Updated release notes for Taverna 2.2.0
git-svn-id: https://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-workbench/trunk/workbench-distro@11075 bf327186-88b3-11dd-a302-d386e5130c1c
diff --git a/src/main/resources/known-issues.txt b/src/main/resources/known-issues.txt
index 7f54693..5d21167 100644
--- a/src/main/resources/known-issues.txt
+++ b/src/main/resources/known-issues.txt
@@ -1,61 +1,50 @@
==========================
-Taverna 2.1.2 known issues
+Taverna 2.2.0 known issues
==========================
-This document some of the known issues in Taverna 2.1.2. A full list and
-further details can be found within myGrid's issue tracker Jira at
-http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?mode=hide&requestId=10153
+This document some of the known issues in Taverna 2.2.0. A full list
+and further details can be found within myGrid's issue tracker Jira at
+http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?mode=hide&requestId=10171
General issues
==============
-T2-316: Ability to execute workflow from command line
-
-T2-890: Iteration strategy not always translated correctly from Taverna 1
-workflows (most likely due to Taverna 1 having inconsistent iteration
+T2-890: Iteration strategy not always translated correctly from Taverna
+1 workflows (most likely due to Taverna 1 having inconsistent iteration
strategies)
-T2-895: The dataviewer should be included with the release.
+T2-895: The dataviewer should be included with the release.
T2-1144: Plugin manager only supports HTTP-based sites
Workflow engine
===============
-T2-414: Can't stop a running workflow
+T2-1423: Merges of depth 1 in front of depth 0 can give empty list
Data management
===============
-T2-1003: The degradation of speed when the cache is full needs to be examined.
-
T2-1033: The database can become locked after an abrupt close of Taverna
+T2-1264: Database not starting up could cause NullPointerException in
+StringConstant
+
Provenance capturing
====================
-T2-875: Processor execution start/finish time not recorded
-
-T2-982: If the database is already being used, for example by another instance
-of Taverna, then attempts to use it do not fail gracefully.
-
-T2-1019: The intermediate results display should distinguish between a
-processor that has finished and produced an empty list, and a processor that
-has not yet produced any results.
-
-T2-1051: Provenance does not work correctly if an input and an output port have
-the same name
+T2-982: If the database is already being used, for example by another
+instance of Taverna, then attempts to use it do not fail gracefully.
T2-1062: Failed to start database 't2-database' error
-T2-1082: Sometimes data for previous runs are not shown correctly
-
-T2-1083: Provenance capture can in some cases severely affect run speed
-
T2-1211: Provenance does not capture details of retries
T2-1212: Provenance does not capture details about looping
+T2-1342: Provenance fails if nested workflow's processor name matches
+processor inside nested workflow
+
Security
========
@@ -64,32 +53,24 @@
T2-933: Secured WSDLs should be indicated with padlock in diagram
-
-Testing
-=======
-T2-264: Scalability and memory/thread footprint testing will continue
-
-
-
Workbench issues
================
-
-T2-248, T2-392: No feedback while opening workflow
-
T2-294: Can't add alternative services to processor
T2-495: Removing links to a merge leaves stand-alone merge
-T2-685: Can't open workflow if a service is offline/disappeared
-
T2-766: If/else style branching
-T2-734: Undo should indicate what is to be undone
+T2-1053: If you have a lot of workflows (say over 50) open then the
+workflows menu does not cope
-T2-797: Can't rename workflow
+T2-1302: Registration dialog is too big
-T2-1053: If you have a lot of workflows (say over 50) open then the workflows
-menu does not cope
+T2-1328: Configure available when no selection
+
+T2-1329: File-Open dialogue in Windows has button for creating a folder
+
+T2-1402: Double-clicking Run icon runs workflow w/no inputs twice
Available services
@@ -102,13 +83,13 @@
T2-767: Can't save configured services (Beanshell, BioMart)
-T2-1151: Empty/failing service providers can't be removed (Only by 'Remove all
-user-added')
+T2-1151: Empty/failing service providers can't be removed (Only by
+'Remove all user-added')
T2-1235: Should cache descriptions, should work even starting offline
-T2-1236, T2-1237: Ability to refresh service descriptions (while developing a
-service)
+T2-1236, T2-1237: Ability to refresh service descriptions (while
+developing a service)
Workflow diagram
@@ -121,17 +102,21 @@
T2-505: Port display order not consistent
-T2-508: Show/hide ports menu item does not update correctly on OS X
+T2-508: Show/hide ports menu item does not update correctly on OS X
T2-839: Nested workflow with no inputs shown incorrectly in diagram
T2-991, T2-1044: Diagram too tiny for small workflows
-T2-1001: Arrows to a merge can start from the wrong position when ports are
-displayed
+T2-1001: Arrows to a merge can start from the wrong position when ports
+are displayed
+
+T2-1074: ConcurrentModificationException in GraphMonitor
T2-1120: Diagram does not indicate implicit iteration
+T2-1385: Panning to make a connection does not always work correctly
+
Workflow explorer
=================
@@ -144,17 +129,13 @@
===========
T2-350: Port details should show connections
-T2-416: Can't configure retries and threads for service
-
-T2-1047: Details for services loses HTML formatting and borders
+T2-1290: Undo does not work for annotation
Looping
=======
T2-641: Looping fails if tested output port not connected in workflow
-T2-827: Support for loop testing on lists
-
T2-1119: Looping not indicated in diagram
@@ -174,24 +155,12 @@
Results/runs
============
-T2-504: Can't click on output port to see values
-
T2-969: Need ability to store a run as OPM (Open Provenance Model)
T2-1016: Ability to open workflow from previous run
-T2-1090: Might say "List with 2 values" instead of 3
-
-T2-1123: Total number of invocations not shown
-
T2-1140: Saving of large data not memory-efficient
-T2-1206: Not obvious that service can be clicked for intermediates
-
-T2-1208: Need t1-style processor list/table view
-
-T2-1209: Need filter to show only errors
-
T2-1213: Need workflow run progress report
T2-1215: Colours should be red/green indicating status (as in t1)
@@ -200,8 +169,10 @@
T2-1249: Should auto-select the first value in list
-T2-1251: Workflow outputs not always shown if workflow executes fast (redraw
-issue)
+T2-1251: Workflow outputs not always shown if workflow executes fast
+(redraw issue)
+
+T2-1323: Deleting a workflow run should move to next entry
Output values (Renderers)
@@ -212,25 +183,10 @@
T2-1207: Renderer area is too small for many outputs
-T2-1245: For quite large values, (> 100 MB), selecting runs out of memory
-without showing "Value is large" dialogue
+T2-1245: For quite large values, (> 100 MB), selecting runs out of
+memory without showing "Value is large" dialogue
-T2-1248: Text renderer scrolls to last line, should show first line
-
-
-Provenance/intermediate values
-==============================
-T2-553: Does not distingiush lists and iterations
-
-T2-875: Processor execution start/stop times should be shown
-
-T2-1019: The provenance popup panel should distinguish between the production
-of an empty list and no results being received yet.
-
-T2-1045: Multiple clicks on a service can cause multiple intermediate values
-panels
-
-
+T2-1420: HTML renderer can't show complex web pages
Beanshell scripts
@@ -243,10 +199,8 @@
T2-779: Beanshell configuration needs help/descriptions
-T2-1122: Beanshell configuration dialogue behind main window after switching
-application
-
-T2-1128: Close->Yes does not check if port names are unique
+T2-1122: Beanshell configuration dialogue behind main window after
+switching application
BioMart services
@@ -255,9 +209,6 @@
T2-1046: Empty configuration panel sometimes appears
-T2-1093: BioMart streaming is disabled (for provenance performance reasons)
-
-
BioMoby services
================
@@ -275,6 +226,9 @@
T2-1126: "Save as" in a nested workflow detaches it from parent
+T2-1335: Configure action for nested workflow is incorrect/inconsistent
+
+T2-1340: Nested workflow never completes if input port not connected
Local workers
@@ -295,17 +249,18 @@
=============
T2-486: Can't use lists of lists as input
-T2-587: Can't distinguish between several declared operations with same name
-
-T2-847: XML splitters don't support optional inputs
+T2-587: Can't distinguish between several declared operations with same
+name
T2-1061: Can't upload SOAP attachments (only receive)
-T2-1105: Wrong/invalid element name from XML splitters for inner complex types
+T2-1105: Wrong/invalid element name from XML splitters for inner complex
+types
T2-1106: Can't import cyclic XML schema includes
-T2-1108: Does not support XML attributes (only elements) in XML splitters
+T2-1108: Does not support XML attributes (only elements) in XML
+splitters
T2-1088, T2-1110: Incorrect handling of arrays in result
@@ -313,30 +268,37 @@
T2-1160: XML splitters not updated when XML schema changes on server
-T2-1224: Binary data invalid as input, need 'Encode as base64' local worker
-first
+T2-1224: Binary data invalid as input, need 'Encode as base64' local
+worker first
T2-1229: Security dialogue should remember/guess security profile
-T2-1230: Security dialogue don't indicate if username/password already set
+T2-1230: Security dialogue don't indicate if username/password already
+set
T2-1243: HTTP Digest-protected web services not supported
+T2-1339: Need better error message on Illegal Keysize when JCE policy
+not installed
+
+T2-1471: XML output splitters return wrong elements on maxOccurs=0
+
+
+Disabled services
+=================
+T2-1405: Edit Property does not ask for confirmation on Window Close
+
myExperiment perspective
========================
-T2-1012: The myExperiment login should make it clear that it is for
-myExperiment and not for Taverna
+T2-1036: The perspective should filter out broken workflows. This
+relies on myExperiment's capability being upgraded,
-T2-1036: The perspective should filter out broken workflows. This relies on
-myExperiment's capability being upgraded,
+T2-1068: Does not display processors/services of Taverna 2 workflows
+(only T1)
-T2-1068: Does not display processors/services of Taverna 2 workflows (only T1)
-
-T2-1121: Upload seems to require title/description even when it will be derived
-
-T2-1185: Upload assumes file is saved as .t2flow (breaks for T1 .xml)
-
+T2-1121: Upload seems to require title/description even when it will be
+derived
Documentation
@@ -345,4 +307,5 @@
fail-if-false should be documented.
-Stian Soiland-Reyes, Alan R Williams, 2010-03-23
+Stian Soiland-Reyes, Alan R Williams, 2010-07-05
+
diff --git a/src/main/resources/readme.txt b/src/main/resources/readme.txt
index 4e58f84..03c9e11 100644
--- a/src/main/resources/readme.txt
+++ b/src/main/resources/readme.txt
@@ -1,10 +1,10 @@
=======================
-Taverna workbench 2.1.2
+Taverna workbench 2.2.0
=======================
http://www.taverna.org.uk/
http://www.mygrid.org.uk/
-Released by myGrid, 2010-03-30
+Released by myGrid, 2010-07-05
(c) Copyright 2005-2010 University of Manchester, UK
@@ -23,7 +23,7 @@
Running Taverna
===============
For Windows, if you used the installer you should have
-Taverna->Taverna workbench 2.1.2 in your Start menu. If you used the
+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
@@ -32,14 +32,35 @@
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 couple
-of days.
+workbench. myGrid's support team should respond to your query within a
+week.
Mailing lists
@@ -70,8 +91,7 @@
* Allow us to support you better; future plans will be directed towards
solutions Taverna users require
- * Help sustain Taverna development; out continued funding relies on us
- showing usage
+ * 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
@@ -81,34 +101,13 @@
http://www.taverna.org.uk/about/legal-stuff/terms/
-Examples
-========
-Example Taverna 2.1 workflows can be found in the myExperiment starter pack at
-http://www.myexperiment.org/packs/103
-
-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/
-
-
-
-Documentation
-=============
-See http://www.taverna.org.uk/documentation/taverna-2-1/ 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.
-
-
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/
@@ -126,8 +125,8 @@
implementation by running:
sudo update-alternatives --config java
-Read http://www.taverna.org.uk/download/taverna-2-1/system-requirements/ for
-more requirement details.
+Read http://www.taverna.org.uk/download/workbench/system-requirements/
+for more requirement details.
Secure web services
@@ -138,16 +137,16 @@
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).
+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.
+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:
@@ -179,40 +178,67 @@
Logging
-------
-If you would prefer to see the console log in Windows, instead execute
-"taverna-debug.bat" from the installed Taverna folder.
-In OS X, start /Applications/Utillities/Console, and from Linux run
-"taverna.sh" from a Terminal.
+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.
-You can also find detailed logs in Taverna's home directory. See:
+In OS X, start "/Applications/Utillities/Console".
-Windows XP: C:\Documents and settings\JohnDoe\
- Application Data\taverna-2.1.2\logs
+In Linux run "taverna.sh" from a Terminal.
-Vista/Windows 7: C:\Users\JohnDoe\AppData\Roaming\taverna-2.1.2\logs
+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.
-OS X: /Users/JohnDoe/Library/Application support/taverna-2.1.2/logs
+See:
-Linux: /home/johndoe/.taverna-2.1.2/logs
+ 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 300 MiB. In Windows,
-"taverna-debug.bat" will also use 300 MiB, while "taverna.exe" will use 300 MiB
-or up to 50% of available memory when launching Taverna.
+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 could 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 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 "-Xmx300m" 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.
+"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.
diff --git a/src/main/resources/release-notes.txt b/src/main/resources/release-notes.txt
index 6ae7ab8..b66bfa2 100644
--- a/src/main/resources/release-notes.txt
+++ b/src/main/resources/release-notes.txt
@@ -1,159 +1,204 @@
-Changes in 2.2.0
-================
+Changes in Taverna 2.2.0
+========================
-For a complete list of issues that have been solved for 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 which plugin is
-not installed, can now be opened and edited. (T2-1231, T2-1411)
+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 services are shown faded in the workflow. (T2-1354)
+Unavailable and unrecognized services are shown faded in the workflow.
+(T2-1354)
-The dialogue for adding nested workflows did not always disappear
-(T2-1261)
+New menu item Advanced->Show log folder. (T2-1273)
-Workbench configuration preference tidied up (T2-1463)
+Workbench Configuration preferences tidied up. (T2-1463)
-The preferences window did not always appear on a restricted (ie.
-WiFi) network which present HTML login pages to any URL. (T2-1409)
-
-New menu item: Advanced->Show log folder (T2-1273)
+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
---------------
-New ability to pause and cancel a running workflow (T2-414).
+"executeworkflow" command line tool. (T2-316)
-Provenance handles empty lists correctly. (T2-1019)
+Ability to pause, resume and cancel a running workflow. (T2-414).
-Provenance supports workflows and services which has an
+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)
-Provenance records and shows start/stop/average execution times for
-workflow, services and service iterations. (T2-875)
-
-New "executeworkflow" command line tool (T2-316)
-
-taverna.sh and taverna-debug.bat now handles symlinks to the Taverna
-installation. (T2-1406)
-
-
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)
-Validation Report warns on potential errors in workflow, and
-suggests possible solutions like editing the List Handling. (T2-1238)
+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 for instance if a service is not available, or if a
-beanshell script contains error.
+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)
-Right-click menu to configure looping, retries and threads.
+Added Right-click menu to configure looping, retries and threads.
-Configure Looping dialogue layout modified (T2-1366)
-
-Configure Looping dialogue simplified (T2-824, T2-1349)
+Configure Looping dialogue simplified. (T2-1366, T2-824, T2-1349)
Workflow output port was not always selected correctly. (T2-1288)
-Menu for Insert->Constant value modified (T2-1325)
+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 dialogue per
-workflow at the same time (T2-1221)
+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 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. (T2-863)
+double-clicking Run button. (T2-863)
-Run Workflow shows the filename or name of workflow (T2-1284)
-
-"Load previous values" button in the Run Dialog should remember the last
+"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 runs. (T2-1426)
+to Cancel active workflow runs. (T2-1426)
Results
-------
-New Progress Report shows a table of running services in workflow and
-nested workflows. Table shows status, queued iterations, iterations
-finished, failed iterations, start and stop times, and average
-invocation time. (T2-1213)
+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)
-T2-1248 Workbench - Renderers Text renderer scrolls to bottom
-T2-1263 Workbench - Renderers URL renderer does not work as expected
-T2-1313 Workbench - Renderers HTML renderer does not work as a proper HTML renderer where you can follow hyperlinks etc.
-T2-1317 Workbench - Renderers TIFF renderer is needed
-T2-1320 Workbench - Renderers Rtf renderer renders text as html
-T2-1369 Workbench - Renderers SeqVista messes up look and feel
-T2-1469 Workbench - Provenance previous runs Previous Runs of nested workflows wrongly appear if nested workflow was also individually run
-T2-553 Workbench - Provenance previous runs Provenance does not distinguish between lists and iterations
+Suggested port names should start at 1, not 0. (T2-1387)
-T2-1279 Workbench - Results panel Value-too-large dialogue still renders if pressing Escape in Windows
-T2-1324 Workbench - Results panel "Save values" should say "Save all values"
-T2-1413 Workbench - Results panel Error count for processor inside nested workflow is wrong
-T2-1414 Workbench - Results panel No error count on a nested workflow
-T2-1416 Workbench - Results panel No indication of which invocation failed
-T2-1427 Workbench - Results panel Need to distinguish between invocations that error bounced and those that threw an error
-T2-1459 Refinement Workbench - Results panel Clicking workflow output port in result graph should select output port results
-T2-1460 Workbench - Results panel Intermediate values must allow filtering for errors
-T2-1461 Workbench - Results panel Workflow results must be filterable
-T2-1280 Workbench - Results panel Workbench - Workflow runs panel Binary data not always loaded/saved correctly
+Invalid beanshell scripts detected by validation report. (T2-1375)
+Nested workflows
+----------------
+Import workflow did not always display "Already opened workflows" list
+correctly. (T2-1315)
-X service
----------
-T2-1287 Activity - Beanshell Script should show line numbers
-T2-1375 Activity - Beanshell Beanshell health checker needs tweaking
-T2-1387 Activity - Beanshell Activity - RShell Ports should start at 1
-T2-1093 Activity - Biomart Switch BioMart streaming back on
-T2-674 Activity - Biomart Activity - Biomoby Activity - Soaplab Activity - WSDL and XML splitter Hardcoded default locations
-T2-1314 Activity - Nested workflow Import workflow window pops up 2 file chooser dialogs
-T2-1315 Activity - Nested workflow Import workflow window does not display location of the "Already opened window" nicely
-T2-1376 Activity - Unrecognized Unrecognized activity must be implemented
-T2-1470 Activity - WSDL and XML splitter WSDL activity can take lone time to fail configuration
-T2-847 Activity - WSDL and XML splitter XML splitters don't support optional inputs - WSDL minOccurs ignored
+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
------------------------
-T2-1185 Workbench - Perspectives - myExperiment myExperiment perspective assumes a t2flow is being uploaded
-T2-1333 Workbench - Perspectives - myExperiment when myExperiment perspective loads T1 workflows from a file on a disk they appear as T2 workflows on myExperiment Web site
-T2-1377 Workbench - Perspectives - myExperiment The myExperiment perspective wipes out css settings
+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
-----------
-T2-1336 Engine - Workflow model Placeholder for semantic annotation
-T2-1337 Engine - Workflow model Identification chain for dataflows
+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)
-
-
-Changes in 2.1.2 (including 2.1.1)
-==================================
+Changes in Taverna 2.1.2 (including 2.1.1)
+==========================================
For a complete list of issues that have been solved for 2.1.2,
see http://tinyurl.com/t2-1-2-fixes or
@@ -162,25 +207,27 @@
General user interface
----------------------
-Resolved a memory leak for multiple invocations of nested workflows. (T2-1135)
+Resolved a memory leak for multiple invocations of nested workflows.
+(T2-1135)
-Database cleanup no longer blocks shutdown, done in the background at startup
-instead. (T2-1191)
+Database cleanup no longer blocks shutdown, done in the background at
+startup instead. (T2-1191)
-"Do you want to save" dialogue now appears before database shutdown dialogue.
-(T2-1189)
+"Do you want to save" dialogue now appears before database shutdown
+dialogue. (T2-1189)
-Pressing Enter now closes dialogue in "Add new plugin site" (T2-1150) and "Add
-new WSDL/Biomart/Soaplab service" (T2-1149)
+Pressing Enter now closes dialogue in "Add new plugin site" (T2-1150)
+and "Add new WSDL/Biomart/Soaplab service" (T2-1149)
-Previous workflow runs used to parse every executed workflow at startup, which
-could be slow and error-prone. Now they are parsed individually when a run
-is first selected (T2-1188)
+Previous workflow runs used to parse every executed workflow at startup,
+which could be slow and error-prone. Now they are parsed individually
+when a run is first selected (T2-1188)
Workflow engine
---------------
-Two thread-safety issues with nested workflows were resolved (T2-1137, T2-1124)
+Two thread-safety issues with nested workflows were resolved (T2-1137,
+T2-1124)
"Save value" now saves the correct value after showing "Value too large"
warning (T2-1147)
@@ -188,26 +235,27 @@
Workflow design
---------------
-Empty dot and cross products in list handling could cause workflow execution to
-fail, but are now automatically removed when editing the list handling.
-(T2-1101. T2-1100)
+Empty dot and cross products in list handling could cause workflow
+execution to fail, but are now automatically removed when editing the
+list handling. (T2-1101. T2-1100)
Results
-------
-"Save value" now saves the correct value after switching back to port without
-reselecting value (T2-1156, T2-1147)
+"Save value" now saves the correct value after switching back to port
+without reselecting value (T2-1156, T2-1147)
All renderers are now available, even if not automatically detected.
Non-detected renderers are grayed out, but still selectable. (T2-1228)
-The chosen renderer is now remembered for all items on an output port. (T2-1089)
+The chosen renderer is now remembered for all items on an output port.
+(T2-1089)
-It is now possible to force a re-rendering of the result by clicking "Refresh"
-(T2-1227)
+It is now possible to force a re-rendering of the result by clicking
+"Refresh" (T2-1227)
-The "Value too large" warning for outputs over 1 MB no longer appear more than
-once when selecting the same value again. (T2-1244)
+The "Value too large" warning for outputs over 1 MB no longer appear
+more than once when selecting the same value again. (T2-1244)
WSDL services
@@ -226,15 +274,16 @@
Local workers
-------------
-"Get page/image from URL" now supports HTTPS and Basic/digest authentication
-(T2-1198)
+"Get page/image from URL" now supports HTTPS and Basic/digest
+authentication (T2-1198)
Beanshell scripts
-----------------
Invalid port names are no longer allowed (T2-1129)
-An output port name called the same as an input name is now allowed (T2-1127)
+An output port name called the same as an input name is now allowed
+(T2-1127)
RShell script
@@ -244,46 +293,46 @@
myExperiment perspective
------------------------
-Non-English users now able to log in (avoiding locale-based date parsing)
-(T2-1157)
+Non-English users now able to log in (avoiding locale-based date
+parsing) (T2-1157)
Security
--------
-HTTP Proxy username/password no longer lost if using File -> Open from location
-(T2-1184)
+HTTP Proxy username/password no longer lost if using File -> Open from
+location (T2-1184)
-HTTP Basic Auth and HTTP Digest now supported for opening workflows and "Get
-page/image from URL" local worker. (T2-1225, T2-1183)
+HTTP Basic Auth and HTTP Digest now supported for opening workflows and
+"Get page/image from URL" local worker. (T2-1225, T2-1183)
-An Apple update to Java 6 on OS X change the default trust store password
-(T2-1094)
+An Apple update to Java 6 on OS X change the default trust store
+password (T2-1094)
-Credential manager no longer pops up user interfaces when run outside the
-workbench (T2-1164, T2-698)
+Credential manager no longer pops up user interfaces when run outside
+the workbench (T2-1164, T2-698)
Master password dialogue did not appear in 2.1.1 (T2-1133)
-HTTPS should now generally be supported. A confirmation dialogue will appear if
-an untrusted certificate is used for the first time, and the default Java
-truststore is imported on first run.
+HTTPS should now generally be supported. A confirmation dialogue will
+appear if an untrusted certificate is used for the first time, and the
+default Java truststore is imported on first run.
API changes
-----------
-StartupSPI and ShutdownSPI positionHint flipped, now a low position means early
-execution (T2-1186)
+StartupSPI and ShutdownSPI positionHint flipped, now a low position
+means early execution (T2-1186)
-Running Taverna from workbench-dev no longer gives blank perspectives (T2-1190)
+Running Taverna from workbench-dev no longer gives blank perspectives
+(T2-1190)
Credential Manager now exposes a single SPI CredentialProviderSPI, for
providing master password, certificate approval and username password.
Workbench implementation pops up dialogues. (T2-1193)
-
-Changes in 2.1.0 (since 2.1 beta 2)
-===================================
+Changes in Taverna 2.1.0 (since 2.1 beta 2)
+===========================================
For a complete list of issues solved for 2.1.0, see
http://tinyurl.com/t2-1-0-fixes or
@@ -298,8 +347,8 @@
Recent workflows: Taverna now remembers your recently edited workflows
and you can easily open them.
-Notification of updates: Users are now notified when updates to
-Taverna or to a plugin are available.
+Notification of updates: Users are now notified when updates to Taverna
+or to a plugin are available.
Editing of workflows
@@ -329,8 +378,8 @@
Support for security: secured WSDL services can now be called using
security validated via a credential manager.
-Updated R support: the R service now allows connections to an Rserve
-for the latest R (up to 2.10).
+Updated R support: the R service now allows connections to an Rserve for
+the latest R (up to 2.10).
New spreadsheet service: you can import Excel or csv spreadsheets and
feed the content into your workflow.
@@ -345,15 +394,15 @@
complex trees of values.
Saving and reusing values: You can now save and reuse the input values
-for a workflow run. You can save the output values from a run and
-could use them as inputs for other workflow runs.
+for a workflow run. You can save the output values from a run and could
+ use them as inputs for other workflow runs.
Output value display: Output values are displayed using the correct
renderers. You are now warned if a value is large and could cause
problems for Taverna.
-Output value tree: The tree of output values should now be correct.
-It no longer misses some of the generated data.
+Output value tree: The tree of output values should now be correct. It
+no longer misses some of the generated data.
Runs: You can now access the data associated with previous runs. The
provenance and data from a run can be deleted.
@@ -364,8 +413,8 @@
Provenance and data management: The provenance is now kept in the same
database as the values.
-Improved performance: Workflow execution in 2.1 RC 1 is faster than
-that in 2.1 beta 2.
+Improved performance: Workflow execution in 2.1 RC 1 is faster than that
+in 2.1 beta 2.
myExperiment perspective
