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Author SHA1 Message Date
Martin Cech 9c9c8a5d50 Merge pull request #7239 from dannon/node_ver_pin_18.09 
[18.09] Add/pin configurable node version
 2019-02-11 21:28:46 -05:00
Marius van den Beek c8b3d5e4c4 Merge pull request #7275 from jmchilton/1901_migrate_tools 
[18.09] Stop tool migrations checking by default...
 2019-01-29 15:29:22 +01:00
John Chilton d83db6a537 Stop with tool migrations by default, they are not needed in modern Galaxies... 
... and even problematic in some ways.
 2019-01-27 15:48:16 -05:00
Dannon 6a660e9893 Merge pull request #7253 from mvdbeek/fix_install_in_manage_tools_grid 
[18.09] Fix install operation in installed_repository_grid
 2019-01-24 13:19:27 -05:00
Dannon f0bd2df6d4 Merge pull request #7265 from nsoranzo/release_18.09_sqlalchemy-migrate_0.12.0 
[18.09] Update sqlalchemy-migrate requirement to 0.12.0
 2019-01-24 08:54:29 -05:00
Nicola Soranzo 1a4c1ec514 Merge pull request #7258 from mvdbeek/fix_workflow_uuid_access 
[18.09] Not all workflow outputs have a UUID
 2019-01-24 11:52:04 +00:00
Nicola Soranzo 5adfa81a8b Update sqlalchemy-migrate requirement to 0.12.0 
Fix https://github.com/galaxyproject/galaxy/issues/7159
 2019-01-24 10:56:43 +00:00
mvdbeek f2a454c776 Fix output uuid comparison 2019-01-24 11:25:37 +01:00
mvdbeek 35fe3bf716 Not all workflow outputs have a UUID 2019-01-23 16:00:50 +01:00
mvdbeek eb406cc210 Fix install operation in installed_repository_grid 
The incoming url keywords look like this:
```
operation=install&id=ebfb8f50c6abde6d?async=false&sort=name&page=1&show_item_checkboxes=true&advanced_search=false&operation=install&id=ebfb8f50c6abde6d
```
and the id parameter gets parsed into a list:
```
['ebfb8f50c6abde6d?async=false', 'ebfb8f50c6abde6d']
```

Obviously there's something wrong in the grid or mako,
but this works fine.

Fixes https://github.com/galaxyproject/galaxy/issues/5619
 2019-01-22 20:10:12 +01:00
John Chilton 920f07369d Merge pull request #7252 from mvdbeek/fix_shed_tool_conf_parsing 
[18.09] strip() text when parsing xml
 2019-01-22 13:56:01 -05:00
mvdbeek 31c71fbd6f strip() text when loading xml 
Should fix https://github.com/galaxyproject/galaxy/issues/7250.
 2019-01-22 11:30:49 +01:00
Dannon Baker a10d2c51d3 Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220) 2019-01-18 11:54:59 -05:00
John Chilton 889c1026c0 Merge pull request #7227 from mvdbeek/fix_workflow_loading_saving 
[18.09] Properly deal with missing tools in workflows
 2019-01-18 11:04:16 -05:00
mvdbeek 6f861dec7e Overridde __init__ for ToolMissingException 2019-01-18 13:52:52 +01:00
mvdbeek b1b1d848d3 Fix loading subworkflows 2019-01-17 16:00:36 +01:00
mvdbeek 54aecb3f31 Properly deal with missing tools in subworkflows 
If a subworkflow is missing tools the entire parent workflow couldn't
be loaded into the editor, because we raised an exception. This is now
only logged as an error. On the user side we now prevent running and
saving such workflows by actually implementing the `get_errors` method
for the SubWorkflowModule class.

This should fix https://github.com/galaxyproject/galaxy/issues/7140.
 2019-01-17 13:41:21 +01:00
Dannon 105a1d8a61 Merge pull request #7201 from mvdbeek/fix_view_metadata_error 
[18.09] Fix error in view_tool_metadata
 2019-01-11 09:19:39 -05:00
Martin Cech a7ae521597 Merge branch 'release_18.05' into release_18.09 2019-01-10 13:01:44 -05:00
Martin Cech c17c20b8cf Merge pull request #7181 from dannon/page_save_history_fix 
[18.05] Fix hda accessibility check in Page's renderForSave name fetching
 2019-01-10 13:00:54 -05:00
Nicola Soranzo 141c2a1ef3 Fix indentation 
Broken in commit cf2645f9a6 .
 2019-01-10 16:16:58 +00:00
mvdbeek 338020f2a5 Fix error in view_tool_metadata (https://sentry.galaxyproject.org/sentry/toolshed/issues/294272/) 2019-01-10 16:59:31 +01:00
Nicola Soranzo c4ad6b9e4b Merge branch 'release_18.05' into release_18.09 2019-01-09 18:56:53 +00:00
Dannon ce1a1ee778 Merge pull request #7180 from martenson/security-ts 
[18.09] Prevent XSS on toolshed when browsing repo changeset
 2019-01-09 09:07:35 -05:00
John Chilton 6256ac0f11 Merge pull request #7190 from martenson/fix-permission-api 
[18.09] fix library dataset permission API
 2019-01-09 08:53:09 -05:00
Martin Cech 193f5eae6e call the method through the proper manager 2019-01-08 14:43:52 -05:00
Martin Cech 29abf8f437 refactor approach so the method is inherited to ldda 2019-01-08 14:01:39 -05:00
Martin Cech 5e3ebb13c0 fix import ordering, thanks @nsoranzo 2019-01-08 13:53:40 -05:00
Martin Cech 2e82b7f8c0 fix library dataset permission API 
broken in refactoring
 2019-01-08 13:42:43 -05:00
Martin Cech f6b978be8c prevent XSS on toolshed when browsing repo changeset 
fix invalid changeset ts test, fix flake8

Revert "fix invalid changeset ts test, fix flake8"

This reverts commit 84864fe82a9f3b9ffa1cd5ef272f979e867e2002.

tweak the invalid changeset test and add a new one
 2019-01-08 12:52:28 -05:00
Dannon 2a17860fad Merge pull request #7128 from natefoo/slurm-trace-log-fix 
[18.05] Fix for use of `log.trace` in Slurm runner
 2019-01-07 14:31:35 -05:00
Dannon Baker 998eb85856 Fix hda accessibility check in Page's renderForSave name fetching 2019-01-07 11:47:22 -05:00
Nate Coraor d4c6921862 Fix for use of log.trace in Slurm runner 2018-12-18 13:39:53 -05:00
Nicola Soranzo 65ca25ed66 Merge branch 'release_18.05' into release_18.09 2018-12-16 22:56:39 +00:00
Nicola Soranzo bfc634e415 Merge branch 'release_18.01' into release_18.05 2018-12-16 22:54:49 +00:00
Nicola Soranzo 6feef2a280 Merge branch 'release_17.09' into release_18.01 2018-12-16 22:53:32 +00:00
Nicola Soranzo fdd9a091f8 Merge branch 'release_17.05' into release_17.09 2018-12-16 22:44:54 +00:00
Nicola Soranzo 06cfb7e206 Merge branch 'release_17.01' into release_17.05 2018-12-16 22:43:37 +00:00
Nicola Soranzo 1b30a9a1b9 Merge branch 'release_16.10' into release_17.01 2018-12-16 22:42:04 +00:00
Nicola Soranzo a2e70ef67e Merge branch 'release_16.07' into release_16.10 2018-12-16 22:40:26 +00:00
Nicola Soranzo f3c81816db Merge branch 'release_16.04' into release_16.07 2018-12-16 22:36:18 +00:00
Nicola Soranzo 87fa609396 Merge branch 'release_16.01' into release_16.04 2018-12-16 22:29:19 +00:00
Nicola Soranzo 8f14121518 Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 
[16.01] Backport #2383
 2018-12-16 22:28:21 +00:00
Martin Cech 7dd7d8a5e9 Merge pull request #7078 from mvdbeek/fix_peek_for_running_datasets 
[18.09] Fix set_peek method for copied datasets
 2018-12-12 13:24:08 -05:00
Martin Cech 4df43adae6 Merge pull request #7074 from dannon/fix_for_facebook_auth 
[18.09] Fix welcome on redirect from facebook auth
 2018-12-12 13:23:39 -05:00
Björn Grüning 6db721915f Merge pull request #7041 from erasche/fix-grt 
[18.09] GRT: Rip out all parameters, round file sizes
 2018-12-12 19:22:32 +01:00
Nicola Soranzo efe84751a7 Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 2018-12-11 22:22:01 +00:00
Nate Coraor b10cfa43ac Remove unused $GXPIP_VERSION 2018-12-11 22:01:24 +00:00
Nate Coraor 0e5c96ef37 Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in 
pip >= 8.1).
 2018-12-11 22:01:13 +00:00
John Chilton 3a1bdd0ea6 Merge pull request #7092 from martenson/boto-workaround 
[18.09] boto cfg workaround
 2018-12-11 16:23:59 -05:00