| 15239f1 | John Chilton | 10 June 2019, 19:01:46 UTC | Update version to 19.05 | 10 June 2019, 19:01:46 UTC |
| 097612f | Dannon | 10 June 2019, 14:44:59 UTC | Merge pull request #8106 from Nerdinacan/analytics_load_issue [19.05] Restored google analytics inits in mako templates | 10 June 2019, 14:44:59 UTC |
| 9043dd1 | Enis Afgan | 10 June 2019, 14:31:59 UTC | [19.05] Add recent merges to release notes | 10 June 2019, 14:31:59 UTC |
| 696f9f9 | John Chilton | 10 June 2019, 14:02:56 UTC | Merge pull request #8103 from nuwang/fix_k8s_runasuser [19.05] Fix k8s runasuser | 10 June 2019, 14:02:56 UTC |
| f821d3f | John Chilton | 10 June 2019, 14:01:30 UTC | Merge pull request #8092 from nuwang/fix_k8s_namespace_19_05 [19.05] Filter all pykube queries by namespace | 10 June 2019, 14:01:30 UTC |
| 6b899ce | Nicola Soranzo | 10 June 2019, 13:09:26 UTC | Merge branch 'release_19.01' into release_19.05 | 10 June 2019, 13:09:26 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 |
| 8f5a35e | Martin Cech | 07 June 2019, 19:13:14 UTC | I love RST | 07 June 2019, 19:13:14 UTC |
| 2dad501 | John Chilton | 07 June 2019, 12:30:06 UTC | Merge pull request #8116 from nuwang/fix_default_container_image [19.05] Fix error in recognizing destination default container image | 07 June 2019, 12:30:06 UTC |
| 39d265b | Nuwan Goonasekera | 07 June 2019, 01:49:25 UTC | Fix error in recognizing destination default container image | 07 June 2019, 01:49:25 UTC |
| 3837440 | Nate Coraor | 06 June 2019, 20:21:36 UTC | Merge pull request #8065 from jmchilton/metadata_output_pulsar [19.05] Fix metadata output collection on Pulsar with new metadata strategy. | 06 June 2019, 20:21:36 UTC |
| 1245153 | Mason | 06 June 2019, 17:17:36 UTC | Restored google analytics initialize inside mako templates | 06 June 2019, 17:17:36 UTC |
| dc4785a | John Chilton | 06 June 2019, 15:05:28 UTC | Fixes(?) to galaxy.metadata. | 06 June 2019, 15:05:28 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 |
| aa463ce | Nuwan Goonasekera | 05 June 2019, 17:55:37 UTC | Default to none if run_as_user or group are not specified | 06 June 2019, 11:41:04 UTC |
| 0a32933 | Martin Cech | 05 June 2019, 20:58:53 UTC | fix link to user release notes | 05 June 2019, 20:59:46 UTC |
| 95586c1 | Martin Cech | 05 June 2019, 19:49:39 UTC | Merge pull request #8037 from jmchilton/release_19.05_notes [19.05] 19.05 Release Notes | 05 June 2019, 19:49:39 UTC |
| e831139 | Martin Cech | 05 June 2019, 19:48:33 UTC | minor changes to RN | 05 June 2019, 19:48:33 UTC |
| b0dc3fe | Martin Cech | 05 June 2019, 19:06:43 UTC | Merge branch 'release_19.01' into release_19.05 | 05 June 2019, 19:06:43 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 |
| 91b6774 | Nuwan Goonasekera | 04 June 2019, 05:24:03 UTC | Added support for runAsUser and runAsGroup to k8srunner | 05 June 2019, 18:08:09 UTC |
| 7aa5d56 | Nicola Soranzo | 05 June 2019, 14:16:13 UTC | Merge branch 'release_19.01' into release_19.05 | 05 June 2019, 14:16:13 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 |
| f577541 | Nuwan Goonasekera | 03 June 2019, 09:15:10 UTC | Filter all pykube queries by namespace | 04 June 2019, 17:00:10 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 |
| 5a85147 | John Chilton | 03 June 2019, 17:28:06 UTC | Fix job metrics collection from them returning into metadata/ Ideally all job metrics should be placed here to mimic Pulsar but this is a bug fix to an almost stable branch. | 03 June 2019, 17:36:11 UTC |
| cbb578e | John Chilton | 03 June 2019, 16:42:12 UTC | Spelling fix. | 03 June 2019, 17:36:11 UTC |
| c6e5a86 | John Chilton | 31 May 2019, 15:26:50 UTC | Fix finding datatype's registry for metadata collection on Pulsar. | 03 June 2019, 17:35:59 UTC |
| 5f4bebd | John Chilton | 31 May 2019, 14:32:02 UTC | Fix portable remote metadata output files... ... three features not working together super well. | 03 June 2019, 17:35:58 UTC |
| a80a49b | John Chilton | 30 May 2019, 20:38:36 UTC | Fix metadata output collection on Pulsar. | 03 June 2019, 17:35:58 UTC |
| 4a87bb4 | Nicola Soranzo | 03 June 2019, 17:13:05 UTC | Merge branch 'release_19.01' into release_19.05 | 03 June 2019, 17:13:05 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 |
| 115157c | John Chilton | 03 June 2019, 14:00:38 UTC | Merge pull request #8071 from dannon/axios-sec-upgrade [19.05] Upgrade axios to handle CVE-2019-10742 | 03 June 2019, 14:00:38 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 |
| b346565 | Dannon Baker | 31 May 2019, 11:55:21 UTC | Upgrade axios to handle https://snyk.io/vuln/SNYK-JS-AXIOS-174505 | 31 May 2019, 11:55:21 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 |
| bff203f | Nate Coraor | 30 May 2019, 19:03:00 UTC | Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 | 30 May 2019, 19:03:00 UTC |
| 9c960c2 | John Chilton | 30 May 2019, 18:15:21 UTC | Merge pull request #8056 from mvdbeek/possibly_fix_amqp_issue_on_mules [19.05] Release ampq connection after initial connect | 30 May 2019, 18:15:21 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 |
| 514154e | mvdbeek | 30 May 2019, 09:21:05 UTC | Release ampq connection after initial connect We need to call `connection.connect()` to avoid `'kombu.transport.sqlalchemy.Message' is not mapped`` errrors. This is fine for for sqlalchemy transports, but the connection is still open if we don't release the connection. This is a problem when acquiring the connection with rabbitmq transports. So instead we release the connection and acquire a blocking connection from the connection pool. This sets up the mapping and avoids `'kombu.transport.sqlalchemy.Message' is not mapped`. Not sure if this will fix @natefoo's issue as I haven't exactly been able to reproduce the same error, but acquiring a blocking connection failed outright without releasing the connection, so this is probably a step in the right direction. | 30 May 2019, 13:54:56 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 |
| e0a5e39 | Nicola Soranzo | 30 May 2019, 09:33:51 UTC | Merge branch 'release_19.01' into release_19.05 | 30 May 2019, 09:33:51 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 |
| 4521614 | Helena Rasche | 29 May 2019, 11:03:46 UTC | Enhance user facing release notes with gifs | 29 May 2019, 11:03:46 UTC |
| 530077a | John Chilton | 28 May 2019, 13:37:13 UTC | Merge pull request #8040 from mvdbeek/bwlang_editor_fixes [19.05] Update node.post_job_actions when changing post job actions | 28 May 2019, 13:37:13 UTC |
| ea107d7 | Marius van den Beek | 28 May 2019, 11:28:12 UTC | Merge pull request #8048 from nsoranzo/release_19.05_update_conda [19.05] Update Conda for new installs to v4.6.14 | 28 May 2019, 11:28:12 UTC |
| b1ea3d2 | mvdbeek | 28 May 2019, 10:33:38 UTC | Don't add new outputView because it resets mapOver This means we don't see the forced datataype on the node itself, but we maintain the noodle type, and the connection hints are correct. | 28 May 2019, 10:33:41 UTC |
| c703109 | mvdbeek | 27 May 2019, 16:19:06 UTC | Update node.post_job_actions when changing post job actions I broke persisting pot job actions in https://github.com/galaxyproject/galaxy/pull/7989. The onchange function prevented updating the post job action. | 28 May 2019, 08:14:20 UTC |
| 25ea088 | Nicola Soranzo | 27 May 2019, 22:16:29 UTC | Update Conda for new installs to v4.6.14 and conda-build to v3.17.8 . | 27 May 2019, 23:36:22 UTC |
| 0e33056 | John Chilton | 27 May 2019, 16:09:34 UTC | Merge pull request #8039 from mvdbeek/non_legacy_object_store_fix [19.05] Backport 7939: Fix non-eager object store with nested object stores | 27 May 2019, 16:09:34 UTC |
| 5b05866 | mvdbeek | 17 May 2019, 12:04:23 UTC | Explicitly create extra_files_path when discovering outputs with extra files | 27 May 2019, 12:37:53 UTC |
| 563ae4d | mvdbeek | 12 May 2019, 18:13:57 UTC | Raise ObjectNotFound if file does not exist in object store And return an empty string if a path does not exist when calling `get_filename` or` get_extra_files_path` on a Dataset. | 27 May 2019, 12:37:53 UTC |
| 419bae1 | John Chilton | 18 April 2019, 18:34:25 UTC | Don't calculate real path in tool action code if unused. | 27 May 2019, 12:37:53 UTC |
| 7ea502b | John Chilton | 18 April 2019, 17:24:18 UTC | Run API tests with a nested object store. | 27 May 2019, 12:37:53 UTC |
| 5c2da64 | Nicola Soranzo | 27 May 2019, 11:27:17 UTC | [19.05] Use byte comparison for contains and files_re_match (#8010) [19.05] Use byte comparison for contains and files_re_match | 27 May 2019, 11:27:17 UTC |
| 62f5572 | mvdbeek | 27 May 2019, 09:35:20 UTC | Add carriage return unit test | 27 May 2019, 09:35:20 UTC |
| 1eea5de | Nicola Soranzo | 26 May 2019, 14:55:20 UTC | Merge branch 'release_19.01' into release_19.05 | 26 May 2019, 14:55:20 UTC |
| d9b0f54 | Nicola Soranzo | 26 May 2019, 13:55:14 UTC | Try to verify tool test output first as Unicode | 26 May 2019, 14:07:36 UTC |
| aa4566e | John Chilton | 24 May 2019, 17:27:28 UTC | First pass at writing 19.05 release notes. | 24 May 2019, 20:59:32 UTC |
| 0cf83ef | John Chilton | 24 May 2019, 15:06:35 UTC | Initial bootstrapping of 19.05 release notes... | 24 May 2019, 20:59:32 UTC |
| 038d78a | John Chilton | 24 May 2019, 14:19:40 UTC | Fixes and enhancements for release note generation. - Auto-bootstrap user announcements for datatypes, tools, and viz. (follow up on #7527) - Many fixes for things broken in #7527 - Treat procedures as an enhancment for categorizing things. - Speed up release note generation a bit by not considering really, really old PRs. | 24 May 2019, 20:59:32 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 |
| 877b115 | Dannon | 24 May 2019, 13:15:57 UTC | Merge pull request #8029 from guerler/disable_register_button [19.05] Disable create user button while request is being processed | 24 May 2019, 13:15:57 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 |
| 0949c38 | guerler | 23 May 2019, 23:27:54 UTC | Disable create user button while request is being processed | 23 May 2019, 23:27:54 UTC |
| 12f394c | Nate Coraor | 23 May 2019, 14:34:12 UTC | Merge pull request #8021 from mvdbeek/fix_databaseless_tools [19.05] Fix repo cache when no install database is present | 23 May 2019, 14:34:12 UTC |
| 6ea862f | mvdbeek | 23 May 2019, 12:05:30 UTC | Use sqlalchemy.inspect to find detached repositories Thanks for the suggestion Nicola! | 23 May 2019, 12:05:30 UTC |
| a398127 | mvdbeek | 23 May 2019, 11:43:57 UTC | Work with bytestrings in `files_contains`, `files_re_match_*` But read utf-8 unicode in `lines_diff`. This will replace non-utf8 characters and seems like a reasonable tradeoff for text files mixed with byte contents, like pdfs. | 23 May 2019, 11:43:59 UTC |
| f204b33 | mvdbeek | 23 May 2019, 09:53:31 UTC | Fix repo cache when no install database is present Fixes https://github.com/galaxyproject/galaxy/issues/8015 | 23 May 2019, 09:55:19 UTC |
| 2d71b0b | mvdbeek | 23 May 2019, 09:07:06 UTC | Use io.open with errors="repalce" instead of comparing byte strings | 23 May 2019, 09:07:06 UTC |
| 9f6bc89 | mvdbeek | 22 May 2019, 15:59:49 UTC | Do non-shallow file comparison | 22 May 2019, 15:59:49 UTC |
| 30bec00 | mvdbeek | 22 May 2019, 12:35:01 UTC | Use bytestring comparisons in verify module | 22 May 2019, 15:45:00 UTC |
| ab7a386 | mvdbeek | 22 May 2019, 12:34:28 UTC | Unit test verify module | 22 May 2019, 15:45:00 UTC |
| 8fea7e9 | mvdbeek | 21 May 2019, 09:04:58 UTC | Use byte comparison for contains I don't think there's any drawback open this in byte mode. Fixes https://github.com/galaxyproject/galaxy/issues/7957#issuecomment-493954901 | 21 May 2019, 09:09:13 UTC |
| 47b27be | John Chilton | 20 May 2019, 12:17:41 UTC | Merge pull request #7989 from mvdbeek/fix_force_datatype_changes [19.05] Update tool output datatype in workflow editor if datatype changes | 20 May 2019, 12:17:41 UTC |
| fca2f4f | John Chilton | 19 May 2019, 20:17:46 UTC | Merge pull request #8004 from mvdbeek/add_missing_commits_to_backport [19.05] Add missing commits from #7995 backport | 19 May 2019, 20:17:46 UTC |
| a71a44b | Marius van den Beek | 19 May 2019, 13:12:01 UTC | Merge pull request #8003 from galaxyproject/release_19.01 Merge 19.01 into 19.05 | 19 May 2019, 13:12:01 UTC |
| ecc453b | mvdbeek | 17 May 2019, 15:53:47 UTC | Group with statements and clean up docstring | 19 May 2019, 07:30:26 UTC |
| 9c06527 | mvdbeek | 17 May 2019, 15:38:40 UTC | Simplify convert_newlines_sep2tabs Just call convert_newlines with a compiled regex | 19 May 2019, 07:30:26 UTC |
| b67ddbf | mvdbeek | 17 May 2019, 14:14:44 UTC | Drop (seemingly?) unused sep2tabs function | 19 May 2019, 07:30:26 UTC |
| 0638240 | mvdbeek | 17 May 2019, 09:24:44 UTC | Operate on blocks directly | 19 May 2019, 07:30:26 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 |
| 1543c0b | John Chilton | 17 May 2019, 22:23:47 UTC | Merge pull request #8000 from jmchilton/backport_newline_stuff [19.05] Backport #7995 | 17 May 2019, 22:23:47 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 |
| a5c0104 | John Chilton | 17 May 2019, 19:47:21 UTC | Merge pull request #7967 from mvdbeek/use_node_watch_for_monitoring_db [19.05] Use node-watch instead of fs.watch to watch for db changes | 17 May 2019, 19:47:21 UTC |
| 3c5c7a0 | mvdbeek | 17 May 2019, 10:18:50 UTC | Parametrize sniff_test | 17 May 2019, 19:41:14 UTC |
| b6185fc | mvdbeek | 17 May 2019, 08:58:36 UTC | Fix line counting | 17 May 2019, 19:41:14 UTC |
| 6878e39 | mvdbeek | 17 May 2019, 08:42:43 UTC | Fix test_sniff unittest | 17 May 2019, 19:41:14 UTC |
| 06aa7d2 | mvdbeek | 17 May 2019, 08:42:20 UTC | Use byte replacement strategy | 17 May 2019, 19:41:13 UTC |
| 6887398 | John Chilton | 16 May 2019, 19:12:14 UTC | Binary variant of convert_newlines. | 17 May 2019, 19:41:13 UTC |
| 0e707f2 | John Chilton | 16 May 2019, 19:10:22 UTC | Improve sniffing test cases. | 17 May 2019, 19:41:13 UTC |
| 73b92af | John Chilton | 16 May 2019, 13:57:03 UTC | Binary upload fix for interaction with FilePrefix stuff. | 17 May 2019, 19:41:13 UTC |
| d3f2ce0 | John Chilton | 15 May 2019, 18:49:59 UTC | Attempt binary conversion of newlines if UTF conversion fails. | 17 May 2019, 19:41:13 UTC |
| 85f9ead | John Chilton | 14 May 2019, 19:13:01 UTC | Improved newline conversion handling. - Fix bug where sep2tabs didn't work with '\r\n' - Fix bug where sep2tabs didn't work with '\r' - we were opening it with universal newlines. - Fix memory bug where convert_newlines would read unbounded buffers - other methods still do though :(. - Simplify convert_newlines to just let universal newline handling handle the conversion. | 17 May 2019, 19:41:13 UTC |
| 6000f79 | John Chilton | 13 May 2019, 01:49:14 UTC | Fix extra newlines in peek code. Behavior changes: - Now includes a trailing new line if the input contained a trailing newline. - Now returns only as many lines as are present if the file contains fewer lines than LINE_COUNT. | 17 May 2019, 19:41:13 UTC |
