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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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[galaxyproject/galaxy] 429ef9: WIP pgcleanup improvements
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 429ef96a106d0bf094145a7fd8a65143b113e6e5 https://github.com/galaxyproject/galaxy/commit/429ef96a106d0bf094145a7fd8a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- WIP pgcleanup improvements Commit: 941d68ad358155f6577fb89f1778625b805035fe https://github.com/galaxyproject/galaxy/commit/941d68ad358155f6577fb89f1778… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- WIP pgcleanup improvements Commit: ba83310d53488ccc62dd52907746a3ca63baaf28 https://github.com/galaxyproject/galaxy/commit/ba83310d53488ccc62dd52907746… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Mostly refactored pgcleanup.py Commit: e1a197676ec3f6f35dafaa6cb58d60c7d9d44fb2 https://github.com/galaxyproject/galaxy/commit/e1a197676ec3f6f35dafaa6cb58d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Refactor repetitive HDA purging stuff and add a function to purge HDAs with null history_ids Commit: 4d0538cc4f74c183495c9df33c1055a9441766d8 https://github.com/galaxyproject/galaxy/commit/4d0538cc4f74c183495c9df33c10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py Log Message: ----------- Add a table for logging user cleanup events Commit: e72d52c6dfe9332c5cd1c3f42d4e0276e9a75008 https://github.com/galaxyproject/galaxy/commit/e72d52c6dfe9332c5cd1c3f42d4e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Lint Commit: 3759db3297b2d277ae3039f54e203dc7493cb3dc https://github.com/galaxyproject/galaxy/commit/3759db3297b2d277ae3039f54e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #6877 from natefoo/pgcleanup-inactive-users Refactor pgcleanup.py and add new routines Compare: https://github.com/galaxyproject/galaxy/compare/99bc4b33d2fa...3759db3297b2 **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] 4dd2ec: Fix ``make config-validate``
by GitHub 23 Oct '18

23 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy 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`` Compare: https://github.com/galaxyproject/galaxy/compare/88b840d2c6cc...194358703450 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] c6a4fe: Collect Galaxy handler process stats
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6a4fe030044926479872c4a60f95216887b893b https://github.com/galaxyproject/infrastructure-playbook/commit/c6a4fe03004… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/tacc/group_vars/galaxyservers.yml Log Message: ----------- Collect Galaxy handler process stats **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] aa23d8: Configure workflow schedulers on Main
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa23d8cf0d1d857421b02c98bf278ea0d9923ba7 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa23d8cf0d1d8574… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: R env/common/templates/galaxy/config/workflow_schedulers_conf.xml.j2 A env/main/files/galaxy/config/workflow_schedulers_conf.xml M env/main/group_vars/galaxyjobservers.yml M env/main/group_vars/galaxyservers/vars.yml A env/test/files/galaxy/config/workflow_schedulers_conf.xml M env/test/group_vars/galaxyservers/vars.yml R env/test/templates/galaxy/config/workflow_schedulers_conf.xml.j2 Log Message: ----------- Configure workflow schedulers on 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/usegalaxy-playbook] 796070: Rename uWSGI logs from uwsgi_zerg*.log to zerg*.lo...
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 796070ba4ffacae52de4a889b89f271866a5bec3 https://github.com/galaxyproject/usegalaxy-playbook/commit/796070ba4ffacae5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/common/templates/supervisor/galaxy.j2 M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 Log Message: ----------- Rename uWSGI logs from uwsgi_zerg*.log to zerg*.log Commit: ecce49a63dc603bb6b0f2f4e2c08312179b7e634 https://github.com/galaxyproject/usegalaxy-playbook/commit/ecce49a63dc603bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: A env/common/templates/galaxy/config/workflow_schedulers_conf.xml.j2 M env/common/templates/supervisor/galaxy_group.j2 A env/common/templates/supervisor/galaxy_workflow_scheduler.j2 M env/test/group_vars/galaxyservers/vars.yml A env/test/templates/galaxy/config/workflow_schedulers_conf.xml.j2 Log Message: ----------- Configure a workflow scheduler on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1634bc2fc07f...… **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] 46e564: Use hasattr instead of relying on value
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/0aca12ce96f0...88b840d2c6cc **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] 1634bc: Update Main migrated_tool_conf
by GitHub 22 Oct '18

22 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1634bc2fc07f981a55f6a9302bf429d9ceccf112 https://github.com/galaxyproject/usegalaxy-playbook/commit/1634bc2fc07f981a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/migrated_tools_conf.xml Log Message: ----------- Update Main migrated_tool_conf **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 21 Oct '18

21 Oct '18

Branch: refs/heads/release_18.05 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 Compare: https://github.com/galaxyproject/galaxy/compare/a8fa5a1d4a6c...3411852fedf3 **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] 60d0d9: Add grooming for composite files.
by GitHub 19 Oct '18

19 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60d0d9d5ec36fb1e6a79a4f51ab919325687b10d https://github.com/galaxyproject/galaxy/commit/60d0d9d5ec36fb1e6a79a4f51ab9… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Add grooming for composite files. Add call to groom_dataset_content() for composite files. Commit: 665e11facbf0b9b86fbcde04593fcd49ebe96777 https://github.com/galaxyproject/galaxy/commit/665e11facbf0b9b86fbcde04593f… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add ISA composite data type. Add new data types isa-tab and isa-json. Add isa-rwval library (isatools Python 2 version) in requirements. Commit: 1fb63a1369e8fa75b1f7825693ef286682659a64 https://github.com/galaxyproject/galaxy/commit/1fb63a1369e8fa75b1f7825693ef… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- [ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas (#31) * [ISA datatype] adds logger setting for isatools.isatab to avoid failing uploads when no pandas. * Update isa.py Commit: fe139ad8dfe6c83188c33498d8d2854b33670c04 https://github.com/galaxyproject/galaxy/commit/fe139ad8dfe6c83188c33498d8d2… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Installs isa-rwval from develop Otherwise failing currently when building in the container. Commit: 06c57810d9050ffd4c81ce8e189741f255d6eafc https://github.com/galaxyproject/galaxy/commit/06c57810d9050ffd4c81ce8e1897… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct linting issues detected by Travis-CI run. Commit: 5babb80fc24febbbbed1af5b0bf56c84f16ab8a4 https://github.com/galaxyproject/galaxy/commit/5babb80fc24febbbbed1af5b0bf5… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct again lint errors for Travis-CI. Commit: 84c002283209a5717682c31d1013034e9cfc828b https://github.com/galaxyproject/galaxy/commit/84c002283209a5717682c31d1013… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Correct some more lint errors for Travis-CI. Commit: b9c63df60e12b6220f088645c17bf6d8bd68ab1b https://github.com/galaxyproject/galaxy/commit/b9c63df60e12b6220f088645c17b… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Change ISA Tools web site link. Replace ISA Tools .org web site that has just been hacked, by the GitHub page of the organization. Commit: cf7034399083c77d38e29c2832339776df103983 https://github.com/galaxyproject/galaxy/commit/cf7034399083c77d38e29c283233… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Escape filename in primary file. Commit: a50537cd5a2cb1039bcc7b0fa215d523c6e97499 https://github.com/galaxyproject/galaxy/commit/a50537cd5a2cb1039bcc7b0fa215… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Escape assay information in ISA display_data(). Commit: 86de0d3bc431404d6fca26e7506ec11415411788 https://github.com/galaxyproject/galaxy/commit/86de0d3bc431404d6fca26e7506e… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove unused method _list_archive_files(). Commit: 62ff476a7c3eeaca51147b5ae0cac753b71ba9ee https://github.com/galaxyproject/galaxy/commit/62ff476a7c3eeaca51147b5ae0ca… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Use CompressedFile class. Replace unzip custom code by Galaxy call to CompressedFile class. Commit: abd22c12f22b15c010bcfe6b7dca63d1c2135d18 https://github.com/galaxyproject/galaxy/commit/abd22c12f22b15c010bcfe6b7dca… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove logger configuration. Commit: 55bae21f77c03ebb1d114e9dbe593490b3e07993 https://github.com/galaxyproject/galaxy/commit/55bae21f77c03ebb1d114e9dbe59… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Comment out raw files listing in ISA type. Commit: e9f00065ee190ebdeca5c02d21c068d815674999 https://github.com/galaxyproject/galaxy/commit/e9f00065ee190ebdeca5c02d21c0… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Remove dynamical setting of study name for ISA. Commit: 2be9e1f637180d04d4e085b1c91292df3e09c72e https://github.com/galaxyproject/galaxy/commit/2be9e1f637180d04d4e085b1c912… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Add new lazy table parsing for isa-tab datatype and reintroduce data files Commit: 87cdd2156d46036807134f8d91fde4fcc2ac10de https://github.com/galaxyproject/galaxy/commit/87cdd2156d46036807134f8d91fd… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A test-data/MTBLS6.zip M test/api/test_tools_upload.py Log Message: ----------- Start writing upload test for isa-tab. Do not know how to read zip file content and submit it to uploader for a composite type. Commit: 08ce54fe6e0f3cc178ad41a6fa3c00177cfbfef1 https://github.com/galaxyproject/galaxy/commit/08ce54fe6e0f3cc178ad41a6fa3c… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Introduce new table parsers to get data files back; temporarily puts dependency back to Git repo to test against (updated PyPI package for isa-rwval will be pushed soon). Commit: eac29d55f9567b68ca94b3c2e468c380a64261ba https://github.com/galaxyproject/galaxy/commit/eac29d55f9567b68ca94b3c2e468… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fix requirements again for isa-rwval==0.10.1 Commit: b4fa3d28064e1c527a3b1a3232d10873490b6825 https://github.com/galaxyproject/galaxy/commit/b4fa3d28064e1c527a3b1a3232d1… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Cleanup presentation of data files (unused rendering using datafile id) Commit: 832f51b5168cc9751eecb77a62ff7a06807f92ed https://github.com/galaxyproject/galaxy/commit/832f51b5168cc9751eecb77a62ff… Author: Pierrick Roger <pk.roger(a)icloud.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pinned requirements as a symbolic link as done in dev branch. Commit: 39d4447a97ab8fe8359d3fd2a1df2815014570ea https://github.com/galaxyproject/galaxy/commit/39d4447a97ab8fe8359d3fd2a1df… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Add check so that empty filenames not added to file list. Commit: a98cc55db25492217ff5cb6d91716122e39347fb https://github.com/galaxyproject/galaxy/commit/a98cc55db25492217ff5cb6d9171… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Fix upload test for isa-tab datatype Commit: f2176d395478fe4c4ad41ae3f03747b3967abc6d https://github.com/galaxyproject/galaxy/commit/f2176d395478fe4c4ad41ae3f037… Author: djcomlab <djcomlab(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update isa-rwval version as new update fixes a bug Commit: efc7864cabb0f7adc65929f3bff2f56c3ef14041 https://github.com/galaxyproject/galaxy/commit/efc7864cabb0f7adc65929f3bff2… Author: Pierrick ROGER <pk.roger(a)icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M .ci/flake8_blacklist.txt A .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh A 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test/unit/test_objectstore.py M test/unit/test_remote_shell.py M test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py A tool-data/intermine_simple_display.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample A tools/data_source/intermine.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'dev' into feature/isa_data_type Commit: 35093e38fcfe4f9efc3a2914d694cf4a11f24ace https://github.com/galaxyproject/galaxy/commit/35093e38fcfe4f9efc3a2914d694… Author: Pierrick ROGER <pk.roger(a)icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Remove spaces in blank line. Commit: a9eb587a3e38849c5044700f9f01c47d53f55a87 https://github.com/galaxyproject/galaxy/commit/a9eb587a3e38849c5044700f9f01… Author: Pierrick ROGER <pk.roger(a)icloud.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Various corrections for py34-lint Add second blank line. Remove useless imports. Commit: 99bc4b33d2fa14a42f9ee7f4a9afe4dcf867c851 https://github.com/galaxyproject/galaxy/commit/99bc4b33d2fa14a42f9ee7f4a9af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-19 (Fri, 19 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt A test-data/MTBLS6.zip M test/api/test_tools_upload.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5787 from phnmnl/feature/isa_data_type Feature/isa data type Compare: https://github.com/galaxyproject/galaxy/compare/81f31d1a29e1...99bc4b33d2fa **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] a7f278: Decrease squid memory on cvmfs1-tacc0 and cvmfs1-p...
by GitHub 18 Oct '18

18 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a7f278a59e8a86c8e5a87765432809d0ac2102ca https://github.com/galaxyproject/infrastructure-playbook/commit/a7f278a59e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M env/galaxy/host_vars/cvmfs1-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs1-tacc0.galaxyproject.org.yml Log Message: ----------- Decrease squid memory on cvmfs1-tacc0 and cvmfs1-psu0 until their allocated memory is increased **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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

18 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 554b84542637a868328d7d025977b47dc247b917 https://github.com/galaxyproject/infrastructure-playbook/commit/554b8454263… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M env/galaxy/files/jenkins/jenkins_server_user_ssh_config M env/galaxy/group_vars/jenkinsslaves/vars.yml Log Message: ----------- Fixes for Jenkins **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] d2c78c: Add n1, n2, n5 jenkins workers
by GitHub 18 Oct '18

18 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d2c78c3bc617d0c3940eaf0ad1ab54c795ccaa84 https://github.com/galaxyproject/infrastructure-playbook/commit/d2c78c3bc61… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M common_roles M env/galaxy/inventory Log Message: ----------- Add n1,n2,n5 jenkins workers **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] e66da3: Use hasattr instead of relying on value
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e66da36f60c0d1d2b43fe1a5bd9cdf7da7ddc697 https://github.com/galaxyproject/galaxy/commit/e66da36f60c0d1d2b43fe1a5bd9c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use hasattr instead of relying on value Commit: 81f31d1a29e1b1021f7629008d433797b9367267 https://github.com/galaxyproject/galaxy/commit/81f31d1a29e1b1021f7629008d43… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6884 from guerler/fix_accessible_links Improve resilience on handling sharing attributes Compare: https://github.com/galaxyproject/galaxy/compare/af05cb480b1c...81f31d1a29e1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 973514: add discovered tool vulnerabilities to RN
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9735146f2848beca367ac84c066d10a4b5008a25 https://github.com/galaxyproject/galaxy/commit/9735146f2848beca367ac84c066d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- add discovered tool vulnerabilities to RN Commit: fa212c3c31b78f885b7aff2681430bc9e54fec89 https://github.com/galaxyproject/galaxy/commit/fa212c3c31b78f885b7aff268143… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- specify which gemini tools were fixed Commit: 0aca12ce96f0c2a860453a15022bbd5e693493ed https://github.com/galaxyproject/galaxy/commit/0aca12ce96f0c2a860453a15022b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6892 from martenson/security-notes [18.09] add discovered tool vulnerabilities to RN Compare: https://github.com/galaxyproject/galaxy/compare/89fbe9c9344d...0aca12ce96f0 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] ee4365: It's annual cert update day
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ee4365f8a3e71646b6af91e9e5fe51095f5f2a1b https://github.com/galaxyproject/infrastructure-playbook/commit/ee4365f8a3e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M env/common/files/ssl/athena.galaxyproject.org_cert.pem M env/common/files/ssl/status.galaxyproject.org_cert.pem M env/common/files/ssl/wildcard_cert.pem M env/common/group_vars/sslservers/vault.yml Log Message: ----------- It's annual cert update day **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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