| 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) | |
| 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 | |
| http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?requestId=10154 | |
| 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 Auth support for WSDL service invocation (but not | |
| Digest) (T2-1096) | |
| Username/password dialogue now appears via credential manager, no longer | |
| appears outside 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 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 | |
| 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 |