| 80aa2f8 | Nate Coraor | 05 August 2020, 14:19:48 UTC | Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 | 05 August 2020, 14:19:48 UTC |
| 0299798 | Nate Coraor | 05 August 2020, 14:18:15 UTC | Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 | 05 August 2020, 14:18:15 UTC |
| 9cdfd18 | Dannon | 05 August 2020, 14:05:28 UTC | Merge pull request #10069 from natefoo/semicolon-uwsgi-pass [18.01] Add missing semicolon to uwsgi_pass directive in nginx docs | 05 August 2020, 14:05:28 UTC |
| 10a456b | Nate Coraor | 05 August 2020, 13:41:56 UTC | Add missing semicolon to uwsgi_pass directive in nginx docs | 05 August 2020, 13:41:56 UTC |
| 359fadc | Nicola Soranzo | 12 December 2019, 18:04:22 UTC | Merge branch 'release_18.05' into release_18.09 | 12 December 2019, 18:04:22 UTC |
| b7a2fdb | Nicola Soranzo | 12 December 2019, 18:02:32 UTC | Merge branch 'release_18.01' into release_18.05 | 12 December 2019, 18:02:32 UTC |
| a429433 | Nicola Soranzo | 12 December 2019, 18:00:31 UTC | Merge branch 'release_17.09' into release_18.01 | 12 December 2019, 18:00:31 UTC |
| b04b3d9 | Nicola Soranzo | 12 December 2019, 17:59:09 UTC | Merge branch 'release_17.05' into release_17.09 | 12 December 2019, 17:59:09 UTC |
| e0a06a3 | Nicola Soranzo | 12 December 2019, 17:48:38 UTC | Merge branch 'release_17.01' into release_17.05 | 12 December 2019, 17:48:38 UTC |
| 61e6fd1 | Nicola Soranzo | 12 December 2019, 17:43:26 UTC | Merge branch 'release_16.10' into release_17.01 | 12 December 2019, 17:43:26 UTC |
| 267037f | Nicola Soranzo | 12 December 2019, 17:42:02 UTC | Merge branch 'release_16.07' into release_16.10 | 12 December 2019, 17:42:02 UTC |
| 6c02000 | Nicola Soranzo | 12 December 2019, 17:30:59 UTC | Merge branch 'release_16.04' into release_16.07 | 12 December 2019, 17:30:59 UTC |
| 48510a2 | John Chilton | 12 December 2019, 16:37:38 UTC | Merge pull request #9089 from nsoranzo/release_16.04_extra-index-url [16.04] Explicitly include PyPI as an ``--extra-index-url`` to pip | 12 December 2019, 16:37:38 UTC |
| aca9490 | Nicola Soranzo | 10 December 2019, 23:21:29 UTC | Explicitly include PyPI as an ``--extra-index-url`` to pip Backport combining commits 244fc834cd4dd3980cc3edb755d22ca5a9372421 and 09fdac513d59ca6dad440616a53daa97751ff905 . This is now needed because wheels.galaxyproject.org is not a full-fledged pypiserver any more but just an S3 bucket served via a CDN. | 10 December 2019, 23:29:06 UTC |
| 2f21e73 | Björn Grüning | 01 June 2019, 08:50:02 UTC | [18.09] Backport 8023: Fix ColumnSetAction post job action (#8069) [18.09] Backport 8023: Fix ColumnSetAction post job action | 01 June 2019, 08:50:02 UTC |
| 4425697 | mvdbeek | 23 May 2019, 13:07:17 UTC | Fix ColumnSetAction post job action If columns are specified as integers this would fail currently. Reported by Peter Briggs on the [mailing list](https://lists.galaxyproject.org/archives/list/galaxy-dev@lists.galaxyproject.org/thread/PXLCVKIZ5LW3MLI6333PFMANYGOCDLD2/) | 31 May 2019, 08:44:45 UTC |
| 177a2a1 | Nicola Soranzo | 12 April 2019, 12:02:12 UTC | Merge branch 'release_18.05' into release_18.09 | 12 April 2019, 12:02:12 UTC |
| 5d1df57 | Marius van den Beek | 12 April 2019, 07:51:28 UTC | Merge pull request #7725 from nsoranzo/release_18.05_more_ci_backports [18.05] Backport other CI config changes | 12 April 2019, 07:51:28 UTC |
| d403075 | Nicola Soranzo | 11 April 2019, 18:44:45 UTC | Backport other CI config changes `py35-unit` and `py35-first_startup` jobs were green on CircleCI, but doing nothing. Remove duplicated jobs from TravisCI. | 11 April 2019, 19:04:26 UTC |
| d20cbad | Nicola Soranzo | 01 April 2019, 17:04:36 UTC | Merge pull request #7626 from martenson/18.09.backport-xss [18.09] backport xss | 01 April 2019, 17:04:36 UTC |
| a07c99d | Martin Cech | 29 March 2019, 20:40:35 UTC | prevent XSS on old style-mako and expand to the messageLarge method | 01 April 2019, 15:31:17 UTC |
| 6230d93 | Nicola Soranzo | 29 March 2019, 13:18:33 UTC | Use bleach to clean msg which will not strip safe HTML tags and attributes, which we use. Also, restrict the possible values of `status` instead of trying to escape it. | 29 March 2019, 18:16:40 UTC |
| 76af203 | Nicola Soranzo | 29 March 2019, 03:02:51 UTC | Encode content before writing to temp file | 29 March 2019, 18:15:24 UTC |
| 623a3b8 | Martin Cech | 27 March 2019, 18:04:33 UTC | check for validity of user-given changesets | 29 March 2019, 18:15:16 UTC |
| 2899cf3 | Dannon Baker | 22 March 2019, 20:36:20 UTC | Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 | 22 March 2019, 20:36:20 UTC |
| 76643a2 | Dannon | 22 March 2019, 20:34:56 UTC | Merge pull request #7583 from martenson/backportcci [18.05] backport circleci testing | 22 March 2019, 20:34:56 UTC |
| a9d2119 | Martin Cech | 22 March 2019, 17:31:18 UTC | drop jslint | 22 March 2019, 17:31:18 UTC |
| 173cb18 | Martin Cech | 22 March 2019, 17:08:09 UTC | downgrade to node9 images | 22 March 2019, 17:08:09 UTC |
| 6543d47 | Martin Cech | 22 March 2019, 16:43:14 UTC | backport circleci testing | 22 March 2019, 16:43:14 UTC |
| 7b31621 | Nicola Soranzo | 11 March 2019, 14:07:44 UTC | Merge pull request #7504 from mvdbeek/logging_fix [18.09] Fix warning message formatting in sharing controller | 11 March 2019, 14:07:44 UTC |
| 98a189c | mvdbeek | 11 March 2019, 12:23:37 UTC | Fix warning message formatting in sharing controller Reported by @erasche in https://github.com/galaxyproject/galaxy/issues/7503#issuecomment-471496500, broken in https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae161f031f8da9eb | 11 March 2019, 12:25:54 UTC |
| 8e125b7 | Nicola Soranzo | 10 March 2019, 21:36:15 UTC | Merge branch 'release_18.05' into release_18.09 | 10 March 2019, 21:36:15 UTC |
| 0ab05b3 | Dannon | 10 March 2019, 20:18:56 UTC | Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 [18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins | 10 March 2019, 20:18:56 UTC |
| c1a9095 | Nicola Soranzo | 10 March 2019, 12:51:50 UTC | Restrict loading of JSON files on the server via the workflow API to Galaxy admins Fix https://github.com/galaxyproject/security/issues/29 | 10 March 2019, 12:52:02 UTC |
| 996d7c9 | Martin Cech | 03 March 2019, 15:49:49 UTC | Merge pull request #7448 from mvdbeek/fix_when_default_label_is_none [18.09] Fix loading workflows with steps without default label | 03 March 2019, 15:49:49 UTC |
| 6c80ca5 | Martin Cech | 03 March 2019, 15:46:11 UTC | Merge pull request #7449 from mvdbeek/remove_broken_tool_submission_burst [18.09] Remove broken tool_submission_burst | 03 March 2019, 15:46:11 UTC |
| d960340 | Martin Cech | 02 March 2019, 17:03:10 UTC | fix lint | 02 March 2019, 17:03:10 UTC |
| bc8cf37 | mvdbeek | 02 March 2019, 15:47:40 UTC | Remove broken tool_submission_burst | 02 March 2019, 15:53:36 UTC |
| 5142d0d | mvdbeek | 02 March 2019, 15:13:47 UTC | Fix loading workflows with steps without default label Prior to https://github.com/galaxyproject/galaxy/pull/7422 we'd call str(default_label), so if `default_label` was None we'd get 'None'. Fixes part of https://github.com/galaxyproject/galaxy/issues/7447 | 02 March 2019, 15:13:54 UTC |
| a12d9e3 | John Chilton | 01 March 2019, 16:40:35 UTC | Merge pull request #7438 from mvdbeek/fix_shell_runner [18.09] Fix LocalShellRunner | 01 March 2019, 16:40:35 UTC |
| e8f5a13 | mvdbeek | 01 March 2019, 10:22:50 UTC | Fix LocalShellRunner All the `cmd` coming from the plugins are strings, so if cmd is a string we use `shell=True`, brings this on par with the Remote Shell plugins (which consume strings). Should fix https://github.com/galaxyproject/galaxy/issues/7269. | 01 March 2019, 13:45:32 UTC |
| 68e3568 | Nicola Soranzo | 01 March 2019, 00:03:03 UTC | Merge pull request #7429 from natefoo/slurm-cgroup-message-fix [18.09] Catch another Slurm memory cgroup creation error message | 01 March 2019, 00:03:03 UTC |
| 9a26de1 | Nate Coraor | 28 February 2019, 16:51:36 UTC | Catch another Slurm memory cgroup creation error message | 28 February 2019, 16:51:36 UTC |
| 13c175a | Martin Cech | 28 February 2019, 15:16:44 UTC | Merge pull request #7422 from mvdbeek/fix_workflow_loading [18.09] Fix workflow loading on systems with ASCII locale | 28 February 2019, 15:16:44 UTC |
| 9e0d3b6 | mvdbeek | 27 February 2019, 16:56:26 UTC | Fix workflow loading on systems with ASCII locale Fixes https://github.com/galaxyproject/galaxy/issues/7421, though it's very likely Galaxy won't play well when python is falling back to ASCII as default encoding. WorkflowStep.label is backed by a 255 character unicode string, but tool_inputs is JSONType, which might have integer or float values (in principle), so we play it safe by casting to unicode. | 27 February 2019, 17:02:55 UTC |
| 9b72f5a | Nicola Soranzo | 22 February 2019, 18:16:25 UTC | Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments [18.09] Update configuration samples | 22 February 2019, 18:16:25 UTC |
| 2f973ac | John Chilton | 22 February 2019, 18:11:49 UTC | Merge branch 'release_18.05' into release_18.09 | 22 February 2019, 18:11:49 UTC |
| 1529758 | John Chilton | 22 February 2019, 18:11:19 UTC | Merge branch 'release_18.01' into release_18.05 | 22 February 2019, 18:11:19 UTC |
| 656b3c2 | John Chilton | 04 December 2018, 15:37:57 UTC | Refactor dataset fetching in get/set dataset method in web controller. | 22 February 2019, 18:10:12 UTC |
| 5fc5b4a | Marius van den Beek | 22 February 2019, 16:41:24 UTC | Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions | 22 February 2019, 16:41:24 UTC |
| a83eb67 | Nate Coraor | 22 February 2019, 16:31:44 UTC | Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions. | 22 February 2019, 16:31:44 UTC |
| 351c188 | Nicola Soranzo | 22 February 2019, 12:07:16 UTC | Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports | 22 February 2019, 12:07:16 UTC |
| 1a0f067 | Martin Cech | 21 February 2019, 17:26:31 UTC | change config schema to reflect removing paste options | 21 February 2019, 17:26:31 UTC |
| 8c9c27b | mvdbeek | 21 February 2019, 16:45:56 UTC | Drop filter-with from docs / .sample | 21 February 2019, 16:45:56 UTC |
| 6d24026 | Marius van den Beek | 19 February 2019, 15:42:06 UTC | Merge pull request #11 from martenson/fix_galaxy_yml_prefix_comments remove Paste config option, reword URL prefix | 19 February 2019, 15:42:06 UTC |
| d72f82d | Martin Cech | 19 February 2019, 15:37:34 UTC | remove Paste config option, reword URL prefix | 19 February 2019, 15:37:34 UTC |
| 9c9c8a5 | Martin Cech | 12 February 2019, 02:28:46 UTC | Merge pull request #7239 from dannon/node_ver_pin_18.09 [18.09] Add/pin configurable node version | 12 February 2019, 02:28:46 UTC |
| c8b3d5e | Marius van den Beek | 29 January 2019, 14:29:22 UTC | Merge pull request #7275 from jmchilton/1901_migrate_tools [18.09] Stop tool migrations checking by default... | 29 January 2019, 14:29:22 UTC |
| d83db6a | John Chilton | 27 January 2019, 20:48:16 UTC | Stop with tool migrations by default, they are not needed in modern Galaxies... ... and even problematic in some ways. | 27 January 2019, 20:48:16 UTC |
| 6a660e9 | Dannon | 24 January 2019, 18:19:27 UTC | Merge pull request #7253 from mvdbeek/fix_install_in_manage_tools_grid [18.09] Fix install operation in installed_repository_grid | 24 January 2019, 18:19:27 UTC |
| f0bd2df | Dannon | 24 January 2019, 13:54:29 UTC | Merge pull request #7265 from nsoranzo/release_18.09_sqlalchemy-migrate_0.12.0 [18.09] Update sqlalchemy-migrate requirement to 0.12.0 | 24 January 2019, 13:54:29 UTC |
| 1a4c1ec | Nicola Soranzo | 24 January 2019, 11:52:04 UTC | Merge pull request #7258 from mvdbeek/fix_workflow_uuid_access [18.09] Not all workflow outputs have a UUID | 24 January 2019, 11:52:04 UTC |
| 5adfa81 | Nicola Soranzo | 24 January 2019, 10:56:40 UTC | Update sqlalchemy-migrate requirement to 0.12.0 Fix https://github.com/galaxyproject/galaxy/issues/7159 | 24 January 2019, 10:56:43 UTC |
| f2a454c | mvdbeek | 23 January 2019, 18:29:37 UTC | Fix output uuid comparison | 24 January 2019, 10:25:37 UTC |
| 35fe3bf | mvdbeek | 23 January 2019, 15:00:50 UTC | Not all workflow outputs have a UUID | 23 January 2019, 15:00:50 UTC |
| eb406cc | mvdbeek | 22 January 2019, 12:51:03 UTC | 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 | 22 January 2019, 19:10:12 UTC |
| 920f073 | John Chilton | 22 January 2019, 18:56:01 UTC | Merge pull request #7252 from mvdbeek/fix_shed_tool_conf_parsing [18.09] strip() text when parsing xml | 22 January 2019, 18:56:01 UTC |
| 31c71fb | mvdbeek | 22 January 2019, 09:31:15 UTC | strip() text when loading xml Should fix https://github.com/galaxyproject/galaxy/issues/7250. | 22 January 2019, 10:30:49 UTC |
| a10d2c5 | Dannon Baker | 18 January 2019, 16:54:59 UTC | Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220) | 18 January 2019, 16:54:59 UTC |
| 889c102 | John Chilton | 18 January 2019, 16:04:16 UTC | Merge pull request #7227 from mvdbeek/fix_workflow_loading_saving [18.09] Properly deal with missing tools in workflows | 18 January 2019, 16:04:16 UTC |
| 6f861de | mvdbeek | 18 January 2019, 12:52:52 UTC | Overridde __init__ for ToolMissingException | 18 January 2019, 12:52:52 UTC |
| b1b1d84 | mvdbeek | 17 January 2019, 14:11:32 UTC | Fix loading subworkflows | 17 January 2019, 15:00:36 UTC |
| 54aecb3 | mvdbeek | 17 January 2019, 12:12:31 UTC | 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. | 17 January 2019, 12:41:21 UTC |
| b6d5675 | mvdbeek | 15 January 2019, 11:21:30 UTC | Update galaxy.yml.sample for prefix config | 15 January 2019, 11:32:41 UTC |
| 105a1d8 | Dannon | 11 January 2019, 14:19:39 UTC | Merge pull request #7201 from mvdbeek/fix_view_metadata_error [18.09] Fix error in view_tool_metadata | 11 January 2019, 14:19:39 UTC |
| a7ae521 | Martin Cech | 10 January 2019, 18:01:44 UTC | Merge branch 'release_18.05' into release_18.09 | 10 January 2019, 18:01:44 UTC |
| c17c20b | Martin Cech | 10 January 2019, 18:00:54 UTC | Merge pull request #7181 from dannon/page_save_history_fix [18.05] Fix hda accessibility check in Page's renderForSave name fetching | 10 January 2019, 18:00:54 UTC |
| 141c2a1 | Nicola Soranzo | 10 January 2019, 16:16:56 UTC | Fix indentation Broken in commit cf2645f9a658c5e122fea0309bf73a1f64590c39 . | 10 January 2019, 16:16:58 UTC |
| 338020f | mvdbeek | 10 January 2019, 15:38:58 UTC | Fix error in view_tool_metadata (https://sentry.galaxyproject.org/sentry/toolshed/issues/294272/) | 10 January 2019, 15:59:31 UTC |
| c4ad6b9 | Nicola Soranzo | 09 January 2019, 18:56:53 UTC | Merge branch 'release_18.05' into release_18.09 | 09 January 2019, 18:56:53 UTC |
| ce1a1ee | Dannon | 09 January 2019, 14:07:35 UTC | Merge pull request #7180 from martenson/security-ts [18.09] Prevent XSS on toolshed when browsing repo changeset | 09 January 2019, 14:07:35 UTC |
| 6256ac0 | John Chilton | 09 January 2019, 13:53:09 UTC | Merge pull request #7190 from martenson/fix-permission-api [18.09] fix library dataset permission API | 09 January 2019, 13:53:09 UTC |
| 193f5ea | Martin Cech | 08 January 2019, 19:43:52 UTC | call the method through the proper manager | 08 January 2019, 19:43:52 UTC |
| 29abf8f | Martin Cech | 08 January 2019, 19:01:39 UTC | refactor approach so the method is inherited to ldda | 08 January 2019, 19:01:39 UTC |
| 5e3ebb1 | Martin Cech | 08 January 2019, 18:53:40 UTC | fix import ordering, thanks @nsoranzo | 08 January 2019, 18:53:40 UTC |
| 2e82b7f | Martin Cech | 08 January 2019, 18:42:43 UTC | fix library dataset permission API broken in refactoring | 08 January 2019, 18:42:43 UTC |
| f6b978b | Martin Cech | 07 January 2019, 16:38:39 UTC | 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 | 08 January 2019, 17:52:28 UTC |
| 2a17860 | Dannon | 07 January 2019, 19:31:35 UTC | Merge pull request #7128 from natefoo/slurm-trace-log-fix [18.05] Fix for use of `log.trace` in Slurm runner | 07 January 2019, 19:31:35 UTC |
| 998eb85 | Dannon Baker | 07 January 2019, 16:40:02 UTC | Fix hda accessibility check in Page's renderForSave name fetching | 07 January 2019, 16:47:22 UTC |
| d4c6921 | Nate Coraor | 18 December 2018, 18:39:53 UTC | Fix for use of `log.trace` in Slurm runner | 18 December 2018, 18:39:53 UTC |
| 65ca25e | Nicola Soranzo | 16 December 2018, 22:56:39 UTC | Merge branch 'release_18.05' into release_18.09 | 16 December 2018, 22:56:39 UTC |
| bfc634e | Nicola Soranzo | 16 December 2018, 22:54:49 UTC | Merge branch 'release_18.01' into release_18.05 | 16 December 2018, 22:54:49 UTC |
| 6feef2a | Nicola Soranzo | 16 December 2018, 22:51:40 UTC | Merge branch 'release_17.09' into release_18.01 | 16 December 2018, 22:53:32 UTC |
| fdd9a09 | Nicola Soranzo | 16 December 2018, 22:44:54 UTC | Merge branch 'release_17.05' into release_17.09 | 16 December 2018, 22:44:54 UTC |
| 06cfb7e | Nicola Soranzo | 16 December 2018, 22:43:37 UTC | Merge branch 'release_17.01' into release_17.05 | 16 December 2018, 22:43:37 UTC |
| 1b30a9a | Nicola Soranzo | 16 December 2018, 22:42:04 UTC | Merge branch 'release_16.10' into release_17.01 | 16 December 2018, 22:42:04 UTC |
| a2e70ef | Nicola Soranzo | 16 December 2018, 22:40:26 UTC | Merge branch 'release_16.07' into release_16.10 | 16 December 2018, 22:40:26 UTC |
| f3c8181 | Nicola Soranzo | 16 December 2018, 22:36:18 UTC | Merge branch 'release_16.04' into release_16.07 | 16 December 2018, 22:36:18 UTC |
| 87fa609 | Nicola Soranzo | 16 December 2018, 22:29:19 UTC | Merge branch 'release_16.01' into release_16.04 | 16 December 2018, 22:29:19 UTC |
| 8f14121 | Nicola Soranzo | 16 December 2018, 22:28:21 UTC | Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 | 16 December 2018, 22:28:21 UTC |
