From 5f4334f62576b8f0018f5348d31940ab8781fc17 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 17 Oct 2023 13:19:51 -0400 Subject: [PATCH] Rebuild config schema. --- doc/source/admin/galaxy_options.rst | 72 ++++++++++++------- lib/galaxy/config/sample/galaxy.yml.sample | 48 ++++++++----- lib/galaxy/config/sample/tool_shed.yml.sample | 48 +++++++++++++ 3 files changed, 123 insertions(+), 45 deletions(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 010844a4fa18..44db78d7dd32 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -1650,13 +1650,26 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - URL of the support resource for the galaxy instance. Used in - activation emails. + URL of the support resource for the galaxy instance. Used outside + of web contexts such as in activation emails and in Galaxy + markdown report generation. Example value 'https://galaxyproject.org/' :Default: ``None`` :Type: str +~~~~~~~~~~~~~~~~~~~~~~~ +``instance_access_url`` +~~~~~~~~~~~~~~~~~~~~~~~ + +:Description: + URL used to access this Galaxy server. Used outside of web + contexts such as in Galaxy markdown report generation. + Example value 'https://usegalaxy.org' +:Default: ``None`` +:Type: str + + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``email_domain_blocklist_file`` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4036,35 +4049,35 @@ :Type: str -~~~~~~~~~~~~~~~~~~~~ -``ga4gh_service_id`` -~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~ +``organization_name`` +~~~~~~~~~~~~~~~~~~~~~ :Description: - Service ID for GA4GH services (exposed via the service-info - endpoint for the Galaxy DRS API). If unset, one will be generated - using the URL the target API requests are made against. + The name of the organization that operates this Galaxy instance. + Serves as the default for the GA4GH service organization name and + can be exposed through Galaxy markdown for reports and such. For + instance, "Not Evil Corporation". + For GA4GH APIs, this is exposed via the service-info endpoint for + the Galaxy DRS API. If unset, one will be generated using + ga4gh_service_id (but only in the context of GA4GH APIs). For more information on GA4GH service definitions - check out https://github.com/ga4gh-discovery/ga4gh-service-registry and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml - This value should likely reflect your service's URL. For instance - for usegalaxy.org this value should be org.usegalaxy. Particular - Galaxy implementations will treat this value as a prefix and - append the service type to this ID. For instance for the DRS - service "id" (available via the DRS API) for the above - configuration value would be org.usegalaxy.drs. :Default: ``None`` :Type: str -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -``ga4gh_service_organization_name`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~ +``organization_url`` +~~~~~~~~~~~~~~~~~~~~ :Description: - Service name for host organization (exposed via the service-info - endpoint for the Galaxy DRS API). If unset, one will be generated - using ga4gh_service_id. + The URL of the organization that operates this Galaxy instance. + Serves as the default for the GA4GH service organization name and + can be exposed through Galaxy markdown for reports and such. For + instance, "notevilcorp.com". + For GA4GH APIs, this is exposed via the service-info endpoint. For more information on GA4GH service definitions - check out https://github.com/ga4gh-discovery/ga4gh-service-registry and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml @@ -4072,18 +4085,23 @@ :Type: str -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -``ga4gh_service_organization_url`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~ +``ga4gh_service_id`` +~~~~~~~~~~~~~~~~~~~~ :Description: - Organization URL for host organization (exposed via the - service-info endpoint for the Galaxy DRS API). If unset, one will - be generated using the URL the target API requests are made - against. + Service ID for GA4GH services (exposed via the service-info + endpoint for the Galaxy DRS API). If unset, one will be generated + using the URL the target API requests are made against. For more information on GA4GH service definitions - check out https://github.com/ga4gh-discovery/ga4gh-service-registry and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml + This value should likely reflect your service's URL. For instance + for usegalaxy.org this value should be org.usegalaxy. Particular + Galaxy implementations will treat this value as a prefix and + append the service type to this ID. For instance for the DRS + service "id" (available via the DRS API) for the above + configuration value would be org.usegalaxy.drs. :Default: ``None`` :Type: str diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 3f4d369e9981..a181d693c415 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -1116,11 +1116,17 @@ galaxy: # message, before the 'Your Galaxy Team' signature. #custom_activation_email_message: null - # URL of the support resource for the galaxy instance. Used in - # activation emails. + # URL of the support resource for the galaxy instance. Used outside + # of web contexts such as in activation emails and in Galaxy markdown + # report generation. # Example value 'https://galaxyproject.org/' #instance_resource_url: null + # URL used to access this Galaxy server. Used outside of web contexts + # such as in Galaxy markdown report generation. + # Example value 'https://usegalaxy.org' + #instance_access_url: null + # E-mail domains blocklist is used for filtering out users that are # using disposable email addresses at registration. If their # address's base domain matches any domain on the list, they are @@ -2187,6 +2193,28 @@ galaxy: # production server. #bootstrap_admin_api_key: null + # The name of the organization that operates this Galaxy instance. + # Serves as the default for the GA4GH service organization name and + # can be exposed through Galaxy markdown for reports and such. For + # instance, "Not Evil Corporation". + # For GA4GH APIs, this is exposed via the service-info endpoint for + # the Galaxy DRS API. If unset, one will be generated using + # ga4gh_service_id (but only in the context of GA4GH APIs). + # For more information on GA4GH service definitions - check out + # https://github.com/ga4gh-discovery/ga4gh-service-registry and + # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml + #organization_name: null + + # The URL of the organization that operates this Galaxy instance. + # Serves as the default for the GA4GH service organization name and + # can be exposed through Galaxy markdown for reports and such. For + # instance, "notevilcorp.com". + # For GA4GH APIs, this is exposed via the service-info endpoint. + # For more information on GA4GH service definitions - check out + # https://github.com/ga4gh-discovery/ga4gh-service-registry and + # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml + #organization_url: null + # Service ID for GA4GH services (exposed via the service-info endpoint # for the Galaxy DRS API). If unset, one will be generated using the # URL the target API requests are made against. @@ -2201,22 +2229,6 @@ galaxy: # be org.usegalaxy.drs. #ga4gh_service_id: null - # Service name for host organization (exposed via the service-info - # endpoint for the Galaxy DRS API). If unset, one will be generated - # using ga4gh_service_id. - # For more information on GA4GH service definitions - check out - # https://github.com/ga4gh-discovery/ga4gh-service-registry and - # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml - #ga4gh_service_organization_name: null - - # Organization URL for host organization (exposed via the service-info - # endpoint for the Galaxy DRS API). If unset, one will be generated - # using the URL the target API requests are made against. - # For more information on GA4GH service definitions - check out - # https://github.com/ga4gh-discovery/ga4gh-service-registry and - # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml - #ga4gh_service_organization_url: null - # Service environment (exposed via the service-info endpoint for the # Galaxy DRS API) for implemented GA4GH services. # Suggested values are prod, test, dev, staging. diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample index 3b04d57f94a7..af9726e851ba 100644 --- a/lib/galaxy/config/sample/tool_shed.yml.sample +++ b/lib/galaxy/config/sample/tool_shed.yml.sample @@ -15,6 +15,10 @@ tool_shed: # installation directory. #hgweb_config_dir: null + # Allow pushing directly to mercurial repositories directly and + # without authentication. + #config_hg_for_dev: null + # Where Tool Shed repositories are stored. #file_path: database/community_files @@ -188,6 +192,50 @@ tool_shed: # Address to join mailing list #mailing_join_addr: galaxy-announce-join@bx.psu.edu + # Service ID for GA4GH services. + # If unset, one will be generated using the URL the target API + # requests are made against. + # For more information on GA4GH service definitions - check out + # https://github.com/ga4gh-discovery/ga4gh-service-registry and + # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml + # This value should likely reflect your service's URL. For instance + # for usegalaxy.org this value should be org.usegalaxy. Particular + # Galaxy implementations will treat this value as a prefix and append + # the service type to this ID. For instance for the DRS service "id" + # (available via the DRS API) for the above configuration value would + # be org.usegalaxy.drs. + #ga4gh_service_id: null + + # The name of the organization that operates this Galaxy instance. + # Serves as the default for the GA4GH service organization name and + # can be exposed through Galaxy markdown for reports and such. For + # instance, "Not Evil Corporation". + # For GA4GH APIs, this is exposed via the service-info endpoint for + # the Galaxy DRS API. If unset, one will be generated using + # ga4gh_service_id (but only in the context of GA4GH APIs). + # For more information on GA4GH service definitions - check out + # https://github.com/ga4gh-discovery/ga4gh-service-registry and + # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml + #organization_name: null + + # The URL of the organization that operates this Galaxy instance. + # Serves as the default for the GA4GH service organization name and + # can be exposed through Galaxy markdown for reports and such. For + # instance, "notevilcorp.com". + # For GA4GH APIs, this is exposed via the service-info endpoint. + # For more information on GA4GH service definitions - check out + # https://github.com/ga4gh-discovery/ga4gh-service-registry and + # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml + #organization_url: null + + # Service environment (exposed via the service-info endpoint for the + # Galaxy DRS API) for implemented GA4GH services. + # Suggested values are prod, test, dev, staging. + # For more information on GA4GH service definitions - check out + # https://github.com/ga4gh-discovery/ga4gh-service-registry and + # https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml + #ga4gh_service_environment: null + # Write thread status periodically to 'heartbeat.log' (careful, uses # disk space rapidly!) #use_heartbeat: true