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20966 Commits
Author SHA1 Message Date
mvdbeek 9574de30f6 Fix startup on python 3 if run through uwsgi 
uwsgi options are returned as bytestring, so this avoids:
```
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 12, in <module>
    import galaxy.app
  File "lib/galaxy/app.py", line 8, in <module>
    import galaxy.model
  File "lib/galaxy/model/__init__.py", line 45, in <module>
    import galaxy.exceptions
  File "lib/galaxy/exceptions/__init__.py", line 19, in <module>
    from ..exceptions import error_codes
  File "lib/galaxy/exceptions/error_codes.py", line 9, in <module>
    from galaxy.util import unicodify
  File "lib/galaxy/util/__init__.py", line 1708, in <module>
    executable = _executable()
  File "lib/galaxy/util/__init__.py", line 1700, in _executable
    exe = os.path.join(virtualenv, 'bin', 'python')
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.6/posixpath.py", line 94, in join
    genericpath._check_arg_types('join', a, *p)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.6/genericpath.py", line 151, in _check_arg_types
    raise TypeError("Can't mix strings and bytes in path components") from None
TypeError: Can't mix strings and bytes in path components
```

Broken in https://github.com/galaxyproject/galaxy/commit/891daf4f82eb45c692f3fc5542cea35f94e10118
 2019-07-12 16:53:21 +02:00
Nicola Soranzo e9b6c106d2 Sniff fastqsanger more aggressively (#8322) 
Sniff fastqsanger more aggressively
 2019-07-12 10:03:21 +01:00
Enis Afgan 33f442f0c8 Merge pull request #8311 from telukir/f-kt-r19.05-jwt1 
walltime_limit added for the k8s jobs
 2019-07-12 08:30:29 +02:00
Wolfgang Maier 80b9be3cf5 Clean up code 2019-07-11 21:14:05 +02:00
Martin Cech b415dfddfa Merge pull request #8294 from bwlang/library_date_propagate 
Library date propagate
 2019-07-11 13:55:31 -04:00
Wolfgang Maier ff6f1084a7 Reduce to minimal required change 2019-07-11 16:47:25 +02:00
John Chilton c2ac586669 Merge pull request #8296 from blankenberg/environment_variable-strip 
Add ability to strip whitespace from tool environment_variables.
 2019-07-11 16:28:29 +02:00
John Chilton 6a1c05fac2 Merge pull request #8300 from mvdbeek/skip_migration_for_new_databases 
Skip migrations on entirely clean new databases
 2019-07-11 16:24:07 +02:00
Vahid 731b3eb8d2 add r to regexp to escape \d & satisfy lint. 2019-07-10 13:49:33 -07:00
Vahid 40fe0a3e86 Enable user1 & user2 resolve to different usernames 2019-07-10 12:51:52 -07:00
Wolfgang Maier 37b3a0fe13 Improve readability 2019-07-10 17:37:56 +02:00
Wolfgang Maier 3df7b2591c Avoid previously used test file names 2019-07-10 17:22:14 +02:00
mvdbeek 6fc3d09b60 Fix and simplify k8s error handling 2019-07-10 17:16:37 +02:00
Nicola Soranzo bdee798bc0 Fix kubernetes runner on py3 (#8321) 
Fix kubernetes runner on py3
 2019-07-10 15:59:37 +01:00
Wolfgang Maier 986c1831d3 Add unit test and fix test file 2019-07-10 16:04:05 +02:00
Wolfgang Maier 79f2bb5991 Sniff fastqsanger with telltale low quality scores 
When a fastq file contains quality scores that are too low to be
compatible with any +64 encoding scheme, the assumption should be
that the file is Phred+33 encoded even if some scores are above
the current upper threshold of 44.
 2019-07-10 15:55:58 +02:00
mvdbeek b2cd5ba8d0 Add k8s_walltime_limit to job_conf.xml.sample_advanced 2019-07-10 15:27:25 +02:00
mvdbeek 8fb5936f92 Fix kubernetes runner on py3 
instance_id is a string, so this can't be compared to an integer
on python 3. Broken in ac1b25ed4c,
prior to that the comparison was `len(self._galaxy_instance_id) > 0:`
 2019-07-10 13:55:49 +02:00
mvdbeek 888c03877d Fix kubernetes runner on py3 
instance_id is a string, so this can't be compared to an integer
on python 3. Broken in ac1b25ed4c,
prior to that the comparison was `len(self._galaxy_instance_id) > 0:`
 2019-07-10 13:49:53 +02:00
Kiran Telukunta saraswathi 34bde631f4 * walltime_limit added for the k8s jobs 
* default is also set to the k8s_walltime_limit in job specification
 2019-07-10 12:51:29 +02:00
Brad Langhorst 485e0043a7 implements nicola's suggestion -> snakecase 2019-07-10 05:22:27 -04:00
Marius van den Beek ef9698895a Merge pull request #8319 from nsoranzo/lowercase_boolean_yaml 
Use lowercase true/false in config_schema.yml
 2019-07-10 11:18:19 +02:00
Marius van den Beek db3a1bac1d Merge pull request #8320 from nsoranzo/merge_19.05_20190709 
Merge 19.05 20190709
 2019-07-10 11:15:46 +02:00
Marius van den Beek bc7b48756b Merge pull request #7402 from guerler/activate_toolshed 
Activate api-based Toolshed interface in Admin panel
 2019-07-10 11:06:18 +02:00
guerler 95d69146be Restore tool metadata endpoint for old tool management grid 2019-07-10 08:21:38 +02:00
Nicola Soranzo d0c28f669b Use lowercase true/false in config_schema.yml 
since these are the only allowed values for booleans in YAML 1.2:
https://yaml.org/spec/1.2/spec.html#id2803629

make config-rebuild
 2019-07-09 18:58:51 +01:00
Nicola Soranzo ea32667142 Merge branch 'release_19.05' into dev 2019-07-09 18:43:43 +01:00
John Chilton 7fa24b191b Remove mimeparse package in lib/ root. 
Was added for trackster in 985f7c63fa for a tracks controller that no longer exists. Cannot find any references to this module.
 2019-07-09 14:13:12 +01:00
Marius van den Beek d22d7beaf4 Merge pull request #8305 from jmchilton/axe_log_tempfile 
Remove log_tempfile.
 2019-07-09 14:42:43 +02:00
guerler 4359029ef9 Remove legacy toolshed activation flag in config 2019-07-09 13:59:46 +02:00
guerler deaa583890 Merge branch 'dev' into activate_toolshed 2019-07-09 13:58:01 +02:00
Marius van den Beek ef86713754 Merge pull request #8304 from nsoranzo/remove_temp2.txt 
Use temporary file for sniff tests
 2019-07-09 12:55:25 +02:00
Nate Coraor 97bcd9c46a Merge pull request #8306 from jmchilton/axe_psyco_full 
Remove psyco_full.py - unused as far as I can tell.
 2019-07-09 11:01:09 +02:00
Brad Langhorst 50011c1e98 linting fixes 2019-07-09 04:09:11 -04:00
Brad Langhorst d35df5eca7 Sqlite3 compatible syntax 2019-07-08 13:10:35 -04:00
mvdbeek a01adf6da2 Do actually initialize tool shed mapping 2019-07-08 16:37:28 +02:00
mvdbeek ea0688146d Use correct install db url 2019-07-08 16:37:28 +02:00
mvdbeek d34142e420 Skip migrations on entirely clean new databases 
This should be a very nice speedup for ansible tutorials,
tests, planemo etc.
 2019-07-08 16:37:28 +02:00
John Chilton 1bed6c4931 Remove psyco_full.py - unused as far as I can tell. 
@natefoo didn't object.
 2019-07-08 14:59:52 +02:00
John Chilton 8a327db74d Remove log_tempfile. 
Simplify packaging - @natefoo said I could.
 2019-07-08 14:52:13 +02:00
Nicola Soranzo 8876f165d1 Use temporary file for tests 
Remove `lib/galaxy/datatypes/test/temp2.txt` which was added by
mistake in commit 54d2ca01f8 .
 2019-07-08 12:45:10 +01:00
Daniel BlankenbergandNicola Soranzo a5b3308a89 Update lib/galaxy/tool_util/xsd/galaxy.xsd 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-07-08 13:34:54 +02:00
Nate Coraor 058fabc121 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-08 12:27:21 +02:00
Daniel Blankenberg 3255284fb0 Fix for fetching strip if not defined 2019-07-08 12:17:38 +02:00
Daniel Blankenberg 7db36407cb Merge branch 'dev' of https://github.com/galaxyproject/galaxy into environment_variable-strip 2019-07-08 11:51:01 +02:00
Nate Coraor d187b28951 Stop trying to guess a web port from the config since most configs are not INI anymore anyway. 2019-07-08 11:43:11 +02:00
John Chilton 23241a29d7 Merge pull request #8280 from dglaetzer/dev 
get tests on data package running
 2019-07-08 11:41:36 +02:00
Nate Coraor 906413d07b Rework config locating logic (it was reading the sample again). 2019-07-08 11:28:31 +02:00
Nate Coraor 751503958f Fixes from PR review 2019-07-08 11:28:04 +02:00
Brad Langhorst dc26a388bb removes noisy debug output 2019-07-08 04:48:13 -04:00