August 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] cbae8f: Fix an XSS reflection vulnerability on the workflo...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: cbae8fab672e302094bb5adaa3921e9feae87224 https://github.com/galaxyproject/galaxy/commit/cbae8fab672e302094bb5adaa392… Author: Nate Coraor <nate(a)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/8e7017a6b125ce5a079cc15c5f26… Author: Martin Cech <cech.marten(a)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/25d8a54aeb6c34ebf48d9c3bead4… Author: Nate Coraor <nate(a)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/a454c93fd342783902887ecb66f6… Author: Nate Coraor <nate(a)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/2a1b2dbb5ae83b3c6b7d4360a674… Author: Nicola Soranzo <nicola.soranzo(a)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/e3e9213e28e02ed7439f7458ad07… Author: Nate Coraor <nate(a)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/052b6a6a38fb0bba859d8c591aa7… Author: Nate Coraor <nate(a)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: a6a85cbc4ccbde1a39ebb9b84a47da6332a6a27c https://github.com/galaxyproject/galaxy/commit/a6a85cbc4ccbde1a39ebb9b84a47… Author: Nate Coraor <nate(a)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/f01300d7da5625ac264552258b29… Author: Nate Coraor <nate(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/15b5a336c4c0...f01300d7da56

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[galaxyproject/galaxy] cbae8f: Fix an XSS reflection vulnerability on the workflo...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: cbae8fab672e302094bb5adaa3921e9feae87224 https://github.com/galaxyproject/galaxy/commit/cbae8fab672e302094bb5adaa392… Author: Nate Coraor <nate(a)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/8e7017a6b125ce5a079cc15c5f26… Author: Martin Cech <cech.marten(a)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/25d8a54aeb6c34ebf48d9c3bead4… Author: Nate Coraor <nate(a)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/a454c93fd342783902887ecb66f6… Author: Nate Coraor <nate(a)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: a6a85cbc4ccbde1a39ebb9b84a47da6332a6a27c https://github.com/galaxyproject/galaxy/commit/a6a85cbc4ccbde1a39ebb9b84a47… Author: Nate Coraor <nate(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/444509241061...a6a85cbc4ccb

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[galaxyproject/galaxy] cbae8f: Fix an XSS reflection vulnerability on the workflo...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: cbae8fab672e302094bb5adaa3921e9feae87224 https://github.com/galaxyproject/galaxy/commit/cbae8fab672e302094bb5adaa392… Author: Nate Coraor <nate(a)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/8e7017a6b125ce5a079cc15c5f26… Author: Martin Cech <cech.marten(a)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: 6dc5f022c73d5bde3b4ef1abe31a8d3b37ade9c3 https://github.com/galaxyproject/galaxy/commit/6dc5f022c73d5bde3b4ef1abe31a… Author: Nate Coraor <nate(a)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_15.01 Commit: 096a1686badda620acb507deaf9382ccee37086a https://github.com/galaxyproject/galaxy/commit/096a1686badda620acb507deaf93… Author: Nate Coraor <nate(a)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_15.01 Compare: https://github.com/galaxyproject/galaxy/compare/9f67bdbab5bb...096a1686badd

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[galaxyproject/galaxy] cbae8f: Fix an XSS reflection vulnerability on the workflo...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/release_14.10 Home: https://github.com/galaxyproject/galaxy Commit: cbae8fab672e302094bb5adaa3921e9feae87224 https://github.com/galaxyproject/galaxy/commit/cbae8fab672e302094bb5adaa392… Author: Nate Coraor <nate(a)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.

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[galaxyproject/galaxy] 6a25d9: fix _query method to return a query instead of a l...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a25d979e1329aec4366bf6943aa65d9b41ec18f https://github.com/galaxyproject/galaxy/commit/6a25d979e1329aec4366bf6943aa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- fix _query method to return a query instead of a list Commit: 40f61610f1133e142de32389aad1a04294cb3164 https://github.com/galaxyproject/galaxy/commit/40f61610f1133e142de32389aad1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- introduce new API endpoint&method for published histories Commit: a4274913e195d0c1d6f558f5f877346a18c1e310 https://github.com/galaxyproject/galaxy/commit/a4274913e195d0c1d6f558f5f877… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #594 from martenson/expose-api-pub-hist new API for published histories Compare: https://github.com/galaxyproject/galaxy/compare/01b69e327b52...a4274913e195

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[galaxyproject/usegalaxy-playbook] f891ab: Fix path to zfs for postgres backups from radegast
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f891abde3e3da083bbc9edd8af4bfb7b87daf806 https://github.com/galaxyproject/usegalaxy-playbook/commit/f891abde3e3da083… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml Log Message: ----------- Fix path to zfs for postgres backups from radegast

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[galaxyproject/galaxy] bb6a78: Include valid_tools as part of metadata returned w...
by GitHub 12 Aug '15

12 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb6a784f13ff3f91762244d4488437ffef9e5acf https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Include valid_tools as part of metadata returned with the repository install info. Otherwise, no linkage exists bwtween tool version and a revision that can be used via the API. Commit: 01b69e327b524be014f86b9e98375f3e5d660141 https://github.com/galaxyproject/galaxy/commit/01b69e327b524be014f86b9e9837… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #592 from afgane/dev Include valid_tools as part of metadata returned with the repository … Compare: https://github.com/galaxyproject/galaxy/compare/1d325e217e03...01b69e327b52

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[galaxyproject/galaxy] 790713: Code style cleanup.
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7907136ffd4e3ee293ec96d39bf48357cf433539 https://github.com/galaxyproject/galaxy/commit/7907136ffd4e3ee293ec96d39bf4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Code style cleanup. Commit: f1fc95e3655950a9f2064c5bc1506fecc936e4d4 https://github.com/galaxyproject/galaxy/commit/f1fc95e3655950a9f2064c5bc150… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Use correct formatting for multi-line if. Commit: 1d325e217e03e13fbfcfc8c4ed46a00277382ed9 https://github.com/galaxyproject/galaxy/commit/1d325e217e03e13fbfcfc8c4ed46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py Log Message: ----------- Merge pull request #591 from davebx/ts_lint Code style cleanup. Compare: https://github.com/galaxyproject/galaxy/compare/db4461177162...1d325e217e03

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[galaxyproject/galaxy] d9d365: Fix wrong call to LDAPObject.result() by using sea...
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: d9d365b36e827adf859759fd41113a74204ce376 https://github.com/galaxyproject/galaxy/commit/d9d365b36e827adf859759fd4111… Author: Nicola Soranzo <nicola.soranzo(a)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/15b5a336c4c09524bacdc445ad47… Author: Dannon Baker <dannon.baker(a)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(). Compare: https://github.com/galaxyproject/galaxy/compare/395e103ee5ff...15b5a336c4c0

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[galaxyproject/usegalaxy-playbook] f59034: Mutable configs from Test
by GitHub 11 Aug '15

11 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f59034d1e3dccdfeb7a41a5166de7ba0f8302d31 https://github.com/galaxyproject/usegalaxy-playbook/commit/f59034d1e3dccdfe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Test Commit: 4c97ad68efeb863c6ac2a4c98933b6d5038bf668 https://github.com/galaxyproject/usegalaxy-playbook/commit/4c97ad68efeb863c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Corral is back up Commit: bd7bc13a6a102a798f9b7128f3d381f10a80b045 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd7bc13a6a102a79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 0531e6047534313b1a33b0466b708c7d7edf3272 https://github.com/galaxyproject/usegalaxy-playbook/commit/0531e6047534313b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e22a25d404ed...…

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