| fada8d2 | Nicola Soranzo | 05 July 2017, 14:05:28 UTC | Merge branch 'release_16.07' into release_16.10 | 05 July 2017, 14:05:28 UTC |
| 5a39d47 | John Chilton | 05 July 2017, 13:44:32 UTC | Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 | 05 July 2017, 13:44:32 UTC |
| 0ff61d9 | Nicola Soranzo | 25 June 2017, 23:36:42 UTC | Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. | 26 June 2017, 12:44:36 UTC |
| 490e565 | Martin Cech | 21 March 2017, 16:42:22 UTC | Merge pull request #3790 from galaxyproject/release_16.07 merge 16.07 into 16.10 | 21 March 2017, 16:42:22 UTC |
| 80ecc79 | Martin Cech | 21 March 2017, 16:41:38 UTC | Merge pull request #3789 from galaxyproject/release_16.04 merge 16.04 into 16.07 | 21 March 2017, 16:41:38 UTC |
| 2528a89 | Nicola Soranzo | 20 March 2017, 16:54:24 UTC | Merge pull request #3776 from martenson/xss-fix [16.04] fix xss vuln in grids | 20 March 2017, 16:54:24 UTC |
| 12eb383 | Martin Cech | 20 March 2017, 14:00:41 UTC | fix xss thanks to @erasche | 20 March 2017, 14:00:41 UTC |
| 1b9a286 | John Chilton | 09 March 2017, 13:11:56 UTC | Merge pull request #3728 from martenson/backport-masthead-fix [16.10] backport of webhook masthead fix for datalibs and workflows | 09 March 2017, 13:11:56 UTC |
| 02f3a27 | anuprulez | 21 December 2016, 11:46:14 UTC | Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages | 08 March 2017, 20:17:15 UTC |
| b41b8e3 | Martin Cech | 04 February 2017, 20:04:16 UTC | Merge pull request #3558 from natefoo/toolconf-watch-hash [16.10] Ensure toolbox conf watcher updates cached hash when config change is detected | 04 February 2017, 20:04:16 UTC |
| 934bf6b | Nate Coraor | 04 February 2017, 03:19:55 UTC | Ensure toolbox conf watcher updates cached hash when config change is detected | 04 February 2017, 03:19:55 UTC |
| 4df803a | Marius van den Beek | 03 February 2017, 09:00:43 UTC | Merge pull request #3532 from guerler/fix_new_history_naming [16.10] Fix new history naming for batchmode workflow runs | 03 February 2017, 09:00:43 UTC |
| f985b61 | guerler | 01 February 2017, 18:30:39 UTC | Fix new history naming for batchmode workflow runs | 01 February 2017, 18:30:39 UTC |
| e499951 | Daniel Blankenberg | 30 January 2017, 22:25:58 UTC | Merge pull request #3486 from mvdbeek/converter_reload [16.10] BUG: Reload converter tools after toolbox reload | 30 January 2017, 22:25:58 UTC |
| 36ecf28 | mvdbeek | 25 January 2017, 16:16:42 UTC | Use CONVERTER_fasta_to_tabular as example converter (thx @jmchilton) | 25 January 2017, 16:18:42 UTC |
| 78b4f8f | mvdbeek | 25 January 2017, 16:00:29 UTC | Reload converter tools after toolbox reload | 25 January 2017, 16:18:42 UTC |
| dd77cdb | mvdbeek | 25 January 2017, 12:46:20 UTC | Add API test for converters after toolbox reload | 25 January 2017, 16:18:41 UTC |
| 1c0c378 | Nicola Soranzo | 23 January 2017, 16:58:32 UTC | Merge branch 'release_16.07' into release_16.10 | 23 January 2017, 16:58:32 UTC |
| 915b653 | Martin Cech | 23 January 2017, 15:08:30 UTC | Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers | 23 January 2017, 15:08:30 UTC |
| 3f93b19 | Bjoern Gruening | 22 January 2017, 21:21:00 UTC | fix condor containers | 23 January 2017, 14:23:37 UTC |
| c9fdb6e | John Chilton | 19 January 2017, 16:24:34 UTC | Merge pull request #3449 from dannon/backport_mistargeted_3429 [16.10] Backport of 3429, safestringwrapper | 19 January 2017, 16:24:34 UTC |
| f508260 | Nicola Soranzo | 16 January 2017, 11:14:08 UTC | Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. | 19 January 2017, 15:09:01 UTC |
| 02a8a7d | John Chilton | 16 January 2017, 01:08:35 UTC | Merge pull request #3416 from dannon/ui_misc_message_fixes [16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html | 16 January 2017, 01:08:35 UTC |
| 08454cf | Dannon Baker | 13 January 2017, 19:50:48 UTC | Name function appropriately for Javascript instead of being stuck in Python. | 13 January 2017, 19:50:48 UTC |
| c94ccb3 | John Chilton | 13 January 2017, 13:59:07 UTC | Merge pull request #3414 from erasche/fix-rstudio-login [16.10] Fix RStudio login | 13 January 2017, 13:59:07 UTC |
| b798895 | Dannon Baker | 12 January 2017, 21:38:41 UTC | Swap form-view to use the new UnescapedMessage | 12 January 2017, 21:38:41 UTC |
| 68f5bc7 | Dannon Baker | 12 January 2017, 21:10:50 UTC | Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component. | 12 January 2017, 21:10:50 UTC |
| 2d69909 | John Chilton | 12 January 2017, 21:04:20 UTC | Merge pull request #3415 from dannon/revert_uimisc [16.10]Reversion of ui-misc messagebox changes. | 12 January 2017, 21:04:20 UTC |
| 8901073 | Dannon Baker | 12 January 2017, 21:02:03 UTC | Reversion of ui-misc messagebox changes. | 12 January 2017, 21:02:03 UTC |
| 45a9d58 | Dannon Baker | 12 January 2017, 17:00:43 UTC | Formatting cleanup. | 12 January 2017, 20:51:18 UTC |
| 3060da4 | Dannon Baker | 12 January 2017, 16:45:28 UTC | Export UnescapedMessage from ui-misc. | 12 January 2017, 20:49:30 UTC |
| cc4cd55 | Eric Rasche | 12 January 2017, 20:48:51 UTC | Fix RStudio login Thanks @shiltemann for reporting this | 12 January 2017, 20:48:51 UTC |
| e108313 | Dannon Baker | 12 January 2017, 16:25:34 UTC | Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own. | 12 January 2017, 20:42:05 UTC |
| a5c4459 | Dannon Baker | 12 January 2017, 15:37:54 UTC | Swap the client's ui-misc.Message to escape by default. | 12 January 2017, 17:10:38 UTC |
| b0ac7da | Martin Cech | 11 January 2017, 17:28:04 UTC | Merge pull request #3405 from dannon/remoteuser_logout_fix [16.10] Remoteuser Logout Fix. | 11 January 2017, 17:28:04 UTC |
| d49e014 | Dannon Baker | 11 January 2017, 15:58:37 UTC | The /user/logout endpoint is now used for both remote and internal users to handle logout logic, and should be accessible here. | 11 January 2017, 15:58:37 UTC |
| 535dd7a | Martin Cech | 11 January 2017, 15:16:04 UTC | Merge pull request #3404 from dannon/backport_viz_escape [16.10] Backport of visualization hda.name escapes | 11 January 2017, 15:16:04 UTC |
| 2d991bb | yhoogstrate | 02 January 2017, 15:43:23 UTC | Escapes some variables | 11 January 2017, 14:17:44 UTC |
| 24b250a | Martin Cech | 10 January 2017, 13:56:51 UTC | Merge pull request #3397 from jmchilton/backport_3395 [16.10] Backport #3395 | 10 January 2017, 13:56:51 UTC |
| 79752b5 | John Chilton | 09 January 2017, 20:11:34 UTC | Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. | 10 January 2017, 13:09:19 UTC |
| 63e70f4 | Aysam Guerler | 09 January 2017, 07:28:59 UTC | Merge pull request #3376 from jmchilton/fix_3247 [16.10] Fix workflow extraction of dataset/collections name. | 09 January 2017, 07:28:59 UTC |
| 41f5ff4 | Björn Grüning | 08 January 2017, 11:35:06 UTC | Merge pull request #3375 from jmchilton/fix_3268 [16.10] Fix implicit conversion for sessionless tool API calls. | 08 January 2017, 11:35:06 UTC |
| 4d73dfc | Dannon Baker | 06 January 2017, 15:55:37 UTC | Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 | 06 January 2017, 15:55:37 UTC |
| 5b3debc | Dannon Baker | 06 January 2017, 15:50:44 UTC | Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. | 06 January 2017, 15:50:44 UTC |
| c368711 | John Chilton | 05 January 2017, 14:07:16 UTC | Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. | 05 January 2017, 19:48:53 UTC |
| b6e9f4a | John Chilton | 27 December 2016, 20:45:51 UTC | Fix workflow extraction of dataset/collections name. It works fine if multiple names are chosen, but if only one input is selected and named it doesn't work. This is a temporary workaround until that page is replaced by API calls with superior typing. Fixes #3247 reported by @peterjc. | 27 December 2016, 20:45:51 UTC |
| 06cc5f5 | John Chilton | 27 December 2016, 20:11:03 UTC | Fix implicit conversion for sessionless tool API calls. Also fixes it for backgrounded workflow invocations (fixes #3268 reported by @guerler). Includes a new test tool w/test definition that exercises this functionality. This tool fails without these changes. | 27 December 2016, 20:16:24 UTC |
| 4d84b3f | Martin Cech | 23 December 2016, 22:12:26 UTC | Merge pull request #3357 from jmchilton/backport_3185 [16.10] Backport #3185 | 23 December 2016, 22:12:26 UTC |
| b400a15 | Martin Cech | 23 December 2016, 22:10:47 UTC | Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. | 23 December 2016, 22:10:47 UTC |
| b57a961 | John Chilton | 22 December 2016, 02:48:23 UTC | Merge changes fixing tour from dev commit 10720fa4f9e26b3feec1a90468f4ecc726a99c05 Cannot do a full cherry-pick because the test modified did not exist in 16.10. | 22 December 2016, 02:48:23 UTC |
| 3d155f0 | Dannon Baker | 16 November 2016, 17:24:28 UTC | Fix history list selector | 22 December 2016, 02:47:42 UTC |
| 69fe5ae | John Chilton | 21 December 2016, 17:56:56 UTC | Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). | 22 December 2016, 02:42:59 UTC |
| 42a4613 | John Chilton | 21 December 2016, 17:56:17 UTC | Fix linting of 16.07 broken with security patches. | 22 December 2016, 02:42:59 UTC |
| 17a752d | Björn Grüning | 21 December 2016, 22:00:45 UTC | Merge pull request #3346 from jmchilton/docker_tools_fix [16.10] Fix explicit Docker container resolution. | 21 December 2016, 22:00:45 UTC |
| 14549d0 | Björn Grüning | 21 December 2016, 21:58:55 UTC | Merge pull request #3354 from jmchilton/1610_conda_fixes [16.10] Merge forward #3351. | 21 December 2016, 21:58:55 UTC |
| 8b75305 | Nicola Soranzo | 21 December 2016, 20:18:40 UTC | Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. | 21 December 2016, 20:18:40 UTC |
| 4969c4a | John Chilton | 21 December 2016, 18:52:18 UTC | Merge 16.07 conda fix from #3351 into 16.10. Tricky merge - please review. Conflicts: lib/galaxy/tools/deps/resolvers/conda.py | 21 December 2016, 18:56:43 UTC |
| fe2a1d8 | John Chilton | 21 December 2016, 16:34:14 UTC | Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. | 21 December 2016, 18:32:50 UTC |
| 05cd16f | John Chilton | 20 December 2016, 18:11:18 UTC | Fix explicit Docker container resolution. Fix thanks to @stevecassidy. Fixes #3207. Broken with introduction of container resolution stradegies in #2986. | 20 December 2016, 18:12:25 UTC |
| 5eafa8b | Daniel Blankenberg | 20 December 2016, 01:54:53 UTC | Merge pull request #3335 from nsoranzo/release_16.10_backport_3324 [16.10] Backport #3324 | 20 December 2016, 01:54:53 UTC |
| 553ec58 | Dannon Baker | 19 December 2016, 15:54:49 UTC | Merge pull request #3329 from guerler/fix_workflow_parameters [16.10] Fix workflow parameter handling | 19 December 2016, 15:54:49 UTC |
| 854b24b | John Chilton | 16 December 2016, 13:24:05 UTC | Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. | 19 December 2016, 14:40:55 UTC |
| 5c3a0e1 | guerler | 17 December 2016, 20:22:20 UTC | Identify workflow parameters through regex from original value | 17 December 2016, 20:22:20 UTC |
| 3f07c7b | guerler | 17 December 2016, 20:03:28 UTC | Preserve template value if no workflow parameter value has been specified | 17 December 2016, 20:03:28 UTC |
| 733a53a | guerler | 17 December 2016, 20:00:57 UTC | Replace workflow parameter values in template value string | 17 December 2016, 20:00:57 UTC |
| b6e9ba4 | guerler | 16 December 2016, 20:14:54 UTC | Allow multiple workflow parameters in a single line | 16 December 2016, 20:14:54 UTC |
| c139790 | Nate Coraor | 15 December 2016, 19:09:48 UTC | Update version to 16.10 | 15 December 2016, 19:09:48 UTC |
| 5c01c01 | Nate Coraor | 15 December 2016, 19:07:00 UTC | Add security disclosure to release notes | 15 December 2016, 19:07:00 UTC |
| 42cda96 | Nate Coraor | 15 December 2016, 18:07:39 UTC | Merge branch 'release_16.07' into release_16.10 | 15 December 2016, 18:07:39 UTC |
| 22fda44 | Nate Coraor | 15 December 2016, 18:05:22 UTC | Merge branch 'release_16.04' into release_16.07 | 15 December 2016, 18:05:22 UTC |
| 4cf70ae | Nate Coraor | 15 December 2016, 18:04:29 UTC | Merge branch 'release_16.01' into release_16.04 | 15 December 2016, 18:04:29 UTC |
| 4c07734 | Nate Coraor | 15 December 2016, 17:55:39 UTC | Merge branch 'release_15.10' into release_16.01 | 15 December 2016, 17:55:39 UTC |
| 95daf69 | Nate Coraor | 15 December 2016, 17:49:39 UTC | Merge branch 'release_15.07' into release_15.10 | 15 December 2016, 17:49:39 UTC |
| 790e60a | Nate Coraor | 15 December 2016, 17:46:17 UTC | Merge branch 'release_15.05' into release_15.07 | 15 December 2016, 17:46:17 UTC |
| 7c443ed | Nate Coraor | 15 December 2016, 17:38:28 UTC | Merge branch 'release_15.03' into release_15.05 | 15 December 2016, 17:38:28 UTC |
| da7afb4 | Nate Coraor | 15 December 2016, 17:37:10 UTC | Merge branch 'release_15.01' into release_15.03 | 15 December 2016, 17:37:10 UTC |
| 9ee3d01 | Nate Coraor | 15 December 2016, 17:36:21 UTC | Merge branch 'release_14.10' into release_15.01 | 15 December 2016, 17:36:21 UTC |
| c1e3087 | Nate Coraor | 15 December 2016, 17:34:18 UTC | Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. | 15 December 2016, 17:34:18 UTC |
| d2ab7e7 | Bjoern Gruening | 14 December 2016, 21:46:36 UTC | build the client | 14 December 2016, 21:46:36 UTC |
| 3ab4e1d | Dannon Baker | 14 December 2016, 20:59:18 UTC | The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming / | 14 December 2016, 20:59:18 UTC |
| 329108f | Nate Coraor | 14 December 2016, 18:44:44 UTC | Merge pull request #3310 from jmchilton/shell_fix [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. | 14 December 2016, 18:44:44 UTC |
| bb8a5a2 | John Chilton | 13 December 2016, 18:36:24 UTC | [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309. This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129. | 13 December 2016, 18:36:53 UTC |
| 2c83349 | John Chilton | 12 December 2016, 03:48:29 UTC | Merge pull request #3287 from guerler/fix_chart_datatypes [16.10] Rely on tabular subclass matching through vizframework layer | 12 December 2016, 03:48:29 UTC |
| 22c7fcf | John Chilton | 12 December 2016, 03:40:00 UTC | Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes [16.10] Tool install fixes | 12 December 2016, 03:40:00 UTC |
| 9dda310 | John Chilton | 12 December 2016, 03:39:21 UTC | Merge pull request #3296 from dannon/workflow_editor_toolsearch_messagebox_fix [16.10] Workflow editor 'messagebox' fix. | 12 December 2016, 03:39:21 UTC |
| 5a7f9e8 | Nicola Soranzo | 09 December 2016, 12:38:35 UTC | Correctly update TS repo status Execute build_dependency_cache() only if using a cached dependency manager. Set tool versions only if the TS repo contains tools. Raise exception if fetch_tool_versions() fails, previously the error message never reached the UI. | 11 December 2016, 20:31:38 UTC |
| d6d2a12 | Nicola Soranzo | 09 December 2016, 17:09:28 UTC | Merge branch 'release_16.07' into release_16.10 Conflicts: client/galaxy/scripts/mvc/upload/composite/composite-row.js client/galaxy/scripts/mvc/upload/default/default-row.js static/maps/mvc/upload/composite/composite-row.js.map static/maps/mvc/upload/default/default-row.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js.map static/scripts/mvc/upload/composite/composite-row.js static/scripts/mvc/upload/default/default-row.js | 09 December 2016, 17:09:28 UTC |
| 602f2f2 | Nate Coraor | 09 December 2016, 16:53:23 UTC | Merge pull request #3292 from dannon/backport_upload_fn_escape [16.07] Upload file escaping backport. | 09 December 2016, 16:53:23 UTC |
| 7c9d9d2 | Dannon Baker | 09 December 2016, 14:56:29 UTC | Apply a fix similar to 36134bca694c9dc6b2584fb661dfbce4ddb793e6 for the workflow editor. Not ideal, but this is old code we're replacing as the editor is overhauled. | 09 December 2016, 14:56:29 UTC |
| 879e3d6 | Nicola Soranzo | 07 December 2016, 21:50:53 UTC | Skip building cache if force_rebuild is False Also: - re-raise exception if rmtree() fails - change hash(ed)_requirements to hash(ed)_dependencies | 09 December 2016, 11:45:14 UTC |
| 2268741 | Nicola Soranzo | 07 December 2016, 20:48:10 UTC | Ensure Conda prefix and cached environment are absolute paths Otherwise when Conda commands are executed from the job working directory, they will break. | 09 December 2016, 11:45:14 UTC |
| ca99753 | Martin Cech | 08 December 2016, 22:17:09 UTC | Merge pull request #3281 from nsoranzo/release_16.10_fix_doc_Makefile [16.10] Use OSX-compatible sed syntax | 08 December 2016, 22:17:09 UTC |
| 13ae374 | Nicola Soranzo | 08 December 2016, 20:45:43 UTC | Move sed commands to a script to resolve interferences with Make which happen only under OSX | 08 December 2016, 20:46:06 UTC |
| c315f1d | Dannon Baker | 08 December 2016, 20:31:59 UTC | Upload file escaping backport. | 08 December 2016, 20:31:59 UTC |
| 4431d73 | guerler | 08 December 2016, 16:22:13 UTC | Extend list of tabular datatypes for bar diagrams | 08 December 2016, 17:08:58 UTC |
| 2cbf9a9 | John Chilton | 08 December 2016, 16:00:12 UTC | Merge pull request #3284 from martenson/notes-tinies [16.10] add small touches to release notes | 08 December 2016, 16:00:12 UTC |
| c01e25d | Martin Cech | 08 December 2016, 15:41:26 UTC | missing articles | 08 December 2016, 15:41:26 UTC |
| e3fbbc5 | Martin Cech | 08 December 2016, 15:37:44 UTC | add small touches to release notes | 08 December 2016, 15:37:44 UTC |
| 9c43568 | Dannon Baker | 07 December 2016, 21:31:02 UTC | Don't rely on complex, absolute selector, use local element.find() | 07 December 2016, 21:31:02 UTC |
| 83de83e | John Chilton | 07 December 2016, 21:27:11 UTC | Merge pull request #3282 from martenson/release_16.10 [16.10] work on release notes 16.10 | 07 December 2016, 21:27:11 UTC |
