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 |
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 |
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 |
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 |
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 |
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 |
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 |