Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7e05a012cb8dd3bf90f31f5c5a7df44587e97c0 https://github.com/galaxyproject/galaxy/commit/b7e05a012cb8dd3bf90f31f5c5a7d... Author: Ignacio Eguinoa <igegu@psb.ugent.be> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- otherwise it will overwrite linking source file Commit: 19e5478cb8ffbd9d97db663bb1d04e52bed721a0 https://github.com/galaxyproject/galaxy/commit/19e5478cb8ffbd9d97db663bb1d04... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4911 from jmchilton/backport_4858 [17.09] Backport #4858 Commit: e3be7c31d59b69571bcee04599bdac6693426b89 https://github.com/galaxyproject/galaxy/commit/e3be7c31d59b69571bcee04599bda... Author: Wolfgang Maier <wolfgang.maier@biologie.uni-freiburg.de> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- fix broken link in 17.09 announcement Commit: 222ece4eabb6d080c6b8a0e327f8cf617b8a194f https://github.com/galaxyproject/galaxy/commit/222ece4eabb6d080c6b8a0e327f8c... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-11-03 (Fri, 03 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #4927 from wm75/patch-2 fix broken link in 17.09 announcement Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3 https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3ca... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Tolerate IOError in tool and data table watcher Without these changes the watcher thread may die when manually deleting loc files: ``` Exception in thread Thread-7: Traceback (most recent call last): File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run self.dispatch_events(self.event_queue, self.timeout) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events handler.dispatch(event) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch self.on_any_event(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event self._handle(event) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle cur_hash = md5_hash_file(path) File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file with open(path, 'rb') as afile: IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc' ``` Similar problems could occur when deleting tool xml files. Commit: 231ce40e8154bd44fc1e5a0072489b9b81ad5377 https://github.com/galaxyproject/galaxy/commit/231ce40e8154bd44fc1e5a0072489... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-11-12 (Sun, 12 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Encode file content with utf-8 There shouldn't be any disadvantages over doing this only for specific elements. This also fixes https://github.com/galaxyproject/galaxy/issues/4345#issuecomment-343753378. I have tested this with unicode strings in the name and info fields. Commit: 0c9b42035bc51d6a66f5a6e0746fd28c67996cb3 https://github.com/galaxyproject/galaxy/commit/0c9b42035bc51d6a66f5a6e0746fd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Open files in text-mode (thx @nsoranzo) Commit: 6915007f85482648999768eecb9920da57b42e59 https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb992... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge pull request #4981 from mvdbeek/watcher_error_delete [17.05][BUG] Tolerate IOError in tool and data table watcher Commit: a0b4a2de53793c85a9b0443be4b2e4a8f4421759 https://github.com/galaxyproject/galaxy/commit/a0b4a2de53793c85a9b0443be4b2e... Author: John Chilton <jmchilton@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4987 from mvdbeek/history_import_bug [17.09][Bug] Encode file content with utf-8 Commit: 577d57a69ce0d6d7f7c60ebc98009443cae204a0 https://github.com/galaxyproject/galaxy/commit/577d57a69ce0d6d7f7c60ebc98009... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: e78efe16f4325a8abb7701fc62b5969ef89781db https://github.com/galaxyproject/galaxy/commit/e78efe16f4325a8abb7701fc62b59... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M doc/source/releases/17.09_announce.rst M lib/galaxy/tools/cache.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a18835b5169c...e78efe16f432