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
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>> http://www.opentox.org/mailman/listinfo/development
>>
>
>