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

[galaxyproject/usegalaxy-playbook] 2e50f6: It's annual cert update day
by GitHub 18 Oct '18

18 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 18 Oct '18

18 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 18 Oct '18

18 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 17 Oct '18

17 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 17 Oct '18

17 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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[galaxyproject/galaxy] 429c29: History name not escaped
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 429c29a67166e0718776aee63ee709c60b6130bf https://github.com/galaxyproject/galaxy/commit/429c29a67166e0718776aee63ee7… Author: almahmoud <amahmou4(a)jhu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- History name not escaped Commit: f4088c89a0b110a648fe8f504ff4f26669c63613 https://github.com/galaxyproject/galaxy/commit/f4088c89a0b110a648fe8f504ff4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #6871 from almahmoud/rename-bug History name not escaped Compare: https://github.com/galaxyproject/galaxy/compare/fb0f792f8d50...f4088c89a0b1 **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] a60f5f: Indicate language in client docs to enable syntax ...
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a60f5f6a89bc8139d2f72534f6819bcbcb9cfcc4 https://github.com/galaxyproject/galaxy/commit/a60f5f6a89bc8139d2f72534f681… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md Log Message: ----------- Indicate language in client docs to enable syntax highlighting. Enables syntax highlighting for code blocks in .md files. Commit: 39654146723109d11b33f24c93581feeb36327db https://github.com/galaxyproject/galaxy/commit/39654146723109d11b33f24c9358… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md Log Message: ----------- Minor updates to client dir: indicate language, add/update readme. 1. Add 'vue' as language to .md files in client/galaxy/docs. 2. Add README.md to docs directory. 3. Update main client README.md (LESS >> Sass). Commit: fb0f792f8d50e81b3a2c8b6b9ff49252377c5114 https://github.com/galaxyproject/galaxy/commit/fb0f792f8d50e81b3a2c8b6b9ff4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md Log Message: ----------- Merge pull request #6848 from ic4f/dev Indicate language in client docs to enable syntax highlighting. Compare: https://github.com/galaxyproject/galaxy/compare/1e09f234e77c...fb0f792f8d50 **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] 67ee35: Use small button for editable text fields in histo...
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67ee35874e65e5d2bc40caa7fd3cf143bce084c5 https://github.com/galaxyproject/galaxy/commit/67ee35874e65e5d2bc40caa7fd3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/ui/editable-text.js Log Message: ----------- Use small button for editable text fields in history annotation Commit: 23541fcf2ccc87c22c5529020031f7a5cacfe100 https://github.com/galaxyproject/galaxy/commit/23541fcf2ccc87c22c5529020031… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/ui/editable-text.js Log Message: ----------- Float annotation button to the right Commit: 1e09f234e77cbca06c91dde4c1fc3af483ee6f1e https://github.com/galaxyproject/galaxy/commit/1e09f234e77cbca06c91dde4c1fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/ui/editable-text.js Log Message: ----------- Merge pull request #6878 from guerler/fix_annotation_button Use small button for editable text fields in history annotation Compare: https://github.com/galaxyproject/galaxy/compare/168032ffc82d...1e09f234e77c **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] 4bd6d7: Add fix for rule editor element
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4bd6d71ed71643a9f28db9e41a6cf43e1af9a942 https://github.com/galaxyproject/galaxy/commit/4bd6d71ed71643a9f28db9e41a6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Add fix for rule editor element Commit: da6c452a9d57ca81594c3c9966bfee19aa4bd01e https://github.com/galaxyproject/galaxy/commit/da6c452a9d57ca81594c3c9966bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Left align rule editor button Commit: 168032ffc82d0b19f07cbc101ad8d9273daa3d59 https://github.com/galaxyproject/galaxy/commit/168032ffc82d0b19f07cbc101ad8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6874 from guerler/fix_rules_editor Fix rule editor element alignment Compare: https://github.com/galaxyproject/galaxy/compare/d144523f7c29...168032ffc82d **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] 8edb74: Keep xlsx files compressed
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8edb7499c8d336d727fa751a2097d0356cf5bcbe https://github.com/galaxyproject/galaxy/commit/8edb7499c8d336d727fa751a2097… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Keep xlsx files compressed Fixes https://github.com/galaxyproject/galaxy/issues/6849 Commit: 0c7cc50e73827ac65eabf10400c90a644a15f10b https://github.com/galaxyproject/galaxy/commit/0c7cc50e73827ac65eabf10400c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Only warn about multi-file zips if we don't keep the compressed archive Commit: 03073ed1249d2403994013d9f4486f85d7a23e80 https://github.com/galaxyproject/galaxy/commit/03073ed1249d2403994013d9f448… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Merge pull request #6867 from mvdbeek/fix_xlsx_unpacking [18.09] Keep xlsx files compressed Commit: b9a01761b03e4ad4c06e86a1250c2f33e62ae0be https://github.com/galaxyproject/galaxy/commit/b9a01761b03e4ad4c06e86a1250c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Do not traceback when uploading a TS repo with no changes Fix the following traceback when executing `planemo shed_update`: ``` galaxy.web.framework.decorators ERROR 2018-10-15 18:07:38,736 [p:30249,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 154, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/tool_shed/api/repositories.py", line 1116, in create_changeset_revision new_repo_alert File "lib/tool_shed/util/repository_content_util.py", line 64, in upload_tar undesirable_files_removed) File "lib/tool_shed/util/commit_util.py", line 225, in handle_directory_changes message=commit_message) File "lib/tool_shed/util/hg_util.py", line 65, in commit_changeset raise Exception(error_message) Exception: Error committing '/opt/galaxy/database/community_files/000/repo_1' to repository: Command '['hg', 'commit', '-u', u'earlhaminst', '-m', u'planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 22231ebc4e5e990c61243a3609b3347cf63fa024', '/opt/galaxy/database/community_files/000/repo_1']' returned non-zero exit status 1 Output was: nothing changed 127.0.0.1 - - [15/Oct/2018:18:07:38 +0100] "POST /api/repositories/adb5f5c93f827949/changeset_revision HTTP/1.1" 500 - "-" "python-requests/2.18.4" ``` Commit: d4e2f6d59e15bc06b35824201be30e95209596fb https://github.com/galaxyproject/galaxy/commit/d4e2f6d59e15bc06b35824201be3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #6875 from nsoranzo/release_18.09_fix_commit_changeset [18.09] Do not traceback when uploading a TS repo with no changes Commit: d144523f7c29ae03e48045fd1cff47b0efc50305 https://github.com/galaxyproject/galaxy/commit/d144523f7c29ae03e48045fd1cff… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/519b994d40ef...d144523f7c29 **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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