Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy 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: 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
Compare: https://github.com/galaxyproject/galaxy/compare/7688b057e604...6915007f8548