Re: [galaxy-dev] Workflow param error leads to template error [patch]

2014-09-18 Thread Dannon Baker
Hi Tim,

Thanks for this.  If you still have it handy, what was the exact attribute
error?

-Dannon

On Thu, Sep 18, 2014 at 10:28 AM, Tim Booth  wrote:

> Dear Devs,
>
> I recently ran into a problem where attempting to run a workflow
> resulted in an uninformative error and a traceback in the logs, that I
> put into Google.  This led me to the message below from 2012.  As far as
> I can see it got no reply at the time and I have hit the same issue.
>
> I modified database/compiled_templates/workflow/run.mako.py and this
> resulted in a much more useful error report appearing in the browser.
> Obviously this is a generated file, so attached is a patch for
> templates/webapps/galaxy/workflow/run.mako that I propose you add to
> Galaxy.  As you'll see it just adds a single "try" block and then
> ignores the exception, which I would say in this case is not actually a
> bad thing to do even if it is not the ideal fix.  Should be fairly
> explanatory from the patch.
>
> Cheers,
>
> TIM
>
> Way way back in Jun 2012, Paul-Michael.Agapow at hpa.org.uk wrote:
>
> > Looking for pointers on what might be causing this problem:
> >
> > A user had a moderately complicated workflow that when run under certain
> parameter values results in a traceback that ends:
> >
> >Module workflow_run_mako:232 in render_body
> >>> for ic in oc.input_step.module.get_data_inputs():
> >AttributeError: 'WorkflowStep' object has no attribute 'module'
> >
> > After some puzzling, I realized one of the parameters was outside the
> allowed range (a max on an integer param) and that Galaxy was trying to
> render "run.mako" flagging up the error but erroring out. Why Galaxy tries
> to call this non-existent member is unclear to me. Any insight or places I
> should start exploring?
> >
> > Galaxy version: various (started with an 6-month old one, upgraded to
> latest production to see if it would fix error, it didn't)
> > Hosting OS:  CentOS 6
> >
> > --
> > Paul Agapow (paul-michael.agapow at hpa.org.uk)
> > Bioinformatics, Health Protection Agency (UK)
> >
> --
> Tim Booth 
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>
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Re: [galaxy-dev] find bam index files

2014-09-18 Thread Nate Coraor
Hi Ulf,

Unfortunately, metadata files are assigned an id that is unrelated to the
dataset id. To link the files you'll need to use the database. The
numerical id you see in the filename is the id of the dataset in the
`dataset` table. From this you can go backward to the
history_dataset_association (hda) table, where hda.dataset_id = dataset.id.
Finally, from there, hda.id can be used to find the metadata_file via
metadata_file.hda_id.

More succinctly:

dataset.id = history_dataset_association.dataset_id
history_dataset_association.id = metadata_file.hda_id

--nate

On Mon, Sep 15, 2014 at 6:34 AM, Ulf Schaefer 
wrote:

> Dear all
>
> For each bam file in my history I can download the associated bai (bam
> index) file.
>
> I assume these files are stored somewhere under
> /mount/galaxy/database/files/_metadata_files. Correct? Is there an easy
> way to find the bam index file for a bam file, given only the internal
> file name of the bam (e.g.
> /mont/galaxy/database/files/089/dataset_89231.dat)?
>
> I am asking because I would like to use the files_to_ftp tool to
> automatically download bams together with their associated indices.
>
> Thanks
> Ulf
>
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Re: [galaxy-dev] Workflow param error leads to template error [patch]

2014-09-18 Thread Tim Booth
Dear Devs,

I recently ran into a problem where attempting to run a workflow
resulted in an uninformative error and a traceback in the logs, that I
put into Google.  This led me to the message below from 2012.  As far as
I can see it got no reply at the time and I have hit the same issue.

I modified database/compiled_templates/workflow/run.mako.py and this
resulted in a much more useful error report appearing in the browser.
Obviously this is a generated file, so attached is a patch for
templates/webapps/galaxy/workflow/run.mako that I propose you add to
Galaxy.  As you'll see it just adds a single "try" block and then
ignores the exception, which I would say in this case is not actually a
bad thing to do even if it is not the ideal fix.  Should be fairly
explanatory from the patch.

Cheers,

TIM

Way way back in Jun 2012, Paul-Michael.Agapow at hpa.org.uk wrote:

> Looking for pointers on what might be causing this problem:
> 
> A user had a moderately complicated workflow that when run under certain 
> parameter values results in a traceback that ends:
> 
>Module workflow_run_mako:232 in render_body
>>> for ic in oc.input_step.module.get_data_inputs():
>AttributeError: 'WorkflowStep' object has no attribute 'module'
> 
> After some puzzling, I realized one of the parameters was outside the allowed 
> range (a max on an integer param) and that Galaxy was trying to render 
> "run.mako" flagging up the error but erroring out. Why Galaxy tries to call 
> this non-existent member is unclear to me. Any insight or places I should 
> start exploring?
> 
> Galaxy version: various (started with an 6-month old one, upgraded to latest 
> production to see if it would fix error, it didn't)
> Hosting OS:  CentOS 6
> 
> --
> Paul Agapow (paul-michael.agapow at hpa.org.uk)
> Bioinformatics, Health Protection Agency (UK)
> 
-- 
Tim Booth 
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705
# This patch addresses 
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010303.html
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -582,9 +582,12 @@
   # Filter possible inputs to data types that are valid for 
subsequent steps
   type_filter = []
   for oc in step.output_connections:
+try:
   for ic in oc.input_step.module.get_data_inputs():
   if 'extensions' in ic and ic['name'] == oc.input_name:
   type_filter += ic['extensions']
+except AttributeError:
+  pass
   if not type_filter:
   type_filter = ['data']
   %>
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