Installed tool invisible in Galaxy
Hi there I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error: Error - <type 'exceptions.AttributeError'>: 'Tool' object has no attribute 'citations' A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is not in any of the Tool categories. Deleting and re-installing the tool does not fix this problem - and on installation time I never get asked what group to add it to. It seems as if it is somehow "stuck" in an incorrect state. Any ideas where to go poking? Presumably there is somewhere in the database to go poking to "reset" things. Thanks, Peter P.S. this is with the latest Galaxy from galaxy-central.
Hey Peter, When you are deleting and reinstalling the tool - can you confirm for me that you are definitely deleting the tool and not just deactivating it? I don't know where to hack around from there - I think repositories are tracked in the database (tool_shed_repository) table, in shed_tool_conf.xml, integrated_tool_panel.xml, shed_tools directory, tool_dependencies directory. It would be interesting to know which of these still have references to the tool after you delete it. I am also interested in the underlying bug - are you running multiple Galaxy processes? Can you send me the tool that produced this error? -John On Tue, Aug 12, 2014 at 10:08 AM, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Hi there
I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error:
Error - <type 'exceptions.AttributeError'>: 'Tool' object has no attribute 'citations'
A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is not in any of the Tool categories. Deleting and re-installing the tool does not fix this problem - and on installation time I never get asked what group to add it to. It seems as if it is somehow "stuck" in an incorrect state.
Any ideas where to go poking? Presumably there is somewhere in the database to go poking to "reset" things.
Thanks, Peter P.S. this is with the latest Galaxy from galaxy-central.
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1. Yes, its definitely a delete (checked the box). 2. The tool, once added, creates: a. the correct directory structure in shed_tools/ b. an entry in the tool_shed_repository table that *appears* to be correct c. an entry in shed_tool_conf.xml with the annotation of the Graph section (where it was originally located before being deleted d. *no entry* in integrated_tool_panel.xml 3. When the tool is deleted: a. the shed_tools/ directory is cleaned out except for the top level directory (graph_report) of the tool b. the entry in the tool_shed_repository table remains c. the entry in shed_tool_conf.xml remains d. there is still no integrated_tool_panel.xml In terms of the database, tool_version_association references tool_version which references tool_shed_repository, so you need to delete entries all along that chain to remove an entry from tool_shed_repository. The tool and its type dependency are attached. On 12/08/2014 16:43, John Chilton wrote:
Hey Peter,
When you are deleting and reinstalling the tool - can you confirm for me that you are definitely deleting the tool and not just deactivating it?
I don't know where to hack around from there - I think repositories are tracked in the database (tool_shed_repository) table, in shed_tool_conf.xml, integrated_tool_panel.xml, shed_tools directory, tool_dependencies directory. It would be interesting to know which of these still have references to the tool after you delete it.
I am also interested in the underlying bug - are you running multiple Galaxy processes? Can you send me the tool that produced this error?
-John
On Tue, Aug 12, 2014 at 10:08 AM, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Hi there
I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error:
Error - <type 'exceptions.AttributeError'>: 'Tool' object has no attribute 'citations'
A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is not in any of the Tool categories. Deleting and re-installing the tool does not fix this problem - and on installation time I never get asked what group to add it to. It seems as if it is somehow "stuck" in an incorrect state.
Any ideas where to go poking? Presumably there is somewhere in the database to go poking to "reset" things.
Thanks, Peter P.S. this is with the latest Galaxy from galaxy-central.
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I think your tool has an XML error in it (the in_graph_filename param is not being closed) - I imagine this would prevent Galaxy from displaying the tool - cannot say if it is the only error though: <param format="graphml" name="in_graph_filename" type="data" label="Protein interaction graph" </inputs> -John On Tue, Aug 12, 2014 at 2:00 PM, Peter van Heusden <pvh@sanbi.ac.za> wrote:
1. Yes, its definitely a delete (checked the box).
2. The tool, once added, creates:
a. the correct directory structure in shed_tools/ b. an entry in the tool_shed_repository table that *appears* to be correct c. an entry in shed_tool_conf.xml with the annotation of the Graph section (where it was originally located before being deleted d. *no entry* in integrated_tool_panel.xml
3. When the tool is deleted:
a. the shed_tools/ directory is cleaned out except for the top level directory (graph_report) of the tool b. the entry in the tool_shed_repository table remains c. the entry in shed_tool_conf.xml remains d. there is still no integrated_tool_panel.xml
In terms of the database, tool_version_association references tool_version which references tool_shed_repository, so you need to delete entries all along that chain to remove an entry from tool_shed_repository.
The tool and its type dependency are attached.
On 12/08/2014 16:43, John Chilton wrote:
Hey Peter,
When you are deleting and reinstalling the tool - can you confirm for me that you are definitely deleting the tool and not just deactivating it?
I don't know where to hack around from there - I think repositories are tracked in the database (tool_shed_repository) table, in shed_tool_conf.xml, integrated_tool_panel.xml, shed_tools directory, tool_dependencies directory. It would be interesting to know which of these still have references to the tool after you delete it.
I am also interested in the underlying bug - are you running multiple Galaxy processes? Can you send me the tool that produced this error?
-John
On Tue, Aug 12, 2014 at 10:08 AM, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Hi there
I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error:
Error - <type 'exceptions.AttributeError'>: 'Tool' object has no attribute 'citations'
A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is not in any of the Tool categories. Deleting and re-installing the tool does not fix this problem - and on installation time I never get asked what group to add it to. It seems as if it is somehow "stuck" in an incorrect state.
Any ideas where to go poking? Presumably there is somewhere in the database to go poking to "reset" things.
Thanks, Peter P.S. this is with the latest Galaxy from galaxy-central.
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Aha, that's true! With the XML fixed, the installation dialogue changes, and displays the "Add new tool panel section" and subsequent parts of the page. This would *appear* to come from the check for includes_tools_for_display_in_tool_panel on line 1620 of lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py which in turn is (eventually) pulled from the repository model I think. Peter On 12/08/2014 20:03, John Chilton wrote:
I think your tool has an XML error in it (the in_graph_filename param is not being closed) - I imagine this would prevent Galaxy from displaying the tool - cannot say if it is the only error though:
<param format="graphml" name="in_graph_filename" type="data" label="Protein interaction graph" </inputs>
-John
On Tue, Aug 12, 2014 at 2:00 PM, Peter van Heusden <pvh@sanbi.ac.za> wrote:
1. Yes, its definitely a delete (checked the box).
2. The tool, once added, creates:
a. the correct directory structure in shed_tools/ b. an entry in the tool_shed_repository table that *appears* to be correct c. an entry in shed_tool_conf.xml with the annotation of the Graph section (where it was originally located before being deleted d. *no entry* in integrated_tool_panel.xml
3. When the tool is deleted:
a. the shed_tools/ directory is cleaned out except for the top level directory (graph_report) of the tool b. the entry in the tool_shed_repository table remains c. the entry in shed_tool_conf.xml remains d. there is still no integrated_tool_panel.xml
In terms of the database, tool_version_association references tool_version which references tool_shed_repository, so you need to delete entries all along that chain to remove an entry from tool_shed_repository.
The tool and its type dependency are attached.
On 12/08/2014 16:43, John Chilton wrote:
Hey Peter,
When you are deleting and reinstalling the tool - can you confirm for me that you are definitely deleting the tool and not just deactivating it?
I don't know where to hack around from there - I think repositories are tracked in the database (tool_shed_repository) table, in shed_tool_conf.xml, integrated_tool_panel.xml, shed_tools directory, tool_dependencies directory. It would be interesting to know which of these still have references to the tool after you delete it.
I am also interested in the underlying bug - are you running multiple Galaxy processes? Can you send me the tool that produced this error?
-John
On Tue, Aug 12, 2014 at 10:08 AM, Peter van Heusden <pvh@sanbi.ac.za> wrote:
Hi there
I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error:
Error - <type 'exceptions.AttributeError'>: 'Tool' object has no attribute 'citations'
A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is not in any of the Tool categories. Deleting and re-installing the tool does not fix this problem - and on installation time I never get asked what group to add it to. It seems as if it is somehow "stuck" in an incorrect state.
Any ideas where to go poking? Presumably there is somewhere in the database to go poking to "reset" things.
Thanks, Peter P.S. this is with the latest Galaxy from galaxy-central.
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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John Chilton -
Peter van Heusden