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Author SHA1 Message Date
Nate Coraor 4dbadc26e4 Merge branch 'release_17.05' into release_17.09 2017-09-21 15:27:05 -04:00
Nate Coraor cfabe37d69 Merge branch 'release_17.01' into release_17.05 2017-09-21 15:26:24 -04:00
Nate Coraor 706a5b2cd2 Merge branch 'release_16.10' into release_17.01 2017-09-21 15:25:36 -04:00
Nate Coraor e178879c0f Merge branch 'release_16.07' into release_16.10 2017-09-21 15:25:16 -04:00
Nicola Soranzo 2ffeedfa72 Merge pull request #4663 from natefoo/fix-modules-resolver 
[16.07] Fix modules resolver
 2017-09-21 17:33:50 +01:00
Nate Coraor 5d7b524b57 Merge pull request #4644 from mvdbeek/upload_tool_registry_xml_failure 
[17.05] BUG: Explicitly write registry.xml when creating a job for the upload tool
 2017-09-21 09:30:11 -04:00
John Chilton c9aead91d7 Merge pull request #4656 from dannon/display_link_fixes 
[17.09] Fix links on workflow, history items.
 2017-09-21 09:17:20 -04:00
Nate Coraor 69a87003f7 Fix modules resolver (addition of the resolver_msg property on the base 
class references name and version attributes that were not defined in
the ModuleDependecy).
 2017-09-20 20:26:21 -04:00
Dannon Baker 5404f7cda7 Small (temporary, mako is going away) layer to support modern routes in old display_base pages (workflow, history, etc). 2017-09-20 11:20:01 -04:00
Nicola Soranzo 0e89935460 Merge pull request #4652 from martenson/release_17.09 
[17.09] pin the last missing flake8
 2017-09-20 06:38:23 +01:00
Martin Cech ee6b8b1af8 pin the last flake8 
thanks @nsoranzo 🦅 👀
 2017-09-19 20:15:44 -04:00
John Chilton f46a5c1797 Merge pull request #4650 from martenson/release_17.09 
[17.09] pin flake8 deps for release
 2017-09-19 15:38:09 -04:00
John Chilton a25b6e5b0e Merge pull request #4648 from martenson/version-17.09 
[17.09]Update version to 17.09.rc1
 2017-09-19 15:37:31 -04:00
Martin Cech 7fd6813dd7 pin flake8 deps for release 2017-09-19 14:43:00 -04:00
mvdbeek b7b3ffb181 Fix unit test failure 2017-09-19 20:39:35 +02:00
Martin Cech eee4a17a4c Update version to 17.09.rc1 2017-09-19 14:32:41 -04:00
Martin Cech f154058776 Merge pull request #4639 from guerler/replace_spaces_url 
do not wrap lines in the upload url fetch
 2017-09-19 14:20:52 -04:00
John Chilton 7d394f202d Merge pull request #4640 from martenson/datalibs-optimize-access-checks 
optimize the process of identifying public libraries
 2017-09-19 14:18:18 -04:00
Martin Cech 3f51e7dc1e Merge pull request #4647 from jmchilton/selenium_fixes_28 
Improved state handling for @anatskiy-style Selenium tests.
 2017-09-19 13:49:51 -04:00
Martin Cech c5d29be0a2 avoid mutable default, improve docs 
switch to set comprehension
 2017-09-19 11:44:43 -04:00
John Chilton 87bb576c39 Improved state handling for @anatskiy-style Selenium tests. 
These tests aren't idealized unittest.TestCase because they initialize class level data in instance level methods. While this isn't ideal, it is seems an entirely fair workaround given that SeleniumTestCase setups up the Selenium connection itself in an instance method - so class-level initializers would not be able to setup Galaxy data. Since I think we will continue using this pattern then, probably best to formalize it a bit and improve error handling.

This provides a formal super class for these test cases that provides a uniform method for setting up the class level data and tracks whether this is successful or not. This serves a couple purposes beyond simple uniformity. First, it tracks if the state has actually been setup or not and will skip subsequent tests if it hasn't. Some of these tests aren't passing very consistently on Jenkins and so we get a bunch of extra noise for tests that are attempting to run without their preconditions met - this will fix that and make the original errors much more clear. Moving the "hacky" part of this into the framework itself also means the tests themselves don't have to repeat hacks like seeing if variables are set with ``getattr`` and such - I always prefer one framework hack to a dozen application hacks.
 2017-09-19 10:33:26 -04:00
mvdbeek d980dfa162 Write registry.xml for all tools that require galaxy's python env 
This should cover the upload and data_source tools.
 2017-09-19 16:02:40 +02:00
John Chilton 844f083c7b Merge pull request #4641 from anatskiy/custom_builds_tests 
Custom Builds tests
 2017-09-19 09:53:07 -04:00
John Chilton a17ae7b90c Merge pull request #4617 from mvdbeek/data_manager_watch_new_tables 
Allow adding new data tables without restart
 2017-09-19 09:09:38 -04:00
mvdbeek a3ff129743 Explicitly write registry.xml when creating a job for the upload tool 2017-09-19 11:20:25 +02:00
Evgeny Anatskiy e01b57da58 small improvement 2017-09-18 22:28:04 +02:00
guerler 403cd3ffca Remove line wrap 2017-09-18 15:36:29 -04:00
guerler 8b517e7a03 Restore previous behavior 2017-09-18 15:31:16 -04:00
Evgeny Anatskiy db67d254ed don't test the uploading of fasta files 2017-09-18 21:17:00 +02:00
Evgeny Anatskiy 260a834619 Merge branch 'dev' into custom_builds_tests 2017-09-18 21:02:39 +02:00
Martin Cech 8a4c637388 optimize the process of identifying public libraries 
this aims to speed up the library loading considerably
 2017-09-18 14:50:36 -04:00
guerler 6af7661fb1 Drop manual string replacements, rely on split without parameters 2017-09-18 13:24:46 -04:00
guerler 2bcd46c723 Split by space instead of newline 2017-09-18 13:19:20 -04:00
guerler 0df4db5175 Replace spaces with newlines in multi url upload requests 2017-09-18 13:01:25 -04:00
Marius van den Beek d9a8055368 Merge pull request #4636 from bgruening/find_file 
remove .git and .hg from recursive file search
 2017-09-18 14:21:40 +02:00
Nicola Soranzo ef602e1d1a Merge branch 'release_17.05' into dev 
Conflicts:
	lib/galaxy/datatypes/registry.py
	lib/galaxy/jobs/__init__.py
	lib/galaxy/jobs/command_factory.py
	lib/galaxy/tools/actions/metadata.py
	lib/galaxy/tools/evaluation.py
 2017-09-18 11:09:00 +01:00
Eric Rasche cfb0d06575 Exclude venv 2017-09-18 11:51:30 +02:00
Björn Grüning 5f635bda10 remove .git and .hg from recursive file search 2017-09-17 00:54:33 +02:00
Björn Grüning 8f337f692f Merge pull request #4634 from anatskiy/custom_builds_fix 
Fix data order in Custom Builds
 2017-09-17 00:29:13 +02:00
Evgeny Anatskiy f3c593fc59 fix column order in Custom Builds 2017-09-16 21:22:12 +02:00
mvdbeek 642aaa811b Do cleanup if skip_cleanup is not set 2017-09-16 17:31:01 +02:00
mvdbeek 706434da41 Append temp dirs to test_driver list of temp dirs 
Thanks for the hint @jmchilton.
 2017-09-16 17:31:01 +02:00
Martin Cech 03d9a9c6fb Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir 
[17.05] Backport #4600: Write datatypes registry xml to working directory
 2017-09-16 10:10:35 -04:00
John Chilton 13881bd264 Merge pull request #4625 from dannon/sanitize_whitelist_post 
Swap sanitize whitelist form to use a post.
 2017-09-16 07:12:35 -04:00
John Chilton 4c9cc67a8f Merge pull request #4630 from VJalili/patch-4 
Refactored a dataset variable to hda
 2017-09-16 07:12:14 -04:00
John Chilton 6dbd47e661 Merge pull request #4632 from mvdbeek/fix_unintended_change 
[BUG] Restore tool provided metadata path in setup_external_metdata
 2017-09-16 07:10:33 -04:00
John Chilton 22b0542d0b Merge pull request #4631 from martenson/disable-macos-travis 
disable MacOS CI on travis
 2017-09-16 07:08:48 -04:00
mvdbeek e03ee53f3c Remove references to integrated_datatypes_config 2017-09-16 11:38:42 +02:00
mvdbeek 9d3af63660 Skip DataManagerIntegrationTestCase when watchdog unavailable 2017-09-16 10:06:15 +02:00
mvdbeek 432d7f4405 Restore correct metadata path in setup_external_metdata 
This is a change I shouldn't have touched in
https://github.com/galaxyproject/galaxy/pull/4600
 2017-09-16 09:02:33 +02:00