Hi Everyone
I was recently trying to update tools that I installed from the central tool shed. However, it seems that a temporary redirect on the central tool shed server is causing my galaxy installation to throw a stack trace. Anyone else encountered this? Thanks in advance.
URL: http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_change... Module galaxy.web.framework.middleware.error:149 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# app_iter = self.application(environ, sr_checker)
Module paste.lint:170 in lint_app
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# iterator = application(environ, start_response_wrapper)
Module paste.recursive:84 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:92 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return self.app( environ, start_response )
Module paste.httpexceptions:633 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# body = method( trans, **kwargs )
Module galaxy.web.framework:377 in decorator
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:1926 in update_to_changeset_revision
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return self.prepare_for_install( trans, **new_kwd )
Module galaxy.web.framework:377 in decorator
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:1122 in prepare_for_install
Module tool_shed.util.common_install_util:110 in get_dependencies_for_repository
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
Module tool_shed.util.common_install_util:451 in get_required_repo_info_dicts
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# response = urllib2.urlopen( request ).read()
Module urllib2:126 in urlopen
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# return _opener.open(url, data, timeout)
Module urllib2:397 in open
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# response = meth(req, response)
Module urllib2:510 in http_response
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# 'http', request, response, code, msg, hdrs)
Module urllib2:429 in error
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# result = self._call_chain(*args)
Module urllib2:369 in _call_chain
Module urllib2:595 in http_error_302
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# new = self.redirect_request(req, fp, code, msg, headers, newurl)
Module urllib2:556 in redirect_request
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1# raise HTTPError(req.get_full_url(), code, msg, headers, fp)
HTTPError: HTTP Error 307: Temporary Redirect
Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada Iyad.Kandalaft@agr.gc.ca | (613) 759-1228
I don't believe I received any replies to this, so I will answer my own question for the benefit of others who might run into this problem.
It seems that the tool shed is being served over HTTP SSL now and traffic over HTTP without SSL is being redirected. My tool_sheds_conf.xml defines the tool shed as HTTP:// rather than HTTPS://. I modified the entry to HTTPS:// and restarted galaxy. The problem is "patched" although I don't see why a redirect is problematic for the library dealing with the request.
Regards,
Iyad Kandalaft
From: Kandalaft, Iyad Sent: Monday, October 06, 2014 8:40 AM To: galaxy-dev@bx.psu.edu Subject: Central tool shed installations fail due to redirect
Hi Everyone
I was recently trying to update tools that I installed from the central tool shed. However, it seems that a temporary redirect on the central tool shed server is causing my galaxy installation to throw a stack trace. Anyone else encountered this? Thanks in advance.
URL: http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_change... Module galaxy.web.framework.middleware.error:149 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 app_iter = self.application(environ, sr_checker)
Module paste.lint:170 in lint_app
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 iterator = application(environ, start_response_wrapper)
Module paste.recursive:84 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:92 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return self.app( environ, start_response )
Module paste.httpexceptions:633 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 body = method( trans, **kwargs )
Module galaxy.web.framework:377 in decorator
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:1926 in update_to_changeset_revision
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return self.prepare_for_install( trans, **new_kwd )
Module galaxy.web.framework:377 in decorator
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:1122 in prepare_for_install
Module tool_shed.util.common_install_util:110 in get_dependencies_for_repository
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
Module tool_shed.util.common_install_util:451 in get_required_repo_info_dicts
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 response = urllib2.urlopen( request ).read()
Module urllib2:126 in urlopen
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 return _opener.open(url, data, timeout)
Module urllib2:397 in open
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 response = meth(req, response)
Module urllib2:510 in http_response
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 'http', request, response, code, msg, hdrs)
Module urllib2:429 in error
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 result = self._call_chain(*args)
Module urllib2:369 in _call_chain
Module urllib2:595 in http_error_302
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 new = self.redirect_request(req, fp, code, msg, headers, newurl)
Module urllib2:556 in redirect_request
http://galaxy-devtest.biodiversity.agr.gc.ca/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=t2ps&owner=devteam&changeset_revision=9e2b9ca7f33a&latest_changeset_revision=dee81096ec71&latest_ctx_rev=1 raise HTTPError(req.get_full_url(), code, msg, headers, fp)
HTTPError: HTTP Error 307: Temporary Redirect
Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada Iyad.Kandalaft@agr.gc.camailto:Iyad.Kandalaft@agr.gc.ca | (613) 759-1228
galaxy-dev@lists.galaxyproject.org
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Kandalaft, Iyad