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

[galaxyproject/galaxy] fbf3cf: Fix joiner tool to inherit datatype, restoring pre...
by GitHub 04 Oct '17

04 Oct '17

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

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[galaxyproject/galaxy] a9c23f: replace selector for selecting selected rows
by GitHub 04 Oct '17

04 Oct '17

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

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[galaxyproject/usegalaxy-playbook] 884b81: Temporarily switch to a single docker host for Tes...
by GitHub 04 Oct '17

04 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 884b8129a51a77ca38152e8fb3c7dfb2fd65f44d https://github.com/galaxyproject/usegalaxy-playbook/commit/884b8129a51a77ca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Temporarily switch to a single docker host for Test to test new images.

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[galaxyproject/usegalaxy-playbook] fd7b89: Stop trying to communicate with Jetstream@TACC due...
by GitHub 04 Oct '17

04 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fd7b891fca0cf5b0cb9876ec00346e667ba3f3da https://github.com/galaxyproject/usegalaxy-playbook/commit/fd7b891fca0cf5b0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/group_vars/galaxywebservers.yml Log Message: ----------- Stop trying to communicate with Jetstream@TACC due to extended downtime.

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[galaxyproject/usegalaxy-playbook] 72a1d0: Unicycler fixes for Main
by GitHub 04 Oct '17

04 Oct '17

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

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[galaxyproject/infrastructure-playbook] 296f4a: Switch the docker role to use the common ssl role, ...
by GitHub 04 Oct '17

04 Oct '17

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.

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[galaxyproject/galaxy] 78d1dd: Refactor API upload tests into their own test clas...
by GitHub 04 Oct '17

04 Oct '17

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

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[galaxyproject/galaxy] 1ec0f8: Standardize dict_*_visible_keys to a list.
by GitHub 04 Oct '17

04 Oct '17

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

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[galaxyproject/galaxy] fb0586: Better hanlding of long id secrets when generating...
by GitHub 04 Oct '17

04 Oct '17

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

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[galaxyproject/galaxy] bf5c82: Force onload webhooks to wait for Galaxy object (a...
by GitHub 04 Oct '17

04 Oct '17

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

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