Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 https://github.com/galaxyproject/galaxy/commit/93a8bfc7cb5e9c3395c5057910ec3... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/managers/groups.py Log Message: ----------- Security: Fix issues with path handling in libraries and in general. Commit: 0e698813a96f1ad61d797255686f69cf5e6b1280 https://github.com/galaxyproject/galaxy/commit/0e698813a96f1ad61d797255686f6... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M tools/data_source/data_source.py Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. Commit: ed045cd570cf6b2198fb496852458194c8e28d6f https://github.com/galaxyproject/galaxy/commit/ed045cd570cf6b2198fb496852458... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/managers/groups.py Log Message: ----------- Security: Fix issues with path handling in libraries and in general. Commit: 9e672f94588b8eeecee745665162fc92f0158e27 https://github.com/galaxyproject/galaxy/commit/9e672f94588b8eeecee745665162f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M tools/data_source/data_source.py Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. Commit: 1bccbefbffc02803e93913b145f4214b8eb78d54 https://github.com/galaxyproject/galaxy/commit/1bccbefbffc02803e93913b145f42... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/managers/groups.py Log Message: ----------- Security: Fix issues with path handling in libraries and in general. Commit: 658f126e7a387c11df9b5f0a01e0b75e4d84410b https://github.com/galaxyproject/galaxy/commit/658f126e7a387c11df9b5f0a01e0b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M tools/data_source/data_source.py Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. Commit: e8a72252effa5fdd888abd0e3462dde3b5c70f6e https://github.com/galaxyproject/galaxy/commit/e8a72252effa5fdd888abd0e3462d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/managers/groups.py Log Message: ----------- Security: Fix issues with path handling in libraries and in general. Commit: 9f8d3ee444ad10038add204ed1c1dc11e636dd9d https://github.com/galaxyproject/galaxy/commit/9f8d3ee444ad10038add204ed1c1d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Security: Switch GIE Popen() calls to run without shell=True to fix an ACE vulnerability. Commit: cded49354e5fba4b93432294a4518c93b51f259f https://github.com/galaxyproject/galaxy/commit/cded49354e5fba4b93432294a4518... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M tools/data_source/data_source.py Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. Commit: 646a8d1092541c797238e540d071c4346cc5885b https://github.com/galaxyproject/galaxy/commit/646a8d1092541c797238e540d071c... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Support a log directory argument for pgcleanup.py Commit: 1af06ce6fe2a3e20a240d7159391dd8a3e237b72 https://github.com/galaxyproject/galaxy/commit/1af06ce6fe2a3e20a240d7159391d... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #4837 from natefoo/pgcleanup-log-dir [17.09] Support a log directory argument for pgcleanup.py Commit: f02cd7ddb6cc5ae3c9fe5d1b78abcff471ffc461 https://github.com/galaxyproject/galaxy/commit/f02cd7ddb6cc5ae3c9fe5d1b78abc... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/managers/groups.py Log Message: ----------- Security: Fix issues with path handling in libraries and in general. Commit: c3fd90a36dfa0468447b20a63affbd7a6853f0f7 https://github.com/galaxyproject/galaxy/commit/c3fd90a36dfa0468447b20a63affb... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Security: Switch GIE Popen() calls to run without shell=True to fix an ACE vulnerability. Commit: 391586ba01fc1a01443962d137e9df3fce707434 https://github.com/galaxyproject/galaxy/commit/391586ba01fc1a01443962d137e9d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M tools/data_source/data_source.py Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. Commit: 92d63977a96a048440e05c52379e718f6aa8df13 https://github.com/galaxyproject/galaxy/commit/92d63977a96a048440e05c52379e7... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path/__init__.py A lib/galaxy/util/path/ntpath.py A lib/galaxy/util/path/posixpath.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/managers/groups.py Log Message: ----------- Security: Fix issues with path handling in libraries and in general. Commit: 8bc242abc1adc85487c924bb42b4fd2dff4a0b82 https://github.com/galaxyproject/galaxy/commit/8bc242abc1adc85487c924bb42b4f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Security: Switch GIE Popen() calls to run without shell=True to fix an ACE vulnerability. Commit: 3a70d0c6483407ec69ff84f8c7398584889fc22c https://github.com/galaxyproject/galaxy/commit/3a70d0c6483407ec69ff84f8c7398... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M tools/data_source/data_source.py Log Message: ----------- [GX-2017-0003]: Fix for the reported issue, only allow http, https, and ftp schemes in the data_source tool. Commit: dda175dbf088bb4ba014fbea70b610cb7e2c2ed6 https://github.com/galaxyproject/galaxy/commit/dda175dbf088bb4ba014fbea70b61... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: c4855af7d516b0a955e508cc7e5bc8716028b670 https://github.com/galaxyproject/galaxy/commit/c4855af7d516b0a955e508cc7e5bc... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: b35fe934d4246ae0b4c1b6aa3a446fd5672d55c6 https://github.com/galaxyproject/galaxy/commit/b35fe934d4246ae0b4c1b6aa3a446... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: cfe3dfc6eb93c65f55dd794b742b08762edd5d02 https://github.com/galaxyproject/galaxy/commit/cfe3dfc6eb93c65f55dd794b742b0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: b8dfceb72aa444dcce6d4645c8028c7496eb6c44 https://github.com/galaxyproject/galaxy/commit/b8dfceb72aa444dcce6d4645c8028... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/faa50a23fbd0...b8dfceb72aa4