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Author SHA1 Message Date
John Chilton a25aed5781 Optimization for dataset deletion - don't check jobs if dataset terminal. 2019-04-10 20:59:33 -04:00
John Chilton d89749bad7 Bulk delete and hide operations. 2019-04-10 20:59:33 -04:00
Nate Coraor 8d5b155f1a Merge pull request #7694 from jmchilton/fix_pulsar_metadata 
Fix pulsar remote metadata with metadata_strategy == 'directory'.
 2019-04-10 09:02:31 -04:00
Helena Rasche 6be36b8253 Merge pull request #7690 from guerler/fix_side_panel_styles 
Fix side panel styling, adjust appearance in reports
 2019-04-10 14:07:08 +02:00
Marius van den Beek 45726e64b5 Merge pull request #7708 from nsoranzo/alternative_to_7093 
Improve error message if GFF file is missing attribute col
 2019-04-10 09:12:36 +02:00
Dannon c4486eeb1e Merge pull request #7709 from natefoo/drmaa-runner-param-fix 
Fix runner param validation in the DRMAA runner
 2019-04-09 19:50:22 -04:00
Daniel Blankenberg d05ee64e64 Merge pull request #7703 from mvdbeek/update_pytest_postgresql 
Update pytest-posgresql to 1.4.0, which removes a hard dependency on psycopg2
 2019-04-09 16:02:59 -04:00
Marius van den Beek d8284f1ff5 Merge pull request #7342 from bernt-matthias/topic/verify_bam 
Fall back to binary comparison if BAM conversion fails
 2019-04-09 22:01:13 +02:00
Nate Coraor d4aa845ce7 Fix runner param validation in the DRMAA runner 2019-04-09 15:41:20 -04:00
Nicola Soranzo 2d5db1efb1 More natural checks 2019-04-09 20:23:29 +01:00
Marius van den Beekandnsoranzo 6989746306 More natural check 
Co-Authored-By: nsoranzo <nicola.soranzo@gmail.com>
 2019-04-09 20:20:14 +01:00
Nicola Soranzo 22fe708b8b Improve error message if GFF file is missing attribute col 2019-04-09 19:45:54 +01:00
Nicola Soranzo b8285b6e43 Merge pull request #6437 from martenson/declutter-history-menu 
declutter the history 'cog' menu
 2019-04-09 18:52:33 +01:00
mvdbeek 20492cbe00 Update to 1.4.0, which removes a hard dependency on psycopg2 2019-04-09 18:48:07 +02:00
John Chilton ee770ca78b Merge pull request #7702 from bebatut/fix_mtx_sniff 
Relax the 1st line sniffing for mtx (not only real coordinate)
 2019-04-09 12:42:51 -04:00
John Chilton da26bfdc75 Merge pull request #7683 from mvdbeek/implicit_conversion_for_collection_parameters 
Implicit conversion for input collection parameters
 2019-04-09 10:55:17 -04:00
Martin Cech 1075a0e6bc Merge pull request #7659 from jmchilton/format2_import_default 
Allow import of format2 workflows by default for 19.05.
 2019-04-09 10:50:45 -04:00
John Chilton ecd1ac87e8 Merge pull request #7643 from dannon/popup-cors-errmsg 
popup-menu.js error handling tweaks
 2019-04-09 10:46:32 -04:00
John Chilton 568587bbd2 Merge pull request #7609 from VJalili/cloudauthz_post 
Add a PUT api for CloudAuthz
 2019-04-09 10:35:16 -04:00
John Chilton 49839a07a4 Merge pull request #7597 from VJalili/cloud_api_config_format 
Serialize the config attribute of an authnz record as a json object.
 2019-04-09 10:33:10 -04:00
John Chilton 01e3960c9a Merge pull request #7590 from erasche/fix-rstudio 
Fix RStudio GIE
 2019-04-09 10:32:20 -04:00
John Chilton 16109e8f85 Merge pull request #7587 from jj-umn/datatype_imgtjson 
Add ImgtJson datatype for IMGT immune system libraries
 2019-04-09 10:31:38 -04:00
Bérénice Batut 7816f90bbf Relax the 1st line sniffing for mtx (not only real coordinate) 2019-04-09 16:19:00 +02:00
Daniel Blankenberg ff1313f08b Merge pull request #7697 from dannon/genomespace_error_detection 
Fix genomespace exporter tool
 2019-04-09 09:36:34 -04:00
Dannon 3ed1e638d6 Merge pull request #7698 from nsoranzo/update_citation 
Update CITATION to latest Galaxy update paper
 2019-04-09 09:00:13 -04:00
Dannon 96a8e6abc2 Merge pull request #7569 from bebatut/add_mtx 
Add mtx datatype
 2019-04-09 08:53:03 -04:00
Nicola Soranzo 3e21adfd46 Update CITATION to latest Galaxy update paper 2019-04-09 13:00:59 +01:00
Nicola Soranzo b32626da45 Merge pull request #7696 from bebatut/fix_biom1 
Patch for metadata setting of minimal BIOM1 files
 2019-04-09 12:58:23 +01:00
Dannon 421e77eb65 Merge pull request #7695 from nsoranzo/model_migrations 
More refactoring of model migrations
 2019-04-09 07:28:58 -04:00
Dannon Baker 3366a5805b Specify profile and look for exit codes for genomespace tool -- warnings cause failures otherwise 2019-04-09 07:24:05 -04:00
Bérénice Batut 1e1803d759 Add extra column metadata check for minimal biom1 file 2019-04-09 10:04:41 +02:00
guerler e8fe0556f7 Remove unused styles from reports style definition 2019-04-08 21:42:00 -04:00
Nicola Soranzo 8d8a125a44 More migration refactoring 2019-04-09 01:06:31 +01:00
Nicola Soranzo 7ee93c0995 Fix 4 index names in old migrations 
Prevent the creation of duplicated indexes for new databases:
`ix_user_deleted`, `ix_user_form_values_id`, `ix_user_purged` and
`ix_user_username` are duplicates of `ix_galaxy_user_*` indexes created in
migration 106.

Also:
- use `util` methods
- fix the order of dropping tables in migration 14.
 2019-04-09 00:29:47 +01:00
Nicola Soranzo 9498ae5d4e Refactor migrations adding indexes 2019-04-09 00:29:47 +01:00
John Chilton 74a6615488 Fix pulsar with metadata_strategy == 'directory'. 2019-04-08 16:30:15 -04:00
John Chilton 60c357ecdf Merge pull request #7693 from dannon/fix-custos-authnz 
Deconflict migration versions for custos authnz
 2019-04-08 16:24:42 -04:00
Dannon Baker 6467a72eb7 Deconflict migration versions for custos authnz 2019-04-08 16:23:56 -04:00
Enis Afgan a8dc13da53 Merge pull request #7195 from machristie/keycloak-integration 
Custos integration
 2019-04-08 16:15:41 -04:00
Dannon e705758410 Merge pull request #7647 from blankenberg/genomespace-importer-fix 
Fix genomespace_importer tool
 2019-04-08 15:38:05 -04:00
Aysam Guerler 1efd748d77 Merge pull request #7689 from dannon/plugin_staging_fixes 
Plugin static staging fix
 2019-04-08 15:13:33 -04:00
John Chilton 2206194f9a Merge pull request #7651 from jmchilton/dictifiable_tool_outputs 
Implement functional dict-ifiable tool outputs and error detection.
 2019-04-08 14:04:03 -04:00
guerler 39c1908a0a Restore comments in theme 2019-04-08 14:01:25 -04:00
Dannon Baker a98ded70ba Merge branch 'openid_support' into dev 2019-04-08 14:01:12 -04:00
Dannon Baker 581d8e2b39 Client format 2019-04-08 14:01:04 -04:00
Martin Cech 68ee8e2599 Merge pull request #7691 from VJalili/oidc_docs 
Add docs to OIDC backends configuration file.
 2019-04-08 14:00:55 -04:00
vahid 2786abb70e Add docs to OIDC backends configuration file. 2019-04-08 10:55:21 -07:00
guerler 8ab1dd500e Fix styles in reports app 2019-04-08 13:38:51 -04:00
guerler 34a0f14153 Improve style description of tool panel 2019-04-08 12:56:00 -04:00
mvdbeek 5dc46f9d33 Enable implicit conversion of collection inputs 2019-04-08 18:34:31 +02:00