Branch: refs/heads/master 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: 0207b0186ac7c3d61004718ff7b91c3ea0c52165 https://github.com/galaxyproject/galaxy/commit/0207b0186ac7c3d61004718ff7b91... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py
Log Message: ----------- Specify TagAssociation class when copying a tag
This probably fixes https://github.com/galaxyproject/galaxy/issues/4975. Otherwise if a collection is created from a HDA with a tag (i.e by splitting the dataset) a HistoryDatasetAssociationTag would be added to a collection of HistoryDatasetCollectionAssociationTags.
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: b978acbe62053596e5c2ae736c848a62dc936591 https://github.com/galaxyproject/galaxy/commit/b978acbe62053596e5c2ae736c848... Author: John Chilton jmchilton@gmail.com Date: 2017-11-12 (Sun, 12 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message: ----------- Revert "Remove downloading workflows through controller"
This reverts commit 1a4effa70e9ad8088e19ae334753b7a898d286aa.
This is used when downloading workflows with the save icom from "pages".
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: 3b523260551d15241de5dce3d1023790dcfd2250 https://github.com/galaxyproject/galaxy/commit/3b523260551d15241de5dce3d1023... Author: Martin Cech marten@bx.psu.edu Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message: ----------- Merge pull request #4988 from jmchilton/revert_export_to_file
[17.09] Revert export to file
Commit: e5587dcb64897e53900c05bde2afa32c945ce6a6 https://github.com/galaxyproject/galaxy/commit/e5587dcb64897e53900c05bde2afa... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py
Log Message: ----------- Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags
[17.05][BUG] Specify TagAssociation class when copying a tag
Commit: 1a412bfb1b0497d9e3e2b8f9c348d7aa0f2478d6 https://github.com/galaxyproject/galaxy/commit/1a412bfb1b0497d9e3e2b8f9c348d... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py
Log Message: ----------- Merge branch 'release_17.05' into release_17.09
Commit: 06e9509d3868c885d41d94e455d7245f4af10156 https://github.com/galaxyproject/galaxy/commit/06e9509d3868c885d41d94e455d72... Author: John Chilton jmchilton@gmail.com Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths: M lib/galaxy/work/context.py
Log Message: ----------- Allow get_history calls with create=False when evaluation workflows.
No reasons to prevent this I guess - since create means create if a history isn't available not force the creation of a history.
Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba779... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Add missing ipaddress requirement
Broken in https://github.com/galaxyproject/galaxy/pull/4289 .
Fix https://github.com/galaxyproject/galaxy/issues/4999 .
Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be5... Author: Martin Cech marten@bx.psu.edu Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message: ----------- remove the default override since it is wrong and ignores the access permissions
Commit: 827ac9c0433f581166b5bd06b70a14a39f22ded2 https://github.com/galaxyproject/galaxy/commit/827ac9c0433f581166b5bd06b70a1... Author: guerler aysam.guerler@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/tools/parameters/__init__.py
Log Message: ----------- Do not attempt to visit parameters of invalid conditionals
Commit: 1457fa7f937522d4825bb814a927a87b2e363cc8 https://github.com/galaxyproject/galaxy/commit/1457fa7f937522d4825bb814a927a... Author: guerler aysam.guerler@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/tools/parameters/__init__.py
Log Message: ----------- Check for key/value errors only when testing conditional cases
Commit: 75f84bfc476ea94c22a38097d20f694265fcded6 https://github.com/galaxyproject/galaxy/commit/75f84bfc476ea94c22a38097d20f6... Author: guerler aysam.guerler@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/tools/parameters/__init__.py
Log Message: ----------- Add test cases to cover version changes
Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956 https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf3... Author: John Chilton jmchilton@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message: ----------- Merge pull request #5008 from martenson/fix-ldda-access-check
[16.07] history contents api - remove the default flag override
Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9 https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a64190... Author: John Chilton jmchilton@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into HEAD
Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa9430606040... Author: John Chilton jmchilton@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into HEAD
Commit: eab30c96522a5a558de4232320c87c1ef102d2d2 https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c87... Author: John Chilton jmchilton@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05
Commit: b25de8b003168ebced8fbc3bfce5274d32cc1ab7 https://github.com/galaxyproject/galaxy/commit/b25de8b003168ebced8fbc3bfce52... Author: John Chilton jmchilton@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into HEAD
Commit: 9e9edb7e338bcf6a3d4174fc0d8e420a5184ad6b https://github.com/galaxyproject/galaxy/commit/9e9edb7e338bcf6a3d4174fc0d8e4... Author: guerler aysam.guerler@gmail.com Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths: M lib/galaxy/tools/parameters/__init__.py
Log Message: ----------- Remove unnecessary name setting for non-group parameters
Commit: 64eced315887f19b7efd6334d4a28f91e8fd6116 https://github.com/galaxyproject/galaxy/commit/64eced315887f19b7efd6334d4a28... Author: guerler aysam.guerler@gmail.com Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths: M lib/galaxy/tools/parameters/__init__.py
Log Message: ----------- Fix comments
Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623 https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1f... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement
[17.09] Add missing ipaddress requirement
Commit: de1bd5f5d5af7b9e67180b115407fbc2ccb75a3e https://github.com/galaxyproject/galaxy/commit/de1bd5f5d5af7b9e67180b115407f... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js
Log Message: ----------- Fix workflow editor output attributes.
Commit: 5dc2254417667216dab982a4bc375a85d3b55316 https://github.com/galaxyproject/galaxy/commit/5dc2254417667216dab982a4bc375... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths: M lib/galaxy/work/context.py
Log Message: ----------- Merge pull request #4997 from jmchilton/allow_create_false_in_work_context
[17.09] Allow get_history calls with create=False when evaluation workflows.
Commit: 2a0c7114dfafb0c91e3bafb03ae6ff4370ce9ed8 https://github.com/galaxyproject/galaxy/commit/2a0c7114dfafb0c91e3bafb03ae6f... Author: Martin Cech marten@bx.psu.edu Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js
Log Message: ----------- Merge pull request #5022 from dannon/workflow_editor_fix_backport
[17.09] Fix workflow editor output attributes.
Commit: 1cfdf85879213018affc3ec19142e3ebccdb8c40 https://github.com/galaxyproject/galaxy/commit/1cfdf85879213018affc3ec19142e... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py
Log Message: ----------- add ICM datatype for glimmer
Commit: f44175b03c1671e6db11f1b072c3cd704a95fd58 https://github.com/galaxyproject/galaxy/commit/f44175b03c1671e6db11f1b072c3c... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths: M lib/galaxy/datatypes/binary.py
Log Message: ----------- copy paste mistake...
Commit: f60a75c285830bff963bd31120f3420e9815dbe2 https://github.com/galaxyproject/galaxy/commit/f60a75c285830bff963bd31120f34... Author: E Rasche hxr@hx42.org Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths: M lib/galaxy/jobs/runners/condor.py
Log Message: ----------- extraneous %s
Commit: 59e9809585e2322382eaeb7b3e0270485b7e8db0 https://github.com/galaxyproject/galaxy/commit/59e9809585e2322382eaeb7b3e027... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths: M lib/galaxy/jobs/runners/condor.py
Log Message: ----------- Merge pull request #5048 from erasche/fix-ufr-6206
Remove extraneous %s in condor logging
Commit: a7c8edbaa448805e0211fc75e3888d8426e5fa38 https://github.com/galaxyproject/galaxy/commit/a7c8edbaa448805e0211fc75e3888... Author: John Chilton jmchilton@gmail.com Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml
Log Message: ----------- Bug fix - expose proper element_identifier in tool action template expansions. (#5049)
xref https://github.com/galaxyproject/tools-iuc/commit/f57f1bf4816f212b83c08e0e3c...
Commit: 0bb7612977a44422acdf9c7d559d555ece1d17da https://github.com/galaxyproject/galaxy/commit/0bb7612977a44422acdf9c7d559d5... Author: Anthony Bretaudeau anthony.bretaudeau@inria.fr Date: 2017-11-21 (Tue, 21 Nov 2017)
Changed paths: M lib/galaxy/datatypes/binary.py
Log Message: ----------- don't read too much
Commit: 8db4288ab5dcf379a669a5ae6ececc217b3c9da0 https://github.com/galaxyproject/galaxy/commit/8db4288ab5dcf379a669a5ae6ecec... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt
Log Message: ----------- Fixes galaxy startup when LC_TYPE=UTF-8 on os-x
Closes https://github.com/galaxyproject/galaxy/issues/2645.
Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c8... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message: ----------- Ignore OSError when chmod'ing integrated_tool_panel_conf.xml
This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031: ``` Exception in thread ToolConfWatcher.thread: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(*self.__args, **self.__kwargs) File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check self.reload_callback() File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda> self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache) File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox _get_new_toolbox(app) File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app) File "lib/galaxy/tools/__init__.py", line 226, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__ self._save_integrated_tool_panel() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel self._write_integrated_tool_panel_config_file() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file os.chmod(self._integrated_tool_panel_config, 0o644) OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml' ```
Commit: adfb623224810a0f383dc4ddf88be4ce51d3aa71 https://github.com/galaxyproject/galaxy/commit/adfb623224810a0f383dc4ddf88be... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- Fix metadata setting for Otu datatypes
I broke this in https://github.com/galaxyproject/galaxy/pull/4388. I went through the other changes in that PR, and I believe this should be the only error. Figured out through the great detective work of @abernard.
Commit: a71d5aa2db41a289b9410b129e6e70652f456593 https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e7... Author: John Chilton jmchilton@gmail.com Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message: ----------- Merge pull request #5071 from mvdbeek/installation_fixes
[BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml
Commit: f16491cd6506eb0734c415be1e0456faf9c1dd04 https://github.com/galaxyproject/galaxy/commit/f16491cd6506eb0734c415be1e045... Author: John Chilton jmchilton@gmail.com Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt
Log Message: ----------- Merge pull request #5070 from mvdbeek/docutils_upgrade
[BUG][[17.09] Fixes galaxy startup when LC_TYPE=UTF-8 on os-x
Commit: a58586f0e4973aa6855142222ed8be124add9ad5 https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8b... Author: John Chilton jmchilton@gmail.com Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths: M lib/galaxy/workflow/scheduling_manager.py
Log Message: ----------- Cleanup SA objects between workflow invocation scheduling attempts.
This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more.
Commit: ed162d5a69a3fac061f6becf592e737eed678411 https://github.com/galaxyproject/galaxy/commit/ed162d5a69a3fac061f6becf592e7... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2017-11-27 (Mon, 27 Nov 2017)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- Merge pull request #5072 from mvdbeek/metadata_investigation
[BUG][17.09] Fix metadata setting for Otu datatypes
Commit: 385aaf2bd7e2b1c79f4b21f0449aed98fc9d6446 https://github.com/galaxyproject/galaxy/commit/385aaf2bd7e2b1c79f4b21f0449ae... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-27 (Mon, 27 Nov 2017)
Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
Log Message: ----------- Fix exception in admin panel
TypeError: Non-hexadecimal digit found File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 660, in manage_repositories return self.repository_installation_grid(trans, **kwd) File "galaxy/web/framework/helpers/grids.py", line 85, in __call__ query = self.build_initial_query(trans, **kwargs) File "tool_shed/galaxy_install/grids/admin_toolshed_grids.py", line 334, in build_initial_query clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_shed_repository_id)) File "galaxy/web/security/__init__.py", line 107, in decode_id return int(id_cipher.decrypt(obj_id.decode('hex')).lstrip("!")) File "encodings/hex_codec.py", line 42, in hex_decode output = binascii.a2b_hex(input)
This is due to `tool_shed_repository_ids` being a json dump of a list in certain consitions (noticed this after installing a new repository).
Commit: 0493763938ab6146dc383b735a7b3523914c2342 https://github.com/galaxyproject/galaxy/commit/0493763938ab6146dc383b735a7b3... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message: ----------- Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE
Commit: f6aedb0d2094256eb7f45ce7fc75f327db5b560c https://github.com/galaxyproject/galaxy/commit/f6aedb0d2094256eb7f45ce7fc75f... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py
Log Message: ----------- Merge pull request #5042 from abretaud/icm_dt
[17.09] Add ICM datatype for glimmer
Commit: ff3a6b084931f532dbce9a6d82059cda0137e3e3 https://github.com/galaxyproject/galaxy/commit/ff3a6b084931f532dbce9a6d82059... Author: John Chilton jmchilton@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message: ----------- Merge pull request #5086 from mvdbeek/sentry_report_fix
[17.09] Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE
Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece6... Author: Eric Rasche hxr@hx42.org Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths: M lib/galaxy/workflow/scheduling_manager.py
Log Message: ----------- Merge pull request #5073 from jmchilton/backport_5045
[17.09] Backport #5045
Commit: e903cb708e2f33bccebf5a0dd89b3bfe13667e03 https://github.com/galaxyproject/galaxy/commit/e903cb708e2f33bccebf5a0dd89b3... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths: M lib/galaxy/tools/parameters/__init__.py
Log Message: ----------- Merge pull request #5010 from guerler/fix_pages_workflows
[17.09] Do not visit child inputs of invalid conditionals
Commit: a82d325d18375797ce8ab53366320f3c9a772ab7 https://github.com/galaxyproject/galaxy/commit/a82d325d18375797ce8ab53366320... Author: Martin Cech marten@bx.psu.edu Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
Log Message: ----------- Merge pull request #5079 from mvdbeek/admin_panel_exception_fix
[17.09] Fix exception in admin panel
Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a562... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths: M lib/galaxy/datatypes/molecules.py
Log Message: ----------- Stricter checks for SDF sniffing
I had a bunch of protein FASTA files being sniffed as 'sdf'.
Also fix https://github.com/galaxyproject/galaxy/issues/4558 .
Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab87... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf
Log Message: ----------- More precise SDF sniffer
First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from:
https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_da...
Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d6... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf
Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes
[17.09] Backport stricter checks for SDF sniffing #4729
Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d1... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-12-04 (Mon, 04 Dec 2017)
Changed paths: M config/datatypes_conf.xml.sample
Log Message: ----------- Fix ICM datatype sniffer config
Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108
Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58f... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-12-04 (Mon, 04 Dec 2017)
Changed paths: M config/datatypes_conf.xml.sample
Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config
[17.09] Fix ICM datatype sniffer config
Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325fd... Author: John Chilton jmchilton@gmail.com Date: 2017-12-05 (Tue, 05 Dec 2017)
Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py
Log Message: ----------- Migrate documentation for setting up a production instance to Galaxy.
This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance).
This content currently includes:
- the production configuration page - the cluster configuration page - the job configuration page - the scaling information page - the ftp configuration page - the top-level nginx page (for external auth content still linking out to the hub) - the top-level apache page (for external auth content still linking out to the hub) - the job metrics configuration page
Includes small tweaks to sphinx documentation generation.
- Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs. - Use AutoStructify for better Markdown integration.
Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including:
- Update the job configuration page with information about XML macros. - Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore). - Updated list of dynamic job runner configuration parameters. - Mention the ``raw`` attribute for ``env`` directives in the job configuration page. - Mention the ``total_walltime`` limit added in #3217. - Drop mentions of older URL-based job conf configuration stuff. - Mention newer Local and Paramiko based shell runners in CLI section. - Mention newer slurm job styles in CLI section. - Improved Pulsar links. - Fix dataset security link in Apache display sites config. - Update job metrics page to link to a new Github issue instead of old Trello issues.
Commit: befa077cc444115e0cac738c2bd3ee786f7425d2 https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3e... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M doc/source/admin/jobs.md
Log Message: ----------- Rework headings in jobs docs.
Thanks to comment from @erasche review.
Commit: b0c03240fd96ace2b25680e753fed0237264ec98 https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fed... Author: Martin Cech marten@bx.psu.edu Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py
Log Message: ----------- Merge pull request #5135 from jmchilton/17.09_admin_docs
[17.09] Migrate documentation for setting up a production instance to Galaxy.
Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43 https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba8359... Author: Dannon Baker dannon.baker@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Log Message: ----------- Merge pull request #5141 from jmchilton/master
[17.09] Re-merge master into release_17.09.
Compare: https://github.com/galaxyproject/galaxy/compare/15372f736913...cd1454c40a43