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

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

23 Oct '17

Branch: refs/heads/release_16.10 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/34344a7563a3...dda175dbf088

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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_16.07 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. Compare: https://github.com/galaxyproject/galaxy/compare/8e199a33cf25...0e698813a96f

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[galaxyproject/galaxy] 646a8d: Support a log directory argument for pgcleanup.py
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/5016a2d5251f...1af06ce6fe2a

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[galaxyproject/infrastructure-playbook] ad4f38: Only mailoom 3 times per day
by GitHub 21 Oct '17

21 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ad4f38e0ae6f171a4512cc9c8d5e050d563f1b35 https://github.com/galaxyproject/infrastructure-playbook/commit/ad4f38e0ae6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-21 (Sat, 21 Oct 2017) Changed paths: M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Only mailoom 3 times per day

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[galaxyproject/infrastructure-playbook] b502c1: Fix mailoom days
by GitHub 21 Oct '17

21 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b502c1dedc78c8ce000cb62cc3b9ffae3259bd5e https://github.com/galaxyproject/infrastructure-playbook/commit/b502c1dedc7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-21 (Sat, 21 Oct 2017) Changed paths: M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Fix mailoom days

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[galaxyproject/usegalaxy-playbook] 96f138: Installed tools on test: trinity_contig_exn50_stat...
by GitHub 21 Oct '17

21 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 96f138f2d2fa9dd76fc2b90e9169cff003d32cd5 https://github.com/galaxyproject/usegalaxy-playbook/commit/96f138f2d2fa9dd7… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-10-21 (Sat, 21 Oct 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed tools on test: trinity_contig_exn50_statistic, trinity_align_and_estimate_abundance, trinity_abundance_estimates_to_matrix

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[galaxyproject/galaxy] 17b45f: Fix the case where 'Labels' in a docker node inspe...
by GitHub 20 Oct '17

20 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17b45ff6d1d13097f5ac79c1ba036544aee2f9b0 https://github.com/galaxyproject/galaxy/commit/17b45ff6d1d13097f5ac79c1ba03… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Fix the case where 'Labels' in a docker node inspect exists but is null. Commit: faa50a23fbd01236a4fe526b2dd7d293653474f4 https://github.com/galaxyproject/galaxy/commit/faa50a23fbd01236a4fe526b2dd7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Merge pull request #4838 from natefoo/docker-type-fix Fix the case where 'Labels' in a docker node inspect exists but is null. Compare: https://github.com/galaxyproject/galaxy/compare/206f5ec03414...faa50a23fbd0

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[galaxyproject/usegalaxy-playbook] d429b6: Update Main
by GitHub 20 Oct '17

20 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d429b648e0cd58392f6a4ab0dc2e2f9c186661b5 https://github.com/galaxyproject/usegalaxy-playbook/commit/d429b648e0cd5839… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: 21b5358baad16d096af86348c3ad675ce30e882b https://github.com/galaxyproject/usegalaxy-playbook/commit/21b5358baad16d09… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M env/common/stack.yml M env/main/host_vars/galaxy-web-05.tacc.utexas.edu.yml M env/test/host_vars/galaxy07.tacc.utexas.edu.yml M roles/usegalaxy_admin/tasks/main.yml M roles/usegalaxy_privileged/tasks/main.yml M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 A roles/usegalaxy_privileged/templates/cleanup_datasets.sh.j2 Log Message: ----------- Fix up and move Galaxy cleaning Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/848421472ba8...…

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[galaxyproject/usegalaxy-playbook] 02aeca: Update Main (yesterday)
by GitHub 20 Oct '17

20 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 02aecac733ce1205387e7d3c39e9937f0968bc78 https://github.com/galaxyproject/usegalaxy-playbook/commit/02aecac733ce1205… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Main (yesterday) Commit: 848421472ba83b38ca9bd1a4b8c0ed49e4b3ebee https://github.com/galaxyproject/usegalaxy-playbook/commit/848421472ba83b38… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/98c3e52eeacd...…

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[galaxyproject/galaxy] 3b03b5: Fix for single select list initial value when mult...
by GitHub 20 Oct '17

20 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b03b5b6cca75fb93c114d93c97e29b8157869b8 https://github.com/galaxyproject/galaxy/commit/3b03b5b6cca75fb93c114d93c97e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix for single select list initial value when multiple options are selected by default. Commit: 1f6df5580bc27d89a93755502f792c711d07b4b5 https://github.com/galaxyproject/galaxy/commit/1f6df5580bc27d89a93755502f79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Fix the spinner for the GIE container readiness check. Commit: 9475e9aac1068538131bce8c047f89c3c4546bb8 https://github.com/galaxyproject/galaxy/commit/9475e9aac1068538131bce8c047f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #4834 from blankenberg/multiple-initial-single-select-param [17.09] Fix for single select list initial value when multiple options are selected by default. Commit: 42dc7b361756b096f9d3b17c06e2db1a5cefbe61 https://github.com/galaxyproject/galaxy/commit/42dc7b361756b096f9d3b17c06e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Filter histories for visualization grids by user Commit: 30b9e5e4afa2c646a36213fa10d31fd1bc848c3e https://github.com/galaxyproject/galaxy/commit/30b9e5e4afa2c646a36213fa10d3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #4835 from natefoo/gie-spinner-fix [17.09] Fix the spinner for the GIE container readiness check Commit: 799fda61dbf3ddaad1b386d9d32602ef2b1c8a83 https://github.com/galaxyproject/galaxy/commit/799fda61dbf3ddaad1b386d9d326… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Filter library dataset by user Commit: 5016a2d5251f42c87c22f1ad9d2bf164436f9ffd https://github.com/galaxyproject/galaxy/commit/5016a2d5251f42c87c22f1ad9d2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #4836 from guerler/filter_visualization_grid [17.09] Add filter to visualization dataset queries Commit: 206f5ec03414edac72c4ee9233d240b684e99c6e https://github.com/galaxyproject/galaxy/commit/206f5ec03414edac72c4ee9233d2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/galaxy.interactive_environments.js.map A static/maps/libs/jquery/jquery.complexify.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge remote-tracking branch 'origin/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0447ec7ea0bb...206f5ec03414

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