soaplab-users — Forum for Soaplab users and developers

[Soaplab-users] min & max

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

Hi,

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.

Is it normal ?

Thanks

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

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

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

>> I have an option (string symbcons) in my application that must be used
>> only if another option is chosen (boolean cons).
> 
>     Dear Sebastien,
> 
> I have some experience with writing EMBOSS programs and I think I can 
> help you.   EMBOSS parses the ACD files from top to bottom, so you must 
> write the object "boolean: cons" first and "string: symbcons" later. To 
> make sure that the program at the command line will only prompt for 
> symbcons when cons is set to y, you must include in the objects cons an 
> attribute
> standdard: "Y"
> and in the object "string: symbcons" an attribute
> standard: "$cons"
> Or you put additional instead of standard.
> Note that in case the user chooses n for cons, symbcons will not be 
> prompted for and will be set to its default value. You must hence make 
> sure that the C code of the program does something intelligent with that.
> 
> Note that the objects of type boolean and toggle are handled the same by 
> EMBOSS. The distinction was introduced for the sake of GUI developers. 
> Note also that since there exist "expert" parameters that are neither 
> standard or optional. They are never prompted at the command line. To 
> allow GUI's to hide them the attribute "needed" was invented, but it 
> depends on the GUI whether it is supported.
> 
>     Regards,
>     Guy Bottu,
>     Belgian EMnet Node

This kind of syntax doesn't seem to work properly in soaplab2.

How can I do the same kind of toggle than in emma ?
Here, I need to use symbcons when default value is chosen AND when cons 
is set to true. And use other symbcons values ONLY when cons is set to true.

Now, cons and symbcons seem to work independently.

     boolean: cons [
         additional: "Y"
         default: "false"
         comment: "defaults"
         comment: "method -&&"
     ]

     string: symbcons [
         additional: "$(cons)"
         knowntype: "string"
         default: "B.*"
         minlength: 3
         maxlength: 3
         comment: "defaults"
         comment: 'method -&&=$"$"'
     ]


Thanks.

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

[Soaplab-users] How to use toggle properly ?

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

Hi,

I have an option (string symbcons) in my application that must be used 
only if another option is chosen (boolean cons).

toggle seems to be the right way to do this but its use is a little bit 
confusing for me.

So, I have tried another way
	comment: "method -cons $symbcons"
but it fails, only '-cons' appears in cmd line.


How could I do this in soaplab2 ?

Thanks


Here is the ACD code:
     string: symbcons [
         knowntype: "string"
         default: "B.*"
         minlength: 3
         maxlength: 3
         comment: "defaults"
         prompt: "Consensus symbols ?"
         information: "Consensus symbols for mismatches(B), 
similarity(.) and identical(*) (B means blank & must be used instead of 
blank !)"
         comment: 'method -&&=$"$"'
     ]

     boolean: cons [
         default: "false"
         comment: "defaults"
         prompt: "Create consensus line ?"
         information: "Create consensus line"
         comment: "method -&& $symbcons"
     ]

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

Re: [Soaplab-users] stderr & stdout

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

> 
>     Is there a way to redirect stderr to stdout in ACD syntax for Soaplab2 ?
> 
> 
> No, not really. Theoretically, you can probably use the same way as we 
> discussed recently about he builtin commands:
> 
>   executable: "bash"
>   comment: 'method -c "let ${greeting} 2>&1"'
> 
> but I have not tried (and I doubt it :-)).
> 
> In fact, both stdout and stderr are, by default, redirected to the 
> 'report' result if they are not defined as separate ACD outfile 
> parameters. But the report contains also some added lines by soaplab 
> itself so it is not purely only stdout and stderr.
> 
> Martin

I didn't know that stderr, if not defined, is redirected to the report file.

With this, I can get what I expected.

Thanks

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

Re: [Soaplab-users] stderr & stdout

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

> Is there a way to redirect stderr to stdout in ACD syntax for Soaplab2 ?


No, not really. Theoretically, you can probably use the same way as we
discussed recently about he builtin commands:

  executable: "bash"
  comment: 'method -c "let ${greeting} 2>&1"'

but I have not tried (and I doubt it :-)).

In fact, both stdout and stderr are, by default, redirected to the 'report'
result if they are not defined as separate ACD outfile parameters. But the
report contains also some added lines by soaplab itself so it is not purely
only stdout and stderr.

Martin

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

[Soaplab-users] stderr & stdout

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

Hi,

Is there a way to redirect stderr to stdout in ACD syntax for Soaplab2 ?

I have tried
     comment: 'method ... 2>&1'
but without success.

Thanks

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

Re: [Soaplab-users] shell builtin

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

>     Is there a way to use shell builtin (like type) as executable in
>     application ?
> 
> 
> Not a straightforward way. Java does not support it (as far as I know) 
> so you have to write a wrapper script around your builtin.
> 
> The second option is to use application attribute 'method' in your ACD 
> file. For example, let's assume that you wish to execute builtin 'let' 
> (that returns an exit code depending on the evaluation of its parameters):
> 
> appl: HelloWorld [
>   ...
>   executable: "bash"
>   comment: 'method -c "let ${greeting}"'
> ]
> 
> This works fine - try for example the command-lines (and see that the 
> exit code changes):
> 
> build/run/run-cmdline-client -name classic.helloworld -w -r -protocol 
> local greeting '1+1'
> build/run/run-cmdline-client -name classic.helloworld -w -r -protocol 
> local greeting '1-1'
> 
> But this might be a security risk - a user can send anything and it is 
> evaluated by your bash. I recommend to use it with caution and only when 
> limited access is established.
> 
> Cheers,
> Martin

I know it is a security issue but it is only for internal use, and only 
for type shell builtin which is more reactive than unix which command on 
our file system.

It works perfectly !

Thanks

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

Re: [Soaplab-users] shell builtin

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

> Is there a way to use shell builtin (like type) as executable in
> application ?


Not a straightforward way. Java does not support it (as far as I know) so
you have to write a wrapper script around your builtin.

The second option is to use application attribute 'method' in your ACD file.
For example, let's assume that you wish to execute builtin 'let' (that
returns an exit code depending on the evaluation of its parameters):

appl: HelloWorld [
  ...
  executable: "bash"
  comment: 'method -c "let ${greeting}"'
]

This works fine - try for example the command-lines (and see that the exit
code changes):

build/run/run-cmdline-client -name classic.helloworld -w -r -protocol local
greeting '1+1'
build/run/run-cmdline-client -name classic.helloworld -w -r -protocol local
greeting '1-1'

But this might be a security risk - a user can send anything and it is
evaluated by your bash. I recommend to use it with caution and only when
limited access is established.

Cheers,
Martin

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

[Soaplab-users] shell builtin

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

Hi,

Is there a way to use shell builtin (like type) as executable in 
application ?


It doesn't seem it works as other executable but maybe there is a way to 
get it.

Thanks

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

Re: [Soaplab-users] Description line

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

> I got the same for application, substitute with aplication
>

Yes, I know what causes it. It is a Perl statement (in the metadata
generator) that replaces double whitespaces (like two or more newlines) -
but erroneously it does it not only for whitespaces but for any doubles. I
already fixed it - just not yet committed.

Martin

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

Re: [Soaplab-users] Description line

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

>>            iPCR: Virtual PCR tol
>>
>>
>> Interesting bug :-)
>> Yes, it is a bug - I have just found its cause (it is deep in the 
>> metadata generator). I will fix it and it will be part of the new 
>> version (that I still hope to do this weekend).
>>
>> Thanks for spotting it,
>> Martin
> 
> Thanks

I got the same for application, substitute with aplication

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

Re: [Soaplab-users] Description line

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

>            iPCR: Virtual PCR tol
> 
> 
> Interesting bug :-)
> Yes, it is a bug - I have just found its cause (it is deep in the 
> metadata generator). I will fix it and it will be part of the new 
> version (that I still hope to do this weekend).
> 
> Thanks for spotting it,
> Martin

Thanks

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

Re: [Soaplab-users] Description line

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

>        iPCR: Virtual PCR tol
>

Interesting bug :-)
Yes, it is a bug - I have just found its cause (it is deep in the metadata
generator). I will fix it and it will be part of the new version (that I
still hope to do this weekend).

Thanks for spotting it,
Martin


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

[Soaplab-users] Description line

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

Hi,

I have an ACD file with the word tool inside:
	documentation: "iPCR: Virtual PCR tool"

I get the same phrase in the xml file generated by soaplab:
	<description>iPCR: Virtual PCR tool</description>

Nevertheless, on http://localhost:8080/soaplab2/, the description 
following service name is:
	iPCR: Virtual PCR tol


So, is there a kind of substitution form tool to tol somewhere in the 
web interface ?

Thanks

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

Re: [Soaplab-users] Problem with Infile Path

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

> Okay, let's do the replacement, minus for underscore.
> Thanks, Mahmut.
> 
> Martin

Okay,
I will investigate more deeply to find if it is only pascal code dependent.

Thanks

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

Re: [Soaplab-users] Problem with Infile Path

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

Okay, let's do the replacement, minus for underscore.
Thanks, Mahmut.

Martin

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

Re: [Soaplab-users] Problem with Infile Path

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

Hi Martin,

>         So, could you add this replaceAll("-", "_") method to soaplab2
>         source
>         code to avoid this kind of problem in the future for other
>         users & maybe
>         
>         with other old pascal programs ?
> 
> I am aware that you are waiting for my answer to this. But I
> hesitate... Next time, it may be another character, next time
> another... I probably still feel that this should be dealt with where
> it belongs - meaning in your application, or in wrapping your
> application. The minus sign is a valid character in a filename in all
> major platforms (unix, windows, mac) - at least I think so.
> 
> Mahmut, what is your opinion?

I have noticed that the minus signs related to the numeric value of two
attributes in the UID machinery. Although it would not look pretty it
should not harm the uniqueness of the identifiers if we replace minus
sign characters by some other character. 

Since what we do here is in some sense similar to what Java
File.createTempFile does in getting unique file identifiers, I checked
its source code. Their unique file identifier is based on a static
integer counter which is initialised by a "positive" random number,
however, after the maximum integer value reached the counter does have
minus values and so the unique file names have minus sign.

Regards,
Mahmut

Re: [Soaplab-users] Problem with Infile Path

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

> So, could you add this replaceAll("-", "_") method to soaplab2 source
> code to avoid this kind of problem in the future for other users & maybe
> with other old pascal programs ?


I am aware that you are waiting for my answer to this. But I hesitate...
Next time, it may be another character, next time another... I probably
still feel that this should be dealt with where it belongs - meaning in your
application, or in wrapping your application. The minus sign is a valid
character in a filename in all major platforms (unix, windows, mac) - at
least I think so.

Mahmut, what is your opinion?

Cheers,
Martin

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

Re: [Soaplab-users] Problem with Infile Path

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

>>     More precisely, this is '-', in the path, which makes my program
>>     crashed.
>>
>>     Where can I replace '-' by '_' in the soaplab2 sources ?
>>
>>
>> The name of the directory in question is also the job ID. It is 
>> created in org.soaplab.services.JobManager in method createJobId(). 
>> The minus is given by calling 'new java.rmi.server.UID().toString()'.
>>
>> Martin
> 
> So, it should work if I use 
> java.rmi.server.UID().toString().replaceAll('-', '_')
> but I need to recompile this class and reinstall soaplab2 ?
> 
> I don't know yet if the bug is coming from the application, or from 
> pascal syntax !
> 
> 
> Could you add this replaceAll("-", "_") method to soaplab2 source code 
> to avoid this kind of problem in the future for other users & maybe for 
> other old pascal programs ?
> 
> Thanks

It works perfectly with .replaceAll("-", "_")

So, could you add this replaceAll("-", "_") method to soaplab2 source 
code to avoid this kind of problem in the future for other users & maybe 
with other old pascal programs ?

Thanks

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

Re: [Soaplab-users] Problem with Infile Path

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

>     More precisely, this is '-', in the path, which makes my program
>     crashed.
> 
>     Where can I replace '-' by '_' in the soaplab2 sources ?
> 
> 
> The name of the directory in question is also the job ID. It is created 
> in org.soaplab.services.JobManager in method createJobId(). The minus is 
> given by calling 'new java.rmi.server.UID().toString()'.
> 
> Martin

So, it should work if I use 
java.rmi.server.UID().toString().replaceAll('-', '_')
but I need to recompile this class and reinstall soaplab2 ?

I don't know yet if the bug is coming from the application, or from 
pascal syntax !


Could you add this replaceAll("-", "_") method to soaplab2 source code 
to avoid this kind of problem in the future for other users & maybe for 
other old pascal programs ?

Thanks

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

Re: [Soaplab-users] spinet and EMBOSS

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

Hi Cath,

> But that raises one further question for me. Why did my rebuild of
> soaplab not result in that properties file being automatically
> regenerated correctly? I did make the changes in my soaplab home
> directory, but install doesn't seem to have copied them to the tomcat
> version. Looks like the war file was rebuilt, but not the whole thing.
> I must have misread the install doco; can anyone explain where to look
> for what I need to do to add services to an existing installation?

The soaplab.properties file in the generated war files come from the
my.soaplab.properties property defined in the build.properties file in
your Soaplab project home page.

If you don't have my.soaplab.properties property defined in your
build.properties file then related soaplab.properties file is generated
from src/etc/config/soaplab.properties.template file and soaplab build
machinery doesn't comment out the EMBOSS related applist line
automatically when you have EMBOSS metadata files already generated.

(There was a problem with Spinet working with Internet Explorer which is
now fixed in CVS version, you may update your project to have this fix
in your installation)

Regards,
Mahmut

Re: [Soaplab-users] spinet and EMBOSS

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

Hi all,

Typically for me, I ask a question just before being off line for a
while - this time it was easter holidays, and transferring over to a
new computer... Sorry, Mahmut, your help really is appreciated,
despite my delay in thanking you. It was indeed the right answer.

But that raises one further question for me. Why did my rebuild of
soaplab not result in that properties file being automatically
regenerated correctly? I did make the changes in my soaplab home
directory, but install doesn't seem to have copied them to the tomcat
version. Looks like the war file was rebuilt, but not the whole thing.
I must have misread the install doco; can anyone explain where to look
for what I need to do to add services to an existing installation?

thanks
Cath



On 18/03/2008, Mahmut Uludag <ul...@eb...> wrote:
>  > I've just tried to install EMBOSS on soaplab2, and it seems sorta
>  > kinda successful - the EMBOSS services show up in the info-list, and
>  > they seem to have deployed OK when you look at the list at
>  > http://myserver.myuni.au:8888/soaplab2-axis/services
>  > (not real URL)
>  >
>  > However, entering that same URL in a taverna session as a new soaplab
>  > scavenger returns only the original default soaplab list. And the
>  > spinet web page doesn't have them, either. What have I missed? I guess
>  > it must be some config somewhere that I overlooked.
>  >
>  > How can I make taverna see these, and spinet regenerate itself? Spinet
>  > looks like a nifty little testing page, by the way, and I'd like to
>  > use it.
>
>
> >From your description it seems that the services are recognised by Axis
>  but not Soaplab. This should be related to a missing or wrong 'applist'
>  property line in your soaplab.properties file (under your
>  WEB-INF/classes directory of your soaplab2-axis web application). You
>  should have a property definition similar to the following.
>
>     applist = ${metadata.dir}/EMBOSSApplications.xml
>
>  Make sure that you have ${metadata.dir} defined correctly above in your
>  properties file. It should normally point to the metadata directory of
>  your soaplab2-axis web application.
>
>  Regards,
>
> Mahmut
>
>
>


-- 
Cath Lawrence    ---  cajela at gmail dot com
http://thecanberracook.blogspot.com

Re: [Soaplab-users] Problem with Infile Path

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

> More precisely, this is '-', in the path, which makes my program crashed.
>
> Where can I replace '-' by '_' in the soaplab2 sources ?
>

The name of the directory in question is also the job ID. It is created in
org.soaplab.services.JobManager in method createJobId(). The minus is given
by calling 'new java.rmi.server.UID().toString()'.

Martin

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

Re: [Soaplab-users] Problem with Infile Path

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

>     So, external applications use full paths or relative paths ?
> 
> 
> They are getting from Soaplab always full paths.
> 
> M.

More precisely, this is '-', in the path, which makes my program crashed.

Where can I replace '-' by '_' in the soaplab2 sources ?

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

Re: [Soaplab-users] Problem with Infile Path

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

> So, external applications use full paths or relative paths ?


They are getting from Soaplab always full paths.

M.


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