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Author SHA1 Message Date
Nicola Soranzo efe84751a7 Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 2018-12-11 22:22:01 +00:00
Nate Coraor b10cfa43ac Remove unused $GXPIP_VERSION 2018-12-11 22:01:24 +00:00
Nate Coraor 0e5c96ef37 Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in 
pip >= 8.1).
 2018-12-11 22:01:13 +00:00
John Chilton f3ba9e2b9e Merge pull request #6796 from dannon/peek_drop 
[16.01] Drop unused peek method
 2018-09-28 12:09:38 -04:00
Dannon Baker 814c7f926d Drop unused peek method (this used unencoded ids) 2018-09-28 11:50:18 -04:00
Dannon Baker 2207e7f8aa Merge pull request #4565 from jmchilton/backport_uwsgi_fix 
[16.01] Backport uwsgi fix from #2836.
 2017-09-06 12:35:30 -04:00
John Chilton 02c7792985 [16.01] Backport uwsgi fix from #2836. 
Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy.

https://github.com/galaxyproject/galaxy/pull/2836
 2017-09-06 09:34:11 -04:00
Nate Coraor 4c07734f57 Merge branch 'release_15.10' into release_16.01 2016-12-15 12:55:39 -05:00
Nate Coraor 95daf69b37 Merge branch 'release_15.07' into release_15.10 2016-12-15 12:49:39 -05:00
Nate Coraor 790e60af60 Merge branch 'release_15.05' into release_15.07 2016-12-15 12:46:17 -05:00
Nate Coraor 7c443eda56 Merge branch 'release_15.03' into release_15.05 2016-12-15 12:38:28 -05:00
Nate Coraor da7afb4e22 Merge branch 'release_15.01' into release_15.03 2016-12-15 12:37:10 -05:00
Nate Coraor 9ee3d01c30 Merge branch 'release_14.10' into release_15.01 2016-12-15 12:36:21 -05:00
Nate Coraor c1e3087ca3 Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for 
the disclosure.
 2016-12-15 12:34:18 -05:00
Björn Grüning a274e635a6 Merge pull request #3128 from mvdbeek/backport_3122_3124 
[16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml
 2016-11-05 11:52:03 +01:00
mvdbeek c524521956 Make catching XML parsing errors python2.6 compatible 2016-11-04 20:21:05 +01:00
mvdbeek f6ca913809 Log invalid xml filename 2016-11-04 17:53:12 +01:00
mvdbeek c94b2205b2 Escape section id and name when writing integrated_tool_panel.xml 
This should fix #3084.
 2016-11-04 17:42:16 +01:00
Björn Grüning f7c3e25e5d Merge pull request #3009 from mvdbeek/conda_downgrade 
[16.01] Backport #2869 Fix initial conda version at 4.0.5
 2016-10-05 19:15:14 +02:00
Marius van den Beek 6d27a3c4b6 Fix initial conda version at 4.0.5 
This should prevent missing `activate` in <conda_prefix>/bin when
downgrading to 3.19.3. This is what the conda people use in their CI
environment (
[see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh#L61)
and perhaps why that bug made it into the release in the first place).
 2016-10-05 18:16:24 +02:00
Martin Cech 8bf7256ca8 Merge pull request #2912 from carlfeberhard/dataset.admin-permissions 
[16.01] Allow admin to serialize/deserialize dataset permissions
 2016-09-14 13:20:00 -04:00
carlfeberhard b301fd4202 Dataset perms: correct comment 2016-09-14 13:18:46 -04:00
carlfeberhard e7cb0ac2a1 Datasets: test for anon deserialization 2016-09-13 13:10:42 -04:00
carlfeberhard 9636ea1b6c Datasets: test for anon access/manage 2016-09-13 13:09:11 -04:00
carlfeberhard fc3dcf3b87 Permissions, datasets: allow admin in RBAC 
- Admin are considered permitted when calling
  ** dataset_manager.permssions.access and
  ** dataset_manager.permissions.manage
- Update bad test
- Add admin test to other permission checks
 2016-09-13 13:00:58 -04:00
carlfeberhard b88035955d Datasets: confirm admin ability to set permissions 
The power was inside you all along.
 2016-09-12 11:04:39 -04:00
carlfeberhard 91a190c6eb Datasets: allow admin to serialize permissions 
And updates tests.
 2016-09-12 10:50:57 -04:00
Martin Cech 68f718d53b Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package 
[16.01] Fix misplaced parenthesis
 2016-08-10 11:05:05 -04:00
Nicola Soranzo f4cb63d6f2 Pin flake8 version 
Do not pin when forward-merging to dev branch.
Also ignore .tox/ and eggs/ as in #2650 .
 2016-08-10 15:17:21 +01:00
Nicola Soranzo 33c4025fab Fix misplaced parenthesis 
Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304
 2016-08-10 14:34:08 +01:00
Dannon Baker f4631d2e59 Merge pull request #2629 from carlfeberhard/fix.saved-copy 
[16.01] UI, history: replace copy dialog on grid refresh
 2016-07-19 18:12:17 -04:00
Eric Enns 85671bd466 Fixed E302 2016-07-19 14:27:39 -04:00
Eric Enns 7e389c7d54 Fixed E226 2016-07-19 14:27:26 -04:00
Eric Enns 09b9339569 Fixed to only line_count not line_count + 1 lines and added in really basic test 2016-07-19 14:27:09 -04:00
Eric Enns 5f24afb1b3 Fix off by one error, causing only first line of file to be rendered in peek. 2016-07-19 14:26:58 -04:00
carlfeberhard bc79e9cc4a UI, history: replace copy dialog on grid refresh 
Fixes #2624

init_grid is called from update_grid to rebuild the grid. This patches
that call to replace the copy links with the dialog.

Note:
- related to #1303 which was an effort to make a single code path
for copying histories.
- Uses monkey patching to keep from porting build artifacts.
 2016-07-19 09:51:10 -04:00
Dannon Baker 67c4df712a Merge pull request #2522 from nsoranzo/release_16.01_fix_for_2479 
[16.01] Fix move_directory_files tool dependency action when destination is not empty
 2016-06-21 14:56:07 -04:00
Nicola Soranzo 89890d4f60 Fix move_directory_files tool dependency action when destination is not empty 
Historically this action moves the contents of the source directory to the
destination directory. Commit d38936bd8d
broke the install when e.g. the destination is $INSTALL_DIR, which is
created by Galaxy and is not empty (contains INSTALLATION.log after first
action).
 2016-06-21 17:59:17 +01:00
Nicola Soranzo 4bfa2f62fb Fix for py34-lint 2016-06-21 17:56:42 +01:00
Nicola Soranzo 5aaa1ecdf0 Merge pull request #2518 from dannon/backport_to_1601_pjafix 
[16.01] Copy PJAs when importing a workflow.
 2016-06-20 18:36:29 +01:00
Dannon Baker 8b2ae46467 Copy PJAs when importing a workflow. 2016-06-20 11:33:34 -04:00
Dannon Baker 75cdec9b4b Merge pull request #2479 from nsoranzo/release_16.01_fix_for_1947 
[16.01] Fix move_directory_files tool dependency action when new_file_path is on a different filesystem
 2016-06-15 10:14:32 -04:00
Martin Cech dbbf1edef3 Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 
[16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries
 2016-06-10 12:06:41 -04:00
Nicola Soranzo 933f42619e Log all failed job status checks 2016-06-10 12:34:48 +01:00
Nicola Soranzo 7c40c85034 Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries 2016-06-10 12:31:00 +01:00
Nicola Soranzo d38936bd8d Move the whole directory instead of element by element 
Fix #1947.
 2016-06-09 18:41:10 +01:00
Nicola Soranzo d95e9b840d Refactor move_file() method 2016-06-09 17:59:39 +01:00
John Chilton 47a6516096 Merge pull request #2407 from carlfeberhard/fix.most_recently_used 
[16.01] API, history: fix order in most_recently_used
 2016-05-25 09:41:32 -04:00
carlfeberhard 2a29e92ef9 API, history: fix order in most_recently_used 
- Fix ascending order used in HistoryManager.most_recent to descending
- Slightly update the docs to reflect actual value better
- Add tests
 2016-05-24 17:08:08 -04:00
Dannon Baker 79dd8c82f0 Merge pull request #2312 from nsoranzo/release_16.01_fix_makos 
[16.01] Unicodify pretty datetimes which can contain non-ASCII chars
 2016-05-07 18:11:24 -04:00