opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 10:24:38 +08:00
Code Issues Packages Projects Releases Wiki Activity
44,193 Commits 62 Branches 243 Tags
f5cd88465ec1429205b9132b81eadf0bca3efbb3
Commit Graph
44193 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Nicola Soranzo f5cd88465e Make str.join()s more efficient 
by using generator expressions and tuples instead of lists.
 2020-01-23 11:06:32 +00:00
John Chilton 5ef8b4800c Merge pull request #9208 from OlegZharkov/dev 
implement workflow bookmark selenium test
 2020-01-22 12:09:56 -05:00
John Chilton 5bf73d739a Cleanup workflow bookmark test. 
- Use component abstraction (for atomic retry, establishing an abstract description of interface selectors, etc..)
- Augment the test to pre-check the workflow isn't bookmarked initially.
- More retry during transitions.
 2020-01-22 12:08:09 -05:00
mvdbeek ceb214e1d9 Merge branch 'release_20.01' into dev 2020-01-22 16:14:30 +01:00
mvdbeek 54d6bad26e Merge branch 'release_19.09' into release_20.01 2020-01-22 16:08:45 +01:00
John Chilton a52e24ee3a Merge pull request #9245 from mvdbeek/fix_deletion_of_outputs_before_job 
[20.01] Fix deletion of outputs and working before job
 2020-01-22 09:02:45 -05:00
John Chilton d6a077c75e Merge pull request #9243 from mvdbeek/fix_data_table_moving 
[19.09] Fix moving of data manager output for entries
 2020-01-22 09:02:02 -05:00
John Chilton bb5cdd5d4b Merge pull request #9247 from ic4f/sg_rename_func 
Rename function, params in ConfigSerializer
 2020-01-22 09:01:04 -05:00
Marius van den Beek dc7e2e5f68 Merge pull request #9246 from bernt-matthias/topic/fix-popen-py3 
[19.09] python3 fixes for setups using drmaa and realuser setups
 2020-01-22 13:28:53 +01:00
Nicola Soranzo 093fb52b50 Merge branch 'release_20.01' into dev 2020-01-22 12:26:56 +00:00
Nicola Soranzo 2adf6a8f68 Merge branch 'release_19.09' into release_20.01 2020-01-22 12:24:39 +00:00
mvdbeek 8e81af2e06 Update xsd for filename attribute on configfiles 2020-01-22 11:49:06 +01:00
M BerntandMarius van den Beek 95144e5b8b Add parentheses for import 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2020-01-22 11:29:10 +01:00
mvdbeek 9e76dcd9d3 Things are nicer on python 3 2020-01-22 11:16:06 +01:00
mvdbeek 3568629c71 Ignore FileNotFoundError when deleting extra files 
This worked previously but logged an exception, causing further cleanup
to be skipped.
 2020-01-22 10:59:17 +01:00
mvdbeek 3d868e0a06 Use context manager for writing param_file 2020-01-22 10:54:49 +01:00
M Bernt 5bb2d16533 fix import order 2020-01-22 10:37:20 +01:00
mvdbeek 83a8e1b7eb Test that working dir is intact on resubmission 2020-01-22 10:25:16 +01:00
mvdbeek 9a5004c5ee Place configfiles in working dir if filename set 2020-01-22 09:43:15 +01:00
M Bernt 5de147a181 re-remove the data input 2020-01-22 09:37:24 +01:00
M Bernt fff8d2ec7b inputs configfile: test for filename and data_style attributes 2020-01-22 09:37:19 +01:00
mvdbeek 71788d099c Simplify PREPARE_DIRS logic 2020-01-22 09:35:57 +01:00
John Chilton 4c8918afdf Merge pull request #9232 from dannon/mailto_hrefs_in_menus 
[20.01] Fix mailto hrefs in menus
 2020-01-21 15:16:34 -05:00
M Bernt be3e07fb39 fix Popen/py3 related bugs for real user setups 
- Popen returns bytes in python3
- strings are needed

analoguous to what is happening in slurm I use unicodify here
 2020-01-21 19:12:59 +01:00
Sergey Golitsynskiy 62374dce20 Rename parameter: item > config 
Reason: in ConfigSerializer (unlike in its superclass) the item is
always the config object. Renaming the item parameter, I think, makes
the code easier to understand. Also, that makes it consistent with the
`default_serializer` method definition, which uses config instead of
item.
 2020-01-21 12:26:31 -05:00
Sergey Golitsynskiy 3e72927653 Rename _required_attribute function 
Reason: name caused confusion.
 2020-01-21 12:17:02 -05:00
mvdbeek 28277d2b67 Fix unit test 2020-01-21 11:57:20 +01:00
mvdbeek 9e4545f639 Copy working/ and outputs/ before starting job script 
This seems to be the most robust way to make sure that resubmission by
the DRM will start with proper configfiles and pre-populated outputs
(OutputParameterJSONTool).
The cost should be minimal as most of the time these are empty
directories.
This would also help with https://github.com/galaxyproject/galaxy/pull/9236#issuecomment-576050103
 2020-01-21 11:18:23 +01:00
mvdbeek 8d099ef98b Only delete writable files on job resubmission 2020-01-21 11:18:13 +01:00
mvdbeek db472b2bc0 Only delete working/ and outputs on resubmission 2020-01-21 11:16:38 +01:00
Björn Grüning 8234eb0d5e Merge pull request #9244 from simonbray/tpr 
Add tpr datatype
 2020-01-21 08:06:34 +01:00
Simon Bray 6974fe2884 add tpr datatype 2020-01-20 20:23:00 +01:00
mvdbeek f327189c2b Fix moving of data manager output for entries 
https://github.com/galaxyproject/galaxy/pull/8250 introduced the
add and remove keys for removing items from a data table.
If there is a single data table definition incoming (meaning a
dictionary) that does not specify the `add` key the new code would
just ignore that entry and not move it.

Fixes https://github.com/galaxyproject/tools-iuc/issues/2783?
 2020-01-20 17:36:12 +01:00
Martin Cech 2233a10b1c Merge pull request #9195 from hexylena/user-rename2 
[PROCEDURES] Update my username
 2020-01-20 14:29:59 +01:00
Nicola Soranzo 47c5a0e108 Merge pull request #9239 from mvdbeek/fix_binary_upload_problems_with_faulty_headers 
[19.09] Fallback to binary download if header lies about content encoding
 2020-01-19 23:01:53 +00:00
Marius van den BeekandNicola Soranzo 4d686edb7f Simplify use_source_encoding logic 
Thanks Nicola, very nice!

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-01-19 19:59:20 +01:00
Nicola Soranzo 933c3bafc0 Merge pull request #9240 from mvdbeek/fix_planemo_lint_error 
[20.01] Fix lint warning string formatting
 2020-01-19 18:12:58 +00:00
Björn Grüning 29d73ffa56 Merge pull request #9237 from mvdbeek/remove_fimo_from_galaxy_lib_unversioned_tools 
[20.01] Move meme_fimo out of unversioned lib tools
 2020-01-19 17:59:38 +01:00
mvdbeek 6e8f143124 Fix lint warning string formatting 
Introduced in
https://github.com/mvdbeek/galaxy/commit/c4fabf05e11c033006834fd0bf0d9077c0156134,
causes:
```
ValueError: unsupported format character 'n' (0x6e) at index 16
```
 2020-01-19 17:47:23 +01:00
mvdbeek e6fe571c02 Fallback to binary download if header lies about content encoding 
Fixes https://github.com/galaxyproject/galaxy/issues/9238
 2020-01-19 16:42:10 +01:00
mvdbeek 69ff055843 Move meme_fimo out of unversioned lib tools 2020-01-19 12:46:24 +01:00
Nicola Soranzo cf71e6f365 Merge pull request #9230 from jmchilton/dev_merge_2 
Merge release_20.01 into dev.
 2020-01-17 19:57:25 +00:00
Dannon Baker 6a4a3b89ac Formatting. 2020-01-17 12:57:53 -05:00
Dannon Baker 6218b313a7 Allow mailto addresses (for support/contact) in menu items. 2020-01-17 12:57:20 -05:00
John Chilton 527af29439 Merge remote-tracking branch 'upstream/release_20.01' into dev_merge_2 2020-01-17 12:28:11 -05:00
John Chilton 531ad72032 Starting work on tool-util 20.1.0.dev4 2020-01-17 12:19:48 -05:00
John Chilton 46d772b5c3 Merge pull request #9228 from mvdbeek/extended_base_aonnotation_fixes 
[20.01] More mulled-build-files fixes
 2020-01-17 12:18:45 -05:00
mvdbeek bc9a840d35 Turn off determin_base_image for mulled-build-files 2020-01-17 12:22:13 +01:00
mvdbeek d79e746316 Delete /usr/local before moving conda env 
/usr/local/man already exists and is a symlink in bioconda/extended-base-image:latest,
and so `cp -R /tmp/conda/*` fails with
```
cp: cannot overwrite non-directory '/usr/local/man' with directory '/tmp/conda/man'
```
 2020-01-17 11:20:10 +01:00
Marius van den Beek 798219b3fc Merge pull request #9225 from nuwang/affinity_and_tolerations 
[20.01] Fix: Added support for specifying k8s job affinity and tolerations
 2020-01-17 10:21:15 +01:00