soaplab-users — Forum for Soaplab users and developers

[Soaplab-users] Soaplab 2.3 installation

[Sébastien M. <seb...@un...>]

Hi

Today I wanted to re-install soaplab for it to use our new filesystem 
and use Soaplab 2.3.2/EMBOSS6.3.1 at the same time.

I have a problem during build process.
ACD file parsing looks fine but I have a problem after that step:

BUILD SUCCESSFUL
Total time: 9 seconds
Buildfile: build.xml

tomcat-init:

checkmaven:

initmaven:

init:

axis1init:

axis1dist:

checkmaven:

initmaven:

init:

initeclipse:
      [copy] Copying 1 file to /var/lib/Soaplab2.3

config:
      [copy] Copying 1 file to /var/lib/Soaplab2.3/build/classes
      [copy] Copying 11 files to /var/lib/Soaplab2.3/build/run
       [jar] Building jar: 
/var/lib/Soaplab2.3/build/lib/soaplab-spi-config.jar
      [copy] Copying 1 file to /var/lib/Soaplab2.3/build/classes
      [copy] Copying 1 file to /var/lib/Soaplab2.3/build/classes
      [copy] Copying 11 files to 
/var/lib/Soaplab2.3/build/classes/org/soaplab/clients/wsdl

compile:
     [javac] Compiling 189 source files to /var/lib/Soaplab2.3/build/classes
      [copy] Copying 7 files to /var/lib/Soaplab2.3/build/classes
     [javac] Compiling 38 source files to /var/lib/Soaplab2.3/build/plugins

run-init:

BUILD FAILED
/var/lib/Soaplab2.3/xmls/axis1.xml:37: The following error occurred 
while executing this line:
/var/lib/Soaplab2.3/xmls/run.xml:30: The <tempfile> type doesn't support 
the "deleteonexit" attribute.




Do you know what it could be ?

-- 
Sébastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/

[Soaplab-users] announcement: new Soaplab2 release (2.3.1)

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

Release 2.3.1 is a bug-fix release. Bugs (or missing features) are
related to the character encoding of Soaplab2's services inputs and
outputs.

Details are in the file "docs/ChangeLog" (
http://soaplab.sourceforge.net/soaplab2/ChangeLog).
Project main page stays the same: http://soaplab.sourceforge.net/soaplab2/.

Many thanks for those who contributed. Feedback and suggestions are again
warmly welcome.

Cheers,
Martin

-- 
Martin Senger
email: mar...@gm...,mar...@ka...
skype: martinsenger

Re: [Soaplab-users] Question regarding input and output files

[Daniel B. <Ble...@ma...>]

Hi Martin,

  Thanks for the response.  From reading the docs (very good, btw), I had
come to these same conclusions.  We would like to use Taverna, but our
processing model really doesn¹t fit all that well in the grid model, as this
question indicates.

Best,
-dan


On 10/6/10 5:18 AM, "Martin Senger" <mar...@gm...> wrote:

> This is a good and valid question and concern. There are several options - but
> you have always to keep in mind that this "refusing" was done on purpose, to
> keep Soaplab2 services secure enough. Some of the following options may open
> your file system too much.
> 
> In all options, the input files to be used will need to be referenced as URLs
> - not as a direct data. By default, all input files defined in ACD files are
> specified as working also as URLs (so you do not need to change ACD files).
> 
> But there is another issue: the size of the files. When an input file is
> referenced by its URL the Soaplab2 fetches it and stores it in a server-side
> file and passes this new file name to the application. So the file is actually
> physically copied. If you wish to avoid it, see the last option in the list
> below.
> 
> 1) Soaplab2 can access your input data using a true URL (using http or ftp
> protocols). That can be done only if you have a web server able to serve your
> data. Such server does not need to be visible outside; it could be used just
> by your Tomcat server that contain the Soaplab2 web application. If can be,
> for example, referenced as a 'localhost' (but your users must know it). This
> is probably the "cleanest" way.
> 
> 2) Or one can use the fact that Soaplab2 does not refuse to serve data if they
> sit in its "sandbox". Therefore, you can either make sure that your sandbox is
> where your data are, or you can create symbolic links in the sandbox pointing
> to your data elsewhere (on the same file system). You can define what sandbox
> directory Soaplab2 will be using by the property "working.dir" (see the
> Configuration guide where to put this property). Be careful that this
> directory must be writable for the user running Tomcat. Your users, however,
> need to know the full path to the sandbox (I think that it is a bit
> unfortunate that Soaplab2 does not use a simple file without absolute path as
> a file being in a sandbox - perhaps I should fix this in the next Soaplab2
> release; but I never expected that dealing directly with files in the sandbox
> would be used much).
> 
> 3) Or, you can write your own Java class - a simple extension of the SowaJob
> (or EmbossJob) class that overwrites only the method "isDataReferenceSafe". If
> it return true, all local files will be allowed to read. Or you can return
> true only for some files.
> 
> 4) Last but not least: In ACD file, you can  define your inputs not as inputs
> but as strings. Your application then gets these strings and uses them as file
> names. The Soaplab2 will not know that these strings are actually file names,
> so no checking is done. It will depend on your application what it reads and
> what it does not.
> 
> The all options above are more or less for input files. The output files,
> Soaplab2 creates them in the "result" directory (which can be also defined by
> a property - the "results.dir" property). And these files can be delivered to
> the users also as URLs (which means that big files will be passed by the http
> protocol which does not need to read the whole file first into memory).
> 
> Please do not hesitate to ask for further clarification.
> 
> Cheers,
> Martin

-- 
Daniel Blezek, PhD
Medical Imaging Informatics Innovation Center

P 127 or (77) 8 8886
T 507 538 8886
E ble...@ma...

Mayo Clinic
200 First St. S.W.
Harwick SL-44
Rochester, MN 55905
mayoclinic.org
"It is more complicated than you think." -- RFC 1925

Re: [Soaplab-users] Soaplab2 encoding issue

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

The first finding: The problem is in Spinet - because if I run the same
service from the command-line I get uncorrupted results (with both
protocols: local and jaxws). I will keep you posted.

Martin

-- 
Martin Senger
email: mar...@gm...,mar...@ka...
skype: martinsenger

Re: [Soaplab-users] Soaplab2 encoding issue

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

It is definitely a bug (I can easily reproduce it). I will be working on it
and let you know. Thanks for reporting it.

Martin

-- 
Martin Senger
email: mar...@gm...,mar...@ka...
skype: martinsenger

Re: [Soaplab-users] Question regarding input and output files

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

This is a good and valid question and concern. There are several options -
but you have always to keep in mind that this "refusing" was done on
purpose, to keep Soaplab2 services secure enough. Some of the following
options may open your file system too much.

In all options, the input files to be used will need to be referenced as
URLs - not as a direct data. By default, all input files defined in ACD
files are specified as working also as URLs (so you do not need to change
ACD files).

But there is another issue: the size of the files. When an input file is
referenced by its URL the Soaplab2 fetches it and stores it in a server-side
file and passes this new file name to the application. So the file is
actually physically copied. If you wish to avoid it, see the last option in
the list below.

1) Soaplab2 can access your input data using a true URL (using http or ftp
protocols). That can be done only if you have a web server able to serve
your data. Such server does not need to be visible outside; it could be used
just by your Tomcat server that contain the Soaplab2 web application. If can
be, for example, referenced as a 'localhost' (but your users must know it).
This is probably the "cleanest" way.

2) Or one can use the fact that Soaplab2 does not refuse to serve data if
they sit in its "sandbox". Therefore, you can either make sure that your
sandbox is where your data are, or you can create symbolic links in the
sandbox pointing to your data elsewhere (on the same file system). You can
define what sandbox directory Soaplab2 will be using by the property
"working.dir" (see the Configuration guide where to put this property). Be
careful that this directory must be writable for the user running Tomcat.
Your users, however, need to know the full path to the sandbox (I think that
it is a bit unfortunate that Soaplab2 does not use a simple file without
absolute path as a file being in a sandbox - perhaps I should fix this in
the next Soaplab2 release; but I never expected that dealing directly with
files in the sandbox would be used much).

3) Or, you can write your own Java class - a simple extension of the SowaJob
(or EmbossJob) class that overwrites only the method "isDataReferenceSafe".
If it return true, all local files will be allowed to read. Or you can
return true only for some files.

4) Last but not least: In ACD file, you can  define your inputs not as
inputs but as strings. Your application then gets these strings and uses
them as file names. The Soaplab2 will not know that these strings are
actually file names, so no checking is done. It will depend on your
application what it reads and what it does not.

The all options above are more or less for input files. The output files,
Soaplab2 creates them in the "result" directory (which can be also defined
by a property - the "results.dir" property). And these files can be
delivered to the users also as URLs (which means that big files will be
passed by the http protocol which does not need to read the whole file first
into memory).

Please do not hesitate to ask for further clarification.

Cheers,
Martin

-- 
Martin Senger
email: mar...@gm...,mar...@ka...
skype: martinsenger

[Soaplab-users] Question regarding input and output files

[Daniel B. <Ble...@ma...>]

Hi,

  We have (perhaps) an unusual situation.  I have defined our command line
processes in Soaplab2 and can properly access them from a client.  What we
would like to do is be able to pass filenames of files residing on our
cluster to the services.  The service would process and write out a new
file, also residing on the cluster filesystem.  The reason for this is that
our inputs and outputs tend to be 100¹s of megabytes, and it is not really
feasible to pass them across the network.

  When I tried to specify a filename on the cluster filesystem, I get this
error:

* org.soaplab.share.SoaplabException: Soaplab::NotValidInputs [Input]
Refusing to resolve the reference:
/mi3c/projects/ImageLinks/MRA-0001/MR_20080811/0003_3DTOF/
Is there anyway this can be done using soaplab?

Thanks,
-dan

-- 
Daniel Blezek, PhD
Medical Imaging Informatics Innovation Center

P 127 or (77) 8 8886
T 507 538 8886
E ble...@ma...

Mayo Clinic
200 First St. S.W.
Harwick SL-44
Rochester, MN 55905
mayoclinic.org
"It is more complicated than you think." -- RFC 1925

[Soaplab-users] Soaplab2 encoding issue

[Prokopis P. <pro...@il...>]

Hello all.

I am facing the following encoding problem with a Soaplab2-2.3.0 
installation in a Tomcat6 that shows no similar problems with other webapps.

My small Soaplab2 service takes an input file ("qualifier: i") and 
returns the file after some processing. Now, when I upload to the 
service a UTF-8 test file, the data stored in the i_input file are 
corrupted. What I mean is that the only line in my file

$ more text1.txt
The word "παιδί" in Greek means child.

is stored as

$ more i_input
The word "παιδί" in Greek means child.

The locale in both client and server machines is set to "en_US.UTF-8".  
Tomcat starts with the -Dfile.encoding="UTF-8" parameter.

Thanks in advance for any hints.

Prokopis

[Soaplab-users] Soaplab2 version 2.3.0 released

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

Thanks to work of Soaplab2 developers, especially to people from the EBI, I
can announce a new Soaplab2 release:

Release 2.3.0 is mostly a maintenance release - but it also brings
several new features:

* Strongly typed services.

* Semantically annotated WSDLs.

* Changes made to be compliant with the latest EMBOSS package (version
  6.3).

* More properties to customize Soaplab2 components.

* Updated documentation.

More details about changes are in the file "docs/ChangeLog".

Cheers,
Martin

-- 
Martin Senger
email: mar...@gm...,mar...@ka...
skype: martinsenger

Re: [Soaplab-users] Output files based on input argument

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

I am sorry for a BIG delay in my reply. Somehow I forgot about this email...
In case you still do not have an answer...

I try to define output section for one of my tool but I cannot find the
>
right way:
>
> The tool takes a mandatory argument and returns three different files
> with names starting by the mandatory argument.
> e.g.:    input          ./tool --pdb=2SRC
>         outputs        2SRC.out, 2SRC.gff, 2SRC.bed
>
>
> How to properly code this in ACD format ?
>

Soaplab does not allow users to specify names of the output files (the
reasons are mostly because of the distributed character of web services
where the concept of "files" is blurred; but also some legacy reasons).
Therefore, if an application has to have a fixed names (either hard-coded
names or names based on other parameters, as it is in your example) one must
wrap the application into a wrapper script. The acd file specifies this
wrapper as an executable. The wrapper maps the fixed names into the names
generated by Soaplab. The wrapper knows what names were generated by Soaplab
because it gets the full command line created by Soaplab.

Here is an example - for the "cap3" program (
http://pbil.univ-lyon1.fr/cap3.php). The "cap3" program uses the name of its
input file as a prefix for several output file names. [In your example, the
prefix would be taken from the parameter "-pdb" and not from the input file
name.] The wrapper for cap3 program could use this command-line:

cap3_wrapper
     -I seq
     -q seq.qual
     -C seq.con

     -A seq.cap.ace
     -G seq.cap.contigs
     -Q seq.cap.contigs.qual
     -L seq.cap.contigs.links
     -F seq.cap.info
     -S seq.cap.singlets
     -R seq.con.cap.results

Where "-I" indicates the input file, and -A, -G, -Q, -L, -F, -S, and -R are
all possible output files. The ACD file will reflect this command-line. For
example, the first two outputs will be specified as:

...
outfile: ace [
  additional: "Y"
  qualifier: "A"
]

outfile: contigs [
  additional: "Y"
  qualifier: "G"
]
...

The wrapper itself (a Perl script) is attached (and included also below).

Cheers,
Martin

#!/usr/bin/perl -w
#
# Martin Senger <mar...@gm...>
# ---------------------------------------

use strict;
use Getopt::Std;
use vars qw/ $opt_H $opt_I $opt_q $opt_C $opt_A $opt_G $opt_Q $opt_L $opt_F
$opt_S $opt_R /;

$Getopt::Std::STANDARD_HELP_VERSION = 'true';
getopts ('HI:q:C:A:G:Q:L:F:S:R:');

sub HELP_MESSAGE() {
    print STDOUT <<'END_OF_USAGE';
cap3 seq [cap3-options]
     other (optional) inputs:
seq.qual
seq.con
     outputs:
standard output
seq.cap.ace
seq.cap.contigs
seq.cap.contigs.qual
seq.cap.contigs.links
seq.cap.info
seq.cap.singlets
seq.con.cap.results

cap3_wrapper
     -I seq
     -q seq.qual
     -C seq.con

     -A seq.cap.ace
     -G seq.cap.contigs
     -Q seq.cap.contigs.qual
     -L seq.cap.contigs.links
     -F seq.cap.info
     -S seq.cap.singlets
     -R seq.con.cap.results

Other:
-H ... help
END_OF_USAGE
    exit (0);
}

HELP_MESSAGE() if $opt_H;

# -----------------------------------------------------------

# -- change the input arguments
die "Required input file (option -I) is missing\n" unless defined $opt_I;
#my @cmdline = ('/home/senger/Software/CAP3/cap3', $opt_I);
my @cmdline = ('cap3', $opt_I);
push (@cmdline, @ARGV);

my $inp_qual = $opt_I . '.qual';
`cp $opt_q $inp_qual` if defined $opt_q && -e $opt_q;
my $inp_con = $opt_I . '.con';
`cp $opt_C $inp_con` if defined $opt_C && -e $opt_C;

# -- call the real cap3
system (@cmdline) == 0
    or die "Calling cap3 with the command line [" . join (" ", @cmdline) .
"] failed: $?\n";

# -- rename cap3's outputs
my $out_ace = $opt_I . '.cap.ace';
`mv $out_ace $opt_A` if -e $out_ace && defined $opt_A;
my $out_contigs = $opt_I . '.cap.contigs';
`mv $out_contigs $opt_G` if -e $out_contigs && defined $opt_G;
my $out_qual = $opt_I . '.cap.contigs.qual';
`mv $out_qual $opt_Q` if -e $out_qual && defined $opt_Q;
my $out_links = $opt_I . '.cap.contigs.links';
`mv $out_links $opt_L` if -e $out_links && defined $opt_L;
my $out_info = $opt_I . '.cap.info';
`mv $out_info $opt_F` if -e $out_info && defined $opt_F;
my $out_singlets = $opt_I . '.cap.singlets';
`mv $out_singlets $opt_S` if -e $out_singlets && defined $opt_S;
my $out_results = $opt_I . '.con.cap.results';
`mv $out_results $opt_R` if -e $out_results && defined $opt_R;


-- 
Martin Senger
email: mar...@gm...,mar...@ka...
skype: martinsenger

[Soaplab-users] Output files based on input argument

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

Hi

I try to define output section for one of my tool but I cannot find the 
right way:

The tool takes a mandatory argument and returns three different files 
with names starting by the mandatory argument.
e.g.:    input		./tool --pdb=2SRC
	 outputs        2SRC.out, 2SRC.gff, 2SRC.bed


How to properly code this in ACD format ?

Thanks

-- 
Sébastien Moretti
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4079/4221
http://ch.embnet.org/  http://myhits.vital-it.ch/

Re: [Soaplab-users] soaplab2 plugin problems

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

Hi again - seems the problem is resolved for 1.7.2 - I have uninstalled 
and reinstalled and the plugin appears to be working correctly. I still 
don't know what caused 1.7.1 to break so badly, but at least I can now 
access my Soaplab2 services :)

Many thanks,

Sirisha

Mahmut Uludag wrote:
> Hi Sirisha,
> 
>> I have tried again with Taverna 1.7.2 (was 
>> using 1.7.1) - when I add the plugin site it immediately shows the 
>> message "This plugin site contains no new plugins" - even though this is 
>> a fresh install of a new version!
> 
> I have added a new plugin to usual taverna/soaplab plugin point for
> taverna-1.7.2, version number called 2.1.1.7-beta. I tested it both
> jax-ws and axis1 flavours of soaplab2 and it looks working. You should
> restart taverna after installing the plugin first time.
> 
> Mahmut
> 
> 

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Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Mahmut -

Yesterday evening, I could not get Taverna v 1.7.2 to start at all. 
Today it's starting up, but reporting the following error, so should I 
try to uninstall and reinstall the plugin?

Aug 4, 2009 9:39:32 AM 
net.sf.taverna.raven.repository.impl.LocalRepository ?
WARNING: Could not find artifact 
org.soaplab.plugins.taverna:soaplab2-scavenger:2.1.1.7-beta
net.sf.taverna.raven.repository.ArtifactNotFoundException: Can't find 
artifact for: org.soaplab.plugins.taverna:soaplab2-scavenger:2.1.1.7-beta
         at 
net.sf.taverna.raven.repository.impl.LocalRepository.fetch(LocalRepository.java:819)
         at 
net.sf.taverna.raven.repository.impl.LocalRepository.act(LocalRepository.java:536)
         at 
net.sf.taverna.raven.repository.impl.LocalRepository.update(LocalRepository.java:490)
         at net.sf.taverna.raven.Loader.doRavenMagic(Loader.java:170)
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
         at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at 
net.sf.taverna.tools.Bootstrap.createWorkbenchClass(Bootstrap.java:240)
         at net.sf.taverna.tools.Bootstrap.main(Bootstrap.java:71)


Thanks,

Sirisha


Mahmut Uludag wrote:
> Hi Sirisha,
> 
>> I have tried again with Taverna 1.7.2 (was 
>> using 1.7.1) - when I add the plugin site it immediately shows the 
>> message "This plugin site contains no new plugins" - even though this is 
>> a fresh install of a new version!
> 
> I have added a new plugin to usual taverna/soaplab plugin point for
> taverna-1.7.2, version number called 2.1.1.7-beta. I tested it both
> jax-ws and axis1 flavours of soaplab2 and it looks working. You should
> restart taverna after installing the plugin first time.
> 
> Mahmut
> 
> 

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
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Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Sirisha,

> I have tried again with Taverna 1.7.2 (was 
> using 1.7.1) - when I add the plugin site it immediately shows the 
> message "This plugin site contains no new plugins" - even though this is 
> a fresh install of a new version!

I have added a new plugin to usual taverna/soaplab plugin point for
taverna-1.7.2, version number called 2.1.1.7-beta. I tested it both
jax-ws and axis1 flavours of soaplab2 and it looks working. You should
restart taverna after installing the plugin first time.

Mahmut

Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Sirisha,

> after uninstalling and restarting Taverna, when I 
> add the plugin site (http://soaplab.sourceforge.net/taverna-plugin/) the 
> only available plugin version is 2.1.1.7-beta - should I go ahead with 
> that, or should it say the different version number?

yes it should, looks like there is some caching? just to be make sure i
now also deleted the plugin definition, last time i only delete it from
the available plugins list (when testing here taverna didn't see it so i
was reluctant to delete it completely, i don't know why taverna still
sees it in your case). Can you please try again?

Mahmut

Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Sirisha,

I will this afternoon work on updating the plugin for taverna-1.7.2, it
has not been done yet. I hope to get it soon published.

Mahmut

> Next frustrating problem!! I have tried again with Taverna 1.7.2 (was 
> using 1.7.1) - when I add the plugin site it immediately shows the 
> message "This plugin site contains no new plugins" - even though this is 
> a fresh install of a new version! Bit of a loss as to what to do next :(

Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Mahmut,

Next frustrating problem!! I have tried again with Taverna 1.7.2 (was 
using 1.7.1) - when I add the plugin site it immediately shows the 
message "This plugin site contains no new plugins" - even though this is 
a fresh install of a new version! Bit of a loss as to what to do next :(

Sirisha

Mahmut Uludag wrote:
> Hi Sirisha,
> 
>> after uninstalling and restarting Taverna, when I 
>> add the plugin site (http://soaplab.sourceforge.net/taverna-plugin/) the 
>> only available plugin version is 2.1.1.7-beta - should I go ahead with 
>> that, or should it say the different version number?
> 
> yes it should, looks like there is some caching? just to be make sure i
> now also deleted the plugin definition, last time i only delete it from
> the available plugins list (when testing here taverna didn't see it so i
> was reluctant to delete it completely, i don't know why taverna still
> sees it in your case). Can you please try again?
> 
> Mahmut
> 
> 

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
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Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Mahmut,

Still the same problem and a more worrying issue now - Taverna won't 
start :( getting the following, so perhaps I should take it over to 
taverna-users instead...

Exception occured in getInstance
java.lang.IllegalArgumentException: Host name may not be null
         at org.apache.commons.httpclient.HttpHost.<init>(HttpHost.java:67)
         at org.apache.commons.httpclient.HttpHost.<init>(HttpHost.java:106)
         at 
org.apache.commons.httpclient.HttpMethodBase.setURI(HttpMethodBase.java:276)
         at 
org.apache.commons.httpclient.HttpMethodBase.<init>(HttpMethodBase.java:217)
         at 
org.apache.commons.httpclient.methods.GetMethod.<init>(GetMethod.java:88)
         at 
net.sf.taverna.update.plugin.PluginManager.getPluginsFromSite(PluginManager.java:391)
         at 
net.sf.taverna.update.plugin.PluginManager.checkForUpdates(PluginManager.java:548)
         at 
net.sf.taverna.update.plugin.ui.UpdatesAvailableIcon.pluginUpdateAvailable(UpdatesAvailableIcon.java:151)
         at 
net.sf.taverna.update.plugin.ui.UpdatesAvailableIcon.checkForUpdates(UpdatesAvailableIcon.java:135)
         at 
net.sf.taverna.update.plugin.ui.UpdatesAvailableIcon.<init>(UpdatesAvailableIcon.java:80)
         at 
org.embl.ebi.escience.scuflui.workbench.Workbench.setUI(Workbench.java:336)
         at 
org.embl.ebi.escience.scuflui.workbench.Workbench.<init>(Workbench.java:201)
         at 
org.embl.ebi.escience.scuflui.workbench.Workbench.getInstance(Workbench.java:134)
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
         at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at 
net.sf.taverna.tools.Bootstrap.invokeWorkbench(Bootstrap.java:192)
         at net.sf.taverna.tools.Bootstrap.main(Bootstrap.java:75)


Mahmut Uludag wrote:
> Hi Sirisha,
> 
>> after uninstalling and restarting Taverna, when I 
>> add the plugin site (http://soaplab.sourceforge.net/taverna-plugin/) the 
>> only available plugin version is 2.1.1.7-beta - should I go ahead with 
>> that, or should it say the different version number?
> 
> yes it should, looks like there is some caching? just to be make sure i
> now also deleted the plugin definition, last time i only delete it from
> the available plugins list (when testing here taverna didn't see it so i
> was reluctant to delete it completely, i don't know why taverna still
> sees it in your case). Can you please try again?
> 
> Mahmut
> 
> 

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Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Mahmut,

Thanks for that - but after uninstalling and restarting Taverna, when I 
add the plugin site (http://soaplab.sourceforge.net/taverna-plugin/) the 
only available plugin version is 2.1.1.7-beta - should I go ahead with 
that, or should it say the different version number?

Thanks,

Sirisha

Mahmut Uludag wrote:
> Hi Sirisha,
> 
> I have deleted the beta version of the plugin, it was previously working
> for me i don't know why it is now not able to find that particular
> dependency. If you uninstall and install your Soaplab plugin again it
> should work (using version 2.1.1.6).
> 
> Regards,
> Mahmut
> 
> On Mon, 2009-08-03 at 10:09 +0100, Sirisha Gollapudi wrote:
>> Hi everyone,
>>
>> Is there a problem with the Soaplab2 Taverna plugin? This morning, I 
>> started up Taverna (1.7) and noticed that the Plugin Manager was 
>> reporting that an update was available. I guess I shouldn't have tried 
>> to update, because now the option to add a new Soaplab2 scavenger is no 
>> longer available :(
>>
>> In the Plugin Manager, the "Taverna Soaplab Plugin" is listed (v 
>> 2.1.1.7-beta), but it's now saying that there are no up dates available. 
>>   I have tried disabling/re-enabling, as well as 
>> uninstalling/reinstalling, but no joy.
>>
>> I also got these messages in the terminal, which I haven't seen before, 
>> so not sure if they are anything to do with the problem?
>>
>>
>> Aug 3, 2009 9:54:05 AM 
>> net.sf.taverna.raven.repository.impl.LocalRepository ?
>> WARNING: Could not find artifact org.codehaus.woodstox:wstx-asl:3.2.4
>> net.sf.taverna.raven.repository.ArtifactNotFoundException: Can't find 
>> artifact for: org.codehaus.woodstox:wstx-asl:3.2.4
>>          at 
>> net.sf.taverna.raven.repository.impl.LocalRepository.fetch(LocalRepository.java:727)
>>          at 
>> net.sf.taverna.raven.repository.impl.LocalRepository.act(LocalRepository.java:379)
>>          at 
>> net.sf.taverna.raven.repository.impl.LocalRepository.update(LocalRepository.java:262)
>>          at net.sf.taverna.raven.Loader.doRavenMagic(Loader.java:138)
>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>          at 
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>          at 
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>          at 
>> net.sf.taverna.tools.Bootstrap.createWorkbenchClass(Bootstrap.java:240)
>>          at net.sf.taverna.tools.Bootstrap.main(Bootstrap.java:71)
>> Aug 3, 2009 9:54:06 AM 
>> net.sf.taverna.raven.repository.impl.LocalRepository ?
>> WARNING: Could not find artifact stax:stax-api:1.0.1
> 
> 

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

Re: [Soaplab-users] soaplab2 plugin problems

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

Hi Sirisha,

I have deleted the beta version of the plugin, it was previously working
for me i don't know why it is now not able to find that particular
dependency. If you uninstall and install your Soaplab plugin again it
should work (using version 2.1.1.6).

Regards,
Mahmut

On Mon, 2009-08-03 at 10:09 +0100, Sirisha Gollapudi wrote:
> Hi everyone,
> 
> Is there a problem with the Soaplab2 Taverna plugin? This morning, I 
> started up Taverna (1.7) and noticed that the Plugin Manager was 
> reporting that an update was available. I guess I shouldn't have tried 
> to update, because now the option to add a new Soaplab2 scavenger is no 
> longer available :(
> 
> In the Plugin Manager, the "Taverna Soaplab Plugin" is listed (v 
> 2.1.1.7-beta), but it's now saying that there are no up dates available. 
>   I have tried disabling/re-enabling, as well as 
> uninstalling/reinstalling, but no joy.
> 
> I also got these messages in the terminal, which I haven't seen before, 
> so not sure if they are anything to do with the problem?
> 
> 
> Aug 3, 2009 9:54:05 AM 
> net.sf.taverna.raven.repository.impl.LocalRepository ?
> WARNING: Could not find artifact org.codehaus.woodstox:wstx-asl:3.2.4
> net.sf.taverna.raven.repository.ArtifactNotFoundException: Can't find 
> artifact for: org.codehaus.woodstox:wstx-asl:3.2.4
>          at 
> net.sf.taverna.raven.repository.impl.LocalRepository.fetch(LocalRepository.java:727)
>          at 
> net.sf.taverna.raven.repository.impl.LocalRepository.act(LocalRepository.java:379)
>          at 
> net.sf.taverna.raven.repository.impl.LocalRepository.update(LocalRepository.java:262)
>          at net.sf.taverna.raven.Loader.doRavenMagic(Loader.java:138)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>          at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at 
> net.sf.taverna.tools.Bootstrap.createWorkbenchClass(Bootstrap.java:240)
>          at net.sf.taverna.tools.Bootstrap.main(Bootstrap.java:71)
> Aug 3, 2009 9:54:06 AM 
> net.sf.taverna.raven.repository.impl.LocalRepository ?
> WARNING: Could not find artifact stax:stax-api:1.0.1

[Soaplab-users] soaplab2 plugin problems

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

Hi everyone,

Is there a problem with the Soaplab2 Taverna plugin? This morning, I 
started up Taverna (1.7) and noticed that the Plugin Manager was 
reporting that an update was available. I guess I shouldn't have tried 
to update, because now the option to add a new Soaplab2 scavenger is no 
longer available :(

In the Plugin Manager, the "Taverna Soaplab Plugin" is listed (v 
2.1.1.7-beta), but it's now saying that there are no up dates available. 
  I have tried disabling/re-enabling, as well as 
uninstalling/reinstalling, but no joy.

I also got these messages in the terminal, which I haven't seen before, 
so not sure if they are anything to do with the problem?


Aug 3, 2009 9:54:05 AM 
net.sf.taverna.raven.repository.impl.LocalRepository ?
WARNING: Could not find artifact org.codehaus.woodstox:wstx-asl:3.2.4
net.sf.taverna.raven.repository.ArtifactNotFoundException: Can't find 
artifact for: org.codehaus.woodstox:wstx-asl:3.2.4
         at 
net.sf.taverna.raven.repository.impl.LocalRepository.fetch(LocalRepository.java:727)
         at 
net.sf.taverna.raven.repository.impl.LocalRepository.act(LocalRepository.java:379)
         at 
net.sf.taverna.raven.repository.impl.LocalRepository.update(LocalRepository.java:262)
         at net.sf.taverna.raven.Loader.doRavenMagic(Loader.java:138)
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
         at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at 
net.sf.taverna.tools.Bootstrap.createWorkbenchClass(Bootstrap.java:240)
         at net.sf.taverna.tools.Bootstrap.main(Bootstrap.java:71)
Aug 3, 2009 9:54:06 AM 
net.sf.taverna.raven.repository.impl.LocalRepository ?
WARNING: Could not find artifact stax:stax-api:1.0.1


Anyone else experiencing the same?

Thanks,
Sirisha

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may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

Re: [Soaplab-users] SOAPLab2 - EBI

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

Hi Guillaume,

> I'm looking to interface primer3 in webservice, but when you launch
> the program, this one generates some files...how can I catch this
> results?

>  How can I choose a directory to generate these files, because they
> are generated in tha catalina home...

Did you mean, in directory "${catalina.base}/temp/_R_" ? this is the
default working directory Soaplab uses if users didn't configure their
Soaplab installation by a customised soaplab.properties file.

Relevant Soaplab properties 'working.dir' and 'results.dir' are
explained in Soaplab Configuration Guide.

http://soaplab.sourceforge.net/soaplab2/ConfigurationGuide.html#properties

Soaplab creates a new folder for each job under the 'working.dir'
directory and all job outputs should normally be under that folder.
Collection of these outputs should normally be done by defining
appropriate output types as described in Soaplab Metadata Guide.

http://soaplab.sourceforge.net/soaplab2/MetadataGuide.html#outfiles

EMBOSS has a wrapper for primer3 called eprimer3? You may find it useful
to check how EMBOSS calls eprimer3. I copied below a link to EBI
eprimer3 web service based on Soaplab.

http://www.ebi.ac.uk/soaplab/typed/services/nucleic_primers.eprimer3?wsdl

Regards,
Mahmut

Re: [Soaplab-users] SOAPLab2 - EBI

[Guillaume C. <gco...@gm...>]

Dear all,

I'm looking to interface primer3 in webservice, but when you launch the
program, this one generates some files...how can I catch this results? How
can I choose a directory to generate these files, because they are generated
in tha catalina home...

Best reagards,
GC.

[Soaplab-users] EBI Soaplab Server upgrade

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

Hi,

We are planing to upgrade EBI Soaplab Server to the latest Soaplab
(2.2.0) and EMBOSS (6.1.0). The upgrade will normally take place this
Wednesday afternoon. Since we have two server nodes Soaplab server
should still be reachable during the upgrade process as the nodes will
be upgraded one by one. There is no API changes in Soaplab except
addition of few more methods to the typed interface. There are also few
changes in EMBOSS application parameter names, most in EMBASSY programs.

Regards,
Mahmut

[Soaplab-users] announcement: Soaplab2 - released new version 2.2.0

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

Dear Soaplab users,

The new version was released.

Project: Soaplab  (soaplab)
Package: soaplab2
Date   : 2009-06-26 21:49

Project "Soaplab" ('soaplab') has released the new version of package
'soaplab2'.
You can download it from SourceForge.net by following this link:
<
https://sourceforge.net/project/showfiles.php?group_id=104834&release_id=692718
>
or browse Release Notes and ChangeLog by visiting this link:
<https://sourceforge.net/project/shownotes.php?release_id=692718>


We will appreciate any feedback and bug reports.

Cheers,
Martin

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