soaplab-users

[Soaplab-users] spinet and EMBOSS

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

Hi,
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.

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

Re: [Soaplab-users] spinet and EMBOSS

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

Hi Cath,

> 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

Re: [Soaplab-users] spinet and EMBOSS

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

Hi Cath,

> > 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)

I forgot to say if you don't have special reasons it is better to use
the jax-ws services that would make your Soaplab services interoperable
with more webservices technologies.

If you have decided to use axis services because you want them
accessible from Taverna, you might use the Taverna Soaplab plugin which
supports both jaxws and axis flavours of Soaplab.

http://soaplab.sourceforge.net/soaplab2/TavernaNotes.html

The plugin will probably be part of Taverna-2 and replace the so called
"Soaplab Scavenger".

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] 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