| 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 |
| 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 |
| 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 |
| 3e54b22 | John Chilton | 30 March 2015, 18:07:23 UTC | Merge pull request #55 from martenson/release_15.01-fix-paramget-default [STABLE] [15.01] fix missing defaults for get() | 30 March 2015, 18:07:23 UTC |
| e16e57c | John Chilton | 30 March 2015, 18:07:14 UTC | Merge pull request #54 from martenson/release_14.10-fix-paramget-default [STABLE] [14.10] fix missing defaults for get() | 30 March 2015, 18:07:14 UTC |
| ee611d3 | Martin Cech | 30 March 2015, 17:08:32 UTC | fix missing defaults for get() params class override the method and force default to be included | 30 March 2015, 17:14:50 UTC |
| 69b68c0 | Martin Cech | 30 March 2015, 17:08:32 UTC | fix missing defaults for get() params class override the method and force default to be included | 30 March 2015, 17:08:32 UTC |
| c17a9e5 | Dannon Baker | 12 February 2015, 13:28:37 UTC | Fix path manipulation during fetch_eggs. This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers. | 05 March 2015, 14:57:01 UTC |
| 72f658f | Dannon Baker | 27 February 2015, 16:13:29 UTC | Merge pull request #6 from blankenberg/release_15.01 Fix for ToolShed not having config.shed_tool_data_path | 27 February 2015, 16:13:29 UTC |
| 5099307 | Daniel Blankenberg | 25 February 2015, 17:18:53 UTC | Fix for ToolShed not having config.shed_tool_data_path | 25 February 2015, 17:18:53 UTC |
| 12fb5f4 | John Chilton | 24 February 2015, 17:45:34 UTC | Merge pull request #3 from blankenberg/release_15.01 Fix for installing .loc files from the toolshed to respect shed_tool_dat... | 24 February 2015, 17:45:34 UTC |
| ce3fc2a | Daniel Blankenberg | 24 February 2015, 17:20:34 UTC | Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample. | 24 February 2015, 17:20:34 UTC |
| 664ed02 | Dannon Baker | 23 February 2015, 16:27:01 UTC | Clone .gitignore | 23 February 2015, 16:27:01 UTC |
| 48d5823 | Dannon Baker | 23 February 2015, 16:26:42 UTC | Clone .gitignore | 23 February 2015, 16:26:42 UTC |
| 1304354 | Martin Cech | 16 February 2015, 19:00:52 UTC | back off some over escaping when uploading capsule | 16 February 2015, 19:00:52 UTC |
| d35aa1e | Martin Cech | 16 February 2015, 18:56:59 UTC | Merge | 16 February 2015, 18:56:59 UTC |
| f852463 | Nate Coraor | 13 February 2015, 14:00:30 UTC | Update tag latest_2015.01.13 for changeset a6e9a1d72674 | 13 February 2015, 14:00:30 UTC |
| 212b1f9 | Nate Coraor | 12 February 2015, 18:20:29 UTC | Merged in dannon/galaxy-central/stable (pull request #668) [STABLE] Egg-fetching related bugfixes grafted from default. | 12 February 2015, 18:20:29 UTC |
| 082ff4d | Martin Cech | 12 February 2015, 16:42:29 UTC | Merged in dan/galaxy-central-prs/stable (pull request #667) [STABLE] Fixes for resetting metadata on ToolShed Repositories. | 12 February 2015, 16:42:29 UTC |
| 3961d48 | Dannon Baker | 12 February 2015, 15:34:51 UTC | Fix path insertion vs appending of <galaxy>/lib for all scripts. | 12 February 2015, 15:34:51 UTC |
| 669bdd4 | Nate Coraor | 12 February 2015, 14:00:26 UTC | Update tag latest_2015.01.13 for changeset 577b270034b4 | 12 February 2015, 14:00:26 UTC |
| dce9c1a | Dannon Baker | 12 February 2015, 13:28:37 UTC | Fix path manipulation during fetch_eggs. This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers. | 12 February 2015, 13:28:37 UTC |
| 58e9b20 | Dannon Baker | 12 February 2015, 12:57:51 UTC | Fix at least one error with zipfile downloads and file permissions not being set correctly. | 12 February 2015, 12:57:51 UTC |
| 2332e18 | Daniel Blankenberg | 11 February 2015, 22:36:05 UTC | When resetting repository metadata in the toolshed, don't overwrite the already set relative_install_dir. | 11 February 2015, 22:36:05 UTC |
| 511465b | Daniel Blankenberg | 11 February 2015, 22:31:49 UTC | Always add sample file info to metadata, not only during initial creation.. | 11 February 2015, 22:31:49 UTC |
| 58c4f26 | Daniel Blankenberg | 11 February 2015, 21:50:25 UTC | Fix for resetting repository metadata in the toolshed via UI (pass resetting_all_metadata_on_repository=True flag). | 11 February 2015, 21:50:25 UTC |
| c9f6926 | John Chilton | 11 February 2015, 17:54:36 UTC | Merged in dan/galaxy-central-prs/stable (pull request #666) [STABLE] Several Fixes for Tool Data Tables | 11 February 2015, 17:54:36 UTC |
| 41fcc8e | Daniel Blankenberg | 11 February 2015, 17:40:33 UTC | Fix for parsing Tool Data Table columns that are defined as individual xml elements. | 11 February 2015, 17:40:33 UTC |
| b7e5183 | Daniel Blankenberg | 11 February 2015, 17:37:59 UTC | Fix for TabularToolDataTable.get_named_fields_list() when a data line has extra columns. | 11 February 2015, 17:37:59 UTC |
| 8d82dfb | Daniel Blankenberg | 11 February 2015, 17:33:49 UTC | Fix for Data Tables persisting when .loc file doesn't exist. | 11 February 2015, 17:33:49 UTC |
| 20c0d76 | Martin Cech | 10 February 2015, 17:48:53 UTC | remove incidentally added line | 10 February 2015, 17:48:53 UTC |
| 38641aa | Martin Cech | 10 February 2015, 17:03:19 UTC | removed unnecessary escapes | 10 February 2015, 17:03:19 UTC |
| d6aa0e6 | Martin Cech | 09 February 2015, 23:16:43 UTC | one more batch of escape fixes, mostly amending c2bed0a496f8 https://bitbucket.org/galaxy/galaxy-central/commits/c2bed0a496f8 | 09 February 2015, 23:16:43 UTC |
| 2fbb3d6 | Nate Coraor | 06 February 2015, 14:00:23 UTC | Update tag latest_2015.01.13 for changeset 644deef1a578 | 06 February 2015, 14:00:23 UTC |
| d8875d2 | John Chilton | 05 February 2015, 18:33:59 UTC | Bugfix for bugfix d3b1f6b. d3b1f6b fix the GUI (in an obsecure use) but broke fairly typical uses of the API. | 05 February 2015, 18:33:59 UTC |
| cf16328 | John Chilton | 05 February 2015, 17:14:01 UTC | Fix scheduling_manager.py for unknown attribute reference. Not sure if this was a poor rebasing or a copy and paste error. | 05 February 2015, 17:14:01 UTC |
| 51153c3 | John Chilton | 05 February 2015, 17:14:01 UTC | Workflow scheduling delay fix. There were problems if all three of these conditions were met - 1) workflow from GUI, 2) workflow evaluation delayed, and 3) a delayed step was connected to a input dataset. This fixes these workflows. | 05 February 2015, 17:14:01 UTC |
| accd6f0 | Nate Coraor | 03 February 2015, 14:00:27 UTC | Update tag latest_2015.01.13 for changeset 5e4060f5ac7a | 03 February 2015, 14:00:27 UTC |
| 39baead | John Chilton | 02 February 2015, 21:30:49 UTC | Merged in dan/galaxy-central-prs/stable (pull request #657) [STABLE] Fix for preventing non-admins from running data managers via the api. | 02 February 2015, 21:30:49 UTC |
| 48f77dc | Daniel Blankenberg | 02 February 2015, 21:21:00 UTC | Fix for preventing non-admins from running data managers via the api. | 02 February 2015, 21:21:00 UTC |
| 57ae013 | Nate Coraor | 02 February 2015, 19:00:23 UTC | Update tag latest_2015.01.13 for changeset fd75aaee91cf | 02 February 2015, 19:00:23 UTC |
| c874b23 | John Chilton | 02 February 2015, 14:10:43 UTC | Merged in jmchilton/galaxy-central-backport-2/stable (pull request #638) [STABLE] Backport pull request #636 to all relevant latest_* releases | 02 February 2015, 14:10:43 UTC |
| 9c538ee | Nate Coraor | 30 January 2015, 18:00:22 UTC | Update tag latest_2015.01.13 for changeset c5e7535b4d22 | 30 January 2015, 18:00:22 UTC |
| 9e18e1a | Dave Bouvier | 29 January 2015, 16:23:35 UTC | Set time to epoch instead of throwing server error if repository_metadata.time_last_tested is unset. | 29 January 2015, 16:23:35 UTC |
| 93d377f | Nate Coraor | 29 January 2015, 14:00:24 UTC | Update tag latest_2015.01.13 for changeset a481d17c0448 | 29 January 2015, 14:00:24 UTC |
| 9252d11 | Nate Coraor | 28 January 2015, 18:25:11 UTC | Use subprocess.call() rather than Popen(), thanks Nicola. | 28 January 2015, 18:25:11 UTC |
| fffdaf1 | Nate Coraor | 28 January 2015, 16:58:23 UTC | Use a symlink to the dataset in the same directory as the MetadataTempFile as the input to samtools index so there's no clobber risk. Thanks Dan. | 28 January 2015, 16:58:23 UTC |
| 2f558e3 | Nate Coraor | 28 January 2015, 15:38:22 UTC | Allow BAM's set_meta() to use samtools 1 to generate the index, if the samtools found on $PATH is samtools 1. | 28 January 2015, 15:38:22 UTC |
| 9bed304 | Nate Coraor | 28 January 2015, 14:00:26 UTC | Update tag latest_2015.01.13 for changeset 1b96d3a4ff28 | 28 January 2015, 14:00:26 UTC |
| 43b2f4f | Carl Eberhard | 27 January 2015, 19:32:16 UTC | Remove paragraph tags from history/rename feedback messages | 27 January 2015, 19:32:16 UTC |
| 21409d6 | Nate Coraor | 21 January 2015, 21:00:24 UTC | Update tag latest_2015.01.13 for changeset 4039bfd5584a | 21 January 2015, 21:00:24 UTC |
| df6a7d8 | Dannon Baker | 21 January 2015, 16:46:38 UTC | Merged in carlfeberhard/carlfeberhard-galaxy-central-stable/stable (pull request #642) [STABLE] Fix to allow anon users to view pages with histories | 21 January 2015, 16:46:38 UTC |
| c446be0 | Carl Eberhard | 21 January 2015, 16:33:40 UTC | Fix to allow anon users to view pages with histories | 21 January 2015, 16:33:40 UTC |
| e5db731 | Nate Coraor | 21 January 2015, 14:00:27 UTC | Update tag latest_2015.01.13 for changeset 507edf82ad1d | 21 January 2015, 14:00:27 UTC |
| beec87f | Martin Cech | 20 January 2015, 17:34:26 UTC | Merged in martenson/galaxy-central-stablefix/stable (pull request #641) [STABLE] fix to WF/VIZ links showing when not logged in | 20 January 2015, 17:34:26 UTC |
| 447a48c | Martin Cech | 20 January 2015, 15:12:35 UTC | add ?use_panels=True to the login and register links in WF/VIZ | 20 January 2015, 15:12:35 UTC |
| 071400a | Nate Coraor | 20 January 2015, 14:00:22 UTC | Update tag latest_2015.01.13 for changeset f1cd1bec8272 | 20 January 2015, 14:00:22 UTC |
| 1a02833 | Martin Cech | 19 January 2015, 20:45:50 UTC | Merged in dannon/galaxy-central/stable (pull request #635) [STABLE]Bump bioblend to 0.5.2. | 19 January 2015, 20:45:50 UTC |
| fe273fa | Martin Cech | 19 January 2015, 20:43:13 UTC | galaxy_config.root defaulted from '' to '/' somewhere along the way breaking these links | 19 January 2015, 20:43:13 UTC |
| 27f66b3 | Nate Coraor | 19 January 2015, 14:00:26 UTC | Update tag latest_2015.01.13 for changeset 0cb6cec4ee57 | 19 January 2015, 14:00:26 UTC |
| e1dd5b5 | Dannon Baker | 18 January 2015, 13:39:43 UTC | Merged in guerler/guerler-galaxy-central/stable (pull request #639) Fix for LibraryDatasetToolParameter | 18 January 2015, 13:39:43 UTC |
| 8adba8c | Nate Coraor | 16 January 2015, 14:00:18 UTC | Update tag latest_2015.01.13 for changeset f7235d0ad14f | 16 January 2015, 14:00:18 UTC |
| f5f4049 | Aysam Guerler | 15 January 2015, 21:09:24 UTC | Fix for LibraryDatasetToolParameter | 15 January 2015, 21:09:24 UTC |
| 873ce9e | John Chilton | 15 January 2015, 21:01:37 UTC | Merge head created for backport bug fix on latest_2014.10.06 | 15 January 2015, 21:01:37 UTC |
| bc713eb | John Chilton | 15 January 2015, 21:01:36 UTC | Update tag latest_2014.10.06 for changeset 782fa60fc654 | 15 January 2015, 21:01:36 UTC |
| ed0e764 | John Chilton | 15 January 2015, 21:01:35 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:35 UTC |
| cbfab74 | John Chilton | 15 January 2015, 21:01:34 UTC | Merge head created for backport bug fix on latest_2014.08.11 | 15 January 2015, 21:01:34 UTC |
| 88d4c63 | John Chilton | 15 January 2015, 21:01:34 UTC | Update tag latest_2014.08.11 for changeset 6d6d7f8b3217 | 15 January 2015, 21:01:34 UTC |
| 6304c81 | John Chilton | 15 January 2015, 21:01:33 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:33 UTC |
| bf4381a | John Chilton | 15 January 2015, 21:01:32 UTC | Merge head created for backport bug fix on latest_2014.06.02 | 15 January 2015, 21:01:32 UTC |
| 9dcee02 | John Chilton | 15 January 2015, 21:01:31 UTC | Update tag latest_2014.06.02 for changeset c52dc4c72b77 | 15 January 2015, 21:01:31 UTC |
| cf64a22 | John Chilton | 15 January 2015, 21:01:30 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:30 UTC |
| 29beb00 | John Chilton | 15 January 2015, 21:01:29 UTC | Merge head created for backport bug fix on latest_2014.04.14 | 15 January 2015, 21:01:29 UTC |
| ba78806 | John Chilton | 15 January 2015, 21:01:28 UTC | Update tag latest_2014.04.14 for changeset b2c0570f52e1 | 15 January 2015, 21:01:28 UTC |
| ca34200 | John Chilton | 15 January 2015, 21:01:27 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:27 UTC |
| 9e3da97 | John Chilton | 15 January 2015, 21:01:25 UTC | Merge head created for backport bug fix on latest_2014.02.10 | 15 January 2015, 21:01:25 UTC |
| 3b40397 | John Chilton | 15 January 2015, 21:01:25 UTC | Update tag latest_2014.02.10 for changeset 746db2bf4da0 | 15 January 2015, 21:01:25 UTC |
| baf4b18 | John Chilton | 15 January 2015, 21:01:23 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:23 UTC |
| 327d778 | John Chilton | 15 January 2015, 21:01:22 UTC | Merge head created for backport bug fix on latest_2013.11.04 | 15 January 2015, 21:01:22 UTC |
| d194b20 | John Chilton | 15 January 2015, 21:01:20 UTC | Update tag latest_2013.11.04 for changeset 52a18b44474f | 15 January 2015, 21:01:20 UTC |
| 71ebf96 | John Chilton | 15 January 2015, 21:01:18 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:18 UTC |
| 834eafb | John Chilton | 15 January 2015, 21:01:17 UTC | Merge head created for backport bug fix on latest_2013.08.12 | 15 January 2015, 21:01:17 UTC |
| 647178e | John Chilton | 15 January 2015, 21:01:15 UTC | Update tag latest_2013.08.12 for changeset db967a25c5db | 15 January 2015, 21:01:15 UTC |
| b954cca | John Chilton | 15 January 2015, 21:01:13 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:13 UTC |
| 2ed61bb | John Chilton | 15 January 2015, 21:01:11 UTC | Merge head created for backport bug fix on latest_2013.06.03 | 15 January 2015, 21:01:11 UTC |
| e462c6b | John Chilton | 15 January 2015, 21:01:05 UTC | Update tag latest_2013.06.03 for changeset aae74ee09e46 | 15 January 2015, 21:01:05 UTC |
| 4cd434b | John Chilton | 15 January 2015, 21:01:03 UTC | Bugfix: Skip extra wrapping around template-style macros. | 15 January 2015, 21:01:03 UTC |
| 3f1d9b0 | John Chilton | 15 January 2015, 18:20:34 UTC | Skip extra wrapping around template-style macros. Cheetah wants these to be strings. | 15 January 2015, 18:20:34 UTC |
| a9a1b78 | Nate Coraor | 15 January 2015, 17:00:23 UTC | Update tag latest_2015.01.13 for changeset 3b559c4b9399 | 15 January 2015, 17:00:23 UTC |
| 4623342 | Dannon Baker | 15 January 2015, 16:59:20 UTC | Bump bioblend to 0.5.2. The egg no longer depends on mock, which is sort of a bandaid fix for the startup eggs dependency bug not fetching it correctly. TODO: followup on that bug. | 15 January 2015, 16:59:20 UTC |
| b52817d | Dannon Baker | 15 January 2015, 12:53:44 UTC | Merged in guerler/guerler-galaxy-central/stable (pull request #632) Upload: Fix space_to_tab option | 15 January 2015, 12:53:44 UTC |
| b025470 | Nate Coraor | 14 January 2015, 22:07:57 UTC | Merge head created for backport bug fix on latest_2014.10.06 | 14 January 2015, 22:07:57 UTC |
| 1927fd9 | Nate Coraor | 14 January 2015, 22:07:56 UTC | Update tag latest_2014.10.06 for changeset 9bd6f8b5b815 | 14 January 2015, 22:07:56 UTC |
| 7f62891 | Daniel Blankenberg | 14 January 2015, 22:07:54 UTC | Make DatasetListWrapper and DatasetCollectionWrapper subclasses of ToolParameterValueWrapper. | 14 January 2015, 22:07:54 UTC |
