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Author SHA1 Message Date
Dave B 7090f836a3 Modest refactoring of the migration stages code. 2019-04-12 15:33:49 +01:00
Nicola Soranzo 06ec2d6e4c Merge branch 'release_19.01' into dev 2019-04-12 15:02:11 +01:00
Nicola Soranzo 0bfebb4e84 Merge branch 'release_18.09' into release_19.01 2019-04-12 14:35:03 +01:00
Nicola Soranzo 177a2a1cf3 Merge branch 'release_18.05' into release_18.09 2019-04-12 13:02:12 +01:00
Marius van den Beek 5d1df57f7f Merge pull request #7725 from nsoranzo/release_18.05_more_ci_backports 
[18.05] Backport other CI config changes
 2019-04-12 09:51:28 +02:00
Nicola Soranzo d4030757f9 Backport other CI config changes 
`py35-unit` and `py35-first_startup` jobs were green on CircleCI, but doing
nothing.
Remove duplicated jobs from TravisCI.
 2019-04-11 20:04:26 +01:00
John Chilton 9dfa5d7041 Merge pull request #5495 from jmchilton/batch_operation_optimize 
Batch bulk hide and delete operations when multi-selected.
 2019-04-11 09:01:32 -04:00
John Chilton 8e4ded48b0 Cleanup stray comments, logging 2019-04-10 23:51:30 -04:00
John Chilton fc0b9d9572 Merge pull request #7717 from nsoranzo/followup_on_7569 
Fix mtx datatype sniffer configuration
 2019-04-10 23:50:34 -04:00
John Chilton faeb7aecf1 Merge pull request #7722 from nsoranzo/fix_GALAXY_RUN_ALL_macOS 
Fix (re)starting Galaxy using paste, ``GALAXY_RUN_ALL=1`` and ``--wait`` under macOS
 2019-04-10 23:49:36 -04:00
John Chilton b07027b0ae Merge pull request #7716 from nsoranzo/fix_7714 
Fix uWSGI startup with separate ini file under Python 3
 2019-04-10 23:49:08 -04:00
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
Nicola Soranzo 69ac88f319 Fix (re)starting Galaxy using paste, `GALAXY_RUN_ALL=1 and --wait` under macOS 
xref. https://github.com/galaxyproject/bioblend/commit/99d05e6ad697edc82c58f8ce7302be2a005c6933
 2019-04-11 01:33:21 +01:00
Nicola Soranzo a12db037ca Merge branch 'release_19.01' into dev 2019-04-11 00:43:45 +01:00
Nicola Soranzo aa6993e937 Fix mtx datatype sniffer configuration 
Follow-up on https://github.com/galaxyproject/galaxy/pull/7569

Fix the following exception at Galaxy startup:
```
galaxy.datatypes.registry ERROR 2019-04-10 19:07:33,159 [p:3319,w:0,m:0] [MainThread] Error calling method mtx from class <module 'galaxy.datatypes.tabular' from 'lib/galaxy/datatypes/tabular.pyc'>
Traceback (most recent call last):
  File "lib/galaxy/datatypes/registry.py", line 485, in load_datatype_sniffers
    aclass = getattr(module, datatype_class_name)()
AttributeError: 'module' object has no attribute 'mtx'
```
 2019-04-10 19:00:57 +01:00
Nicola Soranzo 9bbb200f23 Fix uWSGI startup with separate ini file under Python 3 
Ensure ``config_file`` is a Unicode string.

Fix #7714.
 2019-04-10 16:54:48 +01:00
John Chilton 716b8886da Merge pull request #7711 from mvdbeek/fix_workflow_invocations_inaccessible 
[19.01] Restrict workflow invocation index to current user
 2019-04-10 09:50:33 -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
mvdbeek 4c9e4118f5 Restrict workflow invocation index to current user 
If the user is not an admin.
Fixes https://github.com/galaxyproject/galaxy/issues/7710

An alternative would be to skip Accessibility / Ownership
exceptions, but given that we can just restrict the query
this seems like the better approach to me.
 2019-04-10 11:13:59 +02:00
Björn Grüning 78ad61506f Merge pull request #7699 from mvdbeek/fix_sort_tool_too_stringent 
[19.01] Only check for exit code on actual sort command
 2019-04-10 10:33:36 +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 aa008a650b Restore check_call for sed 2019-04-09 20:26:27 +01:00
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
Martin Cech 22c3895bf4 Merge pull request #7705 from dannon/backport-genomespace-fix 
[19.01] Backport GenomeSpace Exporter fix
 2019-04-09 14:08:02 -04:00
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
Dannon Baker c521decf32 Specify profile and look for exit codes for genomespace tool -- warnings cause failures otherwise 2019-04-09 13:34:06 -04:00
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
mvdbeek 68423aa361 Cleanup sorter.py 
Feed open output file to Popen instead of using stdout redirection in
command string.
 2019-04-09 15:35:21 +02:00
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
mvdbeek 45a0ff6173 Only check for exit code on actual sort command 2019-04-09 14:02:10 +02:00
Nicola Soranzo 3e21adfd46 Update CITATION to latest Galaxy update paper 2019-04-09 13:00:59 +01:00