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Author SHA1 Message Date
Nicola Soranzo 44859c7d6d Merge pull request #9290 from nsoranzo/release_19.09_fix_9178 
[19.09] Python3: don't check for has_key attribute
 2020-01-31 14:51:53 +00:00
Nicola Soranzo 2e587f14a7 Python3: don't check for has_key attribute 
Also partially backport commit f892231b8b .
Fix https://github.com/galaxyproject/galaxy/issues/9178 .
 2020-01-31 01:17:02 +00:00
Wolfgang Maier 7135ab307b Python3 compatible SnpEff and SnpSift metadata detection 2020-01-30 11:20:26 +00:00
John Chilton 002964ee17 Merge pull request #9242 from mvdbeek/limit_dataid_in_incoming_special_case 
[19.09] Limit async hack to async tools
 2020-01-27 09:52:23 -05:00
Nicola Soranzo 83bd84842e Merge pull request #9266 from mvdbeek/fix_iteritems_in_workflow_extraction 
[19.09] Fix iteritems use in build_from_current_history.mako
 2020-01-24 17:03:20 +00:00
Marius van den Beek 6bb6aa22b7 Merge pull request #9263 from nsoranzo/release_19.09_backport_9260 
[19.09] Backport #9260 plus refactor
 2020-01-24 16:59:13 +01:00
mvdbeek f405dbf719 Fix iteritems use in build_from_current_history.mako 
Fixes https://github.com/galaxyproject/galaxy/issues/9265
 2020-01-24 15:24:51 +01:00
Nicola Soranzo d67295162a Simplify and refactor 2020-01-23 21:57:54 +00:00
mvdbeek e227b1473f Fix unselected select parameter comparison to empty string 
`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
 2020-01-23 19:24:52 +00:00
Marius van den Beek fc0e31887f Merge pull request #9253 from bernt-matthias/topic/fix-popen-py3-followup 
[19.09] fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
 2020-01-23 16:58:44 +01:00
M BerntandMarius van den Beek c358e3ab69 remove space 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2020-01-22 16:54:48 +01:00
M Bernt db5bd4fac3 fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246 2020-01-22 16:16:45 +01:00
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
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
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
M Bernt 5bb2d16533 fix import order 2020-01-22 10:37:20 +01:00
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
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
mvdbeek 276bf51bf1 Limit async hack to async tools 
Fixes disco tests and https://github.com/galaxyproject/galaxy/issues/9241
 2020-01-20 16:14:40 +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
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
Dannon 56362e3be2 Merge pull request #9217 from kaukrise/bug_fix_trackster_navbar_overflow 
Ensure visible overflow on navbar container
 2020-01-14 15:13:21 -05:00
Dannon 4cbe0cef89 Merge pull request #9216 from kaukrise/bug_fix_trackster_history 
Wrap SQL statement in a text() function as required by sqlalchemy
 2020-01-14 14:58:20 -05:00
kaukriseandNicola Soranzo 01befe12ce Optimise import formatting 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-01-14 15:59:42 +01:00
Kai Kruse 6f68f2a7e2 Ensure visible overflow on nav ba container so that we can push 
the genome navigation into the title element. Fixes #9205
 2020-01-14 15:48:14 +01:00
Kai Kruse 9bf1bf5999 Wrap SQL statement in a text() function as required by sqlalchemy. 
Fixes a history loading issue in Trackster #9205
 2020-01-14 15:46:57 +01:00
Nicola Soranzo 0d1d8f0704 Merge pull request #9198 from natefoo/catch-all-exceptions-in-job-fail 
[19.09] Fix jobs stuck in preparing state when dynamic rules raise arbitrary exceptions
 2020-01-10 20:26:00 +00:00
Nate Coraor 104db46047 Add a comment explaining why the job mapper turns general exceptions 
into JobMappingExceptions.
 2020-01-10 10:44:55 -05:00
Nate Coraor b3910c1b5e Make a new exception class for problems with the dynamic mapper 
configuration itself.
 2020-01-09 16:45:21 -05:00
Nate Coraor 5bd9468281 Don't catch the custom dynamic rule exceptions, just raise them as-is. 2020-01-09 15:36:14 -05:00
Nate Coraor fdd65bbb81 Log exceptions encountered while caching dynamic job rules and raise 
JobMappingException instead.
 2020-01-09 15:18:33 -05:00
Nicola Soranzo f93b5673ca Merge pull request #9182 from jmchilton/fix_ts_tests 
[19.09] Fix tool shed tests for #9168.
 2020-01-07 18:35:02 +00:00
John Chilton f682307d19 Fix tool shed tests for #9168. 2020-01-07 09:23:13 -05:00
Nicola Soranzo fc24bb27b5 Merge pull request #9171 from mvdbeek/fix_shell_runner_returncode 
[19.09] Fix LocalShell returncode
 2019-12-30 09:40:44 +01:00
mvdbeek 3859735c27 Fix LocalShell returncode 
It appears polling once after completionn is necessary to get the
correct returncode.
 2019-12-29 19:25:04 +01:00
mvdbeek 67b7148d09 Test return code 2019-12-29 19:17:27 +01:00
John Chilton 2e91dd121f Starting work on tool-util 19.9.2 2019-12-28 16:43:30 -05:00
John Chilton d6703f54f6 Version 19.9.1 of tool-util (tag galaxy-tool-util-19.9.1). galaxy-tool-util-19.9.1 2019-12-28 16:42:25 -05:00
John Chilton aa47208a7c Merge pull request #9168 from guerler/ensure_role 
[19.09] Ensure that users have a private role before login
 2019-12-28 16:34:36 -05:00
guerler 09a23326ef Use local security agent instead of app in create user roles 2019-12-27 15:07:16 -05:00
guerler b318f6ad08 Create private user role only if user role is not available 2019-12-27 15:01:50 -05:00
guerler fe81adf429 Use parsed local parameter in user role initialization helper 2019-12-27 14:59:04 -05:00
guerler 10c2322662 Move user creation helper from user manager to security model 2019-12-27 14:55:29 -05:00
mvdbeek f12e0844fe Merge branch 'release_19.05' into release_19.09 2019-12-27 20:12:05 +01:00
guerler 6b4f0b4a50 Ensure that the user has a private role before login 2019-12-27 13:40:34 -05:00
Björn Grüning 6e617d2f97 Merge pull request #9156 from mvdbeek/restore_optional_param_none 
[19.05] Cast to None for optional params if not comparing strings
 2019-12-21 21:25:11 +01:00
mvdbeek 9d1cccd14d Cast to None for optional params if not comparing strings 
Proposed by @nsroanzo in https://github.com/galaxyproject/galaxy/pull/9149#discussion_r360225247
 2019-12-21 17:22:34 +01:00
John Chilton 9ae9be077a Merge pull request #9153 from mvdbeek/fix_cool_sniffing 
[19.09] Fix cool sniffing on python3
 2019-12-20 10:04:34 -05:00
mvdbeek e1a1584799 Fix cool & mcool sniffing on python3 
h5py returns bytestrings, so this worked on python 2 but not python 3.
Fixes hicexplorer tests on python 3.
 2019-12-20 12:02:34 +01:00