| 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 |
| 0122040 | Nate Coraor | 24 February 2016, 18:23:36 UTC | Update version to 15.03.4 | 24 February 2016, 18:23:36 UTC |
| f8a1aef | Nate Coraor | 24 February 2016, 16:18:20 UTC | Merge branch 'release_15.01' into release_15.03 | 24 February 2016, 16:18:20 UTC |
| 581808a | Nate Coraor | 24 February 2016, 16:18:20 UTC | Security fixes for tool shed hg push and capsule/tarball uploads | 24 February 2016, 16:18:20 UTC |
| 626cade | Nate Coraor | 24 February 2016, 16:18:20 UTC | Security fixes for tool shed repository browsing | 24 February 2016, 16:18:20 UTC |
| d4b9472 | Nate Coraor | 24 February 2016, 16:18:20 UTC | Remove sample tracking manual external service transfer due to security concerns | 24 February 2016, 16:18:20 UTC |
| c896378 | Nate Coraor | 24 February 2016, 16:18:20 UTC | Security fixes for object store paths | 24 February 2016, 16:18:20 UTC |
| 61cd045 | Nate Coraor | 24 February 2016, 16:18:19 UTC | Merge branch 'release_14.10' into release_15.01 | 24 February 2016, 16:18:19 UTC |
| 4845a39 | Nate Coraor | 24 February 2016, 16:18:19 UTC | Security fixes for tool shed hg push and capsule/tarball uploads | 24 February 2016, 16:18:19 UTC |
| 4f3397f | Nate Coraor | 24 February 2016, 16:18:19 UTC | Security fixes for tool shed repository browsing | 24 February 2016, 16:18:19 UTC |
| 37548ef | Nate Coraor | 24 February 2016, 16:18:19 UTC | Remove sample tracking manual external service transfer due to security concerns | 24 February 2016, 16:18:19 UTC |
| cee85ba | Nate Coraor | 24 February 2016, 16:18:19 UTC | Security fixes for tool shed repository browsing | 24 February 2016, 16:18:19 UTC |
| 78f441b | Nate Coraor | 24 February 2016, 16:18:19 UTC | Remove sample tracking manual external service transfer due to security concerns | 24 February 2016, 16:18:19 UTC |
| 32c910a | Nate Coraor | 24 February 2016, 16:18:19 UTC | Security fixes for object store paths | 24 February 2016, 16:18:19 UTC |
| d650055 | Nate Coraor | 24 February 2016, 16:18:19 UTC | Security fixes for object store paths | 24 February 2016, 16:18:19 UTC |
| 88277c9 | Nate Coraor | 24 February 2016, 16:18:19 UTC | Security fixes for history imports | 24 February 2016, 16:18:19 UTC |
| 5ab53c3 | Nate Coraor | 24 February 2016, 16:18:19 UTC | Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory | 24 February 2016, 16:18:19 UTC |
| ef4a9f6 | Nate Coraor | 24 February 2016, 16:18:19 UTC | Security fixes for history imports | 24 February 2016, 16:18:19 UTC |
| 8468871 | Nate Coraor | 24 February 2016, 16:18:19 UTC | Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory | 24 February 2016, 16:18:19 UTC |
| 3b96322 | Nate Coraor | 24 February 2016, 16:18:18 UTC | Security fixes for history imports | 24 February 2016, 16:18:18 UTC |
| ca123a4 | Nate Coraor | 24 February 2016, 16:18:18 UTC | Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory | 24 February 2016, 16:18:18 UTC |
| b23acda | Nicola Soranzo | 21 August 2015, 18:36:08 UTC | Merge branch 'release_15.01' into release_15.03 | 21 August 2015, 18:36:08 UTC |
| 46e67b5 | Nicola Soranzo | 21 August 2015, 18:31:52 UTC | Merge branch 'release_14.10' into release_15.01 | 21 August 2015, 18:31:52 UTC |
| 360a6ad | Björn Grüning | 21 August 2015, 18:28:25 UTC | Merge pull request #634 from nsoranzo/release_14.10 [14.10] Backport tool lineage fix. | 21 August 2015, 18:28:25 UTC |
| 85c9712 | Nicola Soranzo | 12 August 2015, 17:25:40 UTC | Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. | 21 August 2015, 17:51:24 UTC |
| e06d6a1 | Dannon Baker | 21 August 2015, 13:58:12 UTC | Merge branch 'release_15.01' into release_15.03 | 21 August 2015, 13:58:12 UTC |
| 4d2651a | Dannon Baker | 20 August 2015, 15:41:18 UTC | Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. | 21 August 2015, 13:57:47 UTC |
| b29e810 | Dannon Baker | 20 August 2015, 15:13:44 UTC | Fix for valid height/width definitions in workflow rendering code. | 21 August 2015, 13:57:38 UTC |
| 01278aa | Dannon Baker | 19 August 2015, 23:42:00 UTC | Merge branch 'release_15.01' into release_15.03 | 19 August 2015, 23:42:00 UTC |
| 71f28c9 | Dannon Baker | 19 August 2015, 23:41:39 UTC | Merge pull request #622 from erasche/tool-reloading-fix [15.01] Tool reloading fix | 19 August 2015, 23:41:39 UTC |
| a1bff67 | Eric Rasche | 19 August 2015, 20:26:47 UTC | Fix bug in tool reloading API where ID not passed | 19 August 2015, 20:26:47 UTC |
| a6a85cb | Nate Coraor | 12 August 2015, 21:11:02 UTC | Bump version to 15.03.3 | 12 August 2015, 21:11:02 UTC |
| a454c93 | Nate Coraor | 12 August 2015, 20:52:52 UTC | Merge branch 'security-20150812-xss' into release_15.03 | 12 August 2015, 20:52:52 UTC |
| 25d8a54 | Nate Coraor | 12 August 2015, 20:52:44 UTC | Merge branch 'security-20150812-shed' into release_15.03 | 12 August 2015, 20:52:44 UTC |
| 096a168 | Nate Coraor | 12 August 2015, 20:52:13 UTC | Merge branch 'security-20150812-shed' into release_15.01 | 12 August 2015, 20:52:13 UTC |
| 6dc5f02 | Nate Coraor | 12 August 2015, 20:52:04 UTC | Merge branch 'security-20150812-xss' into release_15.01 | 12 August 2015, 20:52:04 UTC |
| 8e7017a | Martin Cech | 12 August 2015, 20:51:10 UTC | Fix a vulnerability in the Tool Shed API that allowed unauthorized users to upload new repository versions. | 12 August 2015, 20:51:10 UTC |
| cbae8fa | Nate Coraor | 12 August 2015, 20:43:52 UTC | Fix an XSS reflection vulnerability on the workflow import form. | 12 August 2015, 20:43:52 UTC |
| 4445092 | Aysam Guerler | 28 May 2015, 15:44:53 UTC | Merge pull request #293 from jmchilton/history_tag_fix_15.03 [15.03] Fix tag creation via /tags API endpoints. | 28 May 2015, 15:44:53 UTC |
| 2ca8f76 | John Chilton | 26 May 2015, 02:29:44 UTC | Fix tag creation via /tags API endpoints. Add test case to at least check for exceptions such as those reported. Closes galaxyproject/bioblend#145. | 27 May 2015, 16:51:53 UTC |
| 5cf0332 | John Chilton | 05 May 2015, 14:26:45 UTC | Merge pull request #215 from dannon/release_15.03 [15.03] Check to see if toolshed install is actually bound prior to disposing (e... | 05 May 2015, 14:26:45 UTC |
| c1c8259 | Dannon Baker | 10 April 2015, 15:23:46 UTC | Check to see if toolshed install is actually bound prior to disposing (exact same functionality here, but it's less chatty this way, since it might not be bound) | 05 May 2015, 14:10:40 UTC |
| d523d53 | Dannon Baker | 05 May 2015, 13:22:51 UTC | Merge pull request #213 from jmchilton/job_files_fix [STABLE] Job file API fixes | 05 May 2015, 13:22:51 UTC |
| a594b32 | John Chilton | 05 May 2015, 12:22:45 UTC | Fix job files API for case when nginx upload not being used. Fixes regressions introduced with PR #110. | 05 May 2015, 12:22:45 UTC |
| a319329 | John Chilton | 01 May 2015, 20:33:46 UTC | Merge pull request #201 from bgruening/couple_image_to_ie [Stable] Bind the IPython IE to a fixed Docker Image | 01 May 2015, 20:33:46 UTC |
| f417527 | Dannon Baker | 01 May 2015, 19:38:20 UTC | Merge 15.01 into 15.03 | 01 May 2015, 19:38:20 UTC |
| 9f67bdb | Dannon Baker | 01 May 2015, 19:35:17 UTC | Merge branch 'release_14.10' into release_15.01 | 01 May 2015, 19:35:17 UTC |
| 0972c14 | Dannon Baker | 01 May 2015, 19:26:06 UTC | Merge pull request #199 from dannon/release_14.10 [STABLE] Import safe_dumps from galaxy_utils to properly set metadata for interva... | 01 May 2015, 19:26:06 UTC |
| 5f2c364 | Marius van den Beek | 30 April 2015, 17:39:23 UTC | Import safe_dumps from galaxy_utils to properly set metadata for interval files. | 01 May 2015, 18:59:39 UTC |
| 9cdd688 | Bjoern Gruening | 01 May 2015, 18:54:53 UTC | Bind the IPython IE to a fixed Docker Image | 01 May 2015, 18:54:53 UTC |
| 4c7c295 | Nate Coraor | 01 May 2015, 16:11:19 UTC | Merge pull request #195 from natefoo/fix_galaxy_lib_dir [STABLE] Ensure JobWrapper.galaxy_lib_dir is set | 01 May 2015, 16:11:19 UTC |
| f7e4338 | Nate Coraor | 01 May 2015, 15:48:04 UTC | Ensure JobWrapper.galaxy_lib_dir is set, necessary for locally setting metadata externally with Pulsar, which (sometimes?) does not call the wrapper's prepare() method. | 01 May 2015, 15:48:04 UTC |
| f472d9b | Dannon Baker | 28 April 2015, 19:47:17 UTC | Merge pull request #178 from natefoo/release_15.03 [STABLE] Fix job stopping under some conditions | 28 April 2015, 19:47:17 UTC |
| 3211466 | Nate Coraor | 28 April 2015, 19:26:29 UTC | Don't use a bare except | 28 April 2015, 19:26:29 UTC |
| f0fc892 | Nate Coraor | 28 April 2015, 15:43:18 UTC | Fix job stopping under some conditions: 1. track_jobs_in_database is False 2. Jobs being stopped were in the local runner 3. Jobs were deleted with the deleted state and not deleted_new | 28 April 2015, 15:49:18 UTC |
| 78aa8e0 | Dannon Baker | 27 April 2015, 19:07:25 UTC | Merge pull request #174 from natefoo/fix_shed_check [STABLE] Make the `enable_tool_shed_check` option perform as advertised in the sample config file, disable checks at startup. | 27 April 2015, 19:07:25 UTC |
| ffbfcc6 | Nate Coraor | 27 April 2015, 18:56:30 UTC | Make the `enable_tool_shed_check` option perform as advertised in the sample config file. Also disables checks at startup. | 27 April 2015, 18:56:30 UTC |
| af7c97c | Dannon Baker | 25 April 2015, 14:40:50 UTC | Merge pull request #146 from guerler/fix_nested_conditional_defaults [STABLE] Fix default values for nested conditional test parameters | 25 April 2015, 14:40:50 UTC |
| 78ceeae | Dannon Baker | 23 April 2015, 21:02:42 UTC | Merge pull request #153 from guerler/release_15.03 [STABLE] Fix base url tool parameter | 23 April 2015, 21:02:42 UTC |
| 2ab61d7 | Nate Coraor | 23 April 2015, 20:48:58 UTC | Merge pull request #139 from jmchilton/metadata_fixes [STABLE] Metadata Fixes | 23 April 2015, 20:48:58 UTC |
| d3ba1a7 | guerler | 23 April 2015, 19:05:00 UTC | Fix base url tool parameter | 23 April 2015, 19:05:00 UTC |
| 8688099 | Nate Coraor | 22 April 2015, 19:05:21 UTC | Bump version to 15.03.2 | 22 April 2015, 19:05:21 UTC |
| 60a50d0 | Daniel Blankenberg | 22 April 2015, 18:42:50 UTC | Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. Release 14.08..15.01 version | 22 April 2015, 18:42:50 UTC |
| 1029356 | Daniel Blankenberg | 22 April 2015, 18:40:55 UTC | Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. Release 14.08..15.01 version | 22 April 2015, 18:40:55 UTC |
| af81aad | Daniel Blankenberg | 06 April 2015, 14:29:32 UTC | Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. | 22 April 2015, 18:18:15 UTC |
| 3f1cec4 | guerler | 22 April 2015, 16:21:24 UTC | Fix default values for nested conditional test parameters | 22 April 2015, 16:21:24 UTC |
| 305d51a | Dannon Baker | 21 April 2015, 19:20:33 UTC | Merge pull request #141 from jmchilton/remap_typo [STABLE] Bugfix: Typo in remap dataset handling in tools. | 21 April 2015, 19:20:33 UTC |
| 5d3485c | John Chilton | 21 April 2015, 15:41:33 UTC | Bugfix: Typo in remap dataset handling in tools. | 21 April 2015, 15:41:33 UTC |
| 6676535 | John Chilton | 21 April 2015, 13:36:44 UTC | Bugfix: Fix metadata python path when using _handle_metadata_externally. This is used by lwr, pulsar, and task runners and possibly by the local job runner in some configurations. Broken with PR #22 which was merged into 15.03. | 21 April 2015, 13:39:19 UTC |
| fbe9df2 | John Chilton | 21 April 2015, 13:29:50 UTC | Bugfix: Resolve metadata dependencies for task runner. Also deduplicates code for next fix. | 21 April 2015, 13:39:17 UTC |
| 17856e1 | John Chilton | 16 April 2015, 20:31:35 UTC | Merge pull request #122 from blankenberg/genomespace-export-5g-to-stable [STABLE] Genomespace export 5g | 16 April 2015, 20:31:35 UTC |
| 153bef1 | Daniel Blankenberg | 02 April 2015, 14:16:02 UTC | Enable multi-part upload for the GenomeSpace export tool. Files greater than 5gb can once again be send to GenomeSpace from Galaxy. (cherry picked from commit 126ae073afd39a83db90b3f8002f714be9dfdec2) | 16 April 2015, 13:48:42 UTC |
| a25c5c0 | Daniel Blankenberg | 17 March 2015, 17:08:06 UTC | Some basic Caching for the GenomeSpace Export Tool's list of available target directories, so we don't have to reload and download everything every time, especially now that we are calling the parameter's get options method 5 times (6 on reload) when a user loads the tool interface. For now, we'll use 30 seconds as the cache valid time length. (cherry picked from commit feb0a26f8d24c6eb008c02f00230777d978a62cb) | 16 April 2015, 13:48:35 UTC |
| 1b922ea | John Chilton | 10 April 2015, 20:14:12 UTC | Merge pull request #110 from natefoo/release_15.03 [STABLE] Fix job file stageout interruptibility | 10 April 2015, 20:14:12 UTC |
| 7210e5d | Nate Coraor | 10 April 2015, 19:30:31 UTC | Move, rather than copy files staged back to Galaxy via the job files api. Moving is a rename when the source and destination are on the same filesystem, which is nearly instantaneous and greatly reduces the possibility for failure due to mid-copy restarts. | 10 April 2015, 19:30:31 UTC |
| 1167c7d | Nate Coraor | 10 April 2015, 19:29:18 UTC | Enable use of nginx_upload_module for the job files api. | 10 April 2015, 19:29:18 UTC |
| 47c278e | John Chilton | 08 April 2015, 20:09:21 UTC | Merge pull request #96 from dannon/release_15.03 [STABLE] Connection pool disposal fixes for all 3 apps | 08 April 2015, 20:09:21 UTC |
| 3ac5162 | Dannon Baker | 08 April 2015, 17:46:55 UTC | Another pool disposal fix, for reports. | 08 April 2015, 18:21:39 UTC |
| d403c43 | Dannon Baker | 08 April 2015, 15:53:32 UTC | Similar fix as the previous -- Galaxy wasn't disposing of pooled connections prior to returning webapp and (potential) forking. | 08 April 2015, 18:21:34 UTC |
| d6bf6fc | Dannon Baker | 08 April 2015, 15:50:34 UTC | Potential fix for recent uwsgi toolshed database issues. In any event, this current pool disposal is definitely broken (and hidden from view due to blanket passing except) in the current implementation. | 08 April 2015, 18:21:27 UTC |
| 167fb67 | Martin Cech | 08 April 2015, 15:48:04 UTC | Merge pull request #94 from jmchilton/real_user_doc_fix [STABLE] Fix documentation for run-as-real-user parameters. | 08 April 2015, 15:48:04 UTC |
| 54ccd3e | John Chilton | 08 April 2015, 12:47:10 UTC | Fix documentation for real user parameters. I think what was documented was the ideal case - which would be great if these could be set per destination - but they cannot be so they shouldn't be documented that way. Documentation broken in https://github.com/galaxyproject/galaxy/commit/9b7775be03728f724c025a83bc7ffa9e28c2c932. | 08 April 2015, 12:51:20 UTC |
| 9fd27f6 | John Chilton | 07 April 2015, 17:30:26 UTC | Merge pull request #92 from guerler/release_15.03 [STABLE] Fix re-run option for data manager tools | 07 April 2015, 17:30:26 UTC |
| 3207302 | guerler | 07 April 2015, 17:11:39 UTC | Fix re-run option for data manager tools | 07 April 2015, 17:11:39 UTC |
| 2b20641 | John Chilton | 07 April 2015, 16:35:35 UTC | Merge pull request #79 from guerler/pr_dataset_mapping [STABLE] Revise re-run mapping of datasets and collections for imported ... | 07 April 2015, 16:35:35 UTC |
| 7e075a6 | Dannon Baker | 06 April 2015, 20:24:47 UTC | Merge pull request #88 from carlfeberhard/fix.dataset-purge [STABLE] Fix: datasets.purge_async/_purge to allow purging hdas within non-curren... | 06 April 2015, 20:24:47 UTC |
| 05f37ec | Daniel Blankenberg | 06 April 2015, 19:08:57 UTC | Merge pull request #85 from jmchilton/workflow_runtime_bugfixes [STABLE] Bugfixes for runtime parameter handling in the workflow run form. | 06 April 2015, 19:08:57 UTC |
| f4ab1f8 | Dannon Baker | 06 April 2015, 18:35:36 UTC | Merge pull request #81 from blankenberg/ts_tool_display_fix [STABLE] Fixes for displaying certain valid tool interfaces in the ToolShed. | 06 April 2015, 18:35:36 UTC |
| fb3d622 | Carl Eberhard | 06 April 2015, 17:44:21 UTC | Fix: datasets.purge_async/_purge to allow purging hdas within non-current histories | 06 April 2015, 17:44:21 UTC |
| 8b56505 | Dannon Baker | 06 April 2015, 17:22:35 UTC | Merge pull request #83 from blankenberg/igv_local_stable [STABLE] Re-enable IGV local external display application by default. | 06 April 2015, 17:22:35 UTC |
| 6fee45f | John Chilton | 06 April 2015, 15:37:47 UTC | Bugfixes for runtime parameter handling in the workflow run form. The behavior of these forms was modified in PR 433 (https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editing-workflows-on-the-fly-for/diff# - not merged by me :| ) - so that the entire workflow would be submitted as runtime parameters on each submission. In addition to this causing bugs related to unvalidated parameters https://trello.com/c/72WuZ8mu and other problems with select parameters (e.g. http://dev.list.galaxyproject.org/Workflow-bug-when-loc-entries-are-missing-tc4666875.html) - I just discovered it would also cause the modified value to be submitted even if the user opts to undo the selection of a runtime workflow parameter and restore the previous selection (i.e. the form would show the original value but the new value would be submitted). This PR restores the previous behavior of giving the submitted form elements a unique name so every value in the workflow is not replaced as part of the submission - fixing the former problem. The new technique also fixes the other problem as well. | 06 April 2015, 16:29:40 UTC |
| 62c66d3 | Daniel Blankenberg | 26 March 2015, 14:47:58 UTC | Re-enable IGV local external display application by default. Add hg38 as available genome. We should probably update this view to either allow any genome or to function like the current web_link_main. | 06 April 2015, 15:41:44 UTC |
| 3d92202 | Daniel Blankenberg | 03 April 2015, 18:39:40 UTC | Fixes for displaying certain valid tool interfaces in the ToolShed. | 03 April 2015, 18:39:40 UTC |
| 3bca879 | guerler | 03 April 2015, 15:46:17 UTC | [STABLE] Revise re-run mapping of datasets and collections for imported and copied history items. The previous method (from tool_runner.py) had difficulties with consistently hashing history items which caused issues for imported datasets. We fixed that, however now datasets copied back to the same history are shown instead of the original dataset. | 03 April 2015, 15:46:17 UTC |
| acd6700 | John Chilton | 02 April 2015, 20:07:27 UTC | Merge pull request #77 from dannon/workflow_tag_fix [STABLE] More fixes for removal of trans from various manager functions. | 02 April 2015, 20:07:27 UTC |
| fcb35e0 | Dannon Baker | 02 April 2015, 19:42:38 UTC | More fixes for removal of trans from various manager functions. | 02 April 2015, 19:42:38 UTC |
| 93bd09d | Dannon Baker | 02 April 2015, 15:49:41 UTC | Merge pull request #71 from carlfeberhard/release_15.03 [STABLE] Fix: hda manager trans param in visualizations controller and tools api ... | 02 April 2015, 15:49:41 UTC |
| f5e5812 | Carl Eberhard | 02 April 2015, 15:38:30 UTC | Fix: hda manager trans param in visualizations controller and tools api _rerun_tool | 02 April 2015, 15:38:30 UTC |
