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19420 Commits
Author SHA1 Message Date
Nicola Soranzo aef53f6cde Merge branch 'release_18.09' into release_19.01 2019-03-10 21:39:24 +00:00
Nicola Soranzo 8e125b7698 Merge branch 'release_18.05' into release_18.09 2019-03-10 21:36:15 +00:00
Nicola Soranzo c1a9095ad4 Restrict loading of JSON files on the server via the workflow API to Galaxy admins 
Fix https://github.com/galaxyproject/security/issues/29
 2019-03-10 12:52:02 +00:00
mvdbeek 1a636c376f Fix HiddenParameter use 
Broken in
https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5d1e1288315e1
Fixes https://github.com/galaxyproject/galaxy/issues/7454
 2019-03-04 17:39:57 +01:00
Nicola Soranzo 91e49acf37 Merge branch 'release_18.09' into release_19.01 2019-03-03 15:52:13 +00:00
Martin Cech 996d7c9a60 Merge pull request #7448 from mvdbeek/fix_when_default_label_is_none 
[18.09] Fix loading workflows with steps without default label
 2019-03-03 10:49:49 -05:00
Martin Cech d96034062a fix lint 2019-03-02 12:03:10 -05:00
mvdbeek bc8cf37d09 Remove broken tool_submission_burst 2019-03-02 16:53:36 +01:00
mvdbeek 5142d0df07 Fix loading workflows with steps without default label 
Prior to https://github.com/galaxyproject/galaxy/pull/7422
we'd call str(default_label), so if `default_label` was None
we'd get 'None'. Fixes part of https://github.com/galaxyproject/galaxy/issues/7447
 2019-03-02 16:13:54 +01:00
mvdbeek 739bb6310c Merge branch 'release_18.09' into release_19.01 2019-03-01 18:04:44 +01:00
mvdbeek e8f5a13f3b Fix LocalShellRunner 
All the `cmd` coming from the plugins are strings, so if cmd is
a string we use `shell=True`, brings this on par
with the Remote Shell plugins (which consume strings).
Should fix https://github.com/galaxyproject/galaxy/issues/7269.
 2019-03-01 14:45:32 +01:00
Nicola Soranzo 64a0152a6b Merge branch 'release_18.09' into release_19.01 2019-03-01 00:16:18 +00:00
Nate Coraor 9a26de1b4b Catch another Slurm memory cgroup creation error message 2019-02-28 11:51:36 -05:00
mvdbeek 9e0d3b69ca Fix workflow loading on systems with ASCII locale 
Fixes https://github.com/galaxyproject/galaxy/issues/7421,
though it's very likely Galaxy won't play well when python
is falling back to ASCII as default encoding.

WorkflowStep.label is backed by a 255 character unicode string,
but tool_inputs is JSONType, which might have integer or float values
(in principle), so we play it safe by casting to unicode.
 2019-02-27 18:02:55 +01:00
mvdbeek 51d167b85d Fix dependency installation in UI 
We need to pass the install kwarg here.
Broken in https://github.com/galaxyproject/galaxy/commit/2d3ab4ce1205aec24664225d74b2a851cb94b2b0
 2019-02-27 14:15:52 +01:00
John Chilton fdb18045b7 Update version to 19.01 2019-02-26 14:28:25 -05:00
mvdbeek ed375993eb Fix analyze75 hdr file upload when convert newlines is on 2019-02-26 12:22:46 +01:00
Nate Coraor 808aa5bef7 Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 2019-02-22 13:23:16 -05:00
Nicola Soranzo 9b72f5a880 Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments 
[18.09] Update configuration samples
 2019-02-22 18:16:25 +00:00
John Chilton 8651e1eea3 Merge branch 'release_18.09' into release_19.01 2019-02-22 13:12:16 -05:00
John Chilton 2f973ac7fa Merge branch 'release_18.05' into release_18.09 2019-02-22 13:11:49 -05:00
John Chilton 1529758ecb Merge branch 'release_18.01' into release_18.05 2019-02-22 13:11:19 -05:00
John Chilton 656b3c2f87 Refactor dataset fetching in get/set dataset method in web controller. 2019-02-22 13:10:12 -05:00
Nate Coraor a83eb67775 Slight rewording of the cookie_path option description, and corrections 
to file_path and new_file_path descriptions.
 2019-02-22 11:31:44 -05:00
Nicola Soranzo 351c188830 Remove `filter-with and update cookie_path` options also for Tool Shed and Reports 2019-02-22 12:07:16 +00:00
Martin Cech 1a0f067590 change config schema to reflect removing paste options 2019-02-21 12:26:31 -05:00
Martin Cech 648d01685b Merge pull request #7390 from mvdbeek/more_useful_error_message 
[19.01] Report line number mismatch in sort collection tool
 2019-02-20 12:12:27 -05:00
mvdbeek b4fc7c19a8 Report line number mismatch in sort collection tool 
Otherwise this would just fail because sorted_elements is undefined.
I don't think there can be a HDA without metadata, so I've dropped
that check.
 2019-02-20 13:53:26 +01:00
Martin Cech ac9b300df6 Merge pull request #7385 from blankenberg/19.01-anvio-datatypes 
[19.01] Add datatypes for Anvi'o
 2019-02-19 10:55:16 -05:00
Martin Cech d72f82de98 remove Paste config option, reword URL prefix 2019-02-19 10:37:34 -05:00
Nicola Soranzo 737bae8f9b Reword HDF5 attribute test docs 2019-02-19 00:43:12 +00:00
Daniel Blankenberg 51280fbf7d flip a line 2019-02-18 15:26:31 -05:00
Daniel Blankenberg cf31e330e8 Decrease readability. 2019-02-18 14:25:19 -05:00
Daniel Blankenberg 948cdb251a cleanup anvio.py 2019-02-18 13:53:03 -05:00
Daniel Blankenberg 7abd448cbe Add datatypes for Anvi'o 2019-02-18 13:48:13 -05:00
John Chilton 2033535976 Fix HDF5 test assert docs 
Alternative to https://github.com/galaxyproject/galaxy/pull/7382, fix documentation without giving up better validation one gets with actual types for assertion XML elements.
 2019-02-18 13:09:12 -05:00
Dannon b67dc2ba24 Merge pull request #7353 from bgruening/improve_err_message 
Improve error message during tool testing
 2019-02-14 16:56:14 -05:00
John Chilton 728ff2075d Merge pull request #7352 from bgruening/test_data_fix 
fix the filename of saved test-data
 2019-02-14 13:57:44 -05:00
John Chilton 62d8d808eb Merge pull request #7331 from mvdbeek/test_data_managers 
[19.01] Discriminate data managers and allow managed testing
 2019-02-13 14:25:41 -05:00
Bjoern Gruening f311ebd1e2 mention planemo explicitly 2019-02-12 22:28:32 +01:00
Bjoern Gruening 740fc8594e improve test error message 2019-02-12 22:22:43 +01:00
Bjoern Gruening 06d1e5a8b2 fix the name of presevered test-data 2019-02-12 21:12:02 +01:00
Björn Grüning f7322d85a3 Merge pull request #7299 from chambm/feature/rawtar-datatypes 
Add datatypes and sniffers for tar archives of directory-based MS formats and WIFF/SCAN pairs
 2019-02-09 14:42:28 +01:00
mvdbeek d710bb860b Discriminate data managers and allow managed testing 
I am not a big fan of the heuristic in which we fall back
to loading the data manager tool relative to the data_manager_conf.xml
file, but I don't really see a better way here.
 2019-02-07 23:35:02 +01:00
John Chilton 8f7263a1dc Merge pull request #7301 from bgruening/hdf5_tests 
Add new test syntax specific for HDF5 files
 2019-02-07 14:49:33 -05:00
Marius van den Beekanderasche dd917099ba Only block the single category of C characters that is problematic 
Co-Authored-By: erasche <hxr@hx42.org>
 2019-02-06 16:40:40 +01:00
Helena Rasche b59d76eb4a Fix emoji tags 2019-02-06 16:40:40 +01:00
Bjoern Gruening d36cf51f6b change "name" to "key" 2019-02-06 16:31:15 +01:00
Matt Chambers dc303f004f Remove try/except in sniffers 
Add .d/.raw to file_ext
 2019-02-06 10:18:57 -05:00
Matt Chambers d30852b286 Add wiff.tar extension and sniffer 2019-02-05 13:14:06 -05:00