Hi All,
We have an issue with our self-hosted galaxy environment. When we want to share
a workflow (Workflow -> workflow Name -> Share or Download) the links under
'Share' section leads to 'Internal server Error'. Did we miss something ? See
attachment for screenshots and log file.
Thank you for helping us.
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Scientific Institute of Public Health, Brussels, Belgium
Wetenschappelijk Instituut Volksgezondheid, Brussel, België
Institut scientifique de Santé publique, Bruxelles, Belgique
Visit our website: http://www.wiv-isp.be
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[pid: 4812|app: 0|req: 516/3307] 192.168.3.28 () {50 vars in 920 bytes} [Wed
Nov 23 14:35:52 2016] GET /u/bioit/w/imported-resistance-characterization =>
generated 777 bytes in 905 msecs (HTTP/1.1 500) 1 headers in 63 bytes (1
switches on core 2)
10.0.0.26 - - [23/Nov/2016:14:36:45 +0200] "GET / HTTP/1.1" 200 -
"https://galaxy.wiv-isp.be/workflow/list_published"; "Mozilla/5.0 (Windows NT
6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.3
Safari/537.36"
[pid: 4812|app: 0|req: 517/3308] 10.0.0.26 () {50 vars in 903 bytes} [Wed Nov
23 14:36:45 2016] GET / => generated 386037 bytes in 191 msecs (HTTP/1.1 200) 2
headers in 73 bytes (1 switches on core 1)
10.0.0.26 - - [23/Nov/2016:14:36:45 +0200] "GET /api/genomes HTTP/1.1" 200 -
"https://galaxy.wiv-isp.be/"; "Mozilla/5.0 (Windows NT 6.1; Win64; x64)
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.3 Safari/537.36"
[pid: 4812|app: 0|req: 518/3309] 10.0.0.26 () {52 vars in 889 bytes} [Wed Nov
23 14:36:45 2016] GET /api/genomes => generated 9634 bytes in 17 msecs
(HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0)
10.0.0.26 - - [23/Nov/2016:14:36:45 +0200] "GET
/api/datatypes?extension_only=False HTTP/1.1" 200 -
"https://galaxy.wiv-isp.be/"; "Mozilla/5.0 (Windows NT 6.1; Win64; x64)
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.3 Safari/537.36"
[pid: 4813|app: 0|req: 2792/3310] 10.0.0.26 () {52 vars in 933 bytes} [Wed Nov
23 14:36:45 2016] GET /api/datatypes?extension_only=False => generated 21730
bytes in 41 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3)
10.0.0.26 - - [23/Nov/2016:14:36:46 +0200] "GET /welcome HTTP/1.1" 302 -
"https://galaxy.wiv-isp.be/"; "Mozilla/5.0 (Windows NT 6.1; Win64; x64)
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.3 Safari/537.36"
[pid: 4813|app: 0|req: 2794/3311] 10.0.0.26 () {50 vars in 895 bytes} [Wed Nov
23 14:36:46 2016] GET /welcome => generated 304 bytes in 31 msecs (HTTP/1.1
302) 3 headers in 108 bytes (1 switches on core 1)
10.0.0.26 - - [23/Nov/2016:14:36:46 +0200] "GET /history/current_history_json
HTTP/1.1" 200 - "https://galaxy.wiv-isp.be/"; "Mozilla/5.0 (Windows NT 6.1;
Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.3
Safari/537.36"
[pid: 4813|app: 0|req: 2794/3312] 10.0.0.26 () {50 vars in 912 bytes} [Wed Nov
23 14:36:46 2016] GET /history/current_history_json => generated 3360 bytes in
87 msecs (HTTP/1.1 200) 5 headers in 156 bytes (1 switches on core 2)
10.0.0.26 - - [23/Nov/2016:14:36:46 +0200] "GET
/api/histories/73bf562cbe439524/contents?v=dev&details=23477a427001b60d%2Ce48b76eff580fe1e
HTTP/1.1" 200 - "https://galaxy.wiv-isp.be/"; "Mozilla/5.0 (Windows NT 6.1;
Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.3
Safari/537.36"
[pid: 4813|app: 0|req: 2795/3313] 10.0.0.26 () {50 vars in 990 bytes} [Wed Nov
23 14:36:46 2016] GET
/api/histories/73bf562cbe439524/contents?v=dev&details=23477a427001b60d%2Ce48b76eff580fe1e
=> generated 52584 bytes in 197 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1
switches on core 0)
10.0.0.26 - - [23/Nov/2016:14:36:46 +0200] "GET
/api/histories/73bf562cbe439524?keys=size%2Cnon_ready_jobs HTTP/1.1" 200 -
"https://galaxy.wiv-isp.be/"; "Mozilla/5.0 (Windows NT 6.1; Win64; x64)
AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2924.3 Safari/537.36"
[pid: 4813|app: 0|req: 2796/3314] 10.0.0.26 () {50 vars in 969 bytes} [Wed Nov
23 14:36:46 2016] GET
/api/histories/73bf562cbe439524?keys=size%2Cnon_ready_jobs => generated 42
bytes in 26 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3)
192.168.3.28 - - [23/Nov/2016:14:37:01 +0200] "GET
/u/bioit/w/imported-resistance-characterization HTTP/1.1" 500 -
"http://10.0.0.219/workflow/sharing?id=581bf952f093ed97"; "Mozilla/5.0 (Windows
NT 6.1; Win64; x64; rv:50.0) Gecko/20100101 Firefox/50.0"
Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute
'replace'
URL: http://10.0.0.219/u/bioit/w/imported-resistance-characterization
File 'lib/galaxy/web/framework/middleware/error.py', line 151 in __call__
app_iter = self.application(environ, sr_checker)
File '/usr/local/lib/python2.7/dist-packages/paste/recursive.py', line 85 in
__call__
return self.application(environ, start_response)
File '/usr/local/lib/python2.7/dist-packages/paste/httpexceptions.py', line 640
in __call__
return self.application(environ, start_response)
File 'lib/galaxy/web/framework/base.py', line 131 in __call__
return self.handle_request( environ, start_response )
File 'lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File 'lib/galaxy/webapps/galaxy/controllers/workflow.py', line 255 in
display_by_username_and_slug
return self._display( trans, stored_workflow )
File 'lib/galaxy/webapps/galaxy/controllers/workflow.py', line 291 in _display
user_item_rating=user_item_rating, ave_item_rating=ave_item_rating,
num_ratings=num_ratings )
File 'lib/galaxy/web/framework/webapp.py', line 872 in fill_template_mako
return template.render( **data )
File '/usr/local/lib/python2.7/dist-packages/mako/template.py', line 445 in
render
return runtime._render(self, self.callable_, args, data)
File '/usr/local/lib/python2.7/dist-packages/mako/runtime.py', line 829 in
_render
**_kwargs_for_callable(callable_, data))
File '/usr/local/lib/python2.7/dist-packages/mako/runtime.py', line 864 in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File '/usr/local/lib/python2.7/dist-packages/mako/runtime.py', line 890 in
_exec_template
callable_(context, *args, **kwargs)
File '/data/galaxy/database/compiled_templates/base/base_panels.mako.py', line
126 in render_body
__M_writer(unicode(self.center_panel()))
File '/data/galaxy/database/compiled_templates/display_base.mako.py', line 180
in render_center_panel
__M_writer(unicode(self.render_content()))
File '/data/galaxy/database/compiled_templates/display_base.mako.py', line 144
in render_render_content
__M_writer(unicode(self.render_item( item, item_data )))
File '/data/galaxy/database/compiled_templates/workflow/display.mako.py', line
105 in render_render_item
__M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, "", step )))
File '/data/galaxy/database/compiled_templates/workflow/display.mako.py', line
78 in do_inputs
return render_do_inputs(context,inputs,values,prefix,step,other_values)
File '/data/galaxy/database/compiled_templates/workflow/display.mako.py', line
201 in render_do_inputs
__M_writer(unicode(row_for_param( input, values[ input.name ], other_values,
prefix, step )))
File '/data/galaxy/database/compiled_templates/workflow/display.mako.py', line
143 in row_for_param
return render_row_for_param(context,param,value,other_values,prefix,step)
File '/data/galaxy/database/compiled_templates/workflow/display.mako.py', line
265 in render_row_for_param
__M_writer(unicode(cgi.escape( param.value_to_display_text( value, app ) )))
File '/usr/lib/python2.7/cgi.py', line 1043 in escape
s = s.replace("&", "&") # Must be done first!
AttributeError: 'NoneType' object has no attribute 'replace'
CGI Variables
-------------
DOCUMENT_ROOT: '/usr/share/nginx/html'
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=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_COOKIE:
'galaxysession=a03326f355ac0f6b05f7a6c8c6d14ad2da7e40159e5583bf588161c61c7b702154c8679551e6d761'
HTTP_DNT: '1'
HTTP_HOST: '10.0.0.219'
HTTP_REFERER: 'http://10.0.0.219/workflow/sharing?id=581bf952f093ed97'
HTTP_UPGRADE_INSECURE_REQUESTS: '1'
HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; Win64; x64; rv:50.0)
Gecko/20100101 Firefox/50.0'
PATH_INFO: '/u/bioit/w/imported-resistance-characterization'
REMOTE_ADDR: '192.168.3.28'
REMOTE_PORT: '56932'
REQUEST_METHOD: 'GET'
REQUEST_URI: '/u/bioit/w/imported-resistance-characterization'
SERVER_PORT: '80'
SERVER_PROTOCOL: 'HTTP/1.1'
UWSGI_SCHEME: 'http'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0x7fbe9c682f50>
controller_action_key: u'web.workflow.display_by_username_and_slug'
is_api_request: False
paste.cookies: (<SimpleCookie:
galaxysession='a03326f355ac0f6b05f7a6c8c6d14ad2da7e40159e5583bf588161c61c7b702154c8679551e6d761'>,
'galaxysession=a03326f355ac0f6b05f7a6c8c6d14ad2da7e40159e5583bf588161c61c7b702154c8679551e6d761')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at
0x7fbe9c682ed0>
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: 'ea32726eb18111e6beea005056aa18e3'
uwsgi.core: 1
uwsgi.node: 'BioIT-Prod1'
uwsgi.version: '1.9.17.1-debian'
webob._parsed_query_vars: (GET([]), '')
wsgi process: 'Multi process AND threads (?)'
wsgi.file_wrapper: <built-in function uwsgi_sendfile>
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