Hello Björn,

On Apr 6, 2013, at 9:06 AM, Björn Grüning wrote:

> Hi Greg and Dave,
> 
> good to know that it is at least installing :)
> I also tried without apache, fresh checkout and get the same timeouts.
> Maybe my computer is just so slow that its triggers the timeout. Also my
> Memory is very limited and nearly swapped during compilation.
> 
> But with the new API I'm able to install all of them just fine. Is that
> explainable?
> During my experiments I found that im not able to install the tools if a
> new-panel-section is supplied:
> 
> galaxy.web.framework ERROR 2013-04-06 14:29:05,411 Uncaught exception in
> exposed API method:
> 
> Traceback (most recent call last):
>  File
> "/home/bag/projects/galaxy/galaxy-central/lib/galaxy/web/framework/__init__.py",
>  line 196, in decorator
>    rval = func( self, trans, *args, **kwargs)
>  File
> "/home/bag/projects/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py",
>  line 254, in install_repository_revision
>    reinstalling=False )
>  File
> "/home/bag/projects/galaxy/galaxy-central/lib/tool_shed/galaxy_install/repository_util.py",
>  line 358, in install_tool_shed_repository
>    if tool_panel_section_key:
>  File "/usr/lib/python2.7/UserDict.py", line 23, in __getitem__
>    raise KeyError(key)
> KeyError: 'section_chemicaltoolbox'


This issue should be fixed in revision 3a07307 - thanks for reporting this!


> 
> Without that option it works. I tried to understand the code-path but
> found no section where a new entry is created under the toolbox. What I
> found is that: tool_panel_section_keys in repository_dependecy_util.py
> line 235 is updated every time and you will end up with several
> identical instances of 'section_chemicaltoolbox'. Hope that helps a
> little bit.

I'm not able to reproduce this (assuming it is not related to the issue I fixed 
above).  Is this issue now resolved for your?

> 
> Also please see a pull-request for a small typo:
> https://bitbucket.org/galaxy/galaxy-central/pull-request/150/change-error-message/diff


This pull request has been accepted  - thanks for the fixes!


> 
> Thanks for your work!
> Bjoern
> 
> 
> 
> 
>> Hello Björn,
>> 
>> Dave Bouvier (cc'd on this) spent some time yesterday inspecting the logs 
>> for out test tool shed and found no timeouts in either our paster log or our 
>> nginx log.  Dave was also successful in installing your repository and 
>> dependencies.  If I remember correctly, this timeout issue may be 
>> intermittent, but again, Dave found no logged timeout events at our end.  If 
>> you uncover any additional information, please let us know, and we'll 
>> continue to keep an eye on this.
>> 
>> Thanks very much,
>> 
>> Greg Von Kuster
>> 
>> 
>> On Apr 4, 2013, at 5:32 AM, Björn Grüning wrote:
>> 
>>> Hi Greg,
>>> 
>>> sorry forgot to attach the new traceback. Its now attached.
>>> If the grepping with the IP address did not work, maybe you can grep for
>>> the chemicaltoolbox/chemfp/openbabel/osra repositories. Im probably the
>>> only one working with it.
>>> 
>>> Have a nice day!
>>> Bjoern
>>> 
>>>> Hello Björn,
>>>> 
>>>> Thanks very much for your message!  Please see my inline comments.
>>>> 
>>>> 
>>>> On Apr 2, 2013, at 4:33 PM, Björn Grüning wrote:
>>>> 
>>>>> I have tested a few things regarding to the toolshed and prepared a
>>>>> complex module-dependency-beast, with meta-package and
>>>>> orhphan-tool-dependencies and so on. A few problems I encountered are
>>>>> summarized below. You can try it by yourself, if you install the
>>>>> chemicaltoolbox package from the testtoolshed.
>>>>> 
>>>>> - three crashes with traceback attached, during tool-installation
>>>>> 
>>>>> - one 'name' not defined error, with attached patch
>>>> 
>>>> 
>>>> Thanks very much for finding this issue and for the patch.  We've applied 
>>>> it in changeset 9252:da2d6ee29f30 in our stable branch, so it is running 
>>>> on both public Galaxy tool sheds.
>>>> 
>>>> 
>>>>> 
>>>>> - For me the the installation of tools with really complex and long
>>>>> compiling steps are stalled in 'Installing' forever. Try to install the
>>>>> osra package (it often hangs, but not every time). 
>>>>> Its not possible to uninstall/reinstall these dependencies
>>>>> without touching the database. And the error says, tool is already
>>>>> installed. Would be nice if the admin is able to reset that repository
>>>>> easily, even if it is limbo ... (is there a timeout somewhere?)
>>>>> Error: paste.httpserver.ThreadPool WARNING 2013-04-02 22:02:41,256 Thread 
>>>>> 140246687659776 hung (working on task for 1964 seconds)
>>>>> (The SystemExit: traceback attached)
>>>> 
>>>> I've create the following Trello card for this issue:
>>>> 
>>>> https://trello.com/card/toolshed-enable-galaxy-admin-to-reset-tool-dependencies-when-timeout-occurs/506338ce32ae458f6d15e4b3/761
>>>> 
>>>> There are 4 places where this timeout may be occurring: Galaxy tool shed 
>>>> server, Galaxy tool shed nginx, a proxy server at your end, or your local 
>>>> Galaxy server.  There is not enough information in your attached traceback 
>>>> log to determine where the timeout is occurring.  Can you provide me your 
>>>> Galaxy server's IP address so I can look in logs at our end?
>>>> 
>>>> 
>>>>> 
>>>>> - It would be great if the tool-developer or the admin has more control
>>>>> over the location of the tools in the toolbar. Installing meta package
>>>>> leaves you with only one choice, regardless how many tools are bundled. 
>>>> 
>>>> 
>>>> Support for this will be available in the next Galaxy release.  There are 
>>>> Trello cards for this here:
>>>> 
>>>> https://trello.com/card/toolshed-enhance-the-current-galaxy-api-for-installing-repositories-from-the-tool-shed/506338ce32ae458f6d15e4b3/734
>>>> https://trello.com/card/toolshed-add-features-that-leverage-the-galaxy-api-for-installing-repositories-from-the-tool-shed/506338ce32ae458f6d15e4b3/735
>>>> 
>>>> 
>>>>> 
>>>>> - Installing dependencies will leave me with empty folders under
>>>>> galaxy-root with the name of the dependency. My guess is, 
>>>>> that if I manually download a file/folder with wget, the folder is not 
>>>>> purged, but the content is.
>>>> 
>>>> 
>>>> Our intent is that installing repositories from the tool shed is 
>>>> completely automated with no manual intervention required.  Tool 
>>>> dependency definitions should not use utilities like wget to download 
>>>> dependencies because these utilities may not be available in the 
>>>> environments (e.g. vanilla mac os) into which the repositories are being 
>>>> installed.  I'll enhance the tool dependency tag sets as necessary to 
>>>> accommodate additional download and install requirements.  Can you let me 
>>>> know if the current download_by_url needs enhancements?
>>>> 
>>>> 
>>>>> 
>>>>> - Often after upgrading the tool_dependencies.xml file, I was not able
>>>>> to 'get updates' from the toolshed. The version was up-to-data, but it
>>>>> wasn't. Deinstalling and Installing fixed it. But I think its ab bug,
>>>>> isn't it?
>>>> 
>>>> This very well may be a bug.  Can you please provide additional details so 
>>>> that I can reproduce this behavior?  I'll get a fix asap.
>>>> 
>>>> 
>>>>> 
>>>>> - Is there a way, to just download a python file, not zipped and add it 
>>>>> to PYTHONPATH?
>>>>> If I download it with <action type="download_by_url"> I have problems to 
>>>>> copy that file with move.
>>>>> I would like to download it with wget, but one download by URL is 
>>>>> required. My current solution is, 
>>>>> to include a dummy download_by_url and than fetch with wget, or download 
>>>>> a archive version.
>>>> 
>>>> I've created the following Trello card for this issue:
>>>> 
>>>> https://trello.com/card/toolshed-enhance-the-download-by-url-process-for-installing-tool-dependencies/506338ce32ae458f6d15e4b3/760
>>>> 
>>>> 
>>>>> 
>>>>> - Is it correct that a repository referenced only in
>>>>> tool_dependencies.xml is not enough to install? numpy was only
>>>>> referenced as tool_dependency and I got the error that the tool (with
>>>>> owner and revision) was not found. After adding to repository_dependency
>>>>> it was ok.
>>>> 
>>>> Can you provide more details about your question above (e.g., the 
>>>> tool_dependencies.xml fie would help).  I want to make sure i understand 
>>>> the issue.  
>>>> 
>>>> Thanks very much Björn,
>>>> 
>>>> Greg Von Kuster
>>>> 
>>>> 
>>>> 
>>> 
>>> <trackback.txt>
>> 
> 
> 


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