Taverna Workbench Core 2.5.0

Changes in Taverna 2.5.0

Taverna 2.5.0 includes additional functionality (interaction service,
PROV support, components), a simplified installation, user interface
improvements and bug-fixes.

Installation

To simplify installation on common operating systems, Taverna
distributions for Windows/Linux/OSX now come bundled with the Java
Runtime Environment from OpenJDK and the required Graphviz
binaries. The installation no longer requires you to install the JCE
Strong Encryption policy.

Note that installation on OS X currently requires the
XQuartz libraries to be manually installed.
XQuartz-2.7.5.dmg (or newer) should be included on the
Taverna OS X disk image. If not, see
http://xquartz.macosforge.org/landing/

Available services

To improve start-up time and simplify Taverna for users in a wide
range of scientific fields, Available Services are tailored for the
scientific domain. For example, the Astronomy distribution includes
VAMDC services.

Interaction service

The Interaction Service has been added to the Workbench. This provides
the ability to ask questions and inform users during the running of
the workflow. Unlike the previous interactive local workers, this
service uses web pages, and therefore also works if using the Command
Line tool or the Taverna Server.

For details, see
http://www.taverna.org.uk/developers/work-in-progress/interaction/

Provenance

The Taverna-PROV export has been added. This adds a new
button "Save Provenance Bundle" when clicking "Save All"
from the results perspective.

The provenance bundle is a ZIP file containing all input, output and
intermediate values as separate files, along with the provenance of
the workflow run. The bundle is based on the Research Object Bundle
specification, and complies with the W3C PROV-O provenance
specification.

For details, see https://github.com/myGrid/taverna-prov

Component service

The Component capability has been added. This allows the usage of
component services, which encapsulate a nested Taverna workflow that
has been constructed and described for compatiblity with other
components within a chosen Component Family.

This allows for publication of reusable workflow fragments, which
appear as single services within the master workflow.

For details, see
http://www.taverna.org.uk/developers/work-in-progress/components/

Help

Added Help->About, which includes debug information that
can be posted with support requests. (T3-1015)

Help has been added to several dialogs (T3-1074, T3-1075, T3-1076,
T3-1077, T3-1078)

Help and example workflows are now available for services (T3-1069, T3-1072)

Service panel

The Service panel no longer flickers as new services are added (T3-611)

Credential Manager

Rather than requiring a credential manager password at start-up,
the default password "taverna" is used unless explicitly specified. (T3-981)

The bundled OpenJDK includes support for strong cryptography, and thus
the JCE dialogue should no longer appear at startup. (T3-980)

Nested workflow

Nested workflows will now terminate if there are no output ports (T3-986)

The ports of a nested workflow will be correctly synchronized with
those shown in the outer workflow (T3-691)

REST service

Support optional input query parameters (T2-2112)

RShell service

R services running on a local R server no longer ask for the
credential manager password (T3-911)

Ports of R services can now have underscores in their names (T3-1012)

The configuration panel for an R service will retain its size (T3-910)

Spreadsheet service

All changes to the spreadsheet service will be seen as edits (T3-1059)

Text constant

Reading from a file no longer inserts a newline (T3-783)

WSDL service

The WSDL service uses faster iteration (T3-953)

XPath service

Added ability to extract the first matching value (at depth 0).
Additional output ports added. (T3-1019)

Added ability to receive result of XPath functions, e.g.
"count(/foo/bar)" (T3-996)

Plugin manager

Avoid startup screen delays if a plugin's repository URL
fails due to DNS/network errors (T2-2115)

Avoid deadlock in initialization of the logging mechanism
if experiencing network issues while loading
Available Services. (T3-1018)

Plugin versions are now compared numerically (T3-1004)

There is now an "Update all" button (T3-983)

List handling dialog

A simplified list handling dialog has been created (T3-486, T3-1079. T3-480)

Looping

Looping is now indicated in the diagram (T3-494)

Run dialog

On Linux, the Run dialogue should no longer appear
behind the workbench window if it was iconified (T2-2105, T3-994)

Display of error documents has been improved (T3-396)

Saving results

The Workbench Save All values dialog is put into a Scroll pane if
large (T3-1110)

Workflow engine

Resolved a deadlock when validating cross product, which could occur
during command line execution of large workflows. (T2-2102)

Several database locking issues have been resolved (T3-1051, T3-318, T3-1123)

The default memory allocation has been increased (T3-842)

myExperiment perspective

There is now a link for registration on the myExperiment perspective login page (T3-1064)

Uploading of a t2flow workflow now works (T3-804)

Service catalogue perspective

The list of services no longer include archived services (T3-1116)

T2flow format

The calculated port depth of output ports are stored
in the saved t2flow. (T3-1013)