Question: workflow edit issue
0
gravatar for n.goue
15 months ago by
n.goue50
n.goue50 wrote:

Hi, I try to create or edit a workflow but it returned the message

"Internal Server Error

Galaxy was unable to successfully complete your request"

As I suspected a problem with the downloaded workflow.ga, I imported a the TestWorkflow1 from the test/base/data Galaxy folder, but the problem is the same ending with the message

Error - <type 'exceptions.attributeerror'="">: 'module' object has no attribute '_magic_number'

I am using the latest Galaxy version.

My log is below.

Thanks for helping!

127.0.0.1 - - [24/juil./2017:13:45:29 +0200] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" 127.0.0.1 - - [24/juil./2017:13:45:33 +0200] "GET /workflow/import_workflow HTTP/1.1" 200 - "http://localhost:8080/workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" 127.0.0.1 - - [24/juil./2017:13:45:33 +0200] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/workflow/import_workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" /xxx/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:1404: SAWarning: Got None for value of column workflow_step.id; this is unsupported for a relationship comparison and will not currently produce an IS comparison (but may in a future release) "(but may in a future release)" % column) /xxx/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:1404: SAWarning: Got None for value of column stored_workflow.id; this is unsupported for a relationship comparison and will not currently produce an IS comparison (but may in a future release) "(but may in a future release)" % column) 127.0.0.1 - - [24/juil./2017:13:49:26 +0200] "POST /workflow/import_workflow HTTP/1.1" 200 - "http://localhost:8080/workflow/import_workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" 127.0.0.1 - - [24/juil./2017:13:49:27 +0200] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/workflow/import_workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" /xxx/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py:3795: SAWarning: Textual SQL expression u'stored_workflow_id=6' should be explicitly declared as text(u'stored_workflow_id=6') (this warning may be suppressed after 10 occurrences) {"expr": util.ellipses_string(element)}) 127.0.0.1 - - [24/juil./2017:13:49:36 +0200] "GET /workflow/display_by_id?id=a799d38679e985db HTTP/1.1" 200 - "http://localhost:8080/workflow/import_workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" 127.0.0.1 - - [24/juil./2017:13:49:37 +0200] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/workflow/display_by_id?id=a799d38679e985db" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" 127.0.0.1 - - [24/juil./2017:13:49:54 +0200] "GET /workflow HTTP/1.1" 200 - "http://localhost:8080/workflow/display_by_id?id=a799d38679e985db" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" 127.0.0.1 - - [24/juil./2017:13:49:55 +0200] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://localhost:8080/workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" 127.0.0.1 - - [24/juil./2017:13:49:56 +0200] "GET /workflow/editor?id=a799d38679e985db HTTP/1.1" 500 - "http://localhost:8080/workflow" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" Error - <type 'exceptions.attributeerror'="">: 'module' object has no attribute '_magic_number' URL: http://localhost:8080/workflow/editor?id=a799d38679e985db File '/xxx/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__ app_iter = self.application(environ, sr_checker) File '/xxx/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/xxx/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/xxx/galaxy/lib/galaxy/web/framework/base.py', line 135 in __call__ return self.handle_request( environ, start_response ) File '/xxx/galaxy/lib/galaxy/web/framework/base.py', line 214 in handle_request body = method( trans, *kwargs ) File '/xxx/galaxy/lib/galaxy/web/framework/decorators.py', line 74 in decorator return func( self, trans, *args, *kwargs ) File '/xxx/galaxy/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 673 in editor return trans.fill_template( "workflow/editor.mako", workflows=workflows, stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) ) File '/xxx/galaxy/lib/galaxy/web/framework/webapp.py', line 891 in fill_template return self.fill_template_mako( filename, *kwargs ) File '/xxx/galaxy/lib/galaxy/web/framework/webapp.py', line 899 in fill_template_mako template = template_lookup.get_template( filename ) File '/xxx/galaxy/.venv/local/lib/python2.7/site-packages/mako/lookup.py', line 253 in get_template return self._load(srcfile, uri) File '/xxx/galaxy/.venv/local/lib/python2.7/site-packages/mako/lookup.py', line 318 in _load *self.template_args) File '/xxx/galaxy/.venv/local/lib/python2.7/site-packages/mako/template.py', line 322 in __init__ module = self._compile_from_file(path, filename) File '/xxx/galaxy/.venv/local/lib/python2.7/site-packages/mako/template.py', line 381 in _compile_from_file if module._magic_number != codegen.MAGIC_NUMBER: AttributeError: 'module' object has no attribute '_magic_number'

workflow galaxy • 473 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by n.goue50
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Please upgrade your instance to the most current Galaxy 17_05 branch. There were changes between release 17_01 and 17_05 for workflows that involved this variable. Avoid the master or development branches unless you are able to troubleshoot issues that may come up (these are working branches, unlike the full release branches).

Thanks and hopefully this will resolve the problem, Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
0
gravatar for n.goue
15 months ago by
n.goue50
n.goue50 wrote:

Hi Jen, I am already working with the release Galaxy 17_05 that I have installed with the git clone command. I can make a try and reinstall it. I'll let you know the result.

Thanks,

ADD COMMENTlink written 15 months ago by n.goue50
1

Jen, I reinstalled the Galaxy 17_05 and I can edit workflows now. Probably something went wrong at first install... Anyway, it's working now.

Thank you for your suggestion. Have a nice day,

ADD REPLYlink written 15 months ago by n.goue50

Glad it worked!

The release branch will have priority patches made at times that impact usability or security. My guess is that one of these impacted your usage. All is recorded in Github if you ever want to review. Comparing your copy to the current release will reveal any changes since originally cloned.

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson25k
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