Hi again,

Has anyone had time to look into the traceback?

Best,
Martin


From: martinchristiansendk@hotmail.com
To: jmchilton@gmail.com; nate@bx.psu.edu
Date: Tue, 12 Aug 2014 15:59:53 +0200
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] TypeError with 'dict'

Hi guys,

Thanks for the response.

I have been able to work around the from_work_dir option.
And here are the full traceback:

galaxy.tools ERROR 2014-08-12 15:55:35,298 Exception caught while attempting tool execution:
Traceback (most recent call last):
  File "/home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py", line 2004, in handle_single_execution
    job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id )
  File "/home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py", line 2535, in execute
    return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs )
  File "/home/pcm692/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 238, in execute
    data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataid )
  File "/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 767, in get
    instance = self._get_from_identity(self.session, key, False)
  File "/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2437, in _get_from_identity
    instance = session.identity_map.get(key)
  File "/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/identity.py", line 141, in get
    state = dict.get(self, key, default)
TypeError: unhashable type: 'dict'

Best regards,
Martin

> Date: Tue, 12 Aug 2014 08:58:38 -0400
> From: jmchilton@gmail.com
> To: nate@bx.psu.edu
> CC: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] TypeError with 'dict'
>
> Nate is right - full traceback would help. I am not sure it is the
> only problem - but these outputs do not look right:
>
> <outputs>
> <data format="tabular" name="Project" label="Project"
> from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input"/>
> <data format="tabular" name="Samples" label="Samples"
> from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples"/>
> </outputs>
>
> Galaxy isn't going to expand variables ($Project.input /
> $Project.samples) in the from_work_dir attribute so those are going to
> be taken as literal strings. That directory also really needs to be
> relative to the tool directory and I believe this is enforced for
> security reasons.
>
> -John
>
>
> On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor <nate@bx.psu.edu> wrote:
> > Hi Martin,
> >
> > If there's a full traceback instead of just this fragment, that'd certainly
> > help with determining exactly where the problem is coming from.
> >
> > --nate
> >
> > On Aug 12, 2014, at 4:17 AM, bjoern.gruening@googlemail.com
> > <bjoern.gruening@gmail.com> wrote:
> >
> > Hi,
> >
> > Galaxy stores all information about a tool and it's parameters in a
> > database.
> > I suppose if something is wrong with your tool, under some circumstances, it
> > can't be stored in the database.
> >
> > Cheers,
> > Bjoern
> >
> >
> > 2014-08-12 9:23 GMT+02:00 Martin Christiansen
> > <martinchristiansendk@hotmail.com>:
> >>
> >> Hi Björn,
> >>
> >> I'm using galaxy as a front-end to run a larger pipeline in the
> >> background.
> >> Originally I implemented the pipeline which had the same wrapper and was
> >> running fine.
> >> I have now begun to break it down into steps where this is the first step.
> >>
> >> The only thing I've changed is the output.
> >> How would this cause an error in the python egg?
> >>
> >> Martin
> >>
> >> > Date: Tue, 12 Aug 2014 09:06:51 +0200
> >> > From: bjoern.gruening@gmail.com
> >> > To: martinchristiansendk@hotmail.com; galaxy-dev@lists.bx.psu.edu
> >> > Subject: Re: [galaxy-dev] TypeError with 'dict'
> >>
> >> >
> >> > Hi Martin,
> >> >
> >> > please keep galaxy-dev in the CC list.
> >> >
> >> > Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
> >> > > Hi Björn,
> >> > >
> >> > > Most certainly. I have posted it below.
> >> > >
> >> > > <tool id="screen_reads" name="Screen Reads">
> >> >
> >> > -> add here a version number version="0.1"
> >> >
> >> > > <description>against hg19</description>
> >> > >
> >> > > <command interpreter="bash">screen_reads.sh $Project.input
> >> > > $Project.samples $Project $Samples </command>
> >> > >
> >> > > <inputs>
> >> > > <conditional name="Project">
> >> > > <param name="input" type="select" label="Select project">
> >> > > <option value="galaxy_test1">galaxy_test1</option>
> >> > > <option value="Untitled Folder">Untitled Folder</option>
> >> >
> >> > -> is the white space really needed? If so $Project.input will be two
> >> > words. Use "${Project.input}" to convert it to onw argument
> >> >
> >> > > </param>
> >> > > <when value="galaxy_test1">
> >> > > <param name="samples" type="select" label="Select samples"
> >> > > display="checkboxes" multiple="True">
> >> > > <option value="147406386-700171390">147406386-700171390</option>
> >> > > <option value="158256496-700097688">158256496-700097688</option>
> >> > > <option value="158337416-700013715">158337416-700013715</option>
> >> > > <option value="158337416-700097837">158337416-700097837</option>
> >> > > <option value="158357646-700035237">158357646-700035237</option>
> >> > > <option value="158458797-700014562">158458797-700014562</option>
> >> > > <option value="158479027-700014724">158479027-700014724</option>
> >> > > <option value="158479027-700097196">158479027-700097196</option>
> >> > > <option value="158499257-700014837">158499257-700014837</option>
> >> > > <option value="158499257-700098561">158499257-700098561</option>
> >> > > <option value="158742018-700015181">158742018-700015181</option>
> >> > > <option value="158802708-700015245">158802708-700015245</option>
> >> > > <option value="158802708-700015250">158802708-700015250</option>
> >> > > <option value="158802708-700099803">158802708-700099803</option>
> >> > > <option value="158802708-700119165">158802708-700119165</option>
> >> > > <option value="158822939-700014954">158822939-700014954</option>
> >> > > <option value="158883629-700015113">158883629-700015113</option>
> >> > > <option value="158883629-700100227">158883629-700100227</option>
> >> > > <option value="158883629-700112812">158883629-700112812</option>
> >> > > <option value="158924089-700099307">158924089-700099307</option>
> >> > > </param>
> >> > > </when>
> >> > > <when value="Untitled Folder">
> >> > > <param name="samples" type="select" label="Select samples"
> >> > > display="checkboxes" multiple="True">
> >> >
> >> > -> you don't have any <option> here.
> >> >
> >> > > </param>
> >> > > </when>
> >> > > </conditional>
> >> > > </inputs>
> >> > >
> >> > > <outputs>
> >> > > <data format="tabular" name="Project" label="Project"
> >> > > from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input"/>
> >> > > <data format="tabular" name="Samples" label="Samples"
> >> > > from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples"/>
> >> > > </outputs>
> >> >
> >> > -> I'm not sure this will work. workdir is a special dir Galaxy creates
> >> > for you. It will be the working directory where your program get's
> >> > called. So assume your program creates foo.sam files. You can specify it
> >> > like from_work_dir='foo.sam'
> >> >
> >> > The input handling looks also a little bit strange. You do not specify
> >> > any input file in Galaxy. That is not really Galaxy like :)
> >> >
> >> > Cheers,
> >> > Bjoern
> >> >
> >> > > <help>
> >> > > Reads screened against hg19.
> >> > > </help>
> >> > > </tool>
> >> > >
> >> > > Best,
> >> > > Martin
> >> > >
> >> > >
> >
> >
> > ___________________________________________________________
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> >
> >
> >
> > ___________________________________________________________
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___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/