Updating of the master password now works correctly (T2-2004)
Users can now use all the example values with one click (T2-2079)
The minimization of the run dialog has been changed (T2-2005)
Previously, the run dialog could get confused if, after the workflow had been run, ports were removed from the workflow or renamed. (T2-2060)
The My Stuff tab now shows all of a user’s objects (T2-2000)
The default sharing license now agrees with the default on the myExperiment web site (T2-2008)
The myExperiment Perspective has been changed to use the credential manager (T2-2010)
The myExperiment Perspective is more tolerant of different date formats (T2-2020)
Service Catalogue Perspective
The search box is now shown in small windows (T2-1948)
The details of services are now displayed correctly (T2-2001)
The list handling and annotation of a service can now be done by r-clicking on a service (T2-2077 and T2-2078)
Saving a workflow now uses temporary files, so that it it fails it does not lose the original workflow (T2-1998)
The workflow title is now limited in length (T2-2002)
The display of error documents that contain HTML has been improved (T2-1641)
Saving data now closes streams correctly (T2-1997)
The HTML renderer now uses the standard Desktop mechanism (T2-1999)
Annotations of services are now displayed correctly (T2-2009)
The background colour for text has been changed to make it more readable (T2-1984)
The registries have now been changed to point at INAB (T2-1983)
The default port for HTTPS has been corrected (T2-2022)
The REST service can now return the URL that was created by the replacement of the parameters with the input values (T2-2023)
The REST service can now return the headers of the reponse. (T2-2064)
Header values can now be parameterized. The parameters can be set by passing values into the corresponding port of the service. (T2-2072)
The SoapLab service will now fail if the invoked service does not return enough data (T2-1994)
Text constant service
The string constant service has been replaced by the text constant service. The text constant service allows the entry of multi-line text values, and the text can be loaded from and stored to a file.
The SSH connection values are now displayed correctly (T2-1946)
Static URLs are now serialized correctly in tool descriptions (T2-1976)
Configuration now works in Java 1.7 (T2-1985)
The help location for the tool service has been corrected (T2-1986)
The tool service prevents ports being created that overlap with the standard ports (T2-1987)
The tool service now handles binary data (T2-1988 and T2-1981).
The tool service now has the option to retrieve data as soon as the tool invocation has finished. (T2-2003)
The tool service has been made more thread-safe. (T2-2028)
The XML splitters and WSDL service now inherit through extension (T2-511, T2-872 and T2-1109)
Descriptions for WSDL services are now extracted from the WSDL document (T2-1990)
Annotations on web service ports are now included in the corresponding XML splitters (T2-2007)
The XPath service no longer reports problems with attribute namespaces (T2-2018)
The major changes are the addition of REST, XPath and Tool services, the addition of the Service Catalogue Perspective, and the ability to export a workflow run as OPM or Janus.
For a complete list of issues that have been solved for Taverna 2.3.0 (including those for 2.2.1 and 2.2.2) see http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?mode=hide&requestId=10221.
General user interface
Control-click now works on MACs (T2-237)
User-friendly way of reporting bugs (T2-549)
The open workflow dialog has been slightly improved (T2-731)
“Save diagram” has been renamed to “Export diagram” (T2-738)
“Open location” icon is now available in the toolbar (T2-752)
The top level icons have been ordered to agree with the corresponding menu items (T2-753)
The Credential Manager checks for previous versions of Taverna and asks the user to import old Keystore/Truststore (T2-944)
Empty service providers can now be removed (T2-1151)
Important notice mechanism added (T2-1282)
Reduction in the size of the registration dialog (T2-1302)
The “Save as” dialog now suggests a name (T2-1318)
Help is now shown in a standard browser, fixing many issues (T2-1518 and T2-1706)
A problem with service configuration dialog text has been fixed (T2-1592)
Users can now see the “Application data” directory (T2-1612)
Taverna now uses the standard SwingWorker (T2-1683)
The service panel now allows services with identical names (T2-1714)
Taverna now handles up-to-date dot (T2-1874)
A possible ConcurrentModificationException in the service description registry has been removed (T2-1894)
Improved icons are used for most dialogs (T2-1914)
Workflow runs are now removed from memory when deleted (T2-1531 and T2-1596)
Job queues are cleared by the dispatch stack (T2-1597) and cross product, dot product, strategy nodes and the crystalizer no longer cache (T2-1598, T2-1599, T2-1601, T2-1602)
The memory footprint of references has been greatly reduced (T2-1600)
Some mySQL provenance problems have been fixed (T2-1605)
The remote health checker tries a GET if the HEAD fails (T2-1679)
Out-of-date annotations are removed when a workflow is serialized (T2-1697)
A thread deadlock when running nested workflows in parallel has been fixed (T2-1713)
The run-deletion thread no longer hangs (T2-1759)
The timeouts for the plugin manager etc. have been reduced (T2-1783 and T2-1784)
The links within the workflow explorer are now ordered (T2-238)
The name of the current workflow is shown on the diagram border (T2-473); this makes editing a nested workflow less confusing (T2-791)
Undo now unselects a removed processor/port/merge (T2-517)
Validation errors are given if the tested output port involved in making a service loop is not connected within the workflow (T2-641)
The iteration strategy editing has been improved (T2-813)
Can now drag a link to a merge (T2-845)
The details panel attempts to show the same type of information as previously shown (T2-1489)
Nested workflow labels are now shown corrected (T2-1654)
Opening a workflow that uses HTTPS no longer hangs the UI (T2-1659)
An empty workflow is no longer indicated in the workflow explorer as having problems (T2-1717)
Selection of the next annotation field has been improved (T2-1730)
The zoom-related actions now correctly change with the selection of a workflow (T2-1813)
An exception is now shown when addition of a service to the workflow fails (T2-1850)
Larger example values can now be specified (T2-1872)
Import workflow no longer throws null pointer exceptions (T2-1915)
Merging of lists to feed a service that expects a single input value now works (T2-1423)
Pausing a workflow now changes the icon to paused (T2-1530)
Workflow run progress monitor no longer stores a node for each service invocation (T2-1603)
Suggested solutions for failed HTTPS client authentication have been added (T2-1738 and T2-1740)
The credential manager now delays asking for passwords until it is needed (T2-1743)
Users can specify the character encoding and data type of input data (T2-1750)
When the first attempt to give a password for the credential manager fails, it now accepts a correct password (T2-1907)
You can now edit the executed workflow that caused a workflow run (T2-1016)
Deleting a workflow run now moves to the next entry (T2-1323)
The save data dialog has been improved (T2-1498)
The ordering of data for previous runs is correct (T2-1514)
Expansion triangles are shown for top-level data and invocations (T2-1515)
The split pane jumps around less (T2-1516)
Tick box for wrapping result text (T2-633)
Save as OPM and Save as Janus are now available for a workflow run (T2-969)
The hex renderer is now read-only (T2-1569)
The rendering of error documents containing HTML has been improved (T2-1641)
A PDF and an improved HTML (open in browser) renderer have been added (T2-1712)
Virtual machine objects can now be rendered as their string representation (T2-1859)
The scripts now accept Alt-keystrokes on MACs (T2-425)
The Beanshell interpreter now clears its variable bindings (T2-1480)
Existing scripts are shown when loading and saving (T2-1499)
The text of the check script dialog has been improved (T2-1664)
R expressions can now be passed (T2-1695)
R services now use the credential manager to handle authorization (T2-1698)
A NullPointerException is no longer thrown when datasets referenced by filters are missing not when attributes are missing (T2-1513, T2-1913)
The BioMoby port names are now coped with better in provenance (T2-602 and T2-1529)
BioMoby no longer pops up an error message at startup (T2-1496)
The BioMart service provider now loads its services in chunks (T2-1785)
Select and Choose LocalWorkers now throw an exception for an empty list of values (T2-298)
Some local services were changed to close streams (T2-1684)
“Get image from URL” no longer reads contents twice (T2-1685)
A new “Transform XML with parameters” service has been added (T2-1693)
“Read text file” can now take an encoding (T2-1750)
The URL dialog now copes with the lack of a trailing / (T2-1787)
Operations that Taverna could not run are no longer shown in the Service Panel (T2-1116)
XML attributes of top-level SOAP elements are no longer stripped out (T2-1606)
See a complete list of issues that have been solved for 2.2.0.
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 as 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 (i.e. WiFi) network which returned HTML login pages for any URL (T2-1409).
User registration form records the “Purpose” field correctly (T2-1304).
executeworkflow command line tool (T2-316).
Ability to pause, resume and cancel a running workflow (T2-414).
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).
Service descriptions (the Available Services in Service Panel) 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 attempts 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).
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 shows the filename or name of workflow (T2-1284).
Unconnected input ports are no longer shown in the Run Workflow dialogue (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 workflow 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).
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).
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).
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).
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 pops-up two file choosers dialogues (T2-1314).
Biomart is streaming results, enabling pipelining for individual rows in result (T2-1093).
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 did not upload Taverna 1.x workflows correctly (T2-1185, T2-1333).
Using myExperiment perspective could break display of Service Details and other HTML-based components (T2-1377).
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).
See a complete list of issues that have been solved for 2.1.2.
General user interface
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).
“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).
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).
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).
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).
“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).
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).
Support for HTTP Basic authentication support for WSDL service invocation (but not HTTP Digest authentication) (T2-1096).
Username/password dialogue now appears via credential manager, no longer appears outside the Workbench (T2-1165).
Adding a WSDL service to a workflow will pop up the security dialogue if username/password for WSDL already exist in credential manager.
HTTPS protected WSDLs should now work.
“Get page/image from URL” now supports HTTPS and Basic/Digest authentication (T2-1198).
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).
The R script was not always saved when clicking ‘Apply’ (T2-1145).
Non-English users now able to log in (avoiding locale-based date parsing) (T2-1157).
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).
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).
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.
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).
Credential Manager now exposes a single SPI CredentialProviderSPI, for providing master password, certificate approval and username password. Workbench implementation pops up dialogues (T2-1193).
For a complete list of issues solved for 2.1.0, see http://tinyurl.com/t2-1-0-fixes.
General user interface
Keyboard shortcuts: There are now keyboard shortcuts for many of the common workflow editing and running tasks.
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.
Editing of workflows
Importation of workflows: You now have the ability to merge a workflow into a currently edited workflow.
Animated diagram: The diagram can now be made animated so it is easier to see what changes are being made.
Diagram problems: The workflow diagram will no longer throw exceptions and refuse to display some workflows.
Iteration strategy: The iteration strategy of services in Taverna 1 workflows is now interpreted correctly within Taverna.
Customized looping: Customized loop conditions are now displayed and saved correctly.
Copy/cut/paste: You can copy/cut and then paste services. This allows you to copy services from one workflow to another or within the same workflow.
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).
New spreadsheet service: you can import Excel or csv spreadsheets and feed the content into your workflow.
Biomoby services: The BioMoby objects are now shown in the normal service panel and can be added to the workflow just as other services.
Running of workflows
Improved run dialog: The dialog for entering run values now copes with 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.
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.
Runs: You can now access the data associated with previous runs. The provenance and data from a run can be deleted.
Workflow completion: Taverna now correctly detects when a workflow run has finished.
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.
Users can now:
- browse workflows on myExperiment
- open a workflow from myExperiment in Taverna
- merge a workflow from myExperiment into the current workflow
- upload a workflow from Taverna to myExperiment
- download a workflow from myExperiment