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Author SHA1 Message Date
will 924dedd734 add right margin for form field 2019-07-22 14:24:24 -04:00
will b7cb02664e Use bootstrap classes to fix css issue 2019-07-22 14:18:13 -04:00
Marius van den Beek 9606690ac2 Merge pull request #8360 from mvdbeek/fix_default_involucro_path 
Fix default involucro path
 2019-07-22 10:44:26 +02:00
Marius van den Beek 15c8fdd88c Merge pull request #8362 from wm75/zipfile-fix 
Fix autodetection of zip file format (including xlsx)
 2019-07-22 10:43:03 +02:00
Wolfgang Maier 652f19a422 Use more elegant way to test stream type 2019-07-21 10:59:09 +02:00
Wolfgang Maier b66eeea526 Fix and improve unit tests 2019-07-21 10:48:15 +02:00
Wolfgang Maier 2c20eeba3f Add unit test for get_fileobj_raw 2019-07-21 00:09:17 +02:00
Wolfgang Maier 31869d385d Fix zipped files autodetection 2019-07-21 00:08:12 +02:00
Nicola Soranzo e565ef043c Merge branch 'release_19.05' into dev 2019-07-20 01:33:10 +01:00
John Chilton 614a4ee0a2 Merge pull request #8357 from nsoranzo/app_galaxy_config 
Fix broken link in ``galaxy-app`` package
 2019-07-19 12:00:17 -04:00
mvdbeek 7be55d36f2 Fix default involucro path 
BaseAppConfiguration.root is now an absolute path, and so is
BaseAppConfiguration.data_dir, so the result of
`resolve_path(kwargs.get("tool_dependency_dir", "dependencies"), self.data_dir)`
is not "none" as it used to be, but `"<galaxy_data_dir>/none"` and so
the fallback will not be used.

This can be fixed by setting the default target dir to `dependencies`
and join it to self.data_dir, which defaults to `galaxy_root/database`
on classic installations.

Fixes the issues in https://github.com/galaxyproject/galaxy/pull/8195#issuecomment-513246346
 2019-07-19 17:01:40 +02:00
Nicola Soranzo bbf17354c5 Fix broken link in `galaxy-app` package 
Broken in commit 42cf61fd36 .
 2019-07-19 02:36:36 +01:00
Martin Cech 3ae9207ba3 Merge pull request #8355 from jmchilton/copy_to_working_pulsar 
Better config isolation for integration tests.
 2019-07-18 20:37:37 -04:00
John Chilton a70595a23e Better separation for integration tests. 2019-07-18 18:31:17 -04:00
Martin Cech 00600e4006 Merge pull request #8298 from jmchilton/selenium_package 
Create galaxy-selenium package.
 2019-07-18 15:17:42 -04:00
Martin Cech 3e630bfae0 Merge pull request #8316 from guerler/fix_panel_spacing 
Adjustments for panel spacing changes
 2019-07-18 15:09:39 -04:00
Martin Cech c6bc618f8c Merge pull request #8335 from jmchilton/copy_to_working_pulsar 
Integration test for 'outputs_to_working_directory' with Pulsar.
 2019-07-18 15:08:30 -04:00
Martin Cech 0a51ea326b Merge pull request #8301 from juleengraham/zoom_function 
Zoom reset feature
 2019-07-18 15:06:48 -04:00
Martin Cech 354b73a141 Merge pull request #8351 from ic4f/dev_add_links_admin_mainpage 
Add links to admin entry page
 2019-07-18 12:56:57 -04:00
John Chilton 2b5f9e2f96 Merge pull request #8347 from blankenberg/icn3d-geda 
Add GEDA for iCn3D
 2019-07-18 10:35:26 -04:00
Sergey Golitsynskiy 0e3950ab53 Merge remote-tracking branch 'upstream/dev' into dev_add_links_admin_mainpage 2019-07-17 22:17:23 -04:00
Sergey Golitsynskiy e8c017892f Add links to admin entry page 
This is a temporary solution. Ideally, this should be generated using
the same logic that is used for generating the links on the left menu
panel. And no page reloads, of course.
 2019-07-17 19:49:46 -04:00
John Chilton a788eee913 Merge pull request #8346 from nsoranzo/startup_fixes 
Startup fixes
 2019-07-17 16:48:47 -04:00
John Chilton be7e881961 Merge pull request #8345 from ic4f/dev_toolutil_tests_restruct 
Restructure unit tests for tool_util package
 2019-07-17 16:47:59 -04:00
John Chilton da28369526 Merge pull request #8342 from nsoranzo/galaxy-tool-test 
Add ``galaxy-tool-test`` entry-point to ``galaxy-tool-util`` package
 2019-07-17 16:46:08 -04:00
Daniel Blankenberg 0b90afcfcb Enable iCn3D for mol2 and sdf files 2019-07-17 11:54:15 -04:00
Daniel Blankenberg 8dd9b2fe8c Missing space 2019-07-17 09:58:17 -04:00
Daniel Blankenberg dfb5a988e4 Add GEDA for iCn3D 2019-07-17 09:54:43 -04:00
Nicola Soranzo 397be57d0c Make `self.root` an absolute path 
Fix comparisons of relative and absolute paths like the one described
at https://github.com/galaxyproject/galaxy/pull/921#discussion_r304356880
 2019-07-17 12:52:08 +01:00
Nicola Soranzo e7165c37e3 Fix issues reported by shellcheck 2019-07-17 12:46:46 +01:00
Sergey Golitsynskiy 6fb6727d6d Merge remote-tracking branch 'upstream/dev' into dev_toolutil_tests_restruct 2019-07-16 23:16:59 -04:00
Sergey Golitsynskiy 65490868fb Fix linting errors 2019-07-16 20:54:01 -04:00
Sergey Golitsynskiy 0e4e1d9249 Restructure unit tests for tool_util package 
This replaces a previous (now closed) PR:
https://github.com/galaxyproject/galaxy/pull/8279

A few changes:
- tests for code in galaxy/tool_util moved under test/unit/tool_util
- common parts (used in both tools and tool_util) factored out into
  unittest_utils/sample_data.py
- symlink to sample_data.py in test/unit/tool_util/ is needed to make
  the tool_util package tests run. This is not an ideal solution, but it
  avoids duplication of the sample data used by tests in tools/ and
  tool_util/.
 2019-07-16 20:15:45 -04:00
Nicola Soranzo 600f8db5a5 Merge pull request #8343 from nsoranzo/pip_progress_bar 
Fix use of ``PIP_PROGRESS_BAR`` env variable
 2019-07-16 22:05:12 +01:00
Nicola Soranzo 8e8c64308a Fix use of `PIP_PROGRESS_BAR` env variable 
`PIP_PROGRESS_BAR` environment variable is used by `pip` to set the value
for the `--progress-bar` option. It seems that specifying it also only the
command line does not override it in some configurations, e.g. on TravisCI
Linux builds of BioBlend, see e.g.

https://travis-ci.org/galaxyproject/bioblend/jobs/558857557
 2019-07-16 17:17:32 +01:00
John Chilton ef29b72e00 Integration test for 'outputs_to_working_directory' with Pulsar. 2019-07-16 10:23:33 -04:00
Nicola Soranzo 751806d371 Add `galaxy-tool-test entry-point to galaxy-tool-util` package 
As it was in galaxy-lib.
 2019-07-16 11:19:31 +01:00
Nicola Soranzo f7b37516d7 Fix bug in a unit test (#8314) 
Fix bug in a unit test
 2019-07-16 10:52:09 +01:00
Sergey Golitsynskiy ac5d7dfd46 Merge remote-tracking branch 'upstream/dev' into dev_unittest_bugfix 2019-07-15 19:17:44 -04:00
Martin Cech 868d3bd103 Merge pull request #8339 from natefoo/uwsgi-socket-docs-fix 
[19.05] Correct uWSGI socket path in nginx/Apache docs
 2019-07-15 19:14:26 -04:00
Martin Cech e45d7959a7 Merge pull request #8308 from jmchilton/push_scripts_into_subpackages 
Push galaxy-meta scripts into appropiate subpackages.
 2019-07-15 18:45:13 -04:00
Juleen Graham 19c5fac23b Add hover text to reset button 2019-07-16 00:05:18 +02:00
John Chilton 8b52e9de4a Merge pull request #8287 from martenson/fix-sorting 
Fix library folder sorting
 2019-07-15 16:41:04 -04:00
John Chilton b893054e65 Merge pull request #8303 from martenson/admin-users-nonpurged 
make admin/users grid filter on purged
 2019-07-15 16:27:28 -04:00
Sergey Golitsynskiy f90c8c7bfb Merge remote-tracking branch 'upstream/dev' into dev_unittest_bugfix 2019-07-15 16:18:13 -04:00
John Chilton 574a7da326 Merge pull request #8327 from guerler/remove_backbone_toolshed 
Remove legacy backbone toolshed code and entry points
 2019-07-15 16:00:08 -04:00
Nate Coraor a914200965 Correct uWSGI socket path in nginx/Apache docs 2019-07-15 15:43:26 -04:00
John Chilton 6c48dc28b6 Merge pull request #8326 from scholtalbers/fix/modify_library_check_correct_permission 
check correct permission for allowing a user to modify lib folder
 2019-07-15 15:41:52 -04:00
Nicola Soranzo b578b0a793 test removing uwsgi weird python package from circleci (#8337) 
test removing uwsgi weird python package from circleci
 2019-07-15 19:34:32 +01:00
Martin Cech 568feb56a6 remove libpython requirement for uwsgi building 2019-07-15 13:57:00 -04:00