- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/54b9b09fb2d2...fa7f2a4f5c18 **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.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/4a2814227cd7...809ae58c52ed **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.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/9a13a4af7fe4...8a1616aaf816 **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.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/dad5563cac85...482f1ea35971 **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.

1 0

[galaxyproject/galaxy] 814c7f: Drop unused peek method (this used unencoded ids)
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Compare: https://github.com/galaxyproject/galaxy/compare/2207e7f8aa20...f3ba9e2b9e92 **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.

1 0

[galaxyproject/galaxy] ff6526: Add 6789
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: ff65263ab2ee1351bbed11709d8536de694a5776 https://github.com/galaxyproject/galaxy/commit/ff65263ab2ee1351bbed11709d85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6789 **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.

1 0

[galaxyproject/galaxy] c51178: Four more PRs
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: c51178578dcf67c8dbe16d3d8320f660e0c80027 https://github.com/galaxyproject/galaxy/commit/c51178578dcf67c8dbe16d3d8320… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more PRs **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.

1 0

[galaxyproject/galaxy] b0dff4: allow making all datasets within history public, w...
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b0dff4444085668cc3359b73d9d4d13b6da74cf6 https://github.com/galaxyproject/galaxy/commit/b0dff4444085668cc3359b73d9d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- allow making all datasets within history public, when sharing this is a one-off operation so notable behavior is that if you create a new dataset in the shared history, it still won't be public when there are default permissions set on history Commit: e4399021520440a8f58e33dbae161f031f8da9eb https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/web/base/controller.py Log Message: ----------- show warning to user if some of the items within were not published Commit: 29a3b6bbfbde469e59f6a896dc8a4f76a8d3ea3d https://github.com/galaxyproject/galaxy/commit/29a3b6bbfbde469e59f6a896dc8a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6793 from martenson/fix-sharing-by-link [18.09] allow making all datasets within history public, when sharing Compare: https://github.com/galaxyproject/galaxy/compare/5a98515df88b...29a3b6bbfbde **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.

1 0

[galaxyproject/galaxy] 53b062: Add bam upload test
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 53b062f804c6d495b187656c84597f953210a2b0 https://github.com/galaxyproject/galaxy/commit/53b062f804c6d495b187656c8459… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Add bam upload test `test_upload_bam_file` fails on release_18.09 but passes on 18.05. Commit: 57fe3a741a9c3ac9c09513e21d44984ba046322e https://github.com/galaxyproject/galaxy/commit/57fe3a741a9c3ac9c09513e21d44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata spontaneuosly reverting Similar to https://github.com/galaxyproject/galaxy/pull/6631/files. This fixes https://github.com/galaxyproject/galaxy/issues/6769 Commit: 70e325574cb82be62b1be8090e714ce44441686b https://github.com/galaxyproject/galaxy/commit/70e325574cb82be62b1be8090e71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use with statement for all file uploads Commit: 5a98515df88b68483ad59bb7208a57f1a7f71664 https://github.com/galaxyproject/galaxy/commit/5a98515df88b68483ad59bb7208a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6789 from mvdbeek/fix_bam_upload [18.09] Fix bam upload resulting in 'auto' datatype Compare: https://github.com/galaxyproject/galaxy/compare/c5a325d01535...5a98515df88b **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.

1 0

[galaxyproject/usegalaxy-playbook] 12f035: Main: mutable configs for Gemini install
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 12f035accb4d027ae548f415bdc89e1c07374a8f https://github.com/galaxyproject/usegalaxy-playbook/commit/12f035accb4d027a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_data_manager_conf.xml Log Message: ----------- Main: mutable configs for Gemini install **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.

1 0

[galaxyproject/usegalaxy-playbook] ed2d7a: Stop attempting to load broken and unusable report...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ed2d7a112cefff46a01de39152153a6726f8d994 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed2d7a112cefff46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxywebservers.yml M env/test/files/nginx/tacc-protected/index.html M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/nginx/tacc_protected.j2 Log Message: ----------- Stop attempting to load broken and unusable reports, remove most references. Commit: 8fdf33572ac1880c6e8a996aba55be25380307c7 https://github.com/galaxyproject/usegalaxy-playbook/commit/8fdf33572ac1880c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M README.md M env/common/backup.yml M env/common/config.yml A env/common/group_vars/pulsargalaxyservers.yml A env/common/host_vars/br005.bridges.psc.edu.yml A env/common/host_vars/jetstream-iu0.galaxyproject.org.yml A env/common/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/common/host_vars/login2.stampede2.tacc.utexas.edu.yml M env/common/templates/supervisor/galaxy_impersonate.j2 M env/common/templates/supervisor/galaxy_reports.j2 M env/common/update.yml M env/main/group_vars/all.yml M env/main/group_vars/galaxyservers/vars.yml A env/main/group_vars/pulsargalaxyservers.yml M env/main/group_vars/pulsarservers/vars.yml A env/main/host_vars/br005.bridges.psc.edu.yml R env/main/host_vars/br005.bridges.psc.edu.yml A env/main/host_vars/jetstream-iu0.galaxyproject.org.yml R env/main/host_vars/jetstream-iu0.galaxyproject.org.yml A env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml R env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/main/host_vars/login2.stampede2.tacc.utexas.edu.yml R env/main/host_vars/login2.stampede2.tacc.utexas.edu.yml A env/test/group_vars/pulsargalaxyservers.yml M env/test/group_vars/pulsarservers/vars.yml A env/test/host_vars/br005.bridges.psc.edu.yml R env/test/host_vars/br005.bridges.psc.edu.yml A env/test/host_vars/jetstream-iu0.galaxyproject.org.yml R env/test/host_vars/jetstream-iu0.galaxyproject.org.yml A env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml R env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml R env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml Log Message: ----------- Main: - Move Galaxy to /pylon5 and Pulsar persistence dir to /home on Bridges - Deduplicate host vars - Get rid of instance_root and shared_root Commit: ca624a917495743923e16f08fd3bf17303ecf541 https://github.com/galaxyproject/usegalaxy-playbook/commit/ca624a9174957439… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/group_vars/pulsarservers/vars.yml Log Message: ----------- Set pulsar_port for Main pulsar on Jetstream Commit: ad1c1c7c3d759d0a6739e162a76097e77bff58df https://github.com/galaxyproject/usegalaxy-playbook/commit/ad1c1c7c3d759d0a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Main: update job_conf.xml for Bridges dir move Commit: 9c0270c4ddd43132dd0a024f881f99c4668393a9 https://github.com/galaxyproject/usegalaxy-playbook/commit/9c0270c4ddd43132… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove erroneous space that caused a YAML parsing error Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/97b3bb137b92...… **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.

1 0

[galaxyproject/usegalaxy-playbook] 97b3bb: Upgrade dexseq to 1.24
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 97b3bb137b92eb02fa97ebd46fbf1eb39893371b https://github.com/galaxyproject/usegalaxy-playbook/commit/97b3bb137b92eb02… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgrade dexseq to 1.24 **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.

1 0

[galaxyproject/galaxy] 34bc18: Add PB and EB to util.size_to_bytes, reorder match...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 34bc18025bfd63a916ff748fdfce98a139c1c2dd https://github.com/galaxyproject/galaxy/commit/34bc18025bfd63a916ff748fdfce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add PB and EB to util.size_to_bytes, reorder match check so that the sizes more likely to be encountered are first. Commit: 3cd71b4864d2148e7bcdd18b7e12964ad409254a https://github.com/galaxyproject/galaxy/commit/3cd71b4864d2148e7bcdd18b7e12… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #6786 from natefoo/more-size-to-bytes Add PB and EB to util.size_to_bytes Compare: https://github.com/galaxyproject/galaxy/compare/5a9cdfe82694...3cd71b4864d2 **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.

1 0

[galaxyproject/usegalaxy-playbook] 270ee3: Add .yml extension to stampede2 host file
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 270ee3ee36a49da066dfd3f8c00edd99d908e802 https://github.com/galaxyproject/usegalaxy-playbook/commit/270ee3ee36a49da0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: R env/test/host_vars/login2.stampede2.tacc.utexas.edu A env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml Log Message: ----------- Add .yml extension to stampede2 host file Commit: a236263404a0e65505b29b7ed8109aa1fd2aad97 https://github.com/galaxyproject/usegalaxy-playbook/commit/a236263404a0e655… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/common/templates/supervisor/galaxy_datamanager.j2 M env/test/group_vars/all.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/pulsarservers/vars.yml M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml Log Message: ----------- Test: - Stop using the confusing/limiting `shared_root` and `instance_root`. - Move Pular's state directory on Bridges to /home and move the Galaxy clone to /pylon5. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ede6eea39c12...… **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.

1 0

[galaxyproject/usegalaxy-playbook] ede6ee: Changelog update for DESeq2 deps
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ede6eea39c12c658f52335bac9acc8071bf93e39 https://github.com/galaxyproject/usegalaxy-playbook/commit/ede6eea39c12c658… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M CHANGELOG.md Log Message: ----------- Changelog update for DESeq2 deps **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.

1 0

[galaxyproject/galaxy] e9e2b6: Minor reminders that would have been nice (for me, ...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9e2b6d9e22a141d6af1e47c2b77c0544f00b1ea https://github.com/galaxyproject/galaxy/commit/e9e2b6d9e22a141d6af1e47c2b77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Minor reminders that would have been nice (for me, at least) to have on the release scaffold. Commit: 5a9cdfe82694a5bb6be0eedce6502229779dd283 https://github.com/galaxyproject/galaxy/commit/5a9cdfe82694a5bb6be0eedce650… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6778 from dannon/minor_rn_reminders Release issue scaffold tweaks Compare: https://github.com/galaxyproject/galaxy/compare/872b6f57ed7c...5a9cdfe82694 **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.

1 0

[galaxyproject/galaxy] becb92: Strip all control characters from rules
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: becb922dc1e8c2d48e03a2badcb940ab1661e247 https://github.com/galaxyproject/galaxy/commit/becb922dc1e8c2d48e03a2badcb9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Strip all control characters from rules Similar to 366701cfb23d8de31eac3c4312c6accca2e74ef1, which is valid on its own, but here we just apply it to all rules. Commit: c5a325d01535d9b46e28165c531a119d5f51b2d6 https://github.com/galaxyproject/galaxy/commit/c5a325d01535d9b46e28165c531a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Merge pull request #6785 from mvdbeek/escape_all_rules [18.09] Strip all control characters from rules Compare: https://github.com/galaxyproject/galaxy/compare/f54cba043354...c5a325d01535 **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.

1 0

[galaxyproject/galaxy] bf0370: Fix __encode_invocation signature and passthrough ...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: bf0370c1929def91bc69e1ab252dc0e8bfc2a387 https://github.com/galaxyproject/galaxy/commit/bf0370c1929def91bc69e1ab252d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix __encode_invocation signature and passthrough to manager that I busted in merging 18.05 forward Commit: da3b6a1566dc0bb2665b2781cdb3c76551d68613 https://github.com/galaxyproject/galaxy/commit/da3b6a1566dc0bb2665b2781cdb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- encode_invocation defers to manager and doesn't require trans passing anymore Commit: f54cba043354aa8fac339052462f7302613ca24a https://github.com/galaxyproject/galaxy/commit/f54cba043354aa8fac339052462f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6782 from dannon/fix-bad-workflow-invocation-merge [18.09] Fix __encode_invocation signature Compare: https://github.com/galaxyproject/galaxy/compare/b44379c3d9da...f54cba043354 **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.

1 0

[galaxyproject/usegalaxy-playbook] 3a5012: Test: Move Galaxy from /home to /pylon5 on Bridges...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3a5012154ba4a3c759bb0b2da1dfcd96b59a7c5f https://github.com/galaxyproject/usegalaxy-playbook/commit/3a5012154ba4a3c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Test: Move Galaxy from /home to /pylon5 on Bridges now that there is no quota on /pylon5 (and there is one on /home) **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.

1 0

[galaxyproject/galaxy] 0743c7: All extracted datasets should be visible
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 0743c7ba04fa6e61e2c48386a49a61f41d1eb493 https://github.com/galaxyproject/galaxy/commit/0743c7ba04fa6e61e2c48386a49a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- All extracted datasets should be visible Commit: b44379c3d9da4b7916b3c5a4fdf5eff39ee2267d https://github.com/galaxyproject/galaxy/commit/b44379c3d9da4b7916b3c5a4fdf5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6780 from mvdbeek/visible_extracted_datasets [18.09] All extracted datasets should be visible Compare: https://github.com/galaxyproject/galaxy/compare/04d2d2ef4672...b44379c3d9da **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.

1 0

[galaxyproject/galaxy] a18db4: Warn job runner plugin writers not to emulate cond...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a18db4513ad9e3f7b2d08e70ffc4d810137c2480 https://github.com/galaxyproject/galaxy/commit/a18db4513ad9e3f7b2d08e70ffc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Warn job runner plugin writers not to emulate condor.py. Better to write a CLI plugin I think (https://github.com/galaxyproject/galaxy/pull/6751#issuecomment-425079201) Commit: 872b6f57ed7c588b8ae58891253a1a584cd98952 https://github.com/galaxyproject/galaxy/commit/872b6f57ed7c588b8ae58891253a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #6783 from jmchilton/drm_cli_warn Warn job runner plugin writers not to emulate condor.py. Compare: https://github.com/galaxyproject/galaxy/compare/7787d3ae8e3f...872b6f57ed7c **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.

1 0

[galaxyproject/galaxy] 6cb4c3: Add 6768
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 6cb4c32eb4e613b4d90680450d11804779e5b4a5 https://github.com/galaxyproject/galaxy/commit/6cb4c32eb4e613b4d90680450d11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6768 Commit: ee47fdb50cef70dd2b940c42594611863e51bde7 https://github.com/galaxyproject/galaxy/commit/ee47fdb50cef70dd2b940c425946… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6753, 6771 Compare: https://github.com/galaxyproject/galaxy/compare/d3db21fa82a8...ee47fdb50cef **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.

1 0

[galaxyproject/galaxy] 384a16: Allow schema to validate
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Commit: 2209c3171de52dbe83683d2644b0ec6befbaa763 https://github.com/galaxyproject/galaxy/commit/2209c3171de52dbe83683d2644b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor cleanup. Commit: 037ddfeab5decd47d4d2bd8771e975dc1857703a https://github.com/galaxyproject/galaxy/commit/037ddfeab5decd47d4d2bd8771e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Fix active content setting for views with explicitly defined models Commit: 96593cb444063d6cc6819dd77d7b2fb89c250054 https://github.com/galaxyproject/galaxy/commit/96593cb444063d6cc6819dd77d7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Import cleanup and documentation for dataset-li-edit. Commit: 11b5157825ee318b763f6c48b674b968f114aebb https://github.com/galaxyproject/galaxy/commit/11b5157825ee318b763f6c48b674… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use standard faIconButton for visualize. Commit: 806beaca9b4b51322214e68619407e8a0545a19d https://github.com/galaxyproject/galaxy/commit/806beaca9b4b51322214e6861940… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: c8552970dd7c2eeb9d765911843ed3e866b84ce3 https://github.com/galaxyproject/galaxy/commit/c8552970dd7c2eeb9d765911843e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 94082a878dca784eb57c6be1fd552a63f85bcfad https://github.com/galaxyproject/galaxy/commit/94082a878dca784eb57c6be1fd55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: 3ea9d086bfe295a210d6f249ef2c39d8a65ef042 https://github.com/galaxyproject/galaxy/commit/3ea9d086bfe295a210d6f249ef2c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: f6f526a0a50a98143d4845f8907067b6f42e1dea https://github.com/galaxyproject/galaxy/commit/f6f526a0a50a98143d4845f89070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 3017568e77cf950b8b611a16ea7ce9fcc2159e81 https://github.com/galaxyproject/galaxy/commit/3017568e77cf950b8b611a16ea7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test Commit: 4aa2b8f919f28b798ba9a2401c602990287338b6 https://github.com/galaxyproject/galaxy/commit/4aa2b8f919f28b798ba9a2401c60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Disentangle this/self/frames in scratchbook's events. Commit: 077f3088ece5c8617b044d53764aebff1768b34f https://github.com/galaxyproject/galaxy/commit/077f3088ece5c8617b044d53764a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Correct visualization link to use router or scratchbook as appropriate. Commit: 3f29d32898efd121f315b2147e917584e9dec28f https://github.com/galaxyproject/galaxy/commit/3f29d32898efd121f315b2147e91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Strip unused function, cleanup. Commit: 0018ab989b117c953dd2b02e1e06cc80af1ddff2 https://github.com/galaxyproject/galaxy/commit/0018ab989b117c953dd2b02e1e06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Add event hook for non-bb-view center panel id setting, use it for dataset visualization. Commit: d17ea03442448472f1e5e5d4e12e73459f1736e7 https://github.com/galaxyproject/galaxy/commit/d17ea03442448472f1e5e5d4e12e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor formatting tweaks. Commit: 87ecf1428e841bced376e504d1d468319a7853c9 https://github.com/galaxyproject/galaxy/commit/87ecf1428e841bced376e504d1d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use pre-fetched dataset id Commit: b5e221929687809adfb30cad8280767f3a8412c5 https://github.com/galaxyproject/galaxy/commit/b5e221929687809adfb30cad8280… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Fix page editor height for flex panels. Commit: f65e616c1afe6d9ec0bb9680fa90ee8e9d311900 https://github.com/galaxyproject/galaxy/commit/f65e616c1afe6d9ec0bb9680fa90… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Use mapped-over collectionType when inferring collectionType through format_source Commit: 02c177152bd7dbef02d4ea5d40449745e913b38b https://github.com/galaxyproject/galaxy/commit/02c177152bd7dbef02d4ea5d4044… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes [18.05] Backport tool version select fixes Commit: 3ffbf5b4b6138177ed7581d7845432bec138ee23 https://github.com/galaxyproject/galaxy/commit/3ffbf5b4b6138177ed7581d78454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Append mapped-over collection type to output collection type So if for instance the connected input is a regular input with a list:list input and the output is a paired collection we set the output collection type to list:list:paired. Commit: eb37ad3752f5dbe4806e74f85b4fcee63ab407fa https://github.com/galaxyproject/galaxy/commit/eb37ad3752f5dbe4806e74f85b4f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Only reset the right hand side of a connection on disconnect Commit: 30728899054dde65ddd9fe99dc8424166ee0c5ad https://github.com/galaxyproject/galaxy/commit/30728899054dde65ddd9fe99dc84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 287648f5d9f95ccd1b625037e30de0ab3e62e7f5 https://github.com/galaxyproject/galaxy/commit/287648f5d9f95ccd1b625037e30d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Merge pull request #6725 from dannon/fix_active_highlight [18.09] Fix active highlight Commit: 9b5045a05c882c652935d9daaf589a10d776190c https://github.com/galaxyproject/galaxy/commit/9b5045a05c882c652935d9daaf58… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6747 from dannon/fix_page_editor_height [18.09] Fix page editor height for flex panels. Commit: 7eac08979b1f474254e9a6a0b2005d365e09c143 https://github.com/galaxyproject/galaxy/commit/7eac08979b1f474254e9a6a0b200… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Undo auto-propagation of group tags. @mvdbeek and I discussed this in the Galaxy project gitter a few weeks ago and decided the propagation is too aggressive and should likely be done manually at the end of a workflow for now - using for instance the set tags collection operation tool. Commit: f3298953d41cb0e2b37812242a88d226a890e8aa https://github.com/galaxyproject/galaxy/commit/f3298953d41cb0e2b37812242a88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't skip build on release/master moving forward. Commit: bd5d12049b238c4475f267fbbf63bd3a124b0a58 https://github.com/galaxyproject/galaxy/commit/bd5d12049b238c4475f267fbbf63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Swap nodeenv to a pinned requirement. Commit: 4d6d984fbd8d66b30c7da3cd5022903f11218b09 https://github.com/galaxyproject/galaxy/commit/4d6d984fbd8d66b30c7da3cd5022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/README.md Log Message: ----------- Update client/README Commit: 3f8c2beff252587cd1347142ab84ad20afd57b03 https://github.com/galaxyproject/galaxy/commit/3f8c2beff252587cd1347142ab84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Swap to a production w/ sourcemaps build by default for autobuilder (though, of course, folks can manually do whatever -- seems like the most sensible default though) Commit: 0fb115e046b3a492db6b592d8b38459104d696bf https://github.com/galaxyproject/galaxy/commit/0fb115e046b3a492db6b592d8b38… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6750 from jmchilton/1809_tags_walkback [18.09] Undo auto-propagation of group tags. Commit: e10180dea108785a017b7be37b7ff5d85a2eebf1 https://github.com/galaxyproject/galaxy/commit/e10180dea108785a017b7be37b7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- (minor) client-format Commit: 8a4fe72f6710270ca453b75d61e8dbc96feadcc5 https://github.com/galaxyproject/galaxy/commit/8a4fe72f6710270ca453b75d61e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'collection_type_source_followup' into release_18.09 Commit: 679603b7c9a2b1f8c136dcc29d2eb41174bd6b31 https://github.com/galaxyproject/galaxy/commit/679603b7c9a2b1f8c136dcc29d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok, so that it doesn't interrupt processing other jobs. That was discovered because attempting to delete purged job outputs on failure was raising ObjectNotFound since dataset object store assignment is done later now. So also, catch that ObjectNotFound. Commit: 1a19043789498f1d45725840b0761939d5dad2a5 https://github.com/galaxyproject/galaxy/commit/1a19043789498f1d45725840b076… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add graph DOT datatype Commit: 8d025aa4ed75f63924d9e11f9d0c65ca3aca7be0 https://github.com/galaxyproject/galaxy/commit/8d025aa4ed75f63924d9e11f9d0c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- add graph_dot datatype to graphvis Commit: ac65832cb5e4fa7a3e57af3722a09c7dfa4ac2ea https://github.com/galaxyproject/galaxy/commit/ac65832cb5e4fa7a3e57af3722a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- Merge pull request #6760 from bgruening/graph_dot [18.09] Add graph dot datatype and enable it in visualisations Commit: 611764b81a761c034bfd040b76818187a555807e https://github.com/galaxyproject/galaxy/commit/611764b81a761c034bfd040b7681… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Remove cruft releated to upgrading from 17.05 Galaxies. These interact poorly with recent changes in 18.09 and in nearly all cases should no longer be needed at this point. Commit: ea7359b08b21a9e0febe6cd98a9fd4488c133546 https://github.com/galaxyproject/galaxy/commit/ea7359b08b21a9e0febe6cd98a9f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6761 from jmchilton/remove_upgrade_cruft [18.09] Remove upgrade cruft related to datatypes. Commit: de6dc00236ad2947d3bef479b5d7df5c3bef7ba4 https://github.com/galaxyproject/galaxy/commit/de6dc00236ad2947d3bef479b5d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Commit: a0ad5adf6fc02c6a0864308f8d6f8a612a83f308 https://github.com/galaxyproject/galaxy/commit/a0ad5adf6fc02c6a0864308f8d6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Increase the maximum number of stderr lines that will be scanned for slurm warnings to strip to 3. Commit: a89184aa707a477f14905bd44b368006c7cae427 https://github.com/galaxyproject/galaxy/commit/a89184aa707a477f14905bd44b36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6766 from natefoo/remove-more-slurm-warnings [18.09] Increase the maximum number of stderr lines that will be scanned for slurm warnings Commit: 529ed61c3b48e2d8a830e6a890d93b16a4f42ea4 https://github.com/galaxyproject/galaxy/commit/529ed61c3b48e2d8a830e6a890d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6765 from natefoo/job-stdout-none-fix [18.09] Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Commit: 9f688b2f9141683e02ea9aa759a15ebd46174042 https://github.com/galaxyproject/galaxy/commit/9f688b2f9141683e02ea9aa759a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6755 from natefoo/job-object-store-fixes [18.09] Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok Commit: 300d316ad1bcd0ec1a7b762e859232bbe8c9548c https://github.com/galaxyproject/galaxy/commit/300d316ad1bcd0ec1a7b762e8592… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Resilience of success message handling Commit: 46dd1801cbc11cb24bb7fdd0d8a4f8e71fa9ef9e https://github.com/galaxyproject/galaxy/commit/46dd1801cbc11cb24bb7fdd0d8a4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #6768 from martenson/backport_resilience_of_success_message_handling [18.09] backport of: Resilience of success message handling Commit: 2d9b803025828869c50a70db25fb7654caa17368 https://github.com/galaxyproject/galaxy/commit/2d9b803025828869c50a70db25fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Use UserRoleAssociation to get private roles If I understand this correctly this should work even if the user email changes. Commit: 5a97e4fcea77426eab0a7ca22402cdf8b638f79b https://github.com/galaxyproject/galaxy/commit/5a97e4fcea77426eab0a7ca22402… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #6771 from mvdbeek/fix_private_role_none [18.05] Use UserRoleAssociation to get private roles Commit: eb1980ec087d7a2c3da6d138155f6c11895a8b26 https://github.com/galaxyproject/galaxy/commit/eb1980ec087d7a2c3da6d138155f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/README.md M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #6753 from dannon/client-build-startup-changes [18.09] Client build startup changes Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Commit: cf62a1dafd90df9b65f811bed74d1d173542babc https://github.com/galaxyproject/galaxy/commit/cf62a1dafd90df9b65f811bed74d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: c3d4be2e2cb1ccbdfc68ea14ebf3fb71bdec2e97 https://github.com/galaxyproject/galaxy/commit/c3d4be2e2cb1ccbdfc68ea14ebf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 04d2d2ef4672d3ee5f24d7dffe68a7f24238a7f0 https://github.com/galaxyproject/galaxy/commit/04d2d2ef4672d3ee5f24d7dffe68… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6772 from dannon/release_18.09 [18.09] Merge forward from 18.01, 18.05 Commit: 7787d3ae8e3fb9a69c4a5bab129051e59e104b2a https://github.com/galaxyproject/galaxy/commit/7787d3ae8e3fb9a69c4a5bab1290… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/README.md M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/datatypes_conf.xml.sample M config/plugins/visualizations/graphviz/config/graphviz.xml M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/common_startup.sh M templates/webapps/galaxy/page/editor.mako M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cb5b054aa0c9...7787d3ae8e3f **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.

1 0

[galaxyproject/galaxy] 384a16: Allow schema to validate
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Commit: 2d9b803025828869c50a70db25fb7654caa17368 https://github.com/galaxyproject/galaxy/commit/2d9b803025828869c50a70db25fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Use UserRoleAssociation to get private roles If I understand this correctly this should work even if the user email changes. Commit: 5a97e4fcea77426eab0a7ca22402cdf8b638f79b https://github.com/galaxyproject/galaxy/commit/5a97e4fcea77426eab0a7ca22402… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #6771 from mvdbeek/fix_private_role_none [18.05] Use UserRoleAssociation to get private roles Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Commit: cf62a1dafd90df9b65f811bed74d1d173542babc https://github.com/galaxyproject/galaxy/commit/cf62a1dafd90df9b65f811bed74d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: c3d4be2e2cb1ccbdfc68ea14ebf3fb71bdec2e97 https://github.com/galaxyproject/galaxy/commit/c3d4be2e2cb1ccbdfc68ea14ebf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 04d2d2ef4672d3ee5f24d7dffe68a7f24238a7f0 https://github.com/galaxyproject/galaxy/commit/04d2d2ef4672d3ee5f24d7dffe68… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6772 from dannon/release_18.09 [18.09] Merge forward from 18.01, 18.05 Compare: https://github.com/galaxyproject/galaxy/compare/eb1980ec087d...04d2d2ef4672 **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.

1 0

[galaxyproject/galaxy] 384a16: Allow schema to validate
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Commit: cf62a1dafd90df9b65f811bed74d1d173542babc https://github.com/galaxyproject/galaxy/commit/cf62a1dafd90df9b65f811bed74d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/5a97e4fcea77...cf62a1dafd90 **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.

1 0