| ed282c2 | Nate Coraor | 05 August 2020, 14:21:30 UTC | Merge remote-tracking branch 'upstream/release_18.09' into release_19.01 | 05 August 2020, 14:21:30 UTC |
| 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 |
| 90a6e55 | Dannon | 20 February 2020, 22:07:30 UTC | Merge pull request #9408 from nsoranzo/release_19.01_update_bleach [19.01] Update bleach to 3.1.1 | 20 February 2020, 22:07:30 UTC |
| 7e8c851 | Martin Cech | 15 July 2019, 17:57:00 UTC | remove libpython requirement for uwsgi building | 20 February 2020, 15:16:14 UTC |
| 324c0b9 | Nicola Soranzo | 20 February 2020, 14:17:22 UTC | Update bleach to 3.1.1 due to security fixes explained in https://github.com/mozilla/bleach/blob/master/CHANGES | 20 February 2020, 14:17:24 UTC |
| dc38dad | Nicola Soranzo | 12 December 2019, 18:05:25 UTC | Merge branch 'release_18.09' into release_19.01 | 12 December 2019, 18:05:25 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 |
| 53383bf | John Chilton | 17 June 2019, 18:27:54 UTC | Merge pull request #8164 from natefoo/workflow-scheduler-default-required-fix [19.01] Do not require a default attrib on the workflow scheduler config's handlers tag | 17 June 2019, 18:27:54 UTC |
| dc2e288 | Nate Coraor | 17 June 2019, 16:28:38 UTC | Do not require a default attrib on the workflow scheduler config's handlers tag. | 17 June 2019, 16:28:38 UTC |
| 3e01f1a | Marius van den Beek | 10 June 2019, 11:33:03 UTC | Merge pull request #8108 from nsoranzo/release_19.01_fix_iter_methods_py3 [19.01] Do not use dict iter methods for Python3 compatibility | 10 June 2019, 11:33:03 UTC |
| 9ec952c | Nicola Soranzo | 06 June 2019, 14:58:15 UTC | Do not use dict iter methods for Python3 compatibility | 06 June 2019, 14:58:15 UTC |
| cb53c73 | Martin Cech | 05 June 2019, 19:04:58 UTC | Merge pull request #8085 from dannon/fix-multipanel-history-search [19.01] Fix multipanel history search. | 05 June 2019, 19:04:58 UTC |
| 2a19b21 | Marius van den Beek | 05 June 2019, 13:48:00 UTC | Merge pull request #8097 from bgruening/fix_macro_backport_19.01 [19.01] Fix nested macro/token expansion | 05 June 2019, 13:48:00 UTC |
| fc2bff6 | Nicola Soranzo | 26 April 2019, 23:00:01 UTC | Remove recursion from ``expand_nested_tokens()`` Also add test for recursive nested token. | 05 June 2019, 11:54:18 UTC |
| 574d9ad | mvdbeek | 25 April 2019, 16:41:48 UTC | Fix nested macro/token expansion on python 3 I noticed that in multiqc @ESCAPE_IDENTIFIER@ wasn't being replaced. It's surprising that this didn't cause any issues on python 2, but might have to do with the iteration order changes. | 05 June 2019, 11:44:46 UTC |
| 8edffb1 | Dannon Baker | 04 June 2019, 15:47:21 UTC | const, formatting | 04 June 2019, 15:47:21 UTC |
| b732950 | Dannon Baker | 04 June 2019, 15:45:36 UTC | Actually search in onfirstsearch of history search in multipanel | 04 June 2019, 15:46:24 UTC |
| edcce00 | Dannon Baker | 03 June 2019, 15:54:14 UTC | Fix multipanel history search. | 04 June 2019, 15:46:24 UTC |
| fd02b74 | Nicola Soranzo | 03 June 2019, 17:06:45 UTC | Merge branch 'release_18.09' into release_19.01 | 03 June 2019, 17:06:45 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 |
| da0f5f2 | Björn Grüning | 30 May 2019, 15:16:06 UTC | [19.01] Document the handler max_grab config param (#8060) [19.01] Document the handler max_grab config param | 30 May 2019, 15:16:06 UTC |
| dfb591c | Nate Coraor | 30 May 2019, 13:18:42 UTC | Document the handler max_grab config param | 30 May 2019, 13:18:42 UTC |
| d25dcc4 | Björn Grüning | 30 May 2019, 07:30:40 UTC | [19.01] Fixes for job handler and worklflow scheduler self-assignment grab limits (#8059) [19.01] Fixes for job handler and worklflow scheduler self-assignment grab limits | 30 May 2019, 07:30:40 UTC |
| c0c39d5 | Nate Coraor | 29 May 2019, 19:25:55 UTC | Default the maximum grab limit for handler database preassignment methods to unlimited as intended. Document the config param. | 29 May 2019, 19:25:55 UTC |
| 3745263 | John Chilton | 24 May 2019, 13:29:41 UTC | Merge pull request #8032 from mvdbeek/backport_param_as_output_fix [19.01] Backport #7799 Skip recording workflow outputs for input parameters | 24 May 2019, 13:29:41 UTC |
| e988fde | mvdbeek | 24 April 2019, 16:25:17 UTC | Skip recording workflow outputs for input parameters These can come in as a literal parameter value, or as a dictionary like {'id': 'encoded_id', 'src': 'hda'}, none of which is quite right. | 24 May 2019, 08:45:18 UTC |
| c60613c | Marius van den Beek | 18 May 2019, 08:16:25 UTC | Merge pull request #8002 from natefoo/pgcleanup-purge-user-fix [19.01] Fix use of pgcleanup's purge_deleted_users when there are no users to purge | 18 May 2019, 08:16:25 UTC |
| bd06628 | Nate Coraor | 17 May 2019, 20:37:19 UTC | Fix use of pgcleanup's purge_deleted_users when there are no users to purge | 17 May 2019, 20:37:19 UTC |
| 82052db | Marius van den Beek | 17 May 2019, 17:28:59 UTC | Merge pull request #7999 from natefoo/pgcleanup-work-mem-fix [19.01] Fix variable name for work mem in pgcleanup.py | 17 May 2019, 17:28:59 UTC |
| fc02718 | Nate Coraor | 17 May 2019, 15:30:40 UTC | Fix variable name for work mem in pgcleanup.py | 17 May 2019, 15:30:40 UTC |
| 9b9daff | Nicola Soranzo | 07 May 2019, 14:57:31 UTC | Merge pull request #7766 from natefoo/slurmstepd [19.01] Catch and filter *all* Slurm cgroup-related messages | 07 May 2019, 14:57:31 UTC |
| 7130ae9 | Dannon | 07 May 2019, 13:00:37 UTC | Merge pull request #7824 from tmcgowan/issue_7758 [19.01] Possible fix for WSGI process issue #7758 | 07 May 2019, 13:00:37 UTC |
| ea398cb | John Chilton | 04 May 2019, 15:40:41 UTC | Merge pull request #7857 from natefoo/fix-job-config-get-default [19.01] Fix the job config's shared _get_default() method | 04 May 2019, 15:40:41 UTC |
| b2eb394 | John Chilton | 02 May 2019, 15:39:39 UTC | Merge pull request #7870 from jmchilton/1901_fix_plugin [19.01] Fix bug preventing handler runner plugin handling. | 02 May 2019, 15:39:39 UTC |
| d7b1479 | Dannon | 02 May 2019, 15:13:37 UTC | Merge pull request #7872 from mvdbeek/allow_not_uploading_optional_files [19.01] Allow composite upload if all non-optional files are selected | 02 May 2019, 15:13:37 UTC |
| a52f3f3 | mvdbeek | 02 May 2019, 12:12:05 UTC | Allow upload if all non-optional files are selected Fixes https://github.com/galaxyproject/galaxy/issues/5326 | 02 May 2019, 12:13:31 UTC |
| 1758657 | Björn Grüning | 02 May 2019, 12:08:23 UTC | Update test/unit/jobs/test_job_configuration.py Co-Authored-By: jmchilton <jmchilton@gmail.com> | 02 May 2019, 12:08:23 UTC |
| 98fa693 | John Chilton | 01 May 2019, 18:51:35 UTC | Fix bug preventing handler runner plugin handling. | 01 May 2019, 19:09:25 UTC |
| f6e54b4 | John Chilton | 30 April 2019, 23:45:43 UTC | Add job configuration test for resource groups and handler plugins. | 01 May 2019, 19:09:24 UTC |
| 1410e8c | Nate Coraor | 30 April 2019, 18:44:45 UTC | Fix tests broken by previous commit, also, handler defaults are never required (preassign uses all defined handlers if no default is set). | 30 April 2019, 19:01:45 UTC |
| 1994c35 | Nate Coraor | 30 April 2019, 18:48:40 UTC | Merge pull request #7855 from mvdbeek/fix_workflow_extraction [19.01] Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset | 30 April 2019, 18:48:40 UTC |
| 170bd02 | Nicola Soranzo | 30 April 2019, 18:36:06 UTC | [19.01] Use just the env name when checking ``CONDA_DEFAULT_ENV`` (#7853) [19.01] Use just the env name when checking ``CONDA_DEFAULT_ENV`` | 30 April 2019, 18:36:06 UTC |
| 7ac30ec | Nate Coraor | 30 April 2019, 18:14:18 UTC | Fix the job config's shared _get_default() method so it does the correct thing for destinations | 30 April 2019, 18:14:18 UTC |
| 96ed324 | Nicola Soranzo | 30 April 2019, 16:49:49 UTC | Ensure that also `$CONDA_DEFAULT_ENV` is just the env name That's not the case e.g. for conda 4.1.1 when using `conda_exec` not inside `conda_prefix`. | 30 April 2019, 16:49:49 UTC |
| 4af1c0a | mvdbeek | 30 April 2019, 16:27:45 UTC | Fix workflow extraction for jobs whose JobToDatasetOutputAssociation references a discovered dataset To test this run a tool that generates discovered datsets twice, with the second run taking the first output as input. | 30 April 2019, 16:31:19 UTC |
| 8fd0652 | mvdbeek | 30 April 2019, 12:00:46 UTC | CONDA_DEFAULT_NAME is just the env name This will still write the conda activate part out multiple times, but fix the check that would otherwise lead to repeated activation of the conda env. Fixes the slowness reported in https://github.com/galaxyproject/galaxy/issues/7849 | 30 April 2019, 12:02:42 UTC |
| 7d8ec2b | Marius van den Beek | 30 April 2019, 08:03:58 UTC | Merge pull request #7850 from nsoranzo/release_19.01_backport_7696 [19.01] Backport of #7696 | 30 April 2019, 08:03:58 UTC |
| ce6ee86 | Aysam Guerler | 29 April 2019, 21:39:16 UTC | Merge pull request #7845 from dannon/fix_trackster_overflow_issue [19.01] Fix trackster issue w/ constraining (overflow:non-visible) containers | 29 April 2019, 21:39:16 UTC |
| 3dc68db | Bérénice Batut | 09 April 2019, 08:04:41 UTC | Add extra column metadata check for minimal biom1 file | 29 April 2019, 17:59:25 UTC |
| f09bc22 | Dannon Baker | 29 April 2019, 15:55:35 UTC | Fix trackster issue w/ constraining (overflow:non-visible) containers | 29 April 2019, 16:00:23 UTC |
| 966a46c | Thomas McGowan | 25 April 2019, 19:29:31 UTC | Removed trailing whitespace | 25 April 2019, 19:29:31 UTC |
| d0f07ac | Thomas McGowan | 25 April 2019, 18:36:43 UTC | Processes -> threads to minimize server load | 25 April 2019, 18:36:43 UTC |
| 343e6e4 | John Chilton | 24 April 2019, 18:00:27 UTC | Merge pull request #7786 from natefoo/job-fail-destination-loop [19.01] Fix the use of JobMappingException | 24 April 2019, 18:00:27 UTC |
| 166a83b | John Chilton | 19 April 2019, 20:20:15 UTC | Merge pull request #7783 from natefoo/backport-7667 [19.01] Fix shutdown for Pulsar MQ Runner | 19 April 2019, 20:20:15 UTC |
| 87b7bfd | Nate Coraor | 19 April 2019, 18:09:29 UTC | Fix the use of JobMappingException | 19 April 2019, 18:43:30 UTC |
| ca55cab | John Chilton | 04 April 2019, 20:06:32 UTC | Fix PulsarMQRunner shutdown. | 19 April 2019, 16:44:53 UTC |
| b0f0fdc | John Chilton | 04 April 2019, 20:03:23 UTC | Remove unused variable. | 19 April 2019, 16:44:48 UTC |
| 1ba753c | Nate Coraor | 18 April 2019, 16:53:34 UTC | Catch and filter *all* Slurm cgroup-related messages | 18 April 2019, 16:53:34 UTC |
| 5f65252 | Dannon | 15 April 2019, 18:24:54 UTC | Merge pull request #7675 from gtrack/workflow_btn_dont_jump [19.01] Bugfix: "Run workflow" jumps when clicked | 15 April 2019, 18:24:54 UTC |
| a6c531e | Björn Grüning | 12 April 2019, 20:24:41 UTC | Merge pull request #7723 from nsoranzo/release_19.01_fix_safemembers [19.01] Fix check on links in ``CompressedFile.safemembers()`` | 12 April 2019, 20:24:41 UTC |
| 0bfebb4 | Nicola Soranzo | 12 April 2019, 13:35:03 UTC | Merge branch 'release_18.09' into release_19.01 | 12 April 2019, 13:35:03 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 |
| d545e88 | Nicola Soranzo | 12 April 2019, 11:41:24 UTC | Add test case and use `assertRaises()` Also remove temporary directory. | 12 April 2019, 11:41:48 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 |
| 9bf4a0f | Nicola Soranzo | 11 April 2019, 15:24:02 UTC | Fix check on links in ``CompressedFile.safemembers()`` Reported by @curtisecombsjr Fix the following traceback when installing https://toolshed.g2.bx.psu.edu/view/iuc/package_openssl_1_0/ : ``` File "lib/tool_shed/galaxy_install/install_manager.py", line 121, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package(install_environment, tool_dependency, actions_dict) File "lib/tool_shed/galaxy_install/install_manager.py", line 79, in install_and_build_package initial_download=True) File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download) File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 548, in execute_step dir = self.url_download(work_dir, downloaded_filename, url, extract=True, checksums=checksums) File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 77, in url_download extraction_path = archive.extract(install_dir) File "lib/galaxy/util/compression_utils.py", line 111, in extract self.archive.extractall(extraction_path, members=self.safemembers()) File "/usr/lib64/python2.7/tarfile.py", line 2041, in extractall for tarinfo in members: File "lib/galaxy/util/compression_utils.py", line 135, in safemembers raise Exception(finfo.name + " is blocked.") openssl-1.0.2d/apps/md4.c is blocked. ``` | 11 April 2019, 22:21:07 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 |
| 716b888 | John Chilton | 10 April 2019, 13:50:33 UTC | Merge pull request #7711 from mvdbeek/fix_workflow_invocations_inaccessible [19.01] Restrict workflow invocation index to current user | 10 April 2019, 13:50:33 UTC |
| 4c9e411 | mvdbeek | 10 April 2019, 08:35:47 UTC | Restrict workflow invocation index to current user If the user is not an admin. Fixes https://github.com/galaxyproject/galaxy/issues/7710 An alternative would be to skip Accessibility / Ownership exceptions, but given that we can just restrict the query this seems like the better approach to me. | 10 April 2019, 09:13:59 UTC |
| 78ad615 | Björn Grüning | 10 April 2019, 08:33:36 UTC | Merge pull request #7699 from mvdbeek/fix_sort_tool_too_stringent [19.01] Only check for exit code on actual sort command | 10 April 2019, 08:33:36 UTC |
| aa008a6 | Nicola Soranzo | 09 April 2019, 19:26:27 UTC | Restore check_call for `sed` | 09 April 2019, 19:26:27 UTC |
| 22c3895 | Martin Cech | 09 April 2019, 18:08:02 UTC | Merge pull request #7705 from dannon/backport-genomespace-fix [19.01] Backport GenomeSpace Exporter fix | 09 April 2019, 18:08:02 UTC |
| c521dec | Dannon Baker | 09 April 2019, 11:24:05 UTC | Specify profile and look for exit codes for genomespace tool -- warnings cause failures otherwise | 09 April 2019, 17:34:06 UTC |
| 68423aa | mvdbeek | 09 April 2019, 13:21:51 UTC | Cleanup sorter.py Feed open output file to Popen instead of using stdout redirection in command string. | 09 April 2019, 13:35:21 UTC |
| 45a0ff6 | mvdbeek | 09 April 2019, 12:02:10 UTC | Only check for exit code on actual sort command | 09 April 2019, 12:02:10 UTC |
| 3ec5547 | Dannon Baker | 08 April 2019, 18:28:44 UTC | Add unique identifier to run workflow button, style explicitly instead of on the fly | 08 April 2019, 18:28:44 UTC |
| adfb7e6 | Martin Cech | 08 April 2019, 14:13:26 UTC | Merge pull request #7682 from mvdbeek/fix_format_source_impicit_conversion [19.01] Fix format_source for implicit conversion inputs and fasta.gz upload | 08 April 2019, 14:13:26 UTC |
| 62812dd | mvdbeek | 08 April 2019, 11:20:10 UTC | Use backref to implicitly_converted_parent_datasets Thanks for the suggestion @nsoranzo. | 08 April 2019, 11:38:08 UTC |
| fd61989 | mvdbeek | 07 April 2019, 09:07:17 UTC | Add test-data | 07 April 2019, 21:15:35 UTC |
| 966cad8 | mvdbeek | 07 April 2019, 07:12:57 UTC | Fix fasta.gz uploads This looks like it may probably broke with https://github.com/galaxyproject/galaxy/commit/fce2dd3ae801cd13a542388746b84f9cca2a4c48 | 07 April 2019, 21:15:35 UTC |
| 5f578d4 | mvdbeek | 06 April 2019, 20:45:45 UTC | Add double conversion test | 07 April 2019, 21:15:35 UTC |
| 3e3d15a | mvdbeek | 06 April 2019, 19:10:27 UTC | Add test that verifies ftype is being set correctly | 07 April 2019, 21:15:35 UTC |
| 0d20c03 | mvdbeek | 06 April 2019, 19:06:37 UTC | Fix format_source when input is implicitly converted | 07 April 2019, 21:15:34 UTC |
| 67e0d61 | mvdbeek | 06 April 2019, 20:20:25 UTC | Add implicitly_converted_parent_datasets to LDDA | 07 April 2019, 21:15:19 UTC |
| 587d7e7 | John Chilton | 07 April 2019, 21:05:12 UTC | Merge pull request #7680 from dannon/tags_delete_list_redux [19.01] Tags remove_tags_from_list fix update | 07 April 2019, 21:05:12 UTC |
| db094e8 | Dannon Baker | 06 April 2019, 17:43:56 UTC | Make this slightly more robust by not worrying about whitespace in the source representation. | 06 April 2019, 17:43:56 UTC |
| 769bef1 | Dannon Baker | 06 April 2019, 17:38:02 UTC | Slightly different fix for deleting tags with less potential side effects. | 06 April 2019, 17:38:02 UTC |
| 2b34eb5 | Dannon | 06 April 2019, 17:18:30 UTC | Merge pull request #7679 from mvdbeek/use_exit_code_for_sort_tool [19.01] Detect errors using exit_code for sort tool | 06 April 2019, 17:18:30 UTC |
