Recent problematic change in the Galaxy Toolshed
Hi, I just tried to upload a new version of the Grinder Galaxy wrapper to the Galaxy ToolShed and am encountering difficulties that I did have in previous versions. When I upload my .tar.gz file, the upload is aborted and I get the error:
'GalaxyWebUITransaction' object has no attribute 'tool_data_tables'
When I remove my tool_data_table_conf.xml.sample file from the tarball and try re-uploading, I get this warning:
The file 'grinder-galaxy-0.4.3.tar.gz' has been successfully uncompressed and uploaded to the repository. 1 files were removed from the repository root. Metadata cannot be defined for revision 'c9fee6113b0d' so this revision cannot be automatically installed into a local Galaxy instance. Correct the following problems and reset metadata. grinder.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to resolve this issue.
These two messages are contradictory. Also, if I am not allowed to define a new datatable with this name, how I am suppose to have a tool use data tables? Thanks, Florent
Hello Florent, Sorry you encountered this issue. It results from a recently introduce typo in the tool shed code when uploading into a repo that depends on tool data table entries. I've corrected the problem in the tool shed. I also inspected your repository that contains the grinder tool and noticed that the state of the repository was such that the tool_data_table_conf.xml.sample file was added but not committed, so I committed it for you. I also downloaded and installed this repository into my local instance with no problems, so I believe your grinder repository is now in a good state. Thanks very much for reporting this issue. Greg Von Kuster On Jan 17, 2012, at 8:43 PM, Florent Angly wrote:
Hi,
I just tried to upload a new version of the Grinder Galaxy wrapper to the Galaxy ToolShed and am encountering difficulties that I did have in previous versions.
When I upload my .tar.gz file, the upload is aborted and I get the error:
'GalaxyWebUITransaction' object has no attribute 'tool_data_tables'
When I remove my tool_data_table_conf.xml.sample file from the tarball and try re-uploading, I get this warning:
The file 'grinder-galaxy-0.4.3.tar.gz' has been successfully uncompressed and uploaded to the repository. 1 files were removed from the repository root. Metadata cannot be defined for revision 'c9fee6113b0d' so this revision cannot be automatically installed into a local Galaxy instance. Correct the following problems and reset metadata. grinder.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to resolve this issue.
These two messages are contradictory. Also, if I am not allowed to define a new datatable with this name, how I am suppose to have a tool use data tables?
Thanks,
Florent
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Thank you very much Greg. Florent On 19/01/12 02:50, Greg Von Kuster wrote:
Hello Florent,
Sorry you encountered this issue. It results from a recently introduce typo in the tool shed code when uploading into a repo that depends on tool data table entries. I've corrected the problem in the tool shed. I also inspected your repository that contains the grinder tool and noticed that the state of the repository was such that the tool_data_table_conf.xml.sample file was added but not committed, so I committed it for you. I also downloaded and installed this repository into my local instance with no problems, so I believe your grinder repository is now in a good state. Thanks very much for reporting this issue.
Greg Von Kuster
On Jan 17, 2012, at 8:43 PM, Florent Angly wrote:
Hi,
I just tried to upload a new version of the Grinder Galaxy wrapper to the Galaxy ToolShed and am encountering difficulties that I did have in previous versions.
When I upload my .tar.gz file, the upload is aborted and I get the error:
'GalaxyWebUITransaction' object has no attribute 'tool_data_tables' When I remove my tool_data_table_conf.xml.sample file from the tarball and try re-uploading, I get this warning: The file 'grinder-galaxy-0.4.3.tar.gz' has been successfully uncompressed and uploaded to the repository. 1 files were removed from the repository root. Metadata cannot be defined for revision 'c9fee6113b0d' so this revision cannot be automatically installed into a local Galaxy instance. Correct the following problems and reset metadata. grinder.xml - This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to resolve this issue. These two messages are contradictory. Also, if I am not allowed to define a new datatable with this name, how I am suppose to have a tool use data tables?
Thanks,
Florent
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
participants (2)
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Florent Angly -
Greg Von Kuster