October 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 211366: Update SSL certs
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 211366fb4201713d39ddaa42cb79b6d82a03d93d https://github.com/galaxyproject/infrastructure-playbook/commit/211366fb420… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M common_env/files/ssl/wildcard_cert.pem M common_env/secret_group_vars/sslwebservers.yml M galaxyenv/files/ssl/athena.galaxyproject.org_cert.pem Log Message: ----------- Update SSL certs

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[galaxyproject/infrastructure-playbook] 6923c7: Autoindex updates for depot's patch directory
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6923c7fd02685e6bd33deb557fa2486f71dfa828 https://github.com/galaxyproject/infrastructure-playbook/commit/6923c7fd026… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M galaxyenv/templates/nginx/depot.j2 Log Message: ----------- Autoindex updates for depot's patch directory

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[galaxyproject/usegalaxy-playbook] dca269: Wasn't getting anything at 15 seconds, try 5.
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dca269213288b5a7d2d7b26477b5d0c436825b69 https://github.com/galaxyproject/usegalaxy-playbook/commit/dca269213288b5a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Wasn't getting anything at 15 seconds, try 5.

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[galaxyproject/usegalaxy-playbook] 59ee27: Make uWSGI write to different heartbeat logs...
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 59ee2718fedd57e94a1fc07ad12b5de928aa95f0 https://github.com/galaxyproject/usegalaxy-playbook/commit/59ee2718fedd57e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Make uWSGI write to different heartbeat logs...

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[galaxyproject/usegalaxy-playbook] cd1d65: Enable @dannon's slow query logging for Test and M...
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cd1d65bf8fda5bbb216a241d065e58c28ab68ff9 https://github.com/galaxyproject/usegalaxy-playbook/commit/cd1d65bf8fda5bbb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Enable @dannon's slow query logging for Test and Main

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[galaxyproject/usegalaxy-playbook] a69b02: Enable periodic heartbeats on Main formally so it'...
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a69b029782ca35d89cef50a573d51184fdcc39ac https://github.com/galaxyproject/usegalaxy-playbook/commit/a69b029782ca35d8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Enable periodic heartbeats on Main formally so it's not overwritten again. For tracking down memory usage problems. Commit: 92080edd97149c768adb5276aac709dbcee2aef4 https://github.com/galaxyproject/usegalaxy-playbook/commit/92080edd97149c76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test and Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/96f138f2d2fa...…

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[galaxyproject/galaxy] 93a8bf: Security: Fix issues with path handling in librari...
by GitHub 23 Oct '17

23 Oct '17

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

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[galaxyproject/galaxy] 93a8bf: Security: Fix issues with path handling in librari...
by GitHub 23 Oct '17

23 Oct '17

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

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[galaxyproject/galaxy] 93a8bf: Security: Fix issues with path handling in librari...
by GitHub 23 Oct '17

23 Oct '17

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

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[galaxyproject/galaxy] 93a8bf: Security: Fix issues with path handling in librari...
by GitHub 23 Oct '17

23 Oct '17

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

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