Galaxy ToolShed Update Problem

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Galaxy ToolShed Update Problem

孙兆朕
Hi all,

I want to update some of my tool plug-in and some problem shows, even if I updated my Galaxy instance to the latest. I suppose it is not related to the version of Galaxy. 

The problem occured when I used the administrator's panel and update my plug-in using the  "Get updates" option. The next page reports that an internal Server Error has occured and the update was not successful.  All the plug-in updates seems had the same problem.

I checked the logs where I get the following message:

CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
  HTTP_CONNECTION: 'close'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
  HTTP_HOST: '222.28.163.110'
  HTTP_REFERER: 'http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E.'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
  HTTP_X_FORWARDED_FOR: '222.28.170.89'
  HTTP_X_FORWARDED_HOST: '222.28.163.110'
  ORGINAL_HTTP_HOST: '127.0.0.1:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
  QUERY_STRING: 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10'
  REMOTE_ADDR: '222.28.170.89'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
  is_api_request: False
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650>
  paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'a12a5604dce911e4a05000215e543aa8'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  wsgi process: 'Multithreaded'
------------------------------------------------------------
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 39438)
Traceback (most recent call last):
  File "/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
    self.finish()
  File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
    self.wfile.flush()
  File "/usr/lib64/python2.6/socket.py", line 303, in flush
    self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
----------------------------------------
222.28.170.89 - - [07/Apr/2015:13:47:59 +0800] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 HTTP/1.0" 500 - "http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36"
Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'get'
URL: http://222.28.163.110/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 133 in __call__
  return self.handle_request( environ, start_response )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 191 in handle_request
  body = method( trans, **kwargs )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 87 in decorator
  return func( self, trans, *args, **kwargs )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1954 in update_to_changeset_revision
  persist=True )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 31 in __init__
  metadata_dict=metadata_dict, user=None )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', line 60 in __init__
  self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) }
AttributeError: 'NoneType' object has no attribute 'get'


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
  HTTP_CONNECTION: 'close'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
  HTTP_HOST: '222.28.163.110'
  HTTP_REFERER: 'http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E.'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
  HTTP_X_FORWARDED_FOR: '222.28.170.89'
  HTTP_X_FORWARDED_HOST: '222.28.163.110'
  ORGINAL_HTTP_HOST: '127.0.0.1:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
  QUERY_STRING: 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10'
  REMOTE_ADDR: '222.28.170.89'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
  is_api_request: False
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650>
  paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'a58bb404dce911e481c700215e543aa8'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  wsgi process: 'Multithreaded'
------------------------------------------------------------

Could you please give me some advise to figure out where the problem is and how to fix it?
Thanks,

Zhaozhen



___________________________________________________________
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Re: Galaxy ToolShed Update Problem

Martin Čech
Hello Zhaozhen,

this is a known problem. The shed_tool_conf.xml got moved along with other configs into /config folder but unfortunately some tools stored the path absolutely in the DB. You can use the following script (which you should find in the Galaxy /scripts folder):
to update your DB to have the correct path to the config. 

Sorry for the inconvenience.

Martin, Galaxy Team


On Tue, Apr 7, 2015 at 10:16 AM 孙兆朕 <[hidden email]> wrote:
Hi all,

I want to update some of my tool plug-in and some problem shows, even if I updated my Galaxy instance to the latest. I suppose it is not related to the version of Galaxy. 

The problem occured when I used the administrator's panel and update my plug-in using the  "Get updates" option. The next page reports that an internal Server Error has occured and the update was not successful.  All the plug-in updates seems had the same problem.

I checked the logs where I get the following message:

CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
  HTTP_CONNECTION: 'close'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
  HTTP_HOST: '222.28.163.110'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
  HTTP_X_FORWARDED_FOR: '222.28.170.89'
  HTTP_X_FORWARDED_HOST: '222.28.163.110'
  ORGINAL_HTTP_HOST: '127.0.0.1:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
  REMOTE_ADDR: '222.28.170.89'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
  is_api_request: False
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650>
  paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'a12a5604dce911e4a05000215e543aa8'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  wsgi process: 'Multithreaded'
------------------------------------------------------------
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 39438)
Traceback (most recent call last):
  File "/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
    self.finish()
  File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
    self.wfile.flush()
  File "/usr/lib64/python2.6/socket.py", line 303, in flush
    self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
----------------------------------------
222.28.170.89 - - [07/Apr/2015:13:47:59 +0800] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 HTTP/1.0" 500 - "http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36"
Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'get'
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 133 in __call__
  return self.handle_request( environ, start_response )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 191 in handle_request
  body = method( trans, **kwargs )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 87 in decorator
  return func( self, trans, *args, **kwargs )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1954 in update_to_changeset_revision
  persist=True )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 31 in __init__
  metadata_dict=metadata_dict, user=None )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', line 60 in __init__
  self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) }
AttributeError: 'NoneType' object has no attribute 'get'


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
  HTTP_CONNECTION: 'close'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
  HTTP_HOST: '222.28.163.110'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
  HTTP_X_FORWARDED_FOR: '222.28.170.89'
  HTTP_X_FORWARDED_HOST: '222.28.163.110'
  ORGINAL_HTTP_HOST: '127.0.0.1:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
  REMOTE_ADDR: '222.28.170.89'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
  is_api_request: False
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650>
  paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'a58bb404dce911e481c700215e543aa8'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  wsgi process: 'Multithreaded'
------------------------------------------------------------

Could you please give me some advise to figure out where the problem is and how to fix it?
Thanks,

Zhaozhen


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: Galaxy ToolShed Update Problem

Martin Čech
Hi Zhaozhen,

the --config_file argument needs to point to galaxy.ini config so the script can load the database.

Galaxy continues to support Python 2.6 and 2.7, I am sorry that this script required 2.7 (or you could `pip install argparse`) - we will look into improving it.

Martin, Galaxy Team



On Wed, Apr 8, 2015 at 4:09 AM 孙兆朕 <[hidden email]> wrote:
Hi Martin,

Thanks for the advise. It helped a lot for me to figure out where the problem is. However, there were still error messages there.
I tried to run the update_shed_config_path.py script under the /script folder. At first it says there was no module named argparse, then I found out it was the python version problem, which required python 2.7+. Then I updated my python. Then there was another error said there was no module named galaxy.model.tool_shed_install. Then I tried harder, and found out that it was the path problem. I figured out the sys path was in the above folder. Then I copied and pasted the update_shed_config_path.py to the parent folder and seemed solved the problem. Then I run the update_shed_config_path.py and the command somehow run for a while, with the error message No module named _sqlite3. It must be the DB versions and plug-ins, then I fixed the DB. Then finally there came the following message:

usage: update_shed_config_path.py [-h] --config_file CONFIG_FILE --from
                                  BAD_FILENAME --to GOOD_FILENAME [--force]
update_shed_config_path.py: error: argument --config_file is required

I run the command line in: python2.7 update_shed_config_path.py
I wonder if I need some more input for the command line or something?
By the way, I hope there would be some advise for the new Galaxy administrtators to know their Python should be 2.7+ and file path issues. When I started to deploy Galaxy last year, the requirement in the web page was Python 2.5 or something lower than 2.6 I used. I think that message need to be updated as well.
Thanks in advance,

Yours,

Zhaozhen




argparse


At 2015-04-07 22:43:50, "Martin Čech" <[hidden email]> wrote:
Hello Zhaozhen,

this is a known problem. The shed_tool_conf.xml got moved along with other configs into /config folder but unfortunately some tools stored the path absolutely in the DB. You can use the following script (which you should find in the Galaxy /scripts folder):
to update your DB to have the correct path to the config. 

Sorry for the inconvenience.

Martin, Galaxy Team


On Tue, Apr 7, 2015 at 10:16 AM 孙兆朕 <[hidden email]> wrote:
Hi all,

I want to update some of my tool plug-in and some problem shows, even if I updated my Galaxy instance to the latest. I suppose it is not related to the version of Galaxy. 

The problem occured when I used the administrator's panel and update my plug-in using the  "Get updates" option. The next page reports that an internal Server Error has occured and the update was not successful.  All the plug-in updates seems had the same problem.

I checked the logs where I get the following message:

CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
  HTTP_CONNECTION: 'close'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
  HTTP_HOST: '222.28.163.110'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
  HTTP_X_FORWARDED_FOR: '222.28.170.89'
  HTTP_X_FORWARDED_HOST: '222.28.163.110'
  ORGINAL_HTTP_HOST: '127.0.0.1:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
  REMOTE_ADDR: '222.28.170.89'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
  is_api_request: False
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650>
  paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'a12a5604dce911e4a05000215e543aa8'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  wsgi process: 'Multithreaded'
------------------------------------------------------------
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 39438)
Traceback (most recent call last):
  File "/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
    self.finish()
  File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
    self.wfile.flush()
  File "/usr/lib64/python2.6/socket.py", line 303, in flush
    self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
----------------------------------------
222.28.170.89 - - [07/Apr/2015:13:47:59 +0800] "GET /admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10 HTTP/1.0" 500 - "http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E." "Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36"
Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'get'
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 133 in __call__
  return self.handle_request( environ, start_response )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py', line 191 in handle_request
  body = method( trans, **kwargs )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 87 in decorator
  return func( self, trans, *args, **kwargs )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1954 in update_to_changeset_revision
  persist=True )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 31 in __init__
  metadata_dict=metadata_dict, user=None )
File '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py', line 60 in __init__
  self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) }
AttributeError: 'NoneType' object has no attribute 'get'


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
  HTTP_CONNECTION: 'close'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
  HTTP_HOST: '222.28.163.110'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
  HTTP_X_FORWARDED_FOR: '222.28.170.89'
  HTTP_X_FORWARDED_HOST: '222.28.163.110'
  ORGINAL_HTTP_HOST: '127.0.0.1:8080'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
  REMOTE_ADDR: '222.28.170.89'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
  is_api_request: False
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>, 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xd888fd0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xdcf8650>
  paste.parsed_querystring: ([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')], 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: 'a58bb404dce911e481c700215e543aa8'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner', 'devteam'), ('changeset_revision', 'de11e1a921c4'), ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]), 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10')
  wsgi process: 'Multithreaded'
------------------------------------------------------------

Could you please give me some advise to figure out where the problem is and how to fix it?
Thanks,

Zhaozhen


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