(File) - Constructor for class org.apache.taverna.commandline.data.SaveResultsHandler

saveResultsToDirectory() - Method in class org.apache.taverna.commandline.CommandLineOptionsImpl

Save the results to a directory if -outputdir has been explicitly defined, or if -bundlec has not been defined.

saveResultsToDirectory() - Method in interface org.apache.taverna.commandline.options.CommandLineOptions

Save the results to a directory if -outputdir has been explicitly defined, or if -outputdoc has not been defined.

setCommandLineOptions(CommandLineOptions) - Method in class org.apache.taverna.commandline.CommandLineTool

setCredentialManager(CredentialManager) - Method in class org.apache.taverna.commandline.CommandLineTool

setDatabaseConfiguration(DatabaseConfiguration) - Method in class org.apache.taverna.commandline.CommandLineTool

Sets the databaseConfiguration.

setDatabaseManager(DatabaseManager) - Method in class org.apache.taverna.commandline.CommandLineTool

Sets the databaseManager.

setMasterPassword(String) - Method in class org.apache.taverna.commandline.CommandLineMasterPasswordProvider

setRunService(RunService) - Method in class org.apache.taverna.commandline.CommandLineTool

setupAndExecute() - Method in class org.apache.taverna.commandline.CommandLineTool

setWorkflowBundleIO(WorkflowBundleIO) - Method in class org.apache.taverna.commandline.CommandLineTool

T

TavernaCommandLine - Class in org.apache.taverna.commandline

Main entry point for starting the Taverna Command-line Tool.

TavernaCommandLine() - Constructor for class org.apache.taverna.commandline.TavernaCommandLine

testDatabaseConnection() - Method in class org.apache.taverna.commandline.data.DatabaseConfigurationHandler

U

useOptions() - Method in class org.apache.taverna.commandline.data.DatabaseConfigurationHandler

V

validateWorkflowBundle(WorkflowBundle) - Method in class org.apache.taverna.commandline.CommandLineTool

A B C D E G H I M O R S T U V