Hi Matthias,
this looks like your python installation does not know how to verify SSL certificates.
Redhat have a nice section on troubleshooting that here:
https://access.redhat.com/articles/2039753
I can get your error by specifying a nonexsting cert:
mvandenb@Mariuss-MacBook-Pro:~/src/readtagger/readtagger (master)*$ SSL_CERT_FILE=/does_not_exist python ~/urllib2_test.py https://usegalaxy.org
Traceback (most recent call last):
File "/Users/mvandenb/urllib2_test.py", line 10, in <module>
urllib2.urlopen(req)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen
return opener.open(url, data, timeout)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 429, in open
response = self._open(req, data)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 447, in _open
'_open', req)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 407, in _call_chain
result = func(*args)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1241, in https_open
context=self._context)
File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 1198, in do_open
raise URLError(err)
urllib2.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)>
Hope that helps,
Marius
Dear list,
Currently I get SSL certificate errors when I try to install a tool in Galaxy. I also get the same error when I try to use the galaxy-tools ansible role (when debugging this I thought this might be because my local server is on http, since the error appeared seemingly when a message was posted to the local server -- but I'm not entirely sure).
I'm also missing the "Manage installed tools" link in the admin area (but maybe this is expected in a fresh install?).
Thanks a lot.
Best,
Matthias
This is the stack trace when I try to install through the web frontend:
141.65.27.89 - - [18/Apr/2017:14:58:19 +0000] "GET /admin_toolshed/prepare_for_install?changeset_revisions=9ba8 ebb636f4&repository_ids=d5dd1c 5d2070513e&tool_shed_url= https%3A%2F%2Ftoolshed.g2.bx. psu.edu %2F HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0"
Error - <class 'urllib2.URLError'>: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)>
URL: http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?c hangeset_revisions=9ba8ebb636f 4&repository_ids=d5dd1c5d20705 13e&tool_shed_url=https%3A%2F% 2Ftoolshed.g2.bx.psu.edu%2F
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framewo rk/middleware/error.py', line 154 in __call__
app_iter = self.application(environ, sr_checker)
File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/ site-packages/paste/recursive. py', line 85 in __call__
return self.application(environ, start_response)
File '/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/ site-packages/paste/httpexcept ions.py', line 640 in __call__
return self.application(environ, start_response)
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framewo rk/base.py', line 134 in __call__
return self.handle_request( environ, start_response )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framewo rk/base.py', line 193 in handle_request
body = method( trans, **kwargs )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framewo rk/decorators.py', line 98 in decorator
return func( self, trans, *args, **kwargs )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/gal axy/controllers/admin_toolshed .py', line 1035 in prepare_for_install
raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init __.py', line 1488 in url_get
response = urlopener.open( full_url )
File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/ urllib2.py', line 429 in open
response = self._open(req, data)
File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/ urllib2.py', line 447 in _open
'_open', req)
File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/ urllib2.py', line 407 in _call_chain
result = func(*args)
File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/ urllib2.py', line 1241 in https_open
context=self._context)
File '/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/ urllib2.py', line 1198 in do_open
raise URLError(err)
URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)>
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-US,en;q=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_COOKIE: 'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7d a2cc7e5bd9aff8a0eb130e333f3419 e10fa'
HTTP_DNT: '1'
HTTP_HOST: 'bioinf2-dev:8080'
HTTP_UPGRADE_INSECURE_REQUESTS: '1'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0'
PATH_INFO: '/admin_toolshed/prepare_for_install'
QUERY_STRING: 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d207 0513e&tool_shed_url=https%3A% 2F%2Ftoolshed.g2.bx.psu.edu% 2F'
REMOTE_ADDR: '141.65.27.89'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8080'
SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at 0x7f2dd8bb5190>
controller_action_key: u'web.admin_toolshed.prepare_for_install'
is_api_request: False
paste.cookies: (<SimpleCookie: galaxysession='5d9fe20b2f75201eeee9486487f5942375617bcc89a7d a2cc7e5bd9aff8a0eb130e333f3419 e10fa'>, 'galaxysession=5d9fe20b2f75201 eeee9486487f5942375617bcc89a7d a2cc7e5bd9aff8a0eb130e333f3419 e10fa')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7f2dd8bb5110>
paste.httpserver.proxy.host: 'dummy'
paste.httpserver.proxy.scheme: 'http'
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7f2dd875fe10>
paste.parsed_querystring: ([('changeset_revisions', '9ba8ebb636f4'), ('repository_ids', 'd5dd1c5d2070513e'), ('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/') ], 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d207 0513e&tool_shed_url=https%3A% 2F%2Ftoolshed.g2.bx.psu.edu% 2F')
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIt er from />
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: '7599ea98244711e7941208002755efa5'
webob._parsed_query_vars: (GET([(u'changeset_revisions', u'9ba8ebb636f4'), (u'repository_ids', u'd5dd1c5d2070513e'), (u'tool_shed_url', u'https://toolshed.g2.bx.psu.edu/')] ), 'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d207 0513e&tool_shed_url=https%3A% 2F%2Ftoolshed.g2.bx.psu.edu% 2F')
wsgi process: 'Multithreaded'
------------------------------------------------------------
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
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