{"push_id":1389283640,"size":63,"distinct_size":23,"ref":"refs/heads/curie","head":"d38d5d661d40140a131617c5228c53ddaac0deac","before":"9818b9efaadd836f807d42af4aca8a34d48564c5","commits":[{"sha":"66dec1d580b426ad955db03608ec7da7eb5c5018","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@tgac.ac.uk"},"message":"Add download_to_file function to galaxy.util\n\nUse it in 2 places:\n- test/base/driver_util.py (thus adding timeout and chunking)\n- lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py\n  where the total download timeout is substituted with the usual\n  urllib timeout","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/66dec1d580b426ad955db03608ec7da7eb5c5018"},{"sha":"6082f790438d6fc04f313c2eef273bfa43ff0715","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@tgac.ac.uk"},"message":"Fix path\n\nBroken in #2131.\n\nReported by @dnbenso at\nhttps://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d19e35a6460c65#commitcomment-19642191","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/6082f790438d6fc04f313c2eef273bfa43ff0715"},{"sha":"8f89a04eae27e615434e268f93d492b6c0cd54be","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@tgac.ac.uk"},"message":"Fix job_working_directory commented default\n\nFollow-up to commit 0eab8346b3dd3ee7788c9cdda0f10f8aea4b2726.","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/8f89a04eae27e615434e268f93d492b6c0cd54be"},{"sha":"83760e6a01cd3fa16a17158bb1182ffebb00c5d7","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@tgac.ac.uk"},"message":"Don't skip __init__() methods when generating 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branch 'release_16.07' into dev","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/1d8f31c4f488dc380ffe657e5fa4a9d9cdd697ae"},{"sha":"5e19d6c57465ce79d4ee96e3206542ac655d137d","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Escape section id and name when writing integrated_tool_panel.xml\n\nThis should fix #3084.","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/5e19d6c57465ce79d4ee96e3206542ac655d137d"},{"sha":"4866e72ad22b1772f93c8973e51f32086896277f","author":{"name":"Nicola Soranzo","email":"6a9e18f3f66e690ded93190b2ad69412cf28e60e@tiscali.it"},"message":"Merge pull request #3122 from mvdbeek/escape_sections\n\nEscape section name when writing to xml,","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/4866e72ad22b1772f93c8973e51f32086896277f"},{"sha":"d5132a374c25d17e63a19379bcec1d42b99f8547","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Log invalid xml filename","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/d5132a374c25d17e63a19379bcec1d42b99f8547"},{"sha":"51c586c264f2acd912060297804d61c2539f2483","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Fix tools placed outside of panel section\n\nOccasionally tools were being installed outside of the selected too panel\nsection. In the log one would find contradicting messages such as\n```\n\ntool_shed.util.repository_util DEBUG 2016-11-04 11:06:17,854 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'.\ngalaxy.tools.toolbox.base DEBUG 2016-11-04 11:06:17,886 Appending to tool panel section: NCBI SRA Tools\n172.17.0.1 - - [04/Nov/2016:11:06:15 +0000] \"POST\n/admin_toolshed/prepare_for_install HTTP/1.1\" 200 -\n\"http://localhost/admin_toolshed/prepare_for_install?changeset_revisions=62e4d56ebb6f&repository_ids=cb2d31dfab58ee88&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F\"\n\"\nMozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)\nChrome/54.0.2840.71 Safari/537.36\nnvalid tool_panel_section_key \"ncbi_sra_tools\" specified.  Tools will be\nloaded outside of sections in the tool panel.\n```\nThe intermittent POST is picked up by a different thread, that didn't\nhave its toolbox updated with the new section.\nTo circumvent this, we send the `create_panel_section` task to all\nthreads.","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/51c586c264f2acd912060297804d61c2539f2483"},{"sha":"4365b907293e366d4ad48396bb5c9dc00f134611","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Fix toolbox unittests","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/4365b907293e366d4ad48396bb5c9dc00f134611"},{"sha":"37399049552dd1f2f4492e4eb9f168ac8a9abd5f","author":{"name":"Björn Grüning","email":"0e992fbc137cfbe2bbe7f34a4a9cce8a620c105e@gruenings.eu"},"message":"Merge pull request #3124 from mvdbeek/escape_sections\n\nLog invalid xml filename","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/37399049552dd1f2f4492e4eb9f168ac8a9abd5f"},{"sha":"c94b2205b27d1d527f159bcf13ba62ce937457f6","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Escape section id and name when writing integrated_tool_panel.xml\n\nThis should fix #3084.","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/c94b2205b27d1d527f159bcf13ba62ce937457f6"},{"sha":"f6ca913809330922a3bc96bcf0f77d3f60e9bbe9","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Log invalid xml filename","distinct":false,"url":"https://api.github.com/repos/mvdbeek/galaxy/commits/f6ca913809330922a3bc96bcf0f77d3f60e9bbe9"}]}
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