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18589 Commits
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
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
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
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
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
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 bd5d12049b Swap nodeenv to a pinned requirement. 2018-09-21 11:59:10 -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
Martin Cech 3072889905 Merge branch 'release_18.05' into release_18.09 2018-09-20 11:48:45 -04:00
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
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
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 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
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
Nicola Soranzo 4ce8086c20 Merge branch 'release_18.05' into release_18.09 2018-09-19 16:58:46 +01:00
Martin Cech 420f43645a map the favicon in uwsgi config 2018-09-19 11:52:35 -04:00
mvdbeek 5635a05a2a Look up collection_type if collection_type_source is set 
We do this in the wf-editor and in the backend, so this works for
subworkflows. This should make quite some tools more usable in a
workflow scenario. Should fix
- https://github.com/galaxyproject/galaxy/issues/6514
- https://github.com/galaxyproject/galaxy/issues/6012
- https://github.com/galaxyproject/galaxy/issues/6569
- https://github.com/galaxyproject/galaxy/issues/1889
and perhaps more issues related to this.
 2018-09-19 09:48:25 -04:00
mvdbeek f6f526a0a5 Use tool_version instead of version parameter 
To be consistent with other routes that accept this parameter.
 2018-09-19 15:39:00 +02:00
mvdbeek 3ea9d086bf Sort rval so that newest tool appears last in rval 2018-09-19 15:39:00 +02:00
mvdbeek c8552970dd Sort by tool version when picking a tool with an unavailable version 2018-09-19 15:39:00 +02:00
mvdbeek 806beaca9b Test that newest version will be returned if tool id or version don't match 2018-09-19 15:39:00 +02:00
John Chilton 5121275c1d Remove stray debug statement. 2018-09-19 08:38:41 -04:00
Nicola Soranzo 7f38e61cae Remove again lib/galaxy/dependencies/requirements.txt 
It was reintroduced (empty) by mistake in
https://github.com/galaxyproject/galaxy/pull/4474 .
 2018-09-19 10:18:02 +01:00
Nicola Soranzo 18d99deb95 Decode tool id and version in the client, not in the API 
using `decodeUriComponent` from `decode-uri-component` JS package.

Revert https://github.com/galaxyproject/galaxy/pull/6707

Remove unused `_get_tool()` method in
`lib/galaxy/webapps/galaxy/api/workflows.py` .

Rebuild client with:
```
make client-production-maps
```
 2018-09-19 10:17:26 +01:00
Dannon 8462df83c9 Merge pull request #6723 from blankenberg/18.09-loom 
[18.09] Add Loom datatype and remove rdata.seurat
 2018-09-18 14:10:01 -04:00
Dannon 0974b130ef Merge pull request #6730 from nsoranzo/release_18.09_backport_6722 
[18.09] Partial backport of #6722
 2018-09-18 08:32:16 -04:00
Nicola Soranzo 8982212d39 Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter() 2018-09-18 10:06:13 +01:00
Nicola Soranzo 8ed19a3a09 async is a reserved keyword in Python 3.7 
- Remove unused `async` parameter of `stage_data_async()` method.
- Rename `async` parameter of `quick_load()` method.

Fix https://github.com/galaxyproject/galaxy/issues/6717 .

xref. https://github.com/galaxyproject/galaxy/issues/1715
 2018-09-18 10:06:01 +01:00
Nicola Soranzo 54d137edab Remove deprecated decode_param_names parameter 
It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 .
 2018-09-18 10:05:47 +01:00
Martin Cech 17d67e24c0 use bleach isntead of custom regex 
thanks @nsoranzo
 2018-09-17 15:31:30 -04:00
Martin Cech b7f1622857 replace the replacement for newline 
from empty string to space, that should avoid unwanted word merges
 2018-09-17 13:58:06 -04:00
Martin Cech 072d40f3e9 remove html tags and newlines from the help text 
this should improve the toolsearch for certain keywords
and also make the search index smaller
 2018-09-17 13:52:12 -04:00
Daniel Blankenberg f06da87189 remove comment 2018-09-17 10:19:31 -04:00
Daniel Blankenberg dfff5c9663 Add Loom datatype and remove rdata.seurat. 2018-09-17 09:00:40 -04:00
Martin Cech 6993dbb6fc Merge pull request #6705 from natefoo/slurm-cgroup-enospc 
[18.05] Catch additional permutations of Slurm cgroup creation warnings
 2018-09-14 15:38:18 -04:00
Nate Coraor 3d508a01d3 Improvements from @nsoranzo 2018-09-14 14:39:01 -04:00
Martin Cech 1b6d422afd unquote similarly to previous commit but in the workflow controller 2018-09-13 13:00:18 -04:00
Martin Cech f7c1d31dbc unquote the tool_version in the tools API 
if the tool version includes '+', which is a recommended way
of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-versions
this would fail the comparison down the line in the toolbox.get_tool() method

this commit also downgrades the unquote_plus to unquote for tool_id
for similar reasons since it also contains the version
 2018-09-12 14:49:10 -04:00
Nate Coraor 7e2a77e8af Catch additional permutations of Slurm cgroup creation warnings 2018-09-12 13:59:26 -04:00
Dave B bddabe3029 Add missing route for API endpoint. 2018-09-12 12:28:10 -04:00
John Chilton 471162eadb [18.09] Fix new extract dataset to perserve collection element identifier. 2018-09-11 14:01:36 -04:00
Dannon Baker be04959cf3 Update version to 18.09.rc1 2018-09-10 18:52:44 -04:00
Dannon ebc5858f02 Merge pull request #6660 from VJalili/upgrade_cloudbridge 
Upgrade CloudBridge to v1.0.1
 2018-09-10 17:32:30 -04:00
Dannon Baker b8fe2fe294 Merge branch 'release_18.05' into dev 2018-09-10 17:31:24 -04:00