BioThings SDK
0.12.x
Products
BioThings Studio
BioThings CLI
BioThings Standalone
BioThings Hub
BioThings Web
DataTransform Module
Documentation
biothings.web
biothings.tests
biothings.utils
biothings.hub
biothings.cli
BioThings SDK
Index
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Index
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_ClientPool (class in biothings.web.connections)
A
access_key (biothings.hub.dataindex.snapshooter.CloudStorage attribute)
add() (biothings.hub.datatransform.ciidstruct.CIIDStruct method)
(biothings.hub.datatransform.datatransform.IDStruct method)
(biothings.utils.hub_db.ChangeWatcher class method)
(biothings.web.options.manager.OptionsManager method)
add_api_endpoint() (biothings.hub.HubServer method)
add_update() (biothings.hub.dataload.sync.MongoSync method)
add_watch() (biothings.utils.hub.TornadoAutoReloadHubReloader method)
AddOperation (class in biothings.utils.jsonpatch)
address (biothings.utils.es.Database property)
(biothings.utils.hub_db.IDatabase property)
(biothings.utils.sqlite3.Database property)
addsuffix() (in module biothings.utils.common)
adjust_index() (biothings.web.query.engine.ESQueryBackend method)
AdvancedPluginLoader (class in biothings.hub.dataplugin.assistant)
agg_by_append() (in module biothings.utils.parallel_mp)
agg_by_sum() (in module biothings.utils.parallel_mp)
aggregate() (biothings.utils.parallel_mp.ParallelResult method)
aiogunzipall() (in module biothings.utils.common)
allow_empty() (biothings.web.options.openapi.OpenAPIParameterContext method)
allow_reserved() (biothings.web.options.openapi.OpenAPIParameterContext method)
AlreadyRunningException
alwayslist() (in module biothings.utils.dataload)
am (built-in variable)
AnalyticsMixin (class in biothings.web.analytics.notifiers)
anonymous_download() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
anyfile() (in module biothings.utils.common)
api (built-in variable)
APIDumper (class in biothings.hub.dataload.dumper)
APIManager (class in biothings.hub.api.manager)
APIManagerException
APISpecificationHandler (class in biothings.web.handlers.services)
Application (class in biothings.cli.web_app)
apply()
(biothings.utils.jsonpatch.AddOperation method)
(biothings.utils.jsonpatch.CopyOperation method)
(biothings.utils.jsonpatch.JsonPatch method)
(biothings.utils.jsonpatch.MoveOperation method)
(biothings.utils.jsonpatch.PatchOperation method)
(biothings.utils.jsonpatch.RemoveOperation method)
(biothings.utils.jsonpatch.ReplaceOperation method)
(biothings.utils.jsonpatch.TestOperation method)
apply_diff() (biothings.hub.autoupdate.uploader.BiothingsUploader method)
apply_extras() (biothings.web.query.builder.ESQueryBuilder method)
apply_patch() (in module biothings.utils.jsonpatch)
ARCHIVE (biothings.hub.dataload.dumper.BaseDumper attribute)
archive()
archive_merge() (biothings.hub.databuild.builder.BuilderManager method)
asdict() (biothings.utils.configuration.ConfigAttrMeta method)
ask() (in module biothings.utils.common)
AssistantException
AssistantManager (class in biothings.hub.dataplugin.assistant)
AssistedDumper (class in biothings.hub.dataplugin.assistant)
AssistedUploader (class in biothings.hub.dataplugin.assistant)
async_check() (biothings.web.services.health.ESHealth method)
AsyncESQueryBackend (class in biothings.web.query.engine)
AsyncESQueryPipeline (class in biothings.web.query.pipeline)
at() (biothings.hub.dataindex.indexer_registrar.Stage method)
attach_cold_src_build_reader() (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader method)
ATTRIBUTE_FIELDS (biothings.web.options.openapi.OpenAPIContactContext attribute)
(biothings.web.options.openapi.OpenAPIExternalDocsContext attribute)
(biothings.web.options.openapi.OpenAPIInfoContext attribute)
(biothings.web.options.openapi.OpenAPILicenseContext attribute)
(biothings.web.options.openapi.OpenAPIOperation attribute)
(biothings.web.options.openapi.OpenAPIParameterContext attribute)
audit() (in module biothings.hub.dataindex.snapshot_registrar)
auth_download() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
AUTO_PURGE_INDEX (biothings.hub.autoupdate.uploader.BiothingsUploader attribute)
AUTO_UPLOAD (biothings.hub.autoupdate.dumper.BiothingsDumper attribute)
(biothings.hub.dataload.dumper.BaseDumper attribute)
AutoBuildConfig (class in biothings.hub.databuild.buildconfig)
AutoBuildConfigError
AutoHubFeature (class in biothings.hub.standalone)
AutoHubServer (class in biothings.hub.standalone)
AWS_ACCESS_KEY_ID (biothings.hub.autoupdate.dumper.BiothingsDumper attribute)
AWS_SECRET_ACCESS_KEY (biothings.hub.autoupdate.dumper.BiothingsDumper attribute)
B
backend()
backup()
(in module biothings.utils.hub_db)
base_url (biothings.hub.autoupdate.dumper.BiothingsDumper property)
BaseAPIHandler (class in biothings.web.handlers.base)
BaseAssistant (class in biothings.hub.dataplugin.assistant)
BaseDiffer (class in biothings.hub.databuild.differ)
BaseDumper (class in biothings.hub.dataload.dumper)
BaseHandler (class in biothings.cli.web_app)
(class in biothings.hub.api.handlers.base)
(class in biothings.web.handlers.base)
BaseHubReloader (class in biothings.utils.hub)
BaseManager (class in biothings.utils.manager)
BaseMapper (class in biothings.hub.databuild.mapper)
BaseMode (class in biothings.utils.inspect)
BasePluginLoader (class in biothings.hub.dataplugin.assistant)
BasePreCompiledDataProvider (class in biothings.hub.databuild.prebuilder)
BasePublisher (class in biothings.hub.datarelease.publisher)
BaseQueryHandler (class in biothings.web.handlers.query)
BaseSourceManager (class in biothings.utils.manager)
BaseSourceUploader (class in biothings.hub.dataload.uploader)
BaseStatusRegisterer (class in biothings.utils.manager)
BaseSyncer (class in biothings.hub.databuild.syncer)
batch_size (biothings.hub.datatransform.datatransform.DataTransform attribute)
(biothings.hub.datatransform.datatransform_api.DataTransformAPI attribute)
(biothings.hub.datatransform.datatransform_mdb.DataTransformMDB attribute)
before_configure() (biothings.hub.HubServer method)
before_start() (biothings.hub.HubServer method)
begin_auth() (biothings.hub.HubSSHServer method)
BiothingHandler (class in biothings.web.handlers.query)
BiothingHubMeta (class in biothings.web.services.metadata)
BiothingLicenses (class in biothings.web.services.metadata)
BiothingMappings (class in biothings.web.services.metadata)
BiothingMetaProp (class in biothings.web.services.metadata)
biothings (biothings.web.handlers.base.BaseHandler property)
biothings.cli
module
biothings.cli.dataplugin
module
biothings.cli.dataplugin_hub
module
biothings.cli.utils
module
biothings.cli.web_app
module
biothings.hub
module
biothings.hub.api
module
biothings.hub.api.handlers.base
module
biothings.hub.api.handlers.log
module
biothings.hub.api.handlers.shell
module
biothings.hub.api.handlers.upload
module
biothings.hub.api.handlers.ws
module
biothings.hub.api.manager
module
biothings.hub.autoupdate.dumper
module
biothings.hub.autoupdate.uploader
module
biothings.hub.databuild.backend
module
biothings.hub.databuild.buildconfig
module
biothings.hub.databuild.builder
module
biothings.hub.databuild.differ
module
biothings.hub.databuild.mapper
module
biothings.hub.databuild.prebuilder
module
biothings.hub.databuild.syncer
module
biothings.hub.dataexport.ids
module
biothings.hub.dataindex.idcache
module
biothings.hub.dataindex.indexer
module
biothings.hub.dataindex.indexer_cleanup
module
biothings.hub.dataindex.indexer_payload
module
biothings.hub.dataindex.indexer_registrar
module
biothings.hub.dataindex.indexer_schedule
module
biothings.hub.dataindex.indexer_task
module
biothings.hub.dataindex.snapshooter
module
biothings.hub.dataindex.snapshot_cleanup
module
biothings.hub.dataindex.snapshot_registrar
module
biothings.hub.dataindex.snapshot_repo
module
biothings.hub.dataindex.snapshot_task
module
biothings.hub.datainspect.inspector
module
biothings.hub.dataload.dumper
module
biothings.hub.dataload.source
module
biothings.hub.dataload.storage
module
biothings.hub.dataload.sync
module
biothings.hub.dataload.uploader
module
biothings.hub.dataplugin.assistant
module
biothings.hub.dataplugin.manager
module
biothings.hub.datarelease
module
biothings.hub.datarelease.publisher
module
biothings.hub.datarelease.releasenote
module
biothings.hub.datatransform.ciidstruct
module
biothings.hub.datatransform.datatransform
module
biothings.hub.datatransform.datatransform_api
module
biothings.hub.datatransform.datatransform_mdb
module
biothings.hub.datatransform.histogram
module
biothings.hub.standalone
module
biothings.tests
module
biothings.tests.hub
module
biothings.tests.web
module
biothings.utils
module
biothings.utils.aws
module
biothings.utils.backend
module
biothings.utils.common
module
biothings.utils.configuration
module
biothings.utils.dataload
module
biothings.utils.diff
module
biothings.utils.doc_traversal
module
biothings.utils.docs
module
biothings.utils.dotfield
module
biothings.utils.dotstring
module
biothings.utils.es
module
biothings.utils.exclude_ids
module
biothings.utils.hub
module
biothings.utils.hub_db
module
biothings.utils.info
module
biothings.utils.inspect
module
biothings.utils.jsondiff
module
biothings.utils.jsonpatch
module
biothings.utils.jsonschema
module
biothings.utils.loggers
module
biothings.utils.manager
module
biothings.utils.mongo
module
biothings.utils.parallel
module
biothings.utils.parallel_mp
module
biothings.utils.parsers
module
biothings.utils.redis
module
biothings.utils.serializer
module
biothings.utils.sqlite3
module
biothings.utils.version
module
biothings.web
module
biothings.web.analytics
module
biothings.web.analytics.channels
module
biothings.web.analytics.events
module
biothings.web.analytics.notifiers
module
biothings.web.applications
module
biothings.web.connections
module
biothings.web.handlers
module
biothings.web.handlers.base
module
biothings.web.handlers.query
module
biothings.web.handlers.services
module
biothings.web.launcher
module
biothings.web.options
module
biothings.web.options.manager
module
biothings.web.options.openapi
module
biothings.web.query
module
biothings.web.query.builder
module
biothings.web.query.engine
module
biothings.web.query.formatter
module
biothings.web.query.pipeline
module
biothings.web.services
module
biothings.web.services.health
module
biothings.web.services.metadata
module
biothings.web.services.namespace
module
biothings.web.services.query
module
biothings.web.settings
module
biothings.web.settings.configs
module
biothings.web.settings.default
module
biothings.web.settings.validators
module
biothings.web.templates
module
BiothingsAPI (in module biothings.web.applications)
BiothingsAPIBaseLauncher (class in biothings.web.launcher)
BiothingsAPIEdge (class in biothings.hub.datatransform.datatransform_api)
BiothingsAPILauncher (in module biothings.web.launcher)
BiothingsDataTest (in module biothings.tests.web)
BiothingsDBProxy (class in biothings.web.services.namespace)
BiothingsDumper (class in biothings.hub.autoupdate.dumper)
BiothingsESMetadata (class in biothings.web.services.metadata)
BiothingsJSONEncoder (class in biothings.utils.common)
BiothingsMetadata (class in biothings.web.services.metadata)
BiothingsMongoMetadata (class in biothings.web.services.metadata)
BiothingsNamespace (class in biothings.web.services.namespace)
BiothingsSQLMetadata (class in biothings.web.services.metadata)
BiothingsTestCase (in module biothings.tests.web)
BiothingsUploader (class in biothings.hub.autoupdate.uploader)
BiothingsWebAppTest (class in biothings.tests.web)
BiothingsWebTest (class in biothings.tests.web)
BiothingsWebTestBase (class in biothings.tests.web)
BLOCK_SIZE (biothings.hub.dataload.dumper.FTPDumper attribute)
bm (built-in variable)
boolean_convert() (in module biothings.utils.dataload)
breadth_first_recursive_traversal() (in module biothings.utils.doc_traversal)
breadth_first_traversal() (in module biothings.utils.doc_traversal)
break_received() (biothings.hub.HubSSHServerSession method)
broadcast() (biothings.web.analytics.notifiers.Notifier method)
bucket (biothings.hub.dataindex.snapshooter.RepositoryConfig property)
Bucket (class in biothings.hub.dataindex.snapshooter)
build()
(biothings.utils.loggers.SlackMessage method)
(biothings.web.query.builder.ESQueryBuilder method)
(biothings.web.query.builder.MongoQueryBuilder method)
(biothings.web.query.builder.SQLQueryBuilder method)
build_config (biothings.hub.databuild.builder.DataBuilder property)
build_config_info()
(biothings.hub.databuild.builder.BuilderManager method)
build_diff_report() (biothings.hub.databuild.differ.DifferManager method)
build_id (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader property)
build_index() (biothings.utils.es.ESIndexer method)
build_info() (biothings.hub.databuild.builder.BuilderManager method)
build_release_note() (biothings.hub.datarelease.publisher.ReleaseManager method)
build_save_mapping()
build_stats (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader property)
(biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReaderAdapter property)
BUILD_TYPES (biothings.hub.databuild.buildconfig.AutoBuildConfig attribute)
build_version (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader property)
BuilderException
BuilderManager (class in biothings.hub.databuild.builder)
builds()
bulk_write() (biothings.utils.sqlite3.Collection method)
C
cache (biothings.web.handlers.base.BaseAPIHandler attribute)
cache_control_template (biothings.web.handlers.base.BaseAPIHandler attribute)
call() (biothings.hub.dataload.dumper.DumperManager method)
can_handle() (biothings.hub.dataplugin.assistant.BaseAssistant method)
(biothings.hub.dataplugin.assistant.GithubAssistant method)
(biothings.hub.dataplugin.assistant.LocalAssistant method)
can_load_plugin() (biothings.hub.dataplugin.assistant.AdvancedPluginLoader method)
(biothings.hub.dataplugin.assistant.BasePluginLoader method)
(biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader method)
capturesESExceptions() (in module biothings.web.query.pipeline)
category (biothings.hub.datarelease.publisher.BasePublisher property)
catelog (biothings.hub.dataindex.indexer.Step attribute)
ChangeListener (class in biothings.utils.hub_db)
ChangeWatcher (class in biothings.utils.hub_db)
Channel (class in biothings.web.analytics.channels)
check()
(biothings.utils.redis.RedisClient method)
(biothings.web.services.health.DBHealth method)
(biothings.web.services.health.ESHealth method)
(biothings.web.services.health.MongoHealth method)
(biothings.web.services.health.SQLHealth method)
check_compat() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
check_constraints() (biothings.utils.manager.JobManager method)
check_document_size() (in module biothings.utils.mongo)
check_index() (biothings.utils.es.ESIndexer method)
check_new_version() (in module biothings.utils.version)
check_ready() (biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.dataload.uploader.DummySourceUploader method)
CHILD_CONTEXTS (biothings.web.options.openapi.OpenAPIContext attribute)
(biothings.web.options.openapi.OpenAPIInfoContext attribute)
(biothings.web.options.openapi.OpenAPIPathItemContext attribute)
choose_best_version() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
CIIDStruct (class in biothings.hub.datatransform.ciidstruct)
CIMongoDBEdge (class in biothings.hub.datatransform.datatransform_mdb)
clean() (biothings.hub.dataindex.indexer_cleanup.Cleaner method)
clean_archived_collections() (biothings.hub.autoupdate.uploader.BiothingsUploader method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
clean_data() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
clean_features() (biothings.hub.HubServer method)
clean_field() (biothings.utils.es.ESIndexer method)
clean_old_collections() (biothings.hub.databuild.builder.DataBuilder method)
clean_stale_status() (biothings.hub.databuild.builder.BuilderManager method)
(biothings.hub.databuild.differ.DifferManager method)
(biothings.hub.databuild.syncer.SyncerManager method)
(biothings.hub.dataindex.indexer.IndexManager method)
(biothings.hub.dataindex.snapshooter.SnapshotManager method)
(biothings.hub.datainspect.inspector.InspectorManager method)
(biothings.hub.dataload.dumper.DumperManager method)
(biothings.hub.dataload.uploader.UploaderManager method)
(biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
(biothings.utils.manager.BaseManager method)
clean_staled() (biothings.utils.manager.JobManager method)
clean_temp_collections() (biothings.hub.databuild.builder.BuilderManager method)
Cleaner (class in biothings.hub.dataindex.indexer_cleanup)
cleanup() (biothings.hub.dataindex.indexer.IndexManager method)
(biothings.hub.dataindex.snapshooter.SnapshotManager method)
CleanUpResult (class in biothings.hub.dataindex.indexer_cleanup)
clear() (biothings.utils.configuration.MetaField method)
client (biothings.hub.dataload.dumper.APIDumper property)
(biothings.hub.dataload.dumper.BaseDumper property)
(biothings.hub.datatransform.datatransform_api.BiothingsAPIEdge property)
(biothings.utils.redis.RedisClient attribute)
client_name (biothings.hub.datatransform.datatransform_api.BiothingsAPIEdge attribute)
(biothings.hub.datatransform.datatransform_api.MyChemInfoEdge attribute)
(biothings.hub.datatransform.datatransform_api.MyGeneInfoEdge attribute)
clients (biothings.hub.api.handlers.ws.WebSocketConnection attribute)
CLIJobManager (class in biothings.utils.manager)
close() (biothings.utils.common.LogPrint method)
(biothings.utils.es.ESIndexer method)
CloudStorage (class in biothings.hub.dataindex.snapshooter)
cmd (biothings.utils.hub.HubShell attribute)
cmd_cnt (biothings.utils.hub.HubShell attribute)
code (biothings.web.query.pipeline.QueryPipelineException attribute)
col_entity (biothings.utils.hub_db.ChangeWatcher attribute)
cold_collection_name (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader property)
ColdHotDiffer (class in biothings.hub.databuild.differ)
ColdHotIndexer (class in biothings.hub.dataindex.indexer)
ColdHotJsonDiffer (class in biothings.hub.databuild.differ)
ColdHotJsonDifferBase (class in biothings.hub.databuild.differ)
ColdHotSelfContainedJsonDiffer (class in biothings.hub.databuild.differ)
collapse() (biothings.web.query.formatter.FormatterDict method)
collection (biothings.hub.datarelease.publisher.BasePublisher property)
(biothings.hub.datarelease.publisher.ReleaseManager property)
(biothings.hub.datatransform.datatransform_mdb.MongoDBEdge property)
(biothings.utils.manager.BaseStatusRegisterer property)
Collection (class in biothings.utils.es)
(class in biothings.utils.hub_db)
(class in biothings.utils.mongo)
(class in biothings.utils.sqlite3)
collection_find() (biothings.hub.datatransform.datatransform_mdb.CIMongoDBEdge method)
(biothings.hub.datatransform.datatransform_mdb.MongoDBEdge method)
collection_names() (biothings.utils.hub_db.IDatabase method)
(biothings.utils.mongo.Database method)
(biothings.utils.mongo.DummyDatabase method)
(biothings.utils.sqlite3.Database method)
collection_partition() (in module biothings.utils.parallel)
Colors (class in biothings.utils.loggers)
COLUMNS (biothings.utils.manager.JobManager attribute)
command()
command_info() (biothings.utils.hub.HubShell class method)
CommandDefinition (class in biothings.utils.hub)
CommandError
CommandInformation (class in biothings.utils.hub)
CommandNotAllowed
commands()
commit() (biothings.utils.configuration.ConfigAttrMeta method)
compare_remote_local() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
completed() (biothings.hub.dataindex.indexer_schedule.Schedule method)
compose_dot_fields_by_fields() (in module biothings.utils.dotfield)
CompositeCommand (class in biothings.utils.hub)
compute_metadata() (in module biothings.utils.inspect)
config (biothings.hub.dataload.uploader.BaseSourceUploader attribute)
(biothings.tests.web.BiothingsWebAppTest property)
CONFIG (biothings.utils.es.Database attribute)
(biothings.utils.sqlite3.Database attribute)
config()
ConfigAttrMeta (class in biothings.utils.configuration)
ConfigLine (class in biothings.utils.configuration)
ConfigLines (class in biothings.utils.configuration)
ConfigModule (class in biothings.web.settings.configs)
ConfigPackage (class in biothings.web.settings.configs)
configurate_file_handler() (in module biothings.utils.loggers)
ConfigurationDefault (class in biothings.utils.configuration)
ConfigurationError
ConfigurationValue (class in biothings.utils.configuration)
ConfigurationWrapper (class in biothings.utils.configuration)
configure() (biothings.hub.databuild.builder.BuilderManager method)
(biothings.hub.databuild.differ.DifferManager method)
(biothings.hub.databuild.syncer.SyncerManager method)
(biothings.hub.dataindex.indexer.IndexManager method)
(biothings.hub.dataindex.snapshooter.SnapshotManager method)
(biothings.hub.dataplugin.assistant.AssistantManager method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
(biothings.hub.HubServer method)
(biothings.hub.standalone.AutoHubFeature method)
(biothings.web.services.namespace.BiothingsDBProxy method)
configure_api_endpoints() (biothings.hub.HubServer method)
configure_api_manager() (biothings.hub.HubServer method)
configure_auto_archive_manager() (biothings.hub.HubServer method)
configure_auto_release() (biothings.hub.standalone.AutoHubFeature method)
configure_auto_snapshot_cleaner_manager() (biothings.hub.HubServer method)
configure_autohub_feature() (biothings.hub.HubServer method)
configure_build_manager() (biothings.hub.HubServer method)
configure_commands() (biothings.hub.HubServer method)
configure_config_feature() (biothings.hub.HubServer method)
configure_dataplugin_manager() (biothings.hub.HubServer method)
configure_dataupload_feature() (biothings.hub.HubServer method)
configure_diff_manager() (biothings.hub.HubServer method)
configure_dump_manager() (biothings.hub.HubServer method)
configure_extra_commands() (biothings.hub.HubServer method)
configure_hooks_feature() (biothings.hub.HubServer method)
configure_index_manager() (biothings.hub.HubServer method)
configure_inspect_manager() (biothings.hub.HubServer method)
configure_ioloop() (biothings.hub.HubServer method)
configure_job_manager() (biothings.hub.HubServer method)
configure_managers() (biothings.hub.HubServer method)
configure_readonly_api_endpoints() (biothings.hub.HubServer method)
configure_readonly_feature() (biothings.hub.HubServer method)
configure_release_manager() (biothings.hub.HubServer method)
configure_reloader_feature() (biothings.hub.HubServer method)
configure_remaining_features() (biothings.hub.HubServer method)
configure_snapshot_manager() (biothings.hub.HubServer method)
configure_source_manager() (biothings.hub.HubServer method)
configure_sync_manager() (biothings.hub.HubServer method)
configure_terminal_feature() (biothings.hub.HubServer method)
configure_upgrade_feature() (biothings.hub.HubServer method)
configure_upload_manager() (biothings.hub.HubServer method)
configure_ws_feature() (biothings.hub.HubServer method)
confmod (biothings.utils.configuration.ConfigAttrMeta attribute)
connection_lost() (biothings.hub.HubSSHServer method)
connection_made() (biothings.hub.HubSSHServer method)
(biothings.hub.HubSSHServerSession method)
contact() (biothings.web.options.openapi.OpenAPIInfoContext method)
CONTAINER_NAME (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
convert() (biothings.web.options.manager.Converter method)
convert_to() (biothings.web.options.manager.Converter method)
(biothings.web.options.manager.FormArgCvter method)
(biothings.web.options.manager.JsonArgCvter method)
Converter (class in biothings.web.options.manager)
CopyOperation (class in biothings.utils.jsonpatch)
count() (biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMongoBackend method)
(biothings.utils.es.Collection method)
(biothings.utils.es.ESIndexer method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.mongo.Collection method)
(biothings.utils.mongo.DummyCollection method)
(biothings.utils.sqlite3.Collection method)
count_from_ids() (biothings.utils.backend.DocMongoBackend method)
count_src() (biothings.utils.es.ESIndexer method)
create() (biothings.hub.dataindex.indexer.DynamicIndexerFactory method)
(biothings.hub.dataindex.snapshooter.Bucket method)
(biothings.hub.dataindex.snapshot_repo.Repository method)
(biothings.hub.dataindex.snapshot_task.Snapshot method)
(biothings.hub.dataload.uploader.BaseSourceUploader class method)
create_and_call() (biothings.hub.dataload.dumper.DumperManager method)
create_and_dump() (biothings.hub.dataload.dumper.DumperManager method)
create_and_load() (biothings.hub.dataload.uploader.UploaderManager method)
create_and_update_master() (biothings.hub.dataload.uploader.UploaderManager method)
create_api()
(biothings.hub.api.manager.APIManager method)
create_backend() (in module biothings.hub.databuild.backend)
create_bucket() (biothings.hub.datarelease.publisher.BasePublisher method)
(in module biothings.utils.aws)
create_build_conf()
create_build_configuration() (biothings.hub.databuild.builder.BuilderManager method)
create_collection() (biothings.utils.es.Database method)
(biothings.utils.hub_db.IDatabase method)
(biothings.utils.sqlite3.Database method)
create_data_plugin() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
create_from_options() (biothings.utils.backend.DocESBackend class method)
create_handlers() (in module biothings.hub.api)
create_if_needed() (biothings.utils.sqlite3.Database method)
create_index() (biothings.utils.es.ESIndexer method)
create_instance() (biothings.hub.dataload.dumper.DumperManager method)
(biothings.hub.dataload.uploader.UploaderManager method)
(biothings.hub.dataplugin.assistant.AssistantManager method)
create_logger() (in module biothings.utils.loggers)
create_release_note()
(biothings.hub.datarelease.publisher.ReleaseManager method)
create_release_note_from_build() (biothings.hub.datarelease.publisher.ReleaseManager method)
create_repository() (biothings.utils.es.ESIndexer method)
create_todump_list() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
(biothings.hub.dataload.dumper.APIDumper method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.LastModifiedBaseDumper method)
(biothings.hub.dataload.dumper.WgetDumper method)
CRITICAL (biothings.utils.loggers.Colors attribute)
(biothings.utils.loggers.Squares attribute)
cron_and_strdelta_info() (biothings.hub.JobRenderer method)
CumulativeResult (class in biothings.hub.dataindex.snapshooter)
current_data_folder (biothings.hub.dataload.dumper.BaseDumper property)
current_release (biothings.hub.dataload.dumper.BaseDumper property)
Cursor (class in biothings.utils.sqlite3)
CWD_DIR (biothings.hub.dataload.dumper.FTPDumper attribute)
D
DATA_PATH (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
DATA_PLUGIN_FOLDER (biothings.hub.dataplugin.assistant.AssistedDumper attribute)
(biothings.hub.dataplugin.assistant.AssistedUploader attribute)
data_plugin_manager (biothings.hub.dataplugin.assistant.BaseAssistant attribute)
data_received() (biothings.hub.api.handlers.upload.UploadHandler method)
(biothings.hub.HubSSHServerSession method)
database (biothings.utils.sqlite3.Collection property)
Database (class in biothings.utils.es)
(class in biothings.utils.mongo)
(class in biothings.utils.sqlite3)
database() (biothings.utils.hub_db.Collection method)
DatabaseClient (class in biothings.utils.mongo)
(class in biothings.utils.sqlite3)
DatabaseCollectionTesting (class in biothings.tests.hub)
DataBuilder (class in biothings.hub.databuild.builder)
DATALINE (biothings.utils.manager.JobManager attribute)
DataPluginManager (class in biothings.hub.dataplugin.manager)
datasource_info (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReaderAdapter property)
datasource_mapping (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader property)
datasource_stats (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader property)
datasource_versions (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader property)
DataTransform (class in biothings.hub.datatransform.datatransform)
DataTransformAPI (class in biothings.hub.datatransform.datatransform_api)
DataTransformEdge (class in biothings.hub.datatransform.datatransform)
DataTransformMDB (class in biothings.hub.datatransform)
(class in biothings.hub.datatransform.datatransform_mdb)
DataTransformMyChemInfo (class in biothings.hub.datatransform.datatransform_api)
DataTransformMyGeneInfo (class in biothings.hub.datatransform.datatransform_api)
DBHealth (class in biothings.web.services.health)
DBParamValidator (class in biothings.web.settings.validators)
debug (biothings.hub.datatransform.datatransform.DataTransform attribute)
DEBUG (biothings.utils.loggers.Colors attribute)
(biothings.utils.loggers.Squares attribute)
DeepStatsMode (class in biothings.utils.inspect)
default (biothings.utils.configuration.Flag attribute)
(biothings.utils.configuration.MetaField attribute)
(biothings.utils.configuration.Paragraph attribute)
default() (biothings.utils.common.BiothingsJSONEncoder method)
DEFAULT_API_CONFIG (biothings.hub.HubServer attribute)
DEFAULT_AUTOHUB_CONFIG (biothings.hub.HubServer attribute)
DEFAULT_BRANCH (biothings.hub.dataload.dumper.GitDumper attribute)
DEFAULT_DATAUPLOAD_CONFIG (biothings.hub.HubServer attribute)
DEFAULT_DIFF_PUBLISHER_CLASS (biothings.hub.datarelease.publisher.ReleaseManager attribute)
DEFAULT_DUMPER_CLASS (biothings.hub.standalone.AutoHubFeature attribute)
DEFAULT_FEATURES (biothings.hub.HubServer attribute)
(biothings.hub.standalone.AutoHubServer attribute)
DEFAULT_INDEXER (biothings.hub.dataindex.indexer.IndexManager attribute)
DEFAULT_MANAGERS_ARGS (biothings.hub.HubServer attribute)
default_match_query() (biothings.web.query.builder.ESQueryBuilder method)
DEFAULT_RELOADER_CONFIG (biothings.hub.HubServer attribute)
DEFAULT_SNAPSHOT_PUBLISHER_CLASS (biothings.hub.datarelease.publisher.ReleaseManager attribute)
default_source (biothings.hub.datatransform.datatransform.DataTransform attribute)
(biothings.hub.datatransform.datatransform_api.DataTransformAPI attribute)
(biothings.hub.datatransform.datatransform_mdb.DataTransformMDB attribute)
default_string_query() (biothings.web.query.builder.ESQueryBuilder method)
DEFAULT_UPLOADER_CLASS (biothings.hub.standalone.AutoHubFeature attribute)
DEFAULT_VALIDATOR_CLASS (biothings.hub.standalone.AutoHubFeature attribute)
DEFAULT_WEBSOCKET_CONFIG (biothings.hub.HubServer attribute)
DEFAULT_WEIGHT (biothings.hub.datatransform.datatransform.DataTransform attribute)
DefaultCORSHeaderMixin (class in biothings.hub.api.handlers.log)
DefaultHandler (class in biothings.hub.api.handlers.base)
DEFAULTS (biothings.web.analytics.events.Message attribute)
defer_to_process() (biothings.utils.manager.CLIJobManager method)
(biothings.utils.manager.JobManager method)
defer_to_thread() (biothings.utils.manager.CLIJobManager method)
(biothings.utils.manager.JobManager method)
delete() (biothings.hub.api.handlers.base.GenericHandler method)
(biothings.hub.dataindex.snapshot_repo.Repository method)
(biothings.hub.dataindex.snapshot_task.Snapshot method)
(biothings.hub.dataload.sync.MongoSync method)
(biothings.web.options.openapi.OpenAPIPathItemContext method)
(in module biothings.hub.dataindex.snapshot_cleanup)
delete_api()
(biothings.hub.api.manager.APIManager method)
delete_build_conf()
delete_build_configuration() (biothings.hub.databuild.builder.BuilderManager method)
delete_doc() (biothings.utils.es.ESIndexer method)
delete_docs() (biothings.utils.es.ESIndexer method)
delete_index() (biothings.utils.es.ESIndexer method)
delete_merge() (biothings.hub.databuild.builder.BuilderManager method)
delete_merged_data() (biothings.hub.databuild.builder.BuilderManager method)
delete_or_restore_container() (biothings.hub.dataload.dumper.DockerContainerDumper method)
delete_snapshots() (biothings.hub.dataindex.snapshooter.SnapshotManager method)
deprecated() (biothings.web.options.openapi.OpenAPIParameterContext method)
depth_first_recursive_traversal() (in module biothings.utils.doc_traversal)
depth_first_traversal() (in module biothings.utils.doc_traversal)
description (biothings.utils.configuration.ConfigAttrMeta attribute)
details (biothings.web.query.pipeline.QueryPipelineException attribute)
DevInfo (class in biothings.utils.info)
dict_apply() (in module biothings.utils.dataload)
dict_attrmerge() (in module biothings.utils.dataload)
dict_convert() (in module biothings.utils.dataload)
dict_nodup() (in module biothings.utils.dataload)
dict_sweep() (in module biothings.utils.dataload)
dict_to_list() (in module biothings.utils.dataload)
dict_traverse() (in module biothings.utils.dataload)
dict_walk() (in module biothings.utils.dataload)
diff()
(biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.differ.DifferManager method)
diff_build_stats() (biothings.hub.datarelease.releasenote.ReleaseNoteSource method)
diff_collections() (in module biothings.utils.diff)
diff_collections_batches() (in module biothings.utils.diff)
diff_cols() (biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.differ.ColdHotDiffer method)
diff_datasource_info() (biothings.hub.datarelease.releasenote.ReleaseNoteSource method)
diff_datasource_mapping() (biothings.hub.datarelease.releasenote.ReleaseNoteSource method)
diff_docs_jsonpatch() (in module biothings.utils.diff)
diff_info()
(biothings.hub.databuild.differ.DifferManager method)
diff_report() (biothings.hub.databuild.differ.DifferManager method)
diff_type (biothings.hub.databuild.differ.BaseDiffer attribute)
(biothings.hub.databuild.differ.ColdHotJsonDiffer attribute)
(biothings.hub.databuild.differ.ColdHotSelfContainedJsonDiffer attribute)
(biothings.hub.databuild.differ.JsonDiffer attribute)
(biothings.hub.databuild.differ.SelfContainedJsonDiffer attribute)
(biothings.hub.databuild.syncer.BaseSyncer attribute)
(biothings.hub.databuild.syncer.ESColdHotJsonDiffSelfContainedSyncer attribute)
(biothings.hub.databuild.syncer.ESColdHotJsonDiffSyncer attribute)
(biothings.hub.databuild.syncer.ESJsonDiffSelfContainedSyncer attribute)
(biothings.hub.databuild.syncer.ESJsonDiffSyncer attribute)
(biothings.hub.databuild.syncer.MongoJsonDiffSelfContainedSyncer attribute)
(biothings.hub.databuild.syncer.MongoJsonDiffSyncer attribute)
diff_worker_count() (in module biothings.hub.databuild.differ)
diff_worker_new_vs_old() (in module biothings.hub.databuild.differ)
diff_worker_old_vs_new() (in module biothings.hub.databuild.differ)
DifferException
DifferManager (class in biothings.hub.databuild.differ)
DiffPublisher (class in biothings.hub.datarelease.publisher)
DiffReportRendererBase (class in biothings.hub.databuild.differ)
DiffReportTxt (class in biothings.hub.databuild.differ)
dim (built-in variable)
dispatch() (biothings.hub.dataindex.indexer.Step class method)
(biothings.hub.dataindex.indexer_task.IndexingTask method)
(in module biothings.hub.dataindex.indexer_task)
(in module biothings.hub.dataindex.snapshot_registrar)
dm (built-in variable)
do_clean() (in module biothings.cli.utils)
do_clean_dumped_files() (in module biothings.cli.utils)
do_clean_uploaded_sources() (in module biothings.cli.utils)
do_create() (in module biothings.cli.utils)
do_dump() (biothings.hub.dataload.dumper.BaseDumper method)
(in module biothings.cli.utils)
do_dump_and_upload() (in module biothings.cli.utils)
do_index() (biothings.hub.dataindex.indexer.Indexer method)
do_inspect() (in module biothings.cli.utils)
do_list() (in module biothings.cli.utils)
do_publish (biothings.utils.hub_db.ChangeWatcher attribute)
do_serve() (in module biothings.cli.utils)
do_upload() (in module biothings.cli.utils)
do_work() (in module biothings.utils.manager)
Doc (class in biothings.web.query.formatter)
doc_feeder() (biothings.utils.es.ESIndexer method)
(in module biothings.utils.mongo)
doc_feeder_using_helper() (biothings.utils.es.ESIndexer method)
doc_type (biothings.utils.es.ESIndex property)
DocBackendBase (class in biothings.utils.backend)
DocBackendOptions (class in biothings.utils.backend)
DocESBackend (class in biothings.utils.backend)
DocHandler (class in biothings.cli.web_app)
DOCKER_CLIENT_URL (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
DOCKER_IMAGE (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
docker_source_info_parser() (in module biothings.utils.parsers)
DockerContainerDumper (class in biothings.hub.dataload.dumper)
DockerContainerException
DocMemoryBackend (class in biothings.utils.backend)
DocMongoBackend (class in biothings.utils.backend)
DocMongoDBBackend (in module biothings.utils.backend)
document_cleaner() (biothings.hub.databuild.builder.DataBuilder method)
DONE (biothings.hub.dataindex.indexer_registrar.Stage attribute)
dotdict (class in biothings.utils.common)
download()
(biothings.hub.autoupdate.dumper.BiothingsDumper method)
(biothings.hub.dataload.dumper.APIDumper method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.FilesystemDumper method)
(biothings.hub.dataload.dumper.FTPDumper method)
(biothings.hub.dataload.dumper.GitDumper method)
(biothings.hub.dataload.dumper.GoogleDriveDumper method)
(biothings.hub.dataload.dumper.HTTPDumper method)
(biothings.hub.dataload.dumper.LastModifiedFTPDumper method)
(biothings.hub.dataload.dumper.WgetDumper method)
download_s3_file() (in module biothings.utils.aws)
dpm (built-in variable)
drop() (biothings.hub.databuild.backend.LinkTargetDocMongoBackend method)
(biothings.utils.backend.DocBackendBase method)
(biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMemoryBackend method)
(biothings.utils.backend.DocMongoBackend method)
(biothings.utils.mongo.DummyCollection method)
(biothings.utils.sqlite3.Collection method)
DummyCollection (class in biothings.utils.mongo)
DummyConfig (class in biothings.utils.common)
DummyDatabase (class in biothings.utils.mongo)
DummyDumper (class in biothings.hub.dataload.dumper)
DummySourceUploader (class in biothings.hub.dataload.uploader)
dump()
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DummyDumper method)
(biothings.hub.dataload.dumper.GitDumper method)
(biothings.hub.dataload.dumper.ManualDumper method)
(biothings.hub.dataplugin.manager.ManualDataPlugin method)
(in module biothings.utils.common)
dump2gridfs() (in module biothings.utils.common)
dump_all()
(biothings.hub.dataload.dumper.DumperManager method)
dump_and_upload() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
DUMP_COMMAND (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
dump_data() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
dump_info()
(biothings.hub.dataload.dumper.DumperManager method)
dump_plugin()
dump_src() (biothings.hub.dataload.dumper.DumperManager method)
dumper_manager (biothings.hub.dataplugin.assistant.BaseAssistant attribute)
dumper_registry (biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader attribute)
DumperException
DumperManager (class in biothings.hub.dataload.dumper)
dupline_seperator() (in module biothings.utils.dataload)
DynamicIndexerFactory (class in biothings.hub.dataindex.indexer)
E
edge_lookup() (biothings.hub.datatransform.datatransform.DataTransformEdge method)
(biothings.hub.datatransform.datatransform.RegExEdge method)
(biothings.hub.datatransform.datatransform_api.BiothingsAPIEdge method)
(biothings.hub.datatransform.datatransform_mdb.MongoDBEdge method)
email() (biothings.web.options.openapi.OpenAPIContactContext method)
emit() (biothings.utils.loggers.EventRecorder method)
(biothings.utils.loggers.SlackHandler method)
(biothings.utils.loggers.WSLogHandler method)
end (biothings.utils.loggers.Range attribute)
EndpointDefinition (class in biothings.hub.api)
EndScrollInterrupt
eof_received() (biothings.hub.HubSSHServerSession method)
ERROR (biothings.utils.loggers.Colors attribute)
(biothings.utils.loggers.Squares attribute)
ErrorHandler (class in biothings.utils.parallel_mp)
es (in module biothings.web.connections)
ESColdHotJsonDiffSelfContainedSyncer (class in biothings.hub.databuild.syncer)
ESColdHotJsonDiffSyncer (class in biothings.hub.databuild.syncer)
ESHealth (class in biothings.web.services.health)
ESIndex (class in biothings.hub.dataindex.indexer_task)
(class in biothings.utils.es)
ESIndexer (class in biothings.utils.es)
ESJsonDiffSelfContainedSyncer (class in biothings.hub.databuild.syncer)
ESJsonDiffSyncer (class in biothings.hub.databuild.syncer)
ESQueryBackend (class in biothings.web.query.engine)
ESQueryBuilder (class in biothings.web.query.builder)
ESQueryPipeline (class in biothings.web.query.pipeline)
ESResultFormatter (class in biothings.web.query.formatter)
ESScrollID (class in biothings.web.query.builder)
ESUserQuery (class in biothings.web.query.builder)
ETAG (biothings.hub.dataload.dumper.LastModifiedHTTPDumper attribute)
eval() (biothings.utils.hub.HubShell method)
eval_lines() (biothings.hub.HubSSHServerSession method)
Event (class in biothings.web.analytics.events)
event_queue (biothings.utils.hub_db.ChangeWatcher attribute)
EventRecorder (class in biothings.utils.loggers)
exclude() (biothings.web.query.formatter.FormatterDict method)
exclude_from_reloader() (in module biothings.utils.hub)
ExcludeFieldsById (class in biothings.utils.exclude_ids)
exec_requested() (biothings.hub.HubSSHServerSession method)
execute() (biothings.hub.dataindex.indexer.Step method)
(biothings.web.query.engine.AsyncESQueryBackend method)
(biothings.web.query.engine.ESQueryBackend method)
(biothings.web.query.engine.MongoQueryBackend method)
(biothings.web.query.engine.SQLQueryBackend method)
Existentialist (class in biothings.web.options.manager)
exists() (biothings.hub.dataindex.snapshooter.Bucket method)
(biothings.hub.dataindex.snapshot_repo.Repository method)
(biothings.hub.dataindex.snapshot_task.Snapshot method)
(biothings.utils.es.ESIndexer method)
exists_index() (biothings.utils.es.ESIndexer method)
exists_or_null() (in module biothings.utils.docs)
explode() (biothings.web.options.openapi.OpenAPIParameterContext method)
export() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
(biothings.hub.dataplugin.assistant.AssistantManager method)
export_command_documents()
(biothings.hub.HubServer method)
export_dumper() (biothings.hub.dataplugin.assistant.AssistantManager method)
export_ids() (in module biothings.hub.dataexport.ids)
export_mapping() (biothings.hub.dataplugin.assistant.AssistantManager method)
export_plugin()
export_uploader() (biothings.hub.dataplugin.assistant.AssistantManager method)
expose()
EXTENSION (biothings.web.options.openapi.OpenAPIContactContext attribute)
(biothings.web.options.openapi.OpenAPIContext attribute)
(biothings.web.options.openapi.OpenAPIExternalDocsContext attribute)
(biothings.web.options.openapi.OpenAPIInfoContext attribute)
(biothings.web.options.openapi.OpenAPILicenseContext attribute)
(biothings.web.options.openapi.OpenAPIOperation attribute)
(biothings.web.options.openapi.OpenAPIParameterContext attribute)
(biothings.web.options.openapi.OpenAPIPathItemContext attribute)
extract() (biothings.hub.standalone.AutoHubFeature method)
extract_command_name() (biothings.utils.hub.HubShell method)
extract_pending_info() (biothings.utils.manager.JobManager method)
extract_worker_info() (biothings.utils.manager.JobManager method)
extras() (biothings.web.handlers.query.MetadataSourceHandler method)
F
failed() (biothings.hub.dataindex.indexer_registrar.IndexJobStateRegistrar method)
FastAPIBiothingsAPI (class in biothings.web.applications)
FastAPILauncher (class in biothings.web.launcher)
feed() (biothings.utils.configuration.ConfigAttrMeta method)
(biothings.utils.configuration.Flag method)
(biothings.utils.configuration.MetaField method)
(biothings.utils.configuration.Paragraph method)
(biothings.utils.configuration.Text method)
fetch() (biothings.web.query.pipeline.AsyncESQueryPipeline method)
(biothings.web.query.pipeline.ESQueryPipeline method)
(biothings.web.query.pipeline.QueryPipeline method)
field_name (biothings.utils.inspect.FieldInspection attribute)
field_type (biothings.utils.inspect.FieldInspection attribute)
FieldInspection (class in biothings.utils.inspect)
FieldInspectValidation (class in biothings.utils.inspect)
FieldNote (class in biothings.utils.info)
file_merge() (in module biothings.utils.dataload)
file_newer() (in module biothings.utils.common)
fileno() (biothings.utils.common.LogPrint method)
FilesystemDumper (class in biothings.hub.dataload.dumper)
filter_class() (biothings.hub.dataload.uploader.UploaderManager method)
(biothings.utils.manager.BaseSourceManager method)
filter_dict() (in module biothings.utils.common)
finalize() (biothings.hub.dataindex.indexer_payload.IndexMappings method)
(biothings.hub.dataindex.indexer_payload.IndexSettings method)
(biothings.utils.backend.DocBackendBase method)
(biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMemoryBackend method)
(biothings.utils.backend.DocMongoBackend method)
find() (biothings.hub.dataindex.indexer_cleanup.Cleaner method)
(biothings.hub.datatransform.ciidstruct.CIIDStruct method)
(biothings.hub.datatransform.datatransform.IDStruct static method)
(biothings.utils.es.Collection method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.loggers.LookUpList method)
(biothings.utils.sqlite3.Collection method)
(in module biothings.hub.dataindex.snapshot_cleanup)
find_biggest_doc() (biothings.utils.es.ESIndexer method)
find_builder_classes() (biothings.hub.databuild.builder.BuilderManager method)
find_classes() (biothings.utils.manager.BaseSourceManager method)
find_classes_subclassing() (in module biothings.utils.common)
find_doc() (in module biothings.utils.common)
find_index() (biothings.utils.loggers.LookUpList method)
find_left() (biothings.hub.datatransform.datatransform.IDStruct method)
find_one() (biothings.utils.es.Collection method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.sqlite3.Collection method)
find_process() (in module biothings.utils.manager)
find_right() (biothings.hub.datatransform.datatransform.IDStruct method)
find_sources() (biothings.hub.dataload.source.SourceManager method)
find_update_path() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
find_value_in_doc() (in module biothings.utils.common)
findv2() (biothings.utils.sqlite3.Collection method)
fix_batch_duplicates() (in module biothings.hub.databuild.builder)
Flag (class in biothings.utils.configuration)
FlaskAPILauncher (class in biothings.web.launcher)
FlaskBiothingsAPI (class in biothings.web.applications)
flatten() (biothings.hub.datainspect.inspector.InspectorManager method)
flatten_and_validate() (in module biothings.utils.inspect)
flatten_doc() (in module biothings.utils.docs)
flatten_doc_2() (in module biothings.utils.docs)
flatten_inspection_data() (in module biothings.utils.inspect)
flatten_stats() (biothings.utils.inspect.StatsMode method)
float_convert() (in module biothings.utils.dataload)
flush() (biothings.utils.common.LogPrint method)
flush_and_refresh() (biothings.utils.es.ESIndexer method)
FormArgCvter (class in biothings.web.options.manager)
format (biothings.web.handlers.base.BaseAPIHandler attribute)
format() (biothings.hub.dataindex.snapshooter.RepositoryConfig method)
FormatterDict (class in biothings.web.query.formatter)
from_diff() (biothings.utils.jsonpatch.JsonPatch class method)
from_string() (biothings.utils.jsonpatch.JsonPatch class method)
FrontPageHandler (class in biothings.web.handlers.services)
FS_OP (biothings.hub.dataload.dumper.FilesystemDumper attribute)
FTP_HOST (biothings.hub.dataload.dumper.FTPDumper attribute)
FTP_PASSWD (biothings.hub.dataload.dumper.FTPDumper attribute)
FTP_TIMEOUT (biothings.hub.dataload.dumper.FTPDumper attribute)
FTP_USER (biothings.hub.dataload.dumper.FTPDumper attribute)
FTPDumper (class in biothings.hub.dataload.dumper)
fullname (biothings.hub.dataload.uploader.BaseSourceUploader property)
func (biothings.hub.dataindex.snapshot_registrar.MainSnapshotState attribute)
(biothings.hub.dataindex.snapshot_registrar.PostSnapshotState attribute)
(biothings.hub.dataindex.snapshot_registrar.PreSnapshotState attribute)
G
g (built-in variable)
GA4Channel (class in biothings.web.analytics.channels)
GAChannel (class in biothings.web.analytics.channels)
GAEvent (class in biothings.web.analytics.events)
generate_api_routes() (in module biothings.hub.api)
generate_doc_src_master() (biothings.hub.dataload.uploader.BaseSourceUploader method)
generate_document_query() (biothings.hub.databuild.builder.DataBuilder method)
generate_endpoint_for_callable() (in module biothings.hub.api)
generate_endpoint_for_composite_command() (in module biothings.hub.api)
generate_endpoint_for_display() (in module biothings.hub.api)
generate_es_mapping() (in module biothings.utils.es)
generate_folder() (in module biothings.hub.databuild.backend)
generate_handler() (in module biothings.hub.api)
generate_json_schema() (in module biothings.utils.jsonschema)
generate_remote_file() (biothings.hub.dataload.dumper.DockerContainerDumper method)
generate_target_name() (biothings.hub.databuild.backend.TargetDocBackend method)
GenericHandler (class in biothings.hub.api.handlers.base)
get() (biothings.cli.web_app.DocHandler method)
(biothings.cli.web_app.HomeHandler method)
(biothings.cli.web_app.QueryHandler method)
(biothings.hub.api.handlers.base.GenericHandler method)
(biothings.hub.api.handlers.base.RootHandler method)
(biothings.hub.api.handlers.log.HubLogDirHandler method)
(biothings.hub.api.handlers.log.HubLogFileHandler method)
(biothings.hub.dataindex.snapshooter.CloudStorage method)
(biothings.utils.info.DevInfo method)
(biothings.web.handlers.query.BiothingHandler method)
(biothings.web.handlers.query.MetadataFieldHandler method)
(biothings.web.handlers.query.MetadataSourceHandler method)
(biothings.web.handlers.query.QueryHandler method)
(biothings.web.handlers.services.APISpecificationHandler method)
(biothings.web.handlers.services.FrontPageHandler method)
(biothings.web.handlers.services.StatusHandler method)
(biothings.web.options.openapi.OpenAPIPathItemContext method)
get_alias() (biothings.utils.es.ESIndexer method)
get_all() (biothings.hub.databuild.prebuilder.BasePreCompiledDataProvider method)
(biothings.hub.databuild.prebuilder.MongoDBPreCompiledDataProvider method)
(biothings.hub.databuild.prebuilder.RedisPreCompiledDataProvider method)
get_api() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_apis()
(biothings.hub.api.manager.APIManager method)
get_app() (biothings.tests.web.BiothingsWebAppTest method)
(biothings.web.applications.FastAPIBiothingsAPI class method)
(biothings.web.applications.FlaskBiothingsAPI class method)
(biothings.web.applications.TornadoBiothingsAPI class method)
(biothings.web.launcher.BiothingsAPIBaseLauncher method)
(biothings.web.launcher.FastAPILauncher method)
(biothings.web.launcher.FlaskAPILauncher method)
(biothings.web.launcher.TornadoAPILauncher method)
get_async_client() (biothings.web.connections._ClientPool method)
get_available_routes() (in module biothings.cli.web_app)
get_backend() (in module biothings.utils.diff)
get_backend_provider_info() (biothings.hub.datainspect.inspector.InspectorManager method)
get_backend_url() (biothings.hub.databuild.backend.LinkTargetDocMongoBackend method)
(biothings.hub.databuild.backend.TargetDocBackend method)
get_biothing() (biothings.utils.es.ESIndexer method)
get_biothings_commit() (in module biothings.utils.version)
get_build_configuration() (biothings.hub.databuild.backend.SourceDocBackendBase method)
(biothings.hub.databuild.backend.SourceDocMongoBackend method)
get_build_version() (biothings.hub.databuild.builder.DataBuilder method)
get_builder() (biothings.hub.databuild.builder.BuilderManager method)
get_builder_class() (biothings.hub.databuild.builder.BuilderManager method)
get_cache_filename() (in module biothings.utils.mongo)
get_class_from_classpath() (in module biothings.utils.common)
get_class_name() (biothings.hub.standalone.AutoHubFeature method)
get_classdef() (biothings.hub.dataplugin.assistant.GithubAssistant method)
(biothings.hub.dataplugin.assistant.LocalAssistant method)
get_client() (biothings.utils.redis.RedisClient class method)
(biothings.web.connections._ClientPool method)
get_client_for_url() (biothings.hub.dataload.dumper.LastModifiedFTPDumper method)
get_cmd() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_code_for_mod_name() (biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader method)
get_compressed_outfile() (in module biothings.utils.common)
get_conn() (biothings.utils.sqlite3.Collection method)
(biothings.utils.sqlite3.Database method)
(in module biothings.utils.mongo)
get_converters() (in module biothings.utils.inspect)
get_current_and_new_master() (biothings.hub.dataload.uploader.BaseSourceUploader method)
get_custom_metadata() (biothings.hub.databuild.builder.DataBuilder method)
get_data_plugin() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_db() (biothings.utils.redis.RedisClient method)
get_debug() (biothings.hub.datatransform.datatransform.IDStruct method)
get_doc_type() (in module biothings.utils.es)
get_docs() (biothings.utils.es.ESIndexer method)
get_document() (biothings.hub.dataload.dumper.APIDumper static method)
get_document_id() (biothings.hub.dataload.dumper.GoogleDriveDumper method)
get_dotfield_value() (in module biothings.utils.common)
get_dumper_dynamic_class() (biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader method)
get_es() (in module biothings.utils.es)
get_es_client() (in module biothings.web.connections)
get_event() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_example_queries() (in module biothings.cli.web_app)
get_field_notes() (biothings.utils.info.FieldNote method)
get_filter() (biothings.web.query.builder.ESUserQuery method)
get_folder_name() (biothings.hub.standalone.AutoHubFeature method)
get_from_id() (biothings.utils.backend.DocBackendBase method)
(biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMemoryBackend method)
(biothings.utils.backend.DocMongoBackend method)
get_hub_config() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_hub_db_conn() (in module biothings.utils.es)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_hub_reloader() (in module biothings.utils.hub)
get_id_list() (biothings.utils.backend.DocBackendBase method)
(biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMemoryBackend method)
(biothings.utils.backend.DocMongoBackend method)
(biothings.utils.es.ESIndexer method)
get_indexes_by_name() (biothings.hub.dataindex.indexer.IndexManager method)
get_indice_names_by_settings() (biothings.utils.es.ESIndexer method)
get_indices_from_snapshots() (biothings.utils.es.ESIndexer method)
get_internal_number_of_replicas() (biothings.utils.es.ESIndexer method)
get_last_command() (in module biothings.utils.es)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_licenses() (biothings.web.services.metadata.BiothingsMetadata method)
(biothings.web.services.metadata.BiothingsMongoMetadata method)
get_loadjson() (in module biothings.utils.jsonpatch)
get_log_content() (in module biothings.hub.api.handlers.log)
get_logger() (in module biothings.cli.utils)
(in module biothings.utils.loggers)
get_loop() (in module biothings.utils.common)
get_loop_with_max_workers() (in module biothings.utils.common)
get_manifest_content() (in module biothings.cli.utils)
get_mapper_for_source() (biothings.hub.databuild.builder.DataBuilder method)
get_mapping() (biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.dataload.uploader.BaseSourceUploader class method)
(biothings.utils.es.ESIndexer method)
get_mapping_meta() (biothings.utils.es.ESIndexer method)
get_mappings() (biothings.web.services.metadata.BiothingsMetadata method)
(biothings.web.services.metadata.BiothingsMongoMetadata method)
get_metadata() (biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.differ.ColdHotDiffer method)
(biothings.web.services.metadata.BiothingsMetadata method)
get_mode_layer() (in module biothings.utils.inspect)
get_mongo_client() (in module biothings.web.connections)
get_mongodb_uri() (in module biothings.utils.diff)
get_new_ioloop() (biothings.tests.web.BiothingsWebAppTest method)
get_pending_processes() (biothings.utils.manager.JobManager method)
get_pending_summary() (biothings.utils.manager.JobManager method)
get_pid_files() (biothings.utils.manager.JobManager method)
get_pinfo() (biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.differ.DifferManager method)
(biothings.hub.databuild.syncer.BaseSyncer method)
(biothings.hub.dataindex.indexer.IndexManager method)
(biothings.hub.dataindex.indexer.ProcessInfo method)
(biothings.hub.dataindex.snapshooter.ProcessInfo method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
get_plugin_name() (in module biothings.cli.utils)
get_plugin_name_from_local_manifest() (in module biothings.utils.common)
get_plugin_name_from_remote_manifest() (in module biothings.utils.common)
get_plugin_obj() (biothings.hub.dataplugin.assistant.BasePluginLoader method)
get_pre_post_previous_result() (biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.DiffPublisher method)
(biothings.hub.datarelease.publisher.SnapshotPublisher method)
get_predicates() (biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.differ.DifferManager method)
(biothings.hub.databuild.syncer.BaseSyncer method)
(biothings.hub.databuild.syncer.ThrottlerSyncer method)
(biothings.hub.dataindex.indexer.IndexManager method)
(biothings.hub.dataindex.indexer.ProcessInfo method)
(biothings.hub.dataindex.snapshooter.ProcessInfo method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
get_previous_collection() (in module biothings.utils.mongo)
get_process_summary() (biothings.utils.manager.JobManager method)
get_python_exec_version() (in module biothings.utils.version)
get_python_version() (in module biothings.utils.version)
get_query() (biothings.web.query.builder.ESUserQuery method)
get_query_for_list_merge() (biothings.hub.databuild.builder.BuilderManager method)
get_random_string() (in module biothings.utils.common)
get_release() (biothings.hub.dataload.dumper.APIDumper static method)
get_release_note()
(biothings.hub.datarelease.publisher.ReleaseManager method)
get_release_note_filename() (biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.DiffPublisher method)
get_remote_file() (biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.LastModifiedFTPDumper method)
get_remote_lastmodified() (biothings.hub.dataload.dumper.DockerContainerDumper method)
get_repository() (biothings.utils.es.ESIndexer method)
get_repository_information() (in module biothings.utils.version)
get_restore_status() (biothings.utils.es.ESIndexer method)
get_root_document_sources() (biothings.hub.databuild.builder.DataBuilder method)
get_s3_file() (in module biothings.utils.aws)
get_s3_file_contents() (in module biothings.utils.aws)
get_s3_folder() (in module biothings.utils.aws)
get_s3_static_website_url() (in module biothings.utils.aws)
get_s3_url() (in module biothings.utils.aws)
get_schedule() (biothings.hub.dataload.dumper.DumperManager method)
(in module biothings.hub)
get_server() (biothings.web.launcher.BiothingsAPIBaseLauncher method)
(biothings.web.launcher.FlaskAPILauncher method)
(biothings.web.launcher.TornadoAPILauncher method)
get_settings() (biothings.utils.es.ESIndexer method)
get_snapshot_repository_config() (biothings.hub.autoupdate.uploader.BiothingsUploader method)
get_snapshot_status() (biothings.utils.es.ESIndexer method)
get_snapshots() (biothings.utils.es.ESIndexer method)
get_software_info() (in module biothings.utils.version)
get_source() (biothings.hub.dataload.source.SourceManager method)
get_source_code_info() (in module biothings.utils.version)
get_source_fullname() (in module biothings.utils.es)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_source_fullnames() (in module biothings.utils.mongo)
get_source_ids() (biothings.hub.dataload.dumper.DumperManager method)
(biothings.hub.dataload.uploader.UploaderManager method)
get_sources() (biothings.hub.dataload.source.SourceManager method)
get_sql_client() (in module biothings.web.connections)
get_src_build() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_src_build_config() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_src_conn() (in module biothings.utils.es)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_src_db() (in module biothings.utils.es)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_src_dump() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_src_master() (in module biothings.utils.es)
(in module biothings.utils.hub_db)
(in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
get_src_master_docs() (biothings.hub.databuild.backend.SourceDocBackendBase method)
(biothings.hub.databuild.backend.SourceDocMongoBackend method)
get_src_metadata() (biothings.hub.databuild.backend.SourceDocBackendBase method)
(biothings.hub.databuild.backend.SourceDocMongoBackend method)
get_stats() (biothings.hub.databuild.builder.DataBuilder method)
get_summary() (biothings.utils.manager.JobManager method)
get_target_backend() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
(biothings.hub.databuild.syncer.BaseSyncer method)
get_target_conn() (in module biothings.utils.mongo)
get_target_db() (in module biothings.utils.mongo)
get_target_master() (in module biothings.utils.mongo)
get_target_name() (biothings.hub.databuild.builder.DataBuilder method)
get_template_path() (biothings.web.handlers.base.BaseAPIHandler method)
(biothings.web.handlers.services.FrontPageHandler method)
get_thread_files() (biothings.utils.manager.JobManager method)
get_thread_summary() (biothings.utils.manager.JobManager method)
get_timestamp() (in module biothings.utils.common)
get_uploaded_collections() (in module biothings.cli.utils)
get_uploader_dynamic_class() (biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader method)
get_uploader_dynamic_classes() (biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader method)
get_uploaders() (in module biothings.cli.utils)
get_url() (biothings.tests.web.BiothingsWebAppTest method)
(biothings.tests.web.BiothingsWebTestBase method)
get_value() (biothings.utils.configuration.ConfigurationValue method)
get_value_from_db() (biothings.utils.configuration.ConfigurationWrapper method)
get_value_from_file() (biothings.utils.configuration.ConfigurationWrapper method)
get_version() (in module biothings.utils.version)
GET_VERSION_CMD (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
get_websocket_urls() (biothings.hub.HubServer method)
GIT_REPO_URL (biothings.hub.dataload.dumper.GitDumper attribute)
GitDataPlugin (class in biothings.hub.dataplugin.manager)
GitDumper (class in biothings.hub.dataload.dumper)
GithubAssistant (class in biothings.hub.dataplugin.assistant)
GoogleDriveDumper (class in biothings.hub.dataload.dumper)
Group (class in biothings.web.query.builder)
gunzip() (in module biothings.utils.common)
gunzipall() (in module biothings.utils.common)
GZipRotator (class in biothings.utils.loggers)
H
handle() (biothings.hub.dataplugin.assistant.BaseAssistant method)
(biothings.hub.dataplugin.assistant.GithubAssistant method)
(biothings.hub.dataplugin.assistant.LocalAssistant method)
(biothings.utils.parallel_mp.ErrorHandler method)
handle_autoreconnect() (in module biothings.utils.mongo)
HandleAutoReconnectMixin (class in biothings.utils.mongo)
handles() (biothings.web.analytics.channels.Channel method)
(biothings.web.analytics.channels.GA4Channel method)
(biothings.web.analytics.channels.GAChannel method)
(biothings.web.analytics.channels.SlackChannel method)
has_cold_collection() (biothings.hub.datarelease.releasenote.ReleaseNoteSrcBuildReader method)
has_filter() (biothings.web.query.builder.ESUserQuery method)
has_multiple_types (biothings.utils.inspect.FieldInspectValidation attribute)
has_query() (biothings.web.query.builder.ESUserQuery method)
hash() (biothings.web.connections._ClientPool static method)
head() (biothings.hub.api.handlers.base.GenericHandler method)
(biothings.web.handlers.services.StatusHandler method)
(biothings.web.options.openapi.OpenAPIPathItemContext method)
HEADER (biothings.utils.manager.JobManager attribute)
HEADERLINE (biothings.utils.manager.JobManager attribute)
help()
(biothings.utils.hub.HubShell method)
hidden (biothings.utils.configuration.ConfigAttrMeta attribute)
Histogram (class in biothings.hub.datatransform.histogram)
Hits (class in biothings.web.query.formatter)
HomeHandler (class in biothings.cli.web_app)
host (biothings.tests.web.BiothingsWebTestBase attribute)
http_method (biothings.web.options.openapi.OpenAPIPathItemContext attribute)
HTTPDumper (class in biothings.hub.dataload.dumper)
hub_memory (biothings.utils.manager.JobManager property)
hub_process (biothings.utils.manager.JobManager property)
HubCommands (class in biothings.hub)
HubDBListener (class in biothings.hub.api.handlers.ws)
HubLogDirHandler (class in biothings.hub.api.handlers.log)
HubLogFileHandler (class in biothings.hub.api.handlers.log)
HubServer (class in biothings.hub)
HubShell (class in biothings.utils.hub)
HubSSHServer (class in biothings.hub)
HubSSHServerSession (class in biothings.hub)
I
id_feeder() (in module biothings.utils.mongo)
id_lst (biothings.hub.datatransform.datatransform.IDStruct property)
id_priority_list (biothings.hub.datatransform.datatransform.DataTransform property)
id_strip() (in module biothings.utils.dataload)
IDatabase (class in biothings.utils.hub_db)
IDBaseMapper (class in biothings.hub.databuild.mapper)
IDCache (class in biothings.hub.dataindex.idcache)
IdentifiersMode (class in biothings.utils.inspect)
ids (biothings.utils.inspect.IdentifiersMode attribute)
IDStruct (class in biothings.hub.datatransform.datatransform)
IGNORE_HTTP_CODE (biothings.hub.dataload.dumper.HTTPDumper attribute)
IgnoreDuplicatedSourceUploader (class in biothings.hub.dataload.uploader)
im (built-in variable)
import_debug() (biothings.hub.datatransform.datatransform.IDStruct method)
include() (biothings.web.query.formatter.FormatterDict method)
INDEX (biothings.hub.dataindex.indexer_task.Mode attribute)
index()
(biothings.hub.dataindex.indexer.ColdHotIndexer method)
(biothings.hub.dataindex.indexer.Indexer method)
(biothings.hub.dataindex.indexer.IndexManager method)
(biothings.hub.dataindex.indexer_task.IndexingTask method)
(biothings.utils.es.ESIndexer method)
index_bulk() (biothings.utils.es.ESIndexer method)
index_cleanup()
index_config (built-in variable)
index_info()
(biothings.hub.dataindex.indexer.IndexManager method)
INDEXER (biothings.hub.dataindex.indexer.ColdHotIndexer attribute)
Indexer (class in biothings.hub.dataindex.indexer)
IndexerCumulativeResult (class in biothings.hub.dataindex.indexer)
IndexerException
,
[1]
IndexerStepResult (class in biothings.hub.dataindex.indexer)
indexes_by_name()
IndexingTask (class in biothings.hub.dataindex.indexer_task)
IndexJobStateRegistrar (class in biothings.hub.dataindex.indexer_registrar)
IndexManager (class in biothings.hub.dataindex.indexer)
IndexMappings (class in biothings.hub.dataindex.indexer_payload)
IndexSettings (class in biothings.hub.dataindex.indexer_payload)
inf (class in biothings.utils.common)
INFO (biothings.utils.loggers.Colors attribute)
(biothings.utils.loggers.Squares attribute)
info()
(biothings.hub.autoupdate.dumper.BiothingsDumper method)
(biothings.web.options.openapi.OpenAPIContext method)
ingest_hooks() (biothings.hub.HubServer method)
init_mapper() (biothings.hub.databuild.builder.DataBuilder method)
init_state() (biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.datatransform.datatransform.DataTransformEdge method)
(biothings.hub.datatransform.datatransform_api.BiothingsAPIEdge method)
(biothings.hub.datatransform.datatransform_mdb.MongoDBEdge method)
initialize() (biothings.hub.api.handlers.base.BaseHandler method)
(biothings.hub.api.handlers.base.GenericHandler method)
(biothings.hub.api.handlers.base.RootHandler method)
(biothings.hub.api.handlers.log.HubLogDirHandler method)
(biothings.hub.api.handlers.shell.ShellHandler method)
(biothings.hub.api.handlers.upload.UploadHandler method)
(biothings.utils.redis.RedisClient method)
(biothings.web.handlers.base.BaseAPIHandler method)
(biothings.web.handlers.query.BaseQueryHandler method)
INPUT (biothings.utils.loggers.ShellLogger attribute)
input() (biothings.utils.loggers.ShellLogger method)
inquire() (biothings.web.options.manager.Existentialist method)
insert() (biothings.utils.backend.DocBackendBase method)
(biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMemoryBackend method)
(biothings.utils.backend.DocMongoBackend method)
(biothings.utils.mongo.Collection method)
(biothings.utils.sqlite3.Collection method)
insert_one() (biothings.utils.es.Collection method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.sqlite3.Collection method)
inspect()
(biothings.hub.datainspect.inspector.InspectorManager method)
(in module biothings.utils.inspect)
inspect_data() (in module biothings.hub.datainspect.inspector)
inspect_docs() (in module biothings.utils.inspect)
inspect_source() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
InspectionValidation (class in biothings.utils.inspect)
InspectionValidation.Warning (class in biothings.utils.inspect)
InspectorError
InspectorManager (class in biothings.hub.datainspect.inspector)
install()
(biothings.hub.standalone.AutoHubFeature method)
int_convert() (in module biothings.utils.dataload)
interpret_manifest() (biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader method)
INVALID_CHARACTERS_PATTERN (biothings.utils.inspect.InspectionValidation attribute)
invalidate_cache() (in module biothings.utils.mongo)
invalidate_plugin() (biothings.hub.dataplugin.assistant.BasePluginLoader method)
InvalidJsonPatch
invisible (biothings.utils.configuration.ConfigAttrMeta attribute)
is_filehandle() (in module biothings.utils.common)
is_float() (in module biothings.utils.common)
is_int() (in module biothings.utils.common)
is_jsonable() (in module biothings.utils.configuration)
is_scalar() (in module biothings.utils.common)
is_seq() (in module biothings.utils.common)
is_str() (in module biothings.utils.common)
is_valid_data_plugin_dir() (in module biothings.cli.utils)
isempty() (biothings.utils.doc_traversal.Queue method)
(biothings.utils.doc_traversal.Stack method)
ism (built-in variable)
iter_n() (in module biothings.utils.common)
J
jm (built-in variable)
job_info()
(biothings.utils.manager.JobManager method)
JobManager (class in biothings.utils.manager)
JobRenderer (class in biothings.hub)
jobs() (biothings.hub.dataload.uploader.ParallelizedSourceUploader method)
json_array_parser() (in module biothings.utils.parsers)
json_dumps() (in module biothings.utils.serializer)
json_encode() (in module biothings.utils.common)
json_loads() (in module biothings.utils.serializer)
json_serial() (in module biothings.utils.common)
JsonArgCvter (class in biothings.web.options.manager)
jsondiff()
JsonDiffer (class in biothings.hub.databuild.differ)
JsonPatch (class in biothings.utils.jsonpatch)
JsonPatchConflict
JsonPatchException
JsonPatchTestFailed
jsonreadify() (in module biothings.utils.hub)
K
keep_archive (biothings.hub.databuild.builder.DataBuilder attribute)
(biothings.hub.dataload.uploader.BaseSourceUploader attribute)
KEEP_CONTAINER (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
key (biothings.utils.inspect.BaseMode attribute)
(biothings.utils.inspect.DeepStatsMode attribute)
(biothings.utils.inspect.IdentifiersMode attribute)
(biothings.utils.inspect.StatsMode attribute)
key_exists() (in module biothings.utils.aws)
key_lookup_batch() (biothings.hub.datatransform.datatransform.DataTransform method)
(biothings.hub.datatransform.datatransform_api.DataTransformAPI method)
(biothings.hub.datatransform.datatransform_mdb.DataTransformMDB method)
key_value() (in module biothings.utils.dotstring)
keylookup (biothings.hub.dataplugin.assistant.BaseAssistant attribute)
kwargs (biothings.web.handlers.base.BaseAPIHandler attribute)
(biothings.web.handlers.query.MetadataFieldHandler attribute)
(biothings.web.handlers.query.MetadataSourceHandler attribute)
L
last_element() (in module biothings.utils.dotstring)
LAST_MODIFIED (biothings.hub.dataload.dumper.LastModifiedHTTPDumper attribute)
LastModifiedBaseDumper (class in biothings.hub.dataload.dumper)
LastModifiedFTPDumper (class in biothings.hub.dataload.dumper)
LastModifiedHTTPDumper (class in biothings.hub.dataload.dumper)
launch() (biothings.utils.hub.HubShell method)
launched_commands (biothings.utils.hub.HubShell attribute)
left() (biothings.hub.datatransform.datatransform.IDStruct method)
license() (biothings.web.options.openapi.OpenAPIInfoContext method)
LinkDataBuilder (class in biothings.hub.databuild.builder)
LinkTargetDocMongoBackend (class in biothings.hub.databuild.backend)
list()
list2dict() (in module biothings.utils.common)
(in module biothings.utils.dataload)
list_biothings() (biothings.hub.standalone.AutoHubFeature method)
list_itemcnt() (in module biothings.utils.dataload)
list_length() (in module biothings.utils.dotstring)
list_merge() (biothings.hub.databuild.builder.BuilderManager method)
list_snapshots() (biothings.hub.dataindex.snapshooter.SnapshotManager method)
list_sources() (biothings.hub.databuild.builder.BuilderManager method)
list_split() (in module biothings.utils.dataload)
listeners (biothings.utils.hub_db.ChangeWatcher attribute)
listing() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
listitems() (in module biothings.utils.dataload)
listsort() (in module biothings.utils.dataload)
llist() (in module biothings.utils.dataload)
load() (biothings.hub.autoupdate.uploader.BiothingsUploader method)
(biothings.hub.databuild.mapper.BaseMapper method)
(biothings.hub.databuild.mapper.TransparentMapper method)
(biothings.hub.dataindex.idcache.IDCache method)
(biothings.hub.dataindex.idcache.RedisIDCache method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.dataplugin.assistant.AssistantManager method)
(biothings.hub.dataplugin.manager.DataPluginManager method)
(in module biothings.web.settings.configs)
load_build() (biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
load_class() (in module biothings.web.applications)
(in module biothings.web.services.namespace)
load_data() (biothings.hub.dataload.uploader.BaseSourceUploader method)
load_doc() (biothings.utils.manager.BaseStatusRegisterer method)
load_json() (in module biothings.utils.serializer)
load_metadata() (biothings.hub.databuild.syncer.BaseSyncer method)
load_module() (in module biothings.web.settings.configs)
load_plugin() (biothings.hub.dataplugin.assistant.AdvancedPluginLoader method)
(biothings.hub.dataplugin.assistant.AssistantManager method)
(biothings.hub.dataplugin.assistant.BaseAssistant method)
(biothings.hub.dataplugin.assistant.BasePluginLoader method)
(biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader method)
(in module biothings.cli.utils)
load_plugin_managers() (in module biothings.cli.utils)
load_remote_json() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
loader (biothings.hub.dataplugin.assistant.BaseAssistant property)
loader_type (biothings.hub.dataplugin.assistant.AdvancedPluginLoader attribute)
(biothings.hub.dataplugin.assistant.BasePluginLoader attribute)
(biothings.hub.dataplugin.assistant.ManifestBasedPluginLoader attribute)
LoaderException
loaders (biothings.hub.dataplugin.assistant.BaseAssistant attribute)
loadobj() (in module biothings.utils.common)
LocalAssistant (class in biothings.hub.dataplugin.assistant)
Locator (class in biothings.web.options.manager)
log() (biothings.web.options.manager.OptionsManager method)
logger (biothings.hub.databuild.builder.DataBuilder property)
(biothings.hub.dataload.dumper.BaseDumper property)
(biothings.hub.datatransform.datatransform.DataTransformEdge property)
(biothings.web.query.builder.ESUserQuery property)
LogListener (class in biothings.hub.api.handlers.ws)
LogPrint (class in biothings.utils.common)
lookin() (biothings.web.options.manager.Locator method)
lookup() (biothings.hub.datatransform.datatransform.IDStruct method)
(biothings.web.options.manager.ReqArgs method)
lookup_fields (biothings.hub.datatransform.datatransform_api.DataTransformAPI attribute)
(biothings.hub.datatransform.datatransform_api.DataTransformMyChemInfo attribute)
(biothings.hub.datatransform.datatransform_api.DataTransformMyGeneInfo attribute)
lookup_one() (biothings.hub.datatransform.datatransform.DataTransform method)
LookUpList (class in biothings.utils.loggers)
loop (built-in variable)
lsmerge()
M
main() (biothings.hub.dataload.sync.MongoSync method)
(in module biothings.cli)
(in module biothings.cli.web_app)
(in module biothings.web.launcher)
main_source (biothings.hub.dataload.uploader.BaseSourceUploader attribute)
MainIndexJSR (class in biothings.hub.dataindex.indexer_registrar)
MainIndexStep (class in biothings.hub.dataindex.indexer)
MainSnapshotState (class in biothings.hub.dataindex.snapshot_registrar)
make() (in module biothings.utils.jsondiff)
make_object() (in module biothings.utils.dotfield)
make_patch() (in module biothings.utils.jsonpatch)
make_temp_collection() (biothings.hub.dataload.uploader.BaseSourceUploader method)
ManagerError
ManifestBasedPluginLoader (class in biothings.hub.dataplugin.assistant)
ManualDataPlugin (class in biothings.hub.dataplugin.manager)
ManualDumper (class in biothings.hub.dataload.dumper)
mapdb (biothings.utils.redis.RedisClient property)
MappingError
mark_done() (biothings.hub.dataindex.idcache.IDCache method)
(biothings.hub.dataindex.idcache.RedisIDCache method)
mark_success() (biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DumperManager method)
markdown() (biothings.utils.loggers.SlackMessage method)
match() (biothings.utils.configuration.ConfigLine method)
matchers (biothings.utils.inspect.IdentifiersMode attribute)
(biothings.utils.inspect.RegexMode attribute)
MAX_PARALLEL_DUMP (biothings.hub.dataload.dumper.BaseDumper attribute)
(biothings.hub.dataload.dumper.DockerContainerDumper attribute)
maxminiflist() (biothings.utils.inspect.StatsMode method)
MaxRetryAutoReconnectException
md5sum() (in module biothings.utils.common)
mentions() (biothings.utils.loggers.SlackMentionPolicy method)
MERGE (biothings.hub.dataindex.indexer_task.Mode attribute)
merge()
(biothings.hub.databuild.builder.BuilderManager method)
(biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.dataindex.indexer_task.IndexingTask method)
(biothings.utils.inspect.BaseMode method)
(biothings.utils.inspect.DeepStatsMode method)
(biothings.utils.inspect.RegexMode method)
(biothings.utils.inspect.StatsMode method)
(in module biothings.utils.common)
merge_dict() (in module biothings.utils.dataload)
merge_duplicate_rows() (in module biothings.utils.dataload)
merge_field_inspections_validations() (in module biothings.utils.inspect)
merge_object() (in module biothings.utils.dotfield)
merge_order() (biothings.hub.databuild.builder.DataBuilder method)
merge_record() (in module biothings.utils.inspect)
merge_root_keys() (in module biothings.utils.dataload)
merge_scalar_list() (in module biothings.utils.inspect)
merge_source() (biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.databuild.builder.LinkDataBuilder method)
merge_sources() (biothings.hub.databuild.builder.DataBuilder method)
merge_src_build_metadata() (in module biothings.hub.databuild.backend)
merge_struct() (in module biothings.utils.dataload)
merger_worker() (in module biothings.hub.databuild.builder)
MergerSourceUploader (class in biothings.hub.dataload.uploader)
Message (class in biothings.web.analytics.events)
MetadataFieldHandler (class in biothings.web.handlers.query)
MetadataSourceHandler (class in biothings.web.handlers.query)
MetaField (class in biothings.utils.configuration)
method (biothings.hub.dataindex.indexer.MainIndexStep attribute)
(biothings.hub.dataindex.indexer.PostIndexStep attribute)
(biothings.hub.dataindex.indexer.PreIndexStep attribute)
(biothings.hub.dataindex.indexer.Step attribute)
mexists() (biothings.hub.dataindex.indexer_task.ESIndex method)
(biothings.utils.es.ESIndexer method)
mget() (biothings.hub.dataindex.indexer_task.ESIndex method)
mget_from_ids() (biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMongoBackend method)
mindex() (biothings.hub.dataindex.indexer_task.ESIndex method)
MinType (class in biothings.utils.dataload)
mixargs() (biothings.hub.HubServer method)
Mode (class in biothings.hub.dataindex.indexer_task)
modified (biothings.utils.configuration.ConfigurationWrapper property)
module
biothings.cli
biothings.cli.dataplugin
biothings.cli.dataplugin_hub
biothings.cli.utils
biothings.cli.web_app
biothings.hub
biothings.hub.api
biothings.hub.api.handlers.base
biothings.hub.api.handlers.log
biothings.hub.api.handlers.shell
biothings.hub.api.handlers.upload
biothings.hub.api.handlers.ws
biothings.hub.api.manager
biothings.hub.autoupdate.dumper
biothings.hub.autoupdate.uploader
biothings.hub.databuild.backend
biothings.hub.databuild.buildconfig
biothings.hub.databuild.builder
biothings.hub.databuild.differ
biothings.hub.databuild.mapper
biothings.hub.databuild.prebuilder
biothings.hub.databuild.syncer
biothings.hub.dataexport.ids
biothings.hub.dataindex.idcache
biothings.hub.dataindex.indexer
biothings.hub.dataindex.indexer_cleanup
biothings.hub.dataindex.indexer_payload
biothings.hub.dataindex.indexer_registrar
biothings.hub.dataindex.indexer_schedule
biothings.hub.dataindex.indexer_task
biothings.hub.dataindex.snapshooter
biothings.hub.dataindex.snapshot_cleanup
biothings.hub.dataindex.snapshot_registrar
biothings.hub.dataindex.snapshot_repo
biothings.hub.dataindex.snapshot_task
biothings.hub.datainspect.inspector
biothings.hub.dataload.dumper
biothings.hub.dataload.source
biothings.hub.dataload.storage
biothings.hub.dataload.sync
biothings.hub.dataload.uploader
biothings.hub.dataplugin.assistant
biothings.hub.dataplugin.manager
biothings.hub.datarelease
biothings.hub.datarelease.publisher
biothings.hub.datarelease.releasenote
biothings.hub.datatransform.ciidstruct
biothings.hub.datatransform.datatransform
biothings.hub.datatransform.datatransform_api
biothings.hub.datatransform.datatransform_mdb
biothings.hub.datatransform.histogram
biothings.hub.standalone
biothings.tests
biothings.tests.hub
biothings.tests.web
biothings.utils
biothings.utils.aws
biothings.utils.backend
biothings.utils.common
biothings.utils.configuration
biothings.utils.dataload
biothings.utils.diff
biothings.utils.doc_traversal
biothings.utils.docs
biothings.utils.dotfield
biothings.utils.dotstring
biothings.utils.es
biothings.utils.exclude_ids
biothings.utils.hub
biothings.utils.hub_db
biothings.utils.info
biothings.utils.inspect
biothings.utils.jsondiff
biothings.utils.jsonpatch
biothings.utils.jsonschema
biothings.utils.loggers
biothings.utils.manager
biothings.utils.mongo
biothings.utils.parallel
biothings.utils.parallel_mp
biothings.utils.parsers
biothings.utils.redis
biothings.utils.serializer
biothings.utils.sqlite3
biothings.utils.version
biothings.web
biothings.web.analytics
biothings.web.analytics.channels
biothings.web.analytics.events
biothings.web.analytics.notifiers
biothings.web.applications
biothings.web.connections
biothings.web.handlers
biothings.web.handlers.base
biothings.web.handlers.query
biothings.web.handlers.services
biothings.web.launcher
biothings.web.options
biothings.web.options.manager
biothings.web.options.openapi
biothings.web.query
biothings.web.query.builder
biothings.web.query.engine
biothings.web.query.formatter
biothings.web.query.pipeline
biothings.web.services
biothings.web.services.health
biothings.web.services.metadata
biothings.web.services.namespace
biothings.web.services.query
biothings.web.settings
biothings.web.settings.configs
biothings.web.settings.default
biothings.web.settings.validators
biothings.web.templates
modules (biothings.web.settings.configs.ConfigPackage attribute)
mongo (in module biothings.web.connections)
MongoDBEdge (class in biothings.hub.datatransform)
(class in biothings.hub.datatransform.datatransform_mdb)
MongoDBPreCompiledDataProvider (class in biothings.hub.databuild.prebuilder)
MongoHealth (class in biothings.web.services.health)
MongoJsonDiffSelfContainedSyncer (class in biothings.hub.databuild.syncer)
MongoJsonDiffSyncer (class in biothings.hub.databuild.syncer)
MongoParamValidaor (class in biothings.web.settings.validators)
MongoQueryBackend (class in biothings.web.query.engine)
MongoQueryBuilder (class in biothings.web.query.builder)
MongoQueryPipeline (class in biothings.web.query.pipeline)
MongoResultFormatter (class in biothings.web.query.formatter)
MongoSync (class in biothings.hub.dataload.sync)
monitor() (biothings.utils.hub.TornadoAutoReloadHubReloader method)
(biothings.utils.hub_db.ChangeWatcher class method)
MoveOperation (class in biothings.utils.jsonpatch)
msgpack_ok() (biothings.tests.web.BiothingsWebTestBase static method)
multidict() (in module biothings.utils.jsonpatch)
MyChemInfoEdge (class in biothings.hub.datatransform)
(class in biothings.hub.datatransform.datatransform_api)
MyGeneInfoEdge (class in biothings.hub.datatransform)
(class in biothings.hub.datatransform.datatransform_api)
N
name (biothings.hub.autoupdate.uploader.BiothingsUploader attribute)
(biothings.hub.databuild.backend.LinkTargetDocMongoBackend attribute)
(biothings.hub.dataindex.indexer.MainIndexStep attribute)
(biothings.hub.dataindex.indexer.PostIndexStep attribute)
(biothings.hub.dataindex.indexer.PreIndexStep attribute)
(biothings.hub.dataindex.indexer.Step attribute)
(biothings.hub.dataindex.snapshot_registrar.MainSnapshotState attribute)
(biothings.hub.dataindex.snapshot_registrar.PostSnapshotState attribute)
(biothings.hub.dataindex.snapshot_registrar.PreSnapshotState attribute)
(biothings.hub.dataload.uploader.BaseSourceUploader attribute)
(biothings.utils.backend.DocBackendBase attribute)
(biothings.utils.backend.DocESBackend attribute)
(biothings.utils.backend.DocMemoryBackend attribute)
(biothings.utils.backend.DocMongoBackend attribute)
(biothings.utils.hub_db.Collection property)
(biothings.utils.sqlite3.Collection property)
(biothings.web.handlers.base.BaseAPIHandler attribute)
(biothings.web.handlers.query.BiothingHandler attribute)
(biothings.web.handlers.query.MetadataFieldHandler attribute)
(biothings.web.handlers.query.MetadataSourceHandler attribute)
(biothings.web.handlers.query.QueryHandler attribute)
name() (biothings.web.options.openapi.OpenAPIContactContext method)
(biothings.web.options.openapi.OpenAPILicenseContext method)
nan (class in biothings.utils.common)
ndjson_parser() (in module biothings.utils.parsers)
need_load() (biothings.hub.databuild.mapper.IDBaseMapper method)
need_prepare() (biothings.hub.dataload.dumper.APIDumper method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.FilesystemDumper method)
(biothings.hub.dataload.dumper.FTPDumper method)
(biothings.hub.dataload.dumper.GitDumper method)
(biothings.hub.dataload.dumper.HTTPDumper method)
(biothings.hub.dataload.dumper.WgetDumper method)
nested_lookup() (in module biothings.hub.datatransform.datatransform)
new_data_folder (biothings.hub.dataload.dumper.BaseDumper property)
(biothings.hub.dataload.dumper.GitDumper property)
(biothings.hub.dataload.dumper.ManualDumper property)
newer() (in module biothings.utils.common)
NoBatchIgnoreDuplicatedSourceUploader (class in biothings.hub.dataload.uploader)
NoDataSourceUploader (class in biothings.hub.dataload.uploader)
NoResultError
norm() (in module biothings.utils.manager)
normalized_value() (in module biothings.utils.dataload)
NoSuchCommand
Notifier (class in biothings.web.analytics.notifiers)
NOTSET (biothings.utils.loggers.Colors attribute)
(biothings.utils.loggers.Squares attribute)
NUMERIC_FIELDS (biothings.utils.inspect.InspectionValidation attribute)
O
on_close() (biothings.hub.api.handlers.ws.WebSocketConnection method)
on_finish() (biothings.web.analytics.notifiers.AnalyticsMixin method)
(biothings.web.handlers.base.BaseAPIHandler method)
on_message() (biothings.hub.api.handlers.ws.WebSocketConnection method)
on_open() (biothings.hub.api.handlers.ws.WebSocketConnection method)
open() (biothings.utils.es.ESIndexer method)
open_anyfile() (in module biothings.utils.common)
open_compressed_file() (in module biothings.utils.common)
OpenAPIContactContext (class in biothings.web.options.openapi)
OpenAPIContext (class in biothings.web.options.openapi)
OpenAPIDocumentBuilder (in module biothings.web.options.openapi)
OpenAPIExternalDocsContext (class in biothings.web.options.openapi)
OpenAPIInfoContext (class in biothings.web.options.openapi)
OpenAPILicenseContext (class in biothings.web.options.openapi)
OpenAPIOperation (class in biothings.web.options.openapi)
OpenAPIParameterContext (class in biothings.web.options.openapi)
OpenAPIPathItemContext (class in biothings.web.options.openapi)
operation_id() (biothings.web.options.openapi.OpenAPIOperation method)
optimize() (biothings.utils.es.ESIndexer method)
Option (class in biothings.web.options.manager)
OptionError
options() (biothings.hub.api.handlers.base.DefaultHandler method)
(biothings.hub.api.handlers.log.HubLogFileHandler method)
(biothings.web.handlers.base.BaseAPIHandler method)
(biothings.web.options.openapi.OpenAPIPathItemContext method)
OptionSet (class in biothings.web.options.manager)
OptionsManager (class in biothings.web.options.manager)
order() (biothings.hub.dataindex.indexer.Step static method)
ORIGINAL_CONTAINER_STATUS (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
orjson_default() (in module biothings.utils.serializer)
OUTPUT (biothings.utils.loggers.ShellLogger attribute)
output() (biothings.utils.loggers.ShellLogger method)
output_types (biothings.hub.datatransform.datatransform_api.DataTransformMyChemInfo attribute)
P
Paragraph (class in biothings.utils.configuration)
ParallelizedSourceUploader (class in biothings.hub.dataload.uploader)
ParallelResult (class in biothings.utils.parallel_mp)
parse() (biothings.utils.configuration.ConfigLines method)
(biothings.web.options.manager.Option method)
(biothings.web.options.manager.OptionSet method)
(biothings.web.query.builder.QStringParser method)
parse_dot_fields() (in module biothings.utils.dotfield)
parse_folder_name_from_url() (in module biothings.utils.common)
parse_head() (biothings.hub.api.handlers.upload.UploadHandler method)
password_auth_supported() (biothings.hub.HubSSHServer method)
PASSWORDS (biothings.hub.HubSSHServer attribute)
patch() (biothings.web.options.openapi.OpenAPIPathItemContext method)
PatchOperation (class in biothings.utils.jsonpatch)
path() (biothings.web.options.openapi.OpenAPIContext method)
PathArgCvter (class in biothings.web.options.manager)
PATTERNS (biothings.utils.configuration.ConfigLine attribute)
pause() (biothings.utils.common.LogPrint method)
payload() (biothings.utils.loggers.WSLogHandler method)
(biothings.utils.loggers.WSShellHandler method)
pchildren (biothings.utils.manager.JobManager property)
pending (built-in variable)
pending() (in module biothings.hub.databuild.builder)
pending_outputs (biothings.utils.hub.HubShell attribute)
pending_snapshot() (biothings.hub.dataindex.snapshooter.SnapshotManager static method)
pick_db() (biothings.utils.redis.RedisClient method)
plain_text() (biothings.hub.dataindex.indexer_cleanup.Cleaner static method)
(in module biothings.hub.dataindex.snapshot_cleanup)
plaintext() (biothings.utils.loggers.SlackMessage method)
plugin_name (biothings.hub.dataplugin.assistant.BaseAssistant property)
(biothings.hub.dataplugin.assistant.GithubAssistant property)
(biothings.hub.dataplugin.assistant.LocalAssistant property)
plugin_type (biothings.hub.dataplugin.assistant.BaseAssistant attribute)
(biothings.hub.dataplugin.assistant.GithubAssistant attribute)
(biothings.hub.dataplugin.assistant.LocalAssistant attribute)
poll() (biothings.hub.databuild.builder.BuilderManager method)
(biothings.hub.databuild.differ.DifferManager method)
(biothings.hub.dataindex.snapshooter.SnapshotManager method)
(biothings.hub.dataload.uploader.UploaderManager method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
(biothings.utils.hub.BaseHubReloader method)
(biothings.utils.manager.BaseManager method)
pop() (biothings.utils.doc_traversal.Queue method)
(biothings.utils.doc_traversal.Stack method)
post() (biothings.hub.api.handlers.base.GenericHandler method)
(biothings.hub.api.handlers.upload.UploadHandler method)
(biothings.utils.inspect.BaseMode method)
(biothings.utils.inspect.DeepStatsMode method)
(biothings.web.handlers.query.BiothingHandler method)
(biothings.web.handlers.query.QueryHandler method)
(biothings.web.options.openapi.OpenAPIPathItemContext method)
post_diff_cols() (biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.differ.ColdHotJsonDifferBase method)
post_download() (biothings.hub.dataload.dumper.BaseDumper method)
post_dump() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
post_dump_delete_files() (biothings.hub.dataload.dumper.BaseDumper method)
post_index() (biothings.hub.dataindex.indexer.Indexer method)
post_merge() (biothings.hub.databuild.backend.TargetDocBackend method)
(biothings.hub.databuild.builder.DataBuilder method)
post_publish() (biothings.hub.datarelease.publisher.DiffPublisher method)
(biothings.hub.datarelease.publisher.SnapshotPublisher method)
post_snapshot() (biothings.hub.dataindex.snapshooter.SnapshotEnv method)
post_sync_cols() (biothings.hub.databuild.syncer.BaseSyncer method)
post_update_data() (biothings.hub.dataload.uploader.BaseSourceUploader method)
PostIndexJSR (class in biothings.hub.dataindex.indexer_registrar)
PostIndexStep (class in biothings.hub.dataindex.indexer)
PostSnapshotState (class in biothings.hub.dataindex.snapshot_registrar)
pqueue (built-in variable)
pre_index() (biothings.hub.dataindex.indexer.Indexer method)
pre_publish() (biothings.hub.datarelease.publisher.DiffPublisher method)
(biothings.hub.datarelease.publisher.SnapshotPublisher method)
pre_snapshot() (biothings.hub.dataindex.snapshooter.SnapshotEnv method)
prefix (biothings.tests.web.BiothingsWebTestBase attribute)
PreIndexJSR (class in biothings.hub.dataindex.indexer_registrar)
PreIndexStep (class in biothings.hub.dataindex.indexer)
prepare() (biothings.hub.api.handlers.upload.UploadHandler method)
(biothings.hub.databuild.backend.ShardedTargetDocMongoBackend method)
(biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.ManualDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.datatransform.datatransform.DataTransformEdge method)
(biothings.utils.backend.DocBackendBase method)
(biothings.utils.backend.DocESBackend method)
(biothings.web.handlers.base.BaseAPIHandler method)
(biothings.web.handlers.query.BaseQueryHandler method)
prepare_client() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
(biothings.hub.dataload.dumper.APIDumper method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.DummyDumper method)
(biothings.hub.dataload.dumper.FilesystemDumper method)
(biothings.hub.dataload.dumper.FTPDumper method)
(biothings.hub.dataload.dumper.GitDumper method)
(biothings.hub.dataload.dumper.GoogleDriveDumper method)
(biothings.hub.dataload.dumper.HTTPDumper method)
(biothings.hub.dataload.dumper.LastModifiedFTPDumper method)
(biothings.hub.dataload.dumper.ManualDumper method)
(biothings.hub.dataload.dumper.WgetDumper method)
(biothings.hub.datatransform.datatransform_api.BiothingsAPIEdge method)
prepare_collection() (biothings.hub.datatransform.datatransform_mdb.MongoDBEdge method)
prepare_dumper_params() (biothings.hub.dataload.dumper.DockerContainerDumper method)
prepare_local_folders() (biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
prepare_remote_container() (biothings.hub.dataload.dumper.DockerContainerDumper method)
prepare_src_dump() (biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.dataload.uploader.DummySourceUploader method)
(biothings.hub.dataplugin.manager.GitDataPlugin method)
(biothings.hub.dataplugin.manager.ManualDataPlugin method)
PreSnapshotState (class in biothings.hub.dataindex.snapshot_registrar)
print_pending_info() (biothings.utils.manager.JobManager method)
print_workers() (biothings.utils.manager.JobManager method)
process() (biothings.hub.databuild.mapper.BaseMapper method)
(biothings.hub.databuild.mapper.IDBaseMapper method)
(biothings.hub.databuild.mapper.TransparentMapper method)
process_hook_file() (biothings.hub.HubServer method)
process_inspect() (in module biothings.cli.utils)
ProcessInfo (class in biothings.hub.dataindex.indexer)
(class in biothings.hub.dataindex.snapshooter)
prune() (biothings.hub.dataindex.indexer_registrar.IndexJobStateRegistrar static method)
publish()
(biothings.hub.api.handlers.ws.WebSocketConnection method)
(biothings.hub.datarelease.publisher.DiffPublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
(biothings.hub.datarelease.publisher.SnapshotPublisher method)
(biothings.utils.hub_db.ChangeWatcher class method)
publish_build() (biothings.hub.datarelease.publisher.ReleaseManager method)
publish_data_version() (in module biothings.utils.hub)
publish_diff()
(biothings.hub.datarelease.publisher.ReleaseManager method)
publish_release_notes() (biothings.hub.datarelease.publisher.BasePublisher method)
publish_snapshot()
(biothings.hub.datarelease.publisher.ReleaseManager method)
PublisherException
PURGE (biothings.hub.dataindex.indexer_task.Mode attribute)
push() (biothings.utils.doc_traversal.Queue method)
(biothings.utils.doc_traversal.Stack method)
put() (biothings.hub.api.handlers.base.GenericHandler method)
(biothings.hub.api.handlers.shell.ShellHandler method)
(biothings.web.options.openapi.OpenAPIPathItemContext method)
Q
QStringParser (class in biothings.web.query.builder)
Query (class in biothings.web.query.builder)
query() (biothings.tests.web.BiothingsWebTestBase method)
(biothings.utils.backend.DocESBackend method)
QueryArgCvter (class in biothings.web.options.manager)
QueryHandler (class in biothings.cli.web_app)
(class in biothings.web.handlers.query)
QueryPipeline (class in biothings.web.query.pipeline)
QueryPipelineException
QueryPipelineInterrupt
Queue (class in biothings.utils.doc_traversal)
QueueEmptyError
quick_index()
(biothings.hub.HubServer method)
R
range (biothings.utils.loggers.Record attribute)
Range (class in biothings.utils.loggers)
RawQueryInterrupt
RawResultInterrupt
read() (biothings.hub.api.handlers.ws.HubDBListener method)
(biothings.hub.api.handlers.ws.LogListener method)
(biothings.utils.hub_db.ChangeListener method)
readonly (biothings.utils.configuration.ConfigAttrMeta attribute)
(biothings.utils.configuration.ConfigurationWrapper property)
READY (biothings.hub.dataindex.indexer_registrar.Stage attribute)
reapply_patch() (in module biothings.utils.jsonpatch)
rebuild_diff_file_list() (biothings.hub.databuild.differ.DifferManager method)
rec_handler() (in module biothings.utils.dataload)
ReceiverGroup (class in biothings.utils.loggers)
Record (class in biothings.utils.loggers)
recycle_process_queue() (biothings.utils.manager.JobManager method)
RedisClient (class in biothings.utils.redis)
RedisClientError
RedisIDCache (class in biothings.hub.dataindex.idcache)
RedisPreCompiledDataProvider (class in biothings.hub.databuild.prebuilder)
reduce_diffs() (in module biothings.hub.databuild.differ)
refresh() (biothings.web.services.metadata.BiothingsESMetadata method)
(biothings.web.services.metadata.BiothingsMetadata method)
(biothings.web.services.metadata.BiothingsMongoMetadata method)
(biothings.web.services.metadata.BiothingsSQLMetadata method)
refresh_commands() (biothings.utils.hub.HubShell class method)
regex_name (biothings.hub.dataload.uploader.BaseSourceUploader attribute)
RegExEdge (class in biothings.hub.datatransform)
(class in biothings.hub.datatransform.datatransform)
RegexMode (class in biothings.utils.inspect)
region (biothings.hub.dataindex.snapshooter.CloudStorage attribute)
(biothings.hub.dataindex.snapshooter.RepositoryConfig property)
register() (biothings.hub.databuild.prebuilder.BasePreCompiledDataProvider method)
(biothings.hub.databuild.prebuilder.MongoDBPreCompiledDataProvider method)
(biothings.hub.databuild.prebuilder.RedisPreCompiledDataProvider method)
register_builder() (biothings.hub.databuild.builder.BuilderManager method)
register_classes() (biothings.hub.dataload.dumper.DumperManager method)
(biothings.hub.dataload.uploader.UploaderManager method)
(biothings.hub.dataplugin.assistant.AssistantManager method)
(biothings.utils.manager.BaseSourceManager method)
register_command() (biothings.utils.hub.HubShell method)
register_differ() (biothings.hub.databuild.differ.DifferManager method)
register_loader() (biothings.hub.dataplugin.assistant.BaseAssistant method)
register_managers() (biothings.utils.hub.HubShell method)
register_source() (biothings.utils.manager.BaseSourceManager method)
register_sources() (biothings.utils.manager.BaseSourceManager method)
register_status() (biothings.hub.api.manager.APIManager method)
(biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.syncer.BaseSyncer method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
(biothings.utils.manager.BaseStatusRegisterer method)
register_syncer() (biothings.hub.databuild.syncer.SyncerManager method)
register_url()
(biothings.hub.dataplugin.assistant.AssistantManager method)
regx (biothings.hub.dataindex.snapshot_registrar.MainSnapshotState attribute)
(biothings.hub.dataindex.snapshot_registrar.PostSnapshotState attribute)
reindex() (biothings.utils.es.ESIndexer method)
release_client() (biothings.hub.dataload.dumper.APIDumper method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.FilesystemDumper method)
(biothings.hub.dataload.dumper.FTPDumper method)
(biothings.hub.dataload.dumper.GitDumper method)
(biothings.hub.dataload.dumper.HTTPDumper method)
(biothings.hub.dataload.dumper.LastModifiedFTPDumper method)
(biothings.hub.dataload.dumper.WgetDumper method)
RELEASE_FORMAT (biothings.hub.dataload.dumper.LastModifiedFTPDumper attribute)
(biothings.hub.dataload.dumper.LastModifiedHTTPDumper attribute)
release_info()
(biothings.hub.datarelease.publisher.ReleaseManager method)
RELEASE_TO_BUILD (biothings.hub.databuild.buildconfig.AutoBuildConfig attribute)
RELEASE_TYPES (biothings.hub.databuild.buildconfig.AutoBuildConfig attribute)
ReleaseManager (class in biothings.hub.datarelease.publisher)
ReleaseNoteSource (class in biothings.hub.datarelease.releasenote)
ReleaseNoteSrcBuildReader (class in biothings.hub.datarelease.releasenote)
ReleaseNoteSrcBuildReaderAdapter (class in biothings.hub.datarelease.releasenote)
ReleaseNoteTxt (class in biothings.hub.datarelease.releasenote)
reload() (biothings.hub.dataload.source.SourceManager method)
remote_is_better() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
(biothings.hub.dataload.dumper.APIDumper method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.FilesystemDumper method)
(biothings.hub.dataload.dumper.FTPDumper method)
(biothings.hub.dataload.dumper.GitDumper method)
(biothings.hub.dataload.dumper.GoogleDriveDumper method)
(biothings.hub.dataload.dumper.HTTPDumper method)
(biothings.hub.dataload.dumper.LastModifiedFTPDumper method)
(biothings.hub.dataload.dumper.LastModifiedHTTPDumper method)
(biothings.hub.dataload.dumper.WgetDumper method)
remove() (biothings.utils.es.Collection method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.mongo.Collection method)
(biothings.utils.serializer.URL method)
(biothings.utils.sqlite3.Collection method)
remove_files_in_folder() (in module biothings.cli.utils)
remove_from_ids() (biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMongoBackend method)
remove_key() (in module biothings.utils.dotstring)
RemoveOperation (class in biothings.utils.jsonpatch)
rename() (biothings.utils.sqlite3.Collection method)
render() (biothings.hub.JobRenderer method)
render_cron() (biothings.hub.JobRenderer method)
render_func() (biothings.hub.JobRenderer method)
render_lambda() (biothings.hub.JobRenderer method)
render_method() (biothings.hub.JobRenderer method)
render_partial() (biothings.hub.JobRenderer method)
render_strdelta() (biothings.hub.JobRenderer method)
RenderedStr (class in biothings.hub.dataindex.snapshooter)
replace_one() (biothings.utils.es.Collection method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.sqlite3.Collection method)
ReplaceOperation (class in biothings.utils.jsonpatch)
repo (biothings.hub.dataindex.snapshooter.RepositoryConfig property)
report()
(biothings.utils.inspect.BaseMode method)
(biothings.utils.inspect.DeepStatsMode method)
(biothings.utils.inspect.RegexMode method)
(biothings.utils.inspect.StatsMode method)
Repository (class in biothings.hub.dataindex.snapshot_repo)
RepositoryConfig (class in biothings.hub.dataindex.snapshooter)
ReqArgs (class in biothings.web.options.manager)
ReqArgs.Path (class in biothings.web.options.manager)
ReqResult (class in biothings.web.options.manager)
request() (biothings.tests.web.BiothingsWebAppTest method)
(biothings.tests.web.BiothingsWebTestBase method)
requires_config() (in module biothings.utils.mongo)
(in module biothings.utils.sqlite3)
reset() (biothings.hub.dataload.source.SourceManager method)
(biothings.utils.configuration.ConfigAttrMeta method)
(biothings.utils.configuration.ConfigurationWrapper method)
reset_backend()
reset_synced()
(biothings.hub.datarelease.publisher.DiffPublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
reset_target_backend() (biothings.hub.autoupdate.dumper.BiothingsDumper method)
resetconf()
resolve_builder_class() (biothings.hub.databuild.builder.BuilderManager method)
RESOLVE_FILENAME (biothings.hub.dataload.dumper.HTTPDumper attribute)
(biothings.hub.dataload.dumper.LastModifiedHTTPDumper attribute)
resolve_sources() (biothings.hub.databuild.builder.DataBuilder method)
ResourceError
,
[1]
ResourceNotFound
ResourceNotReady
restart()
(biothings.utils.hub.HubShell method)
restore()
(biothings.utils.es.ESIndexer method)
(in module biothings.utils.hub_db)
restore_running_apis() (biothings.hub.api.manager.APIManager method)
restore_snapshot() (biothings.hub.autoupdate.uploader.BiothingsUploader method)
ResultFormatter (class in biothings.web.query.formatter)
ResultFormatterException
ResultInterrupt
RESUME (biothings.hub.dataindex.indexer_task.Mode attribute)
resume() (biothings.hub.dataindex.indexer_task.IndexingTask method)
(biothings.utils.common.LogPrint method)
ResumeException
right() (biothings.hub.datatransform.datatransform.IDStruct method)
rm (built-in variable)
rmdashfr() (in module biothings.utils.common)
rmmerge()
root (biothings.web.settings.configs.ConfigPackage attribute)
RootHandler (class in biothings.hub.api.handlers.base)
run_converters() (in module biothings.utils.inspect)
run_jobs_on_ipythoncluster() (in module biothings.utils.parallel)
run_jobs_on_parallel() (in module biothings.utils.parallel)
run_once() (in module biothings.utils.common)
run_parallel_on_ids_dir() (in module biothings.utils.parallel_mp)
run_parallel_on_ids_file() (in module biothings.utils.parallel_mp)
run_parallel_on_iterable() (in module biothings.utils.parallel_mp)
run_parallel_on_query() (in module biothings.utils.parallel_mp)
run_post_publish_diff() (biothings.hub.datarelease.publisher.DiffPublisher method)
run_post_publish_snapshot() (biothings.hub.datarelease.publisher.SnapshotPublisher method)
run_pre_post() (biothings.hub.datarelease.publisher.BasePublisher method)
run_pre_publish_diff() (biothings.hub.datarelease.publisher.DiffPublisher method)
run_pre_publish_snapshot() (biothings.hub.datarelease.publisher.SnapshotPublisher method)
run_sync_or_async_job() (in module biothings.cli.utils)
S
safe_type() (in module biothings.utils.dataload)
safe_unicode() (in module biothings.utils.common)
safewfile() (in module biothings.utils.common)
sanitize_settings() (biothings.utils.es.ESIndexer method)
sanitize_tarfile() (in module biothings.utils.common)
save() (biothings.hub.databuild.differ.DiffReportRendererBase method)
(biothings.hub.databuild.differ.DiffReportTxt method)
(biothings.hub.datarelease.releasenote.ReleaseNoteTxt method)
(biothings.utils.es.Collection method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.mongo.Collection method)
(biothings.utils.sqlite3.Collection method)
save_cmd() (biothings.utils.hub.HubShell class method)
save_doc_src_master() (biothings.hub.dataload.uploader.BaseSourceUploader method)
save_mapping() (biothings.hub.databuild.builder.BuilderManager method)
(biothings.hub.dataload.source.SourceManager method)
sch()
SCHEDULE (biothings.hub.dataload.dumper.BaseDumper attribute)
Schedule (class in biothings.hub.dataindex.indexer_schedule)
schedule()
(biothings.utils.manager.JobManager method)
schedule_all() (biothings.hub.dataload.dumper.DumperManager method)
schema() (biothings.web.options.openapi.OpenAPIParameterContext method)
scheme (biothings.tests.web.BiothingsWebTestBase attribute)
scopes (biothings.web.query.builder.Group attribute)
(biothings.web.query.builder.Query attribute)
search() (biothings.web.query.pipeline.AsyncESQueryPipeline method)
(biothings.web.query.pipeline.ESQueryPipeline method)
(biothings.web.query.pipeline.QueryPipeline method)
secret_key (biothings.hub.dataindex.snapshooter.CloudStorage attribute)
section (biothings.utils.configuration.ConfigAttrMeta attribute)
SelfContainedJsonDiffer (class in biothings.hub.databuild.differ)
send() (biothings.utils.loggers.SlackHandler static method)
(biothings.web.analytics.channels.Channel method)
(biothings.web.analytics.channels.GA4Channel method)
(biothings.web.analytics.channels.GAChannel method)
(biothings.web.analytics.channels.SlackChannel method)
send_s3_big_file() (in module biothings.utils.aws)
send_s3_file() (in module biothings.utils.aws)
send_s3_folder() (in module biothings.utils.aws)
serve() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
(in module biothings.cli.utils)
server() (biothings.web.options.openapi.OpenAPIContext method)
session_requested() (biothings.hub.HubSSHServer method)
session_started() (biothings.hub.HubSSHServerSession method)
set_cache_header() (biothings.web.handlers.base.BaseAPIHandler method)
set_command_counter() (biothings.utils.hub.HubShell class method)
set_commands() (biothings.utils.hub.HubShell method)
set_data_path() (biothings.hub.dataload.dumper.DockerContainerDumper method)
set_debug() (biothings.hub.datatransform.datatransform.IDStruct method)
set_default_folder() (in module biothings.utils.configuration)
set_default_headers() (biothings.cli.web_app.BaseHandler method)
(biothings.hub.api.handlers.base.DefaultHandler method)
(biothings.hub.api.handlers.log.DefaultCORSHeaderMixin method)
(biothings.web.handlers.base.BaseAPIHandler method)
set_dump_command() (biothings.hub.dataload.dumper.DockerContainerDumper method)
set_get_version_cmd() (biothings.hub.dataload.dumper.DockerContainerDumper method)
set_internal_number_of_replicas() (biothings.utils.es.ESIndexer method)
set_keep_container() (biothings.hub.dataload.dumper.DockerContainerDumper method)
set_key_value() (in module biothings.utils.dotstring)
set_mapping_src_meta() (biothings.hub.dataload.source.SourceManager method)
set_pending_to_build() (in module biothings.hub.databuild.builder)
set_pending_to_diff() (in module biothings.hub.databuild.differ)
set_pending_to_publish() (in module biothings.hub.datarelease)
set_pending_to_release_note() (in module biothings.hub.datarelease)
set_pending_to_upload() (in module biothings.hub.dataload.uploader)
set_release() (biothings.hub.dataload.dumper.DockerContainerDumper method)
(biothings.hub.dataload.dumper.LastModifiedBaseDumper method)
(biothings.hub.dataload.dumper.LastModifiedFTPDumper method)
(biothings.hub.dataload.dumper.LastModifiedHTTPDumper method)
set_static_website() (in module biothings.utils.aws)
set_target_name() (biothings.hub.databuild.backend.TargetDocBackend method)
(biothings.hub.databuild.backend.TargetDocMongoBackend method)
set_versions() (in module biothings.utils.version)
setconf()
setup() (biothings.hub.api.manager.APIManager method)
(biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
(biothings.web.options.manager.OptionSet method)
(in module biothings.utils.hub_db)
setup_class() (biothings.tests.web.BiothingsWebTest class method)
setup_config() (in module biothings.cli)
setup_default_log() (in module biothings.utils.loggers)
setup_log() (biothings.hub.api.manager.APIManager method)
(biothings.hub.databuild.builder.BuilderManager method)
(biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.databuild.differ.BaseDiffer method)
(biothings.hub.databuild.differ.DifferManager method)
(biothings.hub.databuild.syncer.BaseSyncer method)
(biothings.hub.databuild.syncer.SyncerManager method)
(biothings.hub.dataindex.indexer.Indexer method)
(biothings.hub.dataindex.snapshooter.SnapshotEnv method)
(biothings.hub.datainspect.inspector.InspectorManager method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.dataplugin.assistant.AssistantManager method)
(biothings.hub.dataplugin.assistant.BaseAssistant method)
(biothings.hub.dataplugin.assistant.BasePluginLoader method)
(biothings.hub.datarelease.publisher.BasePublisher method)
(biothings.hub.datarelease.publisher.ReleaseManager method)
(biothings.hub.datatransform.datatransform.DataTransformEdge method)
setup_logfile() (in module biothings.utils.common)
ShardedTargetDocMongoBackend (class in biothings.hub.databuild.backend)
SHELL (biothings.hub.HubSSHServer attribute)
shell_requested() (biothings.hub.HubSSHServerSession method)
ShellHandler (class in biothings.hub.api.handlers.shell)
ShellListener (class in biothings.hub.api.handlers.ws)
ShellLogger (class in biothings.utils.loggers)
should_diff_new_build() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
should_install_new_diff() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
should_install_new_release() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
should_install_new_snapshot() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
should_publish_new_diff() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
should_publish_new_snapshot() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
should_snapshot_new_build() (biothings.hub.databuild.buildconfig.AutoBuildConfig method)
show() (biothings.utils.configuration.ConfigurationWrapper method)
show_dumped_files() (in module biothings.cli.utils)
show_hubdb_content() (in module biothings.cli.utils)
show_pendings() (biothings.utils.manager.JobManager method)
show_uploaded_sources() (in module biothings.cli.utils)
side() (biothings.hub.datatransform.datatransform.IDStruct static method)
simplify() (biothings.web.options.manager.OptionError method)
simplify_inspection_data() (in module biothings.utils.inspect)
sizeof_fmt() (in module biothings.utils.common)
SlackChannel (class in biothings.web.analytics.channels)
SlackHandler (class in biothings.utils.loggers)
SlackMentionPolicy (class in biothings.utils.loggers)
SlackMessage (class in biothings.utils.loggers)
SLEEP_BETWEEN_DOWNLOAD (biothings.hub.dataload.dumper.BaseDumper attribute)
sm (built-in variable)
Snapshot (class in biothings.hub.dataindex.snapshot_task)
snapshot()
(biothings.hub.dataindex.snapshooter.SnapshotEnv method)
(biothings.hub.dataindex.snapshooter.SnapshotManager method)
(biothings.utils.es.ESIndexer method)
snapshot_a_build() (biothings.hub.dataindex.snapshooter.SnapshotManager method)
snapshot_cleanup()
snapshot_config (built-in variable)
snapshot_info()
(biothings.hub.dataindex.snapshooter.SnapshotManager method)
SnapshotEnv (class in biothings.hub.dataindex.snapshooter)
SnapshotManager (class in biothings.hub.dataindex.snapshooter)
SnapshotPublisher (class in biothings.hub.datarelease.publisher)
soft_eof_received() (biothings.hub.HubSSHServerSession method)
sort_input_by_priority_list() (biothings.hub.datatransform.datatransform.DataTransform method)
sort_output_by_priority_list() (biothings.hub.datatransform.datatransform.DataTransform method)
source_backend (biothings.hub.databuild.builder.BuilderManager property)
(biothings.hub.databuild.builder.DataBuilder property)
SOURCE_CLASS (biothings.hub.dataload.dumper.DumperManager attribute)
(biothings.hub.dataload.uploader.UploaderManager attribute)
(biothings.utils.manager.BaseSourceManager attribute)
source_config (biothings.hub.dataload.dumper.DockerContainerDumper property)
source_info()
(biothings.hub.dataload.dumper.DumperManager method)
(biothings.hub.dataload.uploader.UploaderManager method)
source_reset()
source_save_mapping()
SourceDocBackendBase (class in biothings.hub.databuild.backend)
SourceDocMongoBackend (class in biothings.hub.databuild.backend)
SourceManager (class in biothings.hub.dataload.source)
sources()
SPACE_PATTERN (biothings.utils.inspect.InspectionValidation attribute)
split_ids() (in module biothings.utils.common)
splitstr (class in biothings.utils.common)
sql (in module biothings.web.connections)
SQLHealth (class in biothings.web.services.health)
SQLQueryBackend (class in biothings.web.query.engine)
SQLQueryBuilder (class in biothings.web.query.builder)
SQLQueryPipeline (class in biothings.web.query.pipeline)
SQLResultFormatter (class in biothings.web.query.formatter)
Squares (class in biothings.utils.loggers)
src_doc (biothings.hub.dataload.dumper.BaseDumper property)
src_dump (biothings.hub.dataload.dumper.BaseDumper property)
SRC_NAME (biothings.hub.autoupdate.dumper.BiothingsDumper attribute)
(biothings.hub.dataload.dumper.BaseDumper attribute)
SRC_ROOT_FOLDER (biothings.hub.autoupdate.dumper.BiothingsDumper attribute)
(biothings.hub.dataload.dumper.BaseDumper attribute)
SRC_URLS (biothings.hub.dataload.dumper.LastModifiedBaseDumper attribute)
ssm (built-in variable)
Stack (class in biothings.utils.doc_traversal)
StackEmptyError
Stage (class in biothings.hub.dataindex.indexer_registrar)
start (biothings.utils.loggers.Range attribute)
start() (biothings.hub.HubServer method)
(biothings.utils.common.LogPrint method)
(biothings.web.launcher.BiothingsAPIBaseLauncher method)
(biothings.web.launcher.FlaskAPILauncher method)
(biothings.web.launcher.TornadoAPILauncher method)
start_api()
(biothings.hub.api.manager.APIManager method)
(in module biothings.hub.api)
start_ssh_server() (in module biothings.hub)
STARTED (biothings.hub.dataindex.indexer_registrar.Stage attribute)
started() (biothings.hub.dataindex.indexer_registrar.IndexJobStateRegistrar method)
(biothings.hub.dataindex.indexer_registrar.MainIndexJSR method)
(biothings.hub.dataindex.indexer_registrar.PostIndexJSR method)
(biothings.hub.dataindex.indexer_registrar.PreIndexJSR method)
state (biothings.hub.dataindex.indexer.MainIndexStep attribute)
(biothings.hub.dataindex.indexer.PostIndexStep attribute)
(biothings.hub.dataindex.indexer.PreIndexStep attribute)
(biothings.hub.dataindex.indexer.Step attribute)
state() (biothings.hub.dataindex.snapshot_task.Snapshot method)
stats (biothings.utils.inspect.FieldInspection attribute)
stats() (in module biothings.utils.hub)
StatsMode (class in biothings.utils.inspect)
status()
(in module biothings.hub)
StatusHandler (class in biothings.web.handlers.services)
step (biothings.hub.dataindex.snapshot_registrar.MainSnapshotState attribute)
(biothings.hub.dataindex.snapshot_registrar.PostSnapshotState attribute)
(biothings.hub.dataindex.snapshot_registrar.PreSnapshotState attribute)
Step (class in biothings.hub.dataindex.indexer)
step_archive() (biothings.hub.datarelease.publisher.BasePublisher method)
step_upload() (biothings.hub.datarelease.publisher.BasePublisher method)
step_upload_s3() (biothings.hub.datarelease.publisher.BasePublisher method)
StepResult (class in biothings.hub.dataindex.snapshooter)
stop()
(biothings.utils.hub.HubShell method)
(biothings.utils.manager.JobManager method)
stop_api()
(biothings.hub.api.manager.APIManager method)
storage_class (biothings.hub.dataload.uploader.BaseSourceUploader attribute)
(biothings.hub.dataload.uploader.IgnoreDuplicatedSourceUploader attribute)
(biothings.hub.dataload.uploader.MergerSourceUploader attribute)
(biothings.hub.dataload.uploader.NoBatchIgnoreDuplicatedSourceUploader attribute)
(biothings.hub.dataload.uploader.NoDataSourceUploader attribute)
store_metadata() (biothings.hub.databuild.builder.DataBuilder method)
store_value_to_db() (biothings.utils.configuration.ConfigurationWrapper method)
str_to_bool() (biothings.web.options.manager.Converter static method)
(biothings.web.options.manager.QueryArgCvter class method)
str_to_int() (biothings.web.options.manager.Converter method)
str_to_list() (biothings.web.options.manager.Converter static method)
stringify_inspect_doc() (in module biothings.utils.inspect)
style() (biothings.web.options.openapi.OpenAPIParameterContext method)
subclasses (biothings.web.options.openapi.OpenAPIContactContext attribute)
(biothings.web.options.openapi.OpenAPIContext attribute)
(biothings.web.options.openapi.OpenAPIExternalDocsContext attribute)
(biothings.web.options.openapi.OpenAPIInfoContext attribute)
(biothings.web.options.openapi.OpenAPILicenseContext attribute)
(biothings.web.options.openapi.OpenAPIOperation attribute)
(biothings.web.options.openapi.OpenAPIParameterContext attribute)
(biothings.web.options.openapi.OpenAPIPathItemContext attribute)
subclasses() (biothings.web.options.manager.Converter class method)
submit() (biothings.hub.dataplugin.assistant.AssistantManager method)
(biothings.utils.manager.JobManager method)
SubmoduleValidator (class in biothings.web.settings.validators)
SubStr() (in module biothings.utils.common)
succeed() (biothings.hub.dataindex.indexer_registrar.IndexJobStateRegistrar method)
(biothings.hub.dataindex.indexer_registrar.PreIndexJSR method)
suffix() (biothings.hub.dataindex.indexer_schedule.Schedule method)
SUFFIX_ATTR (biothings.hub.dataload.dumper.BaseDumper attribute)
sumiflist() (biothings.utils.inspect.StatsMode method)
summary (biothings.web.query.pipeline.QueryPipelineException attribute)
sumup_source() (biothings.hub.dataload.source.SourceManager method)
supersede() (biothings.utils.configuration.ConfigurationWrapper method)
switch_collection() (biothings.hub.dataload.uploader.BaseSourceUploader method)
sym (built-in variable)
sync()
(biothings.hub.databuild.syncer.BaseSyncer method)
(biothings.hub.databuild.syncer.SyncerManager method)
sync_cols() (biothings.hub.databuild.syncer.BaseSyncer method)
sync_es_coldhot_jsondiff_worker() (in module biothings.hub.databuild.syncer)
sync_es_for_update() (in module biothings.hub.databuild.syncer)
sync_es_jsondiff_worker() (in module biothings.hub.databuild.syncer)
sync_mongo_jsondiff_worker() (in module biothings.hub.databuild.syncer)
SYNCER_FUNC (biothings.hub.autoupdate.uploader.BiothingsUploader attribute)
syncer_func (biothings.hub.autoupdate.uploader.BiothingsUploader property)
SyncerException
SyncerManager (class in biothings.hub.databuild.syncer)
T
tab2dict() (in module biothings.utils.dataload)
tab2dict_iter() (in module biothings.utils.dataload)
tab2list() (in module biothings.utils.dataload)
tabfile_feeder() (in module biothings.utils.dataload)
tabfile_tester() (in module biothings.utils.dataload)
target_alias (biothings.utils.backend.DocESBackend property)
TARGET_BACKEND (biothings.hub.autoupdate.dumper.BiothingsDumper attribute)
target_backend (biothings.hub.autoupdate.dumper.BiothingsDumper property)
TARGET_BACKEND (biothings.hub.autoupdate.uploader.BiothingsUploader attribute)
target_backend (biothings.hub.autoupdate.uploader.BiothingsUploader property)
(biothings.hub.databuild.builder.BuilderManager property)
(biothings.hub.databuild.builder.DataBuilder property)
target_backend_type (biothings.hub.databuild.syncer.BaseSyncer attribute)
(biothings.hub.databuild.syncer.ESColdHotJsonDiffSelfContainedSyncer attribute)
(biothings.hub.databuild.syncer.ESColdHotJsonDiffSyncer attribute)
(biothings.hub.databuild.syncer.ESJsonDiffSelfContainedSyncer attribute)
(biothings.hub.databuild.syncer.ESJsonDiffSyncer attribute)
(biothings.hub.databuild.syncer.MongoJsonDiffSelfContainedSyncer attribute)
(biothings.hub.databuild.syncer.MongoJsonDiffSyncer attribute)
target_collection (biothings.hub.databuild.backend.LinkTargetDocMongoBackend property)
target_db (biothings.utils.backend.DocMongoBackend property)
target_esidxer (biothings.utils.backend.DocESBackend property)
target_name (biothings.hub.databuild.backend.TargetDocBackend property)
(biothings.utils.backend.DocBackendBase property)
(biothings.utils.backend.DocESBackend property)
(biothings.utils.backend.DocMemoryBackend property)
(biothings.utils.backend.DocMongoBackend property)
TargetDocBackend (class in biothings.hub.databuild.backend)
TargetDocMongoBackend (class in biothings.hub.databuild.backend)
tearDown() (biothings.tests.web.BiothingsWebTestBase method)
template (biothings.utils.inspect.BaseMode attribute)
(biothings.utils.inspect.DeepStatsMode attribute)
(biothings.utils.inspect.StatsMode attribute)
template_out() (in module biothings.utils.hub)
template_out_conf() (biothings.hub.datarelease.publisher.BasePublisher method)
TemplateStr (class in biothings.hub.dataindex.snapshooter)
term (biothings.web.query.builder.Group attribute)
(biothings.web.query.builder.Query attribute)
terms_of_service() (biothings.web.options.openapi.OpenAPIInfoContext method)
test() (in module biothings.hub.databuild.buildconfig)
(in module biothings.hub.dataindex.snapshot_registrar)
(in module biothings.utils.jsonschema)
test0() (in module biothings.hub.dataindex.indexer_task)
test1() (in module biothings.hub.dataindex.indexer_task)
test_00() (in module biothings.hub.dataindex.indexer_task)
test_01() (in module biothings.hub.dataindex.indexer_schedule)
(in module biothings.hub.dataindex.snapshot_repo)
(in module biothings.hub.dataindex.snapshot_task)
test_02() (in module biothings.hub.dataindex.indexer_schedule)
(in module biothings.hub.dataindex.snapshot_repo)
(in module biothings.hub.dataindex.snapshot_task)
test_03() (in module biothings.hub.dataindex.indexer_schedule)
test_04() (in module biothings.hub.dataindex.indexer_schedule)
test_clean() (in module biothings.hub.dataindex.indexer_cleanup)
test_clients() (in module biothings.hub.dataindex.indexer_task)
TEST_DATA_DIR_NAME (biothings.tests.web.BiothingsWebAppTest attribute)
test_database_index() (biothings.tests.hub.DatabaseCollectionTesting method)
test_document_name() (biothings.tests.hub.DatabaseCollectionTesting method)
test_documents_taxid() (biothings.tests.hub.DatabaseCollectionTesting method)
test_field_does_not_exist() (biothings.tests.hub.DatabaseCollectionTesting method)
test_field_taxid() (biothings.tests.hub.DatabaseCollectionTesting method)
test_field_unique_id() (biothings.tests.hub.DatabaseCollectionTesting method)
test_find() (in module biothings.hub.dataindex.indexer_cleanup)
(in module biothings.hub.dataindex.snapshot_cleanup)
test_print() (in module biothings.hub.dataindex.snapshot_cleanup)
test_registrar() (in module biothings.hub.dataindex.indexer_registrar)
test_str() (in module biothings.hub.dataindex.indexer_cleanup)
test_total_document_count() (biothings.tests.hub.DatabaseCollectionTesting method)
TestOperation (class in biothings.utils.jsonpatch)
Text (class in biothings.utils.configuration)
ThrottledESColdHotJsonDiffSelfContainedSyncer (class in biothings.hub.databuild.syncer)
ThrottledESColdHotJsonDiffSyncer (class in biothings.hub.databuild.syncer)
ThrottledESJsonDiffSelfContainedSyncer (class in biothings.hub.databuild.syncer)
ThrottledESJsonDiffSyncer (class in biothings.hub.databuild.syncer)
ThrottlerSyncer (class in biothings.hub.databuild.syncer)
TIMEOUT (biothings.hub.dataload.dumper.DockerContainerDumper attribute)
timesofar() (in module biothings.utils.common)
title() (biothings.web.options.openapi.OpenAPIInfoContext method)
to_ADF() (biothings.web.analytics.events.Message method)
to_boolean() (in module biothings.utils.dataload)
to_delete (biothings.hub.dataload.dumper.BaseDumper attribute)
to_dict() (biothings.hub.datarelease.releasenote.ReleaseNoteSource method)
(biothings.utils.inspect.InspectionValidation.Warning method)
(biothings.web.services.metadata.BiothingHubMeta method)
(biothings.web.services.metadata.BiothingLicenses method)
(biothings.web.services.metadata.BiothingMappings method)
(biothings.web.services.metadata.BiothingMetaProp method)
to_email_payload() (biothings.web.analytics.events.Message method)
to_float() (in module biothings.utils.dataload)
to_GA4_payload() (biothings.web.analytics.events.Event method)
(biothings.web.analytics.events.GAEvent method)
to_GA_payload() (biothings.web.analytics.events.Event method)
(biothings.web.analytics.events.GAEvent method)
to_int() (in module biothings.utils.dataload)
to_jira_payload() (biothings.web.analytics.events.Message method)
to_json() (in module biothings.utils.serializer)
to_json_0() (in module biothings.utils.serializer)
to_json_file() (in module biothings.utils.serializer)
to_msgpack() (in module biothings.utils.serializer)
to_number() (in module biothings.utils.dataload)
to_slack_payload() (biothings.web.analytics.events.Message method)
to_string() (biothings.utils.jsonpatch.JsonPatch method)
to_type() (biothings.web.options.manager.Converter static method)
(biothings.web.options.manager.JsonArgCvter method)
to_yaml() (in module biothings.utils.serializer)
top()
(biothings.utils.manager.JobManager method)
TornadoAPILauncher (class in biothings.web.launcher)
TornadoAutoReloadHubReloader (class in biothings.utils.hub)
TornadoBiothingsAPI (class in biothings.web.applications)
tqueue (built-in variable)
trace() (biothings.web.options.openapi.OpenAPIPathItemContext method)
track() (in module biothings.utils.manager)
transfer_debug() (biothings.hub.datatransform.datatransform.IDStruct method)
transform() (biothings.web.query.formatter.ESResultFormatter method)
(biothings.web.query.formatter.MongoResultFormatter method)
(biothings.web.query.formatter.ResultFormatter method)
(biothings.web.query.formatter.SQLResultFormatter method)
transform_aggs() (biothings.web.query.formatter.ESResultFormatter method)
transform_hit() (biothings.web.query.formatter.ESResultFormatter method)
transform_mapping() (biothings.web.query.formatter.ESResultFormatter method)
(biothings.web.query.formatter.ResultFormatter method)
translate() (biothings.hub.databuild.mapper.IDBaseMapper method)
(biothings.web.options.manager.Converter method)
TransparentMapper (class in biothings.hub.databuild.mapper)
trasform_jmespath() (biothings.web.query.formatter.ESResultFormatter method)
travel() (biothings.hub.datatransform.datatransform_mdb.DataTransformMDB method)
traverse() (biothings.web.query.formatter.ESResultFormatter static method)
(in module biothings.utils.common)
traverse_keys() (in module biothings.utils.dataload)
trigger_diff() (biothings.hub.databuild.differ.DifferManager method)
trigger_merge() (biothings.hub.databuild.builder.BuilderManager method)
trigger_release_note() (biothings.hub.datarelease.publisher.BasePublisher method)
two_docs_iterator() (in module biothings.utils.diff)
type (biothings.hub.dataindex.snapshooter.CloudStorage attribute)
type() (biothings.web.options.openapi.OpenAPIParameterContext method)
types (biothings.utils.inspect.FieldInspectValidation attribute)
(biothings.web.services.metadata.BiothingsESMetadata property)
(biothings.web.services.metadata.BiothingsMongoMetadata property)
(biothings.web.services.metadata.BiothingsSQLMetadata property)
typify_inspect_doc() (in module biothings.utils.inspect)
U
um (built-in variable)
uncompressall() (in module biothings.utils.common)
unique_ids() (in module biothings.utils.dataload)
UnknownResource
unlist() (in module biothings.utils.dataload)
unlist_incexcl() (in module biothings.utils.dataload)
unprepare() (biothings.hub.databuild.builder.DataBuilder method)
(biothings.hub.dataload.dumper.BaseDumper method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.datatransform.datatransform.DataTransformEdge method)
unregister_url()
(biothings.hub.dataplugin.assistant.AssistantManager method)
untarall() (in module biothings.utils.common)
untargzall() (in module biothings.utils.common)
unxzall() (in module biothings.utils.common)
unzipall() (in module biothings.utils.common)
update() (biothings.utils.backend.DocBackendBase method)
(biothings.utils.backend.DocESBackend method)
(biothings.utils.backend.DocMemoryBackend method)
(biothings.utils.backend.DocMongoBackend method)
(biothings.utils.configuration.ConfigAttrMeta method)
(biothings.utils.es.Collection method)
(biothings.utils.es.ESIndexer method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.mongo.Collection method)
(biothings.utils.sqlite3.Collection method)
(biothings.web.services.metadata.BiothingsESMetadata method)
update_alias() (biothings.utils.es.ESIndexer method)
update_build_conf()
update_build_configuration() (biothings.hub.databuild.builder.BuilderManager method)
update_data() (biothings.hub.autoupdate.uploader.BiothingsUploader method)
(biothings.hub.dataload.uploader.BaseSourceUploader method)
(biothings.hub.dataload.uploader.DummySourceUploader method)
(biothings.hub.dataload.uploader.NoDataSourceUploader method)
(biothings.hub.dataload.uploader.ParallelizedSourceUploader method)
update_dict_recur() (in module biothings.utils.dataload)
update_diff() (biothings.utils.backend.DocMongoBackend method)
update_docs() (biothings.utils.es.ESIndexer method)
update_edge() (biothings.hub.datatransform.histogram.Histogram method)
update_io() (biothings.hub.datatransform.histogram.Histogram method)
update_many() (biothings.utils.es.Collection method)
update_mapping() (biothings.utils.es.ESIndexer method)
update_mapping_meta() (biothings.utils.es.ESIndexer method)
update_master() (biothings.hub.dataload.uploader.BaseSourceUploader method)
update_metadata()
(biothings.hub.dataindex.indexer.IndexManager method)
update_one() (biothings.utils.es.Collection method)
(biothings.utils.hub_db.Collection method)
(biothings.utils.sqlite3.Collection method)
update_plugin_name() (biothings.hub.dataplugin.assistant.AssistantManager method)
update_settings() (biothings.utils.es.ESIndexer method)
update_source_meta()
(biothings.hub.dataload.uploader.UploaderManager method)
update_src_meta_stats() (biothings.hub.databuild.builder.DataBuilder method)
updated_dict() (in module biothings.utils.dataload)
upgrade()
upload()
upload_all()
(biothings.hub.dataload.uploader.UploaderManager method)
upload_ids() (in module biothings.hub.dataexport.ids)
upload_info()
(biothings.hub.dataload.uploader.UploaderManager method)
upload_source() (in module biothings.cli.dataplugin)
(in module biothings.cli.dataplugin_hub)
upload_src() (biothings.hub.dataload.uploader.UploaderManager method)
uploader_manager (biothings.hub.dataplugin.assistant.BaseAssistant attribute)
UploaderManager (class in biothings.hub.dataload.uploader)
UploadHandler (class in biothings.hub.api.handlers.upload)
upsert_build_conf() (biothings.hub.databuild.builder.BuilderManager method)
URL (class in biothings.utils.serializer)
url() (biothings.web.options.openapi.OpenAPIContactContext method)
(biothings.web.options.openapi.OpenAPIExternalDocsContext method)
(biothings.web.options.openapi.OpenAPILicenseContext method)
use_curl() (biothings.web.launcher.TornadoAPILauncher static method)
V
validate() (biothings.utils.inspect.InspectionValidation static method)
(biothings.web.options.manager.Validator method)
(biothings.web.settings.validators.DBParamValidator method)
(biothings.web.settings.validators.MongoParamValidaor method)
(biothings.web.settings.validators.SubmoduleValidator method)
(biothings.web.settings.validators.WebAPIValidator method)
validate_mapping()
(biothings.hub.dataindex.indexer.IndexManager method)
validate_password() (biothings.hub.HubSSHServer method)
validate_sources() (biothings.hub.databuild.backend.SourceDocBackendBase method)
(biothings.hub.databuild.backend.SourceDocMongoBackend method)
validate_W001() (biothings.utils.inspect.InspectionValidation static method)
validate_W002() (biothings.utils.inspect.InspectionValidation static method)
validate_W003() (biothings.utils.inspect.InspectionValidation static method)
validate_W004() (biothings.utils.inspect.InspectionValidation static method)
Validator (class in biothings.web.options.manager)
value (biothings.utils.configuration.MetaField property)
(biothings.utils.configuration.Paragraph property)
(biothings.utils.loggers.Record attribute)
value_convert() (in module biothings.utils.dataload)
value_convert_incexcl() (in module biothings.utils.dataload)
value_convert_to_number() (in module biothings.utils.dataload)
value_in_result() (biothings.tests.web.BiothingsWebTestBase static method)
verify() (biothings.hub.dataindex.snapshot_repo.Repository method)
VERIFY_CERT (biothings.hub.dataload.dumper.HTTPDumper attribute)
verify_ids() (in module biothings.utils.es)
version (biothings.utils.backend.DocBackendBase property)
(biothings.utils.backend.DocESBackend property)
(biothings.utils.backend.DocMongoBackend property)
version() (biothings.web.options.openapi.OpenAPIInfoContext method)
VERSION_URL (biothings.hub.autoupdate.dumper.BiothingsDumper attribute)
versions()
(biothings.hub.autoupdate.dumper.BiothingsDumper method)
W
W001 (biothings.utils.inspect.InspectionValidation.Warning attribute)
W002 (biothings.utils.inspect.InspectionValidation.Warning attribute)
W003 (biothings.utils.inspect.InspectionValidation.Warning attribute)
W004 (biothings.utils.inspect.InspectionValidation.Warning attribute)
WARNING (biothings.utils.loggers.Colors attribute)
(biothings.utils.loggers.Squares attribute)
warnings (biothings.utils.inspect.FieldInspection attribute)
(biothings.utils.inspect.FieldInspectValidation attribute)
watched_files() (biothings.utils.hub.BaseHubReloader method)
(biothings.utils.hub.TornadoAutoReloadHubReloader method)
WebAPIValidator (class in biothings.web.settings.validators)
WebSocketConnection (class in biothings.hub.api.handlers.ws)
WgetDumper (class in biothings.hub.dataload.dumper)
whatsnew()
(biothings.hub.databuild.builder.BuilderManager method)
wrap() (biothings.utils.hub_db.ChangeWatcher class method)
(biothings.web.query.formatter.FormatterDict method)
wrapper() (in module biothings.utils.es)
write() (biothings.hub.api.handlers.base.DefaultHandler method)
(biothings.utils.common.LogPrint method)
(biothings.web.handlers.base.BaseAPIHandler method)
(biothings.web.handlers.query.BaseQueryHandler method)
write_error() (biothings.hub.api.handlers.base.DefaultHandler method)
(biothings.web.handlers.base.BaseAPIHandler method)
WSLogHandler (class in biothings.utils.loggers)
WSShellHandler (class in biothings.utils.loggers)
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