Hi paul,

I've forwarded this thread to the galaxy-dev mail list as that is where these 
types of issues are discussed.  Please keep the list included in your responses 
so that other interested parties can follow the thread.

Regarding this issue, your initial problem was regarding uploading a file to a 
repository that you successfully created, but your pater log does not include 
anything about uploading.  Can you clarify what the problem is?  I'll need as 
much context as you can provide.  For example, have you successfully created a 
new repository?  If so, is the problem still that you cannot upload a file to 
it?  If this is the case, can you send me the file you are attempting to 
upload?  What are the contents of your hgweb.config file, which is located in 
you Galaxy install directory?

Thanks,

Greg Von Kuster


On Apr 17, 2012, at 4:34 AM, Paul-Michael Agapow wrote:

> Thanks Greg,
>  
> Here’s the last bit, the last two failed attempts. Looks like it’s failing to 
> find a temporary directory. Shouldn’t make any difference, but I’m running 
> this out of a user account as I play round with the toolshed features.
>  
> Cheers
>  
> p
>  
> transaction abort!
> rollback completed
> transaction abort!
> rollback completed
> 158.119.175.46 - - [10/Apr/2012:13:57:08 +0100] "POST 
> /upload/upload?repository_id=adb5f5c93f827949 HTTP/1.1" 500 - 
> "http://158.119.147.40:9009/
> upload/upload?repository_id=adb5f5c93f827949&webapp=community" "Mozilla/5.0 
> (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrom
> e/17.0.963.78 Safari/535.11"
> Error - <type 'exceptions.TypeError'>: array item must be char
> 158.119.175.46 - - [10/Apr/2012:14:00:04 +0100] "GET 
> /repository/browse_repositories?webapp=community&operation=my_repositories 
> HTTP/1.1" 200 -
> "http://158.119.147.40:9009/repository?webapp=community"; "Mozilla/5.0 
> (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrome/17.0
> .963.78 Safari/535.11"
> 158.119.175.46 - - [10/Apr/2012:14:00:06 +0100] "GET 
> /repository/browse_repositories?f-deleted=False&f-email=p...@agapow.net&sort=name&show_item_
> checkboxes=false&async=false&page=1&webapp=community&operation=view_or_manage_repository&id=adb5f5c93f827949&
>  HTTP/1.1" 302 - "http://158.119.14
> 7.40:9009/repository/browse_repositories?webapp=community&operation=my_repositories"
>  "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KH
> TML, like Gecko) Chrome/17.0.963.78 Safari/535.11"
> Exception OSError: (2, 'No such file or directory', '/tmp/tmpxiB8nn') in 
> <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>',
> mode 'w+b' at 0xbc4d2a0>> ignored
> 158.119.175.46 - - [10/Apr/2012:14:00:06 +0100] "GET 
> /repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-dele
> ted=False&show_item_checkboxes=false&async=false&webapp=community&operation=view_or_manage_repository&page=1
>  HTTP/1.1" 200 - "http://158.119.147
> .40:9009/repository/browse_repositories?webapp=community&operation=my_repositories"
>  "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHT
> ML, like Gecko) Chrome/17.0.963.78 Safari/535.11"
> 158.119.175.46 - - [10/Apr/2012:14:00:11 +0100] "GET 
> /upload/upload?repository_id=adb5f5c93f827949&webapp=community HTTP/1.1" 200 
> - "http://158.
> 119.147.40:9009/repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-deleted=False&show_item_checkboxes=false&a
> sync=false&webapp=community&operation=view_or_manage_repository&page=1" 
> "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gec
> ko) Chrome/17.0.963.78 Safari/535.11"
> transaction abort!
> rollback completed
> transaction abort!
> rollback completed
> 158.119.175.46 - - [10/Apr/2012:14:00:30 +0100] "POST 
> /upload/upload?repository_id=adb5f5c93f827949 HTTP/1.1" 500 - 
> "http://158.119.147.40:9009/
> upload/upload?repository_id=adb5f5c93f827949&webapp=community" "Mozilla/5.0 
> (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrom
> e/17.0.963.78 Safari/535.11"
> Error - <type 'exceptions.TypeError'>: array item must be char
> 158.119.175.46 - - [10/Apr/2012:14:00:40 +0100] "GET 
> /repository/browse_repositories?webapp=community&operation=my_repositories 
> HTTP/1.1" 200 -
> "http://158.119.147.40:9009/repository?webapp=community"; "Mozilla/5.0 
> (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHTML, like Gecko) Chrome/17.0
> .963.78 Safari/535.11"
> 158.119.175.46 - - [10/Apr/2012:14:00:44 +0100] "GET 
> /repository/browse_repositories?f-deleted=False&f-email=p...@agapow.net&sort=name&show_item_
> checkboxes=false&async=false&page=1&webapp=community&operation=view_or_manage_repository&id=adb5f5c93f827949&
>  HTTP/1.1" 302 - "http://158.119.14
> 7.40:9009/repository/browse_repositories?webapp=community&operation=my_repositories"
>  "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KH
> TML, like Gecko) Chrome/17.0.963.78 Safari/535.11"
> 158.119.175.46 - - [10/Apr/2012:14:00:44 +0100] "GET 
> /repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-dele
> ted=False&show_item_checkboxes=false&async=false&webapp=community&operation=view_or_manage_repository&page=1
>  HTTP/1.1" 200 - "http://158.119.147
> .40:9009/repository/browse_repositories?webapp=community&operation=my_repositories"
>  "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHT
> ML, like Gecko) Chrome/17.0.963.78 Safari/535.11"
> 158.119.175.46 - - [10/Apr/2012:14:01:08 +0100] "GET 
> /repository/browse_repositories?f-deleted=False&f-email=p...@agapow.net&sort=name&show_item_
> checkboxes=false&async=false&page=1&webapp=community&operation=view_or_manage_repository&id=adb5f5c93f827949&
>  HTTP/1.1" 302 - "http://158.119.14
> 7.40:9009/repository/browse_repositories?webapp=community&operation=my_repositories"
>  "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KH
> TML, like Gecko) Chrome/17.0.963.78 Safari/535.11"
> Exception OSError: (2, 'No such file or directory', '/tmp/tmpTsL0B1') in 
> <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>',
> mode 'w+b' at 0xbc4d840>> ignored
> 158.119.175.46 - - [10/Apr/2012:14:01:08 +0100] "GET 
> /repository/manage_repository?sort=name&f-email=pma%40agapow.net&id=adb5f5c93f827949&f-dele
> ted=False&show_item_checkboxes=false&async=false&webapp=community&operation=view_or_manage_repository&page=1
>  HTTP/1.1" 200 - "http://158.119.147
> .40:9009/repository/browse_repositories?webapp=community&operation=my_repositories"
>  "Mozilla/5.0 (Windows NT 5.2; WOW64) AppleWebKit/535.11 (KHT
> ML, like Gecko) Chrome/17.0.963.78 Safari/535.11"
> Removing PID file community_webapp.pid
>  
>  
>  
>  
> ----
> Paul Agapow (paul-michael.aga...@hpa.org.uk)
> Bioinformatics, Health Protection Agency
>  
> From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Sent: 16 April 2012 14:23
> To: Paul-Michael Agapow
> Cc: 'galaxy-u...@lists.bx.psu.edu'
> Subject: Re: [galaxy-user] Toolshed initial upload errors out
>  
> Hi Paul,
>  
> On Apr 10, 2012, at 9:15 AM, Paul-Michael Agapow wrote:
> 
> 
> As per the title, I’m trying to setup a toolshed for our local use. After 
> creating a repo, I try to upload the initial file only to get:
>  
>     TypeError: array item must be char
>  
> Which seems to happen repeatedly, i.e. it’s not a passing error.
>  
>  
> I'll need to see your paster log to be able to help on this one.  You can 
> view it using "tail -f community_webapp.log" (without the quotes) from your 
> Galaxy install directory.  Can you respond back with the content?
>  
> 
> 
>  
> While I’m here, a perhaps obvious question: where or how does the main Galaxy 
> instance get the list of toolsheds to display? The main and test sheds are 
> hardcoded in, I guess, but how does it pick up the local – simply by virtue 
> of the fact that it is local?
>  
>  
> The list of tool sheds available to any local Galaxy instance is defined in 
> the tool_sheds_conf.xml file in the Galaxy install directory.  For your local 
> shed, you'll simply need to an entry like this:
>  
> <tool_shed name="Bx tool shed" url="http://gvk.bx.psu.edu:9009/"/>
>  
> 
> 
>  
> p
>  
> ----
> Paul Agapow (paul-michael.aga...@hpa.org.uk)
> Bioinformatics, Health Protection Agency
>  
> Thanks,
>  
> Greg Von Kuster
>  
> 
> 
>  
>  
>  
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