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 |