Hi Om,

sorry for replying so late. I was on holidays without internet access.

Should work now. Can you try it again.

Best regards,

Fabian
-------- Original-Nachricht --------
> Datum: Sat, 2 Apr 2011 00:32:51 +0530
> Von: Om <ompandey at gmail.com>
> An: opentox development mailing list <development at opentox.org>
> CC: joerg.wicker at in.tum.de, fabian.buchwald at in.tum.de
> Betreff: [OTDev] OT Structural-Clustering service

> Hi
> 
> Thank you all, for the help.
> 
> I re-tried the task again. I could pass the step of A&A. I could get the
> task URI. However while doing curl -X GET task-uri, I am getting
> NullPointerException message.
> 
> May be I am missing some basic steps.
> 
> I have followed below steps to doing Structural-Clustering on 10 compounds
> 
> [1] Created token as
> curl -i -d "username=ompandey" -d "password=*******"
> http://opensso.in-silico.ch/auth/authenticate?uri=service=openldap
> 
> HTTP/1.0 200 OK
> Server: nginx/0.6.32
> Date: Fri, 01 Apr 2011 17:52:14 GMT
> Content-Type: text/plain;charset=UTF-8
> Proxy-Connection: keep-alive
> Content-Length: 72
> 
> -> token.id=AQIC5wM2LY4SfczCIgXW95HXbv3OzRj0FyU0t5qCev1hMyM=@AAJTSQACMDE=#
> 
> [2] curl -X POST -d 'dataset_uri=
> http://apps.ideaconsult.net:8080/ambit2/dataset/23793?max=10' -d
> 'threshold=0.50' -H
> subjectid:AQIC5wM2LY4SfcwO+CQR0LJXqA/9KC8qLhSTr54WvJFYm7s=@AAJTSQACMDE=#
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/StructuralClustering
> 
> ->
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/task/8ff7322e-a579-480b-82fc-c5be5a34927a
> 
> [3] curl -X GET
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/task/8ff7322e-a579-480b-82fc-c5be5a34927a-H
> subjectid:AQIC5wM2LY4SfcwO+CQR0LJXqA/9KC8qLhSTr54WvJFYm7s=@AAJTSQACMDE=#
> 
> -> Task failed: java.lang.NullPointerException
> 
> Or
> curl -X POST -d 'dataset_uri=
> https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/23793?max=10' -d
> 'threshold=0.50' -H
> subjectid:AQIC5wM2LY4SfcwO+CQR0LJXqA/9KC8qLhSTr54WvJFYm7s=@AAJTSQACMDE=#
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/StructuralClustering
> curl -X GET
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/task/d6dd8195-41a8-4598-b067-55655714f01d
> 
> -> Task failed: java.lang.NullPointerException
> 
> I am following these documents:
> http://www.opentox.org/dev/data/documents/development/opentoxreports/opentoxreportd33
> http://www.opentox.org/dev/apis/api-1.2/Algorithm
> http://lxkramer13.informatik.tu-muenchen.de/trac/TUMOpenTox/wiki/walk-throughExample
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev
> 
> Any help will be appreciated.
> 
> Regards
> Om
> 
> On Fri, Apr 1, 2011 at 8:02 PM, Nina Jeliazkova
> <jeliazkova.nina at gmail.com>wrote:
> 
> >
> >
> > On 1 April 2011 16:20, Om <ompandey at gmail.com> wrote:
> >
> >> Hi Tobias,
> >>
> >> I would like to use the gSPAN modules from your source code for the
> >> structural clustering. I wish to integrate these steps locally (through
> >> netbeans project)  as I have large datasets to work on ( and our
> network
> >> connection is intermittent - so that uploads to ambit are likely to
> fail)
> >> and I also want to run the code as efficiently and natively as
> possible.
> >>
> >> Could you please point out which source files within the source
> directory
> >> (and dependencies) contain the code to do the above ?
> >>
> >> Also I would just like to add that I tried using the OpenTox services
> for
> >> TUM and could not get past the "The server understood the request, but
> is
> >> refusing to fulfill it" etc ... error message. I am assuming it was an
> A&A
> >> issue so i tried the following
> >>
> >> curl -i -d "username=ompandey" -d "password=*******"
> >> http://opensso.in-silico.ch/auth/authenticate?uri=service=openldap
> >>
> >> I got the token and tried (with and without url-encoding)
> >>
> >> curl -i -d
> >>
> >>
> "subjectid=AQIC5wM2LY4SfcwnbJmuQevLWTGO%2BkNqbUaqOdwH1tW0iN0%3D%40AAJTSQACMDE%3D%23"
> >> -d 'dataset_uri=
> >> http://apps.ideaconsult.net:8080/ambit2/dataset/23793?max=10'
> >> -d 'threshold=0.50'
> >>
> >>
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/StructuralClustering
> >
> >
> > tokens should be sent via header, not parameter , i.e.
> >
> > curl -H  "subjectid:thetoken"   (not url encoded).
> >
> > Hope this helps,
> > Nina
> >
> >
> >>
> >>
> >> but it did not work.
> >>
> >> Could you please enumerate the correct set of steps involved in getting
> >> the
> >> result from this algorithm?
> >>
> >> Regards
> >> Om
> >>
> >> On Wed, Feb 23, 2011 at 4:27 PM, Tobias Girschick <
> >> tobias.girschick at in.tum.de> wrote:
> >>
> >> > Hi All,
> >> >
> >> > TUM services running on
> >> > http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev will be
> down
> >> for
> >> > the next 1 or 2 hours. The non-AA secured services are still
> available
> >> at:
> >> >
> >> > http://opentox.informatik.tu-muenchen.de:8080/OpenTox-noAA
> >> >
> >> > When the OpenTox-dev services are up again, this will be the AA
> secured
> >> > version.
> >> >
> >> > best regards,
> >> > Tobias
> >> > --
> >> >
> >> > Dipl.-Bioinf. Tobias Girschick
> >> >
> >> > Technische Universität München
> >> > Institut für Informatik
> >> > Lehrstuhl I12 - Bioinformatik
> >> > Bolzmannstr. 3
> >> > 85748 Garching b. München, Germany
> >> >
> >> > Room: MI 01.09.042
> >> > Phone: +49 (89) 289-18002
> >> > Email: tobias.girschick at in.tum.de <mailto:tobias.girschick at in.tum.de>
> >> > Web: http://wwwkramer.in.tum.de/girschick
> >> >
> >> > _______________________________________________
> >> > Development mailing list
> >> > Development at opentox.org
> >> > http://www.opentox.org/mailman/listinfo/development
> >> >
> >> _______________________________________________
> >> Development mailing list
> >> Development at opentox.org
> >> http://www.opentox.org/mailman/listinfo/development
> >>
> >
> >
> _______________________________________________
> Development mailing list
> Development at opentox.org
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