- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 554b84: Fixes for Jenkins
by GitHub 18 Oct '18

18 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 554b84542637a868328d7d025977b47dc247b917 https://github.com/galaxyproject/infrastructure-playbook/commit/554b8454263… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M env/galaxy/files/jenkins/jenkins_server_user_ssh_config M env/galaxy/group_vars/jenkinsslaves/vars.yml Log Message: ----------- Fixes for Jenkins **NOTE:** This service has 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] d2c78c: Add n1, n2, n5 jenkins workers
by GitHub 18 Oct '18

18 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d2c78c3bc617d0c3940eaf0ad1ab54c795ccaa84 https://github.com/galaxyproject/infrastructure-playbook/commit/d2c78c3bc61… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M common_roles M env/galaxy/inventory Log Message: ----------- Add n1,n2,n5 jenkins workers **NOTE:** This service has 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] e66da3: Use hasattr instead of relying on value
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e66da36f60c0d1d2b43fe1a5bd9cdf7da7ddc697 https://github.com/galaxyproject/galaxy/commit/e66da36f60c0d1d2b43fe1a5bd9c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use hasattr instead of relying on value Commit: 81f31d1a29e1b1021f7629008d433797b9367267 https://github.com/galaxyproject/galaxy/commit/81f31d1a29e1b1021f7629008d43… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6884 from guerler/fix_accessible_links Improve resilience on handling sharing attributes Compare: https://github.com/galaxyproject/galaxy/compare/af05cb480b1c...81f31d1a29e1 **NOTE:** This service has 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] 973514: add discovered tool vulnerabilities to RN
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9735146f2848beca367ac84c066d10a4b5008a25 https://github.com/galaxyproject/galaxy/commit/9735146f2848beca367ac84c066d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- add discovered tool vulnerabilities to RN Commit: fa212c3c31b78f885b7aff2681430bc9e54fec89 https://github.com/galaxyproject/galaxy/commit/fa212c3c31b78f885b7aff268143… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- specify which gemini tools were fixed Commit: 0aca12ce96f0c2a860453a15022bbd5e693493ed https://github.com/galaxyproject/galaxy/commit/0aca12ce96f0c2a860453a15022b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6892 from martenson/security-notes [18.09] add discovered tool vulnerabilities to RN Compare: https://github.com/galaxyproject/galaxy/compare/89fbe9c9344d...0aca12ce96f0 **NOTE:** This service has 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] ee4365: It's annual cert update day
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ee4365f8a3e71646b6af91e9e5fe51095f5f2a1b https://github.com/galaxyproject/infrastructure-playbook/commit/ee4365f8a3e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M env/common/files/ssl/athena.galaxyproject.org_cert.pem M env/common/files/ssl/status.galaxyproject.org_cert.pem M env/common/files/ssl/wildcard_cert.pem M env/common/group_vars/sslservers/vault.yml Log Message: ----------- It's annual cert update day **NOTE:** This service has 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] 2e50f6: It's annual cert update day
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2e50f6845a814a8b59ce9252b50ad3fcd19eb07e https://github.com/galaxyproject/usegalaxy-playbook/commit/2e50f6845a814a8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M env/common/files/ssl/radegast.galaxyproject.org_cert.pem M env/common/files/ssl/usegalaxy.org_cert.pem M env/common/files/ssl/wildcard_cert.pem M env/common/group_vars/sslservers/vault.yml Log Message: ----------- It's annual cert update day **NOTE:** This service has 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] 222225: Fix selenium test selectors for alert messages
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 222225d3b017b4af457eb5c59248145899bc01ef https://github.com/galaxyproject/galaxy/commit/222225d3b017b4af457eb5c59248… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix selenium test selectors for alert messages Commit: 47ad50e1d7738e443c96226f6abe5475c83ef32e https://github.com/galaxyproject/galaxy/commit/47ad50e1d7738e443c96226f6abe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M templates/user/register.mako Log Message: ----------- Align legacy registration mako Commit: d29e3fc3bed92f856d140241fc0807f7283eea5f https://github.com/galaxyproject/galaxy/commit/d29e3fc3bed92f856d140241fc08… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M templates/user/info.mako Log Message: ----------- Align legacy user info template Commit: e5186a811032a2c4e8f52865588a0d9033365768 https://github.com/galaxyproject/galaxy/commit/e5186a811032a2c4e8f52865588a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Align legacy history sharing mako Commit: af05cb480b1c49b4cac560cfc086e9638ab7fb1b https://github.com/galaxyproject/galaxy/commit/af05cb480b1c49b4cac560cfc086… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/history/share.mako M test/galaxy_selenium/navigation.yml Log Message: ----------- Merge pull request #6881 from guerler/fix_selenium Fix selenium test selectors for alert messages Compare: https://github.com/galaxyproject/galaxy/compare/fbe9e97f19d6...af05cb480b1c **NOTE:** This service has 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] d19eff: One last batch of PRs.
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: d19effdf3c042538ffa0ba1351a2f3433ad19fd1 https://github.com/galaxyproject/galaxy/commit/d19effdf3c042538ffa0ba1351a2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- One last batch of PRs. Commit: 89fbe9c9344d1e8ad88fe88a0685cf85aa1edcb3 https://github.com/galaxyproject/galaxy/commit/89fbe9c9344d1e8ad88fe88a0685… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6890 from dannon/18.09_release_notes_updates [18.09] One last batch of PRs added to RN Compare: https://github.com/galaxyproject/galaxy/compare/d4e2f6d59e15...89fbe9c9344d **NOTE:** This service has 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] 116ce0: Specify `GET` action for cloudauthz index.
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 116ce0ddf51654cfbb0923e7afc1ae5b035bd602 https://github.com/galaxyproject/galaxy/commit/116ce0ddf51654cfbb0923e7afc1… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Specify `GET` action for cloudauthz index. Commit: 612e6fc1cfb85e879f846cba90753a50182da5b4 https://github.com/galaxyproject/galaxy/commit/612e6fc1cfb85e879f846cba9075… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Specify `POST` action for cloudauthz create action. Commit: 83bfdf3c95a8ec7afe25b84867ade4f9dca4bd85 https://github.com/galaxyproject/galaxy/commit/83bfdf3c95a8ec7afe25b84867ad… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Unify `create` and `index` cloudauthz apis. Commit: aa20778e0f51b538af684c6b7fc2f39d998c0fb9 https://github.com/galaxyproject/galaxy/commit/aa20778e0f51b538af684c6b7fc2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- remove `/create` from cloudauthz create api docstring. Commit: 73f691e5b51249b71b5f21b1f0faeea102b1c725 https://github.com/galaxyproject/galaxy/commit/73f691e5b51249b71b5f21b1f0fa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- reword to reflect refactor Commit: fbe9e97f19d6f200cdac2548ae5c60e4b9687334 https://github.com/galaxyproject/galaxy/commit/fbe9e97f19d6f200cdac2548ae5c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6876 from VJalili/refactor_cloud_authz_api Specify POST and GET actions for cloudauthz API actions Compare: https://github.com/galaxyproject/galaxy/compare/2310a509b2af...fbe9e97f19d6 **NOTE:** This service has 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] f8c48b: Username filtering for published workflows
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8c48b83d2fadc8e4df008ce0f0e37f173a07b9d https://github.com/galaxyproject/galaxy/commit/f8c48b83d2fadc8e4df008ce0f0e… Author: almahmoud <amahmou4(a)jhu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Username filtering for published workflows Commit: 2310a509b2afdd1903a6a00c3df749b4884e66ab https://github.com/galaxyproject/galaxy/commit/2310a509b2afdd1903a6a00c3df7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Merge pull request #6882 from almahmoud/published_workflow_bug Username filtering for published workflows Compare: https://github.com/galaxyproject/galaxy/compare/f4088c89a0b1...2310a509b2af **NOTE:** This service has 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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