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Author SHA1 Message Date
John Chilton 4a345b99c3 Fix security problems when extracting untrusted tar files. 
Fixes GX-2018-0006.
 2018-10-04 11:32:52 -04:00
John Chilton 87d2c20dbf Merge pull request #6814 from shiltemann/rulebuilder-fix 
[18.05] Fix apply rules bug in filter first/last N rows.
 2018-10-04 08:37:01 -04:00
Saskia Hiltemann e54dd1d19c build client 2018-10-04 13:38:02 +02:00
Saskia Hiltemann 266ebdb225 cast row count to integer in filter first/last N rows rule 2018-10-04 13:29:55 +02:00
John Chilton f6a5cae8e1 Merge pull request #6809 from natefoo/purge-user-fix 
[18.05] Don't delete referenced Datasets when purging users
 2018-10-01 15:50:33 -04:00
Nate Coraor b7187f0e62 Don't delete referenced Datasets when purging users. 2018-10-01 13:25:13 -04:00
Dannon 2aad3b2ced Merge pull request #6802 from mvdbeek/fix_int_parsing_rules 
[18.05] Cast rule.length to int when parsing rules
 2018-10-01 10:47:46 -04:00
Dannon de794dd905 Merge pull request #6774 from mvdbeek/fix_old_wf_name 
[18.05] Update name of Workflow when updating StoredWorkflow name
 2018-09-29 07:57:54 -04:00
mvdbeek 2d78dbb9ec Build client 2018-09-29 12:37:27 +02:00
mvdbeek c6d915b8f2 Parse length to integer 
When using the little up/down button we get strings instead of integers,
and those fail the rule validation. Fixes https://github.com/galaxyproject/galaxy/issues/6800
 2018-09-29 12:17:50 +02:00
Dannon Baker 9bc37c03b6 Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 2018-09-28 12:48:42 -04:00
Dannon Baker ac46d21ece Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 2018-09-28 12:46:20 -04:00
Dannon Baker 40cecf6ff4 Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 2018-09-28 12:43:36 -04:00
Dannon Baker c4150d2002 Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 2018-09-28 12:38:23 -04:00
Dannon Baker fa7f2a4f5c Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 2018-09-28 12:37:49 -04:00
Dannon Baker 809ae58c52 Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 2018-09-28 12:37:20 -04:00
Dannon Baker 8a1616aaf8 Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 2018-09-28 12:36:48 -04:00
Dannon Baker 482f1ea359 Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 2018-09-28 12:35:30 -04:00
John Chilton f3ba9e2b9e Merge pull request #6796 from dannon/peek_drop 
[16.01] Drop unused peek method
 2018-09-28 12:09:38 -04:00
Dannon Baker 814c7f926d Drop unused peek method (this used unencoded ids) 2018-09-28 11:50:18 -04:00
mvdbeek 364e7e1f1f Update name of Workflow when updating StoredWorkflow name 
Fixes https://github.com/galaxyproject/galaxy/issues/6773.
 2018-09-26 16:47:05 +02:00
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 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 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
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
Martin Cech 8400417445 Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 
[18.05] Decode tool id and version in the client, not in the API
 2018-09-19 10:58:42 -04:00
mvdbeek 3017568e77 Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test 2018-09-19 16:40:59 +02:00
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 94082a878d Unit test that fails if we don't return the latest version upon version mismatch 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
Nicola Soranzo 35754dc49a Fix symlinking during plugin staging 
Remove also broken symlinks before creating the new ones.
 2018-09-19 11:16:54 +01:00
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
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
Dannon f513594c31 Merge pull request #6707 from martenson/unqoute_tool_version 
[18.05] unquote the tool_version in the tools API
 2018-09-14 09:16:44 -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
Dannon 1dacc35332 Merge pull request #6703 from davebx/updates_api 
[18.05] Add missing route for API endpoint.
 2018-09-12 13:31:21 -04:00
Dave B bddabe3029 Add missing route for API endpoint. 2018-09-12 12:28:10 -04:00
Marius van den Beek 2a79ae0ce1 Merge pull request #6691 from jmchilton/backport_6326 
[18.05] Backport #6326
 2018-09-12 10:25:03 +02:00
John Chilton a937bc5539 Client build. 2018-09-11 11:22:02 -04:00
Sebastian Kapust 4fc9fe2150 Fix target update for rule collection builder after input selection 2018-09-11 09:39:25 -04:00
Nate Coraor 9217680ab6 Merge pull request #6647 from dannon/page_fixes 
[18.05] Pages - fixes for encoded ids in the database
 2018-09-10 16:21:46 -04:00