Hey Peter,

I've reproduced this here, thanks.  Unfortunately this got missed
previously, once we had the import itself working.  To be clear, though,
the workflow itself is still completely functional, imports and runs, and
the only issue is the inability to view the svg?

I think what's causing this is that generate_workflow_image uses completely
separate workflow modules which didn't have my previous fixes applied.
 This should be refactored so we don't have duplicated code sitting around,
but I'll go ahead and patch it to get it working again shortly.


On Wed, Aug 21, 2013 at 6:45 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> Hi Dannon,
>
> I'm seeing a problem which seems very similar to the one Bjoern
> had back in June with the same workflow (which appeared to have
> been fixed according to the old IUC thread "Workflow import is not
> working").
>
> This server is running the current galaxy-dist release,
>
> $ sudo -u galaxy hg head
> changeset:   10411:c42567f43aa7
> tag:         tip
> user:        greg
> date:        Mon Aug 19 13:19:56 2013 -0400
> summary:     Filter invalid objects when generating the list of
> repository_dependencies objects that are associated with a tool shed
> repository installed into Galaxy.
>
> changeset:   10408:6822f41bc9bb
> branch:      stable
> parent:      10393:d05bf67aefa6
> user:        Dave Bouvier <d...@bx.psu.edu>
> date:        Mon Aug 19 13:06:17 2013 -0400
> summary:     Fix for case where running functional tests might
> overwrite certain files in database/files.
>
> I have just installed this workflow repository with its dependencies
> (some of where I had previously installed via the Tool Shed). Most
> of the tools were actually already manually installed but have been
> commented out in my tool_conf.xml file:
>
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925
>
> Installation appeared to be successful, so I wanted to import the
> workflow into Galaxy. I clicked on the workflow and expected to
> see an SVG of the workflow and the import action to be available.
> In the browser I saw:
>
> <quote>
> Find secreted proteins with TMHMM and SignalP
> (this page displays SVG graphics)
>
> Internal Server Error
> Galaxy was unable to sucessfully complete your request
>
> An error occurred.
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
>
> The error has been logged to our team.
> </quote>
>
> On the terminal I have:
>
> 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] "GET
> /galaxy/admin_toolshed/browse_repositories HTTP/1.1" 200 -
> "http://ppcollab/galaxy/admin"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
> 10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
> 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] "GET
>
> /galaxy/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=false&operation=manage_repository&id=eede92f8a72bf85d&f-deleted=False
> HTTP/1.1" 302 -
> "http://ppcollab/galaxy/admin_toolshed/browse_repositories";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101
> Firefox/22.0"
> 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] "GET
>
> /galaxy/admin_toolshed/manage_repository?sort=name&f-deleted=False&async=false&show_item_checkboxes=false&id=eede92f8a72bf85d&page=1
> HTTP/1.1" 200 -
> "http://ppcollab/galaxy/admin_toolshed/browse_repositories";
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101
> Firefox/22.0"
> 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] "GET
>
> /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50
> HTTP/1.1" 200 -
> "
> http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=name&f-deleted=False&async=false&show_item_checkboxes=false&id=eede92f8a72bf85d&page=1
> "
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101
> Firefox/22.0"
> 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] "GET
>
> /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50
> HTTP/1.1" 500 -
> "
> http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50
> "
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101
> Firefox/22.0"
> Error - <type 'exceptions.KeyError'>: 'header_lines'
> URL:
> http://ppcollab/galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50
> File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
>   app_iter = self.application(environ, sr_checker)
> File '/opt/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
> line 84 in __call__
>   return self.application(environ, start_response)
> File
> '/opt/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
> line 633 in __call__
>   return self.application(environ, start_response)
> File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in
> __call__
>   return self.handle_request( environ, start_response )
> File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in
> handle_request
>   body = method( trans, **kwargs )
> File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221
> in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/opt/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 310 in generate_workflow_image
>   return workflow_util.generate_workflow_image( trans, workflow_name,
> repository_metadata_id=None, repository_id=repository_id )
> File '/opt/galaxy-dist/lib/tool_shed/util/workflow_util.py', line 215
> in generate_workflow_image
>   module_data_inputs = get_workflow_data_inputs( step, module )
> File '/opt/galaxy-dist/lib/tool_shed/util/workflow_util.py', line 317
> in get_workflow_data_inputs
>   return module.get_data_inputs()
> File '/opt/galaxy-dist/lib/tool_shed/util/workflow_util.py', line 111
> in get_data_inputs
>   galaxy.tools.parameters.visit_input_values( self.tool.inputs,
> self.state.inputs, callback )
> File '/opt/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line
> 37 in visit_input_values
>   input_values[input.name],
> KeyError: 'header_lines'
>
>
> CGI Variables
> -------------
>   CONTENT_LENGTH: '0'
>   HTTP_ACCEPT:
> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>   HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>   HTTP_ACCEPT_LANGUAGE: 'en-gb,en;q=0.7,en-us;q=0.3'
>   HTTP_CONNECTION: 'Keep-Alive'
>   HTTP_COOKIE:
> 'galaxysession=fed9265fae01dfd8cf547ef38763dabd7ff6f6411d862840f8437fd67320a093efca06cca1fc50e9'
>   HTTP_DNT: '1'
>   HTTP_HOST: 'ppcollab'
>   HTTP_REFERER:
> '
> http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50
> '
>   HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8;
> rv:22.0) Gecko/20100101 Firefox/22.0'
>   PATH_INFO: '/admin_toolshed/generate_workflow_image'
>   QUERY_STRING:
>
> 'repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50'
>   REMOTE_ADDR: '143.234.97.120'
>   REQUEST_METHOD: 'GET'
>   SCRIPT_NAME: '/galaxy'
>   SERVER_NAME: 'XXX'
>   SERVER_PORT: '8080'
>   SERVER_PROTOCOL: 'HTTP/1.1'
>
>
> WSGI Variables
> --------------
>   application: <paste.recursive.RecursiveMiddleware object at 0xb3994d0>
>   is_api_request: False
>   paste.cookies: (<SimpleCookie:
>
> galaxysession='fed9265fae01dfd8cf547ef38763dabd7ff6f6411d862840f8437fd67320a093efca06cca1fc50e9'>,
>
> 'galaxysession=fed9265fae01dfd8cf547ef38763dabd7ff6f6411d862840f8437fd67320a093efca06cca1fc50e9')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
> object at 0xb399490>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0x53ce0d0>
>   paste.parsed_querystring: ([('repository_id', 'eede92f8a72bf85d'),
> ('workflow_name',
>
> 'eef2c509eb9672ca81f4797561cfd5804652c810:46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50')],
>
> 'repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50')
>   paste.recursive.forward: <paste.recursive.Forwarder from /galaxy>
>   paste.recursive.include: <paste.recursive.Includer from /galaxy>
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
> from /galaxy>
>   paste.recursive.script_name: '/galaxy'
>   paste.throw_errors: True
>   request_id: '7e2437a60a4a11e3b07b000c290c0d9f'
>   webob._parsed_query_vars: (MultiDict([('repository_id',
> 'eede92f8a72bf85d'), ('workflow_name',
>
> 'eef2c509eb9672ca81f4797561cfd5804652c810:46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50')]),
>
> 'repository_id=eede92f8a72bf85d&workflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50')
>   wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
>
> (My intention was to update this workflow to use Tool Shed style
> tool identifiers, instead of the current Tool identifiers is has now
> from manually installed versions of the tools).
>
> Regards,
>
> Peter
>
___________________________________________________________
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/

Reply via email to