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

[galaxyproject/galaxy] 69a870: Fix modules resolver (addition of the resolver_msg...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Commit: e178879c0f9f4351bf0270f1602a60d660a4da04 https://github.com/galaxyproject/galaxy/commit/e178879c0f9f4351bf0270f1602a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/14ceb6d91b57...e178879c0f9f

1 0

[galaxyproject/galaxy] aa68d3: Improve robustness of published workflow display t...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa68d38735acda43a078a3412afef3c604d2e205 https://github.com/galaxyproject/galaxy/commit/aa68d38735acda43a078a3412afe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Improve robustness of published workflow display test case. Failed twice in different ways here https://jenkins.galaxyproject.org/job/selenium/484/ - this should address both cases. Commit: 00677fc0f62cc37732528f2af5ac964ce4239fad https://github.com/galaxyproject/galaxy/commit/00677fc0f62cc37732528f2af5ac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #4653 from jmchilton/selenium_fixes_28 Improve robustness of published workflow display test case. Compare: https://github.com/galaxyproject/galaxy/compare/35cd9339453d...00677fc0f62c

1 0

[galaxyproject/galaxy] 01eb5f: Aggressively retry buggy submit_login() function i...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 01eb5f04e6661d389d8c8f681373b5c50fe259b9 https://github.com/galaxyproject/galaxy/commit/01eb5f04e6661d389d8c8f681373… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Aggressively retry buggy submit_login() function in Selenium tests. I don't get why when we click submit the user does not actually get logged in, but based on the last round of improved error messages this seems to be the case. You might think there is some callback in the login form that doesn't get registered by the time Selenium clicks the submit button - but this doesn't seem to be the case - I don't see any jquery magic happening in login.mako. Should fix failures like this: https://jenkins.galaxyproject.org/job/selenium/482/testReport/junit/seleniu… I'd say at this point this is the most common problem in the Selenium tests. This also introduces a framework for taking state snapshots of the Galaxy interface during tests that will only get written out if the tests fail. We now take screenshots before and after submitting the login form but this is a general purpose debugging mechanism that could be used other places. Commit: 35cd9339453dd245ab4c317517ea1dfafb6af147 https://github.com/galaxyproject/galaxy/commit/35cd9339453dd245ab4c317517ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4655 from jmchilton/selenium_fixes_29 Aggressively retry buggy submit_login() function in Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/24557fdeaab2...35cd9339453d

1 0

[galaxyproject/galaxy] a45e7e: Fix transiently failing saved histories due to suc...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a45e7e196b03b6467ddea0bcacac9914830f0bb9 https://github.com/galaxyproject/galaxy/commit/a45e7e196b03b6467ddea0bcacac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Fix transiently failing saved histories due to success message disappearing. Commit: 24557fdeaab24ca8a763478ca5d5a2303f00243f https://github.com/galaxyproject/galaxy/commit/24557fdeaab24ca8a763478ca5d5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4669 from jmchilton/selenium_fixes_31 Fix transiently failing saved histories due to success message disappearing. Compare: https://github.com/galaxyproject/galaxy/compare/98f2c108238e...24557fdeaab2

1 0

[galaxyproject/galaxy] 69a870: Fix modules resolver (addition of the resolver_msg...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Compare: https://github.com/galaxyproject/galaxy/compare/4345d8e7d7a3...2ffeedfa723c

1 0

[galaxyproject/usegalaxy-playbook] 92278f: Fix metadata on Main until we have 17.09
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 92278f434d7e56312b18c1cc78e332e34648507f https://github.com/galaxyproject/usegalaxy-playbook/commit/92278f434d7e5631… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix metadata on Main until we have 17.09

1 0

[galaxyproject/usegalaxy-playbook] b2c1b7: Fixes for modified destination names
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b2c1b7744a625a565c84d33493314498e61dda54 https://github.com/galaxyproject/usegalaxy-playbook/commit/b2c1b7744a625a56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fixes for modified destination names

1 0

[galaxyproject/galaxy] 095307: Selenium fixes for publishing histories button.
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 095307b6783f39bce7a1f4c6fbb4e603e368ecfb https://github.com/galaxyproject/galaxy/commit/095307b6783f39bce7a1f4c6fbb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Selenium fixes for publishing histories button. Fixes https://jenkins.galaxyproject.org/job/selenium/488/testReport/junit/seleniu…. It looks like a Toastr popup sometimes intercepts the click, this should solve that I believe. Commit: 98f2c108238e07a5379712f22ed8c46467204de6 https://github.com/galaxyproject/galaxy/commit/98f2c108238e07a5379712f22ed8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #4660 from jmchilton/selenium_fixes_30 Selenium fixes for publishing histories button. Compare: https://github.com/galaxyproject/galaxy/compare/87d5d440238e...98f2c108238e

1 0

[galaxyproject/galaxy] ac10e0: Reload tools if a macro changes
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac10e0d2245ed9bfec4893512fb1d46532654146 https://github.com/galaxyproject/galaxy/commit/ac10e0d2245ed9bfec4893512fb1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/xml_macros.py M scripts/validate_tools.sh M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Reload tools if a macro changes We do this by recording any macros that are required to load a tool. When loading a tool we register the macro to be watched, and if the macro changes we reload all corresponding tools. Commit: d3d134030aded5b29e62c4c1d5946f3266a34827 https://github.com/galaxyproject/galaxy/commit/d3d134030aded5b29e62c4c1d594… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/util/xml_macros.py M scripts/validate_tools.sh M test/unit/tools/test_tool_loader.py Log Message: ----------- Rework #4635 to preserve backward compatibility on modules shared via galaxy-lib. Also cleanup comments and such in xml_macros to reflect this doesn't apply just to tools. Commit: 87d5d440238e1ce7f1aaaeb152bc00ecf1f6faf1 https://github.com/galaxyproject/galaxy/commit/87d5d440238e1ce7f1aaaeb152bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #4635 from mvdbeek/reload_on_macro_changes Reload tools if a macro changes Compare: https://github.com/galaxyproject/galaxy/compare/e057d7d88700...87d5d440238e

1 0

[galaxyproject/usegalaxy-playbook] 68cc4c: Use remote datatypes_conf.xml for Main Pulsar unti...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 68cc4c1373c32a927a44f3c8d640fc790493c6d7 https://github.com/galaxyproject/usegalaxy-playbook/commit/68cc4c1373c32a92… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Use remote datatypes_conf.xml for Main Pulsar until bugfixes are merged and we update

1 0