[OTDev] OT Structural-Clustering service
Fabian buchwald FabianBuchwald at gmx.deMon Apr 11 16:16:28 CEST 2011
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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 > http://www.opentox.org/mailman/listinfo/development -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl
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