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Author SHA1 Message Date
vahid 275cc365a5 Move some code from test method to setUp method in OS integration tests. 2019-05-25 17:26:14 -07:00
vahid 6acb9e50eb Remove objectstore from its integration tests filenames. 2019-05-25 17:20:00 -07:00
vahid 52596d186e Organize ObjectStore integration tests under a dedicated package. 2019-05-25 16:36:50 -07:00
Dannon 386a1a4c76 Merge pull request #8025 from WilliamHolden/es6_upgrades 
Es6 upgrades in galaxy.js
 2019-05-24 13:11:20 -04:00
Dannon be147f9ffb Merge pull request #8022 from jmchilton/vuejs_show_params_1 
Rework dataset job properties tables into components+APIs
 2019-05-24 10:04:43 -04:00
Dannon Baker 8efaf565a0 Use default function params, dot notation for attribute access. Fix module comment. 2019-05-24 07:57:24 -04:00
will fc5a1b0d20 remove usage of self = this in galaxy.js 2019-05-23 11:37:53 -04:00
will 8fe6fce7f9 prefer const and let over var in galaxy.js 2019-05-23 10:58:14 -04:00
John Chilton b80cf2744b VueJs component to show tool parameters. 
- Can operate on a job_id or dataset_id.
- New API endpoint to support. This endpoint is very tied to the client and so is documented as being unstable. This API endpoint isn't the most wonderfully general creature but hopefully everyone is excited to see less mako and more use of APIs and reusable JS components.
 2019-05-23 07:10:50 -04:00
John Chilton e461918201 VueJs component to show job metrics. 
- Can operate from a job_id or dataset_id.
- New API endpoint to support this.
 2019-05-23 07:10:49 -04:00
Nicola Soranzo 0585178220 Refactor comments in sample object stores to remove nested comments. (#8016) 
Refactor comments in sample object stores to remove nested comments.
 2019-05-22 10:45:09 +01:00
Will Simpson 738579e432 Refactor comments in sample object stores to remove nested comments. 2019-05-21 14:31:51 -07:00
Dannon 29bd376a96 Merge pull request #8009 from WilliamHolden/change_to_public_name 
Change username to public name
 2019-05-21 10:40:42 -04:00
Dannon f6011bab5b Merge pull request #7992 from jmchilton/more_packages 
Add galaxy-tool-util and galaxy-job-metrics packages.
 2019-05-20 16:36:11 -04:00
will 437833fa8b use es6 features 2019-05-20 16:07:46 -04:00
will 3419083099 Change username to public name 2019-05-20 16:01:40 -04:00
Dannon 6203e8ec9d Merge pull request #7665 from Nerdinacan/authnz 
Authnz UI and associated api
 2019-05-20 11:45:27 -04:00
Dannon Baker 444eb6eb37 Prefer const whenever possible 2019-05-20 08:48:38 -04:00
Dannon Baker 88908aa4a7 Merge remote-tracking branch 'upstream/dev' into authnz 2019-05-20 08:44:12 -04:00
Nicola Soranzo d1153b86b8 Merge branch 'release_19.05' into dev 2019-05-20 13:02:21 +01:00
Dannon cd2f5c7187 Merge pull request #8001 from WilliamHolden/dont_close_menu_on_dropdown_header_click 
Don't close popup menu if header item is clicked
 2019-05-20 07:57:20 -04:00
John Chilton fca2f4fb2b Merge pull request #8004 from mvdbeek/add_missing_commits_to_backport 
[19.05] Add missing commits from #7995 backport
 2019-05-19 16:17:46 -04:00
Nicola Soranzo 8a76eee7cf output_checker: fix superficial condition (#7980) 
output_checker: fix superficial condition
 2019-05-19 17:25:18 +01:00
Marius van den Beek a71a44b2de Merge pull request #8003 from galaxyproject/release_19.01 
Merge 19.01 into 19.05
 2019-05-19 15:12:01 +02:00
mvdbeek ecc453b646 Group with statements and clean up docstring 2019-05-19 09:30:26 +02:00
mvdbeek 9c06527bbb Simplify convert_newlines_sep2tabs 
Just call convert_newlines with a compiled regex
 2019-05-19 09:30:26 +02:00
mvdbeek b67ddbf036 Drop (seemingly?) unused sep2tabs function 2019-05-19 09:30:26 +02:00
mvdbeek 0638240c82 Operate on blocks directly 2019-05-19 09:30:26 +02:00
Marius van den Beek c60613cb9b Merge pull request #8002 from natefoo/pgcleanup-purge-user-fix 
[19.01] Fix use of pgcleanup's purge_deleted_users when there are no users to purge
 2019-05-18 10:16:25 +02:00
Björn Grüning b8f9d9a75c Merge pull request #7993 from msauria/mcooler 
Add mcool datatypeand extend h5 tool output testing
 2019-05-18 10:11:37 +02:00
John Chilton 1543c0b711 Merge pull request #8000 from jmchilton/backport_newline_stuff 
[19.05] Backport #7995
 2019-05-17 18:23:47 -04:00
Nate Coraor bd06628a3d Fix use of pgcleanup's purge_deleted_users when there are no users to 
purge
 2019-05-17 16:37:19 -04:00
John Chilton a5c010413b Merge pull request #7967 from mvdbeek/use_node_watch_for_monitoring_db 
[19.05] Use node-watch instead of fs.watch to watch for db changes
 2019-05-17 15:47:21 -04:00
mvdbeek 3c5c7a0da2 Parametrize sniff_test 2019-05-17 15:41:14 -04:00
mvdbeek b6185fc7e4 Fix line counting 2019-05-17 15:41:14 -04:00
mvdbeek 6878e3973a Fix test_sniff unittest 2019-05-17 15:41:14 -04:00
mvdbeek 06aa7d21a8 Use byte replacement strategy 2019-05-17 15:41:13 -04:00
John Chilton 6887398a49 Binary variant of convert_newlines. 2019-05-17 15:41:13 -04:00
John Chilton 0e707f2901 Improve sniffing test cases. 2019-05-17 15:41:13 -04:00
John Chilton 73b92af8d9 Binary upload fix for interaction with FilePrefix stuff. 2019-05-17 15:41:13 -04:00
John Chilton d3f2ce009e Attempt binary conversion of newlines if UTF conversion fails. 2019-05-17 15:41:13 -04:00
John Chilton 85f9ead2a2 Improved newline conversion handling. 
- Fix bug where sep2tabs didn't work with '\r\n'
- Fix bug where sep2tabs didn't work with '\r' - we were opening it with universal newlines.
- Fix memory bug where convert_newlines would read unbounded buffers - other methods still do though :(.
- Simplify convert_newlines to just let universal newline handling handle the conversion.
 2019-05-17 15:41:13 -04:00
John Chilton 6000f79b6d Fix extra newlines in peek code. 
Behavior changes:
 - Now includes a trailing new line if the input contained a trailing newline.
 - Now returns only as many lines as are present if the file contains fewer lines than LINE_COUNT.
 2019-05-17 15:41:13 -04:00
John Chilton 96d6b0508a Merge pull request #7995 from mvdbeek/jmchilton-newline_fixes 
Datatype I/O fixes
 2019-05-17 15:39:26 -04:00
will 0ad2148c7f Don't close popup menu if header item is clicked, upgrade to es6 features, and removed unused functions. 2019-05-17 15:37:28 -04:00
Nate Coraor cf7116e141 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-17 13:33:32 -04:00
Nate Coraor a6e0158672 Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-17 13:32:42 -04:00
Marius van den Beek 82052db4db Merge pull request #7999 from natefoo/pgcleanup-work-mem-fix 
[19.01] Fix variable name for work mem in pgcleanup.py
 2019-05-17 19:28:59 +02:00
John Chilton 6bcac4a8a9 Merge pull request #7939 from mvdbeek/jmchilton-objectstore_fix 
Fix non-eager object store with nested object stores
 2019-05-17 13:12:07 -04:00
msauria 7934e8e928 Fixed py3 indexing error with h5py 2019-05-17 13:07:16 -04:00