biothings.web

Generate a customized BioThings API given a supported database.

biothings.web.launcher: Launch web applications in different environments. biothings.web.applications: HTTP web application over data services below. biothings.web.services & query: Data services built on top of connections. biothings.web.connections: Elasticsearch, MongoDB and SQL database access.

Layers

• biothings.web.launcher
  • BiothingsAPIBaseLauncher
    • BiothingsAPIBaseLauncher.get_app()
    • BiothingsAPIBaseLauncher.get_server()
    • BiothingsAPIBaseLauncher.start()
  • BiothingsAPILauncher
  • FastAPILauncher
    • FastAPILauncher.get_app()
  • FlaskAPILauncher
    • FlaskAPILauncher.get_app()
    • FlaskAPILauncher.get_server()
    • FlaskAPILauncher.start()
  • TornadoAPILauncher
    • TornadoAPILauncher.get_app()
    • TornadoAPILauncher.get_server()
    • TornadoAPILauncher.start()
    • TornadoAPILauncher.use_curl()
  • main()
• biothings.web.applications
  • BiothingsAPI
  • FastAPIBiothingsAPI
    • FastAPIBiothingsAPI.get_app()
  • FlaskBiothingsAPI
    • FlaskBiothingsAPI.get_app()
  • TornadoBiothingsAPI
    • TornadoBiothingsAPI.get_app()
  • load_class()
• biothings.web.services
  • biothings.web.services.query
  • biothings.web.services.health
    • DBHealth
      • DBHealth.check()
    • ESHealth
      • ESHealth.async_check()
      • ESHealth.check()
    • MongoHealth
      • MongoHealth.check()
    • SQLHealth
      • SQLHealth.check()
  • biothings.web.services.metadata
    • BiothingHubMeta
      • BiothingHubMeta.to_dict()
    • BiothingLicenses
      • BiothingLicenses.to_dict()
    • BiothingMappings
      • BiothingMappings.to_dict()
    • BiothingMetaProp
      • BiothingMetaProp.to_dict()
    • BiothingsESMetadata
      • BiothingsESMetadata.refresh()
      • BiothingsESMetadata.types
      • BiothingsESMetadata.update()
    • BiothingsMetadata
      • BiothingsMetadata.get_licenses()
      • BiothingsMetadata.get_mappings()
      • BiothingsMetadata.get_metadata()
      • BiothingsMetadata.refresh()
    • BiothingsMongoMetadata
      • BiothingsMongoMetadata.get_licenses()
      • BiothingsMongoMetadata.get_mappings()
      • BiothingsMongoMetadata.refresh()
      • BiothingsMongoMetadata.types
    • BiothingsSQLMetadata
      • BiothingsSQLMetadata.refresh()
      • BiothingsSQLMetadata.types
  • biothings.web.services.namespace
    • BiothingsDBProxy
      • BiothingsDBProxy.configure()
    • BiothingsNamespace
    • load_class()
• biothings.web.connections
  • get_es_client()
  • get_mongo_client()
  • get_sql_client()
  • _ClientPool
    • _ClientPool.get_async_client()
    • _ClientPool.get_client()
    • _ClientPool.hash()
  • es
  • sql
  • mongo

Components

• biothings.web.analytics
  • biothings.web.analytics.channels
    • Channel
      • Channel.handles()
      • Channel.send()
    • GA4Channel
      • GA4Channel.handles()
      • GA4Channel.send()
      • GA4Channel.send_request()
    • GAChannel
      • GAChannel.handles()
      • GAChannel.send()
      • GAChannel.send_request()
    • SlackChannel
      • SlackChannel.handles()
      • SlackChannel.send()
      • SlackChannel.send_request()
  • biothings.web.analytics.events
    • Event
      • Event.to_GA4_payload()
      • Event.to_GA_payload()
    • GAEvent
      • GAEvent.to_GA4_payload()
      • GAEvent.to_GA_payload()
    • Message
      • Message.DEFAULTS
      • Message.to_ADF()
      • Message.to_email_payload()
      • Message.to_jira_payload()
      • Message.to_slack_payload()
  • biothings.web.analytics.notifiers
    • AnalyticsMixin
      • AnalyticsMixin.on_finish()
    • Notifier
      • Notifier.broadcast()
• biothings.web.handlers
  • biothings.web.handlers.base
    • BaseAPIHandler
      • BaseAPIHandler.cache
      • BaseAPIHandler.cache_control_template
      • BaseAPIHandler.format
      • BaseAPIHandler.get_template_path()
      • BaseAPIHandler.initialize()
      • BaseAPIHandler.kwargs
      • BaseAPIHandler.name
      • BaseAPIHandler.on_finish()
      • BaseAPIHandler.options()
      • BaseAPIHandler.prepare()
      • BaseAPIHandler.set_cache_header()
      • BaseAPIHandler.set_default_headers()
      • BaseAPIHandler.write()
      • BaseAPIHandler.write_error()
    • BaseHandler
      • BaseHandler.biothings
  • biothings.web.handlers.query
    • BaseQueryHandler
      • BaseQueryHandler.initialize()
      • BaseQueryHandler.prepare()
      • BaseQueryHandler.write()
    • BiothingHandler
      • BiothingHandler.get()
      • BiothingHandler.name
      • BiothingHandler.post()
    • MetadataFieldHandler
      • MetadataFieldHandler.get()
      • MetadataFieldHandler.kwargs
      • MetadataFieldHandler.name
    • MetadataSourceHandler
      • MetadataSourceHandler.extras()
      • MetadataSourceHandler.get()
      • MetadataSourceHandler.kwargs
      • MetadataSourceHandler.name
    • QueryHandler
      • QueryHandler.get()
      • QueryHandler.name
      • QueryHandler.post()
  • biothings.web.handlers.services
    • APISpecificationHandler
      • APISpecificationHandler.get()
    • FrontPageHandler
      • FrontPageHandler.get()
      • FrontPageHandler.get_template_path()
    • StatusHandler
      • StatusHandler.get()
      • StatusHandler.head()
• biothings.web.options
  • biothings.web.options.manager
    • Converter
      • Converter.convert()
      • Converter.convert_to()
      • Converter.str_to_bool()
      • Converter.str_to_int()
      • Converter.str_to_list()
      • Converter.subclasses()
      • Converter.to_type()
      • Converter.translate()
    • Existentialist
      • Existentialist.inquire()
    • FormArgCvter
      • FormArgCvter.convert_to()
    • JsonArgCvter
      • JsonArgCvter.convert_to()
      • JsonArgCvter.to_type()
    • Locator
      • Locator.lookin()
    • Option
      • Option.parse()
    • OptionError
      • OptionError.simplify()
    • OptionSet
      • OptionSet.parse()
      • OptionSet.setup()
    • OptionsManager
      • OptionsManager.add()
      • OptionsManager.log()
    • PathArgCvter
    • QueryArgCvter
      • QueryArgCvter.str_to_bool()
    • ReqArgs
      • ReqArgs.Path
      • ReqArgs.lookup()
    • ReqResult
    • Validator
      • Validator.validate()
  • biothings.web.options.openapi
    • OpenAPIContactContext
      • OpenAPIContactContext.ATTRIBUTE_FIELDS
      • OpenAPIContactContext.EXTENSION
      • OpenAPIContactContext.email()
      • OpenAPIContactContext.name()
      • OpenAPIContactContext.subclasses
      • OpenAPIContactContext.url()
    • OpenAPIContext
      • OpenAPIContext.CHILD_CONTEXTS
      • OpenAPIContext.EXTENSION
      • OpenAPIContext.info()
      • OpenAPIContext.path()
      • OpenAPIContext.server()
      • OpenAPIContext.subclasses
    • OpenAPIDocumentBuilder
    • OpenAPIExternalDocsContext
      • OpenAPIExternalDocsContext.ATTRIBUTE_FIELDS
      • OpenAPIExternalDocsContext.EXTENSION
      • OpenAPIExternalDocsContext.subclasses
      • OpenAPIExternalDocsContext.url()
    • OpenAPIInfoContext
      • OpenAPIInfoContext.ATTRIBUTE_FIELDS
      • OpenAPIInfoContext.CHILD_CONTEXTS
      • OpenAPIInfoContext.EXTENSION
      • OpenAPIInfoContext.contact()
      • OpenAPIInfoContext.license()
      • OpenAPIInfoContext.subclasses
      • OpenAPIInfoContext.terms_of_service()
      • OpenAPIInfoContext.title()
      • OpenAPIInfoContext.version()
    • OpenAPILicenseContext
      • OpenAPILicenseContext.ATTRIBUTE_FIELDS
      • OpenAPILicenseContext.EXTENSION
      • OpenAPILicenseContext.name()
      • OpenAPILicenseContext.subclasses
      • OpenAPILicenseContext.url()
    • OpenAPIOperation
      • OpenAPIOperation.ATTRIBUTE_FIELDS
      • OpenAPIOperation.EXTENSION
      • OpenAPIOperation.operation_id()
      • OpenAPIOperation.subclasses
    • OpenAPIParameterContext
      • OpenAPIParameterContext.ATTRIBUTE_FIELDS
      • OpenAPIParameterContext.EXTENSION
      • OpenAPIParameterContext.allow_empty()
      • OpenAPIParameterContext.allow_reserved()
      • OpenAPIParameterContext.deprecated()
      • OpenAPIParameterContext.explode()
      • OpenAPIParameterContext.schema()
      • OpenAPIParameterContext.style()
      • OpenAPIParameterContext.subclasses
      • OpenAPIParameterContext.type()
    • OpenAPIPathItemContext
      • OpenAPIPathItemContext.CHILD_CONTEXTS
      • OpenAPIPathItemContext.EXTENSION
      • OpenAPIPathItemContext.delete()
      • OpenAPIPathItemContext.get()
      • OpenAPIPathItemContext.head()
      • OpenAPIPathItemContext.http_method
      • OpenAPIPathItemContext.options()
      • OpenAPIPathItemContext.patch()
      • OpenAPIPathItemContext.post()
      • OpenAPIPathItemContext.put()
      • OpenAPIPathItemContext.subclasses
      • OpenAPIPathItemContext.trace()
• biothings.web.query
  • biothings.web.query.builder
    • ESQueryBuilder
      • ESQueryBuilder.apply_extras()
      • ESQueryBuilder.build()
      • ESQueryBuilder.default_match_query()
      • ESQueryBuilder.default_string_query()
    • ESScrollID
    • ESUserQuery
      • ESUserQuery.get_filter()
      • ESUserQuery.get_query()
      • ESUserQuery.has_filter()
      • ESUserQuery.has_query()
      • ESUserQuery.logger
    • Group
      • Group.scopes
      • Group.term
    • MongoQueryBuilder
      • MongoQueryBuilder.build()
    • QStringParser
      • QStringParser.parse()
    • Query
      • Query.scopes
      • Query.term
    • RawQueryInterrupt
    • SQLQueryBuilder
      • SQLQueryBuilder.build()
  • biothings.web.query.engine
    • AsyncESQueryBackend
      • AsyncESQueryBackend.execute()
    • ESQueryBackend
      • ESQueryBackend.adjust_index()
      • ESQueryBackend.execute()
    • EndScrollInterrupt
    • MongoQueryBackend
      • MongoQueryBackend.execute()
    • RawResultInterrupt
    • ResultInterrupt
    • SQLQueryBackend
      • SQLQueryBackend.execute()
  • biothings.web.query.formatter
    • Doc
    • ESResultFormatter
      • ESResultFormatter.transform()
      • ESResultFormatter.transform_aggs()
      • ESResultFormatter.transform_hit()
      • ESResultFormatter.transform_mapping()
      • ESResultFormatter.trasform_jmespath()
      • ESResultFormatter.trasform_jmespath_obj()
      • ESResultFormatter.traverse()
    • FormatterDict
      • FormatterDict.collapse()
      • FormatterDict.exclude()
      • FormatterDict.include()
      • FormatterDict.wrap()
    • Hits
    • MongoResultFormatter
      • MongoResultFormatter.transform()
    • ResultFormatter
      • ResultFormatter.transform()
      • ResultFormatter.transform_mapping()
    • ResultFormatterException
    • SQLResultFormatter
      • SQLResultFormatter.transform()
  • biothings.web.query.pipeline
    • AsyncESQueryPipeline
      • AsyncESQueryPipeline.fetch()
      • AsyncESQueryPipeline.search()
    • ESQueryPipeline
      • ESQueryPipeline.fetch()
      • ESQueryPipeline.search()
    • MongoQueryPipeline
    • QueryPipeline
      • QueryPipeline.fetch()
      • QueryPipeline.search()
    • QueryPipelineException
      • QueryPipelineException.code
      • QueryPipelineException.details
      • QueryPipelineException.summary
    • QueryPipelineInterrupt
    • SQLQueryPipeline
    • capturesESExceptions()
• biothings.web.settings
  • biothings.web.settings.configs
    • ConfigModule
    • ConfigPackage
      • ConfigPackage.modules
      • ConfigPackage.root
    • load()
    • load_module()
  • biothings.web.settings.default
  • biothings.web.settings.validators
    • DBParamValidator
      • DBParamValidator.validate()
    • MongoParamValidaor
      • MongoParamValidaor.validate()
    • SubmoduleValidator
      • SubmoduleValidator.validate()
    • WebAPIValidator
      • WebAPIValidator.validate()
• biothings.web.templates