soaplab-users — Forum for Soaplab users and developers

Re: [Soaplab-users] soaplab2/maven won't build :(

[Sirisha G. <si...@my...>]

Hi Martin,

I have executed ant clean followed by ant install for the current 
installation I have, this output is in the attached file 
soaplab2-cleaninstall-output.txt. I also checked out from CVS and 
executed ant install, this output is in soaplab2-installfrom-cvs.txt. 
Hope these will help - if you are unable to reproduce the error, then it 
seems highly likely this is an issue with the University network :(

Having executed the ant tasks above, my ~/.m2/repository still only 
contains three directories, com, javax and org so for whatever reason 
many required jars are not being downloaded (though why these three are 
successfully fetched and others not is a mystery to me).

Thanks,

Sirisha

Martin Senger wrote:
> Well, I cannot reproduce the error myself. I have tried to build/install 
> soaplab2 both from the latest release (2.1.1) and from the CVS. I have 
> also first removed junit-4.3.1 from my local maven  repository 
> (~/.m2/repository) - just to be sure that this jar file will be 
> downloaded again - and it was).
> 
> I am not sure what would be now the best scenario to solve the problem, 
> to find the cause of the problem. Can you perhaps try the one for the 
> CVS - to see if problems also happens there for you?
> 
> Also, please do this:
> 
> ant clean
> ant install
> 
> and send me the full output that went to your screen.
> 
> Anyone has any more idea please?
> 
> Martin
> 
> -- 
> Martin Senger
> email: mar...@gm... 
> <mailto:mar...@gm...>,m.s...@cg... 
> <mailto:m.s...@cg...>
> skype: martinsenger

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Re: [Soaplab-users] soaplab2/maven won't build :(

[Martin S. <mar...@gm...>]

Well, I cannot reproduce the error myself. I have tried to build/install
soaplab2 both from the latest release (2.1.1) and from the CVS. I have also
first removed junit-4.3.1 from my local maven  repository (~/.m2/repository)
- just to be sure that this jar file will be downloaded again - and it was).

I am not sure what would be now the best scenario to solve the problem, to
find the cause of the problem. Can you perhaps try the one for the CVS - to
see if problems also happens there for you?

Also, please do this:

ant clean
ant install

and send me the full output that went to your screen.

Anyone has any more idea please?

Martin

-- 
Martin Senger
email: mar...@gm...,m.s...@cg...
skype: martinsenger

[Soaplab-users] soaplab2/maven won't build :(

[Sirisha G. <si...@my...>]

Hi everyone,

I've had to rebuild Soaplab2 as the server hosting my services died. 
This has now been fixed, but when I've re-downloaded Soaplab2 and try to 
call any ant tasks (e.g. ant install) I'm running into all sorts of 
problems. For some reason certain dependencies aren't being fetched, is 
anyone aware of a problem on the maven side?

In particular, I'm getting these errors:

[artifact:dependencies]  Diagnosis:
[artifact:dependencies]
[artifact:dependencies] Unable to resolve artifact: Missing:
[artifact:dependencies] ----------
[artifact:dependencies] 1) junit:junit:jar:4.3.1
[artifact:dependencies]
[artifact:dependencies]   Try downloading the file manually from the 
project website.
[artifact:dependencies]
[artifact:dependencies]   Then, install it using the command:
[artifact:dependencies]       mvn install:install-file -DgroupId=junit 
-DartifactId=junit -Dversion=4.3.1 -Dpackaging=jar -Dfile=/path/to/file
[artifact:dependencies]
[artifact:dependencies]   Alternatively, if you host your own repository 
you can deploy the file there:
[artifact:dependencies]       mvn deploy:deploy-file -DgroupId=junit 
-DartifactId=junit -Dversion=4.3.1 -Dpackaging=jar -Dfile=/path/to/file 
-Durl=[url] -DrepositoryId=[id]
[artifact:dependencies]
[artifact:dependencies]   Path to dependency:
[artifact:dependencies]         1) org.soaplab:soaplab:jar:2.1.1
[artifact:dependencies]         2) junit:junit:jar:4.3.1

There are 15 such missing artifacts, the final terminal message is:

15 required artifacts are missing.

for artifact:
   org.soaplab:soaplab:jar:2.1.1

from the specified remote repositories:
   java.net (https://maven-repository.dev.java.net/repository/),
   java.net-m2 (http://download.java.net/maven/2),
   bio.maven.repository (http://biomoby.org/m2repo/),
   central (http://mirrors.sunsite.dk/maven2)


I can connect to all these URLs (except the one for central) in a 
browser, I've set ANT_OPTS to account for our University firewall, and 
I've also set the maven proxy in /.m2/settings.xml.

If anyone can shed any light on this, I'd be really grateful.

Sirisha

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Re: [Soaplab-users] ant error?

[Mahmut U. <ul...@eb...>]

Hi Sirisha,

> I have been using Soaplab2 successfully and have been able to deploy and 
> run services with no issue - however I always get the same error message 
> when I execute "ant jaxdeploy" (this appears right at the end after a 
> bunch of other tasks are successfully completed):
> 
> BUILD FAILED
> /home/sirisha/soaplab2/xmls/jaxws.xml:155: The following error occurred 
> while executing this line:
> /home/sirisha/soaplab2/xmls/deployment.xml:151: The following error 
> occurred while executing this line:
> /home/sirisha/soaplab2/xmls/tomcat.xml:78: Unable to delete file 
> /var/lib/tomcat5/webapps/soaplab2/status.jsp

There is an explanation for this error on Soaplab frequently asked
questions page.

  http://soaplab.sourceforge.net/soaplab2/FAQ.html#004

One additional point i have noticed this morning, Soaplab deletes any
previous web application folders (of the soaplab web application
deployed) after copying the web archive file to tomcat's webapps
directory. It is possible that before Soaplab attempting to delete the
web application folder tomcat notices the new web archive file and
starts extracting it; in your case while tomcat was trying to write the
above file Soaplab ant task possible was trying to delete it?

I remember getting similar errors in early stages of soaplab2 project
but i'm not able to reproduce it any more when i now try it using tomcat
versions 5.5.20 and 6.0.18. Is it possible that you are using an
outdated version of tomcat which is more prone to this error?

One way to avoid this error message, you can shutdown your tomcat server
before calling the "ant jaxdeploy" task and restart it after the ant
task completed.

If you don't want to shutdown your server you can use the "ant jaxwar"
target to let Soaplab produce the web archive file (normally
soaplab2.war when using jaxws) then you can deploy the web archive file
by simply copying it to your ${CATALINA_BASE}/webapps directory or using
tomcat manager web interface. After first time deploying a web archive
file you should normally copy your new web archive file over the
existing one (under ${CATALINA_BASE}/webapps directory), and tomcat
should automatically reload your soaplab web application.

Regards,
Mahmut

[Soaplab-users] ant error?

[Sirisha G. <si...@my...>]

Hi everyone,

I have been using Soaplab2 successfully and have been able to deploy and 
run services with no issue - however I always get the same error message 
when I execute "ant jaxdeploy" (this appears right at the end after a 
bunch of other tasks are successfully completed):

BUILD FAILED
/home/sirisha/soaplab2/xmls/jaxws.xml:155: The following error occurred 
while executing this line:
/home/sirisha/soaplab2/xmls/deployment.xml:151: The following error 
occurred while executing this line:
/home/sirisha/soaplab2/xmls/tomcat.xml:78: Unable to delete file 
/var/lib/tomcat5/webapps/soaplab2/status.jsp


This doesn't seem to affect the actual deployment as I can run services 
from within both Taverna and using the bundled clients, so I guess I'm 
just curious as to what it means!

Many thanks,

Sirisha

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Re: [Soaplab-users] output files not definable on command line

[Mahmut U. <ul...@eb...>]

> > I had a similar problem when i was integrating one application to
> > Soaplab. I used the 'default' attribute of the outfile options to
> > specify the name of the output file my application was expecting. This
> > worked well however i also needed to add a new check in the getFileName
> > method of the IOData class for checking whether the output has a default
> > file name and it is secure to use.

> I will test this.

Don't forget to add the following check as the first sentence in the
getFileName method of IOData class.

        if (StringUtils.isNotBlank(paramDef.dflt) && !
        paramDef.dflt.startsWith(File.separator))
                    return paramDef.dflt;

It includes an attempt to prevent use of absolute paths but the current
version will not work on windows platform. It should probably be safer
if the check also fails when the file name starts with a reference to
parent directories "..".

Mahmut

Re: [Soaplab-users] output files not definable on command line

[Sebastien M. <Seb...@un...>]

>>         How could I define output files in the ACD file ?
>>  
>> You can't (except the file extension). The output file names are
>> hidden to you (because it is somehow against the spirit of a
>> distributed application to deal with files). If your application
>> relies on such file naming schema, you need to write a wrapper (an
>> example of such wrapper - that I can send to you - would be for the
>> program 'cap' - or a similar name, I do not remember now, having it on
>> a different computer).
> 
> I had a similar problem when i was integrating one application to
> Soaplab. I used the 'default' attribute of the outfile options to
> specify the name of the output file my application was expecting. This
> worked well however i also needed to add a new check in the getFileName
> method of the IOData class for checking whether the output has a default
> file name and it is secure to use. This didn't look like against the
> spirit of a distributed application but i wasn't quite sure and thought
> discussing with you (haven't had a chance before).
> 
> Mahmut

I will test this.
Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] output files not definable on command line

[Mahmut U. <ul...@eb...>]

>         How could I define output files in the ACD file ?
>  
> You can't (except the file extension). The output file names are
> hidden to you (because it is somehow against the spirit of a
> distributed application to deal with files). If your application
> relies on such file naming schema, you need to write a wrapper (an
> example of such wrapper - that I can send to you - would be for the
> program 'cap' - or a similar name, I do not remember now, having it on
> a different computer).

I had a similar problem when i was integrating one application to
Soaplab. I used the 'default' attribute of the outfile options to
specify the name of the output file my application was expecting. This
worked well however i also needed to add a new check in the getFileName
method of the IOData class for checking whether the output has a default
file name and it is secure to use. This didn't look like against the
spirit of a distributed application but i wasn't quite sure and thought
discussing with you (haven't had a chance before).

Mahmut

Re: [Soaplab-users] output files not definable on command line

[Martin S. <mar...@gm...>]

> How could I define output files in the ACD file ?


You can't (except the file extension). The output file names are hidden to
you (because it is somehow against the spirit of a distributed application
to deal with files). If your application relies on such file naming schema,
you need to write a wrapper (an example of such wrapper - that I can send to
you - would be for the program 'cap' - or a similar name, I do not remember
now, having it on a different computer).

Martin

-- 
Martin Senger
email: mar...@gm...,m.s...@cg...
skype: martinsenger
Sent from: Pasig Riz Philippines.

Re: [Soaplab-users] output files not definable on command line

[Sebastien M. <Seb...@un...>]

> Hi Sebastien,
> 
>> I use an application which adds an extension to input file for output files.
>> Output files are not sent to stdout
>> I can change the output root name or keep the same than the input.
>>
>>
>> How could I define output files in the ACD file ?
>>
>> Should I directly send them to _R_/RESULTS/.../results/ directory ?
>> But how ?
> 
> Can you give an example? I'm finding it difficult to understand your
> question.
> 
> Regards,
> Mahmut

When it runs, the program creates output files in ../_R_/SANDBOX/.../:
i_infile.pdf
i_infile.out
...


I would like to put these files in _R_/RESULTS/.../results/
But I don't control their extensions nor their location.

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] output files not definable on command line

[Mahmut U. <ul...@eb...>]

Hi Sebastien,

> I use an application which adds an extension to input file for output files.
> Output files are not sent to stdout
> I can change the output root name or keep the same than the input.
> 
> 
> How could I define output files in the ACD file ?
> 
> Should I directly send them to _R_/RESULTS/.../results/ directory ?
> But how ?

Can you give an example? I'm finding it difficult to understand your
question.

Regards,
Mahmut

[Soaplab-users] output files not definable on command line

[Sebastien M. <Seb...@un...>]

Hi

I use an application which adds an extension to input file for output files.
Output files are not sent to stdout
I can change the output root name or keep the same than the input.


How could I define output files in the ACD file ?

Should I directly send them to _R_/RESULTS/.../results/ directory ?
But how ?

Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] timeout settings and waitFor calls

[Mahmut U. <ul...@eb...>]

> of your documentation to the new Soaplab article on Wikipedia as well,
> http://en.wikipedia.org/wiki/Soaplab, which needs attention from Soaplab
> developers.

Sorry for another mail, but i just have noticed that i should above say
"from Soaplab community".

Regards,
Mahmut

Re: [Soaplab-users] timeout settings and waitFor calls

[Mahmut U. <ul...@eb...>]

Hi Peter,

> I can contribute example client code, catching HTTP timeouts for Perl 
> and C# (Java will work similary):

Such examples would be quite useful. In current soaplab2 we don't have
many example clients although we have several examples of job classes in
Java and service descriptions in ACD. I'm not sure which directory would
be best to check in example clients but definitely exiting documentation
"For Soaplab2 clients" can be extended with a brief description of most
used Soaplab operations and with your examples. You can integrate a copy
of your documentation to the new Soaplab article on Wikipedia as well,
http://en.wikipedia.org/wiki/Soaplab, which needs attention from Soaplab
developers.

Sorry for my late reply.
Regards,
Mahmut

Re: [Soaplab-users] timeout settings and waitFor calls

[Peter E. <dr....@go...>]

Hello Mahmut,

I can contribute example client code, catching HTTP timeouts for Perl 
and C# (Java will work similary):

_Perl:_
do {
    $res = undef;
    eval {
      $res = $client->call("waitFor", $jobiddata);
    };
} while ($@ =~ /500 read timeout/);


_C#:_
/*
  requires SoapLabSupport class from
  
http://genome.dkfz-heidelberg.de/menu/hobit/webservice-clients/csharp/domainsweep/SoapLabSupport.cs
*/

string jobid = service.createAndRun(indoc);

//SoapLabSupport.waitForCompleted(service, jobid, true);
SoapLabSupport.ignoreTimeOut(service.waitFor, jobid, true);

Tstatus status = service.getStatus(jobid);

/* ignoreTimeOut() and waitForCompleted() try to solve the same task with
 * with two different technologies:
 * Goal is to ignore HTTP-timeouts while waiting for a job to complete.
 * In order to ignore the timeout, the thrown exception need to be analysed, and in
 * case of a timeout, ignored. Then the original method need to be reinvoked.
 * 
 * ignoreTimeOut() uses a function/method delegate to solve this problem in a general level.
 * waitForCompleted() uses reflection to do the waiting (more complicated than delegates).
 */

Best regards,

Peter


On 15.01.2009 10:54, ul...@eb... wrote:
> Hi,
>
> I have recently learned that we need to be more cautious when using
> runAndWaitFor and the waitFor methods in Soaplab interface. Soaplab web
> applications by default has a connection timeout setting of 5 minutes.
> Also some Soaplab servers may have load-balancer layers that may in turn
> have a maximum reply time setting, as for the EBI Soaplab server. In my
> recent experiences with jobs requiring time longer than the maximum reply
> time setting of the EBI Soaplab server the error messages returned after
> the maximum reply time was not clear enough to reveal that my waitFor
> calls was returning due to maximum reply time timeout.
>
> If you were getting error messages for your Soaplab calls after waiting
> couple of minutes and the error messages was not clear enough to
> understand the reason then it is possible that your calls may have been
> interrupted due to one of the timeout settings. If you want to make sure
> that you don't want to hit timeout limits an alternative would be to use
> createAndRun->getStatus->getResults series of calls rather than the
> createAndRun->waitFor calls or the runAndWaitFor call.
>
> Regards,
> Mahmut
>   

[Soaplab-users] timeout settings and waitFor calls

[<ul...@eb...>]

Hi,

I have recently learned that we need to be more cautious when using
runAndWaitFor and the waitFor methods in Soaplab interface. Soaplab web
applications by default has a connection timeout setting of 5 minutes.
Also some Soaplab servers may have load-balancer layers that may in turn
have a maximum reply time setting, as for the EBI Soaplab server. In my
recent experiences with jobs requiring time longer than the maximum reply
time setting of the EBI Soaplab server the error messages returned after
the maximum reply time was not clear enough to reveal that my waitFor
calls was returning due to maximum reply time timeout.

If you were getting error messages for your Soaplab calls after waiting
couple of minutes and the error messages was not clear enough to
understand the reason then it is possible that your calls may have been
interrupted due to one of the timeout settings. If you want to make sure
that you don't want to hit timeout limits an alternative would be to use
createAndRun->getStatus->getResults series of calls rather than the
createAndRun->waitFor calls or the runAndWaitFor call.

Regards,
Mahmut

[Soaplab-users] typed Soaplab interface work in progress

[Mahmut U. <ul...@eb...>]

Hi,

I just wanted to say that we have started working on typed Soaplab
interface and made some progress. If you would like to see current
development version, the latest build for EMBOSS Soaplab services made
available through the EBI test/development servers on the following
address.

    http://wwwdev.ebi.ac.uk/soaplab/

Modified Spinet interface has links to the individual WSDL files as well
as to the jax-ws page that lists all WSDL files. It has been tested only
with EMBOSS services.

Regards,
Mahmut

[Soaplab-users] Spinet and option help message

[Sebastien M. <Seb...@un...>]

Hi,

Soaplab, as opposed to emboss, seems to allow options with the same name 
but in different cases. E.g.: f and F

I use this for blast options.


In spinet, the help message, appearing when the mouse is over the option 
name, seems to be broken when uppercase letters are used:

It is always the message of the first uppercase option which appears for 
every uppercase option.
The A help message appears over A, B, ..., Z

The help message for lowercase options seems to be fine.


An idea ?
Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] quotes

[Mahmut U. <ul...@eb...>]

Hi Sebastien,

> Double quotes appear in the report file, around the attribute from the 
> list, as it should. But the execution fails.
> 
> If I copy/paste the command line from the report file, the program runs 
> successfully.
> 
> Is the command line in the report file the real one ?

It should be but you can double check it by adding a log line in the run
method of the SowaJob class.

        Thread executeThread = getExecuteThread (pb);
        log.info("program and arguments: "+pb.command());
        executeThread.start();

Regards,
Mahmut

Re: [Soaplab-users] quotes

[Sebastien M. <Seb...@un...>]

Sebastien Moretti a écrit :
>>> I try to use double quotes in the ACD file for a list.
>>> I must do something wrong because double quotes don't appear in the 
>>> report file where the command line is written.
>>
>>> I have tried with \" but nothing appends
>>
>> double escaped quotes seem to work, such as \\"
>> Mahmut
> 
> Thanks
> It is the thing I have missed

Just another problem now.

Double quotes appear in the report file, around the attribute from the 
list, as it should. But the execution fails.

If I copy/paste the command line from the report file, the program runs 
successfully.

Is the command line in the report file the real one ?
Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] quotes

[Sebastien M. <Seb...@un...>]

>> I try to use double quotes in the ACD file for a list.
>> I must do something wrong because double quotes don't appear in the 
>> report file where the command line is written.
> 
>> I have tried with \" but nothing appends
> 
> double escaped quotes seem to work, such as \\" 
> 
> Mahmut

Thanks
It is the thing I have missed

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] quotes

[Mahmut U. <ul...@eb...>]

> I try to use double quotes in the ACD file for a list.
> I must do something wrong because double quotes don't appear in the 
> report file where the command line is written.

> I have tried with \" but nothing appends

double escaped quotes seem to work, such as \\" 

Mahmut

[Soaplab-users] quotes

[Sebastien M. <Seb...@un...>]

Hi,

I try to use double quotes in the ACD file for a list.
I must do something wrong because double quotes don't appear in the 
report file where the command line is written.
But I don't know why.

Here is the code for the list
     list: d [
         standard: "Y"
#        template: '-d "$$"'
         comment: 'method -d "$$"'
         default: "swiss"
         comment: "defaults"
         minimum: 1
         values: "nrcrc:non redundant, swiss:SwissProt, 
swisstrembl:UniProt (SwissProt/TrEMBL), trembl_all:TrEMBL, refseq:RefSeq 
protein, ipi:IPI ENSEMBL, gp:GenPept, shuffled:randomized SwissProt, 
microbial:All microbial proteomes (SP format), nrl3d:non redundant 3D 
structure, UniRef100:UniRef100, UniRef90:UniRef90, UniRef50:UniRef50, 
athpep:A. thaliana (from TIGR), worm:Worm (C. elegans), yeast:Yeast (S. 
cerevisiae)"
         delimiter: ", "
         codedelimiter: ":"
         information: "Peptide database used as target."
     ]

And the command line declared in the ACD:
comment: 'method ... $d ...'


Do you know what could be wrong ?
I have tried with \" but nothing appends

Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] Intermittent error invoking Soaplab2-axis services

[Mahmut U. <ul...@eb...>]

Hi John,

> I've investigated this a bit further and it seems the problem is on the client 
> side (Taverna 1.7.1 / Soaplab plugin 2.1.1.3).  The workflow I'm using has 
> multiple instances of Soaplab2 processors.  When Taverna loads the workflow, 
> the ProcessorLoaderThread(s) each call:
>  
> org.soaplab.clients.axis1.ServiceProviderImpl.getInputSpec()
> 
> These calls don't appear to be syncronized, resulting in a mailformed request 
> such as this:
> 
> http://kraz.omii.ac.uk/~jsr2/getInputSpecBad

I remember this problem reported/discussed in the past. I don't know why
we didn't note and fix it.

It seems Axis connection objects are reused for a while for the calls
made for same services. I will investigate it further. A workaround/fix
on taverna plugin side for now would be convenient as it is easier to
release the plugin for us and taverna has a god way of updating its
plugins.

> This in turn leads to the workflow failing to load, and the server-side errors 
> I initially indicated.

Thanks for locating the problem.

Regards,
Mahmut

Re: [Soaplab-users] Intermittent error invoking Soaplab2-axis services

[Mahmut U. <ul...@eb...>]

Hi John,

> xmlwf refports no problems with  server-config.wsdd.
> 
> As I mentioned, this is an intermittent problem.  It's almost as if something 
> is being uncached after a period of time, and the next call missing the cache 
> but causing the data to be reloaded so that subsequent calls hit.  Does this 
> sound plausible?

Yes. You are right if there is a problem in server-config.wsdd file your
services should not work at all. I sent my message just in case if Axis
working in an unexpected way as its most parts are unknown to me. I'm
sure you already have checked Soaplab log files and they don't include
any useful error messages. If you can temporarily make your Soaplab web
archive file available through your home page I can deploy it on my
tomcat server and try to see whether I'm able to reproduce the problem.

Regards,
Mahmut