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

[galaxyproject/galaxy] d49e01: The /user/logout endpoint is now used for both rem...
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: d49e014a63641db37814ab0b31b7aa4d1eded786 https://github.com/galaxyproject/galaxy/commit/d49e014a63641db37814ab0b31b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- The /user/logout endpoint is now used for both remote and internal users to handle logout logic, and should be accessible here. Commit: b0ac7daecdda4001f6bcd7d70a15bb30375216e5 https://github.com/galaxyproject/galaxy/commit/b0ac7daecdda4001f6bcd7d70a15… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3405 from dannon/remoteuser_logout_fix [16.10] Remoteuser Logout Fix. Compare: https://github.com/galaxyproject/galaxy/compare/535dd7a5f546...b0ac7daecdda

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[galaxyproject/galaxy] aba761: Update the testing image used with ``--dockerize``...
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aba7618a3a110c3c4893d23ddb2a9d3a446c14a0 https://github.com/galaxyproject/galaxy/commit/aba7618a3a110c3c4893d23ddb2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Update the testing image used with ``--dockerize``ed tests. Should prevent Jenkins from writing files as root. Commit: 8041525223b2deeffb4b588afe6e480b62fa6c07 https://github.com/galaxyproject/galaxy/commit/8041525223b2deeffb4b588afe6e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3401 from jmchilton/testing_image_update Update the testing image used with ``--dockerize``ed tests. Compare: https://github.com/galaxyproject/galaxy/compare/1d52e9a32cec...8041525223b2

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[galaxyproject/galaxy] 2d991b: Escapes some variables
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 2d991bba073a9e1f40b18f6c927e4adf6ca1ddb9 https://github.com/galaxyproject/galaxy/commit/2d991bba073a9e1f40b18f6c927e… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Escapes some variables Commit: 535dd7a5f54617b12684eaa179066b4877965dd2 https://github.com/galaxyproject/galaxy/commit/535dd7a5f54617b12684eaa17906… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #3404 from dannon/backport_viz_escape [16.10] Backport of visualization hda.name escapes Compare: https://github.com/galaxyproject/galaxy/compare/24b250ab3369...535dd7a5f546

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[galaxyproject/galaxy] 7a370a: Escapes some variables
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a370a4ff6bb5aa24ca9758cb9bbfadbe808e3b0 https://github.com/galaxyproject/galaxy/commit/7a370a4ff6bb5aa24ca9758cb9bb… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Escapes some variables Commit: 1d52e9a32ceca303b12a1de84604e68069ed0e85 https://github.com/galaxyproject/galaxy/commit/1d52e9a32ceca303b12a1de84604… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #3403 from yhoogstrate/visualizations_escape Escapes some variables Compare: https://github.com/galaxyproject/galaxy/compare/778bcd00451a...1d52e9a32cec

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[galaxyproject/galaxy] 8368b1: fix typo
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8368b1784356112682b4eb93692d57582f009b34 https://github.com/galaxyproject/galaxy/commit/8368b1784356112682b4eb93692d… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- fix typo Commit: 778bcd00451aa863899d520aaac38fad7b9cae35 https://github.com/galaxyproject/galaxy/commit/778bcd00451aa863899d520aaac3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- Merge pull request #3402 from manabuishii/patch-3 fix typo Compare: https://github.com/galaxyproject/galaxy/compare/3c494c42e2b4...778bcd00451a

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[galaxyproject/galaxy] ca40f9: Markdown datatype support.
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca40f984b0dfda58af1aa55d167edf615582192a https://github.com/galaxyproject/galaxy/commit/ca40f984b0dfda58af1aa55d167e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/bower.json A client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py A static/maps/libs/showdown.js.map A static/scripts/libs/showdown.js A templates/webapps/galaxy/dataset/markdown.mako A test/functional/tools/creates_html.xml A test/functional/tools/creates_html_index.html A test/functional/tools/creates_markdown.xml A test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Markdown datatype support. With test tools demonstrating HTML and Markdown outputs from tools. Implements #3396 as part of the Qiime hackathon. Commit: 3c494c42e2b42da7e934b38954df910d20bf286d https://github.com/galaxyproject/galaxy/commit/3c494c42e2b42da7e934b38954df… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json A client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py A static/maps/libs/showdown.js.map A static/scripts/libs/showdown.js A templates/webapps/galaxy/dataset/markdown.mako A test/functional/tools/creates_html.xml A test/functional/tools/creates_html_index.html A test/functional/tools/creates_markdown.xml A test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3399 from jmchilton/markdown Markdown datatype support. Compare: https://github.com/galaxyproject/galaxy/compare/6c4dff3f4604...3c494c42e2b4

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[galaxyproject/infrastructure-playbook] 87ea9a: Change jenkins access lists
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 87ea9ab3b08a743504e6cefc41078f8e4a460eb7 https://github.com/galaxyproject/infrastructure-playbook/commit/87ea9ab3b08… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M galaxyenv/secret_group_vars/jenkinsslaves.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Change jenkins access lists

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[galaxyproject/galaxy] 09f027: Document how to create Docker testing images.
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09f0272ede3a17a5445956179acded53e213a1c4 https://github.com/galaxyproject/galaxy/commit/09f0272ede3a17a5445956179acd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M test/docker/README.md Log Message: ----------- Document how to create Docker testing images. With fix noted by @martenson. Commit: 6c4dff3f4604857f5c067c87a7a568a2e3acf0a5 https://github.com/galaxyproject/galaxy/commit/6c4dff3f4604857f5c067c87a7a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M test/docker/README.md Log Message: ----------- Merge pull request #3400 from jmchilton/document_docker_testing_image Document how to create Docker testing images. Compare: https://github.com/galaxyproject/galaxy/compare/542dc4077f35...6c4dff3f4604

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[galaxyproject/usegalaxy-playbook] 37566d: Update Test and Main
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 37566d989afac47f68666393c3c26732460eb8c2 https://github.com/galaxyproject/usegalaxy-playbook/commit/37566d989afac47f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/galaxy_version.yml M stage/galaxy_version.yml M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update Test and Main

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[galaxyproject/usegalaxy-playbook] ebee65: Remove job limits on Bridges
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ebee6544642ee65d3126e294be92bfc41026d381 https://github.com/galaxyproject/usegalaxy-playbook/commit/ebee6544642ee65d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Remove job limits on Bridges Commit: 3ef2b14e2f3706da505d32575919f1c5e8809a74 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ef2b14e2f3706da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test Commit: fa36467433c88244fdb44b9135c1f807121fd08a https://github.com/galaxyproject/usegalaxy-playbook/commit/fa36467433c88244… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M files/galaxy/usegalaxy.org/config/tool_conf.xml Log Message: ----------- Reenable disabled tools Commit: 53c51d53699cfa25603dd7c46f8fa289eecc97c6 https://github.com/galaxyproject/usegalaxy-playbook/commit/53c51d53699cfa25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- Updated Main (a while ago, forgot to commit) Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1e7c06ad0d53...…

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