Taverna 3 status

Stian Soiland-Reyes

myGrid team

University of Manchester

http://orcid.org/0000-0001-9842-9718

Taverna Open Development workshop, Manchester, 2014-10-30

Architecture

Taverna Platform 3

OSGi-based Java API

Constructing and running workflows
 

Workflow language: scufl2

Workflow input/output/run: databundle

 

Taverna Platform API

  Taverna Engine implementation

  Taverna common activities

  Taverna plugin activities

Taverna Platform: Status

Feature-complete
Used by T3 Command line and T3 Workbench

Most core activities migrated (e.g. wsdl, rest, xpath, beanshell, spreadsheet)

Next:

Migrate remaining core activities (tool, interaction)

Migrate plugin activities (helio/vamdc/astrotaverna)

Simplify 3rd-party usage (common pom incl. activities)
Documentation of platform-api
Reorganize source code/build under taverna-engine-*

Taverna Server Client as alternative execution platform

 

Taverna Command Line 3

Executes Taverna 2/3 workflows

(Almost) same options as in Taverna 2.5

Workflow Data Bundle replaces Baclava

$ sh executeworkflow.sh 
usage: executeworkflow [options] [workflow]
 -bundle <bundle>                        Save outputs to a new Workflow
                                         Run Bundle (zip).
 -clientserver                           Connect as a client to a derby
                                         server instance.
 -cmdir <directory path>                 Absolute path to a directory
                                         where Credential Manager's files
                                         (keystore and truststore) are
                                         located.
 -cmpassword                             Indicate that the master password
                                         for Credential Manager will be
                                         provided on standard input.
 -dbproperties <filename>                Load a properties file to
                                         configure the database.
 -embedded                               Connect to an embedded Derby
                                         database. This can prevent
                                         mulitple invocations.
 -help                                   Display comprehensive help
                                         information.
 -inmemory                               Run the workflow with data stored
                                         in-memory rather than in a
                                         database (this is the default
                                         option). This can give
                                         performance inprovements, at the
                                         cost of overall memory usage.
 -inputdelimiter <inputname delimiter>   Cause an inputvalue or inputfile
                                         to be split into a list according
                                         to the delimiter. The associated
                                         workflow input must be expected
                                         to receive a list.
 -inputdoc <document>                    Load inputs from a Baclava
                                         document.
 -inputfile <inputname filename>         Load the named input from file or
                                         URL.
 -inputvalue <inputname value>           Directly use the value for the
                                         named input.
 -logfile <filename>                     The logfile to which more verbose
                                         logging will be written to.
 -outputdir <directory>                  Save outputs as files in
                                         directory, default is to make a
                                         new directory
                                         workflowName_output.
 -port <portnumber>                      The port that the database is
                                         running on. If set requested to
                                         start its own internal server,
                                         this is the start port that will
                                         be used.
 -provenance                             Generate provenance information
                                         and store it in the database.
 -startdb                                Automatically start an internal
                                         Derby database server.

Command Line: Status

Two beta releases (+ Apache Taverna CL beta 3)

"Compare run between 2.5 and 3.0" testing

Not yet production-ready

Next:

Complete data bundle & provenance support

Installer as in 2.5 (is install4j OK?)

Documentation: How to install plugins?

Bug fixes: https, logging, error handling, configuration

Code reorganizing: Confusing module names taverna-command-line, taverna3-commandline, taverna-commandline-common.

Taverna Server 3

Execute Taverna 2/3 workflows remotely

REST/SOAP API

Security separation and workflow restrictions

Server status:

Same WSDL/REST API as in Taverna Server 2.5

.. except now can also run Taverna 3 wfbundle

Executes Taverna Command Line 3

 

Next:

Migrate databundle support (already in 2.5)

Use Taverna Platform directly

Alternative workflow execution environments

Workflow status reports during run

Dynamic plugin installation

Taverna Workbench 3

Design and run workflows

Look & Feel almost like 2.5

Workbench code fully based on Taverna Platform

Load/Save/Share workflow runs

Taverna Workbench: Status

Open Taverna 2/3 workflows

Feature complete for workflow design/run

Removed perspectives: myExperiment, BioCatalogue

Plugin perspective: bioswr

 

Next:

Installer as in 2.5

Optional plugins and editions - ask on startup

Iteration strategy & looping - simplify UI

Create nested workflow/component from selection

Standalone application to view databundles as Results?

Bugfixes: rest config, logging

2014-10-30 Taverna 3 updates

By Stian Soiland-Reyes

2014-10-30 Taverna 3 updates

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