Quick followup on this one -- had you manually tweaked this workflow prior to upload?  I see all of the tool identifiers are the short form 'signalp3' and not the long-form toolshed included versions.


On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
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.cock@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 <dave@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