Installed tool invisible in Galaxy

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Installed tool invisible in Galaxy

Peter van Heusden
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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Re: Installed tool invisible in Galaxy

John Chilton-4
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 <[hidden email]> 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/
___________________________________________________________
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/

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Re: Installed tool invisible in Galaxy

Peter van Heusden
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 <[hidden email]> 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/

___________________________________________________________
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/

capsule_with_dependencies_graphex.sanbi.ac.za_colon_9009_graph_report_pvanheus_81283dded1d9.tar.gz (4K) Download Attachment
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Re: Installed tool invisible in Galaxy

John Chilton-4
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 <[hidden email]> 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 <[hidden email]> 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/
>
___________________________________________________________
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/
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Re: Installed tool invisible in Galaxy

Peter van Heusden
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 <[hidden email]> 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 <[hidden email]> 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/



___________________________________________________________
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/