galaxy-commits June 2018

galaxy-commits@lists.galaxyproject.org

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170 discussions

[galaxyproject/galaxy] 82c965: Prevent throwing an exception if a dataset doesn't...
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82c965f1c6e05c559bcb3a12706d5714f91783ce https://github.com/galaxyproject/galaxy/commit/82c965f1c6e05c559bcb3a12706d… Author: dpryan79 <dpryan79(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Prevent throwing an exception if a dataset doesn't exist (and never will) due to a job error. This is an alternative (and better) solution to #6337 when jobs set metadata externally. Commit: db11a2549d33b9233d6e17cf6c3888e813bc7ab3 https://github.com/galaxyproject/galaxy/commit/db11a2549d33b9233d6e17cf6c38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-16 (Sat, 16 Jun 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6349 from dpryan79/preventExceptionOnFileAccess Prevent throwing an exception if a dataset doesn't exist (and never w… Compare: https://github.com/galaxyproject/galaxy/compare/b41af6abe9c1...db11a2549d33 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 5df126: Missed slurm.conf changes in the last commit
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5df126f6c5258e214e22073c3346f4399c3ecb93 https://github.com/galaxyproject/infrastructure-playbook/commit/5df126f6c52… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M env/jsiu/templates/slurm/slurm.conf.j2 Log Message: ----------- Missed slurm.conf changes in the last commit **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 8ee358: Create /galaxy and /galaxy-repl symlinks on Jetstr...
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8ee3580a4fb3cc76283f33222c1a5604a2139b8f https://github.com/galaxyproject/infrastructure-playbook/commit/8ee3580a4fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M roles/slurmscale/files/group_vars/all/cluster.yml M roles/slurmscale/files/roles/galaxynodeconfig/tasks/main.yml M roles/slurmscale/tasks/main.yml M roles/slurmscale/templates/suspend_resume.sh.j2 Log Message: ----------- Create /galaxy and /galaxy-repl symlinks on Jetstream for old TS dependency resolution, plus log suspends/resumes seperately by hosts in play **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] f7335f: Re-enable multicore jobs on Jetstream @ IU plus se...
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f7335f4a35a82e8863b9182898360a87c0674d89 https://github.com/galaxyproject/usegalaxy-playbook/commit/f7335f4a35a82e88… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Re-enable multicore jobs on Jetstream @ IU plus set memory limits on submissions **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] fc4761: Initial python-based plugin staging. to be used f...
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fc47618f6798d48f3ab903a8ea6231067bf0fed2 https://github.com/galaxyproject/galaxy/commit/fc47618f6798d48f3ab903a8ea62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: A scripts/plugin_staging.py Log Message: ----------- Initial python-based plugin staging. to be used from common startup. Commit: e110489cc55f25b7d5ec7b9e5cbc5d914215b806 https://github.com/galaxyproject/galaxy/commit/e110489cc55f25b7d5ec7b9e5cbc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently) Commit: 370ea25d2c58b7e55f6bc062062e9a962a08ea7d https://github.com/galaxyproject/galaxy/commit/370ea25d2c58b7e55f6bc062062e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Minor refactoring, comments. Commit: 8364ebebcd81b6f8bf6c1122e5271a5c5eb23868 https://github.com/galaxyproject/galaxy/commit/8364ebebcd81b6f8bf6c1122e527… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Add static-safe mapping for uwsgi for plugin static dirs, which are accessible via symlink Commit: 4cdd210bb27cd1c271e69c8dfd46585f0c232ef9 https://github.com/galaxyproject/galaxy/commit/4cdd210bb27cd1c271e69c8dfd46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Use os.pardir instead of ../. Thanks @nsoranzo Commit: 12a05c782099da0eb846069fe96355fb50212fef https://github.com/galaxyproject/galaxy/commit/12a05c782099da0eb846069fe963… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/common_startup.sh M scripts/get_uwsgi_args.py A scripts/plugin_staging.py Log Message: ----------- Merge pull request #6344 from dannon/python_static_staging [18.05] Visualization static staging Compare: https://github.com/galaxyproject/galaxy/compare/e7b7bee82e60...12a05c782099 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy]
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 504e03: WIP historyimport fixes
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 504e030291d3f7bfb49f62888551d68a43357318 https://github.com/galaxyproject/galaxy/commit/504e030291d3f7bfb49f62888551… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M test/selenium_tests/test_workflow_editor.py Log Message: ----------- WIP historyimport fixes Commit: 7f5206a3b1b880161ca6e3bd38626aabb6c2d528 https://github.com/galaxyproject/galaxy/commit/7f5206a3b1b880161ca6e3bd3862… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add preliminary sharing vue component, redirect routes Commit: 5c6704b8e14c1c0da07b537d01e3274c9746b205 https://github.com/galaxyproject/galaxy/commit/5c6704b8e14c1c0da07b537d01e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Augment user information storage api, separate username from email handling Commit: 718e9bc9d09f915b00910b52a3efe58dc087b242 https://github.com/galaxyproject/galaxy/commit/718e9bc9d09f915b00910b52a3ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: A client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add sharing vue component Commit: 91590243b70e7c7727ff9d83b9589e527b36d9bf https://github.com/galaxyproject/galaxy/commit/91590243b70e7c7727ff9d83b958… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add error flag Commit: 53e67733660a8061a31de1a2a867e46e35fa2465 https://github.com/galaxyproject/galaxy/commit/53e67733660a8061a31de1a2a867… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09.dev Commit: 8b51c30aa7c1e7ea711e22f81a4156ea1bcda769 https://github.com/galaxyproject/galaxy/commit/8b51c30aa7c1e7ea711e22f81a41… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Log Message: ----------- Merge branch 'version-18.05' into version-18.09.dev Commit: 7580a28b39175c221525abf74c0438a89b59f13f https://github.com/galaxyproject/galaxy/commit/7580a28b39175c221525abf74c04… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5982 from martenson/version-18.09.dev start Version 18.09.dev Commit: d16c71bbb03ea0a05baf884009b313ff5c0b1cc5 https://github.com/galaxyproject/galaxy/commit/d16c71bbb03ea0a05baf884009b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Expand sharing vue component Commit: 2abab4f53698eca07ea2508c41a868cf33ddb310 https://github.com/galaxyproject/galaxy/commit/2abab4f53698eca07ea2508c41a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Replace mako style url generation Commit: 7d9c085b03d477fa8322e140732d4d1c804d6a6a https://github.com/galaxyproject/galaxy/commit/7d9c085b03d477fa8322e140732d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: f065ebe903cec29aeca89eb7c9ffe1bf44f13f7e https://github.com/galaxyproject/galaxy/commit/f065ebe903cec29aeca89eb7c9ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add remaining sections to vue component Commit: 4824690ade9042c1c96de469a2c3218d2fc33c9a https://github.com/galaxyproject/galaxy/commit/4824690ade9042c1c96de469a2c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Optimize safe_walk to call realpath a lot less for typical calls... Cuts the time required to load 100,000 FTP files into the rule builder in half on my macbook - could imagine the gains to be even bigger on a network file system? Commit: 24b04bfef06d0de9adbff82ce42e7b486fb0c8e9 https://github.com/galaxyproject/galaxy/commit/24b04bfef06d0de9adbff82ce42e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #5995 from jmchilton/ftp_optimize Optimize safe_walk to call realpath a lot less for typical calls... Commit: 74939a3f11a7b21d95e6da54cc26b53a0af854fc https://github.com/galaxyproject/galaxy/commit/74939a3f11a7b21d95e6da54cc26… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Update release process - do not require merge PRs to have milestones. Commit: 39dd9ac76c4de56dcc0066a08d0beba788a9bc93 https://github.com/galaxyproject/galaxy/commit/39dd9ac76c4de56dcc0066a08d0b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6004 from jmchilton/release_process_tweaks Update release process - do not require merge PRs to have milestones. Commit: 6a8c4dc7e287c83c335879e02caa61493d2aa967 https://github.com/galaxyproject/galaxy/commit/6a8c4dc7e287c83c335879e02caa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/containers/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.05' into dev Commit: acc9889815460b7f7ac4652e226e9f9209f8fc9d https://github.com/galaxyproject/galaxy/commit/acc9889815460b7f7ac4652e226e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/yarn.lock M doc/source/admin/scaling.md M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 2b72bbb19f31c8fa633bbeeab8743ba37f0ca9fa https://github.com/galaxyproject/galaxy/commit/2b72bbb19f31c8fa633bbeeab874… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add button labels, fix bugs Commit: 0875b8e65d6d5d7130c829ec8e5b7f9bffcced3a https://github.com/galaxyproject/galaxy/commit/0875b8e65d6d5d7130c829ec8e5b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- fix bowtie2 link Commit: c2ee91508bcc96cadfd7b23fba8a8d60e6f5547a https://github.com/galaxyproject/galaxy/commit/c2ee91508bcc96cadfd7b23fba8a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6009 from galaxyproject/bowtie2_link fix bowtie2 link Commit: 5e9f5aa46c440cf733d4174298f00380c06f0edc https://github.com/galaxyproject/galaxy/commit/5e9f5aa46c440cf733d4174298f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-29 (Sun, 29 Apr 2018) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add api support for sharing status handling to histories Commit: f50715df8377af74afce2231aa857a98684f6868 https://github.com/galaxyproject/galaxy/commit/f50715df8377af74afce2231aa85… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Remove __global__ Commit: 8c152bda45cbf3b49610a9933bd6c38f1724942a https://github.com/galaxyproject/galaxy/commit/8c152bda45cbf3b49610a9933bd6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Merge pull request #6011 from erasche/remove_global Remove duplicate metric sending Commit: 1f3a8d4954abfc8222976dd2a2bee987936b91c5 https://github.com/galaxyproject/galaxy/commit/1f3a8d4954abfc8222976dd2a2be… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/managers/collections_util.py Log Message: ----------- Fix typos Commit: 0bcb69df456ea903461e712aa8e83b624f779d0e https://github.com/galaxyproject/galaxy/commit/0bcb69df456ea903461e712aa8e8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix link formatting We cannot use backquote characters in the link text, because pandoc generates a broken RST, see https://github.com/jgm/pandoc/issues/3973 Commit: f2ce39323364c9cf578235c00800816b5208956e https://github.com/galaxyproject/galaxy/commit/f2ce39323364c9cf578235c00800… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Small tool XML doc fixes Commit: 479e76ff13c9a2e232efda5b3d3db7b25a2701c3 https://github.com/galaxyproject/galaxy/commit/479e76ff13c9a2e232efda5b3d3d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Add closing old milestone to release issue Commit: 54e89ae4983490da43ab3a1035e2df7f73e11d09 https://github.com/galaxyproject/galaxy/commit/54e89ae4983490da43ab3a1035e2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py Log Message: ----------- Fix broken imports `from galaxy.util import enum` probably never worked. Commit: 65cb42d8d8b45d2d4bc879864bc929fa123a3c16 https://github.com/galaxyproject/galaxy/commit/65cb42d8d8b45d2d4bc879864bc9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/torque.py Log Message: ----------- Fix PBS status reporting Without this commit only very short jobs completed successfully, because the status was always set to complete. This was because the status returned by qstat contains leading spaces before the `job_state = Q` part, so I'm adding a `.strip()`. Imported from https://github.com/galaxyproject/pulsar/commit/9acc5637780e553c3a9d0efb9cf7… Commit: d659058385c3ed52ed4cef43dd277f9917440753 https://github.com/galaxyproject/galaxy/commit/d659058385c3ed52ed4cef43dd27… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Simplify imports Commit: 9f5a1fa9a613bfe6d6b49e3460be1a2e15ca6bce https://github.com/galaxyproject/galaxy/commit/9f5a1fa9a613bfe6d6b49e3460be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/managers/collections_util.py M lib/galaxy/tools/xsd/galaxy.xsd M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6013 from nsoranzo/misc Documentation and typo fixes Commit: 02ffdf0be933b972fbd1dcb2a6b2c210331c520c https://github.com/galaxyproject/galaxy/commit/02ffdf0be933b972fbd1dcb2a6b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/lib/galaxy.web.framework.middleware.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- This strips the graphite-specific middleware; statistic functionality is provided by the statsd middleware and we don't need two separate mechanisms to maintain. Commit: 9cee8e229836b707eacb4b3d6ae5cae65e4d6589 https://github.com/galaxyproject/galaxy/commit/9cee8e229836b707eacb4b3d6ae5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Add sample commentary to the stub in config manage, xref a88e19064a38415d867f4c118dd6938d8e368632 Commit: b7a89eb106b2924b2d0e1db7749db89de46228c9 https://github.com/galaxyproject/galaxy/commit/b7a89eb106b2924b2d0e1db7749d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Config rebuild Commit: a630f13e6d7e9876a3cce2192953c1fe62dc5962 https://github.com/galaxyproject/galaxy/commit/a630f13e6d7e9876a3cce2192953… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- More standard spacing in additional config comments just added. Commit: 44ed208e47f89ad14230d6e72c82d31e48442e92 https://github.com/galaxyproject/galaxy/commit/44ed208e47f89ad14230d6e72c82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Load initial settings through api Commit: 740e1fc05c78ff6c05ae5d128489f1514c2b8e1f https://github.com/galaxyproject/galaxy/commit/740e1fc05c78ff6c05ae5d128489… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/lib/galaxy.web.framework.middleware.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6018 from dannon/kill_graphite_middleware This strips the graphite-specific middleware Commit: 7edef1b0dd79593f170bde2ddd912381a5563df9 https://github.com/galaxyproject/galaxy/commit/7edef1b0dd79593f170bde2ddd91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add and initialize properties Commit: ca77dedf7c46ac124dc2a066d836ca058166ca93 https://github.com/galaxyproject/galaxy/commit/ca77dedf7c46ac124dc2a066d836… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Retrieve class name from api model Commit: 4830587b02eeeaf06d2a9c2e5b005ddbae07ff03 https://github.com/galaxyproject/galaxy/commit/4830587b02eeeaf06d2a9c2e5b00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Use plural name as property Commit: 51389473e0f5b56d8e5ffe85f2f5dad8e5e534cd https://github.com/galaxyproject/galaxy/commit/51389473e0f5b56d8e5ffe85f2f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/histories.py Log Message: ----------- Fix serializer Commit: d0790234bb8cd01875704dd53877ccb16fcc7bd2 https://github.com/galaxyproject/galaxy/commit/d0790234bb8cd01875704dd53877… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M config/job_metrics_conf.xml.sample A lib/galaxy/jobs/metrics/instrumenters/hostname.py Log Message: ----------- Add hostname metric Commit: 0fac69bd59256391d2e99200e4c2915d1e14ff3f https://github.com/galaxyproject/galaxy/commit/0fac69bd59256391d2e99200e4c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6014 from nsoranzo/fix_imports Fix some imports Commit: bd7cd04518a08c695b75cd922b7af006338a8730 https://github.com/galaxyproject/galaxy/commit/bd7cd04518a08c695b75cd922b7a… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/jobs/metrics/instrumenters/hostname.py Log Message: ----------- address review comments Commit: 543d5b2138473fe6936420b6d85dd8ce9c2a6629 https://github.com/galaxyproject/galaxy/commit/543d5b2138473fe6936420b6d85d… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py Log Message: ----------- also change import lines here Commit: 370590f9ed7f7177e10f0762b9c84398c6eb4cad https://github.com/galaxyproject/galaxy/commit/370590f9ed7f7177e10f0762b9c8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/collectl.py Log Message: ----------- Fix import order Commit: 4020ecdb33f55b440ebf12e768f98312dbdf57b8 https://github.com/galaxyproject/galaxy/commit/4020ecdb33f55b440ebf12e768f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add individual users to view, populate table Commit: a5917387b2705ff88a72d5691e804cf1f5a1215f https://github.com/galaxyproject/galaxy/commit/a5917387b2705ff88a72d5691e80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Fix link to published list Commit: 4c22203c8097b1b5bcb40864fdccf4df27ba7c45 https://github.com/galaxyproject/galaxy/commit/4c22203c8097b1b5bcb40864fdcc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py A lib/galaxy/jobs/metrics/instrumenters/hostname.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py Log Message: ----------- Merge pull request #6021 from erasche/hostname Add hostname metric Commit: c31b553b7737986756a6ce205eb36bd779f1f0a3 https://github.com/galaxyproject/galaxy/commit/c31b553b7737986756a6ce205eb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix sharing status api endpoint, connect ui Commit: 6e2f4108c50c11d94cdb8a15afad7a3f66e99176 https://github.com/galaxyproject/galaxy/commit/6e2f4108c50c11d94cdb8a15afad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Fix error message handling, properly reflect server response in ui Commit: 606b6e475a432020c8199bde5fab873d457a2e39 https://github.com/galaxyproject/galaxy/commit/606b6e475a432020c8199bde5fab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Add preliminary support for users having access to the history Commit: 08ffa6ec97df79bbd53e4aa409183a3941682939 https://github.com/galaxyproject/galaxy/commit/08ffa6ec97df79bbd53e4aa40918… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Adjust username handling, fix form submission actions Commit: c281c1a6171383241d6584bbf929beb54c0e6c7b https://github.com/galaxyproject/galaxy/commit/c281c1a6171383241d6584bbf929… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove legacy sharing controller endpoint Commit: 93d9a9dc5682f574cce33b5b945892ae039a65e7 https://github.com/galaxyproject/galaxy/commit/93d9a9dc5682f574cce33b5b9458… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Fix username check flag Commit: 7af3b328f2f0bab6500fdceac6b1c872c28e7670 https://github.com/galaxyproject/galaxy/commit/7af3b328f2f0bab6500fdceac6b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/style/scss/base.scss M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/tool_shed/util/admin_util.py M run_tests.sh M static/style/blue/base.css M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/selenium_tests/test_workflow_editor.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 6006d9bfcad15b4a840594fb8367a6b1a780a3cf https://github.com/galaxyproject/galaxy/commit/6006d9bfcad15b4a840594fb8367… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.05' into dev Commit: d52b1f71bc106c3b402231d68c26a8bdb3575888 https://github.com/galaxyproject/galaxy/commit/d52b1f71bc106c3b402231d68c26… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Incremental refactoring to es6 classes and other fixes while tracking down workflow issue. Commit: b09c6803c36305e8f8634429523970831162091c https://github.com/galaxyproject/galaxy/commit/b09c6803c36305e8f86344295239… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/utils/async-save-text.js Log Message: ----------- Use existing slug editing feature in component Commit: 7a17244acd365be9a10d97961b3c07b9a6382cd7 https://github.com/galaxyproject/galaxy/commit/7a17244acd365be9a10d97961b3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: R templates/sharing_base.mako Log Message: ----------- Remove sharing base mako Commit: 17772d19c5e4f168cba4e9fcb0e83a31e15c7858 https://github.com/galaxyproject/galaxy/commit/17772d19c5e4f168cba4e9fcb0e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Link sharing base from history panel Commit: 3507636a4a3d2acc41fb96d464247854a78ea4f2 https://github.com/galaxyproject/galaxy/commit/3507636a4a3d2acc41fb96d46424… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Move sharing status api endpoint to mixin Commit: f8606a81db718ba19d9ecc3ae05e63d629da5ad7 https://github.com/galaxyproject/galaxy/commit/f8606a81db718ba19d9ecc3ae05e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/model/__init__.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py Log Message: ----------- Increase precision of metric_value on job_metric_numeric to 26. Commit: ab8542a24c55271b08c356b3c242a0dbe729a360 https://github.com/galaxyproject/galaxy/commit/ab8542a24c55271b08c356b3c242… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- Allow selection of specific cgroup params for cgroup metrics plugin Commit: a543b62fd3b966352030a24c7b6dbf0ce4f96146 https://github.com/galaxyproject/galaxy/commit/a543b62fd3b966352030a24c7b6d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Add a note that metrics column sizes can't be changed simply by changing their constants in model Commit: 459384b060e131d897f3d6d5dce6e9f64c45d18d https://github.com/galaxyproject/galaxy/commit/459384b060e131d897f3d6d5dce6… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/model/__init__.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py Log Message: ----------- Merge pull request #5993 from natefoo/cgroup-metric-enhancements Minor enhancements for cgroup metrics Commit: 3e49e31707fc0539b859fb11bbfd841fb38dda44 https://github.com/galaxyproject/galaxy/commit/3e49e31707fc0539b859fb11bbfd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/package.json M client/yarn.lock M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M lib/galaxy/tools/errors.py M run_tests.sh M static/style/blue/base.css M templates/display_common.mako M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge branch 'release_18.05' into dev Commit: bd248933f16ebab3af15e7e264ada3a89ff94337 https://github.com/galaxyproject/galaxy/commit/bd248933f16ebab3af15e7e264ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- More incremental refactoring while tracking down workflow bugs. Commit: 258516c055b9ee5288ccb8e2ca3c24578298d87a https://github.com/galaxyproject/galaxy/commit/258516c055b9ee5288ccb8e2ca3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Get sharable object by class name Commit: 6f25fdebc65aba8b7c258749a235a18d78251576 https://github.com/galaxyproject/galaxy/commit/6f25fdebc65aba8b7c258749a235… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/managers/base.py Log Message: ----------- Generalize class name identifer, toolshed corner case Commit: 17a80e3753ab30e09df17951a6a3bc4cd1c9cdaf https://github.com/galaxyproject/galaxy/commit/17a80e3753ab30e09df17951a6a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use default class name for sharable mixin Commit: c283fd5939ae83140f18df1e2623938421f5e58a https://github.com/galaxyproject/galaxy/commit/c283fd5939ae83140f18df1e2623… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/histories.py M lib/galaxy/managers/sharable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Refactor endpoint, add visualization sharing Commit: ac0db77d2c1b8336862eeb7ab9f9482bf49ca9e5 https://github.com/galaxyproject/galaxy/commit/ac0db77d2c1b8336862eeb7ab9f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Add page sharing routes to client Commit: 9360a1ae0d4410d293d5d404ef88db0e0da8f97d https://github.com/galaxyproject/galaxy/commit/9360a1ae0d4410d293d5d404ef88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/pages.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Reroute pages sharing view Commit: 7a7c6a76f086cc416df4f652f750ddf140f5b1c0 https://github.com/galaxyproject/galaxy/commit/7a7c6a76f086cc416df4f652f750… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Remove user sharing in detailed history serialization Remove unused function Commit: 6c2f1957a9c49943182b8b971097f9a8ef511bab https://github.com/galaxyproject/galaxy/commit/6c2f1957a9c49943182b8b971097… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Rules - test case and bug fixes for adding cols for regex groups. Commit: 898e73eca1eccfb9fb707cdb5af75ee72c3d7565 https://github.com/galaxyproject/galaxy/commit/898e73eca1eccfb9fb707cdb5af7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: 7ce1cc445f427a18cf354360a4284c157e39e5b0 https://github.com/galaxyproject/galaxy/commit/7ce1cc445f427a18cf354360a428… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Remove redundant properties Use consistent naming Fix typo Fix Commit: ec723829bf788b3100bfb56f72c22dd4981e3fdf https://github.com/galaxyproject/galaxy/commit/ec723829bf788b3100bfb56f72c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml Log Message: ----------- Rules - fix poor name for Apply Rules output collection. Commit: 050c9e99c6c981518f160d99aeaa2f395a84e4b5 https://github.com/galaxyproject/galaxy/commit/050c9e99c6c981518f160d99aeaa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Rules - test case for apply rules tutorial. Demonstrates using the Apply Rules collection operation tool against existing collections to: - Use grouping to build nested lists from flat ones. - Invert nested collections. - Filter collections. - Filter while also grouping to build nested collections. Based on count data used in the DESeq2 tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq…), originally from the Bioconductor Pasilla package (http://bioconductor.org/packages/release/data/experiment/html/pasilla.html). Citation: Huber W, Reyes A (2018). pasilla: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.. R package version 1.8.0. Commit: 276a559cf44534361e48a1abddd465fce9217ab2 https://github.com/galaxyproject/galaxy/commit/276a559cf44534361e48a1abddd4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_libraries.py M test/api/test_tools.py Log Message: ----------- Make interactor._{get,post,put,...} less repetitve Also inject api key into params, so that we can use `json.dumps` for the payload instead of writing json strings in python. Commit: c67c4b4b82dd4280e9fcef4003a9956c6c0ca062 https://github.com/galaxyproject/galaxy/commit/c67c4b4b82dd4280e9fcef4003a9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/permutations.py M lib/galaxy/util/rules_dsl.py M scripts/grt/export.py M static/style/blue/base.css M test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 2de4219aae59cd93f7b9891d05d0d94859a9febc https://github.com/galaxyproject/galaxy/commit/2de4219aae59cd93f7b9891d05d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix a bunch of typos in workflow manager. Commit: 1f405d6916e2fdff808f9c65b5b3c5becedd21c9 https://github.com/galaxyproject/galaxy/commit/1f405d6916e2fdff808f9c65b5b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Drop unnecessary workflow enumerate in workflow manager. Commit: a4bf7aca6f5e556777d24d7d61dab31a0cc797e0 https://github.com/galaxyproject/galaxy/commit/a4bf7aca6f5e556777d24d7d61da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Minor refactoring in webapp to clarify history association logic (and maybe reuse it) Commit: 1fa77c38f611351bdc5bece9e9d06a16da08f42b https://github.com/galaxyproject/galaxy/commit/1fa77c38f611351bdc5bece9e9d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Commit: 45ea97eea24adf8fa4043297124399effc50ff33 https://github.com/galaxyproject/galaxy/commit/45ea97eea24adf8fa40432971243… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Move username handling from sharable base controller to workflow controller Commit: 346d2dca3e5b44ba6a37952b632bd1910fd5f468 https://github.com/galaxyproject/galaxy/commit/346d2dca3e5b44ba6a37952b632b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Merge `data` into params I don't think we're parsing GET request payloads. This effectively restore the get behavior prior to the previous commit. Commit: 835c59d109cbca3b58e396bed6ba856caaaf95cf https://github.com/galaxyproject/galaxy/commit/835c59d109cbca3b58e396bed6ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- No request body for DELETE/GET, no params for POST Commit: 0a599089fa3733a22e2f3ed7c7882046255b9a9f https://github.com/galaxyproject/galaxy/commit/0a599089fa3733a22e2f3ed7c788… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M test/api/test_libraries.py M test/api/test_tools.py Log Message: ----------- Don't dump json parameters Commit: 85bf5129b2fdabf1070b475df41190b60a9004f8 https://github.com/galaxyproject/galaxy/commit/85bf5129b2fdabf1070b475df411… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Replace mutable default argument Commit: d09dfca4292f9cf34ef1bad76c39eb21fe984518 https://github.com/galaxyproject/galaxy/commit/d09dfca4292f9cf34ef1bad76c39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- More typos, minor tweak to _associate_user_history Commit: a1c58a708829d79859426ecb7c39b5c5f69ad735 https://github.com/galaxyproject/galaxy/commit/a1c58a708829d79859426ecb7c39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py Log Message: ----------- When JobWrapper.get_destination_configuration() is called, check the JobDestination params in addition to the destination_params persisted on the Job and the app configuration Commit: b43ef5538121360c63b895d2a86dec91070598c0 https://github.com/galaxyproject/galaxy/commit/b43ef5538121360c63b895d2a86d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Drop unused edit_workflow_outputs functionality Commit: 6919da46d876768902b51639b1784c2df797f543 https://github.com/galaxyproject/galaxy/commit/6919da46d876768902b51639b178… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M 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config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.js M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.yml.sample M config/user_preferences_extra_conf.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M create_db.sh M doc/Makefile M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/conf.py A doc/source/conf.versioning.py M doc/source/lib/galaxy.web.framework.middleware.rst A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A 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test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/jobs/test_mapper.py M test/unit/managers/test_HistoryManager.py A test/unit/test_rule_utils.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into dev Commit: c3982fdf4ca9cf12595e02be4f08a074ec52f60c https://github.com/galaxyproject/galaxy/commit/c3982fdf4ca9cf12595e02be4f08… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py Log Message: ----------- Add blib MS spectral library datatype blib is a SQlite schema for MassSpec spectral library Commit: 6373d352a83cb1a1f530cdad288ee90fb2b3ec48 https://github.com/galaxyproject/galaxy/commit/6373d352a83cb1a1f530cdad288e… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- fixed typo Commit: a53551448b756cc90305fad25101a0969b59c292 https://github.com/galaxyproject/galaxy/commit/a53551448b756cc90305fad25101… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #6094 from bernt-matthias/topic/collection-typo fixed small typo Commit: c5828aa67c02689060cbb500fb32bf0ca0585f8f https://github.com/galaxyproject/galaxy/commit/c5828aa67c02689060cbb500fb32… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.blib Log Message: ----------- blib datatype add test file: test.blib include blib version in metadata Commit: 3b027af3df512194929fa6a979b111fccd5b9f6d https://github.com/galaxyproject/galaxy/commit/3b027af3df512194929fa6a979b1… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix flake8 errors Commit: 5d2881db01dbe927eb0c003b36b0e890a3a2da73 https://github.com/galaxyproject/galaxy/commit/5d2881db01dbe927eb0c003b36b0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Fix link to sharing view Commit: 22c640608a06abc0f87ab868ef2909b4f59d2c7e https://github.com/galaxyproject/galaxy/commit/22c640608a06abc0f87ab868ef29… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix routing from share controller Commit: 1516cfb8b5ad8179395f700e66d1cbc7beb887fd https://github.com/galaxyproject/galaxy/commit/1516cfb8b5ad8179395f700e66d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix history sharing routes, import missing module Commit: 41c3dbfdb3b109aea742e4e27e778415708c586e https://github.com/galaxyproject/galaxy/commit/41c3dbfdb3b109aea742e4e27e77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- Add title to serializer Commit: 2a21e273ae06303188cddfdc593cb46184d47234 https://github.com/galaxyproject/galaxy/commit/2a21e273ae06303188cddfdc593c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix lint Commit: 507a60a23062fc037b0893fd23b84980c32fd9ef https://github.com/galaxyproject/galaxy/commit/507a60a23062fc037b0893fd23b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Remove duplicate visualization list entries from masthead Commit: 4e65608431279a2c251a0f76817a578a32d10913 https://github.com/galaxyproject/galaxy/commit/4e65608431279a2c251a0f76817a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/style/scss/history.scss A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'release_18.05' into dev Commit: eeb1dae5b71200ffe9f2056b2a7fd8ed560033c1 https://github.com/galaxyproject/galaxy/commit/eeb1dae5b71200ffe9f2056b2a7f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Make JobWrapper/TaskWrapper's dataset_path_rewriter a property Commit: a4b03d10a96bf6652711a8ac996c5f048ef8e568 https://github.com/galaxyproject/galaxy/commit/a4b03d10a96bf6652711a8ac996c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 2dd301d0b5c0fa69b372b4d5a8a029b385c4e3c3 https://github.com/galaxyproject/galaxy/commit/2dd301d0b5c0fa69b372b4d5a8a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix error due to name mangling. Commit: cd723e4f8efe94cd5c6f885c192dc06e97788a1a https://github.com/galaxyproject/galaxy/commit/cd723e4f8efe94cd5c6f885c192d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Merge pull request #6110 from guerler/remove_duplicate_vis_list Remove duplicate visualization list entries from masthead Commit: cb8f8322c85e90e846c31f9370ca8930504b5298 https://github.com/galaxyproject/galaxy/commit/cb8f8322c85e90e846c31f9370ca… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6087 from natefoo/job-dest-config-fix Fix JobWrapper.get_destination_configuration() so that it actually checks the JobDestination params Commit: b68def3ebe7f4f7d8b8650b9d963d0ed8e56966a https://github.com/galaxyproject/galaxy/commit/b68def3ebe7f4f7d8b8650b9d963… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_libraries.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6070 from mvdbeek/improve_test_api_interactor Make `interactor._{get,post,put,...}` less repetitive Commit: a277a4071df754b800a8e9dc14336aea750ff72e https://github.com/galaxyproject/galaxy/commit/a277a4071df754b800a8e9dc1433… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/utils/async-save-text.js Log Message: ----------- Client-format Commit: f69760d66a46a3679bbc9049b7b42032677c656a https://github.com/galaxyproject/galaxy/commit/f69760d66a46a3679bbc9049b7b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/utils/async-save-text.js M lib/galaxy/managers/base.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/sharable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/ind_share_base.mako R templates/sharing_base.mako Log Message: ----------- Merge branch 'sharing' into dev Commit: 02e8cb65a0b4aabc6ad6f29fca2d99dd2cbe08d0 https://github.com/galaxyproject/galaxy/commit/02e8cb65a0b4aabc6ad6f29fca2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M run_tests.sh A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 69dce8d38a5d151a4239d577def65eb88cc46f0f https://github.com/galaxyproject/galaxy/commit/69dce8d38a5d151a4239d577def6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Use bootstrap-vue for Sharing.mako; convert alert, drop unnecessary component style Commit: 824b5721b051cc490180d9204fbb61ef7a94ab48 https://github.com/galaxyproject/galaxy/commit/824b5721b051cc490180d9204fbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- Fix bug where if username was null (which is allowed), the sharable manager blew up. Commit: c9c7455c6688d9bd4b4862ac2f9854d83bec131b https://github.com/galaxyproject/galaxy/commit/c9c7455c6688d9bd4b4862ac2f98… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 02ffbdd7b1c65c30c00ea86e499ad1b36759a555 https://github.com/galaxyproject/galaxy/commit/02ffbdd7b1c65c30c00ea86e499a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Make cache_directory configurable in mulled singluarity resolvers. Commit: 351709a6ba8cf07ac66e3ea7357f32c6d4c8c996 https://github.com/galaxyproject/galaxy/commit/351709a6ba8cf07ac66e3ea7357f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Swap to bsvue-buttons and table. If we really want this a table, we should restyle it. I think we can probably just kill the table, now that I've converted it. Commit: d2805bb6ca62dd690d1477adc676f1f62dd5577b https://github.com/galaxyproject/galaxy/commit/d2805bb6ca62dd690d1477adc676… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/history.scss M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/job_metrics_conf.xml.sample M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/base.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/permutations.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M run_tests.sh M scripts/grt/export.py M static/style/blue/base.css M templates/display_common.mako M templates/ind_share_base.mako R templates/sharing_base.mako M templates/webapps/galaxy/workflow/editor.mako M test/api/test_libraries.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into workflow_fixes Commit: 9dd6773ced15df7b22d2d23ee0466701c92cfbf3 https://github.com/galaxyproject/galaxy/commit/9dd6773ced15df7b22d2d23ee046… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz M lib/galaxy/visualization/plugins/interactive_environments.py M test/unit/datatypes/test_datatypes_registry.py M tools/data_source/upload.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 1fc06c22f884444543655ffcb66f10d71439283f https://github.com/galaxyproject/galaxy/commit/1fc06c22f884444543655ffcb66f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M test/api/test_tools_upload.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 5d7fc1a379a6a21fb5d401fb726837530a348c50 https://github.com/galaxyproject/galaxy/commit/5d7fc1a379a6a21fb5d401fb7268… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Use from_work_dir in CONVERTER_fasta_to_fai Commit: a4ab17cb0db618b8182a0c48726b1fcce8d17bfe https://github.com/galaxyproject/galaxy/commit/a4ab17cb0db618b8182a0c48726b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Add blib test case for supplied test data, fix RetentionTimes not always available. Commit: 3ec6753f0db67de8fefc162ece7502fe47286d35 https://github.com/galaxyproject/galaxy/commit/3ec6753f0db67de8fefc162ece75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- No need to specify these default entries I don't think. Most new datatypes don't get added here, I'm not really sure what purpose these serve. Commit: 7077851e981312ca3ee0e47627e55496d8b8427a https://github.com/galaxyproject/galaxy/commit/7077851e981312ca3ee0e47627e5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Merge pull request #6135 from nsoranzo/fasta_to_fai_from_work_dir Use from_work_dir in CONVERTER_fasta_to_fai Commit: 6a1057e95f5e46cbd676aaf6dbfe3a4df706d9c3 https://github.com/galaxyproject/galaxy/commit/6a1057e95f5e46cbd676aaf6dbfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: eb7a99edb03d8eca258df59fb6b4231dcdb42eb1 https://github.com/galaxyproject/galaxy/commit/eb7a99edb03d8eca258df59fb6b4… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Make workflow editor toolTitle link include the tools description Include the tools description in the toolTitle link to increase the clickable area. Style similar to how the toolMenu is handled outside the workflow editor. Commit: e52802f8fd0e349b8f222cbf56fd1d9ca4f63491 https://github.com/galaxyproject/galaxy/commit/e52802f8fd0e349b8f222cbf56fd… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/sharable.py Log Message: ----------- Merge pull request #6132 from dannon/bsvue-sharing Sharing.vue bootstrapping and a bugfix Commit: ab05ac94755da11a400c2efd12b95b84ec1ecf15 https://github.com/galaxyproject/galaxy/commit/ab05ac94755da11a400c2efd12b9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.blib Log Message: ----------- Merge pull request #6092 from jj-umn/dev Add blib datatype for Mass Spectrometry spectral library Commit: 14cfb26ca1b888156ae517dc33ebeefc099bac6f https://github.com/galaxyproject/galaxy/commit/14cfb26ca1b888156ae517dc33eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Give NO_REPLACEMENT constant object a str value. Shows up in logging a lot and such - make it more clear. Commit: 95962d9e5aa2b3b8e60755767b0dbc06ef341782 https://github.com/galaxyproject/galaxy/commit/95962d9e5aa2b3b8e60755767b0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M test/base/populators.py Log Message: ----------- More correct file_data handling in populators.py. Any of file_N|file_data fields can have attached data. Commit: 31640840e310f76dc38e24f4147c0d4d1959f178 https://github.com/galaxyproject/galaxy/commit/31640840e310f76dc38e24f4147c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Fix consumption of macro paths from tool spec. Commit: 5551611aff92f55c7b1e00f573c44473b6b2823a https://github.com/galaxyproject/galaxy/commit/5551611aff92f55c7b1e00f573c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Drop old comment, we use this variable now and have for some time. Commit: b50ae948368abae7f91af8e2d4f3cbc69418ab92 https://github.com/galaxyproject/galaxy/commit/b50ae948368abae7f91af8e2d4f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Move workflow api test helpers into base class for more reuse. Commit: 867cdd144448810571bcf23888027800a292c344 https://github.com/galaxyproject/galaxy/commit/867cdd144448810571bcf2388802… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Merge pull request #6122 from jmchilton/singularity_mulled_container_cache Make cache_directory configurable in mulled Singluarity resolvers. Commit: c3f9e0c2a7bb5273228d790b62eaf8626687f420 https://github.com/galaxyproject/galaxy/commit/c3f9e0c2a7bb5273228d790b62ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/tool_shed/util/admin_util.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml M test/integration/test_upload_configuration_options.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 3c965f526b6c2fd32453aef0c61e67def03891fd https://github.com/galaxyproject/galaxy/commit/3c965f526b6c2fd32453aef0c61e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: R lib/galaxy/jobs/runners/util/retry.py Log Message: ----------- Remove unused retry.py, functionality provided in pulsar Commit: b920875ff8b65bb9b5e4e13ac94e282cb09864fc https://github.com/galaxyproject/galaxy/commit/b920875ff8b65bb9b5e4e13ac94e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: R lib/galaxy/jobs/runners/util/drmaa/__init__.py Log Message: ----------- Drop DrmaaSessionFactory, unused and provided by pulsar Commit: 93d83c759d1ade726c407fa4e500455a838f6a47 https://github.com/galaxyproject/galaxy/commit/93d83c759d1ade726c407fa4e500… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: R lib/galaxy/jobs/runners/util/drmaa/__init__.py R lib/galaxy/jobs/runners/util/retry.py Log Message: ----------- Merge pull request #6150 from mvdbeek/drop_unused_files Drop unused files Commit: 60a0e1b8cfac183caef799afbc9e6bb5ffcc6c16 https://github.com/galaxyproject/galaxy/commit/60a0e1b8cfac183caef799afbc9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Fix history import form error display, also bs-vue it. Commit: 6bfc4edc6909c7d4b1949d1aeda657864b76d689 https://github.com/galaxyproject/galaxy/commit/6bfc4edc6909c7d4b1949d1aeda6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Use old-style message -- for now, argh. fix visibility, remove custom style and redundant placeholders. Commit: e920280692e02993e2bd1d5a8b3ec9bd0b351a5f https://github.com/galaxyproject/galaxy/commit/e920280692e02993e2bd1d5a8b3e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Re-enable commented out redir code from debugging Commit: c4ad8ab57c3d8c8e8c2453375292ca405baf2e6a https://github.com/galaxyproject/galaxy/commit/c4ad8ab57c3d8c8e8c2453375292… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Fix response message relay in history archive import; axios uses the response.data object here. Commit: e814b75dc27db739dcfe7d3b43f9c17b6510c1eb https://github.com/galaxyproject/galaxy/commit/e814b75dc27db739dcfe7d3b43f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue Log Message: ----------- Floating this card approach for dialogs like this -- if we design components for display in cards, they'll be portable and usable everywhere. Commit: b70426cea47c8445efee96cc6bfc34f1cbc791ff https://github.com/galaxyproject/galaxy/commit/b70426cea47c8445efee96cc6bfc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Cleanup in history contents while looking for history name change bug Commit: 72c175bef2286192dee750daa7e8fefa6e7f0d62 https://github.com/galaxyproject/galaxy/commit/72c175bef2286192dee750daa7e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Minor refactoring, drop self usage in history-view-edit Commit: da0e5f637c2b4e31ca36cf11fbc4ec4cf2cf3123 https://github.com/galaxyproject/galaxy/commit/da0e5f637c2b4e31ca36cf11fbc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- Bugfix: history serializer was not encoding user_id, which (other than leaking an unencoded uid) was causing ownership comparisons to always fail. Commit: 22774f4f2aa9ca06bd6dff7d7919581df6559313 https://github.com/galaxyproject/galaxy/commit/22774f4f2aa9ca06bd6dff7d7919… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M lib/galaxy/managers/histories.py Log Message: ----------- Merge pull request #6159 from dannon/history_rename_bugfix History click-to-rename bugfix Commit: 2fef59aa46c06aebe42c1f075c2d84a86fc11a30 https://github.com/galaxyproject/galaxy/commit/2fef59aa46c06aebe42c1f075c2d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: 24c32a3180b9214fa1bc55569a069dcbe5f7a4a3 https://github.com/galaxyproject/galaxy/commit/24c32a3180b9214fa1bc55569a06… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #6153 from dannon/history_import_safari_fix History import safari fix, overhaul Commit: 4c4aa11ad469a3a66c1bfa03fb6985a9b0033498 https://github.com/galaxyproject/galaxy/commit/4c4aa11ad469a3a66c1bfa03fb69… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Update @erasche's name Commit: 73fb6785fd7ddd9cf14d41b1f5496b0a2f9a9563 https://github.com/galaxyproject/galaxy/commit/73fb6785fd7ddd9cf14d41b1f549… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Clarify how +1 votes on PRs can be expressed Commit: 41e12f0b9d178641209f5d4c732c9d0bd6131184 https://github.com/galaxyproject/galaxy/commit/41e12f0b9d178641209f5d4c732c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M static/style/blue/base.css M test/api/test_tools.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: d714dfb2fa36c4ee9c067c85782eff4ae1d86f08 https://github.com/galaxyproject/galaxy/commit/d714dfb2fa36c4ee9c067c85782e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Commit: d0cb1d6f3c1c49d690a1b7279c7c1ef30df3593b https://github.com/galaxyproject/galaxy/commit/d0cb1d6f3c1c49d690a1b7279c7c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6168 from guerler/fix_upload_selector [18.05] Fix upload file selector value resetting Commit: 6e78a440b308a0a0df541b6d98891d17b99a2a46 https://github.com/galaxyproject/galaxy/commit/6e78a440b308a0a0df541b6d9889… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add impersonate to main user grid when it's enabled Commit: 96b4532e9999b816df3dcc5de6e7c2d7607b5ec6 https://github.com/galaxyproject/galaxy/commit/96b4532e9999b816df3dcc5de6e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M templates/admin/impersonate.mako Log Message: ----------- Drop emails query we weren't actually even using... Commit: 3bd8b3b18b6032e8844795fae488e501074cd573 https://github.com/galaxyproject/galaxy/commit/3bd8b3b18b6032e8844795fae488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/impersonate.mako M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Impersonation refactoring, condense functionality into user grid, optimize some stuff. Commit: ce2893d50d1e2914fa2193aea26d563258a11bc9 https://github.com/galaxyproject/galaxy/commit/ce2893d50d1e2914fa2193aea26d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add APIKey generation operation to user grid. Commit: 5e9cd276ebbef84a0091ef3b531d4b5553874bff https://github.com/galaxyproject/galaxy/commit/5e9cd276ebbef84a0091ef3b531d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Match existing formatting. Commit: c3d01f0505a42903f4fd2bc42d8e5bdce13315d3 https://github.com/galaxyproject/galaxy/commit/c3d01f0505a42903f4fd2bc42d8e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Actually include new_key in msgstring Commit: fb199c5f8c8083e78cc50d62b1c77c9fec21f249 https://github.com/galaxyproject/galaxy/commit/fb199c5f8c8083e78cc50d62b1c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Slight safeguarding of user selection, respond with a more contextualized message Commit: 61e2e82a09047b5b1d4194259012178bc8dfd7f8 https://github.com/galaxyproject/galaxy/commit/61e2e82a09047b5b1d4194259012… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/apps/admin.js R client/galaxy/scripts/components/admin/UserAPIKeys.vue Log Message: ----------- Drop individual UserAPIKeys.vue; this functionality is included in the standard user grid now. Commit: 9dcb1019c5afe76c864cb4e361509b4f47f215c2 https://github.com/galaxyproject/galaxy/commit/9dcb1019c5afe76c864cb4e36150… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Drop separate APIKeys blurb Commit: a992637de17d36b9b821dabc5342f636c530e4bc https://github.com/galaxyproject/galaxy/commit/a992637de17d36b9b821dabc5342… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/datatypes_conf.xml.sample M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/errors.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: d47e5f25e44405c8bbf5a5fa7a5d62ef709c5e8b https://github.com/galaxyproject/galaxy/commit/d47e5f25e44405c8bbf5a5fa7a5d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 7bf55fc301cb6819b371e25030014cde830c05c9 https://github.com/galaxyproject/galaxy/commit/7bf55fc301cb6819b371e2503001… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix history list bottom border Commit: 029975a9f8abe57b6f4ef9d9a9cc50a07f401113 https://github.com/galaxyproject/galaxy/commit/029975a9f8abe57b6f4ef9d9a9cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- A more accurate version of what was set before, with the same outcome (though, it could change if we toggle the grey) Commit: 8d1cff2bba25c70baeebf8fde0878b4e5caa8b2f https://github.com/galaxyproject/galaxy/commit/8d1cff2bba25c70baeebf8fde087… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix dataset messagesmall display, was a TODO left from migration Commit: bffeacad081678dc56eeb0af54c8e4eb8443e5ce https://github.com/galaxyproject/galaxy/commit/bffeacad081678dc56eeb0af54c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: e06639e9456ba022ce6a12e4eba15a696fb37e51 https://github.com/galaxyproject/galaxy/commit/e06639e9456ba022ce6a12e4eba1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix one more busted fade Commit: eadfd406d238b5ef7ad97c964a44e39d6a9d46e9 https://github.com/galaxyproject/galaxy/commit/eadfd406d238b5ef7ad97c964a44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix (ancient, should replace this, but might as well make it work until we do) tool-shed-only grid search button Commit: 74377074ac12fcadb771f5ea212fa1bd7a048df8 https://github.com/galaxyproject/galaxy/commit/74377074ac12fcadb771f5ea212f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Drop submit-image custom styling, use standard fa; left it as inline style to keep it clean and remove all at once when this grid goes. Commit: 2cf1c00137862fd90ce8ccc2fa34751e65e7f960 https://github.com/galaxyproject/galaxy/commit/2cf1c00137862fd90ce8ccc2fa34… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 162fa3a5bbd52ea75db5ec22c32a7a3d86560029 https://github.com/galaxyproject/galaxy/commit/162fa3a5bbd52ea75db5ec22c32a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix list panel control message margins. Commit: 51b93ebc48b96278342b06583642af14fe48ce3a https://github.com/galaxyproject/galaxy/commit/51b93ebc48b96278342b06583642… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- This is correct now Commit: 94ae2e6a958e611c6cdcfe56dc72d47f2dfb66c3 https://github.com/galaxyproject/galaxy/commit/94ae2e6a958e611c6cdcfe56dc72… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- permit actual numbers in conf file Commit: e950520ab0a5c47296d023d9f20ffbdc55125996 https://github.com/galaxyproject/galaxy/commit/e950520ab0a5c47296d023d9f20f… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/xml.py Log Message: ----------- add sbml datatype Commit: 9c17828e9616161a63ea6c7dfd4ebf0fb64bcae9 https://github.com/galaxyproject/galaxy/commit/9c17828e9616161a63ea6c7dfd4e… Author: MONJEAUD Cyril <Cyril.Monjeaud(a)irisa.fr> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- Add edam format Commit: a57600cadfe4b3f383ce69afaf3dc09c237456f8 https://github.com/galaxyproject/galaxy/commit/a57600cadfe4b3f383ce69afaf3d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Merge pull request #6197 from dannon/1805stylefixes [18.05] Minor style fixes Commit: 2ab75d861bd74ae718893ca6a97015960f9036de https://github.com/galaxyproject/galaxy/commit/2ab75d861bd74ae718893ca6a970… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/deps/containers.py M lib/galaxy_ext/metadata/set_metadata.py A test/unit/test_security_passwords.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.05' into dev Commit: 994d78fde08b7463fc41ec376959871a63f799ea https://github.com/galaxyproject/galaxy/commit/994d78fde08b7463fc41ec376959… Author: greg <ghv2(a)psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add the newick extension for the Newick datatype, setting the nhx extension as a subclass Commit: d80a86b9e7cb7edd61d32c6286318715c061694b https://github.com/galaxyproject/galaxy/commit/d80a86b9e7cb7edd61d32c628631… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 7680181864d3e2b269c5d723532d5fdadead2952 https://github.com/galaxyproject/galaxy/commit/7680181864d3e2b269c5d723532d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M tools/filters/cutWrapper.pl Log Message: ----------- fix wrong path in error message Commit: 21aa40addfb21c22dad676aebe041c77cc4ffd92 https://github.com/galaxyproject/galaxy/commit/21aa40addfb21c22dad676aebe04… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add edam data Commit: fcc5b207ab77a29e17ab13d0ba0d38a420ced659 https://github.com/galaxyproject/galaxy/commit/fcc5b207ab77a29e17ab13d0ba0d… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- fix conflicts Commit: e57ff42e2ef8e61dd5d49e7f91a9ecabcd484706 https://github.com/galaxyproject/galaxy/commit/e57ff42e2ef8e61dd5d49e7f91a9… Author: cmonjeau <cyril.monjeaud(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add blank line Commit: ea0b9fd7f27726a45f3068eb3788bff0721dafa3 https://github.com/galaxyproject/galaxy/commit/ea0b9fd7f27726a45f3068eb3788… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M tools/filters/cutWrapper.pl Log Message: ----------- Merge pull request #6211 from abretaud/tools_sync_genouest cuwrapper: fix wrong path in error message Commit: 03a815a2c379186237a9978d0f3af32f1e69c933 https://github.com/galaxyproject/galaxy/commit/03a815a2c379186237a9978d0f3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.tiff A test-data/1.tiff M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Some more upload/sniff tests. Commit: 38dc3baef128e8d5b45a329552e976fe8a6fab49 https://github.com/galaxyproject/galaxy/commit/38dc3baef128e8d5b45a329552e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_single_in_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test element_identifier usage with single data parameters, in repeat/cond. Commit: 30b5e50ba0079a7dd24d3334cacbde2e4b9c07dc https://github.com/galaxyproject/galaxy/commit/30b5e50ba0079a7dd24d3334cacb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/queue_worker.py A lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Enable dynamic reload of dynamic job rules when configured, using watchdog notifications. Commit: 89bf971aa8cee76bc624536e0896de38556d806c https://github.com/galaxyproject/galaxy/commit/89bf971aa8cee76bc624536e0896… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Link downlaod attributes are well supported and should work here, allowing us to actually name the downloads. Commit: 91dbeebf5f4ea2fd94586a883616e6fc148940ae https://github.com/galaxyproject/galaxy/commit/91dbeebf5f4ea2fd94586a883616… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Fix non-Galaxy webapp unit tests Commit: a5840a89bb71c0c17373c7fdac5498f886483b2c https://github.com/galaxyproject/galaxy/commit/a5840a89bb71c0c17373c7fdac54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Refactoring, cleanup, a few bugfixes. Commit: 1656b48323a3110134d0ba3fcc86c54923a75fdc https://github.com/galaxyproject/galaxy/commit/1656b48323a3110134d0ba3fcc86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Minor filename handling tweak, more explicitly better support empty default Commit: 41a601d5375669bfb612b6a98e289fccd4eac8a9 https://github.com/galaxyproject/galaxy/commit/41a601d5375669bfb612b6a98e28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Watch any objects in job rule directories that are not python bytecode, rather than only watching python source. Commit: 60b5cc5341f2bedd97f6a1da8e187edb1584e2b6 https://github.com/galaxyproject/galaxy/commit/60b5cc5341f2bedd97f6a1da8e18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- SVG download titles, more minor refactoring/reuse Commit: ddb6b8692d0eecdaba27a00921875223cef387ef https://github.com/galaxyproject/galaxy/commit/ddb6b8692d0eecdaba27a0092187… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Formatting fixes. Commit: 2ac83d74fbc34703aa7aafc7737e362c210321bf https://github.com/galaxyproject/galaxy/commit/2ac83d74fbc34703aa7aafc7737e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 46dab7f04dce464cbcbeed901224d2ac11ff452a https://github.com/galaxyproject/galaxy/commit/46dab7f04dce464cbcbeed901224… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Wrap inputs in labels Commit: 31eb306112e3051c54edd14df7df8caee6643abb https://github.com/galaxyproject/galaxy/commit/31eb306112e3051c54edd14df7df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 08372c90d6ef07333599c4a1812bc75f8fbad0d8 https://github.com/galaxyproject/galaxy/commit/08372c90d6ef07333599c4a1812b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6221 from erasche/labels Wrap inputs in labels Commit: 8bd856da5120eb15053e1d32f1964aaa851626ad https://github.com/galaxyproject/galaxy/commit/8bd856da5120eb15053e1d32f196… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Ignore change events for dot files. This could be configurable if it's needed but I can't imagine when it would be. Prevents reloading on vim swapfile writes. Commit: fdfba9dac102cdd62db92b28a57a6d96ce2b52c6 https://github.com/galaxyproject/galaxy/commit/fdfba9dac102cdd62db92b28a57a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix file type error in RuleCollectionBuilder. Commit: 13b5883dd6054304a166a3a8fdfd63ae27ec2eaa https://github.com/galaxyproject/galaxy/commit/13b5883dd6054304a166a3a8fdfd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/tools.py A test/functional/tools/empty_select.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 820712144000f05e088791159ffbd80b14e40999 https://github.com/galaxyproject/galaxy/commit/820712144000f05e088791159ffb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6231 from jmchilton/fix_file_type Fix file type error in RuleCollectionBuilder. Commit: d4cb7c614ecb2cc3193de89a87a1fe9661975d21 https://github.com/galaxyproject/galaxy/commit/d4cb7c614ecb2cc3193de89a87a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: f3dccb7b6c897d44cb3fe94e6e4541f6273fe85c https://github.com/galaxyproject/galaxy/commit/f3dccb7b6c897d44cb3fe94e6e45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Overhaul workflow execution response, including appropriate text for new histories, and multiple executions. With links. Commit: 78fabab53c4e511dc5a3db4d3cc62eb71a5f097d https://github.com/galaxyproject/galaxy/commit/78fabab53c4e511dc5a3db4d3cc6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Drop debug statement Commit: 5845d64a48ad9528a45315cb2252afeaa067911b https://github.com/galaxyproject/galaxy/commit/5845d64a48ad9528a45315cb2252… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Cleanup in tool-form-composite Commit: 3b27d249b2876a8e88691dad2fe42213f8943893 https://github.com/galaxyproject/galaxy/commit/3b27d249b2876a8e88691dad2fe4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/mvc/history/history-structure-view.js M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/structure.mako Log Message: ----------- Strip busted history structure view -- we're goign to start from scratch here Commit: 8d9a21c4e9eeab4f1b947b66688658941c482340 https://github.com/galaxyproject/galaxy/commit/8d9a21c4e9eeab4f1b947b666886… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove unused import. Commit: b17bebcb30cd131ee1aab0f9bebeae5a9f3e6b04 https://github.com/galaxyproject/galaxy/commit/b17bebcb30cd131ee1aab0f9bebe… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Move smart_str() calls inside pbkdf2_bin() Commit: 6b21a35319a2916e9d4fa552ac32d8766d0b7c4e https://github.com/galaxyproject/galaxy/commit/6b21a35319a2916e9d4fa552ac32… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Use unicodify() Commit: 7b5e1903f13de4a245a04d42254f68ac81bfeecd https://github.com/galaxyproject/galaxy/commit/7b5e1903f13de4a245a04d42254f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Make pbkdf2_bin() faster `digest` was needlessly recalculated as `bytearray(u)` in the internal loop, instead make `_pseudorandom()` return both the bytestring and the list of character ordinals. Commit: 2ebe88718aa4c4b6bafcfd7dfc0d29bccf9df614 https://github.com/galaxyproject/galaxy/commit/2ebe88718aa4c4b6bafcfd7dfc0d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Unicodify bytearrays Commit: 9b4697d3eda8243ada0908a03b2e8810642eec04 https://github.com/galaxyproject/galaxy/commit/9b4697d3eda8243ada0908a03b2e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #6242 from nsoranzo/python3 Password encoding improvements Commit: 6c9953cfe2b98f0f23a4496d3a45437029b8945c https://github.com/galaxyproject/galaxy/commit/6c9953cfe2b98f0f23a4496d3a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Clarify/reuse new history target logic, fix links to avoid redundant slash on root Commit: 8fcc9332448add1e55fd6b5831da80b336d63078 https://github.com/galaxyproject/galaxy/commit/8fcc9332448add1e55fd6b5831da… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/mvc/history/history-structure-view.js M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/structure.mako Log Message: ----------- Merge pull request #6241 from dannon/history_structure_cleanup Strip legacy history structure view Commit: f99f8667bcfceea21101d0690d2ba6f5630d34cf https://github.com/galaxyproject/galaxy/commit/f99f8667bcfceea21101d0690d2b… Author: Katrin Leinweber <kalei(a)posteo.de> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/managers/citations.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M tools/sr_mapping/bfast_wrapper.xml Log Message: ----------- Hyperlink DOIs against preferred resolver Commit: a79d6fae43be20dbf79d57e8067a022f877b57be https://github.com/galaxyproject/galaxy/commit/a79d6fae43be20dbf79d57e8067a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/managers/citations.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M tools/sr_mapping/bfast_wrapper.xml Log Message: ----------- Merge pull request #6244 from katrinleinweber/resolve-DOIs-securely Hyperlink DOIs against preferred resolver Commit: 27106c59e5d6d3583f1a11adec1ddd26d0114da1 https://github.com/galaxyproject/galaxy/commit/27106c59e5d6d3583f1a11adec1d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.tiff A test-data/1.tiff M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Merge pull request #6212 from jmchilton/tiff_tests Some more upload/sniff tests. Commit: 5d155617952e0fd6ef5e269ca83704f2f2688cab https://github.com/galaxyproject/galaxy/commit/5d155617952e0fd6ef5e269ca837… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Verify existing of runtime environment for textable mode Commit: b0705a4819cb3a1cb541554798f007d4360f3d87 https://github.com/galaxyproject/galaxy/commit/b0705a4819cb3a1cb541554798f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Combine context test into single function Commit: d91cb1563d2ce9cee78ed33c4cd0709e5da35bdb https://github.com/galaxyproject/galaxy/commit/d91cb1563d2ce9cee78ed33c4cd0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Validate parsed workflow building mode parameter Commit: c4e8f0d21ead864a1800802db44bf01c550257c6 https://github.com/galaxyproject/galaxy/commit/c4e8f0d21ead864a1800802db44b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Make runtime context validator available for use in other inputs e.g. drilldown Commit: 5adac19825263d8c98e8628b7f63f0ca49c76495 https://github.com/galaxyproject/galaxy/commit/5adac19825263d8c98e8628b7f63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indention Commit: bac4169d178eeace51cfdf62d979f8a14ce04101 https://github.com/galaxyproject/galaxy/commit/bac4169d178eeace51cfdf62d979… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Rename disabled flag for consistency with existing naming Commit: 5ae57e28667524086595483ff04674b010d067b1 https://github.com/galaxyproject/galaxy/commit/5ae57e28667524086595483ff046… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Use new collapsible flag in rules editor Commit: fb6dbb27026abfa8832dc821633214882e8ee6e9 https://github.com/galaxyproject/galaxy/commit/fb6dbb27026abfa8832dc8216332… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Parse unmodified options Commit: 292a2096424a207a943457d00bf6540fc84e6a3d https://github.com/galaxyproject/galaxy/commit/292a2096424a207a943457d00bf6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js Log Message: ----------- Remove input specific options handling, unify input update mechanism Commit: d0187ac206219c0fb0cb4767f6c1b5d0dcc68e1f https://github.com/galaxyproject/galaxy/commit/d0187ac206219c0fb0cb4767f6c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js Log Message: ----------- Adjust update handler for list inputs Commit: f3ccf42cab1cca514d4e8e159b4b1338090beaea https://github.com/galaxyproject/galaxy/commit/f3ccf42cab1cca514d4e8e159b4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Adjust handling in text select field Commit: 94220c0ac1c0c2273213355343b7164832d31a1a https://github.com/galaxyproject/galaxy/commit/94220c0ac1c0c2273213355343b7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Adjust update caller in rules editor Commit: c8afba470be865acc96af1d532876b580e1739a6 https://github.com/galaxyproject/galaxy/commit/c8afba470be865acc96af1d53287… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Move options handling into selection fields Commit: 3df2a94dbd9d37c99bde75ef637866683a231618 https://github.com/galaxyproject/galaxy/commit/3df2a94dbd9d37c99bde75ef6378… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Fix library dataset selector Commit: 0bad91c59295626bd577662ac2c80f16868a6a6b https://github.com/galaxyproject/galaxy/commit/0bad91c59295626bd577662ac2c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Parse data as is to select field Commit: 0022615418af51ea6d8b1b00a12855ad4191177c https://github.com/galaxyproject/galaxy/commit/0022615418af51ea6d8b1b00a128… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Handle alternative option formatting in text select wrapper Commit: ac7c6e5d947f42054105b25fe33e490152dd7d2f https://github.com/galaxyproject/galaxy/commit/ac7c6e5d947f42054105b25fe33e… Author: Katrin Leinweber <9948149+katrinleinweber(a)users.noreply.github.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/managers/citations.py Log Message: ----------- Refactor to match domain name (follow-up to #6244) Commit: fd25d51b8e47bda031aa6a490c6e73741ab15fe9 https://github.com/galaxyproject/galaxy/commit/fd25d51b8e47bda031aa6a490c6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/managers/citations.py Log Message: ----------- Merge pull request #6252 from katrinleinweber/patch-1 Refactor dx_url to doi_url to match domain name Commit: 825d7f6fa74384d195739fe7ac0bf4e1d5b9c1cf https://github.com/galaxyproject/galaxy/commit/825d7f6fa74384d195739fe7ac0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: 50c98701b7682d8878cbc2fa1acdc3f28abdad0e https://github.com/galaxyproject/galaxy/commit/50c98701b7682d8878cbc2fa1acd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 99889af1d52a263737dca3c7461baa5ce4fe8ad7 https://github.com/galaxyproject/galaxy/commit/99889af1d52a263737dca3c7461b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: dfd80d7d71a8c99495e751cdddbc27d31bbfe8d1 https://github.com/galaxyproject/galaxy/commit/dfd80d7d71a8c99495e751cdddbc… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indentation Commit: c1614be1ef5abaab241bf9739fb99390a8954343 https://github.com/galaxyproject/galaxy/commit/c1614be1ef5abaab241bf9739fb9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Pause jobs with invalid inputs Otherwise these jobs may hang around forever/until the admin does a cleanup. This is probably preferable for users as well, as the pause message gives a hint of why their job didn't start running. Fixes https://github.com/galaxyproject/galaxy/issues/6022 and would minimize maintenance as outlined in https://github.com/galaxyproject/galaxy/issues/5944. I'm working on tests, but one easy way to test this is create a collection through the list builder interface, then delete the source HDAs. Then run a workflow on the collection and without this commit the outputs get created but the job just hangs around indefinetely. With the PR the steps consuming the collection and the subsequent jobs will be paused. Set to paused Commit: 0e31f97269586b061ce58a9eac75743590e310a3 https://github.com/galaxyproject/galaxy/commit/0e31f97269586b061ce58a9eac75… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add a testcase for pausing jobs with deleted input Fix test Commit: ed0b087926c53f4c2c4293ff6443f997fafa9526 https://github.com/galaxyproject/galaxy/commit/ed0b087926c53f4c2c4293ff6443… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Fail jobs with purged inputs We can't resume these jobs anyway, so better to set them to failed. Also resets the info field for datasets produced by resumed jobs. Commit: f9a65a10eb10fd2942ca3306b461ba7dbae4aa09 https://github.com/galaxyproject/galaxy/commit/f9a65a10eb10fd2942ca3306b461… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Display the info field for paused jobs Commit: f8cc653b3051b93cea446317194fcdd88d1aa674 https://github.com/galaxyproject/galaxy/commit/f8cc653b3051b93cea446317194f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/jobs/handler.py M test/api/test_workflows.py Log Message: ----------- Pause job if input dataset state is paused Commit: ca31222cf87a471648876575f068f4e5ac3cba92 https://github.com/galaxyproject/galaxy/commit/ca31222cf87a471648876575f068… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Optimize job resume function Commit: 05fe17a590d9bdbf3aff54b3f3db8b5da5f256a2 https://github.com/galaxyproject/galaxy/commit/05fe17a590d9bdbf3aff54b3f3db… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix SelectToolParameter doctests Commit: cb98bb23f3121708efa8d948b5e3e39426f2b773 https://github.com/galaxyproject/galaxy/commit/cb98bb23f3121708efa8d948b5e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-drilldown.js Log Message: ----------- Adjust drilldown handler Commit: 5c65012f9c2e41b328483fc28b685ae736cc500a https://github.com/galaxyproject/galaxy/commit/5c65012f9c2e41b328483fc28b68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix list parameter style Commit: fb78fabcd757b80cbe063cddab104f17e2b3a4e2 https://github.com/galaxyproject/galaxy/commit/fb78fabcd757b80cbe063cddab10… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js Log Message: ----------- Merge pull request #6216 from dannon/chart_download_fix Charts filename download fix Commit: 06d0fcc0de1a7634df5cb71f4225e11af2ebb345 https://github.com/galaxyproject/galaxy/commit/06d0fcc0de1a7634df5cb71f4225… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 53d2664b0b7bafc5d91243ad897e7fcd3ab1c13a https://github.com/galaxyproject/galaxy/commit/53d2664b0b7bafc5d91243ad897e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- Merge pull request #6200 from erasche/grt-asdf Permit numeric values of GRT instance ID in config Commit: f690386f0b88fa4f5f94b83e4dea8c97f60747fd https://github.com/galaxyproject/galaxy/commit/f690386f0b88fa4f5f94b83e4dea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Drop unused COLLECTION_ATTRIBUTES Commit: 6ace37e910f041442f8b45b76c143fd0dab5ca8d https://github.com/galaxyproject/galaxy/commit/6ace37e910f041442f8b45b76c14… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M test/functional/tools/identifier_single_in_repeat.xml Log Message: ----------- Use 4-space indent in identifier_single_in_repeat test tool Commit: c401f5a713c1774e2dd8d817de04d48e2864e40f https://github.com/galaxyproject/galaxy/commit/c401f5a713c1774e2dd8d817de04… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Use info style when displaying the reason for pausing a dataset Commit: 48fda8debca521a8803513ba8b19ebd92fdec904 https://github.com/galaxyproject/galaxy/commit/48fda8debca521a8803513ba8b19… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M test/functional/tools/identifier_single_in_repeat.xml Log Message: ----------- Merge pull request #68 from mvdbeek/one_more_identifier_test Use 4-space indent in identifier_single_in_repeat test tool Commit: b908ea4530a44993efb8682281d13ebc87cc339b https://github.com/galaxyproject/galaxy/commit/b908ea4530a44993efb8682281d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Fix collection mapping to allow mapping over multi-data inputs. It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work. Commit: 73ea1189e9fae103e367955fc62916e497074b38 https://github.com/galaxyproject/galaxy/commit/73ea1189e9fae103e367955fc629… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Avoid using builtins for variable names. file->file_path, dir->dir_path in generic watcher functions Commit: 1652c4221eacfac2a04955ee6fd4004c84f97ae6 https://github.com/galaxyproject/galaxy/commit/1652c4221eacfac2a04955ee6fd4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M lib/galaxy/util/watcher.py Log Message: ----------- Merge pull request #8 from dannon/dynamic-rule-dynamic-reload Avoid using builtins for variable names. Commit: f19f09b30f607c3af922fcba16ebe0ab95996d2f https://github.com/galaxyproject/galaxy/commit/f19f09b30f607c3af922fcba16eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6248 from guerler/form_fix Align input element update mechanism Commit: a5594551c09250db0dac799711a0d5676817038c https://github.com/galaxyproject/galaxy/commit/a5594551c09250db0dac799711a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6036 from mvdbeek/kill_jobs_with_invalid_input Pause jobs with invalid inputs Commit: 5ba71f580fc861be9c924991a762f0917811b720 https://github.com/galaxyproject/galaxy/commit/5ba71f580fc861be9c924991a762… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/queue_worker.py A lib/galaxy/util/watcher.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Merge pull request #6215 from natefoo/dynamic-rule-dynamic-reload Enable automatic reload of dynamic job rules on change Commit: 1954c9dc633bdf72df446a16f7ec2f2150f92e60 https://github.com/galaxyproject/galaxy/commit/1954c9dc633bdf72df446a16f7ec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/xml.py Log Message: ----------- Merge pull request #6201 from cmonjeau/add_sbml_datatype New datatype: SBML Commit: 9cf66df7a7af0d28b627ad9f24b395a4579cc988 https://github.com/galaxyproject/galaxy/commit/9cf66df7a7af0d28b627ad9f24b3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #6171 from nsoranzo/pr_approval [PROCEDURES] Clarify how +1 votes on PRs can be expressed v.3 Commit: 8f5552f50cda2f5b91bc6fdbfe925726ed6e6077 https://github.com/galaxyproject/galaxy/commit/8f5552f50cda2f5b91bc6fdbfe92… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix up subcollection_type Commit: 78d290c9fbf26adc0a4621174502e50047bbd843 https://github.com/galaxyproject/galaxy/commit/78d290c9fbf26adc0a4621174502… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-03 (Sun, 03 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Do not install py2-ipaddress under Python 3 Commit: 662682c14818dfbc52579e96ff4aae4a8e047070 https://github.com/galaxyproject/galaxy/commit/662682c14818dfbc52579e96ff4a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-03 (Sun, 03 Jun 2018) Changed paths: M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- unicodify bytestrings from uwsgi.opt Fix the 2 following tracebacks: ``` added lib/ to pythonpath. Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 180, in uwsgi_app return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "galaxy") File "lib/galaxy/web/framework/webapp.py", line 968, in build_native_uwsgi_app app_kwds = get_app_kwds(config_section) File "lib/galaxy/web/stack/__init__.py", line 434, in get_app_kwds return application_stack_class().get_app_kwds(config_section, app_name=app_name) File "lib/galaxy/web/stack/__init__.py", line 260, in get_app_kwds has_ini_config = has_ini_config or (config_file and has_ext(config_file, "ini", aliases=True, ignore="sample")) File "lib/galaxy/util/path/__init__.py", line 290, in has_ext root, _ext = __splitext_ignore(path, ignore=ignore) File "lib/galaxy/util/path/__init__.py", line 387, in __splitext_ignore root, ext = __splitext_no_sep(path) File "lib/galaxy/util/path/__init__.py", line 381, in __splitext_no_sep return (path.rsplit(extsep, 1) + [''])[0:2] TypeError: a bytes-like object is required, not 'str' unable to load app 0 (mountpoint='') (callable not found or import error) ``` ``` galaxy.queue_worker INFO 2018-06-03 02:12:51,186 [p:2150,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1 Traceback (most recent call last): File "lib/galaxy/web/stack/__init__.py", line 456, in _do_uwsgi_postfork f(*args, **kwargs) File "lib/galaxy/webapps/galaxy/buildapp.py", line 190, in postfork_setup app.application_stack.log_startup() File "lib/galaxy/web/stack/__init__.py", line 351, in log_startup for s in UWSGIApplicationStack._serving_on(): File "lib/galaxy/web/stack/__init__.py", line 237, in _serving_on yield UWSGIApplicationStack._socket_opt_to_str(opt, val) File "lib/galaxy/web/stack/__init__.py", line 208, in _socket_opt_to_str if val.startswith('='): TypeError: startswith first arg must be bytes or a tuple of bytes, not str ``` Commit: e81931cd753e4c85e624d80e3901c97d6064f9e1 https://github.com/galaxyproject/galaxy/commit/e81931cd753e4c85e624d80e3901… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-03 (Sun, 03 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix loading of tools under Python 3 Tools containing a text parameter fail with a traceback like: ``` [pid: 2433|app: 0|req: 15/28] 127.0.0.1 () {42 vars in 905 bytes} [Sun Jun 3 02:24:59 2018] GET /api/tools/addValue/build?version=1.0.0&__identifer=nv6x1qdhzxo&tool_version=1.0.0 => generated 71 bytes in 58 msecs (HTTP/1.1 500) 3 headers in 143 bytes (1 switches on core 1) galaxy.web.framework.decorators ERROR 2018-06-03 02:25:01,999 [p:2433,w:1,m:0] [uWSGIWorker1Core0] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 281, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 113, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "lib/galaxy/tools/__init__.py", line 1913, in to_json 'state_inputs' : params_to_strings(self.inputs, state_inputs, self.app), File "lib/galaxy/tools/parameters/__init__.py", line 207, in params_to_strings rval[key] = value if nested else str(dumps(value)) File "/usr/lib/python3.5/json/__init__.py", line 230, in dumps return _default_encoder.encode(obj) File "/usr/lib/python3.5/json/encoder.py", line 198, in encode chunks = self.iterencode(o, _one_shot=True) File "/usr/lib/python3.5/json/encoder.py", line 256, in iterencode return _iterencode(o, 0) File "/usr/lib/python3.5/json/encoder.py", line 179, in default raise TypeError(repr(o) + " is not JSON serializable") TypeError: b'c1,c2' is not JSON serializable ``` Commit: 2f6c184e6f5c614e36f8100648b1a5f5a8f6ac94 https://github.com/galaxyproject/galaxy/commit/2f6c184e6f5c614e36f8100648b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6253 from mvdbeek/mapping_over_from_param_fixes Mapping over from_param fixes Commit: b08455ecab5fa068b7f8b93fe08c9c552c8c25a0 https://github.com/galaxyproject/galaxy/commit/b08455ecab5fa068b7f8b93fe08c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #6265 from nsoranzo/python3 Python3 fixes Commit: f59b13c1cdb8e688d6738463ce54027e53d61cb7 https://github.com/galaxyproject/galaxy/commit/f59b13c1cdb8e688d6738463ce54… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Replace non-existent `tab` format with `tabular` in 2 tools Also: - Remove deprecated `interpreter` attribute of `<command>` - Single-quote text and data parameters inside the command - Fix wrong `name` attribute of `output` in 3 tests - Linting and cleanups Commit: b454bef75de0730b80820326eb53c2501b8baa05 https://github.com/galaxyproject/galaxy/commit/b454bef75de0730b80820326eb53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Fix indentation Commit: 6911153c307ba25525df7c165b4f10b4260964ac https://github.com/galaxyproject/galaxy/commit/6911153c307ba25525df7c165b4f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_single_in_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6213 from jmchilton/one_more_identifier_test Test element_identifier usage with single data parameters, in repeat/cond. Commit: 671c4d4f5fad7d15e6b9f70d595cf9f14ec6aeda https://github.com/galaxyproject/galaxy/commit/671c4d4f5fad7d15e6b9f70d595c… Author: Björn Grüning <bjoern.gruening(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- fix link to workflow list Commit: bd0e1f534e33816302fb1e8ed4d44bbbae278c88 https://github.com/galaxyproject/galaxy/commit/bd0e1f534e33816302fb1e8ed4d4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove bundle_to_json() and other unused functions Last usage was removed in commit af4fab16f58c36ea66328725e5bdcfaa3acbacda . Commit: eb67e4a627ea413af87dc341b32932e0b0fea9e0 https://github.com/galaxyproject/galaxy/commit/eb67e4a627ea413af87dc341b329… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove unused hg_util.get_config() function Commit: 644824c499080648dcfce73693b1235b331c2def https://github.com/galaxyproject/galaxy/commit/644824c499080648dcfce73693b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove todo Commit: 8b31cb1b1a90bbc70c5efc352349cea0149a24bb https://github.com/galaxyproject/galaxy/commit/8b31cb1b1a90bbc70c5efc352349… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix help text for renaming operation in workflows Commit: eaec9d248e8557bb8f03808f2e6940749c11314f https://github.com/galaxyproject/galaxy/commit/eaec9d248e8557bb8f03808f2e69… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Use Mercurial CLI instead of API for archive_repository_revision() Commit: c8e483e7b3ff1cf7899ee750eda244fa4e5e9a80 https://github.com/galaxyproject/galaxy/commit/c8e483e7b3ff1cf7899ee750eda2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Remove files only if created If an exception is raised in the `try` block before the files are created, an exception was generated in the `finally` block: ``` File "/home/nicola/software/nsoranzo_galaxy/lib/galaxy/webapps/tool_shed/controllers/repository.py", line 945, in export repositories_archive, error_message = erm.export_repository() File "/home/nicola/software/nsoranzo_galaxy/lib/tool_shed/capsule/capsule_manager.py", line 109, in export_repository if os.path.exists(tmp_export_info): UnboundLocalError: local variable 'tmp_export_info' referenced before assignment ``` Commit: 0ba8090d22c6f7e8b9aff863bb6d37723db46492 https://github.com/galaxyproject/galaxy/commit/0ba8090d22c6f7e8b9aff863bb6d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6255 from jmchilton/subcollection_mapping_with_multi_data_inputs Fix collection mapping to allow subcollection mapping over multi-data inputs. Commit: 6e0a2213c6bfb6be656bce9677b09a671d1d4889 https://github.com/galaxyproject/galaxy/commit/6e0a2213c6bfb6be656bce9677b0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #6273 from nsoranzo/mercurial_api_removal Use Mercurial CLI instead of API for archive_repository_revision() Commit: 5ddb6fc17988c359984115bb6990ae51b9e81118 https://github.com/galaxyproject/galaxy/commit/5ddb6fc17988c359984115bb6990… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6251 from guerler/check_context Check context for textable mode of select fields Commit: 17d7c0fb1f43a8cf377a76ea9484630d1c7be7f1 https://github.com/galaxyproject/galaxy/commit/17d7c0fb1f43a8cf377a76ea9484… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Consolidate use of get_repo_for_repository() Commit: a777c39b1eee65179bc1ae2e817ef269f22f2cd4 https://github.com/galaxyproject/galaxy/commit/a777c39b1eee65179bc1ae2e817e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Consolidate use of clone_repository() Commit: 64ce15f6cfd49ee0667e96402cbfaf8e9e358e96 https://github.com/galaxyproject/galaxy/commit/64ce15f6cfd49ee0667e96402cbf… Author: greg <ghv2(a)psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py Log Message: ----------- Change Newick ext to be newick instead of nhx Commit: 3ec5787f59eca7843dbb9e48bb6bcf8232fc3115 https://github.com/galaxyproject/galaxy/commit/3ec5787f59eca7843dbb9e48bb6b… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix tool search overlay link Commit: 7a7560ad731e7e4ab39e405ef9cf3f2185844850 https://github.com/galaxyproject/galaxy/commit/7a7560ad731e7e4ab39e405ef9cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 031ce67e996edc3c363bca1fbaf8572e92b5cbc7 https://github.com/galaxyproject/galaxy/commit/031ce67e996edc3c363bca1fbaf8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Fix delete "Collection Only" option in history menu. Broken with https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d73…. Commit: 1d52f04807a2f887a5d4d26939ebffb5076ba989 https://github.com/galaxyproject/galaxy/commit/1d52f04807a2f887a5d4d26939eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Merge pull request #6279 from scrathat/tool.search.overlay.selector.fix Fix tool search overlay selector Commit: 43d23b24d14b72bc59f98b4faa89a54dd1e58b25 https://github.com/galaxyproject/galaxy/commit/43d23b24d14b72bc59f98b4faa89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Stop listening to history changes after job submission Commit: 936c165818880bacd17416c7e848d6fba292e586 https://github.com/galaxyproject/galaxy/commit/936c165818880bacd17416c7e848… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Index select2 field values Commit: 1ab71ff1901d9b3c231947171f4611f6e3dcbf56 https://github.com/galaxyproject/galaxy/commit/1ab71ff1901d9b3c231947171f46… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Only update options if provided in parameter definition Commit: 57f319531e9c05c6a30dc8f6ffbe507831dbc7c6 https://github.com/galaxyproject/galaxy/commit/57f319531e9c05c6a30dc8f6ffbe… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- To clear workflow tool search field press ESC or click the X button Commit: 8cecfe30422d7ef8539b34b1237aa9e2acf498d3 https://github.com/galaxyproject/galaxy/commit/8cecfe30422d7ef8539b34b1237a… Author: greg <ghv2(a)psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml Log Message: ----------- Add the newick ext to the phylocanvas plugin Commit: 118e0d00518a1c4e68c25dbf8a584dc3111d207a https://github.com/galaxyproject/galaxy/commit/118e0d00518a1c4e68c25dbf8a58… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Update tabular.py just some cosmetics in the comments...I was looking for something and stumbled over these typos Commit: 9c58c51ea68eb38232610cac5cf8a3d6634269f2 https://github.com/galaxyproject/galaxy/commit/9c58c51ea68eb38232610cac5cf8… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M lib/galaxy/datatypes/data.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py Log Message: ----------- Merge pull request #6206 from gregvonkuster/newick Add the newick extension for the Newick datatype, Commit: 39dc8cfac9a9f090e433ef94e01025329ba421e7 https://github.com/galaxyproject/galaxy/commit/39dc8cfac9a9f090e433ef94e010… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise job success message Commit: d330a79c8d7b47db7d0f8ab49e5cdfbb42260611 https://github.com/galaxyproject/galaxy/commit/d330a79c8d7b47db7d0f8ab49e5c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Merge branch 'release_18.05' into dev Commit: d95dcecbea3499a55c531f40045661b4e3fe1db4 https://github.com/galaxyproject/galaxy/commit/d95dcecbea3499a55c531f400456… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 8e55b22542ff4a7118294efeab296ccc5849db84 https://github.com/galaxyproject/galaxy/commit/8e55b22542ff4a7118294efeab29… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Sort history items by history id in success message Commit: afa62a25e1340f6ed9340a8b30e7ef53a9364262 https://github.com/galaxyproject/galaxy/commit/afa62a25e1340f6ed9340a8b30e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Merge pull request #6289 from guerler/fix_update_handler Only update options if provided in parameter definition Commit: 086bf43eeb3362a775a62420f430156b19b1df19 https://github.com/galaxyproject/galaxy/commit/086bf43eeb3362a775a62420f430… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Hide inputs for tools without inputs Commit: 97fd079255dacbb085e89988d78a6f67cc99d342 https://github.com/galaxyproject/galaxy/commit/97fd079255dacbb085e89988d78a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #6274 from guerler/fix_help Fix help text for renaming operation in workflows Commit: d2723428391a9355e5cd8bc34776d8bf589685a9 https://github.com/galaxyproject/galaxy/commit/d2723428391a9355e5cd8bc34776… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Merge pull request #6281 from jmchilton/fix_delete_collection_only_2 Fix delete "Collection Only" option in history menu. Commit: ee56e570e027eb7306becc95890c68fcb415c1fb https://github.com/galaxyproject/galaxy/commit/ee56e570e027eb7306becc95890c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #6286 from guerler/column_performance Index select2 field values Commit: fae66e65f40b6d8c03fea1236e12a420fbb2058e https://github.com/galaxyproject/galaxy/commit/fae66e65f40b6d8c03fea1236e12… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #6240 from dannon/workflow_submit_text_links Workflow submit text links Commit: eb6cefc514a0ec96fbbb820e14712782653210c7 https://github.com/galaxyproject/galaxy/commit/eb6cefc514a0ec96fbbb820e1471… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 060d3f0ffdefa9903d33847346a823acfdbaa969 https://github.com/galaxyproject/galaxy/commit/060d3f0ffdefa9903d33847346a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Test list collection mapping over multidata input Commit: baa42fa8c6f867c6d2a1adcce9d8f3b946d10f0c https://github.com/galaxyproject/galaxy/commit/baa42fa8c6f867c6d2a1adcce9d8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix mapping list over multidata input Commit: e42e0c39a7d723ab9b99038b2d863c04848ff3e7 https://github.com/galaxyproject/galaxy/commit/e42e0c39a7d723ab9b99038b2d86… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6270 from galaxyproject/fix_workflow_link fix link to workflow list Commit: 0dcca1a727cf3678386b319bd94d5421798e6eff https://github.com/galaxyproject/galaxy/commit/0dcca1a727cf3678386b319bd94d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6300 from mvdbeek/multidata_list_input Make simple lists selectable again in multidata inputs Commit: db5dc5580c6e62d98207cfef6db78929d5c02a88 https://github.com/galaxyproject/galaxy/commit/db5dc5580c6e62d98207cfef6db7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #6277 from nsoranzo/mercurial_api_removal2 Consolidate use of get_repo_for_repository() and clone_repository() Commit: 9a798395d13a061bf5355a88c154975da6a516cf https://github.com/galaxyproject/galaxy/commit/9a798395d13a061bf5355a88c154… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #6076 from dannon/workflow_fixes Workflow and remote-user related refactoring and a bug fix Commit: 940ed5f5dd1f34456d81513db8bbf0a66476e683 https://github.com/galaxyproject/galaxy/commit/940ed5f5dd1f34456d81513db8bb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M test/functional/tools/for_workflows/cat_collection.xml Log Message: ----------- Break test by adding "list" to collection_type This will break tests trying to map over list:pair collections, for instance test_extract_workflows_with_dataset_collections. Commit: cb97f89d129cf7f0b7cf7146c0c15309b3dcb0c7 https://github.com/galaxyproject/galaxy/commit/cb97f89d129cf7f0b7cf7146c0c1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py Log Message: ----------- Fix can_map_over for mapping over paired inputs We'd only try mapping over the first collection type description otherwise. I suppose we didn't notice because the first type is `list` and therefore much more common. Noticed this while working on https://github.com/galaxyproject/galaxy/pull/5640. Commit: 4b99dca85cd277e12fd8213d6abdf6e283fe4fb6 https://github.com/galaxyproject/galaxy/commit/4b99dca85cd277e12fd8213d6abd… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Fix default job script by moving env setup The part where pythonpath was evaluated totally ignored any variables set in the env setup. That is now fixed. All credits go to @mvdbeek for finding the cause of the issue and proposing the solution. Commit: bbce9a1e6f1a077dfbbb795f643f5578b40436f2 https://github.com/galaxyproject/galaxy/commit/bbce9a1e6f1a077dfbbb795f643f… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Change location of env setup Commit: 1825ea53c981e7cf3d0206e63a534e3f288b90b8 https://github.com/galaxyproject/galaxy/commit/1825ea53c981e7cf3d0206e63a53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/app.py Log Message: ----------- Put import at the top Commit: 178a94ad2a8bce2fe80372fb1790b903683fddd3 https://github.com/galaxyproject/galaxy/commit/178a94ad2a8bce2fe80372fb1790… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Move `get_mercurial_default_options_dict()` where it's used Commit: 6c56467641d6eea97aaefd5bf8370f06665bb03f https://github.com/galaxyproject/galaxy/commit/6c56467641d6eea97aaefd5bf837… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Use Mercurial CLI instead of API for `commit_changeset()` Commit: 1831dbe3f30fe18a5bef7e51034494cc7f70f3ee https://github.com/galaxyproject/galaxy/commit/1831dbe3f30fe18a5bef7e510344… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Use Mercurial CLI instead of API for `add_changeset()` Commit: bd31c3e7b63a7d2f7266f1b964c566c87c100cc2 https://github.com/galaxyproject/galaxy/commit/bd31c3e7b63a7d2f7266f1b964c5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Use Mercurial CLI instead of API for `pull_repository()` Merge `get_configured_ui()` into `get_repo_for_repository()`. Commit: 0ca83cbc7c7e10023e3e967b08510c7d7e83cf94 https://github.com/galaxyproject/galaxy/commit/0ca83cbc7c7e10023e3e967b0851… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Use Mercurial CLI instead of API for `remove_file()` Commit: fa78aeab876faac14d1c1ee9ff80c59dd7c6d839 https://github.com/galaxyproject/galaxy/commit/fa78aeab876faac14d1c1ee9ff80… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Remove unnecessary calls to `get_repo_for_repository()` Commit: bba60a05359f4c19e53dd3360402076a0e399e74 https://github.com/galaxyproject/galaxy/commit/bba60a05359f4c19e53dd3360402… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Use `hg init` to create a Mercurial repository This allows removing a call to `hg_util.get_repo_for_repository()`, which uses the discouraged Mercurial API. Commit: 7c75c230bf7b4ff0c132a814b50f10cc8c31671b https://github.com/galaxyproject/galaxy/commit/7c75c230bf7b4ff0c132a814b50f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Remove unused functions Commit: 42999955f74388ef639464879f48c08f92985657 https://github.com/galaxyproject/galaxy/commit/42999955f74388ef639464879f48… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Use `hg id` to map a changeset to a revision number This allows removing a lot of calls to `hg_util.get_repo_for_repository()`, which uses the discouraged Mercurial API. Commit: db4c5a97eded69c6b76ced2bcada1801cad3bd85 https://github.com/galaxyproject/galaxy/commit/db4c5a97eded69c6b76ced2bcada… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix `reversed_upper_bounded_changelog()` calls `hg_util.reversed_upper_bounded_changelog()` expects a changeset revision string as second parameter, not a `changectx` object. Commit: 77cd1fc30a6beabc3cde7ae22e1f62dd2560b94c https://github.com/galaxyproject/galaxy/commit/77cd1fc30a6beabc3cde7ae22e1f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-10 (Sun, 10 Jun 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Need to set default HOME/TMP before env_setup_commands Otherwise the defaults take precedence Commit: 7f2117b26b531edc52b564f7435503c6072a233c https://github.com/galaxyproject/galaxy/commit/7f2117b26b531edc52b564f74355… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #1 from mvdbeek/rhpvorderman-patch-1 Need to set default HOME/TMP before env_setup_commands Commit: 9b19d5c267900409b5aace9f2c554b2da13ce8e7 https://github.com/galaxyproject/galaxy/commit/9b19d5c267900409b5aace9f2c55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- Fix inferring output structure when mapping over Previously this would have always generated `list:list` structures, even when the input is a list:pair. I'm not 100% convinced this is correct, but this seems to work. Commit: fd16302d65193f13eb04456b610044343ca54adb https://github.com/galaxyproject/galaxy/commit/fd16302d65193f13eb04456b6100… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test tool and workflow for mapping over with mapping output This doesn't quite work because of the dynamic output collection, which fails with: ``` galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms) galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs collection_builder.populate() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate elements = self.build_elements() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements new_elements[identifier] = element.build() AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build' ``` This seems to happen because the inner collection is wrongly detected as nested. In general I doubt that mapping over colleciton output works with dynamically discovered output collections. Commit: f270f7abfbe885b4d8dc198f100e26856a5cadec https://github.com/galaxyproject/galaxy/commit/f270f7abfbe885b4d8dc198f100e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Merge pull request #6307 from nsoranzo/mercurial_api_removal3 More use of Mercurial CLI instead of API Commit: e61a05ebf4678ca34aa52d917bc3a5e74f2426c6 https://github.com/galaxyproject/galaxy/commit/e61a05ebf4678ca34aa52d917bc3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #6292 from hrhotz/patch-1 Update tabular.py Commit: c78d7ef5131ee807660e032f865a355459c0dfb0 https://github.com/galaxyproject/galaxy/commit/c78d7ef5131ee807660e032f865a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Missing semicolon. Commit: 544cc610fd07376c961ab3b4a38d1c6b28eeb6ad https://github.com/galaxyproject/galaxy/commit/544cc610fd07376c961ab3b4a38d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss Log Message: ----------- Client format Commit: 1df5959d216a812e344716c94cd836649da042ee https://github.com/galaxyproject/galaxy/commit/1df5959d216a812e344716c94cd8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'workflow.tool.search.clear' into dev Commit: ada8a7f6fb78c53f54cd3dc3c156fd8476c2840f https://github.com/galaxyproject/galaxy/commit/ada8a7f6fb78c53f54cd3dc3c156… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Client format (from the merge) Commit: 47c03ab2514d833225b41ff0c67f3652aa4c6b22 https://github.com/galaxyproject/galaxy/commit/47c03ab2514d833225b41ff0c67f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #6305 from rhpvorderman/patch-1 Fix default job script by moving env setup Commit: 258ccb89bd5190e703f9d1705ec888b65ce77724 https://github.com/galaxyproject/galaxy/commit/258ccb89bd5190e703f9d1705ec8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Consider mapping-over when picking collection_type for dynamically discovered collections Commit: 46ebdce0adc0ba3f28cd268605d8406bbffca9dd https://github.com/galaxyproject/galaxy/commit/46ebdce0adc0ba3f28cd268605d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Remove stray doublequote (which was showing up in the link) Commit: 44275a2b722f68f6d77c9875ca373a146fb35e3c https://github.com/galaxyproject/galaxy/commit/44275a2b722f68f6d77c9875ca37… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6142 from scrathat/workflow_toollink_area Make workflow editor toolTitle link include the tools description Commit: 106dda140f322734c6c4917a54b137c418840a99 https://github.com/galaxyproject/galaxy/commit/106dda140f322734c6c4917a54b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Missing semicolon. Commit: 99c1da2f62739654d72a598908ea07b7d2e699a7 https://github.com/galaxyproject/galaxy/commit/99c1da2f62739654d72a598908ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/slurm.py M scripts/grt/grt.yml.sample M static/style/blue/base.css Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 80e1590869527627ede01954d0a4271ca05304bf https://github.com/galaxyproject/galaxy/commit/80e1590869527627ede01954d0a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Client format Commit: cd2feb7dcb81424e753ef371879c3f4b397555b6 https://github.com/galaxyproject/galaxy/commit/cd2feb7dcb81424e753ef371879c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge branch 'job_success_message' into dev Commit: fc06a7a168d5d36fabb3f6f420a4ef0b12363f2c https://github.com/galaxyproject/galaxy/commit/fc06a7a168d5d36fabb3f6f420a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over Commit: 178486b840b64c2bfb1b4cffefd44c945a8ccb3e https://github.com/galaxyproject/galaxy/commit/178486b840b64c2bfb1b4cffefd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/history_query.py M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/for_workflows/cat_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6278 from mvdbeek/fix_paired_mapping_over Various fixes for mapping over collections Commit: b46ab962adcaef54b75b8e9bf3e5647b59b128cc https://github.com/galaxyproject/galaxy/commit/b46ab962adcaef54b75b8e9bf3e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix typo (UnitializedTree -> UninitializedTree) Commit: 1b50504678dc5c84fa292236ac58697591611aa4 https://github.com/galaxyproject/galaxy/commit/1b50504678dc5c84fa292236ac58… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #6066 from jmchilton/apply_rules_tutorials Rules - test case for apply rules tutorial. Commit: 6ad41928093c033568eeb3e530f32a813accb24e https://github.com/galaxyproject/galaxy/commit/6ad41928093c033568eeb3e530f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js Log Message: ----------- Fix undefined success_message Commit: 254a6bc8d7939a385783795aba6f1fb4a7c4677d https://github.com/galaxyproject/galaxy/commit/254a6bc8d7939a385783795aba6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6315 from mvdbeek/fix_uninitialized_typo Fix typo (UnitializedTree -> UninitializedTree) Commit: 713bca04f63f464ccbb47ced90d971624ed075b6 https://github.com/galaxyproject/galaxy/commit/713bca04f63f464ccbb47ced90d9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Allow #if $datasets #end if patern for file lists Otherwise the following exception occurs: ``` Traceback (most recent call last): File "/home/wolffj/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 191, in prepare_job job_wrapper.prepare() File "/home/wolffj/src/galaxy/lib/galaxy/jobs/__init__.py", line 858, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/wolffj/src/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build raise e AttributeError: 'DatasetListWrapper' object has no attribute 'value' ``` This is because DatasetListWrapper inherits `__bool__` from ToolParameterValueWrapper which defines bool as ``` def __bool__(self): return bool(self.value) __nonzero__ = __bool__ ``` while DatasetListWrapper has no `value` attribute. Fixes https://github.com/galaxyproject/galaxy/issues/6314 reported by @joachimwolff (many thanks for the detailed report!). Commit: 0a29e533d3362e3a0dd7bfc202e8fff799a9e6ee https://github.com/galaxyproject/galaxy/commit/0a29e533d3362e3a0dd7bfc202e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M test/functional/tools/multi_data_optional.xml Log Message: ----------- Use #if $datasets #end if pattern in test tool Commit: c08f7c9a4cfdf4da4771b7f891892ea1332666dc https://github.com/galaxyproject/galaxy/commit/c08f7c9a4cfdf4da4771b7f89189… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js Log Message: ----------- Merge pull request #6316 from mvdbeek/success_message_fix Fix undefined success_message Commit: 6f213b36975b5b8f66b0b02f8920744a5e2d0064 https://github.com/galaxyproject/galaxy/commit/6f213b36975b5b8f66b0b02f8920… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix __bool__ for empty optional multidata parameters Commit: 550eb882100a3a9210689dbe789b67a1eb2ba5c2 https://github.com/galaxyproject/galaxy/commit/550eb882100a3a9210689dbe789b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M test/functional/tools/multi_data_optional.xml Log Message: ----------- Add a test for not providing an optional input Commit: 9b9ab6a1cf4485920c88b252d27642f6f20c3525 https://github.com/galaxyproject/galaxy/commit/9b9ab6a1cf4485920c88b252d276… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/multi_data_optional.xml Log Message: ----------- Merge pull request #6317 from mvdbeek/fix_6314 Allow #if $datasets #end if pattern for file lists Commit: 542dbe63e89689daec88ab0d075ad7f1f77bf0b0 https://github.com/galaxyproject/galaxy/commit/542dbe63e89689daec88ab0d075a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Merge pull request #6269 from nsoranzo/phenotype_association_tools Fixes for phenotype association tools Commit: d514ebce3bfe936091f57d22bbafbca48d419fa8 https://github.com/galaxyproject/galaxy/commit/d514ebce3bfe936091f57d22bbaf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js R client/galaxy/scripts/components/admin/UserAPIKeys.vue M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/impersonate.mako M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Merge pull request #6176 from dannon/user_grid_impersonate Add impersonate to main user grid when it's enabled Commit: 5a27b0cf4d4105f61c7660b63de97d812346df13 https://github.com/galaxyproject/galaxy/commit/5a27b0cf4d4105f61c7660b63de9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Merge pull request #6148 from jmchilton/cwl-small-stuff-2 Small fixes and small refactorings toward reuse in CWL branch (retry) Commit: 81864e9713e63b3478a3e8ec8ed672516b2c6853 https://github.com/galaxyproject/galaxy/commit/81864e9713e63b3478a3e8ec8ed6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update dependencies to versions with Python3 manylinux wheels on PyPI Commit: d66a63012af8f538572458650d47801a5d2cd396 https://github.com/galaxyproject/galaxy/commit/d66a63012af8f538572458650d47… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/api/common.py M test/unit/test_security_helper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Replace unmaintained pycrypto dependency with pycryptodome Minimum secret key length for Blowfish was increased from 4 to 5 bytes. First argument to Blowfish.new() must be a bytestring, and the `mode` argument is no more optional. Remove unused `encode_id` function from `scripts/api/common.py` . Documentation updated, then rebuilt with `make config-rebuild` . Commit: 39b70d7193c223e4013391afcb90cc932f7ac650 https://github.com/galaxyproject/galaxy/commit/39b70d7193c223e4013391afcb90… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py Log Message: ----------- Python3 Unicode/binary fixes Commit: cffeb6edc8b72534385d6aa5e978d25cb20b5479 https://github.com/galaxyproject/galaxy/commit/cffeb6edc8b72534385d6aa5e978… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Move mercurial imports inside the functions that use them Because Galaxy under Python3 would fail otherwise. Commit: 6120183182bf643b6abb995283c7798da71f0211 https://github.com/galaxyproject/galaxy/commit/6120183182bf643b6abb995283c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M scripts/check_python.py Log Message: ----------- Allow Python 3 if in a virtualenv Commit: 594daa85bf5de0acfb0a76aeea8cb55d7aa4684a https://github.com/galaxyproject/galaxy/commit/594daa85bf5de0acfb0a76aeea8c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Add py34-first_startup to Travis and default tox tests. Commit: 847d0e987e21056948a2859d91b39c3b7d41ab69 https://github.com/galaxyproject/galaxy/commit/847d0e987e21056948a2859d91b3… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: b5214867c9ffea3cb9008acc3efa9928781ff513 https://github.com/galaxyproject/galaxy/commit/b5214867c9ffea3cb9008acc3efa… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6326 from scrathat/rule.builder.selection.update Fix target update for rule collection builder after input selection Commit: f8bc0656f9cf5336cac667b1be46ad2bb5bfb7ff https://github.com/galaxyproject/galaxy/commit/f8bc0656f9cf5336cac667b1be46… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M .travis.yml M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M scripts/api/common.py M scripts/check_python.py M test/unit/test_security_helper.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Merge pull request #6325 from mvdbeek/py3_fixes2 Add py34-first_startup to Travis and default tox tests Commit: b41af6abe9c144c76fbedff7d6a5e41d9a3d6071 https://github.com/galaxyproject/galaxy/commit/b41af6abe9c144c76fbedff7d6a5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #6303 from guerler/history_polling Stop listening to history changes after job submission Compare: https://github.com/galaxyproject/galaxy/compare/e7b7bee82e60...b41af6abe9c1 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9ac016: Update description for installing pbs-python
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 9ac0161891a92db7a359e13a74e831ec17a79317 https://github.com/galaxyproject/galaxy/commit/9ac0161891a92db7a359e13a74e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update description for installing pbs-python Commit: 37ad1a8bdce963b4152331685e3755a60777e633 https://github.com/galaxyproject/galaxy/commit/37ad1a8bdce963b4152331685e37… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #6345 from mvdbeek/update_pbs_python_doc [18.01] Update description for installing pbs-python Compare: https://github.com/galaxyproject/galaxy/compare/3007c93d7c5b...37ad1a8bdce9 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] b701ec: FIXME: hack cgroup metrics and logging fixes for p...
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b701ec9dc34a94910083b7a666c737319ec805e7 https://github.com/galaxyproject/usegalaxy-playbook/commit/b701ec9dc34a9491… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M roles/galaxyproject.pulsar/templates/job_metrics_conf.xml.j2 M roles/galaxyproject.pulsar/templates/server.ini.j2 Log Message: ----------- FIXME: hack cgroup metrics and logging fixes for pulsar, need to fix these upstream in the role **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 340a50: More Jetstream autoscaling @ IU stuff
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 340a508e7b48d756fc6fcc8fa32b3af02246bf3c https://github.com/galaxyproject/usegalaxy-playbook/commit/340a508e7b48d756… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml Log Message: ----------- More Jetstream autoscaling @ IU stuff **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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