Workflow import is not working, KeyError: 'header_lines'
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/606da4e... 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
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/606da4e...
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
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/606da4e...
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
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?
Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page? I could manually import the workflow from the *.ga file on disk, and it runs OK.
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.
Sounds good. On Wed, Aug 21, 2013 at 1:47 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
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.
These are not tweaked - it is an old workflow created with manually installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc. I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds). Peter
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page?
Yep, that's where it was. These are not tweaked - it is an old workflow created with manually
installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc.
I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds).
Ok, thanks for the extra info, just wanted to make sure I knew what I was dealing with :)
Hey Peter, The reason it's actually failing has to do with the tool Filter1, and your particular version of the filter tool not having the header lines parameter. This was added in 8678:a14006775b08. In this instance, we should have just used the default value. Once all tools and versions are in the toolshed, this sort of thing shouldn't crop up because you'll have the correct version available. I've committed a temporary fix in 10423:3c60f6a7dedc. On Wed, Aug 21, 2013 at 9:14 AM, Dannon Baker <dannon.baker@gmail.com>wrote:
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page?
Yep, that's where it was.
These are not tweaked - it is an old workflow created with manually
installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc.
I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds).
Ok, thanks for the extra info, just wanted to make sure I knew what I was dealing with :)
n Wed, Aug 21, 2013 at 2:59 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Peter,
The reason it's actually failing has to do with the tool Filter1, and your particular version of the filter tool not having the header lines parameter. This was added in 8678:a14006775b08. In this instance, we should have just used the default value.
Yes - I realised later that the header_lines was from the Filter1 tool, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016224.html
Once all tools and versions are in the toolshed, this sort of thing shouldn't crop up because you'll have the correct version available.
I was under the impression at GCC2013 that Galaxy would continue to keep a set of 'core' tools with no dependencies (like Filter1), but perhaps the goal is more a set of tools installed from the Tool Shed by default?
I've committed a temporary fix in 10423:3c60f6a7dedc.
Thanks, Peter
participants (2)
-
Dannon Baker -
Peter Cock