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Author SHA1 Message Date
Dannon Baker ce4584956b Merge pull request #5050 from erasche/fix-ufr-7036 
Safely handle possible None value encountered in processing and execution of post-job action arguments
 2017-11-21 13:19:52 -05:00
Martin Cech 1d72b260fe Merge pull request #5051 from jmchilton/fast_client_test_setup 
Document fastest way to iterate on client & client tests together.
 2017-11-21 11:44:32 -05:00
John Chilton 306be82a13 Document fastest way to iterate on client and client tests. 
As fast as I've been able to make it anyway.
 2017-11-21 11:26:28 -05:00
E Rasche 070ab533bd Address comments 2017-11-21 17:21:41 +01:00
Martin Cech e9ef110a81 Merge pull request #5045 from jmchilton/scheduler_memory 
Cleanup SA objects between workflow invocation scheduling attempts.
 2017-11-21 10:14:51 -05:00
E Rasche ddfbf2c3f0 Handle None v 2017-11-21 15:58:07 +01:00
M Bernt b2cc634e8a python3 fix (#5043) 
strings can not be written to byte mode file handlers.
writing resulted in: TypeError: a bytes-like object is required, not 'str'

Alternative would be to make string byte.
 2017-11-20 22:34:02 +01:00
John Chilton efd762e18c Cleanup SA objects between workflow invocation scheduling attempts. 
This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more.
 2017-11-20 10:54:14 -05:00
John Chilton 3e2e149325 Merge pull request #5023 from bgruening/cooler 
add cool datatype
 2017-11-19 20:42:02 -05:00
John Chilton db2c3a43e2 Merge pull request #5018 from martenson/api-for-admin-decode 
add API that allows admins to decode galaxy objects' ids
 2017-11-19 20:40:34 -05:00
Aysam Guerler 299ae5c9f5 Merge pull request #5021 from dannon/fix-workflow-editor-outputs 
Workflow editor outputs fixes
 2017-11-18 15:40:39 -05:00
Björn Grüning 83e9e07bd5 Merge pull request #5016 from natefoo/memory-mb-metric 
Add metric to the core plugin to collect $GALAXY_MEMORY_MB
 2017-11-17 08:50:53 +01:00
Martin Cech b5864ad4f7 Merge pull request #5004 from jmchilton/collection_copy_api 
More HDCA copying tests, add option to copy HDAs into new history.
 2017-11-16 14:37:56 -05:00
Nate Coraor 36dc1560e5 Merge pull request #5007 from jmchilton/problematic_data_manager 
Use github instead of NCBI for problematic data manager test FASTA.
 2017-11-16 12:12:31 -05:00
Marius van den Beek a9685d3acd Merge pull request #5017 from jmchilton/test_renaming_multiple_workflows 
Test renaming multiple different outputs in workflows.
 2017-11-16 17:51:59 +01:00
John Chilton 7745897e59 Merge pull request #5020 from martenson/wiki-cleanup 
fix few stray wiki links
 2017-11-16 08:12:11 -05:00
Bjoern Gruening 1718f8dc8e add test file 2017-11-16 12:58:19 +01:00
Bjoern Gruening 32a7dfc20b add cooler file format binary class 2017-11-16 12:41:10 +01:00
Bjoern Gruening e568141170 add cooler fileformat to datatypes_conf.xml 2017-11-16 12:38:27 +01:00
Dannon Baker 5bcd59944d Unpack options in functions in keeping with previous style here (dunno about this long term though) 2017-11-15 18:41:31 -05:00
Dannon Baker ec7c060a90 Formatting. 2017-11-15 18:31:28 -05:00
Dannon Baker f1348c15c7 Fix workflow editor output attributes (var shadowing was silently making *everything* the first output attribute...) 2017-11-15 18:27:04 -05:00
Martin Cech 7157600f85 fix few stray wiki links 2017-11-15 16:39:26 -05:00
Martin Cech 8a35b940de add API that allows admins to decode galaxy objects' ids 2017-11-15 14:09:01 -05:00
John Chilton 5c28618a27 Merge pull request #5015 from nsoranzo/fix_parse_interpreter 
parse_interpreter: log a warning only if interpreter is set
 2017-11-15 14:04:40 -05:00
John Chilton d3b5fac751 Test renaming multiple different outputs in workflows. 
Attempting to exercise a bug reported by @lparsons.
 2017-11-15 13:46:01 -05:00
Nate Coraor d5aa2595aa Add metric to the core plugin to collect $GALAXY_MEMORY_MB 2017-11-15 13:02:29 -05:00
John Chilton 38c620c62b Merge pull request #4998 from martenson/lib-to-colllection 
enhance hdca creation API endpoint to accept lddas
 2017-11-15 12:49:56 -05:00
John Chilton abe1b240c3 Fix broken library test I recently added. 2017-11-15 12:49:21 -05:00
Aysam Guerler f44cbd5d82 Merge pull request #5014 from dannon/remove_search_templates 
Remove unused search template
 2017-11-15 12:34:29 -05:00
Nicola Soranzo d5390350b8 parse_interpreter: log a warning only if interpreter is set 
Also return None instead of False if there is no `<command>`.
Fix typo in warning.
 2017-11-15 17:10:25 +00:00
Dannon Baker ae48c9a3c1 Remove search templates (unused) 2017-11-15 11:08:31 -05:00
Martin Cech 87987b4c94 Merge pull request #25 from jmchilton/lib-to-colllection 
Merge with dev and add more tests.
 2017-11-15 10:47:25 -05:00
Nicola Soranzo 7bede53bef Merge branch 'release_17.09' into dev 
Conflicts:
	lib/galaxy/dependencies/pinned-requirements.txt
	lib/galaxy/dependencies/requirements.txt
 2017-11-15 15:09:33 +00:00
Dannon Baker f34e6a1e2e Merge pull request #4737 from xgaia/askomics-ie 
AskOmics Interactive Environment
 2017-11-15 10:01:45 -05:00
Xavier Garnier 8d3c8c6d40 Merge pull request #1 from dannon/askomics-fixes 
Small javascript fixes for askomics IE integration
 2017-11-15 15:49:34 +01:00
Dannon Baker 7d674e1de0 Left off semicolon. 2017-11-15 09:40:52 -05:00
Dannon Baker 1d5f0d2b61 Fixes to askomics javascript 2017-11-15 09:39:54 -05:00
Dannon Baker e27a16953d Merge pull request #4961 from jmchilton/job_delete_api 
Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint.
 2017-11-15 08:12:19 -05:00
Nicola Soranzo bbd96c435b Merge pull request #4903 from jmchilton/dev_at_same_time 
Install dev and regular dependencies at the same time.
 2017-11-15 11:47:40 +00:00
Dannon Baker 18467e9b2c Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement 
[17.09] Add missing ipaddress requirement
 2017-11-15 06:31:25 -05:00
Dannon Baker 54c6a794e9 Merge pull request #4909 from anatskiy/tdt_tests 
Selenium test for Tool-Describing-Tours
 2017-11-15 05:56:13 -05:00
Nicola Soranzo a12b50c08e Merge pull request #5011 from jmchilton/remove_skip_install_tox 
Removed unneeded skip_install tags in tox.ini.
 2017-11-15 10:10:19 +00:00
John Chilton b4e041d14d Removed unneeded skip_install tags in tox.ini. 
Alternative to #4995 thanks to @nsoranzo's detective work.
 2017-11-14 22:45:02 -05:00
John Chilton 4773765974 Merge remote-tracking branch 'jmchilton/dev' into lib-to-colllection 2017-11-14 22:26:10 -05:00
John Chilton fb91302458 Fix TDT fors ES6 module switchover. 2017-11-14 22:07:20 -05:00
John Chilton 9273d7a1c7 Add screenshots for TDT Selenium tests. 2017-11-14 21:54:58 -05:00
John Chilton cecef90915 Merge remote-tracking branch 'jmchilton/dev' into tdt_tests 2017-11-14 21:49:15 -05:00
John Chilton c52ebfca26 Improvements for tour generator Selenium tests. 
- Replace test using Cut1 with two tests each using framework test tools loaded with Selenium tests by default.
- Create a symbolic link so that tour generator is configured with default test webhooks.
- Establish and use components and navigates_galaxy.py abstractions for tour generation and navigation.
- In one of the tool tests actually walk the tour (previously we only verified the initial tour popover).
 2017-11-14 21:41:09 -05:00
John Chilton 482ff776e5 Merge pull request #5006 from martenson/decode_for_admins 
dataset info: present decoded IDs for admins and add peek
 2017-11-14 20:35:21 -05:00