Taverna

Simon Felix wrote:
> Hi there,

Hello,

> using Taverna 2.1b2:

> 1.       Execute a workflow that will return a list to an output port
> 
> 2.       Select the first list entry in the results pane (lower half of 
> the screen)
> 
> 3.       You will notice that the content of the list item will be shown 
> in the right half of the result pane
> 
> 4.       Press the cursor down key
> 
> 5.       You will notice that the right half of the result pane didn’t 
> refresh.
> 
> I think that the content-pane (in the bottom right corner) should be 
> updated if the selection of the list changes. Be it by mouse or by keyboard.

Thanks for spotting this.  I've added it into Jira as 
http://www.mygrid.org.uk/dev/issues/browse/T2-888

I think the problem is that the method 
net.sf.taverna.t2.workbench.views.results.PortResultsViewTab.initComponents 
puts a MouseListener on the tree which then listens for mouse clicks. 
It probably should be putting a TreeSelectionListener on the tree.

> Regards,
> 
> Simon

Alan

Hi,

The Taverna startup script has a shebang line of /bin/sh, and assumes 
that this program will be Bourne-shell compatible.  It's quite possible 
for /bin/sh to be something else (e.g. C-shell), in which case it fails 
on a syntax error (happens on our Solaris system).  The solution would 
be to change the shebang to explicitly ask for something 
syntax-compatible and widely available, e.g. /bin/ksh.

Cheers,

Paul

Paul Gordon wrote:
> Hi,

Hello,

> The Taverna startup script has a shebang line of /bin/sh, and assumes 
> that this program will be Bourne-shell compatible.  It's quite possible 
> for /bin/sh to be something else (e.g. C-shell), in which case it fails 
> on a syntax error (happens on our Solaris system).  The solution would 
> be to change the shebang to explicitly ask for something 
> syntax-compatible and widely available, e.g. /bin/ksh.

Thanks for reporting this.  The script needs to be rewritten as David 
Withers has also found some problems.  I've added your report to the 
issue, http://www.mygrid.org.uk/dev/issues/browse/T2-430  The issue is 
down as a blocker for 2.1 so will be fixed

If anyone would like to suggest alternative scripts, they'll be very 
welcome.

> Cheers,
> 
> Paul

Alan

Wei Tan wrote:
 > Hi,
 >
 >    We have developed a plug-in activity (let's call it activity C) which
 > will connect to a WSDL activity. In C we need to know the URL of the
 > WSDL activity which it connects.

What happens if it is connected to more than one activity?  What if it 
is connected to, say, a Beanshell or a workflow output port?

 > Is there a API to get it? I guess a feasible approach is to parse the
 > current editing workflow model, get the link starts from C and then find
 > the target WSDL activity?

Yes, you would need to get the connections of the port and see what is 
at the end of those connections.

It sounds as if you are "asking the wrong question" :-)  Are you sure 
you want to do this as a stand-alone activity?

 >    Any suggestion is appreciated.
 >
 >    Best regards,
 >
 > Wei

Alan

Alan Williams wrote:
> Wei Tan wrote:
>  > Hi,
>  >
>  >    We have developed a plug-in activity (let's call it activity C) which
>  > will connect to a WSDL activity. In C we need to know the URL of the
>  > WSDL activity which it connects.
>
> What happens if it is connected to more than one activity?  What if it 
> is connected to, say, a Beanshell or a workflow output port?
>   
It could connect to more than one activities (beanshell, output port, 
etc), but it should connect to one WSDL activity.
>  > Is there a API to get it? I guess a feasible approach is to parse the
>  > current editing workflow model, get the link starts from C and then find
>  > the target WSDL activity?
>
> Yes, you would need to get the connections of the port and see what is 
> at the end of those connections.
>
> It sounds as if you are "asking the wrong question" :-)  Are you sure 
> you want to do this as a stand-alone activity?
>   
You can think it as a helper activity to generate an input soap msg for 
a wsdl activity more easily.
I can embed it into a wsdl activity (and then I will have a new combo 
activity) but users may be
confused of so many activity types...


Thanks Alan,

Wei
>  >    Any suggestion is appreciated.
>  >
>  >    Best regards,
>  >
>  > Wei
>
> Alan
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> taverna-hackers mailing list
> taverna-hackers@...
> Web site: http://www.taverna.org.uk
> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
> Developers Guide: http://www.mygrid.org.uk/tools/developer-information
>   

-- 
Wei Tan, Ph.D.
Computation Institute
the University of Chicago|Argonne National Laboratory
http://www.mcs.anl.gov/~wtan

another question is that, the code which defines the activity does not 
know the exact name of the activity instance in the workflow definition 
file

Wei Tan wrote:
> Alan Williams wrote:
>   
>> Wei Tan wrote:
>>  > Hi,
>>  >
>>  >    We have developed a plug-in activity (let's call it activity C) which
>>  > will connect to a WSDL activity. In C we need to know the URL of the
>>  > WSDL activity which it connects.
>>
>> What happens if it is connected to more than one activity?  What if it 
>> is connected to, say, a Beanshell or a workflow output port?
>>   
>>     
> It could connect to more than one activities (beanshell, output port, 
> etc), but it should connect to one WSDL activity.
>   
>>  > Is there a API to get it? I guess a feasible approach is to parse the
>>  > current editing workflow model, get the link starts from C and then find
>>  > the target WSDL activity?
>>
>> Yes, you would need to get the connections of the port and see what is 
>> at the end of those connections.
>>
>> It sounds as if you are "asking the wrong question" :-)  Are you sure 
>> you want to do this as a stand-alone activity?
>>   
>>     
> You can think it as a helper activity to generate an input soap msg for 
> a wsdl activity more easily.
> I can embed it into a wsdl activity (and then I will have a new combo 
> activity) but users may be
> confused of so many activity types...
>
>
> Thanks Alan,
>
> Wei
>   
>>  >    Any suggestion is appreciated.
>>  >
>>  >    Best regards,
>>  >
>>  > Wei
>>
>> Alan
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
>> trial. Simplify your report design, integration and deployment - and focus on 
>> what you do best, core application coding. Discover what's new with 
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> taverna-hackers mailing list
>> taverna-hackers@...
>> Web site: http://www.taverna.org.uk
>> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
>> Developers Guide: http://www.mygrid.org.uk/tools/developer-information
>>   
>>     
>
>   

-- 
Wei Tan, Ph.D.
Computation Institute
the University of Chicago|Argonne National Laboratory
http://www.mcs.anl.gov/~wtan

I would like to resend this post in case anybody know the answer.
Thanks,

Wei

Wei Tan wrote:
>
> another question is that, the code which defines the activity does not 
> know the exact name of the activity instance in the workflow 
> definition file
>
> Wei Tan wrote:
>> Alan Williams wrote:
>>  
>>> Wei Tan wrote:
>>>  > Hi,
>>>  >
>>>  >    We have developed a plug-in activity (let's call it activity 
>>> C) which
>>>  > will connect to a WSDL activity. In C we need to know the URL of the
>>>  > WSDL activity which it connects.
>>>
>>> What happens if it is connected to more than one activity?  What if 
>>> it is connected to, say, a Beanshell or a workflow output port?
>>>       
>> It could connect to more than one activities (beanshell, output port, 
>> etc), but it should connect to one WSDL activity.
>>  
>>>  > Is there a API to get it? I guess a feasible approach is to parse 
>>> the
>>>  > current editing workflow model, get the link starts from C and 
>>> then find
>>>  > the target WSDL activity?
>>>
>>> Yes, you would need to get the connections of the port and see what 
>>> is at the end of those connections.
>>>
>>> It sounds as if you are "asking the wrong question" :-)  Are you 
>>> sure you want to do this as a stand-alone activity?
>>>       
>> You can think it as a helper activity to generate an input soap msg 
>> for a wsdl activity more easily.
>> I can embed it into a wsdl activity (and then I will have a new combo 
>> activity) but users may be
>> confused of so many activity types...
>>
>>
>> Thanks Alan,
>>
>> Wei
>>  
>>>  >    Any suggestion is appreciated.
>>>  >
>>>  >    Best regards,
>>>  >
>>>  > Wei
>>>
>>> Alan
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 
>>> 30-Day trial. Simplify your report design, integration and 
>>> deployment - and focus on what you do best, core application coding. 
>>> Discover what's new with Crystal Reports now.  
>>> http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> taverna-hackers mailing list
>>> taverna-hackers@...
>>> Web site: http://www.taverna.org.uk
>>> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
>>> Developers Guide: http://www.mygrid.org.uk/tools/developer-information
>>>       
>>
>>   
>

-- 
Wei Tan, Ph.D.
Computation Institute
the University of Chicago|Argonne National Laboratory
http://www.mcs.anl.gov/~wtan

Wei Tan wrote:
> I would like to resend this post in case anybody know the answer.
> Thanks,
> 
> Wei
> 
> Wei Tan wrote:
>> another question is that, the code which defines the activity does not 
>> know the exact name of the activity instance in the workflow 
>> definition file

I think that is deliberate.  As far as I know the enactment of the 
activity is not meant to know anything about its context.  It only knows 
  its configuration and the values on the input ports.

I think you would need to alter the configuration of the activity to 
pass in the information you want.  To be able to do that you probably 
need to alter part of the dispatch stack so that it altered the 
configuration of the activity before it was called.

It does not sound easy to do.

I think the easiest thing is for the API to be changed so that the 
Activity knows the Processor it is in.  I'm not sure what the 
consequences of that would be.  It would prevent an Activity being 
shared by several Processors, which is theoretically possible at the moment.

Alan

Alan Williams wrote:
> Wei Tan wrote:
>   
>> I would like to resend this post in case anybody know the answer.
>> Thanks,
>>
>> Wei
>>
>> Wei Tan wrote:
>>     
>>> another question is that, the code which defines the activity does not 
>>> know the exact name of the activity instance in the workflow 
>>> definition file
>>>       
>
> I think that is deliberate.  As far as I know the enactment of the 
> activity is not meant to know anything about its context.  It only knows 
>   its configuration and the values on the input ports.
>
> I think you would need to alter the configuration of the activity to 
> pass in the information you want.  To be able to do that you probably 
> need to alter part of the dispatch stack so that it altered the 
> configuration of the activity before it was called.
>
>   
Hmm, I guess it is a build-time issue rather than a run-time one?
To make it simple, the new activity serves as a input for a WSDL 
activity, so it needs to know which WSDL activity it connects to.
(mostly it connects to only one WSDL activity)

Thanks Alan!

Wei

Wei Tan wrote:
> 
> Hmm, I guess it is a build-time issue rather than a run-time one?
> To make it simple, the new activity serves as a input for a WSDL 
> activity, so it needs to know which WSDL activity it connects to.
> (mostly it connects to only one WSDL activity)

Is the idea that if it was passing data to an activity on the same grid 
(for example) then it would do something different to passing data to an 
activity elsewhere?

> Thanks Alan!
> 
> Wei

Alan

Alan Williams wrote:
> Wei Tan wrote:
>   
>> Hmm, I guess it is a build-time issue rather than a run-time one?
>> To make it simple, the new activity serves as a input for a WSDL 
>> activity, so it needs to know which WSDL activity it connects to.
>> (mostly it connects to only one WSDL activity)
>>     
>
> Is the idea that if it was passing data to an activity on the same grid 
> (for example) then it would do something different to passing data to an 
> activity elsewhere?
>   
Actually it is not that complex. The scenario is, you have a WSDL 
service and the input is a "SQL" clause to query data from this service.
The newly added activity is like a visual SQL builder to construct the 
SQL. -- it needs the URL of the WSDL service so that it knows the 
metadata of it.

Thanks.

Wei
>   
>> Thanks Alan!
>>
>> Wei
>>     
>
> Alan
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> taverna-hackers mailing list
> taverna-hackers@...
> Web site: http://www.taverna.org.uk
> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
> Developers Guide: http://www.mygrid.org.uk/tools/developer-information
>   

-- 
Wei Tan, Ph.D.
Computation Institute
the University of Chicago|Argonne National Laboratory
http://www.mcs.anl.gov/~wtan

José María Fernández González wrote:
> Thanks!

> I have been inspecting the t2platform artifacts, and I found a copy
> of artifact-support-0.2.xsd inside the
> net.sf.taverna.t2.infrastructure:platform-spring artifact (both in
> version p0.1b1 and version p0.1b2). Those copies differ a lot from
> the one you have put online, even on the namespace, so it complains:

It's confusing.  There is also one with t2platform.  For the moment, 
I've replaced the upload with the one from t2.infrastructure.

I'll try to find out which is the correct one.

> Regards,

> José María

Alan

Yes, AFAIHS there is some inconsistency somewhere between t2platform (p0.1b1, p0.1b2) and Taverna 2.1b2 developments. I have found that artifact net.sf.taverna.t2.core:workflowmodel-impl version 0.8 (used by Taverna 2.1b2) contains provenanceContext.xml, which uses the namespace http://taverna.sf.net/schema/artifact-support , declared on the XSD file you originaly uploaded. If it is a clue, the namespace declarations inside provenanceContext.xml points to the declaration of the schema associated to that namespace as http://taverna.sf.net/schema/artifact-support/artifact-support.xsd

Regards,
	José María

Alan Williams wrote:
> José María Fernández González wrote:
>> Thanks!
> 
>> I have been inspecting the t2platform artifacts, and I found a copy
>> of artifact-support-0.2.xsd inside the
>> net.sf.taverna.t2.infrastructure:platform-spring artifact (both in
>> version p0.1b1 and version p0.1b2). Those copies differ a lot from
>> the one you have put online, even on the namespace, so it complains:
> 
> It's confusing.  There is also one with t2platform.  For the moment, 
> I've replaced the upload with the one from t2.infrastructure.
> 
> I'll try to find out which is the correct one.
> 
>> Regards,
> 
>> José María
> 
> Alan
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> taverna-hackers mailing list
> taverna-hackers@...
> Web site: http://www.taverna.org.uk
> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
> Developers Guide: http://www.mygrid.org.uk/tools/developer-information
> 

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981 
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

José María Fernández González
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez@...		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinformática
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Centro Nacional de Investigaciones Oncológicas
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José María Fernández González wrote:
> Yes, AFAIHS there is some inconsistency somewhere between t2platform
> (p0.1b1, p0.1b2) and Taverna 2.1b2 developments. I have found that
> artifact net.sf.taverna.t2.core:workflowmodel-impl version 0.8 (used
> by Taverna 2.1b2) contains provenanceContext.xml, which uses the
> namespace http://taverna.sf.net/schema/artifact-support , declared on
> the XSD file you originaly uploaded. If it is a clue, the namespace
> declarations inside provenanceContext.xml points to the declaration
> of the schema associated to that namespace as
> http://taverna.sf.net/schema/artifact-support/artifact-support.xsd

Yes I think the problem was due to me getting confused between the two 
platforms.  That's probably due to me having far too many Eclipse 
projects open at the same time :-)

The one that is up there now matches what is in the googlecode svn 
repository.  Sorry for all the confusion.

This should go away when we combine the platform and the main trunk.

> Regards, José María

Alan

Hi Ingo,

> Other services that are not available anymore:
> http://dbk-ed.mib.man.ac.uk:8080/HumanAffymapper/services/HumanAffymappe
> r?wsdl

This service was requested by Paul Fisher. It's currently down as I didn't
think he was using it anymore.

> And all services hosted at:
> http://mygrid.ncl.ac.uk/

These services are down because the server they were deployed on at
Newcastle University is now out of commission.

Cheers, Pete.

Simon Felix wrote:
>>> Why isn't Raven/Taverna downloading those dependencies itself? What
>>> am I doing wrong?
>> It may be because you have specified them as system artifacts.  That
>> means that the platform expects to find them in the classpath and not
>> to have to download them.
> 
> I found out that it is trying to download them, but gets 404 (File not found) on all three repositories:
> http://www.mygrid.org.uk/maven/repository/
> http://mirrors.sunsite.dk/maven2/
> http://mirrors.ibiblio.org/maven2/
> 
> By specifying this additional server (the Maven2 main repository) http://repo1.maven.org/maven2/ the automatic download of all JARs works.
> 
> 
> Maybe you want to include this additional server in the docs: http://www.mygrid.org.uk/dev/wiki/display/developer/T2+Reference+Service+%28Data+Manager%29, chapter 2.2

I'll ask Alex to alter the documentation.  Thanks for spotting this.

> Thanks for helping,
> Simon

Alan

> i4ds.ch

On Thu, Aug 13, 2009 at 15:31, Alan Williams<alanrw@...> wrote:

>> I found out that it is trying to download them, but gets 404 (File not found) on all three repositories:
>> http://www.mygrid.org.uk/maven/repository/
>> http://mirrors.sunsite.dk/maven2/
>> http://mirrors.ibiblio.org/maven2/
>> By specifying this additional server (the Maven2 main repository) http://repo1.maven.org/maven2/ the automatic download of all JARs works.

Also adding our mirror of the repo1 repository should work (and
depending on where in the world you are might perform better):
http://www.mygrid.org.uk/maven/repo1/

The sunsite and ibiblio mirrors, although earlier quite reliant maven
archives, have for some reason ceased to exist..


-- 
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester