Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4
https://github.com/galaxyproject/galaxy/commit/93a8bfc7cb5e9c3395c5057910ec…
Author: Nate Coraor <nate(a)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/0e698813a96f1ad61d797255686f…
Author: Nate Coraor <nate(a)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/ed045cd570cf6b2198fb49685245…
Author: Nate Coraor <nate(a)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/9e672f94588b8eeecee745665162…
Author: Nate Coraor <nate(a)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/1bccbefbffc02803e93913b145f4…
Author: Nate Coraor <nate(a)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/658f126e7a387c11df9b5f0a01e0…
Author: Nate Coraor <nate(a)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/e8a72252effa5fdd888abd0e3462…
Author: Nate Coraor <nate(a)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/9f8d3ee444ad10038add204ed1c1…
Author: Nate Coraor <nate(a)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/cded49354e5fba4b93432294a451…
Author: Nate Coraor <nate(a)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/646a8d1092541c797238e540d071…
Author: Nate Coraor <nate(a)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/1af06ce6fe2a3e20a240d7159391…
Author: John Chilton <jmchilton(a)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/f02cd7ddb6cc5ae3c9fe5d1b78ab…
Author: Nate Coraor <nate(a)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/c3fd90a36dfa0468447b20a63aff…
Author: Nate Coraor <nate(a)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/391586ba01fc1a01443962d137e9…
Author: Nate Coraor <nate(a)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/92d63977a96a048440e05c52379e…
Author: Nate Coraor <nate(a)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/8bc242abc1adc85487c924bb42b4…
Author: Nate Coraor <nate(a)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/3a70d0c6483407ec69ff84f8c739…
Author: Nate Coraor <nate(a)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/dda175dbf088bb4ba014fbea70b6…
Author: Nate Coraor <nate(a)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/c4855af7d516b0a955e508cc7e5b…
Author: Nate Coraor <nate(a)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/b35fe934d4246ae0b4c1b6aa3a44…
Author: Nate Coraor <nate(a)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/cfe3dfc6eb93c65f55dd794b742b…
Author: Nate Coraor <nate(a)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/b8dfceb72aa444dcce6d4645c802…
Author: Nate Coraor <nate(a)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
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4
https://github.com/galaxyproject/galaxy/commit/93a8bfc7cb5e9c3395c5057910ec…
Author: Nate Coraor <nate(a)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/0e698813a96f1ad61d797255686f…
Author: Nate Coraor <nate(a)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/ed045cd570cf6b2198fb49685245…
Author: Nate Coraor <nate(a)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/9e672f94588b8eeecee745665162…
Author: Nate Coraor <nate(a)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/1bccbefbffc02803e93913b145f4…
Author: Nate Coraor <nate(a)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/658f126e7a387c11df9b5f0a01e0…
Author: Nate Coraor <nate(a)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/e8a72252effa5fdd888abd0e3462…
Author: Nate Coraor <nate(a)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/9f8d3ee444ad10038add204ed1c1…
Author: Nate Coraor <nate(a)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/cded49354e5fba4b93432294a451…
Author: Nate Coraor <nate(a)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: f02cd7ddb6cc5ae3c9fe5d1b78abcff471ffc461
https://github.com/galaxyproject/galaxy/commit/f02cd7ddb6cc5ae3c9fe5d1b78ab…
Author: Nate Coraor <nate(a)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/c3fd90a36dfa0468447b20a63aff…
Author: Nate Coraor <nate(a)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/391586ba01fc1a01443962d137e9…
Author: Nate Coraor <nate(a)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/dda175dbf088bb4ba014fbea70b6…
Author: Nate Coraor <nate(a)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/c4855af7d516b0a955e508cc7e5b…
Author: Nate Coraor <nate(a)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/b35fe934d4246ae0b4c1b6aa3a44…
Author: Nate Coraor <nate(a)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/cfe3dfc6eb93c65f55dd794b742b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-23 (Mon, 23 Oct 2017)
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Compare: https://github.com/galaxyproject/galaxy/compare/1af06ce6fe2a...cfe3dfc6eb93
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4
https://github.com/galaxyproject/galaxy/commit/93a8bfc7cb5e9c3395c5057910ec…
Author: Nate Coraor <nate(a)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/0e698813a96f1ad61d797255686f…
Author: Nate Coraor <nate(a)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/ed045cd570cf6b2198fb49685245…
Author: Nate Coraor <nate(a)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/9e672f94588b8eeecee745665162…
Author: Nate Coraor <nate(a)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/1bccbefbffc02803e93913b145f4…
Author: Nate Coraor <nate(a)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/658f126e7a387c11df9b5f0a01e0…
Author: Nate Coraor <nate(a)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/e8a72252effa5fdd888abd0e3462…
Author: Nate Coraor <nate(a)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/9f8d3ee444ad10038add204ed1c1…
Author: Nate Coraor <nate(a)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/cded49354e5fba4b93432294a451…
Author: Nate Coraor <nate(a)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: dda175dbf088bb4ba014fbea70b610cb7e2c2ed6
https://github.com/galaxyproject/galaxy/commit/dda175dbf088bb4ba014fbea70b6…
Author: Nate Coraor <nate(a)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/c4855af7d516b0a955e508cc7e5b…
Author: Nate Coraor <nate(a)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/b35fe934d4246ae0b4c1b6aa3a44…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-23 (Mon, 23 Oct 2017)
Log Message:
-----------
Merge branch 'release_17.01' into release_17.05
Compare: https://github.com/galaxyproject/galaxy/compare/f0e9767912f9...b35fe934d424
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4
https://github.com/galaxyproject/galaxy/commit/93a8bfc7cb5e9c3395c5057910ec…
Author: Nate Coraor <nate(a)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/0e698813a96f1ad61d797255686f…
Author: Nate Coraor <nate(a)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/ed045cd570cf6b2198fb49685245…
Author: Nate Coraor <nate(a)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/9e672f94588b8eeecee745665162…
Author: Nate Coraor <nate(a)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/1bccbefbffc02803e93913b145f4…
Author: Nate Coraor <nate(a)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/658f126e7a387c11df9b5f0a01e0…
Author: Nate Coraor <nate(a)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: dda175dbf088bb4ba014fbea70b610cb7e2c2ed6
https://github.com/galaxyproject/galaxy/commit/dda175dbf088bb4ba014fbea70b6…
Author: Nate Coraor <nate(a)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/c4855af7d516b0a955e508cc7e5b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-23 (Mon, 23 Oct 2017)
Log Message:
-----------
Merge branch 'release_16.10' into release_17.01
Compare: https://github.com/galaxyproject/galaxy/compare/ae140949a869...c4855af7d516