galaxy.tools.data WARNING 2016-07-20 09:00:41,816 Cannot find index file '/work/projects/galaxy/internal/database/tmp/tmp-toolshed-gmfcrzeL1mn/fasta_indexes.loc' for tool data table 'fasta_indexes' galaxy.tools.data DEBUG 2016-07-20 09:00:41,816 Loading another instance of data table 'fasta_indexes', attempting to merge content. galaxy.tools.data DEBUG 2016-07-20 09:00:41,898 Loading another instance of data table 'fasta_indexes', attempting to merge content. galaxy.tools.data DEBUG 2016-07-20 09:00:41,898 Attempted to add fields (['hg19', 'hg19', 'Human (Homo sapiens): hg19', '/work/projects/galaxy/internal/references/hg19/sam_index/hg19.fa']) to data table 'fasta_indexes', but this entry already exists and allow_duplicates is False. galaxy.tools.data DEBUG 2016-07-20 09:00:41,899 Attempted to add fields (['hg38', 'hg38', 'Human (Homo sapiens): hg38', '/work/projects/galaxy/internal/references/hg38/sam_index/hg38.fa']) to data table 'fasta_indexes', but this entry already exists and allow_duplicates is False. galaxy.tools.data DEBUG 2016-07-20 09:00:41,899 Attempted to add fields (['dm3', 'dm3', 'Fruit Fly (Drosophila melanogaster): dm3', '/work/projects/galaxy/internal/references/dm3/sam_index/dm3.fa']) to data table 'fasta_indexes', but this entry already exists and allow_duplicates is False. galaxy.tools.data DEBUG 2016-07-20 09:00:41,899 Attempted to add fields (['mm9', 'mm9', 'Mouse (Mus musculus): mm9', '/work/projects/galaxy/internal/references/mm9/sam_index/mm9.fa']) to data table 'fasta_indexes', but this entry already exists and allow_duplicates is False. galaxy.tools.data DEBUG 2016-07-20 09:00:41,899 Attempted to add fields (['mm10', 'mm10', 'Mouse (Mus Musculus): mm10', '/work/projects/galaxy/internal/references/mm10/sam_index/mm10.fa']) to data table 'fasta_indexes', but this entry already exists and allow_duplicates is False. galaxy.tools.search DEBUG 2016-07-20 09:00:42,191 Starting to build toolbox index. galaxy.tools.search DEBUG 2016-07-20 09:00:44,375 Toolbox index finished. 10.184.148.22 - - [20/Jul/2016:09:00:39 +0200] "GET /admin_toolshed/update_to_changeset_revision?name=cuffdiff&latest_ctx_rev=12&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=5ce5197de50c&latest_changeset_revision=0f32ad418df8 HTTP/1.1" 500 - "https://galaxy-server.uni.lu/admin_toolshed/browse_repositories" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:47.0) Gecko/20100101 Firefox/47.0" Error - : 'list' object has no attribute 'get' URL: https://galaxy-server.uni.lu/admin_toolshed/update_to_changeset_revision?name=cuffdiff&latest_ctx_rev=12&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=5ce5197de50c&latest_changeset_revision=0f32ad418df8 File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/mnt/gaiagpfs/projects/galaxy/internal/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 175 in __call__ return self.app( environ, start_response ) File '/mnt/gaiagpfs/projects/galaxy/internal/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 131 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py', line 89 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 2058 in update_to_changeset_revision updated_ctx_rev=latest_ctx_rev ) File '/home/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/update_repository_manager.py', line 113 in update_repository_record suc.clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url) File '/home/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 136 in clean_dependency_relationships if can_eliminate_tool_dependency(metadata_dict, td.name, td.type, td.version): File '/home/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 109 in can_eliminate_tool_dependency n = td_val.get('name', None) AttributeError: 'list' object has no attribute 'get' 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, br' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_AUTHORIZATION: 'Basic c2RpZWhsOmd3MmlzdHN1cGVyIQ==' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: '__utma=1.479521409.1425985924.1425985924.1425985924.1; galaxysession=0566cd694b3116df0715903d0e6c46690a4defa2b26fa5472466910d02487ae703ed10636e313888' HTTP_HOST: 'galaxy-server.uni.lu' HTTP_REFERER: 'https://galaxy-server.uni.lu/admin_toolshed/browse_repositories' HTTP_REMOTE_USER: 'sdiehl@galaxy-server.uni.lu' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:47.0) Gecko/20100101 Firefox/47.0' HTTP_VIA: '1.1 galaxy-server.uni.lu' HTTP_X_FORWARDED_FOR: '10.184.148.22' HTTP_X_FORWARDED_HOST: 'galaxy-server.uni.lu' HTTP_X_FORWARDED_SERVER: 'galaxy-server.uni.lu' HTTP_X_URL_SCHEME: 'https' ORGINAL_HTTP_HOST: 'localhost:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/admin_toolshed/update_to_changeset_revision' QUERY_STRING: 'name=cuffdiff&latest_ctx_rev=12&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=5ce5197de50c&latest_changeset_revision=0f32ad418df8' REMOTE_ADDR: '10.184.148.22' REQUEST_METHOD: 'GET' SERVER_NAME: '127.0.0.1' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: controller_action_key: u'web.admin_toolshed.update_to_changeset_revision' is_api_request: False original_wsgi.url_scheme: 'http' paste.cookies: (, '__utma=1.479521409.1425985924.1425985924.1425985924.1; galaxysession=0566cd694b3116df0715903d0e6c46690a4defa2b26fa5472466910d02487ae703ed10636e313888') paste.expected_exceptions: [] paste.httpexceptions: paste.httpserver.proxy.host: 'dummy' paste.httpserver.proxy.scheme: 'http' paste.httpserver.thread_pool: paste.parsed_querystring: ([('name', 'cuffdiff'), ('latest_ctx_rev', '12'), ('tool_shed_url', 'https://toolshed.g2.bx.psu.edu/'), ('owner', 'devteam'), ('changeset_revision', '5ce5197de50c'), ('latest_changeset_revision', '0f32ad418df8')], 'name=cuffdiff&latest_ctx_rev=12&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=5ce5197de50c&latest_changeset_revision=0f32ad418df8') paste.recursive.forward: paste.recursive.include: paste.recursive.include_app_iter: paste.recursive.script_name: '' paste.throw_errors: True request_id: 'aa9890ae4e4711e6ae18f8bc124c1d80' webob._parsed_query_vars: (GET([(u'name', u'cuffdiff'), (u'latest_ctx_rev', u'12'), (u'tool_shed_url', u'https://toolshed.g2.bx.psu.edu/'), (u'owner', u'devteam'), (u'changeset_revision', u'5ce5197de50c'), (u'latest_changeset_revision', u'0f32ad418df8')]), 'name=cuffdiff&latest_ctx_rev=12&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&owner=devteam&changeset_revision=5ce5197de50c&latest_changeset_revision=0f32ad418df8') wsgi process: 'Multithreaded' ------------------------------------------------------------