Toolshed error with proprietary datatypes
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
Hello Bjoern, What version of Galaxy are you using? Your code base should be tracking the galaxy-central repository on bitbucket in order to use the tool shed with your local Galaxy instance. The galaxy-central repo is currently around 7201:62bdb265d300, and you can see the version you are running by typing the following in your Galaxy installation directory. %hg heads I believe this behavior will be resolved if you update to the latest code, but let me know if you continue to bump into problems. Thanks, Greg Von Kuster 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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Hi Greg,
What version of Galaxy are you using?
I could reproduce it with latest galaxy-central 7202:f4c4ba7be3d1. Same error and the converters are displayed in the tool menu. I will send you my tarball off the list, if you are interested in reproducing. Thanks, Bjoern
Your code base should be tracking the galaxy-central repository on bitbucket in order to use the tool shed with your local Galaxy instance. The galaxy-central repo is currently around 7201:62bdb265d300, and you can see the version you are running by typing the following in your Galaxy installation directory.
%hg heads
I believe this behavior will be resolved if you update to the latest code, but let me know if you continue to bump into problems.
Thanks,
Greg Von Kuster
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
___________________________________________________________ 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:
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 name description version requirements Convert inchi to mol2 1.0.0 none Convert inchi to mol 1.0.0 none Convert inchi to sdf 1.0.0 none Convert inchi to smiles 1.0.0 none Convert sdf to inchi 1.0.0 none Convert sdf to SMILES 1.0.0 none Convert SMILES to inchi 1.0.0 none Convert SMILES to MOL2 1.0.0 none Convert SMILES to MOL 1.0.0 none Convert SMILES to sdf 1.0.0 none Data types extension type mimetype subclass mol galaxy.datatypes.molFiles:SDF mol2 galaxy.datatypes.molFiles:MOL2 inchi galaxy.datatypes.molFiles:InChI smi galaxy.datatypes.molFiles:SMILES sdf galaxy.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
___________________________________________________________ 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:
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 name description version requirements Convert inchi to mol2 1.0.0 none Convert inchi to mol 1.0.0 none Convert inchi to sdf 1.0.0 none Convert inchi to smiles 1.0.0 none Convert sdf to inchi 1.0.0 none Convert sdf to SMILES 1.0.0 none Convert SMILES to inchi 1.0.0 none Convert SMILES to MOL2 1.0.0 none Convert SMILES to MOL 1.0.0 none Convert SMILES to sdf 1.0.0 none Data types extension type mimetype subclass mol galaxy.datatypes.molFiles:SDF mol2 galaxy.datatypes.molFiles:MOL2 inchi galaxy.datatypes.molFiles:InChI smi galaxy.datatypes.molFiles:SMILES sdf galaxy.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
___________________________________________________________ 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:
___________________________________________________________ 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:
Hello Bjoern, This should be resolved in change set 7211:16a93eb6eaf6, which is available from our central repository. Thanks for reporting this, and please let me know if you encounter additional issues. Greg Von Kuster 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
___________________________________________________________ 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:
Hi Greg, thanks! I can confirm that it is working now. I can upload new datatypes. What is not working is the update of such tools from the toolshed. I get the following error. URL: http://localhost/toolshed/repository/check_for_updates?galaxy_url=http://localhost/&name=molecule_datatypes&owner=admin&changeset_revision=2a638740087d&webapp=galaxy&no_reset=true Module paste.exceptions.errormiddleware:143 in __call__
app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.webapps.community.controllers.repository:684 in check_for_updates url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) UnboundLocalError: local variable 'latest_ctx' referenced before assignment
Removing and installing works fine. If you need more information to track that bug done, let me know. Cheers, Bjoern
Hello Bjoern,
This should be resolved in change set 7211:16a93eb6eaf6, which is available from our central repository. Thanks for reporting this, and please let me know if you encounter additional issues.
Greg Von Kuster
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
___________________________________________________________ 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:
-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
Hi Bjoren, What revision are you seeing this in? I don't think this issues exists in Galaxy central's tip, but let me know. Thanks! Greg On Jun 8, 2012, at 10:44 AM, Björn Grüning wrote:
Hi Greg,
thanks! I can confirm that it is working now. I can upload new datatypes. What is not working is the update of such tools from the toolshed. I get the following error.
URL: http://localhost/toolshed/repository/check_for_updates?galaxy_url=http://localhost/&name=molecule_datatypes&owner=admin&changeset_revision=2a638740087d&webapp=galaxy&no_reset=true Module paste.exceptions.errormiddleware:143 in __call__
app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.webapps.community.controllers.repository:684 in check_for_updates url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) UnboundLocalError: local variable 'latest_ctx' referenced before assignment
Removing and installing works fine. If you need more information to track that bug done, let me know.
Cheers, Bjoern
Hello Bjoern,
This should be resolved in change set 7211:16a93eb6eaf6, which is available from our central repository. Thanks for reporting this, and please let me know if you encounter additional issues.
Greg Von Kuster
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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-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br.
Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
participants (2)
-
Björn Grüning -
Greg Von Kuster