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Author SHA1 Message Date
Nate Coraor ce88f2f81c Security fixes for object store paths 2016-02-24 11:18:20 -05:00
Nate Coraor 6e3b74869a Security fixes for history imports 2016-02-24 11:18:20 -05:00
Nate Coraor 2a8089749c Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory 2016-02-24 11:18:20 -05:00
Nicola Soranzo 0bf60a5205 Merge pull request #794 from jmchilton/release_15.05.output.fix 
[15.05] Fix problem maintaining input maps when rescheduling workflows.
 2015-09-25 18:18:52 +01:00
John Chilton bf60693ed0 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.
 2015-09-24 15:44:46 +01:00
Nicola Soranzo 6827aed9ef Merge pull request #635 from bgruening/perl_env_15.05 
[15.05] Add temporary $HOME directory during perl installations
 2015-08-22 15:56:15 +01:00
Bjoern Gruening 98a3b47265 add temporary $HOME directory during perl installations 2015-08-22 11:39:18 +02:00
Nicola Soranzo 5b60425336 Merge branch 'release_15.03' into release_15.05 2015-08-21 19:38:38 +01:00
Nicola Soranzo b23acda7d8 Merge branch 'release_15.01' into release_15.03 2015-08-21 19:36:08 +01:00
Nicola Soranzo 46e67b5bfa Merge branch 'release_14.10' into release_15.01 2015-08-21 19:31:52 +01:00
Björn Grüning 360a6ad76d Merge pull request #634 from nsoranzo/release_14.10 
[14.10] Backport tool lineage fix.
 2015-08-21 20:28:25 +02:00
Nicola Soranzo 85c971287b 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.
 2015-08-21 18:51:24 +01:00
Dannon Baker c569f7856d Merge branch 'release_15.03' into release_15.05 2015-08-21 09:58:39 -04:00
Dannon Baker e06d6a1cca Merge branch 'release_15.01' into release_15.03 2015-08-21 09:58:12 -04:00
Dannon Baker 4d2651a085 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. 2015-08-21 09:57:47 -04:00
Dannon Baker b29e810149 Fix for valid height/width definitions in workflow rendering code. 2015-08-21 09:57:38 -04:00
Dannon Baker 14a8ee95f3 Merge pull request #616 from nsoranzo/release_15.05 
[15.05] Fix purging datasets whose total_size is None.
 2015-08-20 08:33:09 -04:00
Nicola Soranzo baf8fe6759 Merge pull request #1 from jmchilton/release_fix 
Fix failing tests for 238d908cce.
 2015-08-20 13:21:14 +01:00
John Chilton a9827fae31 Fix failing tests for 238d908cce. 2015-08-20 06:45:11 +01:00
Dannon Baker 483ea9e735 Merge branch 'release_15.03' into release_15.05 2015-08-19 19:42:16 -04:00
Dannon Baker 01278aa956 Merge branch 'release_15.01' into release_15.03 2015-08-19 19:42:00 -04:00
Dannon Baker 71f28c99e5 Merge pull request #622 from erasche/tool-reloading-fix 
[15.01] Tool reloading fix
 2015-08-19 19:41:39 -04:00
Eric Rasche a1bff672f3 Fix bug in tool reloading API where ID not passed 2015-08-19 15:26:47 -05:00
Nicola Soranzo 238d908cce 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
 2015-08-19 15:33:54 +01:00
Nate Coraor f01300d7da Bump version to 15.05.1. 
Merge branch 'release_15.03' into release_15.05

Conflicts:
	lib/galaxy/version.py
v15.05.1 		2015-08-12 17:12:44 -04:00
Nate Coraor a6a85cbc4c Bump version to 15.03.3 v15.03.3 2015-08-12 17:11:02 -04:00
Nate Coraor 052b6a6a38 Merge branch 'security-20150812-shed' into release_15.05 2015-08-12 17:00:02 -04:00
Nate Coraor e3e9213e28 Merge branch 'security-20150812-xss' into release_15.05 
Conflicts:
	lib/galaxy/webapps/galaxy/controllers/workflow.py
 2015-08-12 16:59:44 -04:00
Nicola Soranzo 2a1b2dbb5a 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.
 2015-08-12 16:58:05 -04:00
Nate Coraor a454c93fd3 Merge branch 'security-20150812-xss' into release_15.03 2015-08-12 16:52:52 -04:00
Nate Coraor 25d8a54aeb Merge branch 'security-20150812-shed' into release_15.03 2015-08-12 16:52:44 -04:00
Nate Coraor 096a1686ba Merge branch 'security-20150812-shed' into release_15.01 v15.01.3 2015-08-12 16:52:13 -04:00
Nate Coraor 6dc5f022c7 Merge branch 'security-20150812-xss' into release_15.01 2015-08-12 16:52:04 -04:00
Martin Cech 8e7017a6b1 Fix a vulnerability in the Tool Shed API that allowed unauthorized users 
to upload new repository versions.
 2015-08-12 16:51:10 -04:00
Nate Coraor cbae8fab67 Fix an XSS reflection vulnerability on the workflow import form. v14.10.2 2015-08-12 16:43:52 -04:00
Dannon Baker 15b5a336c4 Merge pull request #590 from nsoranzo/release_15.05 
[15.05] Fix wrong call to LDAPObject.result() by using search_ext_s().
 2015-08-11 19:29:38 -04:00
Nicola Soranzo d9d365b36e 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.
 2015-08-11 20:21:25 +01:00
Aysam Guerler 395e103ee5 Merge pull request #570 from ericenns/new-tool-form-batch-collection 
[15.05] Fix batch mode input in new tool form ui
 2015-08-07 09:50:19 -04:00
Eric Enns 864e2b5111 Fix batch mode for collection, when collection maps to multiple inputs 2015-08-06 14:29:51 -05:00
carlfeberhard ba265074de Merge pull request #456 from jmchilton/fix_expect_outputs 
[15.05] Fix expect_num_outputs parsing on tool test elements.
 2015-08-04 16:39:31 -04:00
Eric Rasche 8f175ef466 Merge pull request #497 from dannon/release_15.05 
SCRIPT_NAME can be empty or not in the environment at all.  This reso…
 2015-07-24 09:20:16 -05:00
Dannon Baker 5788066a6d 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. 2015-07-24 10:04:47 -04:00
Dannon Baker 558a590e18 Merge pull request #475 from blankenberg/custom_builds_objectstore_15.05 
[15.05] Fix for users creating Custom DBKeys when objectstore is being used.
 2015-07-22 13:41:04 -04:00
Nitesh Turaga bcd1f74db1 Merge pull request #483 from dannon/old_cloudlaunch_errormsg 
Catch and return error message during key verification in cloudlaunch.
 2015-07-22 12:36:12 -04:00
Dannon Baker 6049a74468 Catch and return error message during key verification in cloudlaunch. 2015-07-21 14:03:22 -04:00
John Chilton 08136a8b04 Merge pull request #477 from blankenberg/15.05_metadata_autodect_fix 
[15.05]  Fix autodection of metadata, from edit dataset attributes.
 2015-07-20 13:48:01 +01:00
Daniel Blankenberg 807dd81fef 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. 2015-07-17 16:31:56 -04:00
Daniel Blankenberg b11f5a53d3 Minor white-space change. 2015-07-17 11:29:55 -04:00
Daniel Blankenberg 0afcfcbb54 Fix for users creating Custom DBKeys when objectstore is being used. 2015-07-17 11:26:30 -04:00
Daniel Blankenberg 4d0a9a85b1 Merge pull request #474 from jmchilton/metadata_quoting 
[15.05] Quote more paths when building metadata command lines.
 2015-07-17 10:54:52 -04:00