Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 70ac429f22899684d80190e576b176dbef6be1d7 https://github.com/galaxyproject/galaxy/commit/70ac429f22899684d80190e576b17... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Disentangle 'view' handling in trackster track initialization. This is a step towards making Trackster work again. Commit: 4112bd51cc59a0a16845fcfeba2b9b8cb3c3925b https://github.com/galaxyproject/galaxy/commit/4112bd51cc59a0a16845fcfeba2b9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix undefined incomplete_features reference, use correct 'this.view' for tiledtrack Commit: 975e41a0372c85d1caf86c5fde5492e2fa3c4ec9 https://github.com/galaxyproject/galaxy/commit/975e41a0372c85d1caf86c5fde549... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Removal of self reference and unused import in visualization.js Commit: ac872cccf5465a3f3fce197870222168d5b1f550 https://github.com/galaxyproject/galaxy/commit/ac872cccf5465a3f3fce197870222... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Trackster painters overhaul, fixes. Commit: 9c54765e6fb6164816c16ed79628ad37f73a9192 https://github.com/galaxyproject/galaxy/commit/9c54765e6fb6164816c16ed79628a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/slotting.js Log Message: ----------- Scope and minor cleanup in slotting.js Commit: 00f4ffe166716d91fefb6078881d3d79e014c2bb https://github.com/galaxyproject/galaxy/commit/00f4ffe166716d91fefb6078881d3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/filters.js Log Message: ----------- Fix undefined var in trackster/filters -- still exists one that I need to fix here, but that'll take some digging. Commit: 2c51bdd5d04f267b5282ee06ed2312e1b3a44d25 https://github.com/galaxyproject/galaxy/commit/2c51bdd5d04f267b5282ee06ed231... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Incremental fixes and work on trackster/tracks.js -- still not painting.... Commit: 4d7539dbeccc2a51bb36a21b8b34733e7345ae8a https://github.com/galaxyproject/galaxy/commit/4d7539dbeccc2a51bb36a21b8b347... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More trackster/tracks work. More variable scoping issues fixed, function definitions standardized. One callback issue resolved. Commit: 4a7487400aa45a558a87982888c7ce75a234efa1 https://github.com/galaxyproject/galaxy/commit/4a7487400aa45a558a87982888c7c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Minor regex fix, drop a debug statement. Commit: 80c7f369148919c93132c08e19e993b290cc4a84 https://github.com/galaxyproject/galaxy/commit/80c7f369148919c93132c08e19e99... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Fix another regex; var scoping adjustments for trackster. Commit: 43d632d16c2edee3080baa5008269526fc671898 https://github.com/galaxyproject/galaxy/commit/43d632d16c2edee3080baa5008269... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Painter fixes, trying to track down initialization bug w/ this.prefs. Commit: 391ac34d5f1bc479b168b6187bd91bc1b21230fe https://github.com/galaxyproject/galaxy/commit/391ac34d5f1bc479b168b6187bd91... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More cleanup in tracks.js, still trying to track down painter initialization bug. Commit: 5d180ba5191f6c427448f836f44c2b3ca15b5d82 https://github.com/galaxyproject/galaxy/commit/5d180ba5191f6c427448f836f44c2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Rewrite painters using ES6 classes, for my sanity and future maintenance. Still won't paint, but it's easier to track through the hierarchy now. Commit: 33d17bcbe6b6a7dc85ed35849b7dce95ba04a8fe https://github.com/galaxyproject/galaxy/commit/33d17bcbe6b6a7dc85ed35849b7dc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Slight reorg in painters, post-rewrite Commit: 3ac2cabce822ff71ba2fbbb23b1f71ec5428c1e2 https://github.com/galaxyproject/galaxy/commit/3ac2cabce822ff71ba2fbbb23b1f7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Spello Commit: 76c8dae70138e113774c43b54c68babfe26b0ed9 https://github.com/galaxyproject/galaxy/commit/76c8dae70138e113774c43b54c68b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- TracksterUI class-ification, minor cleanup. Disentangling globals next. Commit: d7b2e4942fa2e940cce236d0b87c0b48e3c83508 https://github.com/galaxyproject/galaxy/commit/d7b2e4942fa2e940cce236d0b87c0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Global var refactoring, removal of some unused stuff. Commit: 9bd112bd9169f6fb782cc9fdd86cbb46824df49a https://github.com/galaxyproject/galaxy/commit/9bd112bd9169f6fb782cc9fdd86cb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Trackster refactoring; this pulls apart using a global view. There is a trackster ui, which holds the main view, and should be accessed through it when necessary. Commit: 0e6e468608fd85c3a8bdb41bf329523c821152b0 https://github.com/galaxyproject/galaxy/commit/0e6e468608fd85c3a8bdb41bf3295... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Import fixes in main trackster.js Commit: 7c9c9775753d539527ff4d74a2108563fe06a945 https://github.com/galaxyproject/galaxy/commit/7c9c9775753d539527ff4d74a2108... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Misc cleanup while trying to debug nonexistent paint vars. Commit: ec8c92604239bdb5b7e92717586bc305fbbf8db3 https://github.com/galaxyproject/galaxy/commit/ec8c92604239bdb5b7e92717586bc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Refactoring in feature painter draw. Commit: f0df326e2cdb2c90fb78e0a18dbaadee3d62de17 https://github.com/galaxyproject/galaxy/commit/f0df326e2cdb2c90fb78e0a18dbaa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Use static getters for default painter preferences, fix 'defailt' ironic typo. Commit: 2270f728c421b81ea14f022beb96203f007180dd https://github.com/galaxyproject/galaxy/commit/2270f728c421b81ea14f022beb962... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Consistent sniffing regardless of in_place. Previously sniffing would happen on the original file (before carriage returns and tabular spaces were converted) if in_place was false and on the converted file if it was true. Commit: 4bca4a056cdf766eec8108db4aaa43ddbfb57c0e https://github.com/galaxyproject/galaxy/commit/4bca4a056cdf766eec8108db4aaa4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Config.js fixes; it was trying to import itself and not use it. Commit: f33eee105f02d189cc68914dd72ed0a77f05cfcd https://github.com/galaxyproject/galaxy/commit/f33eee105f02d189cc68914dd72ed... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix config parameter default building in tracks.js; ideally this turns into classes when the multiple inheritance is fixed/refactored, and we can use simple static getter/setter methods. Commit: 2846fa0aa1e92e770e01af15008ed76b93b41b52 https://github.com/galaxyproject/galaxy/commit/2846fa0aa1e92e770e01af15008ed... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Use target file path when adding missing indexes Previously we would load a TS tool during installation and ask if any of its tool datat tables are missing loc files. If thats the case we copy the sample file and call `handle_found_index_file` for the particular missing *.loc path of this data table. This does not work if the data table already existed (e.g for built-in data tables), but was missing the *.loc file, since we would atempt to load that path. Instead we do now load the path to the loc file that we just copied. Should fix https://github.com/galaxyproject/galaxy/issues/5648. Commit: b655a499f82a73f82f89bc8f962d4f0f0097cabc https://github.com/galaxyproject/galaxy/commit/b655a499f82a73f82f89bc8f962d4... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- re-add erroneously removed line Commit: b601bcc429b47617e684158a62166575c244fd61 https://github.com/galaxyproject/galaxy/commit/b601bcc429b47617e684158a62166... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5659 from martenson/merge-in-17.09 [18.01] Merge with 17.09 Commit: 206182ea8f1ae437f4a5016fc49f74d5bf68f378 https://github.com/galaxyproject/galaxy/commit/206182ea8f1ae437f4a5016fc49f7... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #5650 from mvdbeek/missing_index_file_fixes [18.01] Use sample file path when adding missing indexes Commit: cdae68907bdacc4f290f561bff89f3b4525a7b4d https://github.com/galaxyproject/galaxy/commit/cdae68907bdacc4f290f561bff89f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Fix exception if user preference value undefined Fixes the following traceback on main: ``` AttributeError: 'NoneType' object has no attribute 'strip' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/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/webapps/galaxy/controllers/root.py", line 110, in index config.update(self._get_extended_config(trans)) File "galaxy/webapps/galaxy/controllers/root.py", line 57, in _get_extended_config 'toolbox' : app.toolbox.to_dict(trans, in_panel=False), File "galaxy/tools/toolbox/base.py", line 963, in to_dict filter_method = self._build_filter_method(trans) File "galaxy/tools/toolbox/base.py", line 1004, in _build_filter_method filters = self._filter_factory.build_filters(trans) File "galaxy/tools/toolbox/filters/__init__.py", line 37, in build_filters if value.strip(): ``` Commit: 706efdc186177c36871aa47059de64aa0112f1a0 https://github.com/galaxyproject/galaxy/commit/706efdc186177c36871aa47059de6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix exception if email is not specified We render a regular error a few lines lower. Commit: d60b80a537ae4b9d580805014c99d74bb6598896 https://github.com/galaxyproject/galaxy/commit/d60b80a537ae4b9d580805014c99d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if user tries purging datasets without having an associated history. This can be seen by pasting http://<gx_instance>/history/purge_deleted_datasets into an anonymous browser session (be careful to not delete something important ;)). Traceback is: ``` AttributeError: 'NoneType' object has no attribute 'datasets' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/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/webapps/galaxy/controllers/history.py", line 1108, in purge_deleted_datasets for hda in trans.history.datasets: ``` Commit: 17e1786521e458819f2cdb9821fd3e96c18bc3a7 https://github.com/galaxyproject/galaxy/commit/17e1786521e458819f2cdb9821fd3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Avoid exception if email is wrong Avoids: ``` AttributeError: 'NoneType' object has no attribute 'active' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/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/webapps/galaxy/controllers/user.py", line 938, in activate if user.active is True: ``` Commit: fe444ab3ef6bf37761859e09a0baf3ec38e7c6c4 https://github.com/galaxyproject/galaxy/commit/fe444ab3ef6bf37761859e09a0baf... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if history structure can't be shown Fixes: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/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/webapps/galaxy/controllers/history.py", line 494, in display_structured assert (history.user and (history.user.id == trans.user.id) or ``` Commit: 3ce1273d7cc447d9088f9c056649d16c188d509d https://github.com/galaxyproject/galaxy/commit/3ce1273d7cc447d9088f9c056649d... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Merge pull request #5662 from mvdbeek/fix_build_filters [18.01] Fix exception if user preference value undefined Commit: 0a95f20f5ba7e41282a29afb21a41290033cfed8 https://github.com/galaxyproject/galaxy/commit/0a95f20f5ba7e41282a29afb21a41... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #5663 from mvdbeek/user_activation_fix [18.01] Fix exception if email is not specified or email is wrong Commit: a0fd6307562b38a7ef93291c6450cb92bd0eaf59 https://github.com/galaxyproject/galaxy/commit/a0fd6307562b38a7ef93291c6450c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5665 from mvdbeek/show_error_msg_when_history_structure_cannot_be_shown [18.01] Show error message if history structure can't be shown Commit: 1761d85e7299ddd34565794c43b0c761b44a0bc5 https://github.com/galaxyproject/galaxy/commit/1761d85e7299ddd34565794c43b0c... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5664 from mvdbeek/show_error_message_if_no_history_associated [18.01] Show error message if user tries purging datasets Commit: 9c9c69ca29fd820263181ab9f92349658aa74d33 https://github.com/galaxyproject/galaxy/commit/9c9c69ca29fd820263181ab9f9234... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- iniital work on RN Commit: 0229bf532981394ea3e97fd9f62bcef83789bc25 https://github.com/galaxyproject/galaxy/commit/0229bf532981394ea3e97fd9f62bc... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- announce removal of planttribe datatypes Commit: fa3ec5f60b9a4b6bed0ee771166c6e49c8fa02d0 https://github.com/galaxyproject/galaxy/commit/fa3ec5f60b9a4b6bed0ee771166c6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Merge pull request #5261 from dannon/trackster_fixes [18.01] Trackster fixes. Commit: 63292de10a608d624c3cababad741325386226d9 https://github.com/galaxyproject/galaxy/commit/63292de10a608d624c3cababad741... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- add trackster fix to RN Commit: 02bf18f33b93eac5e6fdd4e163cbed0563196f82 https://github.com/galaxyproject/galaxy/commit/02bf18f33b93eac5e6fdd4e163cbe... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Some initial work on release highlights, still completely broken. Commit: 3515d6040514fdb91b5a8780bb48d0a26ade4ee1 https://github.com/galaxyproject/galaxy/commit/3515d6040514fdb91b5a8780bb48d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Another couple sentences of release docs. Commit: e923c61a0726d6d5201e01a017b841d61933f744 https://github.com/galaxyproject/galaxy/commit/e923c61a0726d6d5201e01a017b84... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More progress on release notes, still very rough. Commit: cb477ddcf02749e8d949d237ac8945c9bbd13d36 https://github.com/galaxyproject/galaxy/commit/cb477ddcf02749e8d949d237ac894... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few. Commit: 1a68096cfa29631beca467acf9bd82c57546d938 https://github.com/galaxyproject/galaxy/commit/1a68096cfa29631beca467acf9bd8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 2 of 1003. Commit: 1923786a6545bcef1c381baf39bf931b9b9ec8af https://github.com/galaxyproject/galaxy/commit/1923786a6545bcef1c381baf39bf9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Condense many 18.01 release bullets, expand a few - part 3 of 1003. Commit: b964722acc83d52ae0a107becf02dcee09dae6f4 https://github.com/galaxyproject/galaxy/commit/b964722acc83d52ae0a107becf02d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- More release 18.01 release note tweaks. Commit: 6d4b83990f60f79003f7b6d33446cc9d38eb24a3 https://github.com/galaxyproject/galaxy/commit/6d4b83990f60f79003f7b6d33446c... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Spell check 18.01 release notes and small tweaks. Commit: 9e274278f13e970c46f21b26e7e283f262d1c29b https://github.com/galaxyproject/galaxy/commit/9e274278f13e970c46f21b26e7e28... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Small language tweaks. Including fixes from :eagle::eyes:. Commit: e68ac4a3c8aeb259b348a6b2f606a207786038fd https://github.com/galaxyproject/galaxy/commit/e68ac4a3c8aeb259b348a6b2f606a... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Highlights fixes Commit: 804f815eee221723e1dc35e451783415386d7f6a https://github.com/galaxyproject/galaxy/commit/804f815eee221723e1dc35e451783... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Fix bullet list indentation Commit: 235d6c3269a53191bde7a41e9fda2422df4e28d1 https://github.com/galaxyproject/galaxy/commit/235d6c3269a53191bde7a41e9fda2... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Condense some entries Commit: e72e02cc7a98f6c721dbd14a52f5f18f5de33d5f https://github.com/galaxyproject/galaxy/commit/e72e02cc7a98f6c721dbd14a52f5f... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5643 from jmchilton/sniff_fix [18.01] Consistent sniffing regardless of in_place. Commit: c5ead795b5f0105b75f56914e7c601aa5983b61b https://github.com/galaxyproject/galaxy/commit/c5ead795b5f0105b75f56914e7c60... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst Log Message: ----------- Add #5643 to release notes Commit: df03a59c53250bae402b24e4a6d4a607a32b6cd7 https://github.com/galaxyproject/galaxy/commit/df03a59c53250bae402b24e4a6d4a... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- move some sections deeper in the document to make the highlights more focused Commit: c034ab3f0b6357628f2b7727e42146b84e9f57b5 https://github.com/galaxyproject/galaxy/commit/c034ab3f0b6357628f2b7727e4214... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #5668 from martenson/18.01_release_notes [18.01] Release Notes Commit: 83fa18deb794909afde5e3f21ceeb24fe68335fe https://github.com/galaxyproject/galaxy/commit/83fa18deb794909afde5e3f21ceeb... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Display error message on IE template fill exception Commit: 2db95b4d1dd8c72fbf20439ac473d8a2b15f5c1a https://github.com/galaxyproject/galaxy/commit/2db95b4d1dd8c72fbf20439ac473d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Rename datatype extension 'bam_native' to 'unsorted.bam'. We handle other bam types this way and other more specific variants of an extension (e.g. thermo.raw) so this feels like the more consistent thing to do. Commit: 9c0c8ee679571cc037f77b60f03a95760ddca29d https://github.com/galaxyproject/galaxy/commit/9c0c8ee679571cc037f77b60f03a9... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst Log Message: ----------- Mention self.current_pr in release notes. Commit: d632b41b8600604f143d6f6677d83d41ee735abc https://github.com/galaxyproject/galaxy/commit/d632b41b8600604f143d6f6677d83... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix GIE launch for cases when the published port isn't available immediately (seems to happen with Swarm Mode occasionally) Commit: 4fea3904ab616088ac71a9ac10a3b1656c13f1c0 https://github.com/galaxyproject/galaxy/commit/4fea3904ab616088ac71a9ac10a3b... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5674 from jmchilton/unsorted_bam_rename [18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. Commit: 1a5f6a3499091182797693bc1bb06a82095bc788 https://github.com/galaxyproject/galaxy/commit/1a5f6a3499091182797693bc1bb06... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Merge pull request #5677 from natefoo/docker-swarm-race [18.01] Additional error handling for GIE container launching Commit: 4fc6380708454c15360f0940ee56998c08fc6c8a https://github.com/galaxyproject/galaxy/commit/4fc6380708454c15360f0940ee569... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M config/datatypes_conf.xml.sample A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/tool_util.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dc6b22fc74f4...4fc638070845