Hi Vedrin,

thanks a lot for testing.

On Fri, Aug 20, 2010 at 2:14 PM, Vedrin Jeliazkov <
vedrin.jeliazkov at gmail.com> wrote:

> Hi Martin,
>
> On 19 August 2010 12:58, Martin Guetlein <martin.guetlein at googlemail.com>
> wrote:
> > Hello All,
> >
> > the first version of the qmrf report service is available.
>
> Well done!
>
> > See below for
> > example curl calls. More functionality and a better documentation on the
> > opentox-webpage will be available soon.
> >
> > I would be happy if you could give it a try (with your own model /
> > qmrf-report) and give some feedback to me.
> >
> > create new qmrf-report from model:
> > --------------------------------------------------
> > curl -X POST -d model_uri=
> http://apps.ideaconsult.net:8080/ambit2/model/33
> > http://opentox.informatik.uni-freiburg.de/validation/reach_report/QMRF
> > (The content is very sparse yet, will be extended soon)
>
> Works fine for http://apps.ideaconsult.net:8080/ambit2/model/33, but
> results in an error for models that don't include a reference to a
> dependent variable (e.g.
> http://apps.ideaconsult.net:8080/ambit2/model/2) -- I'm not sure
> whether this is expected or not.
>


Your are right it should work without dependent variables, I fixed that, it
now works with your model.


>
> > alternatively, create new qmrf-report from file:
> > -----------------------------------------------------------------
> > curl -X POST -T QMRF_v1.2_FishTox.xml
> > http://opentox.informatik.uni-freiburg.de/validation/reach_report/QMRF
> > (file is available at http://ecb.jrc.ec.europa.eu/qsar/qsar-tools/qrf)
>
> Couldn't locate and download QMRF_v1.2_FishTox.xml (the URL seems to
> be broken).


Sorry the correct link was:
http://ecb.jrc.ec.europa.eu/qsar/qsar-tools/index.php?c=QRF




> Tried instead the following most recent QMRFs, submitted
> and published in the QMRF Inventory (http://qsardb.jrc.it/qmrf/):
>
>
> http://qsardb.jrc.it/qmrf/download.jsp?filetype=xml&id=245&action=dbattachments
>
> http://qsardb.jrc.it/qmrf/download.jsp?filetype=xml&id=242&action=dbattachments
>
> http://qsardb.jrc.it/qmrf/download.jsp?filetype=xml&id=241&action=dbattachments
>
> In all the 3 cases, the creation of a new qmrf-report at
> http://opentox.informatik.uni-freiburg.de/validation/reach_report/QMRF
> resulted in an error (full output, allong with the corresponding
> input, is attached in the 7z archive). Here is an relevant excerpt
> from the returned exceptions:
>
> - - - - - - - - - 8< - - - - - - - -
> RuntimeError at /validation/reach_report/QMRF
> node not found: attachment_documents
>  (ReachReports::QsarMiscelaneous.from_xml)
> ./reach_reports/reach_persistance.rb: in from_xml, line 115
>


Thanks, I fixed this bug. The attachments are now converted to/from XML
correctly.




> - - - - - - - - - 8< - - - - - - - -
>
> > get report as qmrf-xml:
> > --------------------------------
> > curl -H "accept:application/qmrf-xml"
> > http://opentox.informatik.uni-freiburg.de/validation/reach_report/QMRF/3
> > (This format can be edited with the qmrf editor at
> > http://ambit.sourceforge.net/qmrf/jws/qmrfeditor.jnlp)
>
> Works fine.
>
> > update changes (made with editor) to report at web service:
> >
> -----------------------------------------------------------------------------------
> > curl -X POST -T QMRF_v1.2_FishTox.xml
> > http://opentox.informatik.uni-freiburg.de/validation/reach_report/QMRF/3
>
> Also works fine. However, I would like to mention that the XML
> generated by the service is not strictly identical to the one from the
> qmrf editor. This can be seen when comparing the following files, also
> attached in the zip archive:
>
> 33a.xml --> original file returned by the service
> 33b.xml --> a version of 33a.xml, which was edited with the qmrf
> editor and submitted back to the service
> 33c.xml --> a version of 33b.xml, returned by the service
>
> As you will notice, 33b.xml and 33c.xml differ, however this might be
> a rather cosmetic issue if it does not result in different semantics
> of the content.
>


Indeed, the xml-file provided by the service might differ from the xml-file
you sent to the service. The changes are due to conversion issues (the
reference-id to the catalog entries may change, as well as line breaks, ..
). The content does not change.
I compared 33b.xml and 33c.xml in the editor, the content seams to be equal.

Best regards,
Martin



>
> Kind regards,
> Vedrin
>
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>
>


-- 
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 8442 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetlein at informatik.uni-freiburg.de