Changes in 2.2.0
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).
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 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).
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 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).
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 pops-up two 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.x 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).
Changes in 2.1.2 (including 2.1.1)
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).
Workflow engine
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).
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).
Results
“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).
WSDL services
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.
Local workers
“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).
Rshell script
The R script was not always saved when clicking ‘Apply’ (T2-1145).
myExperiment perspective
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 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.
API changes
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).
Changes in 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 http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?reset=true&pid=10040&resolution=1&resolution=11&fixfor=10112&fixfor=10131&sorter/field=issuekey&sorter/order=DESC
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.
Services
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.
myExperiment perspective
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
