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.ba...@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.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 >> > >
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