| c8e9845 | Nate Coraor | 24 February 2016, 18:34:05 UTC | Update version to 15.05.2 | 24 February 2016, 18:34:05 UTC |
| 3516e94 | Nate Coraor | 24 February 2016, 18:25:57 UTC | Merge branch 'release_15.03' into release_15.05 | 24 February 2016, 18:25:57 UTC |
| 0122040 | Nate Coraor | 24 February 2016, 18:23:36 UTC | Update version to 15.03.4 | 24 February 2016, 18:23:36 UTC |
| f65bcb3 | Nate Coraor | 24 February 2016, 16:18:21 UTC | Merge branch 'release_15.03' into release_15.05 | 24 February 2016, 16:18:21 UTC |
| 2bda436 | 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 |
| 91f5fa8 | Nate Coraor | 24 February 2016, 16:18:20 UTC | Security fixes for tool shed repository browsing | 24 February 2016, 16:18:20 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 |
| fcd8f50 | 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 |
| ce88f2f | Nate Coraor | 24 February 2016, 16:18:20 UTC | Security fixes for object store paths | 24 February 2016, 16:18:20 UTC |
| 6e3b748 | Nate Coraor | 24 February 2016, 16:18:20 UTC | Security fixes for history imports | 24 February 2016, 16:18:20 UTC |
| 2a80897 | Nate Coraor | 24 February 2016, 16:18:20 UTC | Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory | 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 |
| 0bf60a5 | Nicola Soranzo | 25 September 2015, 17:18:52 UTC | Merge pull request #794 from jmchilton/release_15.05.output.fix [15.05] Fix problem maintaining input maps when rescheduling workflows. | 25 September 2015, 17:18:52 UTC |
| bf60693 | John Chilton | 24 September 2015, 14:35:17 UTC | Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. | 24 September 2015, 14:44:46 UTC |
| 6827aed | Nicola Soranzo | 22 August 2015, 14:56:15 UTC | Merge pull request #635 from bgruening/perl_env_15.05 [15.05] Add temporary $HOME directory during perl installations | 22 August 2015, 14:56:15 UTC |
| 98a3b47 | Bjoern Gruening | 22 August 2015, 09:37:59 UTC | add temporary $HOME directory during perl installations | 22 August 2015, 09:39:18 UTC |
| 5b60425 | Nicola Soranzo | 21 August 2015, 18:38:38 UTC | Merge branch 'release_15.03' into release_15.05 | 21 August 2015, 18:38:38 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 |
| c569f78 | Dannon Baker | 21 August 2015, 13:58:39 UTC | Merge branch 'release_15.03' into release_15.05 | 21 August 2015, 13:58:39 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 |
| 14a8ee9 | Dannon Baker | 20 August 2015, 12:33:09 UTC | Merge pull request #616 from nsoranzo/release_15.05 [15.05] Fix purging datasets whose total_size is None. | 20 August 2015, 12:33:09 UTC |
| baf8fe6 | Nicola Soranzo | 20 August 2015, 12:21:14 UTC | Merge pull request #1 from jmchilton/release_fix Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. | 20 August 2015, 12:21:14 UTC |
| a9827fa | John Chilton | 20 August 2015, 05:45:11 UTC | Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. | 20 August 2015, 05:45:11 UTC |
| 483ea9e | Dannon Baker | 19 August 2015, 23:42:16 UTC | Merge branch 'release_15.03' into release_15.05 | 19 August 2015, 23:42:16 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 |
| 238d908 | Nicola Soranzo | 19 August 2015, 11:39:41 UTC | Fix purging datasets whose total_size is None. Fix the error: Removing disk, file /opt/galaxy/database/files/000/dataset_192.dat Error attempting to purge data file: /opt/galaxy/database/files/000/dataset_192.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType' when running: python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 10 -3 -r | 19 August 2015, 14:33:54 UTC |
| f01300d | Nate Coraor | 12 August 2015, 21:12:44 UTC | Bump version to 15.05.1. Merge branch 'release_15.03' into release_15.05 Conflicts: lib/galaxy/version.py | 12 August 2015, 21:12:44 UTC |
| a6a85cb | Nate Coraor | 12 August 2015, 21:11:02 UTC | Bump version to 15.03.3 | 12 August 2015, 21:11:02 UTC |
| 052b6a6 | Nate Coraor | 12 August 2015, 21:00:02 UTC | Merge branch 'security-20150812-shed' into release_15.05 | 12 August 2015, 21:00:02 UTC |
| e3e9213 | Nate Coraor | 12 August 2015, 20:59:44 UTC | Merge branch 'security-20150812-xss' into release_15.05 Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py | 12 August 2015, 20:59:44 UTC |
| 2a1b2db | Nicola Soranzo | 05 June 2015, 14:48:23 UTC | Prevent login with valid username/email and empty password via LDAP auth when anonymous bind is allowed. Also decreased the log level of LDAP bind exception to warning. | 12 August 2015, 20:58:05 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 |
| 15b5a33 | Dannon Baker | 11 August 2015, 23:29:38 UTC | Merge pull request #590 from nsoranzo/release_15.05 [15.05] Fix wrong call to LDAPObject.result() by using search_ext_s(). | 11 August 2015, 23:29:38 UTC |
| d9d365b | Nicola Soranzo | 05 June 2015, 15:03:33 UTC | Fix wrong call to LDAPObject.result() by using search_ext_s(). result() second parameter is 'all', which should be 0 or 1. result() call was passing 60 as second parameter, which was probably intended to be a timeout (third parameter). By using search_ext_s(), the search() and result() calls are combined in one and the number of search results retrieved is limited to 1. Also, if the search return no results, this is now logged separately at warning level. | 11 August 2015, 19:21:25 UTC |
| 395e103 | Aysam Guerler | 07 August 2015, 13:50:19 UTC | Merge pull request #570 from ericenns/new-tool-form-batch-collection [15.05] Fix batch mode input in new tool form ui | 07 August 2015, 13:50:19 UTC |
| 864e2b5 | Eric Enns | 06 August 2015, 19:29:51 UTC | Fix batch mode for collection, when collection maps to multiple inputs | 06 August 2015, 19:29:51 UTC |
| ba26507 | carlfeberhard | 04 August 2015, 20:39:31 UTC | Merge pull request #456 from jmchilton/fix_expect_outputs [15.05] Fix expect_num_outputs parsing on tool test elements. | 04 August 2015, 20:39:31 UTC |
| 8f175ef | Eric Rasche | 24 July 2015, 14:20:16 UTC | Merge pull request #497 from dannon/release_15.05 SCRIPT_NAME can be empty or not in the environment at all. This reso… | 24 July 2015, 14:20:16 UTC |
| 5788066 | Dannon Baker | 24 July 2015, 14:04:47 UTC | SCRIPT_NAME can be empty or not in the environment at all. This resolves http://dev.list.galaxyproject.org/NGINX-uWSGI-with-require-login-needs-uwsgi-param-SCRIPT-NAME-td4666901.html. Thanks to @dctrud and @ericenns for the help tracking it down. | 24 July 2015, 14:04:47 UTC |
| 558a590 | Dannon Baker | 22 July 2015, 17:41:04 UTC | Merge pull request #475 from blankenberg/custom_builds_objectstore_15.05 [15.05] Fix for users creating Custom DBKeys when objectstore is being used. | 22 July 2015, 17:41:04 UTC |
| bcd1f74 | Nitesh Turaga | 22 July 2015, 16:36:12 UTC | Merge pull request #483 from dannon/old_cloudlaunch_errormsg Catch and return error message during key verification in cloudlaunch. | 22 July 2015, 16:36:12 UTC |
| 6049a74 | Dannon Baker | 21 July 2015, 18:03:22 UTC | Catch and return error message during key verification in cloudlaunch. | 21 July 2015, 18:03:22 UTC |
| 08136a8 | John Chilton | 20 July 2015, 12:48:01 UTC | Merge pull request #477 from blankenberg/15.05_metadata_autodect_fix [15.05] Fix autodection of metadata, from edit dataset attributes. | 20 July 2015, 12:48:01 UTC |
| 807dd81 | Daniel Blankenberg | 17 July 2015, 20:31:56 UTC | Turn of sanitizer for in __SET_METADATA__ autodetect metadata tool. Fixes issue that appears as a result of PR #474, but also could occur under corner-cases with interestlying named temp filenames. Also, add quotes around configfile filename. | 17 July 2015, 20:31:56 UTC |
| b11f5a5 | Daniel Blankenberg | 17 July 2015, 15:29:55 UTC | Minor white-space change. | 17 July 2015, 15:29:55 UTC |
| 0afcfcb | Daniel Blankenberg | 17 July 2015, 15:26:30 UTC | Fix for users creating Custom DBKeys when objectstore is being used. | 17 July 2015, 15:26:30 UTC |
| 4d0a9a8 | Daniel Blankenberg | 17 July 2015, 14:54:52 UTC | Merge pull request #474 from jmchilton/metadata_quoting [15.05] Quote more paths when building metadata command lines. | 17 July 2015, 14:54:52 UTC |
| 341a2f1 | John Chilton | 17 July 2015, 09:33:17 UTC | Quote more paths when building metadata command lines. Tested and fixes linked library uploads with spaces in the file path. Probably fixes other more obsecure problems like if the temp directory had a space in it, etc.... | 17 July 2015, 09:38:49 UTC |
| 8c37677 | Daniel Blankenberg | 15 July 2015, 18:49:22 UTC | Merge pull request #466 from natefoo/default-metadata-limit [15.05] Set a default limit for metadata key size | 15 July 2015, 18:49:22 UTC |
| 212b083 | Nate Coraor | 15 July 2015, 18:28:40 UTC | Set the default metadata key limit to 5MB | 15 July 2015, 18:28:40 UTC |
| 13a40b3 | Daniel Blankenberg | 15 July 2015, 14:25:46 UTC | Merge pull request #461 from carlfeberhard/release_15.05 [15.05] UI, Collections: use Galaxy.options.root for API URL | 15 July 2015, 14:25:46 UTC |
| 6e8bfc6 | Carl Eberhard | 15 July 2015, 14:13:22 UTC | UI, Collections: use Galaxy.options.root for API URL | 15 July 2015, 14:13:22 UTC |
| 0cbf97a | John Chilton | 14 July 2015, 09:00:55 UTC | Fix expect_num_outputs parsing on tool test elements. Broken with abstracting XML parsing out into its own module. | 14 July 2015, 09:21:21 UTC |
| 5b8fe57 | Nicola Soranzo | 13 July 2015, 14:38:31 UTC | Merge pull request #451 from carlfeberhard/fix.tools-api-hda-mgr [15.05] API, tools: fix use of trans in _rerun_tool hda manager | 13 July 2015, 14:38:31 UTC |
| 7002f65 | Carl Eberhard | 13 July 2015, 14:27:33 UTC | API, tools: fix use of trans in _rerun_tool hda manager | 13 July 2015, 14:27:33 UTC |
| cf51e0b | Dannon Baker | 01 July 2015, 15:54:05 UTC | Merge conflict due to pep8'ifying, resolved by applying changes. | 01 July 2015, 18:26:49 UTC |
| c00da2a | Dannon Baker | 01 July 2015, 15:34:41 UTC | One flake8 spacing fix. | 01 July 2015, 18:25:15 UTC |
| 8a9af02 | Dannon Baker | 01 July 2015, 15:05:42 UTC | cluster-side filtering of metadata keys. Still done once the final dict is assembled, to allow for all three passes to work correctly with their dependent keys, etc. | 01 July 2015, 18:24:51 UTC |
| f12bb33 | John Chilton | 01 July 2015, 14:59:12 UTC | Merge pull request #411 from guerler/fix_charts_config [15.05] Disable custom tooltips for histograms in charts, repack scripts | 01 July 2015, 14:59:12 UTC |
| bbe5ede | Nate Coraor | 01 July 2015, 14:25:25 UTC | Merge pull request #415 from jmchilton/workflow_fix_fix [15.05] Fix for PR #409. | 01 July 2015, 14:25:25 UTC |
| edf73b7 | John Chilton | 01 July 2015, 13:12:32 UTC | More fixes for force_queue. Document two additional fixes that should be done but I don't have time for pre-GCC. | 01 July 2015, 13:12:32 UTC |
| 267b250 | Daniel Blankenberg | 30 June 2015, 18:51:24 UTC | Merge pull request #409 from jmchilton/1505_workflow_output_fix [15.05] Fix workflow run for certain kinds of explicit output collections. | 30 June 2015, 18:51:24 UTC |
| 8b7a455 | guerler | 30 June 2015, 17:46:12 UTC | Disable custome tooltips for histograms | 30 June 2015, 17:46:12 UTC |
| af62976 | John Chilton | 30 June 2015, 15:41:00 UTC | Add log statement in previous fix for consistency. Thanks for the tip @dannon. | 30 June 2015, 15:41:00 UTC |
| 0357a43 | John Chilton | 30 June 2015, 15:29:44 UTC | Fix workflow run for certain kinds of explicit output collections. Workflows with steps that produce an unknown number of datasets must explicitly be sent to the new workflow engine - since the workflow needs be re-evaluated after such steps have completed. This change updates the force_queue to check workflow steps for such collections and return True if any are found - this is what causes certain GUI driven workflows to use the new workflow engine. | 30 June 2015, 15:33:12 UTC |
| daae187 | Dannon Baker | 27 June 2015, 14:28:28 UTC | Fix managers to pass context necessary down the chain when purging. This should fix at least one quota calc error. Fix another bug in hda manager regarding quota reduction -- quota usage must be calculated prior to actually purging, otherwise the disk usage is 0 and this does nothing. Slight refactoring in manager purge -- we don't need to pass the user via context since we can just grab it where applicable from the history. Fix purge when handling an anonymous user | 30 June 2015, 12:41:52 UTC |
| 9059c4c | Aysam Guerler | 26 June 2015, 16:21:40 UTC | Merge pull request #401 from jmchilton/backport_testname_fix [15.05] Fix function names for dynamic tool test functions. | 26 June 2015, 16:21:40 UTC |
| afbadc0 | John Chilton | 15 May 2015, 19:47:35 UTC | Fix function names for dynamic tool test functions. When finding methods to invoke it seems nose uses the raw function name instead of the class's attribute name (I guess this terminology makes sense), but when reporting results it uses the latter. Synchronizing these names therefore allows calling specific tool test methods from the command-line. This change is required to implement galaxyproject/planemo#145. | 26 June 2015, 14:36:38 UTC |
| ab228c8 | Dannon Baker | 23 June 2015, 13:52:36 UTC | Merge pull request #387 from jmchilton/tsbootstrap_backport Exclude curly braces from API-key to fix toolshed bootstrapping. | 23 June 2015, 13:52:36 UTC |
| f835a74 | Marius van den Beek | 01 June 2015, 14:19:14 UTC | Exclude curly braces from API-key to fix toolshed bootstrapping. | 22 June 2015, 19:05:01 UTC |
| 6e8011d | John Chilton | 17 June 2015, 05:42:05 UTC | Merge pull request #363 from dannon/dirty_env_fix [15.05] Add PyYAML require prior to kombu import, which now depends on it (as… | 17 June 2015, 05:42:05 UTC |
