Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a7cc34e1b1ade9580e464570fc6b83a488e941f https://github.com/galaxyproject/galaxy/commit/6a7cc34e1b1ade9580e464570fc6b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh Log Message: ----------- Bring Galaxy, reports, and shed run scripts in sync. - They now uniformly handle server option processing. - Reports and Tool Shed now respect many new and important options such as --skip_venv. - Reports and Tool Shed now do extra checking around Python version that Galaxy does. In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting. Commit: 72e5a00ba0ad9c1a8e56ad9544bec23c843d900d https://github.com/galaxyproject/galaxy/commit/72e5a00ba0ad9c1a8e56ad9544bec... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Centralize launching server for reports and tool shed. Initial outline of allowing launch via uwsgi. Commit: 1bdb99bbd76d0827cd3a7e617d288564584863ea https://github.com/galaxyproject/galaxy/commit/1bdb99bbd76d0827cd3a7e617d288... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M scripts/manage_tools.py Log Message: ----------- Update galaxy.util.properties to allow YAML. Commit: 8189a1f1e289e14d362fcb8871b9339c3355e8b2 https://github.com/galaxyproject/galaxy/commit/8189a1f1e289e14d362fcb8871b93... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A lib/galaxy/webapps/config_manage.py A scripts/config_sample_to_kwalify.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py Log Message: ----------- Scripts to manage configuration infrastructure. This has been rebased several times and includes a variety of fixes (some thanks to martenson). Commit: 7973a914e0beef9680475d54947bd953c0b062cd https://github.com/galaxyproject/galaxy/commit/7973a914e0beef9680475d54947bd... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- Add uwsgi_schema.yml. Commit: 90e899d68fbf21effad1cf309efbd786c54be556 https://github.com/galaxyproject/galaxy/commit/90e899d68fbf21effad1cf309efbd... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R config/tool_shed.ini.sample A config/tool_shed.yml.sample M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml M run_tool_shed.sh Log Message: ----------- Update tool shed to use newer configuration schema. - Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/tool_shed.yml.sample). Commit: 102566dd5e1c5903726057f1077a1d7fc614b815 https://github.com/galaxyproject/galaxy/commit/102566dd5e1c5903726057f1077a1... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: R config/reports.ini.sample A config/reports.yml.sample M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M run_reports.sh Log Message: ----------- Update Galaxy Reports to use newer configuration schema. - Implement kwalify schema to validate/define the schema. - Replace ini configuration with YAML (completely backward compatible). - Rebuild a sample configuration from the schema (config/reports.yml.sample). Commit: 50d426ed2b9ae2aff8b243143478ce84c7731816 https://github.com/galaxyproject/galaxy/commit/50d426ed2b9ae2aff8b243143478c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst Log Message: ----------- Add reports documentation to ``doc/``. - Automatically generate RST docs from config schema. - Describe older functionality as well as new YAML-based configuration. - Replace https://wiki.galaxyproject.org/Admin/UsageReports. Commit: 4945f55e4fe28842b58c025b37c4d6c96a07028f https://github.com/galaxyproject/galaxy/commit/4945f55e4fe28842b58c025b37c4d... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M Makefile Log Message: ----------- Makefile shortcuts for configuration script. Commit: ef46a60a829e3dae44d935f6f886feef39b873e3 https://github.com/galaxyproject/galaxy/commit/ef46a60a829e3dae44d935f6f886f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add required dependency on uwsgi. Required for the new out-of-the-box configuration of tool shed and reports. Commit: 8191fd492819214b12c0aa28b35e5b6c4ea7bfa1 https://github.com/galaxyproject/galaxy/commit/8191fd492819214b12c0aa28b35e5... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add pykwalify as dependency for the new config validation stuff. xref https://github.com/galaxyproject/starforge/pull/110 Commit: ffe295e96dbd82615c987a2b9ba9bd15ea253826 https://github.com/galaxyproject/galaxy/commit/ffe295e96dbd82615c987a2b9ba9b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M test/unit/config/test_config_manage.py Log Message: ----------- Fix Python 3 linting problem with test_config_manage.py. Commit: 1ce93ccfdf7b54ec1efcf08b04c9f28b67ab0615 https://github.com/galaxyproject/galaxy/commit/1ce93ccfdf7b54ec1efcf08b04c9f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pin version of uWSGI to freshly released 2.0.15 available on wheels.galaxyproject.org. Commit: 539a62f642ada1f2d832f1f88ab339cafe672c1f https://github.com/galaxyproject/galaxy/commit/539a62f642ada1f2d832f1f88ab33... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py Log Message: ----------- Fix ORM scripts for #3179. Commit: 98ca8ce7a68d18533f3bf85097490c5b66e9f876 https://github.com/galaxyproject/galaxy/commit/98ca8ce7a68d18533f3bf85097490... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Update config overhaul branch for introduction of galaxy.web.stack package. Commit: 331851b0495d429220450ceb3a540fbba900143a https://github.com/galaxyproject/galaxy/commit/331851b0495d429220450ceb3a540... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M Makefile R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py Log Message: ----------- Merge pull request #3179 from jmchilton/web_config_overhaul_0 Configuration & Server Overhaul - Tool Shed and Reports Compare: https://github.com/galaxyproject/galaxy/compare/c6e45e7b0720...331851b0495d