soaplab-users — Forum for Soaplab users and developers

[Soaplab-users] embl.ebi.utils.GException: Child POA creation failed

[Tim T. <tim...@ed...>]

Hi,

I have soaplab installed locally. I start soaplab from the  
commandline using:

./run-AppLab-server&

I check the terminal used to issue this command every day or so. Most  
days I see the following exception listed:

[Prg] Something wrong in unknown_adapter():  
embl.ebi.utils.GException: Child POA creation failed.  
org.omg.PortableServer.POAPackage.AdapterAlreadyExists: IDL:omg.org/ 
PortableServer/POA/AdapterAlreadyExists:1.0

Is there something wrong with my set up?

Can I safely ignore this message?

Thanks, Tim

RE: [Soaplab-users] Output Formats

[Marc L. <Mar...@DE...>]

Hi Tim,
Martin, correct me if I'm wrong, but currently this is not possible.
A workaround is that you hardcode the rformat to gff in the fuzznuc.acd
file. In that way the default will be gff (good for soaplab) but it can
be overridden at the command line by setting the rformat explicitely in
case gff is not appropriate (extra typing, but one can live with that
;-).
HTH,
Marc


> Hi,
>=20
> When running EMBOSS tools  directly from the command-line I=20
> can in many cases specify the output format via the -rformat2=20
> or osformat2 switch.
>=20
> However I notice that I cannot specify the output format for=20
> many of the EMBOSS services wrapped by Soaplab. In particular=20
> I am intersted in having fuzznuc output GFF format files=20
> instead of the default seqtable format.
>=20
> Is there anyway to achieve this?
>=20
> I am co-ordinating the execution of these Soaplab services=20
> through Taverna and no input is specified for output format=20
> in many cases.
>=20
> Thanks, Tim
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> Soaplab-users mailing list
> Soa...@li...
> https://lists.sourceforge.net/lists/listinfo/soaplab-users
>=20

[Soaplab-users] Output Formats

[Tim T. <Tim...@ed...>]

Hi,

When running EMBOSS tools  directly from the command-line I can in  
many cases specify the output format via the -rformat2 or osformat2  
switch.

However I notice that I cannot specify the output format for many of  
the EMBOSS services wrapped by Soaplab. In particular I am intersted  
in having fuzznuc output GFF format files instead of the default  
seqtable format.

Is there anyway to achieve this?

I am co-ordinating the execution of these Soaplab services through  
Taverna and no input is specified for output format in many cases.

Thanks, Tim

Re: [Soaplab-users] SoaplabException: Cannot create a DB connection

[Martin S. <se...@eb...>]

> I recently had a scan through my catalina.out file in my tomcat logs  
> and noticed a huge number of "Cannot create a DB connection"  
> exceptions. I have attached a typical stack trace below.
> 
> Is this normal? or is there something wrong with my Soaplab  
> installation?
>
   It should not be there, but it is not your fault. It is an old bug that
I have not fixed. I hope to look at it soon. I will post it here when it's
done. Thanks for reporting it.

   Cheers,
   Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

[Soaplab-users] SoaplabException: Cannot create a DB connection

[Tim T. <Tim...@ed...>]

Hi,

I recently had a scan through my catalina.out file in my tomcat logs  
and noticed a huge number of "Cannot create a DB connection"  
exceptions. I have attached a typical stack trace below.

Is this normal? or is there something wrong with my Soaplab  
installation?

The reason I ask is because I have a number of Taverna workflows  
which use soaplab services. Quite frequently these workflows will  
fail to complete normally. At first I suspected there may be a bug in  
the Taverna/Freefluo software but when I saw the number of these  
stack traces in my catalina log I began to suspect that perhaps I had  
failed tos et up Soaplab correctly.

Any advice would be greatly appreciated.

Thanks, Tim

PS: When I set up Soaplab I chose not to set up a mysql database to  
store data.


org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in setJob/applab).
         at  
org.embl.ebi.SoaplabServer.applab.PersistenceAppLabImpl.setJob 
(PersistenceAppLabImpl.java:117)
         at  
org.embl.ebi.SoaplabServer.applab.JobAppLab.connectToAppLab 
(JobAppLab.java:212)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab.<init> 
(JobAppLab.java:115)
         at  
org.embl.ebi.SoaplabServer.applab.JobManagerAppLab.createJob 
(JobManagerAppLab.java:65)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.createAndRun 
(AnalysisWSAppLabImpl.java:594)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.createAndRun 
(AnalysisWSAppLabImpl.java:591)
         at sun.reflect.GeneratedMethodAccessor73.invoke(Unknown Source)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke 
(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:585)
         at org.apache.axis.providers.java.RPCProvider.invokeMethod 
(RPCProvider.java:388)
         at org.apache.axis.providers.java.RPCProvider.processMessage 
(RPCProvider.java:283)
         at org.apache.axis.providers.java.JavaProvider.invoke 
(JavaProvider.java:323)
         at org.apache.axis.strategies.InvocationStrategy.visit 
(InvocationStrategy.java:32)
         at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
         at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
         at org.apache.axis.handlers.soap.SOAPService.invoke 
(SOAPService.java:453)
         at org.apache.axis.server.AxisServer.invoke(AxisServer.java: 
281)
         at org.apache.axis.transport.http.AxisServlet.doPost 
(AxisServlet.java:699)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
         at org.apache.axis.transport.http.AxisServletBase.service 
(AxisServletBase.java:327)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
         at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter 
(ApplicationFilterChain.java:252)
         at org.apache.catalina.core.ApplicationFilterChain.doFilter 
(ApplicationFilterChain.java:173)
         at org.apache.catalina.core.StandardWrapperValve.invoke 
(StandardWrapperValve.java:213)
         at org.apache.catalina.core.StandardContextValve.invoke 
(StandardContextValve.java:178)
         at org.apache.catalina.core.StandardHostValve.invoke 
(StandardHostValve.java:126)
         at org.apache.catalina.valves.ErrorReportValve.invoke 
(ErrorReportValve.java:105)
         at org.apache.catalina.core.StandardEngineValve.invoke 
(StandardEngineValve.java:107)
         at org.apache.catalina.connector.CoyoteAdapter.service 
(CoyoteAdapter.java:148)
         at org.apache.coyote.http11.Http11Processor.process 
(Http11Processor.java:856)
         at org.apache.coyote.http11.Http11Protocol 
$Http11ConnectionHandler.processConnection(Http11Protocol.java:744)
         at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket 
(PoolTcpEndpoint.java:527)
         at  
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt 
(LeaderFollowerWorkerThread.java:80)
         at org.apache.tomcat.util.threads.ThreadPool 
$ControlRunnable.run(ThreadPool.java:684)
         at java.lang.Thread.run(Thread.java:613)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in getResult).
         at  
org.embl.ebi.SoaplabServer.PersistenceManagerImpl.getResult 
(PersistenceManagerImpl.java:246)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab.getResults 
(JobAppLab.java:647)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.getSomeResults 
(AnalysisWSAppLabImpl.java:769)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.getSomeResults 
(AnalysisWSAppLabImpl.java:768)
         at sun.reflect.GeneratedMethodAccessor77.invoke(Unknown Source)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke 
(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:585)
         at org.apache.axis.providers.java.RPCProvider.invokeMethod 
(RPCProvider.java:388)
         at org.apache.axis.providers.java.RPCProvider.processMessage 
(RPCProvider.java:283)
         at org.apache.axis.providers.java.JavaProvider.invoke 
(JavaProvider.java:323)
         at org.apache.axis.strategies.InvocationStrategy.visit 
(InvocationStrategy.java:32)
         at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
         at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
         at org.apache.axis.handlers.soap.SOAPService.invoke 
(SOAPService.java:453)
         at org.apache.axis.server.AxisServer.invoke(AxisServer.java: 
281)
         at org.apache.axis.transport.http.AxisServlet.doPost 
(AxisServlet.java:699)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
         at org.apache.axis.transport.http.AxisServletBase.service 
(AxisServletBase.java:327)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
         at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter 
(ApplicationFilterChain.java:252)
         at org.apache.catalina.core.ApplicationFilterChain.doFilter 
(ApplicationFilterChain.java:173)
         at org.apache.catalina.core.StandardWrapperValve.invoke 
(StandardWrapperValve.java:213)
         at org.apache.catalina.core.StandardContextValve.invoke 
(StandardContextValve.java:178)
         at org.apache.catalina.core.StandardHostValve.invoke 
(StandardHostValve.java:126)
         at org.apache.catalina.valves.ErrorReportValve.invoke 
(ErrorReportValve.java:105)
         at org.apache.catalina.core.StandardEngineValve.invoke 
(StandardEngineValve.java:107)
         at org.apache.catalina.connector.CoyoteAdapter.service 
(CoyoteAdapter.java:148)
         at org.apache.coyote.http11.Http11Processor.process 
(Http11Processor.java:856)
         at org.apache.coyote.http11.Http11Protocol 
$Http11ConnectionHandler.processConnection(Http11Protocol.java:744)
         at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket 
(PoolTcpEndpoint.java:527)
         at  
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt 
(LeaderFollowerWorkerThread.java:80)
         at org.apache.tomcat.util.threads.ThreadPool 
$ControlRunnable.run(ThreadPool.java:684)
         at java.lang.Thread.run(Thread.java:613)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in localize).
         at org.embl.ebi.SoaplabServer.PersistenceManagerImpl.localize 
(PersistenceManagerImpl.java:485)
         at  
org.embl.ebi.SoaplabServer.applab.PersistenceAppLabImpl.localize 
(PersistenceAppLabImpl.java:148)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab 
$ResultFetcherThread.run(JobAppLab.java:1003)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in setResults).
         at  
org.embl.ebi.SoaplabServer.PersistenceManagerImpl.setResults 
(PersistenceManagerImpl.java:345)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab 
$ResultFetcherThread.run(JobAppLab.java:999)

org.embl.ebi.SoaplabShare.SoaplabException: Cannot create a DB  
connection (in removeJob).
         at  
org.embl.ebi.SoaplabServer.PersistenceManagerImpl.removeJob 
(PersistenceManagerImpl.java:136)
         at org.embl.ebi.SoaplabServer.applab.JobAppLab.destroy 
(JobAppLab.java:711)
         at org.embl.ebi.SoaplabServer.JobManager.removeJob 
(JobManager.java:56)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.destroy 
(AnalysisWSAppLabImpl.java:790)
         at  
org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl.destroy 
(AnalysisWSAppLabImpl.java:788)
         at sun.reflect.GeneratedMethodAccessor78.invoke(Unknown Source)
         at sun.reflect.DelegatingMethodAccessorImpl.invoke 
(DelegatingMethodAccessorImpl.java:25)
         at java.lang.reflect.Method.invoke(Method.java:585)
         at org.apache.axis.providers.java.RPCProvider.invokeMethod 
(RPCProvider.java:388)
         at org.apache.axis.providers.java.RPCProvider.processMessage 
(RPCProvider.java:283)
         at org.apache.axis.providers.java.JavaProvider.invoke 
(JavaProvider.java:323)
         at org.apache.axis.strategies.InvocationStrategy.visit 
(InvocationStrategy.java:32)
         at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
         at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
         at org.apache.axis.handlers.soap.SOAPService.invoke 
(SOAPService.java:453)
         at org.apache.axis.server.AxisServer.invoke(AxisServer.java: 
281)
         at org.apache.axis.transport.http.AxisServlet.doPost 
(AxisServlet.java:699)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
         at org.apache.axis.transport.http.AxisServletBase.service 
(AxisServletBase.java:327)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
         at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter 
(ApplicationFilterChain.java:252)
         at org.apache.catalina.core.ApplicationFilterChain.doFilter 
(ApplicationFilterChain.java:173)
         at org.apache.catalina.core.StandardWrapperValve.invoke 
(StandardWrapperValve.java:213)
         at org.apache.catalina.core.StandardContextValve.invoke 
(StandardContextValve.java:178)
         at org.apache.catalina.core.StandardHostValve.invoke 
(StandardHostValve.java:126)
         at org.apache.catalina.valves.ErrorReportValve.invoke 
(ErrorReportValve.java:105)
         at org.apache.catalina.core.StandardEngineValve.invoke 
(StandardEngineValve.java:107)
         at org.apache.catalina.connector.CoyoteAdapter.service 
(CoyoteAdapter.java:148)
         at org.apache.coyote.http11.Http11Processor.process 
(Http11Processor.java:856)
         at org.apache.coyote.http11.Http11Protocol 
$Http11ConnectionHandler.processConnection(Http11Protocol.java:744)
         at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket 
(PoolTcpEndpoint.java:527)
         at  
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt 
(LeaderFollowerWorkerThread.java:80)
         at org.apache.tomcat.util.threads.ThreadPool 
$ControlRunnable.run(ThreadPool.java:684)
         at java.lang.Thread.run(Thread.java:613)

Re: [Soaplab-users] Managing soaplab output data written to disk

[Martin S. <se...@eb...>]

> Eventually this data will be redundant and should be deleted to save  
> disk space. Does soaplab contain any utility to administer this data  
> cache?
>
   Well, yes and no :-)
   Soaplab has two parts: AppLab and classes running within Tomcat. AppLab
is responsible for storing result in the place you notice. For these files
there is no utility provided but the following two-line script will do it:
The following should remove all files that are older than 3 days:

       cd /ebi/extserv/soaplab-work/a
       find ./ type f -and -mtime +3 -exec /bin/rm {} \;

   If you install also mySql (which is optional) then classes within
Tomcat stores results in mySQL and in the same time they clean (at least I
hope so :-)) the AppLab results. For clearing the mySql database there is
a sql script in the soaplab/utils directory (in the Soaplab CVS version).

   Cheers,
   Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

[Soaplab-users] Managing soaplab output data written to disk

[Tim T. <tim...@ed...>]

Hi,

I have successfully setup a soaplab installation locally and  
performed a number of analyses. I notice that the output of these  
analyses gets written to disk usually somewhere within the "a"  
directory. For my install this equates to:

/usr/local/soaplab/analysis-interfaces/a

Eventually this data will be redundant and should be deleted to save  
disk space. Does soaplab contain any utility to administer this data  
cache?

Thanks, Tim

Re: [Soaplab-users] Soaplab error: Can't communicate with the application launcher

[Tim T. <Tim...@ed...>]

Hi,

Thanks for replying so quickly. I recursively changed permissions on / 
usr/local/soaplab/analysis-interfaces/a from 755 to 777 and this  
fixed the issue.

Cheers, Tim


On 4 Nov 2005, at 08:16, Martin Senger wrote:

> Hi,
>> I then configured Taverna to pickup my soaplab install
>>
>    Try your services first from your own machine using a command-line
> clients:
>    cd ...analysis-interfaces
>    ws/run-factory-client -a
>
> Does it work? Or what error message you see here?
>
>> Can't communicate with the application launcher.
>> Problem: java.io.FileNotFoundException: /usr/local/soaplab/analysis-
>> interfaces/a/unknown/Projects/default/Data
>> /PROP1131037271065 (No such file or directory)
>>
>    Check if the scripts (especially the script ALGenLauncher and
> EmbossLauncher) in analysis-interfaces/run has valid first line;  
> meaning
> the perl path there points to an existing perl on your machine.
>    Check if the path /usr/local/soaplab/analysis-interfaces/a/ really
> exists, and if the owner of the Applab process has permission to write
> here.
>
>    Cheers,
>    Martin
>
> -- 
> Martin Senger
>    email: mar...@gm...
>    skype: martinsenger
> consulting for:
>    International Rice Research Institute
>    Biometrics and Bioinformatics Unit
>    DAPO BOX 7777, Metro Manila
>    Philippines, phone: +63-2-580-5600 (ext.2324)
>
>

Re: [Soaplab-users] Soaplab error: Can't communicate with the application launcher

[Martin S. <se...@eb...>]

Hi,
> I then configured Taverna to pickup my soaplab install
>
   Try your services first from your own machine using a command-line
clients:
   cd ...analysis-interfaces
   ws/run-factory-client -a
 
Does it work? Or what error message you see here?

> Can't communicate with the application launcher.
> Problem: java.io.FileNotFoundException: /usr/local/soaplab/analysis- 
> interfaces/a/unknown/Projects/default/Data
> /PROP1131037271065 (No such file or directory)
>
   Check if the scripts (especially the script ALGenLauncher and
EmbossLauncher) in analysis-interfaces/run has valid first line; meaning
the perl path there points to an existing perl on your machine.
   Check if the path /usr/local/soaplab/analysis-interfaces/a/ really
exists, and if the owner of the Applab process has permission to write
here.

   Cheers,
   Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

[Soaplab-users] Soaplab error: Can't communicate with the application launcher

[Tim T. <Tim...@ed...>]

Hi,

I am using soaplab to make a local install of emboss available as web  
services. I followed the guidelines outlined at:

http://www.ebi.ac.uk/soaplab/BinaryGuide.html

and

http://www.ebi.ac.uk/soaplab/ServiceSets.html

I then configured Taverna to pickup my soaplab install. When running  
a simple workflow through Taverna using services installed on my  
soaplab install I get the following error message (see below). Any  
suggestions as to what is causing this would be greatly appreciated.



<workflowReport workflowID="1" workflowStatus="COMPLETE">
   <processorList>
     <processor name="seqret">
       <ServiceFailure TimeStamp="Nov 3, 2005 5:01:11 PM" />
       <ServiceError Message="Soaplab call returned an error :  
Summary:&#xA;&#x9;Completed: Unknown&#xA;&#x9;Te
rmination status: &#xA;Report:&#xA;Can't communicate with the a..."  
TimeStamp="Nov 3, 2005 5:01:11 PM">Soaplab
call returned an error : Summary:
         Completed: Unknown
         Termination status:
Report:
Can't communicate with the application launcher.
Problem: java.io.FileNotFoundException: /usr/local/soaplab/analysis- 
interfaces/a/unknown/Projects/default/Data
/PROP1131037271065 (No such file or directory)
&lt;br&gt;   SoaplabTask.execute(..) : line 151  
&amp;lt;SoaplabTask.java&amp;gt;&lt;br&gt;   ProcessorTask.run
AndGenerateTemplates(..) : line 444  
&amp;lt;ProcessorTask.java&amp;gt;&lt;br&gt;    
ProcessorTask.doInvocationW
ithRetryLogic(..) : line 397  
&amp;lt;ProcessorTask.java&amp;gt;&lt;br&gt;    
ProcessorTask.invokeOnce(..) : lin
e 319 &amp;lt;ProcessorTask.java&amp;gt;&lt;br&gt;    
ProcessorTask.invokeWithoutIteration(..) : line 503 &amp;
lt;ProcessorTask.java&amp;gt;&lt;br&gt;   ProcessorTask.invoke(..) :  
line 251 &amp;lt;ProcessorTask.java&amp;g
t;&lt;br&gt;   ProcessorTask.handleRun(..) : line 199  
&amp;lt;ProcessorTask.java&amp;gt;&lt;br&gt;   NewState$
1.run(..) : line 67 &amp;lt;NewState.java&amp;gt;&lt;br&gt;</ 
ServiceError>
       <Invoking TimeStamp="Nov 3, 2005 5:01:11 PM" />
       <ProcessScheduled TimeStamp="Nov 3, 2005 5:01:10 PM">
         <s:soaplabwsdl xmlns:s="http://org.embl.ebi.escience/xscufl/ 
0.1alpha">http://wilkie226.dmed.ed.ac.uk:8
080/axis/services/edit.seqret</s:soaplabwsdl>
       </ProcessScheduled>
     </processor>
     <processor name="String_Constant">
       <ProcessComplete TimeStamp="Nov 3, 2005 5:01:11 PM" />
       <Invoking TimeStamp="Nov 3, 2005 5:01:11 PM" />
       <ProcessScheduled TimeStamp="Nov 3, 2005 5:01:10 PM">
         <s:stringconstant xmlns:s="http://org.embl.ebi.escience/ 
xscufl/0.1alpha">gb:AC073855</s:stringconstant
 >
       </ProcessScheduled>
     </processor>
   </processorList>
</workflowReport>



Thanks, Tim

RE: [Soaplab-users] "Allowed values" in metadata

[Marc L. <Mar...@DE...>]

> >    The way how to define is the same as for emboss=20
> appliactions. You=20
> > use standard ACD keys for that. For example:
> >=20
> >   values: "20;30;40;50;60;70;80;90;100;110;120;130;140;150"
> >=20
> > will give you allowed values: 20, 30, 40, 50, 60, 70, 80, 90, 100,=20
> > 110, 120, 130, 140, 150. But you have also to say:
> >   min: 1
> >   max: 1
> >=20
> Do you have to set the min and max also for strings ? In my=20
> case, the parameter is of type 'string'.
> Actually, I tried it before, in the way you suggest, except=20
> using a comma instead of a semi colon. But I also added=20
> "delimiter =3D ','" to indicate that.
> Unfortunately I will not be able to test your suggestion immediately.
> I'am stuck in a meating for a whole day. Yikes :-( I'll come=20
> back to you as soon as I've done a few tests.

Wait!
The attributes you mention ("values","minimum" and "maximum") are only
valid for the types "list" and "selection". I was talking about a
parameter of type "string".
Just like you have e.g. the sformat parameter in EMBOSS applications,
which is also of type "string" (at least according to the metadata you
get when you run 'run/run-analysis -name edit.seqret -ii'). According to
ACDParser.pm these attributes are not valid to type "string".
For that reason (see my previous mails) I was trying my luck with
general attributes like "valid" and "expected".

Marc

RE: [Soaplab-users] "Allowed values" in metadata

[Martin S. <se...@eb...>]

> Do you have to set the min and max also for strings ?
>
   Yes. The min and max does not refer to the value itself, but to the
number of values that can be selected from the list.

   Cheers,
   Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

RE: [Soaplab-users] "Allowed values" in metadata

[Marc L. <Mar...@DE...>]

>    The way how to define is the same as for emboss=20
> appliactions. You use standard ACD keys for that. For example:
>=20
>   values: "20;30;40;50;60;70;80;90;100;110;120;130;140;150"
>=20
> will give you allowed values: 20, 30, 40, 50, 60, 70, 80, 90,=20
> 100, 110, 120, 130, 140, 150. But you have also to say:
>   min: 1
>   max: 1
>=20
Do you have to set the min and max also for strings ? In my case, the
parameter is of type 'string'.
Actually, I tried it before, in the way you suggest, except using a
comma instead of a semi colon. But I also added "delimiter =3D ','" to
indicate that.
Unfortunately I will not be able to test your suggestion immediately.
I'am stuck in a meating for a whole day. Yikes :-(
I'll come back to you as soon as I've done a few tests.
Thanks Martin !
Marc

Re: [Soaplab-users] "Allowed values" in metadata

[Martin S. <se...@eb...>]

> How do you define that in the acd for a non emboss application ?
>
   The way how to define is the same as for emboss appliactions. You use
standard ACD keys for that. For example:

  values: "20;30;40;50;60;70;80;90;100;110;120;130;140;150"

will give you allowed values: 20, 30, 40, 50, 60, 70, 80, 90, 100, 110,
120, 130, 140, 150. But you have also to say:
  min: 1
  max: 1

Otherwise, soaplab generates boolean values for individual values (so you
can set more of them to true).

   Cheers,
   Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

RE: [Soaplab-users] "Allowed values" in metadata

[Marc L. <Mar...@DE...>]

>=20
> How do you define that in the acd for a non emboss application ?
> I tried something like:
> Comment: "listvalue =3D item1,item2,item3"
> But that did not do the trick.
> All suggestions welcome !
These also fail:

1) Comment: "allowed_values =3D item1,item2,item3"
 =3D> not even possible to build !
2) Valid: "item1,item2,item3"
3) Expected: "item1,item2,item3"
4) Comment: "allowed =3D item1,item2,item3"

In the latter case, where the comment syntax is followed (comment: "key
=3D val"), the key/val combination shows up when you run run-analysis =
with
the  -ii option. However, it is not shown in the taverna metadata.

Marc

[Soaplab-users] "Allowed values" in metadata

[Marc L. <Mar...@DE...>]

Hi,
When you look at te metadata of an EMBOSS application like e.g. seqret
you can find a list of allowed data for the sformat option.
sformat
Type string
Mandatory false
Allowed  gcg, gcg8, embl, swiss, fasta, ncbi, genbank, nbrf, pir,
codata, strider, clustal, phylip, acedb, msf, jackknifer, jackknifernon,
nexus, nexusnon, treecon, mega, meganon, ig, staden, text, raw

How do you define that in the acd for a non emboss application ?
I tried something like:
Comment: "listvalue =3D item1,item2,item3"
But that did not do the trick.
All suggestions welcome !
Regards,
Marc
=20

RE: [Soaplab-users] Cvs connection refused

[Martin S. <se...@eb...>]

> BTW, a fresh install of soaplab solved my previous issue.
>
   Perfect - I like emails like this :-)
   Cheers, Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

RE: [Soaplab-users] Cvs connection refused

[Marc L. <Mar...@DE...>]

It appeared to be a temporary sourceforge problem.
Everything works fine now. According to Google this seems to happen now =
and then.
BTW, a fresh install of soaplab solved my previous issue.
Tnx.
Regards,
Marc


-----Original Message-----
From: Martin Senger [mailto:se...@eb...]
Sent: Thu 10/13/2005 11:03 PM
To: Marc Logghe
Cc: soa...@li...
Subject: Re: [Soaplab-users] Cvs connection refused
=20
> Is this only me having problems ?
>
   works fine for me (but I am using :ext: access, not an anonymous
:pserver)...

   Martin

--=20
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

Re: [Soaplab-users] Cvs connection refused

[Martin S. <se...@eb...>]

> Is this only me having problems ?
>
   works fine for me (but I am using :ext: access, not an anonymous
:pserver)...

   Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

[Soaplab-users] Cvs connection refused

[Marc L. <Mar...@DE...>]

Is this only me having problems ?
cvs [login aborted]: connect to cvs.sourceforge.net(66.35.250.207):2401
failed: Connection refused

The web site does work but unfortunately the feature of downloading
tarballs is not implemented :-(
Marc

RE: [Soaplab-users] Help! soaplab broken :-(

[Marc L. <Mar...@DE...>]

> > Fault - Could not find class for the service named:
> > org.embl.ebi.SoaplabServer.AnalysisWSAppLabImpl
> >
>    This is a very old class name - and it should not be used=20
> anymore.=20

It has been a while since I have installed soaplab. Must be a year ago
or something.

>I do not know how it happened that you have it at=20
> all :-) The class name should be=20
> org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl. You=20
> said that you were deploying new services - how have you done=20

I still have the binary emboss distribution + the soaplab installation
(both 1 year old).
The first to have the emboss services straight out of the box, the
latter to build packages.
I just followed my SOP I always use to follow:
1) create ACD file
2) build package with build-dev.sh
3) merge service metadata with metadata in EMBOSS distro with
ws/add-services.pl
I don't know all the things that are happening at this step. Anyhow,
what I needed to do after this is manually merging the produced xml
files.
Cos, the EMBOSS distro uses Emboss.xml, the package contains
Applications.xml. No problem so far.
4) ./ws/deploy-web-services -a
5) restart applab server
6) restart tomcat server
No errors so far.
Run-analysis works fine (meaning on applab level all is OK).
But when I want to check via tomcat/axis I get that nasty error message.

What did I do wrong ?=20

Cheers,
Marc

Re: [Soaplab-users] Help! soaplab broken :-(

[Martin S. <se...@eb...>]

> Fault - Could not find class for the service named:
> org.embl.ebi.SoaplabServer.AnalysisWSAppLabImpl
>
   This is a very old class name - and it should not be used anymore. I do
not know how it happened that you have it at all :-) The class name should
be org.embl.ebi.SoaplabServer.applab.AnalysisWSAppLabImpl. You said that
you were deploying new services - how have you done it? From the CVS
soplab local copy or from the binary distribution? Have you updated any of
them recently? If yes, from where?

   Cheers,
   Martin

-- 
Martin Senger
   email: mar...@gm...
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

[Soaplab-users] Help! soaplab broken :-(

[Marc L. <Mar...@DE...>]

Hi,
Don't understand this. Did not change anything related to Tomcat/axis,
honest !
But in the process of deploying new soaplab services I ran into this:

<error>
Sorry, something seems to have gone wrong... here are the details:

Fault - Could not find class for the service named:
org.embl.ebi.SoaplabServer.AnalysisWSAppLabImpl
Hint: you may need to copy your class files/tree into the right location
(which depends on the servlet system you are using).; nested exception
is:=20
	java.lang.ClassNotFoundException:
org.embl.ebi.SoaplabServer.AnalysisWSAppLabImpl

AxisFault
 faultCode:
{http://schemas.xmlsoap.org/soap/envelope/}Server.generalException
 faultSubcode:=20
 faultString: Could not find class for the service named:
org.embl.ebi.SoaplabServer.AnalysisWSAppLabImpl
Hint: you may need to copy your class files/tree into the right location
(which depends on the servlet system you are using).; nested exception
is:=20
	java.lang.ClassNotFoundException:
org.embl.ebi.SoaplabServer.AnalysisWSAppLabImpl
 faultActor:=20
 faultNode:=20
 faultDetail:=20
</error>

This is the error I get when I try to view  the list of deployed Web
services.
This class is in soaplab.jar, right ? It is still there, at the same
place as usual, so why can't axis find it ?
I don't have a clue. Anybody else ?

Marc

RE: [Soaplab-users] Embossdata soaplab service

[Marc L. <Mar...@DE...>]

> But I am afraid I bumped into another 'problem'. I used a=20
> workaround to get to the content of Cut.index. I just copied=20
> it to the web folder so that is fetched by taverna using that=20
> url. OK so far so good, the user can select a codon table and=20
> the resulting string like "Ebacst.cut" is passed to the next=20
> processor. The string value is passed to the cfile_url port=20
> of backtranseq. Unfortunately the execution fails because the=20
> Eacc.cut file can not be found.
> The issue becomes clear when you look at the report and more=20
> precisely at the -cfile argument:
>=20
> Report:
> Name: backtranseq
> Started: 05-09-26 15:48:09
> Program and parameters:
> backtranseq
> /transfer/results/soaplab/unknown/Projects/default/Data/in1127
> 742489009
> /transfer/results/soaplab/unknown/Projects/default/Data/out112
> 7742489011
> -cfile
> /transfer/results/soaplab/unknown/Projects/default/Data/Ebacst.cut
> --- end of parameters
>=20
> As you can see it is not the string "Ebacst.cut" that is=20
> passed as an argument but actually=20
> "/transfer/results/soaplab/unknown/Projects/default/Data/Ebacs
> t.cut", which does not exist. I expected the first behaviour=20
> not the latter. Or am I using it the wrong way ?

I probably did. Just found out you have to give file:Ebacst.cut to the
cfile_url option.
Cheers,
Marc

RE: [Soaplab-users] Embossdata soaplab service

[Marc L. <Mar...@DE...>]

> Marc,
>    I am today (and part of the tomorrow) on email but then I=20
> will travelling to Europe and I am not sure how often I will=20
> be able to read emails. So bear please with me if I am delayed.
No problem.
But I am afraid I bumped into another 'problem'. I used a workaround to
get to the content of Cut.index. I just copied it to the web folder so
that is fetched by taverna using that url. OK so far so good, the user
can select a codon table and the resulting string like "Ebacst.cut" is
passed to the next processor. The string value is passed to the
cfile_url port of backtranseq. Unfortunately the execution fails because
the Eacc.cut file can not be found.
The issue becomes clear when you look at the report and more precisely
at the -cfile argument:

Report:
Name: backtranseq
Started: 05-09-26 15:48:09
Program and parameters:
backtranseq
/transfer/results/soaplab/unknown/Projects/default/Data/in1127742489009
/transfer/results/soaplab/unknown/Projects/default/Data/out1127742489011
-cfile
/transfer/results/soaplab/unknown/Projects/default/Data/Ebacst.cut
--- end of parameters

As you can see it is not the string "Ebacst.cut" that is passed as an
argument but actually
"/transfer/results/soaplab/unknown/Projects/default/Data/Ebacst.cut",
which does not exist. I expected the first behaviour not the latter. Or
am I using it the wrong way ?
Cheers,
Marc