soaplab-users — Forum for Soaplab users and developers

Re: [Soaplab-users] Soaplab2, WSDLs and third-party clients

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

>> Soaplab use the following line of code to find out name of the service
>> called.
>>
>>  String serviceName = StringUtils.substringAfterLast (requestURI, "/");
>>
>> service names should normally include group name as well. for example
>> when using the default helloworld service it should be
>> "classic.helloworld".
> 
> Success! Thanks :-)
> 
> Have a good weekend,
> 
> Andrew.

Hi,
I have the same problem than you had but I cannot get success.
I can only use AnalysisList because some of its functions do not need 
arguments.


With SoapUI, if I want to run 'getCharacteristics' how do you pass 
'classic.helloworld' ?

Where should I write 'classic.helloworld' ? It does not work between 
arg0 tags for me.

<soapenv:Envelope 
xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" 
xmlns:org="http://org.soaplab.2">
    <soapenv:Header/>
    <soapenv:Body>
       <org:getCharacteristics>
          <!--Optional:-->
          <arg0></arg0>
       </org:getCharacteristics>
    </soapenv:Body>
</soapenv:Envelope>


And with perl SOAP::Lite
my $client = 
SOAP::Lite->service('http://localhost:8080/soaplab2/services?wsdl');

$client->getCharacteristics();

How to pass 'classic.helloworld' ?


Thanks

-- 
Sébastien Moretti

Re: [Soaplab-users] Program with return code non zero

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

>>>> I have a program which returns -1 as success code (instead of 0).
>>>>
>>>> How can I use it in soaplab ?
>>> Wrap it in a shell script that adds 1 to its return code?
>>>
>>> Andrew.
>> It is maybe the best thing to do, because change accept.any.exitcode 
>> property could have some bad side effects.
> 
> You should be able to use this setting specific to your service. For
> example, for service edit.seqret, the full property name should be
> edit.seqret.accept.any.exitcode.
> 
> Regards,
> Mahmut

Good to know !
Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221

Re: [Soaplab-users] Program with return code non zero

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

> >> I have a program which returns -1 as success code (instead of 0).
> >>
> >> How can I use it in soaplab ?
> > 
> > Wrap it in a shell script that adds 1 to its return code?
> > 
> > Andrew.
> 
> It is maybe the best thing to do, because change accept.any.exitcode 
> property could have some bad side effects.

You should be able to use this setting specific to your service. For
example, for service edit.seqret, the full property name should be
edit.seqret.accept.any.exitcode.

Regards,
Mahmut

Re: [Soaplab-users] Program with return code non zero

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

>> Hi,
>>
>> I have a program which returns -1 as success code (instead of 0).
>>
>> How can I use it in soaplab ?
> 
> Wrap it in a shell script that adds 1 to its return code?
> 
> Andrew.

It is maybe the best thing to do, because change accept.any.exitcode 
property could have some bad side effects.

Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221

Re: [Soaplab-users] Program with return code non zero

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

> I have a program which returns -1 as success code (instead of 0).
>
> How can I use it in soaplab ?
>

Set the property "accept.any.exitcode" to true, either by putting into
soaplab.properties this line:

accept.any.exitcode

or this line:

accept.any.exitcode = true

More about various properties (including this one) can be found in
http://soaplab.sourceforge.net/soaplab2/ConfigurationGuide.html.

Martin

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

Re: [Soaplab-users] Program with return code non zero

[Andrew C. <cl...@bi...>]

2008/6/19 Sebastien Moretti <Seb...@un...>:
> Hi,
>
> I have a program which returns -1 as success code (instead of 0).
>
> How can I use it in soaplab ?

Wrap it in a shell script that adds 1 to its return code?

Andrew.

[Soaplab-users] Program with return code non zero

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

Hi,

I have a program which returns -1 as success code (instead of 0).

How can I use it in soaplab ?


I get this error message:
Summary:
	Completed: Erroneously
	Termination status: -1
	Ended:     2008-Jun-19 16:32:25 (CEST)
Report:
Not able to execute an external program ...
...


Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221

Re: [Soaplab-users] Soaplab2, WSDLs and third-party clients

[Andrew C. <cl...@bi...>]

On Friday 06 June 2008 15:41, Mahmut Uludag wrote:
>
> Soaplab use the following line of code to find out name of the service
> called.
>
>  String serviceName = StringUtils.substringAfterLast (requestURI, "/");
>
> service names should normally include group name as well. for example
> when using the default helloworld service it should be
> "classic.helloworld".

Success! Thanks :-)

Have a good weekend,

Andrew.

Re: [Soaplab-users] Soaplab2, WSDLs and third-party clients

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

> I'm still not clear about how to access *specific* services 
> (e.g. helloworld) via that generic interface definition.
> 
> If I load up that WSDL in SoapUI, and create a new 'describe' request for 
> example, there's no parameter into which I can put the name of the service 
> I want to describe -- so how does Soaplab know *which* service I want to 
> get the description for? (Or run any other method on...)

Soaplab use the following line of code to find out name of the service
called.

 String serviceName = StringUtils.substringAfterLast (requestURI, "/");

service names should normally include group name as well. for example
when using the default helloworld service it should be
"classic.helloworld".

Regards,
Mahmut

Re: [Soaplab-users] Soaplab2, WSDLs and third-party clients

[Andrew C. <cl...@bi...>]

On Friday 06 June 2008 15:04, Mahmut Uludag wrote:
>
> not sure I understood you correctly but if you are looking for the
> replacement url in the WSDL file of the Analysis service it is
> "http://localhost:8080/soaplab2/services" in my dynamically generated
> WSDL file (which I can access using the following url of my local
> server)
>
> http://localhost:8080/soaplab2/services?wsdl

Okay -- I didn't realise you could access the WSDL dynamically like that, 
thanks. But I'm still not clear about how to access *specific* services 
(e.g. helloworld) via that generic interface definition.

If I load up that WSDL in SoapUI, and create a new 'describe' request for 
example, there's no parameter into which I can put the name of the service 
I want to describe -- so how does Soaplab know *which* service I want to 
get the description for? (Or run any other method on...)

And if I run 'describe' without any parameters, I still get the same error 
message as when I loaded the WSDL file locally:


<S:Envelope xmlns:S="http://schemas.xmlsoap.org/soap/envelope/">
   <S:Body>
      <S:Fault xmlns:ns3="http://www.w3.org/2003/05/soap-envelope">
         <faultcode>S:Server</faultcode>
         <faultstring>Unknown service 'services'</faultstring>
         <detail>
            <ns2:SoaplabException xmlns:ns2="http://org.soaplab.2" 
xmlns:ns3="http://services.soaplab.org/">
               <message>Unknown service 'services'</message>
            </ns2:SoaplabException>
            <ns2:exception class="org.soaplab.share.SoaplabException" 
note="To disable this feature, set 
com.sun.xml.ws.fault.SOAPFaultBuilder.disableCaptureStackTrace system 
property to false" xmlns:ns2="http://jax-ws.dev.java.net/">
               <message>Unknown service 'services'</message>
               <ns2:stackTrace>
                  <ns2:frame 
class="org.soaplab.services.metadata.MetadataAccessorXML" 
file="MetadataAccessorXML.java" line="118" method="&lt;init>"/>
                  <!-- blah blah blah -->
                  <ns2:frame class="java.lang.Thread" file="Thread.java" 
line="619" method="run"/>
               </ns2:stackTrace>
            </ns2:exception>
         </detail>
      </S:Fault>
   </S:Body>
</S:Envelope>


Just to experiment, I tried changing the WSDL location to:

http://localhost:8080/soaplab2/services/helloworld?wsdl

and this did indeed give me a valid WSDL. However, calling 'describe' still 
resulted in the same exception (whether I changed the endpoint to 
services/helloworld or kept it as just services).

Forgive me if I've missed something obvious -- I'm new to webservices in 
Java, having only done them in C# and (to a lesser extent) Perl before...

Thanks for your help,

Andrew.

Re: [Soaplab-users] Soaplab2, WSDLs and third-party clients

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

> Not really sure what I'm doing 
> with Analysis.wsdl though, to be honest.
> 
> If I put the name of a specific service in there 
> (e.g. /soaplab2/services/helloworld) I get "unknown service 'helloworld'".

not sure I understood you correctly but if you are looking for the
replacement url in the WSDL file of the Analysis service it is
"http://localhost:8080/soaplab2/services" in my dynamically generated
WSDL file (which I can access using the following url of my local
server)

http://localhost:8080/soaplab2/services?wsdl

Regards,
Mahmut

Re: [Soaplab-users] Soaplab2, WSDLs and third-party clients

[Andrew C. <cl...@bi...>]

On Thursday 05 June 2008 17:14, Mahmut Uludag wrote:
>
> if I look at how jaxws replaces the same string in the dynamic wsdl it
> generates
>
> http://localhost:8080/soaplab2/services/list?wsdl
>
> i found it is replaced by "http://localhost:8080/soaplab2/services/list"
>
> you may try appending "/list" to your replacement url

Okay, that works for AnalysisList.wsdl, thanks. Not really sure what I'm doing 
with Analysis.wsdl though, to be honest.

If I put the name of a specific service in there 
(e.g. /soaplab2/services/helloworld) I get "unknown service 'helloworld'".

This is despite the fact that I haven't changed any defaults, and my web.xml 
in Tomcat says:

  <!-- Soaplab2 all other services -->
  <servlet-mapping>
    <servlet-name>soaplab2</servlet-name>
    <url-pattern>/services/*</url-pattern>
  </servlet-mapping>

which suggests to me that /soaplab2/services/helloworld should work.

(These are just calling the describe method, nothing with parameters yet.)

Am I missing something? Do I need to do something else to let Tomcat or 
Soaplab know which URLs relate to which services?

Thanks again,

Andrew.

Re: [Soaplab-users] Soaplab2, WSDLs and third-party clients

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

> However, what I really need to do is ensure that I can consume Soaplab2 
> services in other clients. So I got the WSDL files in src/etc/wsdl and edited 
> them to have
> 
> http://localhost:8080/soaplab2/services
> 
> instead of REPLACE_WITH_ACTUAL_URL.


if I look at how jaxws replaces the same string in the dynamic wsdl it
generates

http://localhost:8080/soaplab2/services/list?wsdl

i found it is replaced by "http://localhost:8080/soaplab2/services/list"

you may try appending "/list" to your replacement url

Regards,
Mahmut

[Soaplab-users] Soaplab2, WSDLs and third-party clients

[Andrew C. <cl...@bi...>]

Hi everyone,

I'm a brand-new Soaplab user so apologies if I've missed something obvious 
here, but I've looked through the website and Google and haven't found any 
solutions.

I've installed Soaplab2 and gone through the instructions in the first part 
of "Soaplab 2: Step by Step" successfully. So, I can connect to

http://localhost:8080/soaplab2/

and see all the standard services supplied with the system, and get sensible 
results out.

However, what I really need to do is ensure that I can consume Soaplab2 
services in other clients. So I got the WSDL files in src/etc/wsdl and edited 
them to have

http://localhost:8080/soaplab2/services

instead of REPLACE_WITH_ACTUAL_URL.

I then downloaded SoapUI to test them with (http://soapui.org/) and loaded up 
AnalysisList.wsdl, and it correctly parsed the service definitions and gave 
me request templates for each of them. However, I can't get anything out 
except faults. For example, when I try to call getAvailableAnalyses with the 
following request:

<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" 
xmlns:org="http://org.soaplab.2">
   <soapenv:Header/>
   <soapenv:Body>
      <org:getAvailableAnalyses/>
   </soapenv:Body>
</soapenv:Envelope>

I just get this response:

<S:Envelope xmlns:S="http://schemas.xmlsoap.org/soap/envelope/">
   <S:Body>
      <S:Fault xmlns:ns3="http://www.w3.org/2003/05/soap-envelope">
         <faultcode>S:Client</faultcode>
         <faultstring>Cannot find dispatch method for 
{http://org.soaplab.2}getAvailableAnalyses</faultstring>
      </S:Fault>
   </S:Body>
</S:Envelope>

What am I doing wrong? I know it's not a SoapUI-specific fault because the 
same thing happens when I try to call methods with the Perl module SOAP::WSDL 
too. wsdl2perl.pl generates client proxy classes quite happily, with no 
errors, but I just get the same exceptions about missing dispatch methods.

I'd really appreciate any suggestions you can throw my way because Soaplab2 
looks like exactly what we need for this project (exposing various analytical 
processes from the CATH database).

Thanks in advance,

Dr Andrew Clegg
CATH Group
Research Dept. of Structural & Molecular Biology
University College London
http://cathdb.info/

Re: [Soaplab-users] Fwd: [SourceForge.net Release] soaplab2 - 2.1.1 released

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

Thanks for your enquiry. But I am a bit confused I must admit - because...

This is the error message I refer to-
> The following error occurred while executing this line:
> /home/myhomedir/soaplab2/xmls/maven.xml:48: Can't get
> http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar to
> /home/myhomedir/soaplab2/lib/maven-ant-tasks-2.0.8.jar


...in the new Soaplab2 release there is no place where the "
http://apache.hoxt.com/"<http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar>server
is used. Or it should not be. It was replaced by the server open-bio
(you should see it in xmls/maven.xml -  http://biomoby.org/jmoby-jars). The
replacement was made because on the new server we can keep the old versions
of maven-ant-task library as long as we want. Therefore, I am not sure why
you see still the message above...

Martin

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

Re: [Soaplab-users] Fwd: [SourceForge.net Release] soaplab2 - 2.1.1 released

[cajela <ca...@gm...>]

Hi Martin et al,

Thanks for the announcement. I assume this also includes the file
formerly at http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar?
I see it's now 2.0.9 up on that page. I discovered this when I tried a
rebuild. (I was tweaking my emboss install as spinet was failing to
see the database info, but that's another thing).

May I suggest that you amend the error message from the build to
indicate that it's a probably an update issue?  Or perhaps maintain
the old version for a month or two?

This is the error message I refer to-
The following error occurred while executing this line:
/home/myhomedir/soaplab2/xmls/maven.xml:48: Can't get
http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar to
/home/myhomedir/soaplab2/lib/maven-ant-tasks-2.0.8.jar

thanks,
Cath

2008/5/17 Martin Senger <mar...@gm...>:
> FYI...
> Martin
>
> ---------- Forwarded message ----------
> From: SourceForge.net <no...@so...>
> Date: Sat, May 17, 2008 at 12:00 AM
> Subject: [SourceForge.net Release] soaplab : soaplab2
> To: no...@so...
>
>
> Project: Soaplab  (soaplab)
> Package: soaplab2
> Date   : 2008-05-16 23:00
>
> 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=599721
>>
> or browse Release Notes and ChangeLog by visiting this link:
> <https://sourceforge.net/project/shownotes.php?release_id=599721>
-- 
Cath Lawrence --- cajela at gmail dot com
http://thecanberracook.blogspot.com

Re: [Soaplab-users] BUILD FAILED

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

>> since last 'cvs -dP update' (this morning), I cannot run 'ant install' 
>> or 'ant jaxdeploy' without an error:
>>
>> BUILD FAILED
>> /opt/soaplab2/xmls/jaxws.xml:95: The following error occurred while 
>> executing this line:
>> /opt/soaplab2/build.xml:212: Compile failed; see the compiler error 
>> output for details.
>>
>> Here is the full log file.
>>
>> What is this ?
> 
> it looks like a CVS merge problem, best to delete
> the /opt/soaplab2/src/main/org/soaplab/services/JobManager.java file and
> call cvs-update again. (backup the Java file before deleting if you
> think you might have your changes in it)
> 
> Mahmut

It's perfect.

Thanks

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221

Re: [Soaplab-users] BUILD FAILED

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

> since last 'cvs -dP update' (this morning), I cannot run 'ant install' 
> or 'ant jaxdeploy' without an error:
> 
> BUILD FAILED
> /opt/soaplab2/xmls/jaxws.xml:95: The following error occurred while 
> executing this line:
> /opt/soaplab2/build.xml:212: Compile failed; see the compiler error 
> output for details.
> 
> Here is the full log file.
> 
> What is this ?

it looks like a CVS merge problem, best to delete
the /opt/soaplab2/src/main/org/soaplab/services/JobManager.java file and
call cvs-update again. (backup the Java file before deleting if you
think you might have your changes in it)

Mahmut

[Soaplab-users] BUILD FAILED

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

Hi,

since last 'cvs -dP update' (this morning), I cannot run 'ant install' 
or 'ant jaxdeploy' without an error:

BUILD FAILED
/opt/soaplab2/xmls/jaxws.xml:95: The following error occurred while 
executing this line:
/opt/soaplab2/build.xml:212: Compile failed; see the compiler error 
output for details.

Here is the full log file.

What is this ?

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221

[Soaplab-users] Fwd: [SourceForge.net Release] soaplab2 - 2.1.1 released

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

FYI...
Martin

---------- Forwarded message ----------
From: SourceForge.net <no...@so...>
Date: Sat, May 17, 2008 at 12:00 AM
Subject: [SourceForge.net Release] soaplab : soaplab2
To: no...@so...


Project: Soaplab  (soaplab)
Package: soaplab2
Date   : 2008-05-16 23:00

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=599721
>
or browse Release Notes and ChangeLog by visiting this link:
<https://sourceforge.net/project/shownotes.php?release_id=599721>



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

Re: [Soaplab-users] [Fwd: Re: [EMBOSS] How to use toggle properly ?]

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

Hi Sebastien,

> Now I can get a syntax in ACD where a toggle "data type" controls the 
> use of a string data type (with EMBOSS acd tools).
> 
> I cannot get the same kind of behaviour, an attribute controls the use 
> of another one on the http://localhost:8080/soaplab2/ application page.

This should be normal, as I'm aware current Spinet doesn't support it
(an attribute controls the use of another one).

Regards,
Mahmut

Re: [Soaplab-users] [Fwd: Re: [EMBOSS] How to use toggle properly ?]

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

> Hi Sebastien,

Hi Mahmut,

>> Now, cons and symbcons seem to work independently.
> 
> I read your related posts here and in the EMBOSS email list but not able
> to follow all discussed. Based on what you stated above can I assume
> this issue is resolved?

It is not resolved.

Now I can get a syntax in ACD where a toggle "data type" controls the 
use of a string data type (with EMBOSS acd tools).

I cannot get the same kind of behaviour, an attribute controls the use 
of another one on the http://localhost:8080/soaplab2/ application page.
Maybe it works with command line clients ?

-- 
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221

Re: [Soaplab-users] min & max

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

> Hi Sebastien,

Hi Mahmut

>> I use minlength/maxlength for strings and minimum/maximum for floats and 
>> integers.
>> They appear in xml generated file but don't seem to be used on the 
>> http://localhost:8080/soaplab2/ page in applications.
> 
> I have checked in javascript validation for the minimum/maximum values
> of numeric inputs. However there is a problem in passing the
> minlength/maxlength attribute values to the XML metadata files that
> doesn't allow similar validation for strings. I will discuss this with
> Martin and hopefully in the coming release we will have
> minlength/maxlength validation support as well.

It could be useful for tests to activate minlength/maxlength (strings) 
and minimum/maximum (floats & integers) checks.

But the most important is that these checks are activated with the 
client. I have not tested it yet.

Thanks

-- 
Sébastien Moretti
SIB, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221

Re: [Soaplab-users] [Fwd: Re: [EMBOSS] How to use toggle properly ?]

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

Hi Sebastien,

> Now, cons and symbcons seem to work independently.

I read your related posts here and in the EMBOSS email list but not able
to follow all discussed. Based on what you stated above can I assume
this issue is resolved?

Regards,
Mahmut

Re: [Soaplab-users] min & max

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

Hi Sebastien,

> I use minlength/maxlength for strings and minimum/maximum for floats and 
> integers.
> They appear in xml generated file but don't seem to be used on the 
> http://localhost:8080/soaplab2/ page in applications.

I have checked in javascript validation for the minimum/maximum values
of numeric inputs. However there is a problem in passing the
minlength/maxlength attribute values to the XML metadata files that
doesn't allow similar validation for strings. I will discuss this with
Martin and hopefully in the coming release we will have
minlength/maxlength validation support as well.

Regards,
Mahmut