Commit Graph
40506 Commits
Author SHA1 Message Date
guerler ddae8f1c2b Hide Ok button if only one item can be selected 2019-05-09 20:07:09 -04:00
Martin Cech eaacd9e8a1 Merge pull request #7878 from inkuzmin/look-and-feel-in-dataset-libraries
Look and Feel in Dataset Libraries
2019-05-09 13:04:53 -04:00
Ivan Kuzmin b50d5c8709 handle case with no libraries 2019-05-09 17:56:00 +03:00
Dannon 1d5bddd8f8 Merge pull request #7908 from guerler/fix_ftp_dialog
Fix help text in ftp-uploader dialog
2019-05-09 10:29:40 -04:00
Marius van den Beek ceb8c7a637 Merge pull request #7918 from nsoranzo/update_conda_update_docs
Update instructions on conda upgrade
2019-05-09 13:59:33 +02:00
Ivan Kuzmin 07b1dadf48 try to use more specific selectors 2019-05-09 13:39:02 +03:00
Martin Cech 3fcc0bed37 Merge branch 'release_19.05' into dev 2019-05-08 14:18:09 -04:00
Martin Cech 5dec2a3c56 Merge pull request #7867 from mvdbeek/fix_scope_issue_for_py3_list_comprehensions
[19.05] Run futurize for python2 cheetah templates, fix scope issue for py3 comprehensions
2019-05-08 14:17:54 -04:00
Martin Cech 64b7fd603e Merge pull request #7909 from jmchilton/dev_merge_2
Merge release_19.05 into dev.
2019-05-08 14:14:28 -04:00
Nicola Soranzo 8a2abb867f Update instructions on conda upgrade
Reported by @William-Brown .
2019-05-08 18:54:55 +01:00
Martin Cech 375e65ef2b add default to test job_conf 2019-05-08 11:55:13 -04:00
Martin Cech a1feeaed46 Merge pull request #7911 from nsoranzo/remove_bibtex_file
Remove ``file`` attribute of bibtex citation
2019-05-08 10:18:26 -04:00
Ivan Kuzmin a5df0c346e remove test for deleted button 2019-05-08 16:03:29 +03:00
Ivan Kuzmin d982436515 fix libraries pagination 2019-05-08 15:50:07 +03:00
Ivan Kuzmin 215f4911e1 fix formatting 2019-05-08 15:43:37 +03:00
Ivan Kuzmin 6173b07766 fix for selenium tests 2019-05-08 15:41:42 +03:00
Ivan Kuzmin 14fb7f947e shorten the pagination text 2019-05-08 15:34:07 +03:00
Ivan Kuzmin ed39c4f870 lazy change for pagination control 2019-05-08 15:26:25 +03:00
mvdbeek ccea1eeb8f Delete running jobs after each API-style test
Should prevent https://jenkins.galaxyproject.org/job/docker-integration-py3/159/testReport/junit/test.integration.test_upload_configuration_options/AdminsCanPasteFilePathsTestCase/test_admin_path_paste_libraries/
2019-05-08 13:40:59 +02:00
Nicola Soranzo 6e01d465c4 Remove `file` attribute of bibtex citation
Introduced in commit cb9fc095fc but
never documented, tested or used in any known tool.
2019-05-08 11:42:22 +01:00
guerler 6d12999efe Remove unused import 2019-05-07 18:54:48 -04:00
John Chilton 199062cc4b Merge remote-tracking branch 'galaxyproject/release_19.05' into dev 2019-05-07 17:08:21 -04:00
guerler 35f8640b3a Revise help text in ftp uploader 2019-05-07 16:35:19 -04:00
Nicola Soranzo 89f54e59d6 Merge pull request #7808 from jmchilton/fix_gff
Remove GFF headers during conversion.
2019-05-07 20:53:35 +01:00
Martin Cech 3451a60acb remove pagination overrides 2019-05-07 15:44:24 -04:00
guerler 1f778b049f Merge branch 'dev' into fix_ftp_dialog 2019-05-07 15:34:37 -04:00
Martin Cech 54c7cbe7ca relabels few things, remove outdated help buttons
and format client
2019-05-07 14:59:52 -04:00
mvdbeek e828dada3f Don't encode string, this is unnecessary and fails on python 3 2019-05-07 20:57:46 +02:00
Martin Cech 7a4ca3a825 Merge pull request #7904 from natefoo/login-apply-history-permissions
[19.05] Fix application of history default permissions to anonymous histories carried over upon login
2019-05-07 14:42:11 -04:00
Ivan Kuzmin 5aaee6926e fix for selenium tests 2019-05-07 21:25:10 +03:00
Ivan Kuzmin 94dc712e03 fix toolbar buttons consistency 2019-05-07 21:24:12 +03:00
Nate Coraor 48c5b58ac6 Fix application of history default permissions to anonymous histories
carried over upon login.
2019-05-07 12:23:20 -04:00
mvdbeek a05d24cdde Use lib2to3 RefactoringTool instead of external process
We use a list of fixers from past.translation. This is just a
list of strings pointing to fixers to import. Currently this is
```
['libfuturize.fixes.fix_absolute_import',
 'libfuturize.fixes.fix_print_with_import',
 'libfuturize.fixes.fix_raise',
 'libfuturize.fixes.fix_next_call',
 'lib2to3.fixes.fix_reduce',
 'lib2to3.fixes.fix_sys_exc',
 'lib2to3.fixes.fix_throw',
 'lib2to3.fixes.fix_tuple_params',
 'lib2to3.fixes.fix_exec',
 'lib2to3.fixes.fix_standarderror',
 'lib2to3.fixes.fix_apply',
 'lib2to3.fixes.fix_paren',
 'lib2to3.fixes.fix_types',
 'lib2to3.fixes.fix_methodattrs',
 'lib2to3.fixes.fix_renames',
 'lib2to3.fixes.fix_ws_comma',
 'lib2to3.fixes.fix_repr',
 'lib2to3.fixes.fix_intern',
 'lib2to3.fixes.fix_numliterals',
 'lib2to3.fixes.fix_funcattrs',
 'lib2to3.fixes.fix_ne',
 'lib2to3.fixes.fix_exitfunc',
 'lib2to3.fixes.fix_has_key',
 'lib2to3.fixes.fix_isinstance',
 'lib2to3.fixes.fix_idioms',
 'lib2to3.fixes.fix_xreadlines',
 'lib2to3.fixes.fix_except',
 'libfuturize.fixes.fix_execfile',
 'libfuturize.fixes.fix_future_standard_library',
 'libfuturize.fixes.fix_metaclass',
 'libfuturize.fixes.fix_future_builtins',
 'libpasteurize.fixes.fix_newstyle',
 'libfuturize.fixes.fix_basestring',
 'libfuturize.fixes.fix_future_standard_library_urllib',
 'libfuturize.fixes.fix_xrange_with_import',
 'libfuturize.fixes.fix_cmp',
 'libfuturize.fixes.fix_unicode_keep_u',
 'libfuturize.fixes.fix_division_safe',
 'libfuturize.fixes.fix_object',
 'lib2to3.fixes.fix_input',
 'lib2to3.fixes.fix_operator',
 'lib2to3.fixes.fix_zip',
 'lib2to3.fixes.fix_dict',
 'lib2to3.fixes.fix_next',
 'lib2to3.fixes.fix_filter',
 'lib2to3.fixes.fix_raw_input',
 'lib2to3.fixes.fix_getcwdu',
 'lib2to3.fixes.fix_itertools_imports',
 'lib2to3.fixes.fix_nonzero',
 'lib2to3.fixes.fix_itertools',
 'lib2to3.fixes.fix_long',
 'lib2to3.fixes.fix_map']
```
And then we drop pasterurize, which we don't need for our purposes.
2019-05-07 18:20:05 +02:00
Nicola Soranzo 1d1f72799b Use packaging.version.parse() instead of float() for version comparisons 2019-05-07 18:20:05 +02:00
mvdbeek d25a5dda10 Only run python 3 fixers if profile version < 19.05
or python_template_version < 3.
2019-05-07 18:20:05 +02:00
mvdbeek 510f23f85a Non-list comprehensions can't refer to non-iteration variables from surrounding scope
While fixable this seems to not work on python 2 either, so we will not
attempt to fix it.
2019-05-07 18:20:05 +02:00
mvdbeek 0062bce79f Work around list comprehension scope issues 2019-05-07 18:20:05 +02:00
mvdbeek 5ef41e7dce Run futurize on Compiled Cheetah Module 2019-05-07 18:20:05 +02:00
mvdbeek 85e13d2dc4 Add test that unfortunately shows that the global variable isn't updated
Now if we could figure out the exact position in the template source
where a NotFound error is raised we could replace `$variable`
with `variable` and add `#variable = $variable` just before the failing
statement.
2019-05-07 18:20:05 +02:00
mvdbeek 9ff9d55b7a Make variables that have not been found global
This will allow tools to work that access variables from
the enclosing scope in a list/dict/tuple comprehension.
2019-05-07 18:20:05 +02:00
Nicola Soranzo 43c6ae8c48 Merge branch 'release_19.01' into release_19.05 2019-05-07 16:51:58 +01:00
Martin Cech 7e9b3a2330 Merge pull request #7880 from WilliamHolden/allow-e-in-float-field
[19.05] Allow typing e in float param field
2019-05-07 11:40:09 -04:00
Ivan Kuzmin e870205e09 fix for eslint 2019-05-07 18:08:40 +03:00
Martin Cech 9bd89c279e Merge pull request #7906 from jmchilton/1905_fix_multi_history_hdca_copy_2
[19.05] Fix multi-history copying of collections.
2019-05-07 11:08:20 -04:00
Marius van den Beek 3dbab3dab2 Merge pull request #7854 from jmchilton/job_conf_from_dict
Allow YAML/JSON job configuration.
2019-05-07 17:04:39 +02:00
Nicola Soranzo 9b9daffd41 Merge pull request #7766 from natefoo/slurmstepd
[19.01] Catch and filter *all* Slurm cgroup-related messages
2019-05-07 15:57:31 +01:00
Ivan Kuzmin d0aebc2492 granularize paginator 2019-05-07 17:44:01 +03:00
Ivan Kuzmin f37e1f34cb try pagination control at the bottom 2019-05-07 16:56:06 +03:00
John Chilton 7a046d56f6 Fix multi-history copying of collections.
Previously it would copy the collection but not the elements, so if the original HDAs were deleted or purged they'd be deleted in the new history as well. This was not the behavior of the "Copy Datasets" page for instance that would do a deep copy.

There are downsides of doing it this way but this is probably the most intuitive behavior for the GUI for now. Fixes #7493.
2019-05-07 09:06:20 -04:00
Dannon 7130ae9411 Merge pull request #7824 from tmcgowan/issue_7758
[19.01] Possible fix for WSGI process issue #7758
2019-05-07 09:00:37 -04:00