Re: [galaxy-dev] [galaxy-user] Toolshed initial upload errors out
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=pma@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=pma@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=pma@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.agapow@hpa.org.uk) Bioinformatics, Health Protection Agency
From: Greg Von Kuster [mailto:greg@bx.psu.edu] Sent: 16 April 2012 14:23 To: Paul-Michael Agapow Cc: 'galaxy-user@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.agapow@hpa.org.uk) Bioinformatics, Health Protection Agency
Thanks,
Greg Von Kuster
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Greg Von Kuster