On Tue, Oct 13, 2009 at 08:25, Yoshinobu Kano <[email protected]> wrote:
>>> ERROR 2009-10-06 12:40:51,396
>>> (net.sf.taverna.t2.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer:166)
>>> - Could not forget [...@48d334]
> Generally speaking, what does "could not forget" in the error message mean?
> Since this error is generated by Taverna, I would like to have any clue to
> solve it -- at least to know whether it is something critical or not.
> No stack trace, or any other information was dumped.
It has to do with cleaning up state in the dispatch stack after an
execution has finished.
For some reason this clean-up is executed twice, but as the call is
already finished this should not affect anything.
Taverna developers: We could have a look at how the platform-version
handles state.
> Yes, assuming that my activity recieves a streamed input iteratively,
> how can I notice the end of the iteration, from inside my activity code?
Then you could make your activity expect depth 1 at the activity input
port, with a granular depth at 0. (1: list of values, 0: individual
values).
That means that you expect the full list, but you don't mind being fed
item by item.
That means that you should get something like:
[0] value0
[1] value1
[2] value2
[] {value0, value1, value2}
So the 'end of the iteration' if you like would be when you receive
the full list in the end.
I'm not sure if we've done an activity that receives inputs in this
way, but it should be possible.
> I am sorry I am not really familar with maven related settings.
> Where should I put the plugins.xml file in my repository (assuming that it
> is the same format of the one which Taverna's local folder contains) -- the
> root directory of the repository?
> Under http://www.mygrid.org.uk/maven/,
> http://www.mygrid.org.uk/maven/repository/, etc. I could not find any such
> file.
> And how about the update detection, is it simply based on the version number
> in the plugins.xml file?
There are two different repositories, which could be the source of
some confusion.
The Maven repository is where Taverna is to find your JAR and POM
files. While developing you might want to use
file:///your/home/directory/.m2/repository as the URL. (Browse to that
folder using something like Firefox to get the URL syntax right!)
Taverna looks for plugin definitions in plugin sites. Each known
pluginsite is decribed in $HOME/.taverna-2.1b2/conf/plugin-sites.xml -
typically you would need to add your own plugin-site.
All the plugin-site needs to contain is a file pluginlist.xml - see
http://www.mygrid.org.uk/taverna/updates/2.1-beta-2/plugins/pluginlist.xml
for an example. - as you see there are then references to individual
plugin files in the same folder, like to
http://www.mygrid.org.uk/taverna/updates/2.1-beta-2/plugins/spreadsheet-plugin-0.2.0.xml
What you see in there is the definition of the plugin. The version
number and name etc. here are just used by the plugin manager. If you
list a plugin with a plugin version higher than Taverna has installed,
Taverna will allow you do an upgrade of that plugin.
Internally in the plugin file you need to list which Maven
repositories to use to find the software components, and also which
components to include into Taverna. Int he case of the spreadsheet
plugins the components are stated as these Maven dependencies:
<dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>spreadsheet-import-activity</artifactId>
<version>0.2</version>
</dependency>
<dependency>
<groupId>net.sf.taverna.t2.ui-activities</groupId>
<artifactId>spreadsheet-import-activity-ui</artifactId>
<version>0.2</version>
</dependency>
Now when you do a new plugin version you will also need to deploy a
new version of those dependencies. As you see in this plugin there are
two independent software components - meaning that you need to make a
new plugin version when you have changed the version of at least one
of those dependencies - allowing for you to upgrade in this case
spreadsheet-import-activity-ui without updating
spreadsheet-import-activity
Be careful to not redeploy Maven artifacts with the same version
number. Both Maven and Raven in Taverna will trust the version number,
so if it finds that it has blablabla:0.2 downloaded in its local
repository, it will not redownload it from your repository.
While developing you would probably keep the Maven components in
SNAPSHOT versions, like 0.3-SNAPSHOT. If you are using the
file:///home/stain/.m2/repository/ in your plugins file then Taverna
will not copy them to its own repository folder, so a new 'mvn
install' would overwrite the JAR files picked up by Taverna. This
means that you would not need to change the version number locally.
However, if you suspect Taverna is using an older version, inspect the
repository/ folder inside .taverna-2.1b2.
> A bug report, probably you already know;
> after running any workflow, "Workflow running" is still shown with a
> rounding icon on the left.
Is this for when the workflow has no outputs? - I believe that would
be http://www.mygrid.org.uk/dev/issues/browse/T2-597 which Alex has
just fixed
If not, could you possibly send us the workflow that don't finish..?
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
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