From f1f935200b85d09c496b6d8d888aa940dfe7e203 Mon Sep 17 00:00:00 2001 From: davelopez <46503462+davelopez@users.noreply.github.com> Date: Wed, 23 Aug 2023 20:11:01 +0200 Subject: [PATCH] Annotate more non-required config params as optional --- lib/galaxy/schema/configuration.py | 275 ++++++++++++++--------------- 1 file changed, 137 insertions(+), 138 deletions(-) diff --git a/lib/galaxy/schema/configuration.py b/lib/galaxy/schema/configuration.py index 93e910ab02fa..9834eb74624d 100644 --- a/lib/galaxy/schema/configuration.py +++ b/lib/galaxy/schema/configuration.py @@ -1087,7 +1087,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None database_engine_option_pool_size: Annotated[ - int, + Optional[int], Field( title="Database Engine Option Pool Size", description="""If the server logs errors about not having enough database pool connections, @@ -1096,7 +1096,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 5 database_engine_option_max_overflow: Annotated[ - int, + Optional[int], Field( title="Database Engine Option Max Overflow", description="""If the server logs errors about not having enough database pool connections, @@ -1105,7 +1105,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 10 database_engine_option_pool_recycle: Annotated[ - int, + Optional[int], Field( title="Database Engine Option Pool Recycle", description="""If using MySQL and the server logs the error "MySQL server has gone away", @@ -1114,7 +1114,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = -1 database_engine_option_server_side_cursors: Annotated[ - bool, + Optional[bool], Field( title="Database Engine Option Server Side Cursors", description="""If large database query results are causing memory or response time issues in @@ -1125,7 +1125,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False database_query_profiling_proxy: Annotated[ - bool, + Optional[bool], Field( title="Database Query Profiling Proxy", description="""Log all database transactions, can be useful for debugging and performance @@ -1147,7 +1147,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None database_log_query_counts: Annotated[ - bool, + Optional[bool], Field( title="Database Log Query Counts", description="""Log number of SQL queries executed and total time spent dispatching SQL statements for @@ -1161,7 +1161,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False slow_query_log_threshold: Annotated[ - float, + Optional[float], Field( title="Slow Query Log Threshold", description="""Slow query logging. Queries slower than the threshold indicated below will @@ -1172,7 +1172,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 0.0 enable_per_request_sql_debugging: Annotated[ - bool, + Optional[bool], Field( title="Enable Per Request Sql Debugging", description="""Enables a per request sql debugging option. If this is set to true, @@ -1200,7 +1200,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None database_auto_migrate: Annotated[ - bool, + Optional[bool], Field( title="Database Auto Migrate", description="""Setting the following option to true will cause Galaxy to automatically @@ -1210,7 +1210,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False database_wait: Annotated[ - bool, + Optional[bool], Field( title="Database Wait", description="""Wait for database to become available instead of failing immediately.""", @@ -1218,7 +1218,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False database_wait_attempts: Annotated[ - int, + Optional[int], Field( title="Database Wait Attempts", description="""Number of attempts before failing if database_wait is enabled.""", @@ -1226,7 +1226,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 60 database_wait_sleep: Annotated[ - float, + Optional[float], Field( title="Database Wait Sleep", description="""Time to sleep between attempts if database_wait is enabled (in seconds).""", @@ -1234,7 +1234,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1.0 history_audit_table_prune_interval: Annotated[ - int, + Optional[int], Field( title="History Audit Table Prune Interval", description="""Time (in seconds) between attempts to remove old rows from the history_audit database table. @@ -1266,7 +1266,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "tmp" maximum_upload_file_size: Annotated[ - int, + Optional[int], Field( title="Maximum Upload File Size", description="""Maximum size of uploadable files, specified in bytes (default: 100GB). @@ -1391,7 +1391,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None conda_debug: Annotated[ - bool, + Optional[bool], Field( title="Conda Debug", description="""Pass debug flag to conda commands.""", @@ -1409,7 +1409,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "conda-forge,bioconda,defaults" conda_use_local: Annotated[ - bool, + Optional[bool], Field( title="Conda Use Local", description="""Use locally-built conda packages.""", @@ -1417,7 +1417,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False conda_auto_install: Annotated[ - bool, + Optional[bool], Field( title="Conda Auto Install", description="""Set to true to instruct Galaxy to look for and install missing tool @@ -1427,7 +1427,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False conda_auto_init: Annotated[ - bool, + Optional[bool], Field( title="Conda Auto Init", description="""Set to true to instruct Galaxy to install Conda from the web automatically @@ -1437,7 +1437,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True conda_copy_dependencies: Annotated[ - bool, + Optional[bool], Field( title="Conda Copy Dependencies", description="""You must set this to true if conda_prefix and job_working_directory are not on the same @@ -1470,7 +1470,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "environment_modules_mapping.yml" use_cached_dependency_manager: Annotated[ - bool, + Optional[bool], Field( title="Use Cached Dependency Manager", description="""Certain dependency resolvers (namely Conda) take a considerable amount of @@ -1500,7 +1500,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None precache_dependencies: Annotated[ - bool, + Optional[bool], Field( title="Precache Dependencies", description="""By default, when using a cached dependency manager, the dependencies are cached @@ -1582,7 +1582,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "short_term_web_storage" short_term_storage_default_duration: Annotated[ - int, + Optional[int], Field( title="Short Term Storage Default Duration", description="""Default duration before short term web storage files will be cleaned up by Galaxy @@ -1592,7 +1592,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 86400 short_term_storage_maximum_duration: Annotated[ - int, + Optional[int], Field( title="Short Term Storage Maximum Duration", description="""The maximum duration short term storage files can hosted before they will be marked for @@ -1602,7 +1602,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 0 short_term_storage_cleanup_interval: Annotated[ - int, + Optional[int], Field( title="Short Term Storage Cleanup Interval", description="""How many seconds between instances of short term storage being cleaned up in default @@ -1628,7 +1628,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None enable_mulled_containers: Annotated[ - bool, + Optional[bool], Field( title="Enable Mulled Containers", description="""Enable Galaxy to fetch containers registered with quay.io generated @@ -1679,7 +1679,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "involucro" involucro_auto_init: Annotated[ - bool, + Optional[bool], Field( title="Involucro Auto Init", description="""Install involucro as needed to build Docker or Singularity containers for tools. Ignored if @@ -1697,7 +1697,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "conda-forge,bioconda" enable_tool_shed_check: Annotated[ - bool, + Optional[bool], Field( title="Enable Tool Shed Check", description="""Enable automatic polling of relative tool sheds to see if any updates @@ -1709,7 +1709,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False hours_between_check: Annotated[ - int, + Optional[int], Field( title="Hours Between Check", description="""Enable automatic polling of relative tool sheds to see if any updates @@ -1834,7 +1834,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "datatypes_conf.xml" sniff_compressed_dynamic_datatypes_default: Annotated[ - bool, + Optional[bool], Field( title="Sniff Compressed Dynamic Datatypes Default", description="""Enable sniffing of compressed datatypes. This can be configured/overridden @@ -1906,7 +1906,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "compiled_templates" check_job_script_integrity: Annotated[ - bool, + Optional[bool], Field( title="Check Job Script Integrity", description="""Set to false to disable various checks Galaxy will do to ensure it @@ -1916,7 +1916,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True check_job_script_integrity_count: Annotated[ - int, + Optional[int], Field( title="Check Job Script Integrity Count", description="""Number of checks to execute if check_job_script_integrity is enabled.""", @@ -1924,7 +1924,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 35 check_job_script_integrity_sleep: Annotated[ - float, + Optional[float], Field( title="Check Job Script Integrity Sleep", description="""Time to sleep between checks if check_job_script_integrity is enabled (in seconds).""", @@ -1946,7 +1946,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "/bin/bash" enable_tool_document_cache: Annotated[ - bool, + Optional[bool], Field( title="Enable Tool Document Cache", description="""Whether to enable the tool document cache. This cache stores @@ -1988,7 +1988,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None biotools_use_api: Annotated[ - bool, + Optional[bool], Field( title="Biotools Use Api", description="""Set this to true to attempt to resolve bio.tools metadata for tools for tool not @@ -2150,11 +2150,10 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "mulled/locks" mulled_resolution_cache_expire: Annotated[ - int, + Optional[int], Field( title="Mulled Resolution Cache Expire", - description="""Seconds until the beaker cache is considered old and a new value is created. -""", + description="""Seconds until the beaker cache is considered old and a new value is created.""", ), ] = 3600 @@ -2203,7 +2202,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "object_store_conf.xml" object_store_cache_monitor_driver: Annotated[ - Literal["auto", "external", "celery", "inprocess"], + Optional[Literal["auto", "external", "celery", "inprocess"]], Field( title="Object Store Cache Monitor Driver", description="""Specify where cache monitoring is driven for caching object stores @@ -2222,7 +2221,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "auto" object_store_cache_monitor_interval: Annotated[ - int, + Optional[int], Field( title="Object Store Cache Monitor Interval", description="""For object store cache monitoring done by Galaxy, this is the interval between @@ -2245,7 +2244,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "object_store_cache" object_store_cache_size: Annotated[ - int, + Optional[int], Field( title="Object Store Cache Size", description="""Default cache size for caching object stores if cache not configured for @@ -2304,7 +2303,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None smtp_ssl: Annotated[ - bool, + Optional[bool], Field( title="Smtp Ssl", description="""If your SMTP server requires SSL from the beginning of the connection""", @@ -2410,7 +2409,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None user_activation_on: Annotated[ - bool, + Optional[bool], Field( title="User Activation On", description="""User account activation feature global flag. If set to false, the rest of @@ -2422,7 +2421,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False activation_grace_period: Annotated[ - int, + Optional[int], Field( title="Activation Grace Period", description="""Activation grace period (in hours). Activation is not forced (login is not @@ -2433,7 +2432,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 3 password_expiration_period: Annotated[ - int, + Optional[int], Field( title="Password Expiration Period", description="""Password expiration period (in days). Users are required to change their @@ -2445,7 +2444,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 0 session_duration: Annotated[ - int, + Optional[int], Field( title="Session Duration", description="""Galaxy Session Timeout @@ -2480,7 +2479,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu" enable_old_display_applications: Annotated[ - bool, + Optional[bool], Field( title="Enable Old Display Applications", description="""Set this to false to disable the old-style display applications that @@ -2497,7 +2496,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True interactivetools_upstream_proxy: Annotated[ - bool, + Optional[bool], Field( title="Interactivetools Upstream Proxy", description="""Set this to false to redirect users of Interactive tools directly to the Interactive tools proxy. `interactivetools_upstream_proxy` should only be set to false in development.""", @@ -2539,7 +2538,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "interactivetool" interactivetools_shorten_url: Annotated[ - bool, + Optional[bool], Field( title="Interactivetools Shorten Url", description="""Shorten the uuid portion of the subdomain or path for interactive tools. @@ -2550,7 +2549,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False retry_interactivetool_metadata_internally: Annotated[ - bool, + Optional[bool], Field( title="Retry Interactivetool Metadata Internally", description="""Galaxy Interactive Tools (GxITs) can be stopped from within the Galaxy @@ -2563,7 +2562,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True display_galaxy_brand: Annotated[ - bool, + Optional[bool], Field( title="Display Galaxy Brand", description="""This option has been deprecated, use the `logo_src` instead to change the @@ -2636,7 +2635,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "http://localhost:8080" galaxy_infrastructure_web_port: Annotated[ - int, + Optional[int], Field( title="Galaxy Infrastructure Web Port", description="""If the above URL cannot be determined ahead of time in dynamic environments @@ -2651,7 +2650,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 8080 static_enabled: Annotated[ - bool, + Optional[bool], Field( title="Static Enabled", description="""Serve static content, which must be enabled if you're not serving it via a @@ -2663,7 +2662,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True static_cache_time: Annotated[ - int, + Optional[int], Field( title="Static Cache Time", description="""Serve static content, which must be enabled if you're not serving it via a @@ -2746,7 +2745,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "static/robots.txt" display_chunk_size: Annotated[ - int, + Optional[int], Field( title="Display Chunk Size", description="""Incremental Display Options""", @@ -2754,7 +2753,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 65536 apache_xsendfile: Annotated[ - bool, + Optional[bool], Field( title="Apache Xsendfile", description="""For help on configuring the Advanced proxy features, see: @@ -2778,7 +2777,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None upstream_gzip: Annotated[ - bool, + Optional[bool], Field( title="Upstream Gzip", description="""If using compression in the upstream proxy server, use this option to disable @@ -2790,7 +2789,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False upstream_mod_zip: Annotated[ - bool, + Optional[bool], Field( title="Upstream Mod Zip", description="""If using the mod-zip module in nginx, use this option to assemble @@ -2867,7 +2866,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None dynamic_proxy_manage: Annotated[ - bool, + Optional[bool], Field( title="Dynamic Proxy Manage", description="""Have Galaxy manage dynamic proxy component for routing requests to other @@ -2881,7 +2880,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True dynamic_proxy: Annotated[ - Literal["node", "golang"], + Optional[Literal["node", "golang"]], Field( title="Dynamic Proxy", description="""As of 16.04 Galaxy supports multiple proxy types. The original NodeJS @@ -2902,7 +2901,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "session_map.sqlite" dynamic_proxy_bind_port: Annotated[ - int, + Optional[int], Field( title="Dynamic Proxy Bind Port", description="""Set the port and IP for the dynamic proxy to bind to, this must match @@ -2922,7 +2921,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "0.0.0.0" dynamic_proxy_debug: Annotated[ - bool, + Optional[bool], Field( title="Dynamic Proxy Debug", description="""Enable verbose debugging of Galaxy-managed dynamic proxy.""", @@ -2930,7 +2929,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False dynamic_proxy_external_proxy: Annotated[ - bool, + Optional[bool], Field( title="Dynamic Proxy External Proxy", description="""The dynamic proxy is proxied by an external proxy (e.g. apache frontend to @@ -2952,7 +2951,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "gie_proxy" dynamic_proxy_golang_noaccess: Annotated[ - int, + Optional[int], Field( title="Dynamic Proxy Golang Noaccess", description="""This attribute governs the minimum length of time between consecutive HTTP/WS @@ -2963,7 +2962,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 60 dynamic_proxy_golang_clean_interval: Annotated[ - int, + Optional[int], Field( title="Dynamic Proxy Golang Clean Interval", description="""In order to kill containers, the golang proxy has to check at some interval @@ -2996,7 +2995,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None auto_configure_logging: Annotated[ - bool, + Optional[bool], Field( title="Auto Configure Logging", description="""If true, Galaxy will attempt to configure a simple root logger if a @@ -3029,7 +3028,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "0" log_rotate_count: Annotated[ - int, + Optional[int], Field( title="Log Rotate Count", description="""Number of log file backups to keep, per the documentation in @@ -3063,7 +3062,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None database_engine_option_echo: Annotated[ - bool, + Optional[bool], Field( title="Database Engine Option Echo", description="""Print database operations to the server log (warning, quite verbose!).""", @@ -3071,7 +3070,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False database_engine_option_echo_pool: Annotated[ - bool, + Optional[bool], Field( title="Database Engine Option Echo Pool", description="""Print database pool operations to the server log (warning, quite verbose!).""", @@ -3079,7 +3078,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False log_events: Annotated[ - bool, + Optional[bool], Field( title="Log Events", description="""Turn on logging of application events and some user events to the database.""", @@ -3087,7 +3086,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False log_actions: Annotated[ - bool, + Optional[bool], Field( title="Log Actions", description="""Turn on logging of user actions to the database. Actions currently logged @@ -3098,7 +3097,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False fluent_log: Annotated[ - bool, + Optional[bool], Field( title="Fluent Log", description="""Fluentd configuration. Various events can be logged to the fluentd instance @@ -3118,7 +3117,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "localhost" fluent_port: Annotated[ - int, + Optional[int], Field( title="Fluent Port", description="""Fluentd configuration. Various events can be logged to the fluentd instance @@ -3128,7 +3127,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 24224 sanitize_all_html: Annotated[ - bool, + Optional[bool], Field( title="Sanitize All Html", description="""Sanitize all HTML tool output. By default, all tool output served as @@ -3153,7 +3152,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "sanitize_allowlist.txt" serve_xss_vulnerable_mimetypes: Annotated[ - bool, + Optional[bool], Field( title="Serve Xss Vulnerable Mimetypes", description="""By default Galaxy will serve non-HTML tool output that may potentially @@ -3179,7 +3178,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None trust_jupyter_notebook_conversion: Annotated[ - bool, + Optional[bool], Field( title="Trust Jupyter Notebook Conversion", description="""Set to true to use Jupyter nbconvert to build HTML from Jupyter @@ -3192,7 +3191,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False debug: Annotated[ - bool, + Optional[bool], Field( title="Debug", description="""Debug enables access to various config options useful for development @@ -3204,7 +3203,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False use_lint: Annotated[ - bool, + Optional[bool], Field( title="Use Lint", description="""Check for WSGI compliance.""", @@ -3212,7 +3211,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False use_profile: Annotated[ - bool, + Optional[bool], Field( title="Use Profile", description="""Run the Python profiler on each request.""", @@ -3220,7 +3219,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False use_printdebug: Annotated[ - bool, + Optional[bool], Field( title="Use Printdebug", description="""Intercept print statements and show them on the returned page.""", @@ -3228,7 +3227,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True monitor_thread_join_timeout: Annotated[ - int, + Optional[int], Field( title="Monitor Thread Join Timeout", description="""When stopping Galaxy cleanly, how much time to give various monitoring/polling @@ -3243,7 +3242,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 30 use_heartbeat: Annotated[ - bool, + Optional[bool], Field( title="Use Heartbeat", description="""Write thread status periodically to 'heartbeat.log', (careful, uses disk @@ -3254,7 +3253,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False heartbeat_interval: Annotated[ - int, + Optional[int], Field( title="Heartbeat Interval", description="""Control the period (in seconds) between dumps. Use -1 to disable. Regardless @@ -3296,7 +3295,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "ERROR" sentry_traces_sample_rate: Annotated[ - float, + Optional[float], Field( title="Sentry Traces Sample Rate", description="""Set to a number between 0 and 1. With this option set, every transaction created @@ -3331,7 +3330,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None statsd_port: Annotated[ - int, + Optional[int], Field( title="Statsd Port", description="""Log to statsd @@ -3359,7 +3358,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "galaxy" statsd_influxdb: Annotated[ - bool, + Optional[bool], Field( title="Statsd Influxdb", description="""If you are using telegraf to collect these metrics and then sending @@ -3371,7 +3370,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False statsd_mock_calls: Annotated[ - bool, + Optional[bool], Field( title="Statsd Mock Calls", description="""Mock out statsd client calls - only used by testing infrastructure really. @@ -3381,7 +3380,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False user_library_import_dir_auto_creation: Annotated[ - bool, + Optional[bool], Field( title="User Library Import Dir Auto Creation", description="""If user_library_import_dir is set, this option will auto create a library @@ -3405,7 +3404,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None user_library_import_check_permissions: Annotated[ - bool, + Optional[bool], Field( title="User Library Import Check Permissions", description="""In conjunction or alternatively, Galaxy can restrict user library imports to @@ -3416,7 +3415,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False allow_path_paste: Annotated[ - bool, + Optional[bool], Field( title="Allow Path Paste", description="""Allow admins to paste filesystem paths during upload. For libraries this @@ -3444,7 +3443,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None tool_name_boost: Annotated[ - float, + Optional[float], Field( title="Tool Name Boost", description="""In tool search, a query match against a tool's name text will receive @@ -3454,7 +3453,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 20.0 tool_name_exact_multiplier: Annotated[ - float, + Optional[float], Field( title="Tool Name Exact Multiplier", description="""If a search query matches a tool name exactly, the score will be @@ -3464,7 +3463,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 10.0 tool_id_boost: Annotated[ - float, + Optional[float], Field( title="Tool Id Boost", description="""In tool search, a query match against a tool's ID text will receive @@ -3475,7 +3474,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 20.0 tool_section_boost: Annotated[ - float, + Optional[float], Field( title="Tool Section Boost", description="""In tool search, a query match against a tool's section text will @@ -3485,7 +3484,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 3.0 tool_description_boost: Annotated[ - float, + Optional[float], Field( title="Tool Description Boost", description="""In tool search, a query match against a tool's description text will @@ -3495,7 +3494,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 8.0 tool_label_boost: Annotated[ - float, + Optional[float], Field( title="Tool Label Boost", description="""In tool search, a query match against a tool's label text will @@ -3505,7 +3504,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1.0 tool_stub_boost: Annotated[ - float, + Optional[float], Field( title="Tool Stub Boost", description="""A stub is parsed from the GUID as "owner/repo/tool_id". @@ -3516,7 +3515,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 2.0 tool_help_boost: Annotated[ - float, + Optional[float], Field( title="Tool Help Boost", description="""In tool search, a query match against a tool's help text will receive @@ -3526,7 +3525,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1.0 tool_help_bm25f_k1: Annotated[ - float, + Optional[float], Field( title="Tool Help Bm25F K1", description="""The lower this parameter, the greater the diminishing reward for @@ -3539,7 +3538,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 0.5 tool_search_limit: Annotated[ - int, + Optional[int], Field( title="Tool Search Limit", description="""Limits the number of results in toolbox search. Use to set the @@ -3549,7 +3548,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 20 tool_enable_ngram_search: Annotated[ - bool, + Optional[bool], Field( title="Tool Enable Ngram Search", description="""Disabling this will prevent partial matches on tool names. @@ -3562,7 +3561,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True tool_ngram_minsize: Annotated[ - int, + Optional[int], Field( title="Tool Ngram Minsize", description="""Set minimum character length of ngrams""", @@ -3570,7 +3569,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 3 tool_ngram_maxsize: Annotated[ - int, + Optional[int], Field( title="Tool Ngram Maxsize", description="""Set maximum character length of ngrams""", @@ -3578,7 +3577,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 4 tool_ngram_factor: Annotated[ - float, + Optional[float], Field( title="Tool Ngram Factor", description="""Ngram matched scores will be multiplied by this factor. Should always @@ -3654,7 +3653,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "USING THE DEFAULT IS NOT SECURE!" normalize_remote_user_email: Annotated[ - bool, + Optional[bool], Field( title="Normalize Remote User Email", description="""If your proxy and/or authentication source does not normalize e-mail @@ -3678,7 +3677,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None show_user_prepopulate_form: Annotated[ - bool, + Optional[bool], Field( title="Show User Prepopulate Form", description="""When using LDAP for authentication, allow administrators to pre-populate users @@ -3688,7 +3687,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False new_user_dataset_access_role_default_private: Annotated[ - bool, + Optional[bool], Field( title="New User Dataset Access Role Default Private", description="""By default, users' data will be public, but setting this to true will cause @@ -3700,7 +3699,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False expose_user_name: Annotated[ - bool, + Optional[bool], Field( title="Expose User Name", description="""Expose user list. Setting this to true will expose the user list to @@ -3732,7 +3731,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None enable_beta_gdpr: Annotated[ - bool, + Optional[bool], Field( title="Enable Beta Gdpr", description="""Enables GDPR Compliance mode. This makes several changes to the way @@ -3754,7 +3753,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False enable_beta_workflow_modules: Annotated[ - bool, + Optional[bool], Field( title="Enable Beta Workflow Modules", description="""Enable beta workflow modules that should not yet be considered part of Galaxy's @@ -3805,7 +3804,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "ga" parallelize_workflow_scheduling_within_histories: Annotated[ - bool, + Optional[bool], Field( title="Parallelize Workflow Scheduling Within Histories", description="""If multiple job handlers are enabled, allow Galaxy to schedule workflow invocations @@ -3816,7 +3815,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False maximum_workflow_invocation_duration: Annotated[ - int, + Optional[int], Field( title="Maximum Workflow Invocation Duration", description="""This is the maximum amount of time a workflow invocation may stay in an active @@ -3827,7 +3826,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 2678400 maximum_workflow_jobs_per_scheduling_iteration: Annotated[ - int, + Optional[int], Field( title="Maximum Workflow Jobs Per Scheduling Iteration", description="""Specify a maximum number of jobs that any given workflow scheduling iteration can create. @@ -3841,7 +3840,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1000 flush_per_n_datasets: Annotated[ - int, + Optional[int], Field( title="Flush Per N Datasets", description="""Maximum number of datasets to create before flushing created datasets to database. @@ -3853,7 +3852,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1000 max_discovered_files: Annotated[ - int, + Optional[int], Field( title="Max Discovered Files", description="""Set this to a positive integer value to limit the number of datasets that can be discovered by @@ -3865,7 +3864,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 10000 history_local_serial_workflow_scheduling: Annotated[ - bool, + Optional[bool], Field( title="History Local Serial Workflow Scheduling", description="""Force serial scheduling of workflows within the context of a particular history""", @@ -3987,7 +3986,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None enable_tool_tags: Annotated[ - bool, + Optional[bool], Field( title="Enable Tool Tags", description="""Enable tool tags (associating tools with tags). This has its own option @@ -4032,7 +4031,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None ftp_upload_purge: Annotated[ - bool, + Optional[bool], Field( title="Ftp Upload Purge", description="""Set to false to prevent Galaxy from deleting uploaded FTP files @@ -4042,7 +4041,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True expose_dataset_path: Annotated[ - bool, + Optional[bool], Field( title="Expose Dataset Path", description="""This option allows users to see the full path of datasets via the "View @@ -4061,7 +4060,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "job_metrics_conf.xml" expose_potentially_sensitive_job_metrics: Annotated[ - bool, + Optional[bool], Field( title="Expose Potentially Sensitive Job Metrics", description="""This option allows users to see the job metrics (except for environment @@ -4071,7 +4070,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False enable_legacy_sample_tracking_api: Annotated[ - bool, + Optional[bool], Field( title="Enable Legacy Sample Tracking Api", description="""Enable the API for sample tracking""", @@ -4079,7 +4078,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False enable_data_manager_user_view: Annotated[ - bool, + Optional[bool], Field( title="Enable Data Manager User View", description="""Allow non-admin users to view available Data Manager options.""", @@ -4190,7 +4189,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = None track_jobs_in_database: Annotated[ - bool, + Optional[bool], Field( title="Track Jobs In Database", description="""This option is deprecated, use the `mem-self` handler assignment option in the @@ -4200,7 +4199,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True use_tasked_jobs: Annotated[ - bool, + Optional[bool], Field( title="Use Tasked Jobs", description="""This enables splitting of jobs into tasks, if specified by the particular tool @@ -4211,7 +4210,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False local_task_queue_workers: Annotated[ - int, + Optional[int], Field( title="Local Task Queue Workers", description="""This enables splitting of jobs into tasks, if specified by the particular tool @@ -4222,7 +4221,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 2 job_handler_monitor_sleep: Annotated[ - float, + Optional[float], Field( title="Job Handler Monitor Sleep", description="""Each Galaxy job handler process runs one thread responsible for discovering jobs and @@ -4235,7 +4234,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1.0 job_runner_monitor_sleep: Annotated[ - float, + Optional[float], Field( title="Job Runner Monitor Sleep", description="""Each Galaxy job handler process runs one thread per job runner plugin responsible for @@ -4248,7 +4247,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1.0 workflow_monitor_sleep: Annotated[ - float, + Optional[float], Field( title="Workflow Monitor Sleep", description="""Each Galaxy workflow handler process runs one thread responsible for @@ -4261,7 +4260,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 1.0 metadata_strategy: Annotated[ - Literal["directory", "extended", "directory_celery", "extended_celery", "legacy"], + Optional[Literal["directory", "extended", "directory_celery", "extended_celery", "legacy"]], Field( title="Metadata Strategy", description="""Determines how metadata will be set. Valid values are `directory`, `extended`, @@ -4277,7 +4276,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "directory" retry_metadata_internally: Annotated[ - bool, + Optional[bool], Field( title="Retry Metadata Internally", description="""Although it is fairly reliable, setting metadata can occasionally fail. In @@ -4290,7 +4289,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = True max_metadata_value_size: Annotated[ - int, + Optional[int], Field( title="Max Metadata Value Size", description="""Very large metadata values can cause Galaxy crashes. This will allow @@ -4303,7 +4302,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 5242880 outputs_to_working_directory: Annotated[ - bool, + Optional[bool], Field( title="Outputs To Working Directory", description="""This option will override tool output paths to write outputs to the job @@ -4318,7 +4317,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = False retry_job_output_collection: Annotated[ - int, + Optional[int], Field( title="Retry Job Output Collection", description="""If your network filesystem's caching prevents the Galaxy server from seeing @@ -4588,7 +4587,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "workflow_schedulers_conf.xml" cache_user_job_count: Annotated[ - bool, + Optional[bool], Field( title="Cache User Job Count", description="""If using job concurrency limits (configured in job_config_file), several @@ -4692,7 +4691,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE" celery_conf: Annotated[ - Any, + Optional[Any], Field( title="Celery Conf", description="""Configuration options passed to Celery. @@ -4712,7 +4711,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = {"task_routes": {"galaxy.fetch_data": "galaxy.external", "galaxy.set_job_metadata": "galaxy.external"}} celery_user_rate_limit: Annotated[ - float, + Optional[float], Field( title="Celery User Rate Limit", description="""If set to a non-0 value, upper limit on number of @@ -4722,7 +4721,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = 0.0 use_pbkdf2: Annotated[ - bool, + Optional[bool], Field( title="Use Pbkdf2", description="""Allow disabling pbkdf2 hashing of passwords for legacy situations. @@ -4757,7 +4756,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "vault_conf.yml" display_builtin_converters: Annotated[ - bool, + Optional[bool], Field( title="Display Builtin Converters", description="""Display built-in converters in the tool panel.""", @@ -4775,7 +4774,7 @@ class FullGalaxyConfig(AdminExposableGalaxyConfig, SchemaCompatibleConfigValues) ] = "themes_conf.yml" expired_notifications_cleanup_interval: Annotated[ - int, + Optional[int], Field( title="Expired Notifications Cleanup Interval", description="""The interval in seconds between attempts to delete all expired notifications from the database (every 24 hours by default). Runs in a Celery task.""",