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Author SHA1 Message Date
Dannon Baker c3d4be2e2c Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 2018-09-26 09:25:54 -04:00
Dannon Baker cf62a1dafd Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 2018-09-26 09:17:26 -04:00
Dannon 71b561512d Merge pull request #6559 from jmchilton/wf_api_legacy 
[18.01] Restore the ability to track jobs for a WF invocation step.
 2018-09-26 09:02:20 -04:00
John Chilton eb1980ec08 Merge pull request #6753 from dannon/client-build-startup-changes 
[18.09] Client build startup changes
 2018-09-26 08:41:59 -04:00
John Chilton 5a97e4fcea Merge pull request #6771 from mvdbeek/fix_private_role_none 
[18.05] Use UserRoleAssociation to get private roles
 2018-09-26 08:40:59 -04:00
mvdbeek 2d9b803025 Use UserRoleAssociation to get private roles 
If I understand this correctly this should work even if the user email
changes.
 2018-09-26 13:20:06 +02:00
Dannon 46dd1801cb Merge pull request #6768 from martenson/backport_resilience_of_success_message_handling 
[18.09] backport of: Resilience of success message handling
 2018-09-25 16:50:51 -04:00
guerler 300d316ad1 Resilience of success message handling 2018-09-25 16:15:37 -04:00
John Chilton 9f688b2f91 Merge pull request #6755 from natefoo/job-object-store-fixes 
[18.09] Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok
 2018-09-25 14:19:41 -04:00
Martin Cech 529ed61c3b Merge pull request #6765 from natefoo/job-stdout-none-fix 
[18.09] Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams().
 2018-09-25 13:46:17 -04:00
Dannon a89184aa70 Merge pull request #6766 from natefoo/remove-more-slurm-warnings 
[18.09] Increase the maximum number of stderr lines that will be scanned for slurm warnings
 2018-09-25 13:13:35 -04:00
Nate Coraor a0ad5adf6f Increase the maximum number of stderr lines that will be scanned for 
slurm warnings to strip to 3.
 2018-09-25 12:57:20 -04:00
Nate Coraor de6dc00236 Don't attempt len(None), ensure stdout/stderr are strings in 
Job(Like).set_streams().
 2018-09-25 11:13:53 -04:00
Martin Cech ea7359b08b Merge pull request #6761 from jmchilton/remove_upgrade_cruft 
[18.09] Remove upgrade cruft related to datatypes.
 2018-09-24 15:55:12 -04:00
John Chilton 611764b81a Remove cruft releated to upgrading from 17.05 Galaxies. 
These interact poorly with recent changes in 18.09 and in nearly all cases should no longer be needed at this point.
 2018-09-24 14:28:46 -04:00
Dannon ac65832cb5 Merge pull request #6760 from bgruening/graph_dot 
[18.09] Add graph dot datatype and enable it in visualisations
 2018-09-24 10:42:19 -04:00
Bjoern Gruening 8d025aa4ed add graph_dot datatype to graphvis 2018-09-23 19:57:44 +02:00
Bjoern Gruening 1a19043789 add graph DOT datatype 2018-09-23 19:56:31 +02:00
Nate Coraor 679603b7c9 Catch any failures encountered while pausing/stopping jobs whose inputs 
are terminal and non-ok, so that it doesn't interrupt processing other
jobs. That was discovered because attempting to delete purged job
outputs on failure was raising ObjectNotFound since dataset object store
assignment is done later now. So also, catch that ObjectNotFound.
 2018-09-21 13:28:11 -04:00
Dannon Baker 8a4fe72f67 Merge branch 'collection_type_source_followup' into release_18.09 2018-09-21 12:55:19 -04:00
Dannon Baker e10180dea1 (minor) client-format 2018-09-21 12:52:26 -04:00
Dannon 0fb115e046 Merge pull request #6750 from jmchilton/1809_tags_walkback 
[18.09] Undo auto-propagation of group tags.
 2018-09-21 12:40:10 -04:00
Dannon Baker 3f8c2beff2 Swap to a production w/ sourcemaps build by default for autobuilder (though, of course, folks can manually do whatever -- seems like the most sensible default though) 2018-09-21 12:24:15 -04:00
Dannon Baker 4d6d984fbd Update client/README 2018-09-21 12:15:24 -04:00
Dannon Baker bd5d12049b Swap nodeenv to a pinned requirement. 2018-09-21 11:59:10 -04:00
Dannon Baker f3298953d4 Don't skip build on release/master moving forward. 2018-09-21 11:42:51 -04:00
John Chilton 7eac08979b Undo auto-propagation of group tags. 
@mvdbeek and I discussed this in the Galaxy project gitter a few weeks ago and decided the propagation is too aggressive and should likely be done manually at the end of a workflow for now - using for instance the set tags collection operation tool.
 2018-09-20 14:15:29 -04:00
Aysam Guerler 9b5045a05c Merge pull request #6747 from dannon/fix_page_editor_height 
[18.09] Fix page editor height for flex panels.
 2018-09-20 13:52:02 -04:00
Aysam Guerler 287648f5d9 Merge pull request #6725 from dannon/fix_active_highlight 
[18.09] Fix active highlight
 2018-09-20 13:41:05 -04:00
Martin Cech 3072889905 Merge branch 'release_18.05' into release_18.09 2018-09-20 11:48:45 -04:00
mvdbeek eb37ad3752 Only reset the right hand side of a connection on disconnect 2018-09-20 17:45:05 +02:00
mvdbeek 3ffbf5b4b6 Append mapped-over collection type to output collection type 
So if for instance the connected input is a regular input with a list:list input
and the output is a paired collection we set the output collection type to
list:list:paired.
 2018-09-20 17:17:05 +02:00
Dannon 02c177152b Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes 
[18.05] Backport tool version select fixes
 2018-09-20 09:41:15 -04:00
mvdbeek f65e616c1a Use mapped-over collectionType when inferring collectionType through format_source 2018-09-20 14:14:07 +02:00
Nicola Soranzo d312c48ea7 Merge pull request #6748 from jmchilton/1809_robust_sleep 
[18.09] Make newer unit tests more robust with a looped wait...
 2018-09-20 10:16:13 +01:00
Nicola Soranzo 5eb7e5ce6f Merge branch 'release_18.05' into release_18.09 2018-09-20 09:49:39 +01:00
Martin Cech d014469f07 Merge pull request #6742 from mvdbeek/fix_error_reporting 
[18.05] Fix and test anonymous error reports
 2018-09-19 21:02:05 -04:00
John Chilton 56f5bf743a Make newer unit tests more robust with a looped wait... 
... instead of raw sleep.
 2018-09-19 20:14:08 -04:00
Dannon Baker b5e2219296 Fix page editor height for flex panels. 2018-09-19 16:09:41 -04:00
Dannon Baker 87ecf1428e Use pre-fetched dataset id 2018-09-19 15:45:04 -04:00
mvdbeek f5dcf60561 Fix and test anonymous error reports 
Fixes https://github.com/galaxyproject/galaxy/issues/6675
 2018-09-19 21:00:50 +02:00
Dannon 7a22f38a2e Merge pull request #6744 from martenson/dispose-tooltip-on-delete 
[18.09] dispose of dataset tooltip when the delete is being called
 2018-09-19 13:46:33 -04:00
Dannon Baker d17ea03442 Minor formatting tweaks. 2018-09-19 13:09:48 -04:00
Dannon b64754dee9 Merge pull request #6743 from martenson/fix-favicon-uwsgi 
[18.09] fix favicon.ico for uwsgi deployments
 2018-09-19 13:00:53 -04:00
Dannon Baker 0018ab989b Add event hook for non-bb-view center panel id setting, use it for dataset visualization. 2018-09-19 12:58:46 -04:00
Dannon Baker 3f29d32898 Strip unused function, cleanup. 2018-09-19 12:54:11 -04:00
Dannon Baker 077f3088ec Correct visualization link to use router or scratchbook as appropriate. 2018-09-19 12:53:29 -04:00
Dannon Baker 4aa2b8f919 Disentangle this/self/frames in scratchbook's events. 2018-09-19 12:37:22 -04:00
Martin Cech 33eb06c9b8 remove something that should have never been where it was 
look at me, I do not know what I am doing
 2018-09-19 12:33:15 -04:00
Martin Cech b45c3531de dispose of tooltip when the delete is being called 2018-09-19 12:23:27 -04:00