Taverna 2.2.0

Milestone information

Project:
Taverna
Series:
t2
Version:
2.2.0
Released:
2010-07-07  
Registrant:
Stian Soiland-Reyes
Release registered:
2010-07-01
Active:
No. Drivers cannot target bugs and blueprints to this milestone.  

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Release notes 

=======================
Taverna workbench 2.2.0
=======================
http://www.taverna.org.uk/
http://www.mygrid.org.uk/

Released by myGrid, 2010-07-05
(c) Copyright 2005-2010 University of Manchester, UK

Licence
=======
Taverna is licenced under the GNU Lesser General Public Licence. (LGPL) 2.1.
See the file LICENCE.txt for details.

If the source code was not included in this download, you can download it from
http://www.taverna.org.uk/download/source-code/

Taverna uses various third-party libraries that are included under compatible
open source licences such as Apache Licence.

Running Taverna
===============
For Windows, if you used the installer you should have
Taverna->Taverna workbench 2.2.0 in your Start menu. If you used the
self-extracting archive, double-click on "taverna.exe" in the extracted folder.

For OS X, copy the Taverna application bundle to /Applications or your
preference. Eject the disk image, and run Taverna from the installed location.

For Linux, either double-click on "taverna.sh", or start a Terminal and execute
"./taverna.sh" or "sh taverna.sh" from the folder where you extracted Taverna.

Documentation
=============
See http://www.taverna.org.uk/documentation/taverna-2-x/ for
documentation and tutorials on using Taverna.

See the file known-issues.txt for known issues with this release, and the file
release-notes.txt for improvements since the previous version of Taverna.

Examples
========
Example Taverna 2.2 workflows can be found in the myExperiment starter pack at
http://www.myexperiment.org/packs/122

You can also access these as the tab 'Starter pack' under the *myExperiment*
view inside Taverna.

You can share and find other workflows at http://www.myexperiment.org/

You can find and describe web services at http://www.biocatalogue.org/

Support
=======
See http://www.taverna.org.uk/about/contact-us/ for contact details.

You may email support@mygrid.org.uk for any questions on using Taverna
workbench. myGrid's support team should respond to your query within a
week.

Mailing lists
-------------

We also encourage you to sign up to the public *taverna-users* mailing list,
where you may post about any problem or give us feedback on using Taverna.
myGrid developers are actively monitoring the list.

 * http://lists.sourceforge.net/lists/listinfo/taverna-users
 * http://taverna-users.markmail.org/search/?q=

If you are a developer, writing plugins for Taverna, dealing with the code
behind Taverna or integrating Taverna with other software, you might find it
interesting to also sign up for the public *taverna-hackers* mailing list,
where you can also track the latest developments of Taverna.

  * http://lists.sourceforge.net/lists/listinfo/taverna-hackers
  * http://taverna-hackers.markmail.org/search/?q=

Registration
============
Taverna might ask if you would like to register as a Taverna user. The myGrid
team would appreciate if you do, as it would:

  * Allow us to support you better; future plans will be directed towards
    solutions Taverna users require

  * Help sustain Taverna development

By registering, you will *not* be giving us access to your data or service
usage. We will *not* be monitoring your usage of Taverna, we will only record
the information you provide at registration time.

For full terms and condition of our registration, see
http://www.taverna.org.uk/about/legal-stuff/terms/

Requirements
============
Taverna requires the Java Runtime Environment (JRE) version 5 or 6 from Sun.
No other versions of Java are officially tested with Taverna.

*Note that future versions of Taverna will require Java 6.*

Mac OS X 10.5 (Leopard) and later should come with Java 5 or newer.

Windows users might need to download Java from http://java.com/

Linux users have different options to install Java depending on their Linux
distribution. Some distributions, such as Ubuntu, might come with alternative
open source implementations of Java, like Gnu GCJ and OpenJDK. We've identified
some issues with these implementations, and recommend using the official Java
implementation from Sun.

To download Sun Java 6 for Ubuntu, start a Terminal, and type the following:
  sudo aptitude install sun-java6-jre

and follow the instructions. You might also need to change the default Java
implementation by running:
  sudo update-alternatives --config java

Read http://www.taverna.org.uk/download/workbench/system-requirements/
for more requirement details.

Secure web services
-------------------
If you need to invoke secure services or access secured data from your
workflows (e.g. if you need to provide username and password to gain access to
your service/data or your service's URL starts with HTTPS), then you need to
allow Taverna to communicate securely to such resources using the strongest
possible cryptography.

To do so, you have to install the 'Unlimited Strength Java Cryptography
Extension' policy instead of the default restrictive policy that is
shipped with Java; the default policy will for export reasons only
allows the use of "weak" cryptography (e.g. short passwords and keys).

Java by default only comes with limited-strength cryptography support
because of import control restrictions in some countries, where
unlimited-strength cryptography is classified as a "weapon technology".
Thus, you must determine whether your country's laws allow you to
install such software and you are responsible for doing so.

The policy files on your system are located in:

   <java-home>/lib/security/local_policy.jar
   <java-home>/lib/security/US_export_policy.jar

where <java-home> is the jre directory of the Java Development Kit (JDK) or the
top-level directory of the JRE (Java Runtime Environment) on your system.

If eligible, you may download the unlimited strength versions of the above
policy files and replace the ones that were installed by default. This will
effectively "turn on" the use of unlimited-strength security in Java on your
system. Not installing these files will most probably cause invoking of secure
services from Taverna to fail. Note that if you switch to another Java version
you will have to install the policy files again in the appropriate directory of
your new Java installation.

For Java 6, you can download the unlimited cryptography policy jar files from:
  http://tinyurl.com/java6sec -or-
  https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jce_policy-6-oth-JPR@CDS-CDS_Developer

For Java 5, you can download the unlimited cryptography policy jar files from:
  http://tinyurl.com/java5sec -or-
  https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jce_policy-1.5.0-oth-JPR@CDS-CDS_Developer

Advanced
========

Logging
-------

If you are using a Windows operating system and want to see Taverna's
logging information, then run "taverna-debug.bat" from the installed
Taverna folder.

In OS X, start "/Applications/Utillities/Console".

In Linux run "taverna.sh" from a Terminal.

You can also find detailed logs in Taverna's home directory. You can
view this directory from within Taverna by choosing
Advanced->Show Log Folder in the menu.

See:

    Windows XP: C:\Documents and settings\JohnDoe\
                   Application Data\taverna-2.2.0\logs

    Vista/Windows 7: C:\Users\JohnDoe\AppData\Roaming\taverna-2.2.0\logs

    OS X: /Users/JohnDoe/Library/Application support/taverna-2.2.0/logs

    Linux: /home/johndoe/.taverna-2.2.0/logs

Note that "Application data" and "AppData" are hidden folders in Windows.

To modify the log levels, edit "conf/log4j.properties" in the Taverna
installation folder.

Default services and plugins
----------------------------

You can edit the default service list for the Taverna installation by
editing "conf/default_service_providers.xml". You can generate this
service list from within Taverna by right-clicking on "Available
Services" and selecting "Export Services To File".

Similarly you can replace the installation "plugins/plugins.xml" with
"plugins.xml" from the Taverna home directory to force installation of a
plugin by default. Note that in this case it is also recommended to copy
the full content of "repository" from the Taverna home directory to
append the installation directory's "repository".

Memory usage
------------
For OS X and Linux, Taverna will use a maximum of 400 MB. In Windows,
"taverna-debug.bat" will also use 400 MB, while "taverna.exe" will use
400 MB or up to 50% of available memory when launching Taverna.

If Taverna happens to run out of memory while running a workflow with
large data (or large number of data), you can set Taverna to store data
in a database by going to Preferences->Data and Provenance and remove
the tick for "In-memory storage". This will reduce execution speed
slightly, but should consume less memory. Also remember to click
'Remove' on old runs you are no longer interested in.

If you need to increase the available memory, edit "taverna.sh" or
"taverna-debug.bat" and replace "-Xmx400m" with say "-Xmx600m" to use
600 MiB.

For OS X you would need to right click on "Taverna.app" and go inside
the application bundle to edit Contents/Info.plist and change the same
parameter using the Property List Editor.

Changelog 

View the full changelog

Changes in Taverna 2.2.0
========================

For a complete list of issues that have been solved for Taverna 2.2.0,
see http://tinyurl.com/t2-2-0-fixes or
http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?mode=hide&requestId=10175

General user interface
----------------------
Workflows with services that are offline/unavailable, or for which the
appropriate plugin is not installed, can now be opened and edited.
(T2-1231, T2-1411, T2-1376)

Unavailable and unrecognized services are shown faded in the workflow.
(T2-1354)

New menu item Advanced->Show log folder. (T2-1273)

Workbench Configuration preferences tidied up. (T2-1463)

Preferences window did not always appear on a restricted (ie. WiFi)
network which returned HTML login pages for any URL. (T2-1409)

User registration form records the "Purpose" field correctly. (T2-1304)

Workflow engine
---------------
"executeworkflow" command line tool. (T2-316)

Ability to pause, resume and cancel a running workflow. (T2-414).

taverna.sh and taverna-debug.bat now handle symbolic links to the
Taverna installation. (T2-1406)

Shows start/stop/average execution times for workflow, services and
individual service iterations. (T2-875)

Intermediate values display empty lists correctly. (T2-1019)

Intermediate values supports workflows and services which has an
input port with the same name as an output port. (T2-1051)

Workflow design
---------------
Service descriptions (the Available Services) can be exported to and
imported from an XML file. Default Services are no longer hard-coded,
but can be customised per Taverna installations. (T2-674)

Added Validation Report, warns on potential errors in workflow, and
suggests possible solutions like editing the List Handling or enabling
retries. (T2-1238)

A full validation is performed before running a workflow, which will
attempt to connect to external services in the workflow - giving an
early warning if a service is not available.

Ability to configure retries and threads. (T2-416)

Added Right-click menu to configure looping, retries and threads.

Configure Looping dialogue simplified. (T2-1366, T2-824, T2-1349)

Workflow output port was not always selected correctly. (T2-1288)

Confusing Insert->Constant value removed as it was always disabled
except when selecting an input port. Still available on right-click
menu. (T2-1325)

Running workflows
-----------------
Run Workflow dialogue is no longer modal, allowing one dialog per
workflow at the same time. (T2-1221)

Run Workflow dialogue warns if the workflow has potential problems.
(T2-1363)

Run Workflow shows the filename or name of workflow. (T2-1284)

Unconnected input ports are no longer shown in Run Workflow. (T2-1285)

Run Workflow dialogue could appear twice for same workflow if
double-clicking Run button. (T2-863)

"Load/Save previous values" button in the Run Dialog remembers the last
used folder. (T2-1252)

Exiting Taverna while a workflow is running will warn the user, asking
to Cancel active workflow runs. (T2-1426)

Results
-------
Added Progress Report, shows a table of running services (including
nested workflows). Table shows status, queued iterations, iterations
finished, failed iterations, first and last invocation times, and average
invocation time. (T2-1213)

Intermediate values for a service shows iterations separately from
output lists. (T2-553)

Iterations indicate if they failed by colour and label. (T2-1416)

Iterations indicate if they were skipped due to incoming errors.
(T2-1427)

Possibility to filter iterations and outputs to show only results or
only errors. (T2-1460, T2-1461)

Clicking a workflow output port in diagram selects the resulting output
tab. (T2-1459)

Added error count on nested workflows, showing number of nested workflow
iterations which contained one or more errors. (T2-1414)

"Save values" button renamed to "Save all values". (T2-1324)

Value-is-too-large dialogue would still render the full value if
pressing Escape in Windows. (T2-1279)

Error count for services inside a nested workflow could be wrong.
(T2-1413)

Previous runs of nested workflows could wrongly reappear as an
individual run. (T2-1469)

Binary data was not always saved correctly on Windows. (T2-1280)

Result renderers
----------------
Added renderer for TIFF and JPEG2000. (T2-1317)

HTML renderer now follows (absolute) hyperlinks. (T2-1313)

Text renderer no longer scrolls to the bottom. (T2-1248)

Updated RTF renderer. (T2-1320)

SeqVista renderer could break look and feel on Linux. (T2-1369)

Non-functioning URL renderer disabled. (T2-1263)

Beanshell/RShell scripts
------------------------
Script editors show line number. (T2-1287)

Suggested port names should start at 1, not 0. (T2-1387)

Invalid beanshell scripts detected by validation report. (T2-1375)

Nested workflows
----------------
Import workflow did not always display "Already opened workflows" list
correctly. (T2-1315)

The dialogue for adding nested workflows did not always disappear.
(T2-1261)

Import workflow could pop-up 2 file choosers dialogues. (T2-1314)

Biomart service
---------------
Biomart is streaming results, enabling pipelining for individual rows in
result. (T2-1093)

WSDL service
------------
XML splitters support optional and nillable inputs. (T2-847)

Loading a workflow with a WSDL service which is unreachable could take a
long time while timing out. (T2-1470)

myExperiment perspective
------------------------
myExperiment perspective did not upload Taverna 1 workflows correctly.
(T2-1185, T2-1333)

Using myExperiment perspective could break display of Service Details
and other HTML-based components. (T2-1377)

API changes
-----------
Added a placeholder to keep semantic annotations of workflow components.
Suggested format is RDF/N3 using <> as subject. (T2-1336)

Workflow definition keeps chain of previous workflow identifiers.
(T2-1337)

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