Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fbf3cf30d7df5673ebbc098a2561e26a5486a18a
https://github.com/galaxyproject/galaxy/commit/fbf3cf30d7df5673ebbc098a2561…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-03 (Tue, 03 Oct 2017)
Changed paths:
M tools/filters/joiner.xml
Log Message:
-----------
Fix joiner tool to inherit datatype, restoring previous behavior.
Commit: 7ce0d87a597353d7915a29708a440939e73bb7a3
https://github.com/galaxyproject/galaxy/commit/7ce0d87a597353d7915a29708a44…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-10-03 (Tue, 03 Oct 2017)
Changed paths:
M tools/filters/joiner.xml
Log Message:
-----------
Merge pull request #4745 from dannon/joiner_fix
[17.09] Fix joiner tool to inherit datatype from the input format
Commit: 096b387f8e97a3620855793cb0d257dd3a56883f
https://github.com/galaxyproject/galaxy/commit/096b387f8e97a3620855793cb0d2…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M lib/galaxy/dependencies/conditional-requirements.txt
Log Message:
-----------
update python-ldap with fix for ldaps
Commit: d788bfb80ae1140ecb7757eea2d192de0a7e4045
https://github.com/galaxyproject/galaxy/commit/d788bfb80ae1140ecb7757eea2d1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M lib/galaxy/dependencies/conditional-requirements.txt
Log Message:
-----------
Merge pull request #4748 from abretaud/ldap
[17.09] Fix auth with ldaps://
Commit: fb0586398d81a39734ee1f2031375d547b2da6c1
https://github.com/galaxyproject/galaxy/commit/fb0586398d81a39734ee1f203137…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/security/__init__.py
M test/unit/test_security_helper.py
Log Message:
-----------
Better hanlding of long id secrets when generating per-kind encryption keys.
Generally more validation and more testing as well. Test cases layout the reasons for some of these changes.
Thanks to @nsoranzo for the Python 3 fix.
Commit: bf5c8248b340a0f60519f3c40afb05b8020ddcf3
https://github.com/galaxyproject/galaxy/commit/bf5c8248b340a0f60519f3c40afb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Force onload webhooks to wait for Galaxy object (and root) resolution.
Commit: 95d5ffc71d5c373b92252e1ea1ec4d119ebbf636
https://github.com/galaxyproject/galaxy/commit/95d5ffc71d5c373b92252e1ea1ec…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Merge pull request #4750 from dannon/onloadjs_webhooks_fix
[17.09] Force onload webhooks to wait for Galaxy object (and root) resolution.
Commit: c3f7f391cbca37624566ca99fa1c8e0e5c525a83
https://github.com/galaxyproject/galaxy/commit/c3f7f391cbca37624566ca99fa1c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/security/__init__.py
M test/unit/test_security_helper.py
Log Message:
-----------
Merge pull request #4713 from jmchilton/id_secret_fix
[17.09] Better handling of long id secrets when generating per-kind encryption keys.
Commit: a9c23f0ba97b1a5560642b6106aa9236c7645682
https://github.com/galaxyproject/galaxy/commit/a9c23f0ba97b1a5560642b6106aa…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
replace selector for selecting selected rows
muhaha
Commit: 9a954ca3432e3da8f002bc901bfd723f8caa3aef
https://github.com/galaxyproject/galaxy/commit/9a954ca3432e3da8f002bc901bfd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4752 from martenson/fix-library-allselect
[17.09] replace selector for selecting selected rows
Commit: 562465ffe9c6d1ecb8e67375798d35acce441475
https://github.com/galaxyproject/galaxy/commit/562465ffe9c6d1ecb8e67375798d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/onload.js
M config/galaxy.ini.sample
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/web/security/__init__.py
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/onload.js
M test/unit/test_security_helper.py
M tools/filters/joiner.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/f4eb2dca9642...562465ffe9c6
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: a9c23f0ba97b1a5560642b6106aa9236c7645682
https://github.com/galaxyproject/galaxy/commit/a9c23f0ba97b1a5560642b6106aa…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
replace selector for selecting selected rows
muhaha
Commit: 9a954ca3432e3da8f002bc901bfd723f8caa3aef
https://github.com/galaxyproject/galaxy/commit/9a954ca3432e3da8f002bc901bfd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/admin.bundled.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #4752 from martenson/fix-library-allselect
[17.09] replace selector for selecting selected rows
Compare: https://github.com/galaxyproject/galaxy/compare/c3f7f391cbca...9a954ca3432e
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 72a1d024e73460babd9a484ba9d6a374add85763
https://github.com/galaxyproject/usegalaxy-playbook/commit/72a1d024e73460ba…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M CHANGELOG.md
M env/main/files/galaxy/var/integrated_tool_panel.xml
M env/main/files/galaxy/var/shed_tool_conf.xml
M env/main/templates/galaxy/config/job_conf.xml.j2
Log Message:
-----------
Unicycler fixes for Main
Branch: refs/heads/docker-test
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 296f4adeeec6962e94d9c4014b39773fcf743e88
https://github.com/galaxyproject/infrastructure-playbook/commit/296f4adeeec…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
A common_env/files/ssl/docker/ca-key.pem
A common_env/files/ssl/docker/ca.pem
A common_env/files/ssl/docker/ca.srl
A common_env/files/ssl/docker/client.pem
A common_env/files/ssl/docker/client_privatekey.yml
A common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem
A common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey…
A common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem
A common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek…
A common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p…
A common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat…
A common_env/files/ssl/docker_test/ca-key.pem
A common_env/files/ssl/docker_test/ca.pem
A common_env/files/ssl/docker_test/ca.srl
A common_env/files/ssl/docker_test/client.pem
A common_env/files/ssl/docker_test/client_privatekey.yml
A common_env/files/ssl/docker_test/gie-standalone/server.pem
A common_env/files/ssl/docker_test/gie-standalone/server_privatekey.yml
R common_env/group_vars/dockersslclients.yml
M common_env/group_vars/sslservers/vars.yml
R common_env/secret_group_vars/dockersslclients.yml
M common_roles
M galaxyenv/playbook.yml
A jetstreamdockerenv/files/ssl
R jetstreamdockerenv/group_vars/all.yml
A jetstreamdockerenv/group_vars/all/vars.yml
A jetstreamdockerenv/group_vars/all/vault.yml
M jetstreamdockerenv/group_vars/baseinstances.yml
M jetstreamdockerenv/group_vars/imageinstances.yml
A jetstreamdockerenv/group_vars/sslservers
A jetstreamdockerenv/host_vars/gie-standalone/vars.yml
A jetstreamdockerenv/host_vars/gie-standalone/vault.yml
M jetstreamdockerenv/inc_clouds_yaml.yml
M jetstreamdockerenv/inc_spawn.yml
M jetstreamdockerenv/inventory
A jetstreamdockerenv/inventory.standalone
M jetstreamdockerenv/snapshot_docker_base.yml
M jetstreamdockerenv/snapshot_docker_image.yml
M jetstreamdockerenv/ssh_config.jetstream_iu
A jetstreamdockerenv/standalone.yml
R roles/docker/README.md
M roles/docker/tasks/main.yml
R roles/docker/tasks/ssl-ca-passphrase.yml
R roles/docker/tasks/ssl-ca.yml
R roles/docker/tasks/ssl-client.yml
R roles/docker/tasks/ssl-gen-ca.yml
R roles/docker/tasks/ssl-gen-client-cert.yml
R roles/docker/tasks/ssl-gen-server-cert.yml
R roles/docker/tasks/ssl-server.yml
A taccenv/group_vars/dockerclients.yml
R taccenv/group_vars/dockersslclients.yml
M taccenv/host_vars/galaxy07.tacc.utexas.edu.yml
M taccenv/inventory
M taccenv/playbook.yml
Log Message:
-----------
Switch the docker role to use the common ssl role, and create a
docker_test CA for testing new GIE docker images on Test.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 78d1dda69e71f55193bb3db328c959a8220c105d
https://github.com/galaxyproject/galaxy/commit/78d1dda69e71f55193bb3db328c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M test/api/test_tools.py
A test/api/test_tools_upload.py
Log Message:
-----------
Refactor API upload tests into their own test class.
Commit: 8eac80a51bc426c8eefaab89419aef4bc76b8cc0
https://github.com/galaxyproject/galaxy/commit/8eac80a51bc426c8eefaab89419a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M test/api/test_tools_upload.py
Log Message:
-----------
More upload API tests.
Commit: 108e94c9c2205d817d10986432d7dcb6c54666be
https://github.com/galaxyproject/galaxy/commit/108e94c9c2205d817d10986432d7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M test/api/test_tools_upload.py
M test/base/api.py
M test/base/api_util.py
A test/base/constants.py
M test/base/populators.py
M test/integration/test_upload_configuration_options.py
Log Message:
-----------
FTP upload integration tests.
Test various configuration options (ftp_upload_dir, ftp_upload_identifier, ftp_upload_dir_template) and various upload API parameters (space_to_tab, to_posix_lines, auto_decompress).
Commit: f4eb2dca96426a434fee47463734118ec2837f96
https://github.com/galaxyproject/galaxy/commit/f4eb2dca96426a434fee47463734…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M test/api/test_tools.py
A test/api/test_tools_upload.py
M test/base/api.py
M test/base/api_util.py
A test/base/constants.py
M test/base/populators.py
M test/integration/test_upload_configuration_options.py
Log Message:
-----------
Merge pull request #4746 from jmchilton/upload_tests_2
Many more upload tests.
Compare: https://github.com/galaxyproject/galaxy/compare/c478716f3b26...f4eb2dca9642
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1ec0f8ea6679625ca51c4fde6d6690498ed3b4de
https://github.com/galaxyproject/galaxy/commit/1ec0f8ea6679625ca51c4fde6d66…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-03 (Tue, 03 Oct 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
Log Message:
-----------
Standardize dict_*_visible_keys to a list.
Commit: 7145035d6c2d45aeb97fc29d7f160bfc80af9e5d
https://github.com/galaxyproject/galaxy/commit/7145035d6c2d45aeb97fc29d7f16…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-03 (Tue, 03 Oct 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Two more spots needing standardization on list for _visible_keys (this concat would fail, another reason for using the same type everywhere)
Commit: c478716f3b26332fcc3d1770b7dc04fe3d0c26a3
https://github.com/galaxyproject/galaxy/commit/c478716f3b26332fcc3d1770b7dc…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
Log Message:
-----------
Merge pull request #4744 from dannon/visible_keys_standardization
Visible keys standardization
Compare: https://github.com/galaxyproject/galaxy/compare/c49adb15184c...c478716f3b26
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: fb0586398d81a39734ee1f2031375d547b2da6c1
https://github.com/galaxyproject/galaxy/commit/fb0586398d81a39734ee1f203137…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/security/__init__.py
M test/unit/test_security_helper.py
Log Message:
-----------
Better hanlding of long id secrets when generating per-kind encryption keys.
Generally more validation and more testing as well. Test cases layout the reasons for some of these changes.
Thanks to @nsoranzo for the Python 3 fix.
Commit: c3f7f391cbca37624566ca99fa1c8e0e5c525a83
https://github.com/galaxyproject/galaxy/commit/c3f7f391cbca37624566ca99fa1c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/web/security/__init__.py
M test/unit/test_security_helper.py
Log Message:
-----------
Merge pull request #4713 from jmchilton/id_secret_fix
[17.09] Better handling of long id secrets when generating per-kind encryption keys.
Compare: https://github.com/galaxyproject/galaxy/compare/95d5ffc71d5c...c3f7f391cbca
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: bf5c8248b340a0f60519f3c40afb05b8020ddcf3
https://github.com/galaxyproject/galaxy/commit/bf5c8248b340a0f60519f3c40afb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Force onload webhooks to wait for Galaxy object (and root) resolution.
Commit: 95d5ffc71d5c373b92252e1ea1ec4d119ebbf636
https://github.com/galaxyproject/galaxy/commit/95d5ffc71d5c373b92252e1ea1ec…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-04 (Wed, 04 Oct 2017)
Changed paths:
M client/galaxy/scripts/onload.js
M static/maps/onload.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/onload.js
Log Message:
-----------
Merge pull request #4750 from dannon/onloadjs_webhooks_fix
[17.09] Force onload webhooks to wait for Galaxy object (and root) resolution.
Compare: https://github.com/galaxyproject/galaxy/compare/d788bfb80ae1...95d5ffc71d5c