soaplab-users — Forum for Soaplab users and developers

[Soaplab-users] seqretsplit

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

The same kind of question for seqretsplit.

It runs completely but fails to create links to output files.

Should it be disabled ?

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

Re: [Soaplab-users] seqretall, seqretallfeat and seqretset

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

Idem for seqrettype !


> P.S.: seqretallfeat is already disabled !
> 
> 
> Hello,
> 
> It seems that these three software are not available by default in EMBOSS:
> cf. src/ChangeLog
> (Since) Version 2.3.0
> 
>     Seqretall, seqretallfeat and seqretset moved to 'make check'.
>     Seqret has all the functionality of the above.
> 
> 
> You need to make a 'make check' then to copy manually these programs to
> your PATH because 'make install' does not seem to do this.
> 
> 
> So, ACD files for them are with the other ACD files.
> I mean that they become available via soaplab.
> But they cannot be run by default.
> 
> It fails for me locally and it is the same from
> http://www.ebi.ac.uk/soaplab/
> 
> 
> So, should these three programs be disabled in the xmls/emboss.xml file ?
> Else you should add a remark in the Soaplab documentation
> (EmbossNotes.html).
> 
> Best regards
> 


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

Re: [Soaplab-users] undeployment

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

Hi Mahmut,

it is exactly what I need.
It works perfectly and split Soaplab default services from our home made 
services.

Thanks
See you at Uppsala for EMBRACE meeting

P.S.: 	In http://soaplab.sourceforge.net/soaplab2/EmbossNotes.html
	it seems that build/run/run-batch-test should be replaced by
	build/run/run-batch-client

> Hi Sebastien,
> 
> You can move your ACD files to a new folder, for example
> src/etc/acd/project1/ folder under your soaplab2 home directory.
> 
> Then you can call ant similar to the following example to translate your
> ACD files into the XML form Soaplab requires.
> 
>   > ant _gen -Dacd.dir=src/etc/acd/project1/ -Dsl=Project1.xml
> 
> You should remember to disable default sowa applications
> (OtherApplications.xml) in your soaplab.properties file and instead
> should add the Project1.xml file to the applist property.
> 
>   applist = ${metadata.dir}/EBIApplications.xml
> 
> 
> As a side note.
> Instead of modifying the soaplab.properties.template file you may 
> use a customised soaplab.properties file that can be used directly in
> your Soaplab web applications. If in your build.properties file you set
> the my.soaplab.properties property to your customised soaplab.properties
> file, Soaplab will not generate the runtime soaplab.properties file from
> the template but will instead use your customised soaplab.properties
> file.
> 
>   my.soaplab.properties = my.customised.soaplab.properties.file
> 
> However, Soaplab still applies the following transformations when
> copying your customised soaplab.properties file to the class
> directories.
> 
>         <filter token="PROJECT_HOME" value="${basedir.unix}"/>
>         <filter token="METADATA_DIR"
> value="$${base.dir}/metadata/generated"/>
>         <filter token="RUNTIME_DIR"  value="$${base.dir}/_R_"/>
>         <filter token="SCRIPTS_DIR"  value="$${base.dir}/run"/>
>         <filter token="TOMCAT_HOST"  value="${tomcat.host}"/>
>         <filter token="TOMCAT_PORT"  value="${tomcat.port}"/>
> 
> Regards,
> Mahmut
> 
> 
>> I would like to undeploy testing services from my soaplab2 installation.
>>
>> It is quite easy for Gowlab Applications because there is only to 
>> comment the right line in soaplab.properties.template
>>
>>
>> It is more difficult for other testing and examples services (in sowa 
>> and testing directories) because our own applications are located in the 
>> sowa directory.
>> I cannot comment the Other Applications line in 
>> soaplab.properties.template because this will disable our applications.
>>
>> If I remove ACD files for these applications, a CVS update will 
>> re-create them.
>>
>> I have tried to use gen.disabled.apps in build.properties but this 
>> activates disabled applications defined in xmls/emboss.xml
>>
>>
>> We use a script to update soaplab2 source, then to build metadata, then 
>> to deploy soaplab war and to restart tomcat.
>>
>>
>> So, is there a way to disable testing and examples services without 
>> manually editing application list files after every update or restart ?
>> Thanks

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

Re: [Soaplab-users] undeployment

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

Hi Sebastien,

You can move your ACD files to a new folder, for example
src/etc/acd/project1/ folder under your soaplab2 home directory.

Then you can call ant similar to the following example to translate your
ACD files into the XML form Soaplab requires.

  > ant _gen -Dacd.dir=src/etc/acd/project1/ -Dsl=Project1.xml

You should remember to disable default sowa applications
(OtherApplications.xml) in your soaplab.properties file and instead
should add the Project1.xml file to the applist property.

  applist = ${metadata.dir}/EBIApplications.xml


As a side note.
Instead of modifying the soaplab.properties.template file you may 
use a customised soaplab.properties file that can be used directly in
your Soaplab web applications. If in your build.properties file you set
the my.soaplab.properties property to your customised soaplab.properties
file, Soaplab will not generate the runtime soaplab.properties file from
the template but will instead use your customised soaplab.properties
file.

  my.soaplab.properties = my.customised.soaplab.properties.file

However, Soaplab still applies the following transformations when
copying your customised soaplab.properties file to the class
directories.

        <filter token="PROJECT_HOME" value="${basedir.unix}"/>
        <filter token="METADATA_DIR"
value="$${base.dir}/metadata/generated"/>
        <filter token="RUNTIME_DIR"  value="$${base.dir}/_R_"/>
        <filter token="SCRIPTS_DIR"  value="$${base.dir}/run"/>
        <filter token="TOMCAT_HOST"  value="${tomcat.host}"/>
        <filter token="TOMCAT_PORT"  value="${tomcat.port}"/>

Regards,
Mahmut


> I would like to undeploy testing services from my soaplab2 installation.
> 
> It is quite easy for Gowlab Applications because there is only to 
> comment the right line in soaplab.properties.template
> 
> 
> It is more difficult for other testing and examples services (in sowa 
> and testing directories) because our own applications are located in the 
> sowa directory.
> I cannot comment the Other Applications line in 
> soaplab.properties.template because this will disable our applications.
> 
> If I remove ACD files for these applications, a CVS update will 
> re-create them.
> 
> I have tried to use gen.disabled.apps in build.properties but this 
> activates disabled applications defined in xmls/emboss.xml
> 
> 
> We use a script to update soaplab2 source, then to build metadata, then 
> to deploy soaplab war and to restart tomcat.
> 
> 
> So, is there a way to disable testing and examples services without 
> manually editing application list files after every update or restart ?
> Thanks
> 

[Soaplab-users] undeployment

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

Hello,

I would like to undeploy testing services from my soaplab2 installation.

It is quite easy for Gowlab Applications because there is only to 
comment the right line in soaplab.properties.template


It is more difficult for other testing and examples services (in sowa 
and testing directories) because our own applications are located in the 
sowa directory.
I cannot comment the Other Applications line in 
soaplab.properties.template because this will disable our applications.

If I remove ACD files for these applications, a CVS update will 
re-create them.

I have tried to use gen.disabled.apps in build.properties but this 
activates disabled applications defined in xmls/emboss.xml


We use a script to update soaplab2 source, then to build metadata, then 
to deploy soaplab war and to restart tomcat.


So, is there a way to disable testing and examples services without 
manually editing application list files after every update or restart ?
Thanks

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

Re: [Soaplab-users] How to add limits in ACD ?

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

Martin Senger a écrit :
> Hi,
> 
>     I would like to add some limits to user inputs.
> 
> 
> A lot depends of what is the meant by the user inputs. For the examples 
> you mentioned:
>  
> 
>     Max number of sequences
> 
>     Max sequence length
> 
> 
> If these maximums are values of the command-line options, Soaplab should 
> be able to define it in the ACD files. But I am not sure now if this 
> kind of validation was already implemented.
> 
> But it is likely that you think rather about limits of the contents of 
> an input file. One can limit it by writing her/his own data input 
> adapter. But even with an adapter, the original input is transmitted 
> anyway to the Soaplab service - whcih may be what you want to avoid. In 
> such case, Soaplab cannot help - it must be validated on the client size.

What a pity !

>     Max upload size
> 
> 
> The only file uploading in Soaplab2 is in the Spinet web interface. At 
> the moment, it does not provide a property that can limit the size of 
> the uploaded size, but it would be very easy to add it there. It is a 
> good idea, and I will do it (but not in the next two weeks - I will be 
> on a conference and on a vacation in the remote parts of Asia).

I think it should be a good think for security purpose.
Maybe we can do this kind of think via Tomcat parameters.

> Cheers,
> Martin

Best regards
Sébastien

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

Re: [Soaplab-users] How to add limits in ACD ?

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

Hi,

I would like to add some limits to user inputs.


A lot depends of what is the meant by the user inputs. For the examples you
mentioned:


> Max number of sequences

Max sequence length
>

If these maximums are values of the command-line options, Soaplab should be
able to define it in the ACD files. But I am not sure now if this kind of
validation was already implemented.

But it is likely that you think rather about limits of the contents of an
input file. One can limit it by writing her/his own data input adapter. But
even with an adapter, the original input is transmitted anyway to the
Soaplab service - whcih may be what you want to avoid. In such case, Soaplab
cannot help - it must be validated on the client size.


> Max upload size


The only file uploading in Soaplab2 is in the Spinet web interface. At the
moment, it does not provide a property that can limit the size of the
uploaded size, but it would be very easy to add it there. It is a good idea,
and I will do it (but not in the next two weeks - I will be on a conference
and on a vacation in the remote parts of Asia).

Cheers,
Martin

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

[Soaplab-users] How to add limits in ACD ?

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

Hi,

I would like to add some limits to user inputs.
e.g.: 	Max number of sequences
	Max sequence length
	Max upload size
	...

Is there a way to do this ?

Thanks

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

[Soaplab-users] EBI Soaplab services upgrade

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

Hi,

Existing EBI Soaplab services based on Soaplab-1 and EMBOSS-2.8.0 will
be upgraded to Soaplab-2 and EMBOSS-6.0.1 in the coming weeks. If you
are using any of the EBI Soaplab services please test your Soaplab
service calls using the service endpoint below.

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

As one major change, upgraded services will not include legacy 'derived'
services that were part of Soaplab-1. Derived services part of the EBI
Soaplab EMBOSS-4 services will remain intact.

   http://wwwdev.ebi.ac.uk/soaplab/emboss4/

Regards,
Mahmut

Re: [Soaplab-users] How to cite SoapLab2 ?

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

Thanks

>> How to cite SoapLab2 ?
> 
> There was a Soaplab2 talk in BOSC conference this year.
> 
> http://www.open-bio.org/wiki/BOSC_2008_schedule
> 
> http://www.open-bio.org/w/images/3/3c/Rice_Soaplab2_abstract.pdf
> 
> Regards,
> Mahmut

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

Re: [Soaplab-users] How to cite SoapLab2 ?

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

> How to cite SoapLab2 ?

There was a Soaplab2 talk in BOSC conference this year.

http://www.open-bio.org/wiki/BOSC_2008_schedule

http://www.open-bio.org/w/images/3/3c/Rice_Soaplab2_abstract.pdf

Regards,
Mahmut

[Soaplab-users] How to cite SoapLab2 ?

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

Hi,

How to cite SoapLab2 ?

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

Re: [Soaplab-users] attributes with blank and quotes

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

> And do you have a way to pass quotes in command lines ?


Yes and no:

1) There is no problem to pass quotes in input values. It depends only on
the client used how to specified the values (for example, for the linux
command-line client you need to escape some quotes in order not to be
interpreted by the linux shell as metacharacters - but it has nothing to do
with Soaplab itself).

2) You can also use quotes in the ACD files - both in the default values or
in the list values. But you can use only either single quotes (having the
whole value quoted by the double quotes), or double quotes (having the whole
value quoted by the single quotes). You cannot mix both types of quotes in
one value because Soaplab's ACD parser does not use a concept of "escaping"
characters. Perhaps the new one will have this feature.

Martin

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

Re: [Soaplab-users] attributes with blank and quotes

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

And do you have a way to pass quotes in command lines ?

Thanks

> Thanks for this report. Unfortunately, it shows a bug in Soaplab2 
> metadata parser. I will fix it in the next release (but I am not sure 
> how, at least not now :-( ).
> 
> The workaround, in order to get what you want on the command line, is to 
> manually edit the XML metadata file (after it is create by the ACD 
> converter). Do not put any 'separator' option in your ACD file - which 
> will result in the comma separator in the created XML metadata file, and 
> edit it to a space. This line in bold is the one to be changed:
> 
>                 <choice_list
>                     grouptype = "zero_or_more"
> *                    separator = " "
> *                    >
> 
> Your report also shows that there is a bug in the matada guide (in 
> documentation). There is no keyword 'separator' (as shown in the 
> documentation) - but you have (as you did) to use the "comment: 
> "separator=<char>" syntax (but, as mentioned above, even this syntax 
> doesnot wotk for a space; sorry for that).
> 
> Cheers,
> Martin

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

Re: [Soaplab-users] attributes with blank and quotes

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

Thanks for this report. Unfortunately, it shows a bug in Soaplab2 metadata
parser. I will fix it in the next release (but I am not sure how, at least
not now :-( ).

The workaround, in order to get what you want on the command line, is to
manually edit the XML metadata file (after it is create by the ACD
converter). Do not put any 'separator' option in your ACD file - which will
result in the comma separator in the created XML metadata file, and edit it
to a space. This line in bold is the one to be changed:

                <choice_list
                    grouptype = "zero_or_more"
*                    separator = " "
*                    >

Your report also shows that there is a bug in the matada guide (in
documentation). There is no keyword 'separator' (as shown in the
documentation) - but you have (as you did) to use the "comment:
"separator=<char>" syntax (but, as mentioned above, even this syntax doesnot
wotk for a space; sorry for that).

Cheers,
Martin

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

[Soaplab-users] attributes with blank and quotes

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

Hi,

I have a list in ACD format from which we can select 1 or several values:

     list: d [
         standard: "Y"
         template: '-&& "$$ "'
         minimum: 1 # Multiple db can be selected at the same time
         values: "nrcrc:non redundant, swiss:SwissProt, 
swisstrembl:UniProt (SwissProt/TrEMBL), trembl_all:TrEMBL, refseq:RefSeq 
protein, ipi:IPI ENSEMBL, gp:GenPept, gpupdate:GenPept updates, 
shuffled:randomized SwissProt"
       	delimiter: ", "
         codedelimiter: ":"
#        separator: " "
         comment: "separator  "
         information: "Peptide database used as target."
     ]

I would like to get
	-d "swiss gp"
in command lines.


In fact, how to print quotes around attribute value(s) in command lines 
? (back-slash + quote fails)

And how to print a blank (a space) between values, as separator ?


With this syntax, I get this
	-d
	swisstruegp

Thus, no visible quotes, and 'true' instead of ' ' between values as 
separator.

Thanks

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

Re: [Soaplab-users] Visibility of individual services and their WSDL

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

Hi Tom,

> With the current version of soaplab2, it is not possible to access the
> individual services and their WSDL? I see you can view something at:
> 
> http://<url>/soaplab2/services
> 
> but is it possible to access/specify/deploy WSDL for each individual
> soaplab2 service?

It is possible to access WSDL files for individual services by
specifying the service name on the URL, for example in my local host I
can reach seqret's WSDL file using the following URL.

http://localhost:8080/soaplab2/services/edit.seqret?wsdl

Soaplab2 web applications (using the default jaxws option) has 2 WSDL
files shared by all applications/services, both WSDL files can be found
under the WEB-INF/wsdl directory in your soaplab2 web application
folder. You shouldn't normally change these 2 wsdl files. However you
can for example add documentation as the current version unfortunately
doesn't have any documentation. If you really want to have a separate
WSDL file for one of your services you can copy the Analysis.wsdl file
and make your application specific changes on it (should normally be
limited to documentation changes, or in the extreme cases you might
disable some of the less used methods). You should also update web.xml
and sun-jaxws.xml files (found in the WEB-INF folder) to set an endpoint
for your service and let jaxws know your new wsdl file.

Regards,
Mahmut

Re: [Soaplab-users] Visibility of individual services and their WSDL

[John S. R. <J.S...@so...>]

I'd be interested to know the answer to this too, so can any replies be 
on-list, please!


Thanks,

JohnR.

Tom Crick wrote:
> Dear all,
> 
> With the current version of soaplab2, it is not possible to access the
> individual services and their WSDL? I see you can view something at:
> 
> http://<url>/soaplab2/services
> 
> but is it possible to access/specify/deploy WSDL for each individual
> soaplab2 service?
> 
> Thanks,
> 
> Tom
> 
> 
> 

-- 
----------------------------------------
John S. Robinson, BSc. (Hons)
OMII-UK | www.omii.ac.uk
School of Electronics & Computer Science
University of Southampton, SO17 1BJ, UK
J.S...@so...
----------------------------------------

[Soaplab-users] Visibility of individual services and their WSDL

[Tom C. <tc...@cs...>]

Dear all,

With the current version of soaplab2, it is not possible to access the
individual services and their WSDL? I see you can view something at:

http://<url>/soaplab2/services

but is it possible to access/specify/deploy WSDL for each individual
soaplab2 service?

Thanks,

Tom



-- 
Tom Crick
Mathematical Foundations Group
Department of Computer Science
University of Bath
tc...@cs...
http://www.cs.bath.ac.uk/tom/

Re: [Soaplab-users] ACD outfile problem: how do you return a file? (soaplab2)

[Tom C. <tc...@cs...>]

Mahmut Uludag wrote:
>> I'm trying to expose a Java program as a web service using soaplab2
>> (2.1.1), but I am unable to return the wav audio output file that it
>> generates. It uses a -dumpAudio flag to output to a file, otherwise the
>> audio is played on the server (sent to the audio stream - not ideal for
>> a web service). This is how I have encoded the dumpAudio parameter in
>> the ACD file:
>>
>> # -dumpAudio <file> flag
>> string: dump_audio [
>>   qualifier: dumpAudio
>>   standard: "Y"
>>   default: "output.wav"
>>   information: "dump audio to this file (default: output.wav)"
>>   comment: defaults
>>   comment: "display false"
>> ]
>>
>> it's hidden from the user so will always output to a file. My outfile
>> definition is:
>>
>> outfile: output [
>>   comment: "mimetype audio/x-wav"
>>   comment: bindata
>>   comment: "make_url yes"
>> ]
> 
> It looks like you should combine above two options into one. your Java
> programs output seems not connected to the Soaplab service output. You
> should have something similar to the following option.
> 
> # -dumpAudio <file> flag
> outfile: dump_audio [
>   qualifier: dumpAudio
>   standard: "Y"
>   default: "output.wav"
>   information: "dump audio to this file (default: output.wav)"
>   comment: defaults
> #  comment: "display false"
>   comment: "mimetype audio/x-wav"
>   comment: bindata
>   comment: "make_url yes"
> ]

That works great Mahmut, thanks. The soaplab2 docs are slightly
confusing with regards to how outfiles work, but this definitely makes
sense now! Martin Senger also replied to an email I sent to the
soaplab2-dev list, which reiterated how one should think about
parameters, inputs and outputs of soaplab2 services.

Regards,

Tom

Re: [Soaplab-users] ACD outfile problem: how do you return a file? (soaplab2)

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

Hi Tom,

> I'm trying to expose a Java program as a web service using soaplab2
> (2.1.1), but I am unable to return the wav audio output file that it
> generates. It uses a -dumpAudio flag to output to a file, otherwise the
> audio is played on the server (sent to the audio stream - not ideal for
> a web service). This is how I have encoded the dumpAudio parameter in
> the ACD file:
> 
> # -dumpAudio <file> flag
> string: dump_audio [
>   qualifier: dumpAudio
>   standard: "Y"
>   default: "output.wav"
>   information: "dump audio to this file (default: output.wav)"
>   comment: defaults
>   comment: "display false"
> ]
> 
> it's hidden from the user so will always output to a file. My outfile
> definition is:
> 
> outfile: output [
>   comment: "mimetype audio/x-wav"
>   comment: bindata
>   comment: "make_url yes"
> ]

It looks like you should combine above two options into one. your Java
programs output seems not connected to the Soaplab service output. You
should have something similar to the following option.

# -dumpAudio <file> flag
outfile: dump_audio [
  qualifier: dumpAudio
  standard: "Y"
  default: "output.wav"
  information: "dump audio to this file (default: output.wav)"
  comment: defaults
#  comment: "display false"
  comment: "mimetype audio/x-wav"
  comment: bindata
  comment: "make_url yes"
]

Regards,
Mahmut

> but when I run the process, it succeeds but I am unable to access
> output.wav:
> 
> --------------------------------------
> Summary:
> 	Completed: Successfully
> 	Termination status: 0
> 	Started:   2008-Jul-09 11:08:18 (BST)
> 	Ended:     2008-Jul-09 11:08:21 (BST)
> 	Duration:  0:00:03.210
> Report:
> Name: text_to_speech.freetts
> Job ID: [text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe
> Program and parameters:
> java
> -jar
> /opt/freetts-1.2.1/lib/freetts.jar
> -dumpAudio
> output.wav
> -text
> Hello World!
> -output
> /home/tc/apache-tomcat-6.0.16/temp/_R_/SANDBOX/[text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe/o_output
> --- end of parameters
> Exit: 0
> 
> Standard output stream:
> Wrote synthesized speech to output.wav
> --------------------------------------
> 
> no URL or output is generated, only the "report" and "detailed_status".
> When I looking in the location above on the server there is the output
> file, but why is no URL generated? Am I doing something incorrect with
> the outfile definition? Is it possible to return the file via Spinet?

[Soaplab-users] ACD outfile problem: how do you return a file? (soaplab2)

[Tom C. <tc...@cs...>]

Hi,

I'm trying to expose a Java program as a web service using soaplab2
(2.1.1), but I am unable to return the wav audio output file that it
generates. It uses a -dumpAudio flag to output to a file, otherwise the
audio is played on the server (sent to the audio stream - not ideal for
a web service). This is how I have encoded the dumpAudio parameter in
the ACD file:

# -dumpAudio <file> flag
string: dump_audio [
  qualifier: dumpAudio
  standard: "Y"
  default: "output.wav"
  information: "dump audio to this file (default: output.wav)"
  comment: defaults
  comment: "display false"
]

it's hidden from the user so will always output to a file. My outfile
definition is:

outfile: output [
  comment: "mimetype audio/x-wav"
  comment: bindata
  comment: "make_url yes"
]

but when I run the process, it succeeds but I am unable to access
output.wav:

--------------------------------------
Summary:
	Completed: Successfully
	Termination status: 0
	Started:   2008-Jul-09 11:08:18 (BST)
	Ended:     2008-Jul-09 11:08:21 (BST)
	Duration:  0:00:03.210
Report:
Name: text_to_speech.freetts
Job ID: [text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe
Program and parameters:
java
-jar
/opt/freetts-1.2.1/lib/freetts.jar
-dumpAudio
output.wav
-text
Hello World!
-output
/home/tc/apache-tomcat-6.0.16/temp/_R_/SANDBOX/[text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe/o_output
--- end of parameters
Exit: 0

Standard output stream:
Wrote synthesized speech to output.wav
--------------------------------------

no URL or output is generated, only the "report" and "detailed_status".
When I looking in the location above on the server there is the output
file, but why is no URL generated? Am I doing something incorrect with
the outfile definition? Is it possible to return the file via Spinet?

Thanks for your help,

Tom


-- Tom Crick
Mathematical Foundations Group
Department of Computer Science
University of Bath
tc...@cs...
http://www.cs.bath.ac.uk/tom/

[Soaplab-users] Soaplab2 Outfile question

[John S R. <J.S...@so...>]

Hi,

I've been scratching my head over this for a couple of days, so I'm hoping 
someone can give a clue...

I have two python scripts that I'd like to wrap using soaplab2.  At the 
simplest level, they both produce text/csv output files in the working 
directory.  The parameter 'resfile' is used to determine the name of the 
output file.  Here's the relevant extract from the ACD file:

outfile: resfile [
comment: "mimetype text/csv"
template: "resfile=$$"
extension: "csv"
additional: "Y"
default: foo.csv"
]

Both ACD files are identical with the exception of the executable name, both 
are correctly converted to XML and are deployed and executed correctly, but 
while app1 returns foo.csv as expected, app2 does not.

For app1, I can see that the results in 
tomcat/temp/_R_/SANDBOX/[app1]/<UID>/o_resfilecsv

However, app2 produces tomcat/temp/_R_/SANDBOX/[app2]/<UID>/foo.csv
and the result is never returned, despite the content being as expected and 
the script returning 0;

I think I need to better understand how soaplab operates on output files.  Is 
this covered somewhere in the documentation in more detail than in the 
Metadata guide?

Thanks in advance,

JohnR.

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

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

> Hi Sebastian,
> 
>> my $client = 
>> SOAP::Lite->service('http://localhost:8080/soaplab2/services?wsdl');
>>
>> $client->getCharacteristics();
>>
>> How to pass 'classic.helloworld' ?
> 
> You should specify the service name within the endpoint you use, similar
> to the following example
> 
> http://localhost:8080/soaplab2/services/classic.helloworld?wsdl
> 
> Regards,
> Mahmut

Thanks.
It will be easier to reach a specific application.


But what should be arguments for 'describe', 'getCharacteristics' or 
'run' by example ?
It is not clear in my mind as it is for simpler WSDL file 
(http://prodom.prabi.fr/prodom/current/wsdl/essairunmkdom.wsdl).


In a word, how can I get a list of application arguments, and how to run 
an application ?

-- 
Sébastien Moretti

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

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

Hi Sebastian,

> my $client = 
> SOAP::Lite->service('http://localhost:8080/soaplab2/services?wsdl');
> 
> $client->getCharacteristics();
> 
> How to pass 'classic.helloworld' ?

You should specify the service name within the endpoint you use, similar
to the following example

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

Regards,
Mahmut