Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple="true" input datasets

5 Jul 2011

      Hi Leandro,

Thanks! I had to change one line to get it working:

<command interpreter="perl">
     ...
     #for $i in $add_inputs
     ${i.extra_table.file_name}
     #end for
</command>

<repeat name="add_inputs" title="Extra Fitness Tables">
    <param format="txt"             name="extra_table"      type="data"
label="Another fitness table" />
</repeat>

Now galaxy will provide a list of files as the last parameters to the
script.

Best,

Kip

On Fri, Jul 1, 2011 at 3:53 AM, Leandro Hermida
<softdev@leandrohermida.com>wrote:
...
Hi Kip,
For the time being we are using this method to achieve the same
result, although its not as nice as just having a multi-select menu in
the form:
<command>
   ...
   $input1
   #for $r in $add_inputs
   $r.$input2
   #end for
   ...
</command>
In <inputs>:
<param name="input1" type="data"/>
<repeat name="add_inputs">
       <param name="input2" type="data" />
</repeat>
best,
Leandro
...
Sorry, I tried to edit that, to make it simpler, but missed the <param>
block. The 'name' does match the one in the 'command' on my end
(list_of_items_in_history).
On Thu, Jun 30, 2011 at 10:45 AM, Kip Bodi <kip.bodi@tufts.edu> wrote:
...
Hi all,
I'm having the same problem. I have a script that tries to take several
history data sets as a single input:
<command interpreter="perl">aggregate.pl --out $outfile
$list_of_items_in_history</command>
<inputs>
    <param format="txt" name="fitness_tables" type="data"
multiple="true"
...
label="Fitness score table, per site"/>
  </inputs>
<outputs>
    <data format="tabular" name="outfile" />
  </outputs>
If I select only one history item it works, but if I press 'ctrl' to
select multiple items, it fails:
File
'/storage/apps/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
...
line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File '/usr/lib/python2.6/site-packages/paste/debug/prints.py', line 106
in
__call__
  environ, self.app)
File '/usr/lib/python2.6/site-packages/paste/wsgilib.py', line 543 in
intercept_output
  app_iter = application(environ, replacement_start_response)
File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in
__call__
  return self.application(environ, start_response)
File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line
633
in __call__
  return self.application(environ, start_response)
File '/storage/apps/galaxy_dist/lib/galaxy/web/framework/base.py', line
145 in __call__
  body = method( trans, **kwargs )
File
'/storage/apps/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py',
On Thu, Jun 30, 2011 at 4:52 PM, Kip Bodi <kip.bodi@tufts.edu> wrote:
line
...
...
68 in index
  template, vars = tool.handle_input( trans, params.__dict__ )
File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 979
in
handle_input
  _, out_data = self.execute( trans, incoming=params, history=history )
File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1271
in execute
  return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid, history=history, **kwargs )
File '/storage/apps/galaxy_dist/lib/galaxy/tools/actions/__init__.py',
line 360 in execute
  for name, value in tool.params_to_strings( incoming, trans.app
).iteritems():
File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1274
in params_to_strings
  return params_to_strings( self.inputs, params, app )
File
'/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/__init__.py',
line 79 in params_to_strings
  value = params[ key ].value_to_basic( value, app )
File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py',
line 110 in value_to_basic
  return self.to_string( value, app )
File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py',
line 1457 in to_string
  return value.id
AttributeError: 'list' object has no attribute 'id'
Is using multiple history items as a single input not currently
supported,
or is there something else I'm doing wrong?
Cheers,
Kip
On Thu, Jun 9, 2011 at 7:05 AM, Leandro Hermida
<softdev@leandrohermida.com> wrote:
...
Hi again,
Sorry to ping again about this, just very interested in knowing if
this is a missing feature in Galaxy or if I had configured something
wrong.
Is it possible in Galaxy to have a tool with a multiple="true" input
dataset parameter?  It doesn't seem so?
best,
Leandro
On Tue, May 24, 2011 at 1:31 PM, Leandro Hermida
<softdev@leandrohermida.com> wrote:
...
Hi Nate,
Thanks for the ping, have fun at the conference!
On Tue, May 24, 2011 at 11:22 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
...
...
...
Hi Leandro,
The Galaxy Team has recently been preparing for and traveling in
advance
of the Galaxy Community Conference, which begins today.
Unfortunately
...
I
don't have an answer for you, but when we're all back at work next
week,
someone should be able to respond.
Thanks,
--nate
Leandro Hermida wrote:
> Hi again,
>
> Very sorry to ask again, just gotten no repsonse, but is this a
> Galaxy
> bug
> or does anyone have a functioning tool that takes multiple
datasets
> as
> an
> input parameter??? i.e.
>
> <param type="data" multiple="true" ...  />
>
> regards,
> Leandro
>
> On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida
> <softdev@leandrohermida.com
> > wrote:
>
> > Hi again,
> >
> > I tried changing the format to txt and tabular which I have
other
> > datasets
> > in my history and still the same error and stack trace in
Galaxy.
> >
> > Is it possible at all to have a select multiple of datasets as
an
> > input
> > parameter??
> >
> > best,
> > Leandro
> >
> >
> > On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida <
> > softdev@leandrohermida.com> wrote:
> >
> >> Hi Galaxy developers,
> >>
> >> Something seems maybe to be wrong with the format="html"
type...
> >> I
> >> forgot
> >> to add before that my tool input param the format="html"
> >> attribute:
> >>
> >> <param type="data" multiple="true" format="html" name="input1"
/>
> >>
> >> In another tool I have it outputs format="html" and this works
> >> and
> >> displays in Galaxy just fine. I would like to use multiple of
> >> these
> >> output
> >> datasets in my history as the input for this other tool but
> >> something
> >> seems
> >> to be wrong if you try to do this?
> >>
> >> a bit lost,
> >> Leandro
> >>
> >>
> >> On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida <
> >> softdev@leandrohermida.com> wrote:
> >>
> >>> Hi,
> >>>
> >>> I have a tool where the input is multi-select of datasets,
e.g.:
> >>>
> >>> <param type="data" multiple="true" name="input1" />
> >>>
> >>> I tested it to see what it would pass to my command and I get
> >>> the
> >>> following debug page and error in Galaxy:
> >>>
> >>> AttributeError: 'list' object has no attribute 'missing_meta'
> >>>
> >>> The last part of the stack trace looks like:
> >>>
> >>> >>  validator.validate( value, history )
> >>> Module galaxy.tools.parameters.validation:185 in validate
> >>>
> >>> history <galaxy.model.History object at 0xb8ea190>
> >>> self
> >>>  <galaxy.tools.parameters.validation.MetadataValidator
> >>> object
> >>> at 0xb8e6250>
> >>> value [<galaxy.model.HistoryDatasetAssociation object at
> >>> 0xa255550>,
> >>> <galaxy.model.HistoryDataset ... Association object at
> >>> 0xb8ea210>]
> >>>
> >>> >>  if value and value.missing_meta( check = self.check, skip
=
> >>> >> self.skip
> >>> ):
> >>> AttributeError: 'list' object has no attribute 'missing_meta'
> >>>
> >>> What am I doing wrong?
> >>>
> >>> regards,
> >>> Leandro
> >>>
> >>>
> >>
> >
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--
Kip Lord Bodi Jr.
Tufts University School of Medicine
136 Harrison Avenue, South Cove 502
Boston, MA 02118
617-636-3763
kip.bodi@tufts.edu
www.tucf.org | genomics.med.tufts.edu
--
Kip Lord Bodi Jr.
Tufts University School of Medicine
136 Harrison Avenue, South Cove 502
Boston, MA 02118
617-636-3763
kip.bodi@tufts.edu
www.tucf.org | genomics.med.tufts.edu
-- 
Kip Lord Bodi Jr.
Tufts University School of Medicine
136 Harrison Avenue, South Cove 502
Boston, MA 02118
617-636-3763
kip.bodi@tufts.edu
www.tucf.org | genomics.med.tufts.edu

Kip Bodi

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