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

[galaxyproject/galaxy] 6a072a: Four more RN PRs.
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6a072ab29d842f79ea0ba46f0f0bc30aa43fd577 https://github.com/galaxyproject/galaxy/commit/6a072ab29d842f79ea0ba46f0f0b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more RN PRs. Commit: 5a71a744edeea3691b04cbd18680eadea90f78bc https://github.com/galaxyproject/galaxy/commit/5a71a744edeea3691b04cbd18680… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add client artifact note Commit: b6e716b289e36ec62cdada07e356552e1388f618 https://github.com/galaxyproject/galaxy/commit/b6e716b289e36ec62cdada07e356… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Correct javascript caps Commit: 17f4f7955f84830f87c21c0027d487a291da66c4 https://github.com/galaxyproject/galaxy/commit/17f4f7955f84830f87c21c0027d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- s/sources/artifacts Commit: 3263aba44a95e2a5e50e5050893628ba618fd306 https://github.com/galaxyproject/galaxy/commit/3263aba44a95e2a5e50e50508936… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add a warning to the 18.09 release notes informing admins that job handling will block until old `new` state jobs have been migrated to a terminal state. Commit: 43d978729593818c5abf2b9a09bd7cb2852f0ffd https://github.com/galaxyproject/galaxy/commit/43d978729593818c5abf2b9a09bd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6923 from dannon/18.09_final_notes [18.09] Final release notes updates Compare: https://github.com/galaxyproject/galaxy/compare/843474e5e375...43d978729593 **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] 280a8e: Update Test and Main
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 280a8e9fb4c53baa86c3e99949ac7b7d27c09335 https://github.com/galaxyproject/usegalaxy-playbook/commit/280a8e9fb4c53baa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test and Main **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] 949dcf: Do not log exceptions twice
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 949dcfdbc34331de7f0aa321e67e1255a7627306 https://github.com/galaxyproject/galaxy/commit/949dcfdbc34331de7f0aa321e67e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/cloud.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/readme_util.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M test/base/populators.py M tools/data_source/upload.py Log Message: ----------- Do not log exceptions twice `logging.exception()` already adds the the exception information after the supplied message. Also: the `message` attribute of `Exception` class has been dropped in Python 3, always use `str(e)`. xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 210cdc998a8f8929362d881bfaded32ac1e45aef https://github.com/galaxyproject/galaxy/commit/210cdc998a8f8929362d881bfade… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/cloud.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/readme_util.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M test/base/populators.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6916 from nsoranzo/fix_exception_logging Do not log exception info twice Compare: https://github.com/galaxyproject/galaxy/compare/2dcd126e82fc...210cdc998a8f **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] cd92dd: add isa-rwal to default pipfile
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd92dd2819ef3e789e0f25e9b1c99dcc8404d486 https://github.com/galaxyproject/galaxy/commit/cd92dd2819ef3e789e0f25e9b1c9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- add isa-rwal to default pipfile it is in pinned already Commit: 4a82c43270670d4d4cc7bd30e6301c4a3516f48c https://github.com/galaxyproject/galaxy/commit/4a82c43270670d4d4cc7bd30e630… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- make update-dependencies Commit: 2dcd126e82fc6db51c8ab9cacb39abd496504d51 https://github.com/galaxyproject/galaxy/commit/2dcd126e82fc6db51c8ab9cacb39… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6906 from martenson/isa-req add isa-rwal to default pipfile Compare: https://github.com/galaxyproject/galaxy/compare/014b9d76f76c...2dcd126e82fc **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] 5dfb74: Allow ``remove_value`` filter on data tables
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5dfb743ae160f873db670bff26d3ba19d85d4ce9 https://github.com/galaxyproject/galaxy/commit/5dfb743ae160f873db670bff26d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Allow ``remove_value`` filter on data tables The `RemoveValueFilter.filter_options()` method was expecting `options` to be a list of lists, where each inner list contains exactly 3-elements (name, value, selected), which is the format returned by the `data_meta` filter. In fact, the only known use of the `remove_falue` filter is in the tool `tools/maf/maf_to_interval.xml`, to filter dataset metadata. This commit generalises the filter to look for a column of the dynamic options named `value`, and use it during the filtering. Fix https://github.com/galaxyproject/tools-iuc/issues/2151 Commit: 26680e0ca1ace0ad8c857ab712f60d2fc4bf8c1b https://github.com/galaxyproject/galaxy/commit/26680e0ca1ace0ad8c857ab712f6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test for remove_value form dynamic options Unfortunately you can select an invalid value (in the API, not the UI) and Galaxy will replace the invalid value with the first valid value. Commit: 7c81daa073dea39785144b9228b53b2cd9f6fdbe https://github.com/galaxyproject/galaxy/commit/7c81daa073dea39785144b9228b5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix assertion in ``RemoveValueFilter`` Commit: 19c98b27455862e7f50570bbc147a28667182e31 https://github.com/galaxyproject/galaxy/commit/19c98b27455862e7f50570bbc147… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M test/functional/tools/remove_value.xml Log Message: ----------- Fix tests and name tool more appropriately Commit: 014b9d76f76c2eb959266bc271ad0539a1ab0f6d https://github.com/galaxyproject/galaxy/commit/014b9d76f76c2eb959266bc271ad… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6914 from nsoranzo/remove_value Allow ``remove_value`` filter on data tables Compare: https://github.com/galaxyproject/galaxy/compare/51ca8dc0f5d4...014b9d76f76c **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] 794d1e: Fix messed up printing of shed_tool_conf.xml file
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 794d1e03be57fdc0cde02bab79f8404c0eed7626 https://github.com/galaxyproject/galaxy/commit/794d1e03be57fdc0cde02bab79f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix messed up printing of shed_tool_conf.xml file This drops xml_to_string from lib/tool_shed/util/xml_util.py and uses xml_to_string form lib/galaxy/utils/__init__.py. Also reduces plain string manipulation of xml structures. Uses xml.dom.minidom to make xml pretty if necessary. Commit: 8a39f27b3c8d20c5adf933f6a3782525b3925432 https://github.com/galaxyproject/galaxy/commit/8a39f27b3c8d20c5adf933f6a378… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix toolshed tests Commit: a4655432604a758f2725c5badc120f4836ffcbda https://github.com/galaxyproject/galaxy/commit/a4655432604a758f2725c5badc12… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Drop threading lock and global try/except The Lock wasn't actually preventing anything, and I don't think anything would need ot be protected here. mkdtemp should be thread-safe. We also remove the try/except Statement. I think it'd be better to expose any exceptions here instead of producing broken capsules and logging an exception. Commit: 57a4e50d8cfe038632bbe25ed6cbb69662491f2e https://github.com/galaxyproject/galaxy/commit/57a4e50d8cfe038632bbe25ed6cb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix capsule export in docker testing Found this by removing the blank try/except in the previous commit. This only affects testing when python can't determine the correct locale and falls back to ASCII. Commit: 3f172cc9880e58396e7f71b7480bea9e7163dda4 https://github.com/galaxyproject/galaxy/commit/3f172cc9880e58396e7f71b7480b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix job stopping from DRMAA jobs broken in a1c58a708829d79859426ecb7c39b5c5f69ad735 and improve logging around it. Commit: 36383785697bed5db7e99461c3483f19836a016b https://github.com/galaxyproject/galaxy/commit/36383785697bed5db7e99461c348… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #6912 from natefoo/fix-drmaa-job-stop [18.09] Fix stopping DRMAA jobs Commit: 328c410fdcad8a870816dea307499fef31c812e7 https://github.com/galaxyproject/galaxy/commit/328c410fdcad8a870816dea30749… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6904 from mvdbeek/fix_weird_xml [18.09] Fix pretty printing of shed_tool_conf.xml file Commit: c862d55ec8fe99e950df7984127461eaedd6f438 https://github.com/galaxyproject/galaxy/commit/c862d55ec8fe99e950df79841274… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Use with statement when handling NamedTemporaryFile Commit: 91a9dbaf5cf093ff72f39d9ea606bef59ecfc45a https://github.com/galaxyproject/galaxy/commit/91a9dbaf5cf093ff72f39d9ea606… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Revert unncessary double logging of exception Commit: 843474e5e375a2359979a8f9ae46fb0e58ac148b https://github.com/galaxyproject/galaxy/commit/843474e5e375a2359979a8f9ae46… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6915 from mvdbeek/6904_followup [18.09] Small followup to #6904 Commit: 51ca8dc0f5d4cb9ba4221cba5d2067f467087caa https://github.com/galaxyproject/galaxy/commit/51ca8dc0f5d4cb9ba4221cba5d20… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/096fe9b7b9c3...51ca8dc0f5d4 **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] c862d5: Use with statement when handling NamedTemporaryFil...
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: c862d55ec8fe99e950df7984127461eaedd6f438 https://github.com/galaxyproject/galaxy/commit/c862d55ec8fe99e950df79841274… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Use with statement when handling NamedTemporaryFile Commit: 91a9dbaf5cf093ff72f39d9ea606bef59ecfc45a https://github.com/galaxyproject/galaxy/commit/91a9dbaf5cf093ff72f39d9ea606… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Revert unncessary double logging of exception Commit: 843474e5e375a2359979a8f9ae46fb0e58ac148b https://github.com/galaxyproject/galaxy/commit/843474e5e375a2359979a8f9ae46… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6915 from mvdbeek/6904_followup [18.09] Small followup to #6904 Compare: https://github.com/galaxyproject/galaxy/compare/328c410fdcad...843474e5e375 **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] a38fc5: Simplify imports
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a38fc541d14712b4a81e9aaf42a8041efc17c803 https://github.com/galaxyproject/galaxy/commit/a38fc541d14712b4a81e9aaf42a8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Simplify imports Commit: cbf8a6658d8bf386c6133213883d0f833049d445 https://github.com/galaxyproject/galaxy/commit/cbf8a6658d8bf386c6133213883d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- Update Bug Reports docs to use YAML syntax Commit: 096fe9b7b9c37e066abe1d31f4a1eeb360b95097 https://github.com/galaxyproject/galaxy/commit/096fe9b7b9c37e066abe1d31f4a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #6909 from nsoranzo/error_reports Update Bug Reports docs to use YAML syntax Compare: https://github.com/galaxyproject/galaxy/compare/ade72dd8b638...096fe9b7b9c3 **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] 794d1e: Fix messed up printing of shed_tool_conf.xml file
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 794d1e03be57fdc0cde02bab79f8404c0eed7626 https://github.com/galaxyproject/galaxy/commit/794d1e03be57fdc0cde02bab79f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix messed up printing of shed_tool_conf.xml file This drops xml_to_string from lib/tool_shed/util/xml_util.py and uses xml_to_string form lib/galaxy/utils/__init__.py. Also reduces plain string manipulation of xml structures. Uses xml.dom.minidom to make xml pretty if necessary. Commit: 8a39f27b3c8d20c5adf933f6a3782525b3925432 https://github.com/galaxyproject/galaxy/commit/8a39f27b3c8d20c5adf933f6a378… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix toolshed tests Commit: a4655432604a758f2725c5badc120f4836ffcbda https://github.com/galaxyproject/galaxy/commit/a4655432604a758f2725c5badc12… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Drop threading lock and global try/except The Lock wasn't actually preventing anything, and I don't think anything would need ot be protected here. mkdtemp should be thread-safe. We also remove the try/except Statement. I think it'd be better to expose any exceptions here instead of producing broken capsules and logging an exception. Commit: 57a4e50d8cfe038632bbe25ed6cbb69662491f2e https://github.com/galaxyproject/galaxy/commit/57a4e50d8cfe038632bbe25ed6cb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix capsule export in docker testing Found this by removing the blank try/except in the previous commit. This only affects testing when python can't determine the correct locale and falls back to ASCII. Commit: 328c410fdcad8a870816dea307499fef31c812e7 https://github.com/galaxyproject/galaxy/commit/328c410fdcad8a870816dea30749… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6904 from mvdbeek/fix_weird_xml [18.09] Fix pretty printing of shed_tool_conf.xml file Compare: https://github.com/galaxyproject/galaxy/compare/36383785697b...328c410fdcad **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] 77f742: Adjust scatterplot interface style
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77f742d7ffd95167b3c4905ef4bdcb4e678e8158 https://github.com/galaxyproject/galaxy/commit/77f742d7ffd95167b3c4905ef4bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js Log Message: ----------- Adjust scatterplot interface style Commit: 4e426ce25621736c6e6c7a7d91fcf1845f46db03 https://github.com/galaxyproject/galaxy/commit/4e426ce25621736c6e6c7a7d91fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Fix scatterplot saving feature Commit: ade72dd8b638292392f057767ad41f9ed4330eb9 https://github.com/galaxyproject/galaxy/commit/ade72dd8b638292392f057767ad4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #6905 from guerler/viz_frame Fixes for built-in Scatterplot plugin Compare: https://github.com/galaxyproject/galaxy/compare/02c71e2429ba...ade72dd8b638 **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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