| 99c8f54 | John Chilton | 18 May 2016, 11:43:10 UTC | Update version to 16.04 | 18 May 2016, 11:43:10 UTC |
| 8195d81 | John Chilton | 18 May 2016, 11:28:01 UTC | Merge pull request #2353 from martenson/16.04_release_notes [16.04] Release notes for 16.04 | 18 May 2016, 11:28:01 UTC |
| f887c05 | John Chilton | 18 May 2016, 11:26:25 UTC | Expand 16.04 highlights... | 18 May 2016, 11:26:25 UTC |
| 9d5bf7b | Martin Cech | 17 May 2016, 19:56:50 UTC | minor release notes touch | 17 May 2016, 19:56:50 UTC |
| 50e596f | Martin Cech | 17 May 2016, 19:51:23 UTC | reorder sections, un-quote bitbucket paragraph | 17 May 2016, 19:51:23 UTC |
| afb9027 | Martin Cech | 17 May 2016, 19:48:00 UTC | final touch of release notes from my side | 17 May 2016, 19:48:00 UTC |
| cc86096 | Martin Cech | 16 May 2016, 22:26:46 UTC | Merge pull request #2362 from dannon/slurm_complete_job_fix [16.04] Fix for slurm's complete_terminal_job where if unable to inspect the … | 16 May 2016, 22:26:46 UTC |
| 62b6eaa | Martin Cech | 16 May 2016, 21:08:32 UTC | Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes | 16 May 2016, 21:08:32 UTC |
| 3b7f6cb | Martin Cech | 16 May 2016, 21:07:32 UTC | add some highlights, seems tough for this release | 16 May 2016, 21:07:32 UTC |
| 2390da5 | Dannon Baker | 16 May 2016, 15:48:33 UTC | Fix for slurm's complete_terminal_job where if unable to inspect the failed job with scontrol drmaajobrunner's _complete_terminal_job was called twice. | 16 May 2016, 15:48:33 UTC |
| 38209bb | John Chilton | 14 May 2016, 19:30:38 UTC | Merge pull request #2350 from natefoo/fix-ajs-red-herring [16.04] Properly handle AsynchronousJobState objects in the job runner work queue | 14 May 2016, 19:30:38 UTC |
| 76fb9b7 | Nicola Soranzo | 13 May 2016, 15:08:58 UTC | Add some missing PRs and merge some entries | 13 May 2016, 15:12:15 UTC |
| dc5a5eb | Nate Coraor | 13 May 2016, 14:30:52 UTC | Add Bitbucket deprecation details | 13 May 2016, 14:30:52 UTC |
| c516c9f | Nicola Soranzo | 13 May 2016, 11:34:02 UTC | Fix truncated PR titles and some acknowledgements | 13 May 2016, 11:34:12 UTC |
| b85d604 | Nicola Soranzo | 13 May 2016, 11:11:25 UTC | Move some PRs that were merged in 16.01 before its release Galaxy 16.01 was officially released on 2016/02/24. | 13 May 2016, 11:11:30 UTC |
| db5c0d9 | Martin Cech | 12 May 2016, 21:43:14 UTC | reorde notes a bit more based on impact/importance | 12 May 2016, 21:43:14 UTC |
| 65e1d68 | Martin Cech | 12 May 2016, 21:37:08 UTC | typo | 12 May 2016, 21:37:08 UTC |
| 633162c | Martin Cech | 12 May 2016, 21:31:22 UTC | fix wrong merge | 12 May 2016, 21:31:22 UTC |
| edbc82c | Martin Cech | 12 May 2016, 21:28:00 UTC | Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes Conflicts: doc/source/releases/16.04_announce.rst | 12 May 2016, 21:28:00 UTC |
| e0a9efc | Martin Cech | 12 May 2016, 21:25:07 UTC | include security note for hg upgrade; some reordering | 12 May 2016, 21:25:07 UTC |
| 86127cd | carlfeberhard | 12 May 2016, 21:20:06 UTC | Update 16.04_announce.rst Fix my rst syntax. | 12 May 2016, 21:20:06 UTC |
| 40e596f | carlfeberhard | 12 May 2016, 21:12:45 UTC | Update 16.04_announce.rst Added more deprecations from #1757 | 12 May 2016, 21:12:45 UTC |
| 93d1d56 | Martin Cech | 12 May 2016, 20:40:01 UTC | add deprecation notices | 12 May 2016, 20:40:01 UTC |
| d8430e5 | Martin Cech | 12 May 2016, 20:22:56 UTC | generated notes with basic manual curation | 12 May 2016, 20:22:56 UTC |
| e28d305 | Daniel Blankenberg | 12 May 2016, 18:01:45 UTC | Merge pull request #2345 from nsoranzo/release_16.04_fix_for_2029 [16.04] Do not pollute param_dict with a non JSONifiable dict | 12 May 2016, 18:01:45 UTC |
| 35a716b | Nate Coraor | 12 May 2016, 14:43:48 UTC | Not all objects added to the runner work queue are JobWrappers/TaskWrappers as claimed in the comment. AsynchronousJobStates could also be added, and if the fail method was called this would result in the AttributeError of attempting to access an AJS' non-existent `get_id_tag` being logged in job.exeception as a red herring. | 12 May 2016, 14:43:48 UTC |
| 8255e72 | Nicola Soranzo | 11 May 2016, 16:22:48 UTC | Do not pollute param_dict with a non JSONifiable dict When running a data manager with a dataset parameter, the job fails with the following backtrace: Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job job_wrapper.prepare() File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 885, in prepare tool_evaluator.set_compute_environment( compute_environment, get_special=get_special ) File "/opt/galaxy/lib/galaxy/tools/evaluation.py", line 107, in set_compute_environment self.tool.exec_before_job( self.app, inp_data, out_data, param_dict ) File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1956, in exec_before_job out.write( json.dumps( (json_params) ).encode('utf8') ) File "/usr/lib/python2.7/json/__init__.py", line 243, in dumps return _default_encoder.encode(obj) File "/usr/lib/python2.7/json/encoder.py", line 207, in encode chunks = self.iterencode(o, _one_shot=True) File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode return _iterencode(o, 0) TypeError: keys must be a string The bug was introduced in PR #2029. | 11 May 2016, 16:28:07 UTC |
| 0138136 | Dannon Baker | 11 May 2016, 15:06:13 UTC | Merge pull request #2339 from natefoo/gie-proxy-path [16.04] Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix | 11 May 2016, 15:06:13 UTC |
| bd25ae9 | Nate Coraor | 10 May 2016, 18:24:17 UTC | Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix | 10 May 2016, 18:24:17 UTC |
| d0830e0 | Eric Rasche | 10 May 2016, 13:20:55 UTC | Merge pull request #2333 from bgruening/proxy_fix Fixes the proxy naming | 10 May 2016, 13:20:55 UTC |
| 443a9e2 | Bjoern Gruening | 10 May 2016, 11:26:52 UTC | fix proxy name | 10 May 2016, 11:26:52 UTC |
| 8ee9ad2 | John Chilton | 09 May 2016, 18:37:42 UTC | Merge pull request #2316 from guerler/fix_accept_000 [16.04] Relax default value acceptance condition | 09 May 2016, 18:37:42 UTC |
| 5710506 | Nicola Soranzo | 09 May 2016, 09:48:17 UTC | Merge branch 'release_16.01' into release_16.04 Conflicts: templates/show_params.mako | 09 May 2016, 09:48:17 UTC |
| 79dd8c8 | Dannon Baker | 07 May 2016, 22:11:24 UTC | Merge pull request #2312 from nsoranzo/release_16.01_fix_makos [16.01] Unicodify pretty datetimes which can contain non-ASCII chars | 07 May 2016, 22:11:24 UTC |
| 5bb7c1d | Björn Grüning | 07 May 2016, 15:52:07 UTC | Merge pull request #2317 from nsoranzo/release_16.04_tsv_fix [16.04] Do not sniff one-line files as CSV/TSV | 07 May 2016, 15:52:07 UTC |
| 427804f | Nicola Soranzo | 05 May 2016, 16:59:59 UTC | Do not sniff one-line files as CSV/TSV | 05 May 2016, 17:21:16 UTC |
| ff903ac | Nicola Soranzo | 05 May 2016, 17:16:12 UTC | Merge branch 'release_16.01' into release_16.04 | 05 May 2016, 17:16:12 UTC |
| 37c50d0 | guerler | 05 May 2016, 17:11:37 UTC | Relax default value acceptance condition | 05 May 2016, 17:12:34 UTC |
| 41e6f22 | John Chilton | 05 May 2016, 16:47:20 UTC | Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit [16.01] Remove SLURM memory limit warning from stderr if the job was successful | 05 May 2016, 16:47:20 UTC |
| ce8fa33 | John Chilton | 05 May 2016, 16:45:56 UTC | Merge pull request #2311 from natefoo/drmaa-failed [16.04] If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue | 05 May 2016, 16:45:56 UTC |
| 0f984d3 | Nicola Soranzo | 05 May 2016, 10:49:05 UTC | Unicodify pretty datetimes which can contain non-ASCII chars | 05 May 2016, 10:49:05 UTC |
| ad0647d | Nicola Soranzo | 04 May 2016, 19:12:03 UTC | Change elif to if because drmaa_state can be changed inside the if | 04 May 2016, 19:12:03 UTC |
| 338d254 | Nicola Soranzo | 04 May 2016, 16:39:04 UTC | Use partial messages to match SLURM memory warnings | 04 May 2016, 18:56:48 UTC |
| d40c237 | Nate Coraor | 04 May 2016, 18:55:14 UTC | If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue. | 04 May 2016, 18:55:14 UTC |
| 3005bba | Lance Parsons | 04 May 2016, 15:17:07 UTC | Remove SLURM memory limit warning from stderr if the job was successful | 04 May 2016, 15:20:39 UTC |
| a54a618 | Dannon Baker | 03 May 2016, 22:18:20 UTC | Merge branch 'release_16.01' into release_16.04 | 03 May 2016, 22:18:20 UTC |
| 063b25f | Dannon Baker | 03 May 2016, 22:18:00 UTC | Merge pull request #2260 from jmchilton/fix_burst_background_workflows [16.01] Fix running workflows in the background when tool bursting is enabled. | 03 May 2016, 22:18:00 UTC |
| 56bd4ad | Dannon Baker | 03 May 2016, 12:38:35 UTC | Merge pull request #2265 from jmchilton/pbs_pro_name_fix [16.04] Truncate job name in DRMAA runner by default for PBSPro. | 03 May 2016, 12:38:35 UTC |
| d282ed9 | Dannon Baker | 02 May 2016, 18:14:57 UTC | Merge branch 'release_16.01' into release_16.04 | 02 May 2016, 18:14:57 UTC |
| cdea922 | Nitesh Turaga | 02 May 2016, 18:12:33 UTC | Merge pull request #2195 from dannon/remoteuser_work [16.01] Prepass on remote user header based on maildomain and normalize confi… | 02 May 2016, 18:12:33 UTC |
| b9b7983 | John Chilton | 02 May 2016, 17:11:17 UTC | Merge pull request #2284 from martenson/backport-2230-04 [16.04] Backport of 2230 | 02 May 2016, 17:11:17 UTC |
| 5cf3297 | Björn Grüning | 02 May 2016, 17:08:42 UTC | Merge pull request #2282 from jmchilton/the_containerz_have_no_bash___doh [16.04] Switch Dockerized commands to use sh instead of bash. | 02 May 2016, 17:08:42 UTC |
| 9290ddc | Eric Rasche | 22 April 2016, 05:44:59 UTC | Fixes #2230 This sanitizes some instances where tool parameters were included directly into the DOM. workflow/run.mako displayed the parameter as a value in a hidden input. This was base64 encoded as there was no better solution apparent at the time. I'm not sure where this parameter is POSTed to but we should figure that out and b64decode it, or remove the hidden parameter. client/... added the parameter value into the DOM. This was easily sanitized using a standard method. workflow/display.mako included the parameter value directly into the HTML. This was cgi.esacped Conflicts: static/scripts/bundled/libs.bundled.js.map | 02 May 2016, 16:25:35 UTC |
| cef9270 | John Chilton | 02 May 2016, 13:11:25 UTC | Switch Dockerized commands to use sh instead of bash. We switched to bash for the conda and that doesn't get sourced in containers - so we should be a bit pragmatic about this and switch back to /bin/sh for containers which is more common than /bin/bash. xref https://github.com/galaxyproject/galaxy/pull/2278 Update galaxy.ini.sample to mention this as suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/2282#issuecomment-216232788. | 02 May 2016, 13:38:55 UTC |
| 787b351 | Martin Cech | 01 May 2016, 14:50:33 UTC | Merge pull request #2208 from guerler/fix_error_message_001 [16.04] Add fixed validation check for data_source tools URL parameter | 01 May 2016, 14:50:33 UTC |
| 630a004 | Martin Cech | 30 April 2016, 16:03:06 UTC | Merge pull request #2255 from bgruening/release_16.04 [16.04] Update `_condarc` automatically | 30 April 2016, 16:03:06 UTC |
| 8b6729e | Nitesh Turaga | 28 April 2016, 14:43:05 UTC | Merge pull request #2266 from dannon/cherrypick_display_encoding [16.04] Cherrypick of encoding fix | 28 April 2016, 14:43:05 UTC |
| 9ba510d | Dannon Baker | 28 April 2016, 12:36:48 UTC | This is a preliminary fix for displaying raw text/html unicodify'd data (html reports, etc). TODO: Push this logic up into the framework so inside the webapp it's all unicode all the time. | 28 April 2016, 14:34:26 UTC |
| 14bd398 | John Chilton | 28 April 2016, 13:59:48 UTC | Truncate job name in DRMAA runner by default for PBSPro. We don't really have a clean way to tell if the DRMAA runner is serving to PBSPro so we make this truncation the default for the DRMAA runner but in the case of the SLURM runner we continue to not truncate. - http://dev.list.galaxyproject.org/Problem-with-DRMAA-and-Pbs-Pro-td4669338.html - http://dev.list.galaxyproject.org/If-you-need-to-use-PBS-Pro-with-Galaxy-16-01-td4669229.html | 28 April 2016, 13:59:48 UTC |
| 615b0b4 | John Chilton | 27 April 2016, 18:34:20 UTC | Fix running workflows in the background when tool bursting is enabled. | 27 April 2016, 19:36:45 UTC |
| f7fa633 | Bjoern Gruening | 27 April 2016, 13:23:50 UTC | it's called conda_ensure_channels | 27 April 2016, 13:23:50 UTC |
| ce31431 | Martin Cech | 23 April 2016, 16:54:27 UTC | Merge pull request #2238 from guerler/fix_collection_reduce_000 [16.04] Encode collection reduce in serializable fashion | 23 April 2016, 16:54:27 UTC |
| 5749e34 | guerler | 22 April 2016, 18:41:13 UTC | Encode collection reduce in serializable fashion | 22 April 2016, 19:43:48 UTC |
| 62bc415 | Dannon Baker | 22 April 2016, 16:30:07 UTC | Merge pull request #2234 from guerler/fix_validator_000 [16.04] Fix js value validator | 22 April 2016, 16:30:07 UTC |
| e5b3c94 | guerler | 22 April 2016, 16:16:19 UTC | Fix js value validator | 22 April 2016, 16:16:19 UTC |
| 0b9ed99 | Dannon Baker | 21 April 2016, 19:38:48 UTC | Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 | 21 April 2016, 19:38:48 UTC |
| 9e98086 | Dannon Baker | 21 April 2016, 19:35:17 UTC | Merge pull request #2220 from martenson/port-tstestfix [16.01] port TS test fix so we can rely on jenkins | 21 April 2016, 19:35:17 UTC |
| 912e6ea | Martin Cech | 21 April 2016, 17:02:09 UTC | port TS test fix so we can rely on jenkins | 21 April 2016, 17:02:09 UTC |
| 2734c2c | Dannon Baker | 21 April 2016, 15:28:40 UTC | Merge pull request #2218 from guerler/fix_cursor_001 [16.04] Avoid reset of cursor position for input fields during manual entry | 21 April 2016, 15:28:40 UTC |
| 3907d83 | Aysam Guerler | 21 April 2016, 15:15:51 UTC | Merge pull request #2214 from dannon/old_library_fixes [16.01] Browse library date handling for non-ascii month abbreviations | 21 April 2016, 15:15:51 UTC |
| 9716134 | guerler | 21 April 2016, 14:15:33 UTC | Avoid reset of cursor position for input fields during manual entry | 21 April 2016, 14:49:40 UTC |
| d0447fe | guerler | 21 April 2016, 04:09:48 UTC | Add validation check for data_source tools URL parameter | 21 April 2016, 13:31:43 UTC |
| f70a2b0 | Dannon Baker | 21 April 2016, 13:10:49 UTC | Merge pull request #2211 from guerler/fix_nondefault_000 [16.04] Fix tool action redirect url for non-default tools | 21 April 2016, 13:10:49 UTC |
| 7e93d46 | Dannon Baker | 21 April 2016, 13:08:38 UTC | Another location where the non-ascii month was breaking display. | 21 April 2016, 13:08:38 UTC |
| ef12ae3 | Dannon Baker | 21 April 2016, 13:00:17 UTC | Test fix for christ-h's french language date abbreviations breaking the old library display | 21 April 2016, 13:00:17 UTC |
| ca5f605 | guerler | 20 April 2016, 17:08:20 UTC | Fix tool action redirects for non-default tools displaying tool forms | 21 April 2016, 04:59:37 UTC |
| 5aefe1b | Martin Cech | 20 April 2016, 17:44:34 UTC | Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. | 20 April 2016, 17:44:34 UTC |
| ebb49d4 | Dannon Baker | 20 April 2016, 17:19:03 UTC | Make client, somehow this got out of sync. | 20 April 2016, 17:19:03 UTC |
| e88e615 | Martin Cech | 20 April 2016, 17:10:46 UTC | Merge pull request #2204 from guerler/fix_error_message_000 [16.04] Improve error message for data source tools, executed through the tool_runner controller | 20 April 2016, 17:10:46 UTC |
| 8749c82 | Nicola Soranzo | 20 April 2016, 15:29:10 UTC | Merge pull request #2197 from dannon/pages_parser_fix [16.04] Pages parser fix | 20 April 2016, 15:29:10 UTC |
| e9df73c | guerler | 20 April 2016, 15:03:09 UTC | Improve error message for data source tools, executed through the tool_runner controller | 20 April 2016, 15:04:11 UTC |
| adbc668 | Martin Cech | 20 April 2016, 15:01:28 UTC | Merge pull request #2203 from jmchilton/doctest_fix [16.04] Sync job_script module with Pulsar to fix doctest. | 20 April 2016, 15:01:28 UTC |
| e5290e1 | Dannon Baker | 20 April 2016, 14:26:57 UTC | Merge pull request #2149 from martenson/fix-biomart [16.04] fix/replace biomart data source | 20 April 2016, 14:26:57 UTC |
| 4ea53d9 | John Chilton | 20 April 2016, 14:15:53 UTC | Merge pull request #2196 from guerler/extend_to_json_000 [16.04] Extend to_json for dataset tool parameters | 20 April 2016, 14:15:53 UTC |
| eac0fb9 | John Chilton | 20 April 2016, 14:12:59 UTC | Merge pull request #2201 from guerler/fix_parameters_000 [16.04] Translate data source tool parameters on parameter expansion | 20 April 2016, 14:12:59 UTC |
| 0cde386 | Dannon Baker | 20 April 2016, 14:00:08 UTC | Remove more unnecessary unicode/text_type, since sanitize_html will always return unicode. | 20 April 2016, 14:00:08 UTC |
| a928064 | John Chilton | 20 April 2016, 13:24:33 UTC | Sync job_script module with Pulsar to fix doctest. Following test fails without this change and is fixed by it. ``` nosetests --with-doctest lib/galaxy/jobs/runners/util/job_script ``` I'm not sure why Travis doesn't pick this up - I should figure that out. | 20 April 2016, 13:24:33 UTC |
| 7c7d6ed | Dannon Baker | 20 April 2016, 00:54:24 UTC | Swap validate_and_sanitize_basestring to use unicodify | 20 April 2016, 00:54:24 UTC |
| 65fa24d | Dannon Baker | 19 April 2016, 23:25:01 UTC | Merge 16.01->16.04, rebuild. | 19 April 2016, 23:25:21 UTC |
| 3737fc9 | Dannon Baker | 19 April 2016, 22:21:21 UTC | Merge pull request #2198 from carlfeberhard/fix.citations-again [16.01] UI, citations: fix bad merge from 15.10 | 19 April 2016, 22:21:21 UTC |
| e137388 | guerler | 19 April 2016, 21:32:41 UTC | Apply parameter translation for data source tools | 19 April 2016, 21:33:22 UTC |
| 659a900 | Dannon Baker | 19 April 2016, 19:39:51 UTC | Simplify expression, trust upstream pieces. | 19 April 2016, 19:39:51 UTC |
| cfb8ed3 | carlfeberhard | 19 April 2016, 19:35:15 UTC | UI, citations: fix bad merge from 15.10 774487d created a difference between the imported name and the one used. | 19 April 2016, 19:35:15 UTC |
| f506062 | Dannon Baker | 19 April 2016, 18:19:45 UTC | Fix pages encoding. Using str on previously unicodify'd extended set values does not work. ``` In [2]: str("Blah blah blah, this breaks the page: ಠ_ಠ") Out[2]: 'Blah blah blah, this breaks the page: \xe0\xb2\xa0_\xe0\xb2\xa0' In [3]: str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) --------------------------------------------------------------------------- UnicodeEncodeError Traceback (most recent call last) <ipython-input-3-4a83f5e5f5c8> in <module>() ----> 1 str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) UnicodeEncodeError: 'ascii' codec can't encode character u'\u0ca0' in position 38: ordinal not in range(128) ``` | 19 April 2016, 18:19:45 UTC |
| cc49110 | guerler | 19 April 2016, 18:00:50 UTC | Enhance to_json such that it can be safely called multiple times | 19 April 2016, 18:00:50 UTC |
| eb15c14 | Dannon Baker | 19 April 2016, 16:25:17 UTC | Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly. | 19 April 2016, 16:25:17 UTC |
| 212f7f4 | Martin Cech | 19 April 2016, 15:02:44 UTC | Merge branch 'release_16.01' into release_16.04 Conflicts: client/galaxy/scripts/mvc/library/library-dataset-view.js static/maps/mvc/library/library-dataset-view.js.map static/maps/mvc/library/library-folder-view.js.map static/maps/mvc/library/library-library-view.js.map static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/library/library-dataset-view.js static/scripts/mvc/library/library-folder-view.js static/scripts/mvc/library/library-library-view.js | 19 April 2016, 15:02:44 UTC |
| 00a55f8 | John Chilton | 19 April 2016, 13:14:14 UTC | Merge pull request #2190 from martenson/fix-import-libraries [16.04] fix a bug with missing history_id in libraries dataset import | 19 April 2016, 13:14:14 UTC |
| e2f8829 | Eric Rasche | 18 April 2016, 21:53:52 UTC | Merge pull request #2176 from martenson/fix-permissions-caching [16.01] libraries: always fetch new permissions as we are reusing the view | 18 April 2016, 21:53:52 UTC |
| 75864e5 | Martin Cech | 18 April 2016, 21:04:31 UTC | Merge pull request #2191 from guerler/fix_message_000 [16.04] Fix message in legacy panel mako | 18 April 2016, 21:04:31 UTC |
