Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0cbf97ac9a30d6006b5a75ab602231af68a4c3d9 https://github.com/galaxyproject/galaxy/commit/0cbf97ac9a30d6006b5a75ab60223... Author: John Chilton <jmchilton@gmail.com> Date: 2015-07-14 (Tue, 14 Jul 2015) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Fix expect_num_outputs parsing on tool test elements. Broken with abstracting XML parsing out into its own module. Commit: ba265074dee13f1dad9b5b728559f4f7bb6cfeb2 https://github.com/galaxyproject/galaxy/commit/ba265074dee13f1dad9b5b728559f... Author: carlfeberhard <carlfeberhard@users.noreply.github.com> Date: 2015-08-04 (Tue, 04 Aug 2015) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #456 from jmchilton/fix_expect_outputs [15.05] Fix expect_num_outputs parsing on tool test elements. Commit: 395e103ee5ffad466ab485c5a1877540a8342d79 https://github.com/galaxyproject/galaxy/commit/395e103ee5ffad466ab485c5a1877... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge pull request #570 from ericenns/new-tool-form-batch-collection [15.05] Fix batch mode input in new tool form ui Commit: d9d365b36e827adf859759fd41113a74204ce376 https://github.com/galaxyproject/galaxy/commit/d9d365b36e827adf859759fd41113... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- 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. Commit: 15b5a336c4c09524bacdc445ad47ce8a0be60168 https://github.com/galaxyproject/galaxy/commit/15b5a336c4c09524bacdc445ad47c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #590 from nsoranzo/release_15.05 [15.05] Fix wrong call to LDAPObject.result() by using search_ext_s(). Commit: cbae8fab672e302094bb5adaa3921e9feae87224 https://github.com/galaxyproject/galaxy/commit/cbae8fab672e302094bb5adaa3921... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix an XSS reflection vulnerability on the workflow import form. Commit: 8e7017a6b125ce5a079cc15c5f26148071b0c366 https://github.com/galaxyproject/galaxy/commit/8e7017a6b125ce5a079cc15c5f261... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix a vulnerability in the Tool Shed API that allowed unauthorized users to upload new repository versions. Commit: 25d8a54aeb6c34ebf48d9c3bead4f6390848a6a3 https://github.com/galaxyproject/galaxy/commit/25d8a54aeb6c34ebf48d9c3bead4f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.03 Commit: a454c93fd342783902887ecb66f63a658ad30270 https://github.com/galaxyproject/galaxy/commit/a454c93fd342783902887ecb66f63... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.03 Commit: 2a1b2dbb5ae83b3c6b7d4360a674432698e216da https://github.com/galaxyproject/galaxy/commit/2a1b2dbb5ae83b3c6b7d4360a6744... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- 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. Commit: e3e9213e28e02ed7439f7458ad079a099064e1b6 https://github.com/galaxyproject/galaxy/commit/e3e9213e28e02ed7439f7458ad079... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.05 Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py Commit: 052b6a6a38fb0bba859d8c591aa78960d8b211db https://github.com/galaxyproject/galaxy/commit/052b6a6a38fb0bba859d8c591aa78... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.05 Commit: d9426dab92ef70528b021adff48e5c67be3b6a94 https://github.com/galaxyproject/galaxy/commit/d9426dab92ef70528b021adff48e5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge branch 'security-20150812-ldap' into release_15.07 Commit: 3c2762b6c7e9532cfbc9bd74ab402f96c77ead58 https://github.com/galaxyproject/galaxy/commit/3c2762b6c7e9532cfbc9bd74ab402... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.07 Commit: 3e4513f195de4e4a8e225d29fe3a9011b0bbc148 https://github.com/galaxyproject/galaxy/commit/3e4513f195de4e4a8e225d29fe3a9... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.07 Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py Commit: accd5ebc8c4cd4dfe707560f6b00ef21ac0cc521 https://github.com/galaxyproject/galaxy/commit/accd5ebc8c4cd4dfe707560f6b00e... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge branch 'security-20150812-ldap' into dev Commit: 95c80f0b342aa08093a7f271f29d50d3df488d1d https://github.com/galaxyproject/galaxy/commit/95c80f0b342aa08093a7f271f29d5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into dev Commit: 28f5021766d618c108f17fccc092925c6c5fe3c8 https://github.com/galaxyproject/galaxy/commit/28f5021766d618c108f17fccc0929... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into dev Conflicts: lib/galaxy/webapps/galaxy/controllers/workflow.py Commit: 8f7f80d295cabc1ecc79e492d463b2f9cc894d08 https://github.com/galaxyproject/galaxy/commit/8f7f80d295cabc1ecc79e492d463b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: c4a12f61fb6e6da499cdb5aa2e96f556ab031a80 https://github.com/galaxyproject/galaxy/commit/c4a12f61fb6e6da499cdb5aa2e96f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Log Message: ----------- Merge branch 'release_15.07' into dev Commit: a6a85cbc4ccbde1a39ebb9b84a47da6332a6a27c https://github.com/galaxyproject/galaxy/commit/a6a85cbc4ccbde1a39ebb9b84a47d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.03.3 Commit: f01300d7da5625ac264552258b29818598d4d535 https://github.com/galaxyproject/galaxy/commit/f01300d7da5625ac264552258b298... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.05.1. Merge branch 'release_15.03' into release_15.05 Conflicts: lib/galaxy/version.py Commit: b3da771a637ac9f7a4778fd115a09da01f432b1c https://github.com/galaxyproject/galaxy/commit/b3da771a637ac9f7a4778fd115a09... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.07 (drop .dev) Merge branch 'release_15.05' into release_15.07 Conflicts: lib/galaxy/version.py Commit: e218a2c72b1b1c9df8ab80f1e8c62833d813125d https://github.com/galaxyproject/galaxy/commit/e218a2c72b1b1c9df8ab80f1e8c62... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge branch 'release_15.07' into dev Commit: d554136658e165c84a42b988f39009c185325919 https://github.com/galaxyproject/galaxy/commit/d554136658e165c84a42b988f3900... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump version to 15.10.dev Compare: https://github.com/galaxyproject/galaxy/compare/a4274913e195...d554136658e1