On 18 April 2017 at 17:13, Matthias Bernt <m.bernt@ufz.de> wrote:

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=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&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?changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/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/httpexceptions.py', line 640 in __call__
  return self.application(environ, start_response)
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 134 in __call__
  return self.handle_request( environ, start_response )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py', line 193 in handle_request
  body = method( trans, **kwargs )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py', line 98 in decorator
  return func( self, trans, *args, **kwargs )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/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=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'
  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=d5dd1c5d2070513e&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='5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'>, 'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa')
  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=d5dd1c5d2070513e&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.IncluderAppIter 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=d5dd1c5d2070513e&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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