Please also see the testing of the previous alpha 2 build
Workbench
Testers:
- Stian - Windows 8.1 and 64-bit Oracle Java - use SY or SN in boxes
- Alex P - Mac Mountain Lion OS X 10.8.5 - use PY or PN in boxes
- Christian windows 7 and 64-bit Oracle Java - testing against 2013-11-27 build except to confirm unexpected Nos against 2013-11-28 as well.
- Chritian Mint 15 inside virtual machine marked using M
- Christian Apple Using A (no comment about workflow image being wrong as I choose to ignore the workaround)
- Shoaib - Mac Mavericks OS X 10.9 - using ShY or ShN in boxes - Java -version -> Java(TM) SE Runtime Environment (build 1.7.0_45-b18), Java HotSpot(TM) 64-Bit Server VM (build 24.45-b08, mixed mode)
Nightly build as of 2013-11-21 is candidate alpha 2 release:
- Download taverna-workbench-product-3.0.1-SNAPSHOT-nightly.zip from t3-taverna-workbench-product build #548
- Unzip and run taverna.bat or taverna.sh – make sure you are inside the folder "taverna-workbench-3.0.1-SNAPSHOT-20131127T1259-nightly" and not an earlier build!
Testing performed:
Workflows from 2.4 starter pack
Workflow file | Load t2flow | Run t2flow | Save wfbundle | Load wfbundle | Run wfbundle | Close and review run bundle | Recreate and run wfbundle | Notes |
|---|---|---|---|---|---|---|---|---|
demonstration_of_configurable_iteration_667929.t2flow | PY,CY,MY | PY,CY,MY | PY,CY,MY | PY,CY,MY | PY,MY,CY | CY, PN5,,MY |
| |
ebi_interproscan_newservices_900329.t2flow | PY,CY,MY | PN2,CN1 ,MN1 | PY,CY,MY | PY,CY,MY | PN2,CN1 | CY, PN5 | ||
example_for_external_tools_with_zip_and_unzip_208995.t2flow | CY, PY,MY | Cn, PN,MN | CY, PY,MY | CY, PY,MY | Cn, PN | Cn/a, PN5 |
| |
| example_of_conditional_invocation_850670.t2flow | CY, PY,MY | CY, PY,MY | CY, PY,MY | CY, PN3,MY | CY, PY,MY | CY, PN5 ,MY | ||
example_of_explicit_looping_253706.t2flow | CY, PY,MY | CY, PY,MY | CY,PY,MY | CY, PN3,MY | CY, PY,MY | CY, PN5,MY | Correct empty list if end < start | |
example_workflow_for_rest_and_xpath_activities_483512.t2flow | CY, PY,MY | CN, PN4,MN | CY, PY,MY | CY, PN3,MY | CN, PN,MN | CY, PN5,MY |
| |
fetch_pdb_flatfile_from_rcsb_server_440785.t2flow | CY, PY,MY | PY, CN3 ,MN3 | CY, PY,MY | CY, PN3,MY | PN3, CN3 ,MN3 | CY, PN5,MY |
| |
fetch_today_s_xkcd_comic_186869.t2flow | CY, PY,MY | CY, PY,MY | CY, PY,MY | CY, PY,MY | CY, PY,MY | CY, PN5,MY |
| |
gbseq_test_310396.t2flow | CY, PY,MY | CY, PY,MY | CY, PY,MY | CY, PY,MY | CY, PY,MY | CY, PN5,MY |
| |
hello_anyone_730275.t2flow | CY, ShY,MY | CY, ShY,MY | CY, ShY3,MY | CY, ShY3,MY | CY, ShY3,MY | CY,ShN5,MY |
| |
hello_world_398701.t2flow | CY, ShY,MY | CY, ShY,MY | CY, ShY,MY | CY, ShY,MY | CY,ShY,MY | CY,ShN5,MY |
| |
multiple_choice_quiz_42858.t2flow | CY, ShN&Y6 | CY, ShY7 | CY, ShY | CY, ShY | CY, ShY | CY,ShN5 |
| |
numerically_adding_two_values._557465.t2flow | CY, ShY8,MY | cn, ShN8,MY | CY, ShY,MY | CY, ShN8,MY | cn, ShN8,MY | Cn/a, Sh-n/a,Mn/a |
| |
pipelined_list_iteration_261838.t2flow | CY, ShY,MY | CY, ShY,MY | CY, ShY<MY | CY, ShY3,MY | CY, ShY38,MY | CY, ShN5,MY |
| |
render_gene_via_biogps_164294.t2flow | CY, ShY,MY | CY, ShY,MY | CY, ShY,MY | CY3, ShY3,MY | CY3, ShY3,MY | CY, ShN5,MY |
| |
secure_rest_service_call_example_323172.t2flow | CY, ShY,My | CY, ShY9,10,11,MY | CY, ShY | CY, ShY12 | CY, ShY | CY, ShN5 |
| |
secure_web_service_call_example_304465.t2flow | CY,MY | Cn,Mn | CY,MY | CY,MY | Cn,Mn | Cn/a,Mn/a |
| |
simple_python_example_285475.t2flow | CY,MY | Cn,Mn | CY,MY | CY,MY | Cn,Mn | Cn/a,Mn/a |
| |
spreadsheet_import_example_166335.t2flow | CY,MY,AY | CY,MY,AY | CY,MY,AY | CY,MY,AY | CY,MY,AY | CY,MY,AY* |
| |
unix_tool_service_using_string_replacement_16330.t2flow lower case n used to say workflow run failed but in the expected way such as no external tool found, (1) Invalid paremeter exception on Sequence.
(2) Alex? (3) Still text output only
| CY,MY | Cn,Mn | CY,MY | CY,MY | Cn,Mn | Cn/a,Mn/a |
|
Note that you will need the saved wfbundles for testing the CLT. Please attach them to the sub-pages of this page.
 | EBI interproscan input data is attached |
| example_of_explicit_looping_253706 input data is end=14 start=-3 step=3 |
| example for render_gene_via_biogps_164294.t2flow is 1016 |
(2) EBI workflow (interproscan): in the 3alpha Taverna fails to invoke "run" service (as if it was down). But when I run the same workflow with the same input data on 2.4 there is no problem. Sorry if that is expected behaviour and again I'm just misinformed. (also reported as problem under 27th Nov)
(3) The workflow was saved but without the example inputs. After reloading, the example input is gone.
(4) Workflow fails on different inputs (London Manchester etc.)
(5) Cannot open workflow run if path includes a space
(6) 29/11/13 - Mac - Shoaib - Get the spinning wheel on load and wb not responding - https://www.dropbox.com/s/6omkucnvv74l747/Screenshot%202013-11-29%2010.24.18.png but when I shutdown the workbench and re-start and re-load it works - weird
(7) 29/11/13 - Mac - Shoaib - Workflows runs when it loads - but saving all the values as XML seems to produce junk in the dataElementData tag - https://dl.dropboxusercontent.com/u/1506138/taverna-testing/wf-results.xml unless this is what is meant to happen
(8) 29/11/13 - Mac - Shoaib - it said there was no environment found - https://www.dropbox.com/s/tnqf1ewkvztenhs/Screenshot%202013-11-29%2011.00.59.png
(9) 29/11/13 - Mac - Shoaib - surely when asking you to install the Crypto extentions it should be referring to Java 7 - https://www.dropbox.com/s/ockyjnt6h058sfp/Screenshot%202013-11-29%2015.16.06.png
(10) 29/11/13 - Mac - Shoaib - after removing the security directory and re-starting Taverna credential manager started working and the workflow ran
(11) 29/11/13 - Mac - Shoaib - on re-starting Taverna and re-loading the workflow get a funny truncated reminded about the credential manager - https://www.dropbox.com/s/li4ss9cj2symhk5/Screenshot%202013-11-29%2016.24.58.png
(12) 29/11/13 - Mac - Shoaib - loads ok in a running Taverna 3 Workbench, but if you close the workbench and start again you get the spinning when you load it in again - https://www.dropbox.com/s/t733bzg4qr4jljl/Screenshot%202013-11-29%2016.36.03.png - although when restarting Taverna the wfbundle loaded fine then with no spinning wheel.
(* ) Workflow run opens if moved to avoid space issue.
Command Line Tool
Testers:
- Stian - Windows 8.1 and 64-bit Oracle Java - use SY or SN in boxes
- Alex P - Mac Mountain Lion OS X 10.8.5 - use PY or PN in boxes
Nightly build as of 2013-11-27 is candidate alpha 2 release:
- Download taverna-command-line-product-3.0.1-SNAPSHOT-nightly.zip from t3-taverna-commandline-product build #214
- Unzip and run executeworkflow.bat or executeworkflow.sh – make sure you are inside the folder "taverna-command-line-3.0.1-SNAPSHOT-20131127T1259-nightly" and not an earlier build!
Workflow file | Run t2flow | Run wfbundle | Notes |
|---|---|---|---|
demonstration_of_configurable_iteration_667929.t2flow | CY | CY | |
ebi_interproscan_newservices_900329.t2flow | Cn/a | Cn/a | |
example_for_external_tools_with_zip_and_unzip_208995.t2flow | Cn/a | Cn/a | |
| example_of_conditional_invocation_850670.t2flow | CY | CY | |
example_of_explicit_looping_253706.t2flow | CY | CY | |
example_workflow_for_rest_and_xpath_activities_483512.t2flow | Cn/a | Cn/a | |
fetch_pdb_flatfile_from_rcsb_server_440785.t2flow | Cy | Cy | |
fetch_today_s_xkcd_comic_186869.t2flow | Cy | Cy | |
gbseq_test_310396.t2flow | Cy | CY | |
hello_anyone_730275.t2flow | CY | CY | |
hello_world_398701.t2flow | CY | CY | |
multiple_choice_quiz_42858.t2flow | CY | CY | |
numerically_adding_two_values._557465.t2flow | Cn/a | Cn/a | |
pipelined_list_iteration_261838.t2flow | CY | CY | |
render_gene_via_biogps_164294.t2flow | CY1 | CY1 | |
secure_rest_service_call_example_323172.t2flow | CY | CY | |
secure_web_service_call_example_304465.t2flow | Cn/a | Cn/a | |
simple_python_example_285475.t2flow | Cn/a | Cn/a | |
spreadsheet_import_example_166335.t2flow | CY | CY | |
unix_tool_service_using_string_replacement_16330.t2flow
Lower case y to remind that without a file extension the output is hard to open (1) Workf but continues to throw errors as previously reported | Cn/a | Cn/a |
Cross-platform testing
Try opening wfbundles from other OSes.
Workflow file | Mint in Windows 7 | Expected |
|---|---|---|
demonstration_of_configurable_iteration_667929.t2flow | ||
ebi_interproscan_newservices_900329.t2flow | ||
example_for_external_tools_with_zip_and_unzip_208995.t2flow | ||
| example_of_conditional_invocation_850670.t2flow | ||
example_of_explicit_looping_253706.t2flow | ||
example_workflow_for_rest_and_xpath_activities_483512.t2flow | ||
fetch_pdb_flatfile_from_rcsb_server_440785.t2flow | ||
fetch_today_s_xkcd_comic_186869.t2flow | ||
gbseq_test_310396.t2flow | ||
hello_anyone_730275.t2flow | ||
hello_world_398701.t2flow | ||
multiple_choice_quiz_42858.t2flow | ||
numerically_adding_two_values._557465.t2flow | ||
pipelined_list_iteration_261838.t2flow | ||
render_gene_via_biogps_164294.t2flow | ||
secure_rest_service_call_example_323172.t2flow | ||
secure_web_service_call_example_304465.t2flow | ||
simple_python_example_285475.t2flow | ||
spreadsheet_import_example_166335.t2flow | ||
unix_tool_service_using_string_replacement_16330.t2flow |
New problems
File extension for workflow runs
Workflow runs are given the file extension .wfRun which I don't think has been discussed, but I (Stian) would have expected the extension .bundle.zip as used by other code like the Taverna-PRO plugin. The file browser (at least in Windows) might have to select on *.zip rather than *.bundle.zip for this though.
Known Problems
Running on Mint and Mac OS (Mountain Lion)
Output values do not appear until a change is made to the UI e.g. resizing, clicking elsewhere. Confirmed in OpenJDK and Oracle#
May be related to the attached part of the log
Progress report
The progress report has a strange highlighting (attached). Confirmed in OpenJDK and Oracle
Check for Updates not working (Christian)
feature advanced -> check for updates
Update failed: Error downloading http://dev.mygrid.org.uk/taverna/updates/taverna-workbencg/updates.xml
No Taverna Logo (Christian)
Recent Workflows not saved if Tarverna 3.0 is closed down.(Christian)
Taverna 2.4 does remember if shutdown.
Are other user settings getting lost too?????
No Annotate Option in the workflow (Christian)
So no way to set title, description ext.
New Nov 25
Workflow tab does not show where workflow sourced/saved (Christian)
In Taverna 2,4 when you save a workflow the tab changes to "wofklow4 from c:\temp\..."
In Taverna 3.0 this does not happen.
Service name with space supported or NOT? (Christian)
In taverna 2.4 spaces are replaced with underscore? in names
In Taverna 3.0 spaces are not replaced and workflow saves fine.
BUT rename services does not allow spaces in names.
Strange error on (re)Run of Workflow Run (without workflow open) (Christian)
throws an InvalidDataflowException
Would expect it either to load and run the workflow or ask the user to load the workflow first!
Intermediate result not shown properly
Based on the ebi_interproscan_newservices_900329.t2flow run (on Mac OS and confirmed on Mint?). See the error log.
new Nov 26
Install dot instructions refer to taverna.org.uk for how to install. (Christian)
Not found on the homepage
Link needs to be exact
Open workflow run can fail with no message, no exception NOTHING (Christian)
manifest warning (attached)
On startup
Preference problem On Windows 8
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0
x80000002. Windows RegCreateKeyEx(...) returned error code 5.
log4j:ERROR A "org.apache.log4j.ConsoleAppender" object is not assignable to a "org.apache.log4j.Appender" variable.
Logger initializaton (also Christian W7 and mint)
log4j:ERROR The class "org.apache.log4j.Appender" was loaded by
log4j:ERROR [org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader@76fdb552[com.springsource.org.apache.log4j:1.2.16(id=42)]] whereas object of type
log4j:ERROR "org.apache.log4j.ConsoleAppender" was loaded by [sun.misc.Launcher$AppClassLoader@404fe94c].
log4j:ERROR Could not instantiate appender named "CONSOLE".
log4j:WARN No appenders could be found for logger (org.springframework.osgi.extender.internal.boot.ChainActivator).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Predicted behavior
Appears not to ever be updated, even after "Validate workflow". Perhaps better to hide the panel. If "Validate workflow" never does anything, perhaps better to disable the menu item.
Loading secure_web_service_call_example_304465.t2flow
Unable to parse the WSDL https://heater.cs.man.ac.uk:7443/axis/services/HelloService-PlaintextPassword?wsdl
Closing a workflow run
had a weird effect on Windows 8.
The runs do not "shuffle over"
Multiple choice problems
Local services are shown as beanshell
Workflow does not show popups
- Due to loop error http://dev.mygrid.org.uk/issues/browse/T3-863
Merges not shown
Is this deliberate?
All previous workflows results load up
After closing all workflows, reopening the bundle and clicking run, tabs with all past runs open up (that is, if I run the bundle twice before, I get 3 tabs open - with the current results and the 2 past ones). I was told this is a feature but I find this annoying. What if I do 50 runs? There must be a possibility to "clear" the workbench.
New Nov 27
"File already exist" over-sized dialogue box
When trying to overwrite an existing bundle ("Save as") the warning box is superwide (the text doesn't wrap) see screenshot. Mac OS X Mountain Lion
Fail to invoke EBI "run" but works in 2.4
EBI workflow (interproscan): in the 3alpha Taverna fails to invoke "run" service (as if it was down). But when I run the same workflow with the same input data on 2.4 there is no problem. Sorry if that is expected behaviour and again I'm just misinformed.
New Nov 28
Cannot open workflow run if path includes a space
Cannot view file submenu
This appeared after running a number of workflows without restarting Taverna. When I click "File" menu the list of previous run workflows shows up hiding the file submenu (see the screenshot). (Incredibly annoying!!)
Run errors not showing up
- (Christian Windows 7) (Alan Mint)
Attempted to run a hacked workflow with an rscript (probably incorrect) and without Rserver running (Definitely incorrct) - confirmed by Alan. Does not even switch to run perspective.
Nothing happened no error no message nothing (except in console there was a null pointer exception)
Bad workflow and stack trace as attachments,
Menu options nonfunctional
Neither "Show Details" nor "Show Validation Report" (from right click on workflow background) work.
Recent workflows not kept between re-starts
"Recent workflows" is not kept between re-starts of Taverna 3. It is kept within a started Taverna 3.
ebi_interproscan_newservices_900329.t2flow failure
WARN 2013-10-08 13:06:22,761 (net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:236) - Failed (INVOCATION) invoking net.sf.taverna.t2.activities.wsdl.WSDLActivity@32ebcda9 for job DispatchJobEvent facade36:EBI_InterproScan_NewServices:run[]: An error occurred invoking the WSDL service
AxisFault
example_workflow_for_rest_and_xpath_activities_483512.t2flow
- Exception occurred evaluting XPath: /query/results/default:place/default:woeid. Exception: XPath expression uses unbound namespace prefix default
- Works in windows 7 Using Taverna 2.4
fetch_pdb_flatfile_from_rcsb_server_440785.t2flow
Output does not display the nice picture Taverna 2.4 does
Workbench GUI
If I choose File->Open Workflow and then click on the main workbench title bar, the file open dialogue goes behind the main window and their is no way of getting it back apart from moving windows around - is this done on purpose ?
Also when there is a dialogue open when moving the main windows the dialogue does not move with it - I found this really irritating and counter to expected behaviour - unless you want to correct me ?
New 29 Nov
Can't close the empty workflow
When you try and close the default empty workflow from the design perspective it won't close (or it may) but the number keeps incrementing - not sure if this is a problem - even close all workflows from the menu does not close it - this was after load/run and close of multiple_choice_quiz_42858.t2flow - https://www.dropbox.com/s/fuebrvbs19r5ix3/Screenshot%202013-11-29%2010.39.59.png - just noted that Taverna 2.4 does the same thing - so I guess it might be a feature ?
Not very clear how to stop a workflow (Christian)
- As a newbie it took me a while to work out that to stop a workflow run I had to close the results tab
- On the positive side the cancelled run was stored correctly
Hugh single line error message with close well off the screen. (Christian)
- Mint doing secure_web_service_call_example_304465.t2flow
- Ugly that I had to drag the error box over to be able to close it with the X in the corner.
- Ok box not centralized!
Labels