Hi all, I just updated our Galaxy from the latest dist to the latest central release. When I had previously updatet to the dist release, the emboss datatypes were installed as a shed tool. However when restarting the server after the update the datatypes_conf.xml in the emboss shed directory got deleted. After some back and forth I ended up with the following error, which I can't seem to resolve. galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File "/galaxy/galaxy_server/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/galaxy/galaxy_server/lib/galaxy/app.py", line 58, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/galaxy/galaxy_server/lib/galaxy/tool_shed/__init__.py", line 21, in load_proprietary_datatypes datatypes_config = metadata[ 'datatypes_config' ] KeyError: 'datatypes_config' Any help would be greatly appreciated! Thanks! Sarah
Hello Sarah, This is due to a known bug (not yet fixed in the distribution). The bug causes the file named "datatypes_conf.xml" included in installed repositories to be deleted. You'll need to go to the directory on disk where your emboss_datatypes repository is installed ( make sure you are in the directory where the file named datatypes_conf.xml exists in the installed repository directory) and type the following command (this will undelete the file). %hg revert datatypes_conf.xml If you'd like to apply a fix to the code in your local instance, do the following. You'll need to apply the fix to the file ~/lib/galaxy/util/shed_util.py. The end of the method named alter_config_and_load_proprietary_datatypes() looks like the following (these lines should be about 601 - 607 in your version of the file, I believe). # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) try: os.unlink( proprietary_datatypes_config ) except: pass return converter_path, display_path You'll need to make this change (note the if statement that now contains the try block): # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) if datatype_files: try: os.unlink( proprietary_datatypes_config ) except: pass return converter_path, display_path Sorry for the inconvenience - I'll get this fix out as soon as I possibly can. Let me know if you bump into any problems with this. Greg Von Kuster On Feb 24, 2012, at 10:42 AM, Sarah Diehl wrote:
Hi all,
I just updated our Galaxy from the latest dist to the latest central release. When I had previously updatet to the dist release, the emboss datatypes were installed as a shed tool. However when restarting the server after the update the datatypes_conf.xml in the emboss shed directory got deleted. After some back and forth I ended up with the following error, which I can't seem to resolve.
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File "/galaxy/galaxy_server/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/galaxy/galaxy_server/lib/galaxy/app.py", line 58, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/galaxy/galaxy_server/lib/galaxy/tool_shed/__init__.py", line 21, in load_proprietary_datatypes datatypes_config = metadata[ 'datatypes_config' ] KeyError: 'datatypes_config'
Any help would be greatly appreciated! Thanks!
Sarah ___________________________________________________________ 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 for the help! However, the error still persists. I tried to play around with lots of things, but nothing seems to change the error. Sarah On 02/24/2012 05:06 PM, Greg Von Kuster wrote:
Hello Sarah,
This is due to a known bug (not yet fixed in the distribution). The bug causes the file named "datatypes_conf.xml" included in installed repositories to be deleted. You'll need to go to the directory on disk where your emboss_datatypes repository is installed ( make sure you are in the directory where the file named datatypes_conf.xml exists in the installed repository directory) and type the following command (this will undelete the file).
%hg revert datatypes_conf.xml
If you'd like to apply a fix to the code in your local instance, do the following.
You'll need to apply the fix to the file ~/lib/galaxy/util/shed_util.py. The end of the method named alter_config_and_load_proprietary_datatypes() looks like the following (these lines should be about 601 - 607 in your version of the file, I believe).
# Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) try: os.unlink( proprietary_datatypes_config ) except: pass return converter_path, display_path
You'll need to make this change (note the if statement that now contains the try block):
# Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) if datatype_files: try: os.unlink( proprietary_datatypes_config ) except: pass return converter_path, display_path
Sorry for the inconvenience - I'll get this fix out as soon as I possibly can. Let me know if you bump into any problems with this.
Greg Von Kuster
On Feb 24, 2012, at 10:42 AM, Sarah Diehl wrote:
Hi all,
I just updated our Galaxy from the latest dist to the latest central release. When I had previously updatet to the dist release, the emboss datatypes were installed as a shed tool. However when restarting the server after the update the datatypes_conf.xml in the emboss shed directory got deleted. After some back and forth I ended up with the following error, which I can't seem to resolve.
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File "/galaxy/galaxy_server/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/galaxy/galaxy_server/lib/galaxy/app.py", line 58, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/galaxy/galaxy_server/lib/galaxy/tool_shed/__init__.py", line 21, in load_proprietary_datatypes datatypes_config = metadata[ 'datatypes_config' ] KeyError: 'datatypes_config'
Any help would be greatly appreciated! Thanks!
Sarah ___________________________________________________________ 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:
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