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/
