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Commit Graph
17340 Commits
Author SHA1 Message Date
Helena Rasche ffe7981cc2 broken access 2018-05-10 17:06:01 +02:00
E Rasche 6872325d80 Remove user IDs from job names 2018-05-01 12:05:28 +02:00
E Rasche d23bb5689e Redact docker logs 2018-04-10 12:34:47 +02:00
E Rasche 75b923b677 do not log usernames 2018-04-10 12:29:02 +02:00
E Rasche abfb69252a Some progress on this 2018-04-10 11:57:46 +02:00
E Rasche 4a6eb37b47 Add config option 2018-04-10 11:36:11 +02:00
Dannon Baker d9efb4ff4c Merge pull request #5864 from guerler/fix_expansion 
Fix conditional parameter handling
 2018-04-09 10:47:51 -04:00
Dannon Baker 075abee766 Merge pull request #5810 from guerler/viz-staging-finalize 
Plugin directory staging
 2018-04-06 09:54:53 -04:00
guerler 02e92e2115 Fix conditional parameter handling for textselect field 2018-04-05 20:17:17 -04:00
John Chilton 4e4dbc8823 Expand selenium test coverage. 
Initial admin app tests including screenshots of display applications, data tables, data types, and job management.
 2018-04-03 20:10:39 -04:00
Nicola Soranzo c9881fdc5c Merge branch 'release_18.01' into dev 2018-04-03 10:54:48 +01:00
John Chilton a8072a1d8b Merge pull request #5816 from dannon/upload_common_bugfix 
Bugfix in upload_common -- ensure hda is added to a session
 2018-03-30 22:29:47 -04:00
Dannon Baker 03287ed195 Bugfix in upload_common -- ensure hda is added to a session prior to state setting. 2018-03-30 14:21:50 -04:00
guerler e99c8ec65c Remove static path mixin 2018-03-30 12:55:57 -04:00
guerler f0dde506d0 Remove unused static url, fix routes in plugins 2018-03-30 12:50:31 -04:00
guerler f21965472c Merge branch 'dev' into viz-staging-finalize 2018-03-29 11:57:48 -04:00
Martin Cech 009921387d Merge pull request #5769 from jmchilton/unify_scripts 
[18.01] Fix scripts/ for YAML/ENV configuration processing
 2018-03-29 11:14:13 -04:00
John Chilton 9e71e1d2f0 Allow anonymous users to view their jobs via the API. 2018-03-29 11:06:42 -04:00
John Chilton 08c2c5b5ac Merge pull request #5698 from dannon/psycopg2_bump 
Bump psycopg2 to 2.7.4;
 2018-03-29 10:47:22 -04:00
John Chilton 241fadc981 Merge pull request #5805 from mvdbeek/fix_cram_metadata 
[18.01] Fix metadata setting for CRAM files
 2018-03-29 10:36:33 -04:00
Nicola Soranzo d5baea1dfc Handle an empty datatypes_registry 
Also transform it to an object attribute for re-use.
 2018-03-29 13:57:16 +01:00
Nicola Soranzo 7e5a90cc1f Use app.datatypes_registry in ValidationContext.from_app() 2018-03-29 13:13:25 +01:00
mvdbeek 288d13b606 Fix metadata setting for CRAM files 
Should fix https://github.com/galaxyproject/galaxy/issues/5801.
 2018-03-29 11:17:58 +02:00
Nicola Soranzo a85b8a83cb Merge pull request #5798 from dannon/lock_pysam 
Lock pysam to 0.14.1 in Pipfile.
 2018-03-28 19:55:14 +01:00
Nicola Soranzo 4f870490f2 Simplify get_datatype_by_extension() method 2018-03-28 19:01:22 +01:00
Nicola Soranzo 96d9d0e5a2 Better re-use of tool attribute 2018-03-28 19:00:20 +01:00
Nicola Soranzo 0ff93b0e53 Merge branch 'release_18.01' into dev 2018-03-28 16:51:45 +01:00
Nate Coraor c6ae97edae Merge pull request #5774 from nsoranzo/release_18.01_fix_pid 
[18.01] Log the pid of the first uWSGI process
 2018-03-28 11:29:25 -04:00
John Chilton 70128b5d69 Merge pull request #5789 from guerler/add_delay_handler 
Add delay attribute to grid handler
 2018-03-28 11:10:47 -04:00
Dannon Baker 0a1ccdba12 Lock pysam to 0.14.1 in Pipfile. 2018-03-28 10:05:05 -04:00
Dannon Baker fa69c7507b Merge pull request #5743 from jmchilton/uwsg-buffer-size 
Revise uwsgi defaults and display.
 2018-03-28 08:28:10 -04:00
Dannon Baker 449e25200b Merge remote-tracking branch 'upstream/release_18.01' into dev 2018-03-27 16:07:25 -04:00
Dannon Baker d6be56256f Merge pull request #5782 from jmchilton/fix_1801 
[18.01] Fix SQL query for "workflows shared with me" as part of workflow index.
 2018-03-27 16:06:33 -04:00
Martin Cech 2558d27801 Merge pull request #5772 from Delphine-L/addGbkgz 
Add genbank.gz datatype
 2018-03-27 16:01:18 -04:00
Martin Cech a97b3a469c fex sniffing of compressed genbank files 
also add doctest for both compressed and uncompressed versions
 2018-03-27 14:43:01 -04:00
Dannon Baker 70915dfc9f Merge remote-tracking branch 'upstream/dev' into viz-staging 2018-03-27 13:49:19 -04:00
Dannon Baker c5beedef6b Merge branch 'visualization_header' into dev 2018-03-27 13:44:23 -04:00
guerler 2b2fd92898 Use visualizations route to link to plugins 2018-03-27 13:39:57 -04:00
Nicola Soranzo bf5d472e28 Merge pull request #5702 from guerler/select_to_text 
Relax validation condition for dynamic parameters
 2018-03-27 15:35:48 +01:00
John Chilton 62d4582ef6 Touch up script unification PR based on @natefoo comments. 2018-03-27 10:34:52 -04:00
Dannon Baker 61adffbd61 Merge pull request #5786 from nsoranzo/default_pipfile 
Use pipenv also for the default dependencies
 2018-03-27 10:32:23 -04:00
guerler db1b8bc64b Use delayed flag for history grid 2018-03-27 08:55:18 -04:00
John Chilton b4a30bcd82 Revise uwsgi defaults and display. 
In https://github.com/galaxyproject/galaxy/issues/1530 we realized that buffer-size needs to be increased for Galaxy requests. Also mention thunder-lock since that should frequently be enabled - https://github.com/galaxyproject/ansible-galaxy-extras/pull/195.
 2018-03-27 08:48:58 -04:00
guerler 528201e56a Add delayed column attribute to grid helper 2018-03-27 08:45:15 -04:00
Dannon Baker 39d5ec89f8 Merge branch 'release_18.01' into dev 2018-03-27 08:42:09 -04:00
Dannon Baker 45dd988965 Merge pull request #5721 from erasche/sentry-reporter 
Sentry bug reports working for anonymous users
 2018-03-27 08:38:54 -04:00
Dannon Baker fbb47f6e03 Merge pull request #5745 from nsoranzo/release_18.01_fix_config 
[18.01] Configuration fixes
 2018-03-27 08:37:19 -04:00
Nicola Soranzo e625b649dc Temporarily pin Mercurial to latest compatible release 2018-03-27 08:53:54 +01:00
Nicola Soranzo f8aa29e280 Temporarily pin WebOb to latest compatible release 2018-03-27 08:53:54 +01:00
Nicola Soranzo fb92257bc7 Exclude 2 problematic h5py versions 
A warning was appearing in the stderr of upload jobs due to
https://github.com/h5py/h5py/issues/995 .
 2018-03-27 08:53:54 +01:00