March 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] c30d61: Installed RSeQC version 2.6.4 on main
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c30d611507f95efafd4b04d92362077373269007 https://github.com/galaxyproject/usegalaxy-playbook/commit/c30d611507f95efa… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed RSeQC version 2.6.4 on main

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[galaxyproject/usegalaxy-playbook] d3334e: Installed tools on test.
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d3334e5f6d16886170dec3e073e1b5d7c93913c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/d3334e5f6d168861… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed tools on test.

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[galaxyproject/galaxy] c73c71: Swap for the constant time comparison algorithm
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c73c7130436097cb9c6db0e3ac24b39515ce5560 https://github.com/galaxyproject/galaxy/commit/c73c7130436097cb9c6db0e3ac24… Author: E Rasche <hxr(a)hx42.org> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Swap for the constant time comparison algorithm Commit: dbf6f58251719f721da13e2d605f616956391076 https://github.com/galaxyproject/galaxy/commit/dbf6f58251719f721da13e2d605f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Merge pull request #5719 from erasche/constant-time-sha-compare Swap for the constant time comparison algorithm Compare: https://github.com/galaxyproject/galaxy/compare/8e95830bca1f...dbf6f5825171

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[galaxyproject/galaxy] d5d1e4: Clarfify that nginx-extras needs to be install for...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: d5d1e4b80d84ebafccfd1e8cc642dbcd1f020d55 https://github.com/galaxyproject/galaxy/commit/d5d1e4b80d84ebafccfd1e8cc642… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Clarfify that nginx-extras needs to be install for the upload_store directive to work Commit: 127d7b8c3c854db7a28c761aee0c3f2d2e211a6e https://github.com/galaxyproject/galaxy/commit/127d7b8c3c854db7a28c761aee0c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #5717 from mvdbeek/nginx_doc_update [18.01] Clarify that nginx-extras needs to be install for the upload_store d… Compare: https://github.com/galaxyproject/galaxy/compare/c58ca749c26b...127d7b8c3c85

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[galaxyproject/galaxy] 393e1d: Remove subclass="true" from Phylip datatype defini...
by GitHub 19 Mar '18

19 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 393e1d85cf4f5c32a63ba8b08977e92f79dc8d48 https://github.com/galaxyproject/galaxy/commit/393e1d85cf4f5c32a63ba8b08977… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove subclass="true" from Phylip datatype definition Introduced in commit 3e63b63720c7c5b2fc672f1bfa9b66bb38851f54 . Commit: 8e95830bca1f2290314733d8723b71f871d52f96 https://github.com/galaxyproject/galaxy/commit/8e95830bca1f2290314733d8723b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5718 from nsoranzo/fix_phylip_datatype Remove subclass="true" from Phylip datatype definition Compare: https://github.com/galaxyproject/galaxy/compare/b821b6a68321...8e95830bca1f

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[galaxyproject/usegalaxy-playbook] 837c03: rev domain blacklist to the latest
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 837c03684890c3ddb206b3d433aab91295231493 https://github.com/galaxyproject/usegalaxy-playbook/commit/837c03684890c3dd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M env/common/files/galaxy/config/disposable_email_blacklist.conf Log Message: ----------- rev domain blacklist to the latest as provided by the https://github.com/martenson/disposable-email-domains project

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[galaxyproject/galaxy] 680cfe: Properly order @flakey and @selenium_test decorato...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 680cfec4c9145e27541744da85948b90c5413133 https://github.com/galaxyproject/galaxy/commit/680cfec4c9145e27541744da8594… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Properly order @flakey and @selenium_test decorators Commit: b821b6a683210391035be133a096ecec736c49cd https://github.com/galaxyproject/galaxy/commit/b821b6a683210391035be133a096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #5711 from nsoranzo/flakey_after_selenium_tests Properly order @flakey and @selenium_test decorators Compare: https://github.com/galaxyproject/galaxy/compare/7c8b24394081...b821b6a68321

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[galaxyproject/galaxy] 200160: Make problematic test test_library_to_collections ...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2001606d33cdbb8bf261f301399e688b6a116aa6 https://github.com/galaxyproject/galaxy/commit/2001606d33cdbb8bf261f301399e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Make problematic test test_library_to_collections more robust potentially. Now that #5701 has been merged we have some more clues on the problem with this test. It is dying on the second upload being changed here. I suspect what is happening is that we are waiting on a history to become okay but we make that check before the first upload has even finished - so there is some chance the history is okay because it is empty - so we are reopening the home page in the middle of the first upload and this is causing something odd to happen - something is popping up an empty alert. I'm not sure what is causing that alert but it isn't what we are testing with this test so it is best to really just wait on the uploads - as we do in other tests (see test_uploads.py for instance). history_panel_wait_for_hid_ok is a stronger assertion and is generally more robust and has better error reporting anyway so this should be a stability win all around. Commit: 7c8b243940810b075d57f5a6625acdabcc38a5fa https://github.com/galaxyproject/galaxy/commit/7c8b243940810b075d57f5a6625a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #5710 from jmchilton/selenium_fixes_39 Make problematic test test_library_to_collections more robust. Compare: https://github.com/galaxyproject/galaxy/compare/6716848a3632...7c8b24394081

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[galaxyproject/galaxy] be0206: Set the role type to SYSTEM for auto generated rol...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: be02063c3fbec79a7e146ef87dbc6e99c80e7754 https://github.com/galaxyproject/galaxy/commit/be02063c3fbec79a7e146ef87dbc… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Set the role type to SYSTEM for auto generated roles, which is similar to the default behavior Commit: c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999 https://github.com/galaxyproject/galaxy/commit/c58ca749c26bbb3c4ca8750f2c37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #5709 from scholtalbers/fix/default_ldap_role_type [18.01] Fix/default role type on auto created roles Compare: https://github.com/galaxyproject/galaxy/compare/ebb7be8d0ec3...c58ca749c26b

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[galaxyproject/infrastructure-playbook] 8f2240: Enable GCC2019 redirect on Hub
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8f224099bde598ead8fd29402b25ed3ec7089f11 https://github.com/galaxyproject/infrastructure-playbook/commit/8f224099bde… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: A env/galaxy/group_vars/sslservers M env/galaxy/templates/nginx/galaxyproject.j2 Log Message: ----------- Enable GCC2019 redirect on Hub

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