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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 23 Oct '18

23 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 23 Oct '18

23 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 23 Oct '18

23 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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[galaxyproject/galaxy] 3f172c: Fix job stopping from DRMAA jobs broken in
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/ecb56d80a103...36383785697b **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] 29d04a: Updated all installed data managers.
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 29d04a9079607b385ecf1e4a275f7d9767386f3c https://github.com/galaxyproject/usegalaxy-playbook/commit/29d04a9079607b38… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated all installed data managers. **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] 8daa82: Fix DM destinations
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8daa82a3c453d3840fb50f75dbcff84424377f46 https://github.com/galaxyproject/usegalaxy-playbook/commit/8daa82a3c453d384… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix DM destinations **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] 126ee5: Create composite file archives in new_file_path in...
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 126ee5fe2bb6d8c1c2874545cd5a583389d45bca https://github.com/galaxyproject/galaxy/commit/126ee5fe2bb6d8c1c2874545cd5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Create composite file archives in new_file_path instead of TMP 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 Commit: 9735146f2848beca367ac84c066d10a4b5008a25 https://github.com/galaxyproject/galaxy/commit/9735146f2848beca367ac84c066d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- add discovered tool vulnerabilities to RN Commit: fa212c3c31b78f885b7aff2681430bc9e54fec89 https://github.com/galaxyproject/galaxy/commit/fa212c3c31b78f885b7aff268143… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- specify which gemini tools were fixed Commit: 0aca12ce96f0c2a860453a15022bbd5e693493ed https://github.com/galaxyproject/galaxy/commit/0aca12ce96f0c2a860453a15022b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6892 from martenson/security-notes [18.09] add discovered tool vulnerabilities to RN Commit: 46e56417dddfa88c9b093c612eb006c9f471579d https://github.com/galaxyproject/galaxy/commit/46e56417dddfa88c9b093c612eb0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use hasattr instead of relying on value Commit: 3411852fedf31c93ec506aa4f8f8a922d4b57ad7 https://github.com/galaxyproject/galaxy/commit/3411852fedf31c93ec506aa4f8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-21 (Sun, 21 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #6885 from mvdbeek/create_in_new_file_path [18.05] Create composite file archives in new_file_path instead of TMP Commit: 88b840d2c6cc18184c71772d96301a9f9a71cbdc https://github.com/galaxyproject/galaxy/commit/88b840d2c6cc18184c71772d9630… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6893 from martenson/backport-6884 [18.09] check presence of attribute in addition to value Commit: 4dd2ecb13f1cac23730debd107dd150e46c47568 https://github.com/galaxyproject/galaxy/commit/4dd2ecb13f1cac23730debd107dd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix ``make config-validate`` Commit: 194358703450ff8fef553d92531fc6e6a0938612 https://github.com/galaxyproject/galaxy/commit/194358703450ff8fef553d92531f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6908 from nsoranzo/release_18.09_config_validate [18.09] Fix ``make config-validate`` Commit: ecb56d80a103dc3b11091beb3de06a086ed48953 https://github.com/galaxyproject/galaxy/commit/ecb56d80a103dc3b11091beb3de0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 02c71e2429bad6caf07ce9a66e788d26af8b21b3 https://github.com/galaxyproject/galaxy/commit/02c71e2429bad6caf07ce9a66e78… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst M lib/galaxy/datatypes/data.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3759db3297b2...02c71e2429ba **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] 126ee5: Create composite file archives in new_file_path in...
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 126ee5fe2bb6d8c1c2874545cd5a583389d45bca https://github.com/galaxyproject/galaxy/commit/126ee5fe2bb6d8c1c2874545cd5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Create composite file archives in new_file_path instead of TMP Commit: 3411852fedf31c93ec506aa4f8f8a922d4b57ad7 https://github.com/galaxyproject/galaxy/commit/3411852fedf31c93ec506aa4f8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-21 (Sun, 21 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #6885 from mvdbeek/create_in_new_file_path [18.05] Create composite file archives in new_file_path instead of TMP Commit: ecb56d80a103dc3b11091beb3de06a086ed48953 https://github.com/galaxyproject/galaxy/commit/ecb56d80a103dc3b11091beb3de0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/194358703450...ecb56d80a103 **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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