From 372430980916ea9e673975b1dc0055dafbe95f90 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 Jul 2024 10:46:44 +0200 Subject: [PATCH 1/4] small docs enhancement --- doc/source/admin/galaxy_options.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index cdf82ab688fd..f07c5abc00a2 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -1606,7 +1606,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Default cache size for caching object stores if cache not + Default cache size, in GB, for caching object stores if the cache is not configured for that object store entry. :Default: ``-1`` :Type: int From 1f4d1dc35d34ce015f3d994f44da970e47666beb Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 5 Jul 2024 09:10:02 -0700 Subject: [PATCH 2/4] reqord desc in schema --- lib/galaxy/config/schemas/config_schema.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml index e18dc2aa28e8..2d67dce794d3 100644 --- a/lib/galaxy/config/schemas/config_schema.yml +++ b/lib/galaxy/config/schemas/config_schema.yml @@ -1146,8 +1146,8 @@ mapping: default: -1 required: false desc: | - Default cache size for caching object stores if cache not configured for - that object store entry. + Default cache size, in GB, for caching object stores if the cache is not + configured for that object store entry. object_store_always_respect_user_selection: type: bool @@ -3828,7 +3828,7 @@ mapping: `result_backend` option in the `celery_conf` option to a valid Celery result backend URL. By default, Galaxy uses an SQLite database at '/results.sqlite' for storing task results. For details, see https://docs.galaxyproject.org/en/master/admin/production.html#use-celery-for-asynchronous-tasks - + celery_conf: type: any required: false From 7b0bf3cae780d6d4a6046232a0a524367380616b Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 5 Jul 2024 09:13:57 -0700 Subject: [PATCH 3/4] proper place to implement https://github.com/galaxyproject/galaxy/pull/18314 --- lib/galaxy/config/schemas/config_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml index 2d67dce794d3..fd3d20c1170a 100644 --- a/lib/galaxy/config/schemas/config_schema.yml +++ b/lib/galaxy/config/schemas/config_schema.yml @@ -1474,7 +1474,7 @@ mapping: This is used to make carbon emissions estimates more accurate as the location effects the carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations, - visit https://galaxyproject.org/admin/carbon_emissions + visit https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html power_usage_effectiveness: type: float From 7264a82589fefa225f84180db815b5f854a1ec14 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 5 Jul 2024 09:19:40 -0700 Subject: [PATCH 4/4] regenerate config sample and docs --- doc/source/admin/galaxy_options.rst | 25 +++------------------ lib/galaxy/config/sample/galaxy.yml.sample | 26 +++++++--------------- 2 files changed, 11 insertions(+), 40 deletions(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index f07c5abc00a2..43469fd2c7fb 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -793,22 +793,6 @@ :Type: seq -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -``user_config_templates_index_by`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -:Description: - Configure URIs for user object stores to use either the object ID - ('id') or UUIDs ('uuid'). Either is fine really, Galaxy doesn't - typically expose database objects by 'id' but there isn't any - obvious disadvantage to doing it in this case and it keeps user - exposed URIs much smaller. The default of UUID feels a little more - like a typical way to do this within Galaxy though. Do not change - this value once user object stores have been created. -:Default: ``uuid`` -:Type: str - - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``user_config_templates_use_saved_configuration`` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1606,8 +1590,8 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Default cache size, in GB, for caching object stores if the cache is not - configured for that object store entry. + Default cache size, in GB, for caching object stores if the cache + is not configured for that object store entry. :Default: ``-1`` :Type: int @@ -2060,7 +2044,7 @@ defaults to "GLOBAL" if not set or the `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations, visit - https://galaxyproject.org/admin/carbon_emissions + https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html :Default: ``GLOBAL`` :Type: str @@ -5597,6 +5581,3 @@ This requires the help_forum_api_url to be set. :Default: ``false`` :Type: bool - - - diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index bb4c6fc32d4f..a09b781abebe 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -1,21 +1,21 @@ # Galaxy is configured by default to be usable in a single-user development # environment. To tune the application for a multi-user production # environment, see the documentation at: -# +# # https://docs.galaxyproject.org/en/master/admin/production.html -# +# # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented # values are set to the default value. Relative paths are relative to the root # Galaxy directory. -# +# # Examples of many of these options are explained in more detail in the Galaxy # Community Hub. -# +# # https://galaxyproject.org/admin/config -# +# # Config hackers are encouraged to check there before asking for help. -# +# # Configuration for Gravity process manager. # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``). gravity: @@ -721,15 +721,6 @@ galaxy: # Configured user file source templates embedded into Galaxy's config. #file_source_templates: null - # Configure URIs for user object stores to use either the object ID - # ('id') or UUIDs ('uuid'). Either is fine really, Galaxy doesn't - # typically expose database objects by 'id' but there isn't any - # obvious disadvantage to doing it in this case and it keeps user - # exposed URIs much smaller. The default of UUID feels a little more - # like a typical way to do this within Galaxy though. Do not change - # this value once user object stores have been created. - #user_config_templates_index_by: uuid - # User defined object stores and file sources are saved in the # database with their last valid configuration. It may be the case # that the admin changes file source and object store templates over @@ -1113,8 +1104,8 @@ galaxy: # . #object_store_cache_path: object_store_cache - # Default cache size for caching object stores if cache not configured - # for that object store entry. + # Default cache size, in GB, for caching object stores if the cache is + # not configured for that object store entry. #object_store_cache_size: -1 # Set this to true to indicate in the UI that a user's object store @@ -2974,4 +2965,3 @@ galaxy: # Enable the integration of the Galaxy Help Forum in the tool panel. # This requires the help_forum_api_url to be set. #enable_help_forum_tool_panel_integration: false -