{"action":"created","issue":{"url":"https://api.github.com/repos/enasequence/enaBrowserTools/issues/35","repository_url":"https://api.github.com/repos/enasequence/enaBrowserTools","labels_url":"https://api.github.com/repos/enasequence/enaBrowserTools/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/enasequence/enaBrowserTools/issues/35/comments","events_url":"https://api.github.com/repos/enasequence/enaBrowserTools/issues/35/events","html_url":"https://github.com/enasequence/enaBrowserTools/issues/35","id":321604040,"number":35,"title":"Fetching genomes sometimes get stuck","user":{"login":"jjkoehorst","id":4471699,"avatar_url":"https://avatars3.githubusercontent.com/u/4471699?v=4","gravatar_id":"","url":"https://api.github.com/users/jjkoehorst","html_url":"https://github.com/jjkoehorst","followers_url":"https://api.github.com/users/jjkoehorst/followers","following_url":"https://api.github.com/users/jjkoehorst/following{/other_user}","gists_url":"https://api.github.com/users/jjkoehorst/gists{/gist_id}","starred_url":"https://api.github.com/users/jjkoehorst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jjkoehorst/subscriptions","organizations_url":"https://api.github.com/users/jjkoehorst/orgs","repos_url":"https://api.github.com/users/jjkoehorst/repos","events_url":"https://api.github.com/users/jjkoehorst/events{/privacy}","received_events_url":"https://api.github.com/users/jjkoehorst/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-05-09T14:54:01Z","updated_at":"2018-05-10T11:10:35Z","closed_at":null,"author_association":"NONE","body":"I have been trying the following command (on a Mac):\r\n\r\n`python3 enaBrowserTools/python3/enaDataGet.py -f embl GCA_000393655.1`\r\n\r\nand notices that it gets stuck on unplaced-scaffold and not sure how to continue.\r\n\r\n```\r\nno sequences: assembled-molecule\r\nno sequences: unlocalised-scaffold\r\nfetching sequences: unplaced-scaffold\r\n```\r\n\r\nThe folder content:\r\n\r\n```\r\n-rw-r--r--  1 me  staff   4.5K May  9 16:51 GCA_000393655.1.xml\r\n-rw-r--r--  1 me  staff    19M May  9 16:51 GCA_000393655.1_sequence_report.txt\r\n-rw-r--r--  1 me  staff     0B May  9 16:51 unplaced-scaffold.dat\r\n```\r\n\r\n**Update**\r\n\r\nOn our ubuntu server it obtains the data but very slowly and shows a lot of:\r\n\r\n`Entry: ASAF01227205 display type is either not supported or entry is not found.`\r\n\r\n**Update 2**\r\n\r\nAs shown on the main page of this git project it indeed states to fix the certificates.\r\n\r\nHowever as I used home-brew to install python3 I needed the following code to run:\r\n\r\n```\r\n# install_certifi.py\r\n#\r\n# sample script to install or update a set of default Root Certificates\r\n# for the ssl module.  Uses the certificates provided by the certifi package:\r\n#       https://pypi.python.org/pypi/certifi\r\n\r\nimport os\r\nimport os.path\r\nimport ssl\r\nimport stat\r\nimport subprocess\r\nimport sys\r\n\r\nSTAT_0o775 = ( stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR\r\n             | stat.S_IRGRP | stat.S_IWGRP | stat.S_IXGRP\r\n             | stat.S_IROTH |                stat.S_IXOTH )\r\n\r\nopenssl_dir, openssl_cafile = os.path.split(\r\n    ssl.get_default_verify_paths().openssl_cafile)\r\n\r\nprint(\" -- pip install --upgrade certifi\")\r\nsubprocess.check_call([sys.executable,\r\n    \"-E\", \"-s\", \"-m\", \"pip\", \"install\", \"--upgrade\", \"certifi\"])\r\n\r\nimport certifi\r\n\r\n# change working directory to the default SSL directory\r\nos.chdir(openssl_dir)\r\nrelpath_to_certifi_cafile = os.path.relpath(certifi.where())\r\nprint(\" -- removing any existing file or link\")\r\ntry:\r\n    os.remove(openssl_cafile)\r\nexcept FileNotFoundError:\r\n    pass\r\nprint(\" -- creating symlink to certifi certificate bundle\")\r\nos.symlink(relpath_to_certifi_cafile, openssl_cafile)\r\nprint(\" -- setting permissions\")\r\nos.chmod(openssl_cafile, STAT_0o775)\r\nprint(\" -- update complete\")\r\n```\r\n\r\nbut it is not yet 100% fixed. Not sure why some genomes do work while others don't."},"comment":{"url":"https://api.github.com/repos/enasequence/enaBrowserTools/issues/comments/388024372","html_url":"https://github.com/enasequence/enaBrowserTools/issues/35#issuecomment-388024372","issue_url":"https://api.github.com/repos/enasequence/enaBrowserTools/issues/35","id":388024372,"user":{"login":"jjkoehorst","id":4471699,"avatar_url":"https://avatars3.githubusercontent.com/u/4471699?v=4","gravatar_id":"","url":"https://api.github.com/users/jjkoehorst","html_url":"https://github.com/jjkoehorst","followers_url":"https://api.github.com/users/jjkoehorst/followers","following_url":"https://api.github.com/users/jjkoehorst/following{/other_user}","gists_url":"https://api.github.com/users/jjkoehorst/gists{/gist_id}","starred_url":"https://api.github.com/users/jjkoehorst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jjkoehorst/subscriptions","organizations_url":"https://api.github.com/users/jjkoehorst/orgs","repos_url":"https://api.github.com/users/jjkoehorst/repos","events_url":"https://api.github.com/users/jjkoehorst/events{/privacy}","received_events_url":"https://api.github.com/users/jjkoehorst/received_events","type":"User","site_admin":false},"created_at":"2018-05-10T11:10:35Z","updated_at":"2018-05-10T11:10:35Z","author_association":"NONE","body":"I just pulled in the latest master branch and it seems to be working perfect. If I encounter any strange behaviour I will let you know."}}
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