Hello Bjoern,

I've reproduced this problem by stopping and attempting to restart my my Galaxy server after installing your repository - very sorry I missed that step in your description.  I'll get back to you with a fix as soon as I have it.

Greg Von Kuster


On May 29, 2012, at 3:34 PM, Greg Von Kuster wrote:

Hello Bjoern,

I've uploaded your tar archive (from your separate email) to my local tool shed, and have the following tools and datatypes displayed in the repository.

Preview tools and inspect metadata by tool version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
namedescriptionversionrequirements
1.0.0none
1.0.0none
1.0.0none
1.0.0none
1.0.0none
1.0.0none
1.0.0none
1.0.0none
1.0.0none
1.0.0none
Data types
extensiontypemimetypesubclass
molgalaxy.datatypes.molFiles:SDF  
mol2galaxy.datatypes.molFiles:MOL2  
inchigalaxy.datatypes.molFiles:InChI  
smigalaxy.datatypes.molFiles:SMILES  
sdfgalaxy.datatypes.molFiles:SDF  

I'm also able to successfully install the repository from my local tool shed to my local galaxy instance, but see some problems - here is the relevant section of the paster log.  It looks like most of the problems are due to the way you are importing modules into your mofFiles.py modules.  Keep in mind that anything you import must be found in the environment in which your repository is installed.   I don't have pybel available in my environment, so the molFiles module won't properly load and also none of the proprietary datatypes are loadable.
###################
galaxy.web.controllers.admin_toolshed DEBUG 2012-05-29 15:05:30,173 Loading new tool panel section: gruning
galaxy.util.shed_util DEBUG 2012-05-29 15:05:30,888 Adding new row (or updating an existing row) for repository 'gruning' in the tool_shed_repository table.
galaxy.datatypes.registry DEBUG 2012-05-29 15:05:31,573 Loading datatypes from /Users/gvk/workspaces_2008/central_051111/database/tmp/tmpFpn0k6
galaxy.datatypes.registry DEBUG 2012-05-29 15:05:31,623 Exception importing proprietary code file /Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gruning/178caf3f76c0/gruning/datatypes/molFiles: No module named pybel
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,624 Error loading datatype with extension 'mol': 'module' object has no attribute 'molFiles'
galaxy.datatypes.registry DEBUG 2012-05-29 15:05:31,625 Exception importing proprietary code file /Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gruning/178caf3f76c0/gruning/datatypes/molFiles: No module named pybel
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,625 Error loading datatype with extension 'mol2': 'module' object has no attribute 'molFiles'
galaxy.datatypes.registry DEBUG 2012-05-29 15:05:31,626 Exception importing proprietary code file /Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gruning/178caf3f76c0/gruning/datatypes/molFiles: No module named pybel
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,627 Error loading datatype with extension 'inchi': 'module' object has no attribute 'molFiles'
galaxy.datatypes.registry DEBUG 2012-05-29 15:05:31,628 Exception importing proprietary code file /Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gruning/178caf3f76c0/gruning/datatypes/molFiles: No module named pybel
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,628 Error loading datatype with extension 'smi': 'module' object has no attribute 'molFiles'
galaxy.datatypes.registry DEBUG 2012-05-29 15:05:31,629 Exception importing proprietary code file /Users/gvk/workspaces_2008/shed_tools/gvk.bx.psu.edu/repos/test/gruning/178caf3f76c0/gruning/datatypes/molFiles: No module named pybel
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,629 Error loading datatype with extension 'sdf': 'module' object has no attribute 'molFiles'
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,629 Error appending sniffer for datatype 'galaxy.datatypes.molFiles:SDF' to sniff_order: No module named molFiles
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,629 Error appending sniffer for datatype 'galaxy.datatypes.molFiles:MOL2' to sniff_order: No module named molFiles
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,629 Error appending sniffer for datatype 'galaxy.datatypes.molFiles:InChI' to sniff_order: No module named molFiles
galaxy.datatypes.registry WARNING 2012-05-29 15:05:31,630 Error appending sniffer for datatype 'galaxy.datatypes.molFiles:SMILES' to sniff_order: No module named molFiles
###################
In any case, I'm still not able to produce the behavior you've logged below, and my line numbers for certain method calls are different from yours.  For example, your 
 File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
   self.installed_repository_manager.load_proprietary_datatypes()

is line 66 in my version of app.py.

Your

 File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
26, in load_proprietary_datatypes
   load_datatype_items( self.app, tool_shed_repository,
relative_install_dir )

is the following line 46 in my version of ~/tools_shed/__init__.py:

galaxy.util.shed_util.load_datatype_items( self.app, tool_shed_repository, relative_install_dir )

I still believe your code base for your Galaxy instance (and perhaps your local tool shed) is not current with that in our galaxy-central repository.  What is the result of typing the following in your Galaxy installation directory?

%hg heads

Also, to answer your question about displaying datatype converters as tools in the tool shed, yes, this is intended behavior.  Since datatype converters are valid Galaxy tools (just loaded differently in the Galaxy toolbox), I don't differentiate between them and other valid Galaxy tools (at least for the current time).


On May 26, 2012, at 10:51 AM, Björn Grüning wrote:

Hi,

has anyone encountered that problem or has an idea how to solve it?

Traceback (most recent call last):
 File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in
app_factory
   app = UniverseApplication( global_conf = global_conf, **kwargs )
 File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
   self.installed_repository_manager.load_proprietary_datatypes()
 File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
26, in load_proprietary_datatypes
   load_datatype_items( self.app, tool_shed_repository,
relative_install_dir )
 File "/home/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036,
in load_datatype_items
   app.datatypes_registry.load_datatype_converters( app.toolbox,
installed_repository_dict=repository_dict, deactivate=deactivate )
AttributeError: 'UniverseApplication' object has no attribute 'toolbox'

All files are in one repository ... xml, the python-class und the
converters. I was able to successfully upload it to our test-toolshed
but after installing it (also successfully) galaxy is not able to start.
Also the converters are recognised as tools in the toolshed is that
intended?

Thanks!
Bjoern

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