Skip to end of metadata
Go to start of metadata

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:

Testing performed:

Workflows from 2.4 starter pack

 

Workflow file

Load t2flowRun t2flowSave wfbundleLoad wfbundleRun wfbundleClose and review run bundleRecreate and run wfbundle

Notes

demonstration_of_configurable_iteration_667929.t2flow

PY,CY,MYPY,CY,MYPY,CY,MYPY,CY,MYPY,MY,CYCY, PN5,,MY 

 

ebi_interproscan_newservices_900329.t2flow

PY,CY,MYPN2,CN1 ,MN1PY,CY,MYPY,CY,MY
PN2,CN1CY, PN5  

example_for_external_tools_with_zip_and_unzip_208995.t2flow

CY, PY,MYCn, PN,MNCY, PY,MYCY, PY,MYCn, PNCn/a, PN5 

 

example_of_conditional_invocation_850670.t2flowCY, PY,MYCY, PY,MYCY, PY,MYCY, PN3,MYCY, PY,MYCY, PN5 ,MY  

example_of_explicit_looping_253706.t2flow

CY, PY,MYCY, PY,MYCY,PY,MYCY, PN3,MYCY, PY,MYCY, PN5,MY 

Correct empty list if end < start

example_workflow_for_rest_and_xpath_activities_483512.t2flow

CY, PY,MYCN, PN4,MNCY, PY,MYCY, PN3,MY CN, PN,MNCY, PN5,MY 

 

fetch_pdb_flatfile_from_rcsb_server_440785.t2flow

CY, PY,MYPY, CN3 ,MN3
CY, PY,MYCY, PN3,MYPN3, CN3 ,MN3CY, PN5,MY 

 

fetch_today_s_xkcd_comic_186869.t2flow

CY, PY,MYCY, PY,MYCY, PY,MYCY, PY,MYCY, PY,MYCY, PN5,MY 

 

gbseq_test_310396.t2flow

CY, PY,MYCY, PY,MYCY, PY,MYCY, PY,MYCY, PY,MYCY, PN5,MY 

 

hello_anyone_730275.t2flow

CY, ShY,MYCY, ShY,MYCY, ShY3,MYCY, ShY3,MYCY, ShY3,MYCY,ShN5,MY 

 

hello_world_398701.t2flow

CY, ShY,MYCY, ShY,MYCY, ShY,MYCY, ShY,MYCY,ShY,MYCY,ShN5,MY 

 

multiple_choice_quiz_42858.t2flow

CY, ShN&Y6CY, ShY7CY, ShYCY, ShYCY, ShYCY,ShN5 

 

numerically_adding_two_values._557465.t2flow

CY, ShY8,MYcn, ShN8,MYCY, ShY,MYCY, ShN8,MYcn, ShN8,MYCn/a, Sh-n/a,Mn/a 

 

pipelined_list_iteration_261838.t2flow

CY, ShY,MYCY, ShY,MYCY, ShY<MYCY, ShY3,MYCY, ShY38,MYCY, ShN5,MY 

 

render_gene_via_biogps_164294.t2flow

CY, ShY,MYCY, ShY,MYCY, ShY,MYCY3, ShY3,MYCY3, ShY3,MYCY, ShN5,MY 

 

secure_rest_service_call_example_323172.t2flow

CY, ShY,MyCY, ShY9,10,11,MYCY, ShY CY, ShY12CY, ShYCY, ShN5 

 

secure_web_service_call_example_304465.t2flow

CY,MYCn,MnCY,MY

CY,MY

Cn,MnCn/a,Mn/a 

 

simple_python_example_285475.t2flow

CY,MYCn,MnCY,MYCY,MYCn,MnCn/a,Mn/a 

 

spreadsheet_import_example_166335.t2flow

CY,MY,AYCY,MY,AYCY,MY,AYCY,MY,AYCY,MY,AYCY,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.

  • Tried using example value
  • Tried using value cut and pasted from Taverna2.4
  • Tried using a file
  • All of the above including the file worked with Taverna 2.4
  • Tried both build 2013-11-27 and 2013-11-28 same thing

(2) Alex?

(3) Still text output only

 

CY,MYCn,MnCY,MYCY,MYCn,MnCn/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:



Workflow file

Run t2flowRun wfbundleNotes

demonstration_of_configurable_iteration_667929.t2flow

CYCY 

ebi_interproscan_newservices_900329.t2flow

Cn/aCn/a 

example_for_external_tools_with_zip_and_unzip_208995.t2flow

Cn/aCn/a 
example_of_conditional_invocation_850670.t2flowCYCY 

example_of_explicit_looping_253706.t2flow

CYCY 

example_workflow_for_rest_and_xpath_activities_483512.t2flow

Cn/aCn/a 

fetch_pdb_flatfile_from_rcsb_server_440785.t2flow

CyCy 

fetch_today_s_xkcd_comic_186869.t2flow

CyCy 

gbseq_test_310396.t2flow

CyCY 

hello_anyone_730275.t2flow

CYCY 

hello_world_398701.t2flow

CYCY 

multiple_choice_quiz_42858.t2flow

CYCY 

numerically_adding_two_values._557465.t2flow

Cn/aCn/a 

pipelined_list_iteration_261838.t2flow

CYCY 

render_gene_via_biogps_164294.t2flow

CY1CY1 

secure_rest_service_call_example_323172.t2flow

CYCY 

secure_web_service_call_example_304465.t2flow

Cn/aCn/a 

simple_python_example_285475.t2flow

Cn/aCn/a 

spreadsheet_import_example_166335.t2flow

CYCY 

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/aCn/a 

Cross-platform testing

Try opening wfbundles from other OSes.

Workflow file

Mint in Windows 7Expected

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

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
  • None