biothings.hub
- class biothings.hub.HubSSHServer[source]
Bases:
SSHServer
- PASSWORDS = {}
- SHELL = None
- begin_auth(username)[source]
Authentication has been requested by the client
This method will be called when authentication is attempted for the specified user. Applications should use this method to prepare whatever state they need to complete the authentication, such as loading in the set of authorized keys for that user. If no authentication is required for this user, this method should return False to cause the authentication to immediately succeed. Otherwise, it should return True to indicate that authentication should proceed.
If blocking operations need to be performed to prepare the state needed to complete the authentication, this method may be defined as a coroutine.
- Parameters:
username (str) – The name of the user being authenticated
- Returns:
A bool indicating whether authentication is required
- connection_lost(exc)[source]
Called when a connection is lost or closed
This method is called when a connection is closed. If the connection is shut down cleanly, exc will be None. Otherwise, it will be an exception explaining the reason for the disconnect.
- connection_made(connection)[source]
Called when a connection is made
This method is called when a new TCP connection is accepted. The conn parameter should be stored if needed for later use.
- Parameters:
conn (
SSHServerConnection
) – The connection which was successfully opened
- password_auth_supported()[source]
Return whether or not password authentication is supported
This method should return True if password authentication is supported. Applications wishing to support it must have this method return True and implement
validate_password()
to return whether or not the password provided by the client is valid for the user being authenticated.By default, this method returns False indicating that password authentication is not supported.
- Returns:
A bool indicating if password authentication is supported or not
- session_requested()[source]
Handle an incoming session request
This method is called when a session open request is received from the client, indicating it wishes to open a channel to be used for running a shell, executing a command, or connecting to a subsystem. If the application wishes to accept the session, it must override this method to return either an
SSHServerSession
object to use to process the data received on the channel or a tuple consisting of anSSHServerChannel
object created withcreate_server_channel
and anSSHServerSession
, if the application wishes to pass non-default arguments when creating the channel.If blocking operations need to be performed before the session can be created, a coroutine which returns an
SSHServerSession
object can be returned instead of the session iself. This can be either returned directly or as a part of a tuple with anSSHServerChannel
object.To reject this request, this method should return False to send back a “Session refused” response or raise a
ChannelOpenError
exception with the reason for the failure.The details of what type of session the client wants to start will be delivered to methods on the
SSHServerSession
object which is returned, along with other information such as environment variables, terminal type, size, and modes.By default, all session requests are rejected.
- Returns:
One of the following:
An
SSHServerSession
object or a coroutine which returns anSSHServerSession
A tuple consisting of an
SSHServerChannel
and the aboveA callable or coroutine handler function which takes AsyncSSH stream objects for stdin, stdout, and stderr as arguments
A tuple consisting of an
SSHServerChannel
and the aboveFalse to refuse the request
- Raises:
ChannelOpenError
if the session shouldn’t be accepted
- validate_password(username, password)[source]
Return whether password is valid for this user
This method should return True if the specified password is a valid password for the user being authenticated. It must be overridden by applications wishing to support password authentication.
If the password provided is valid but expired, this method may raise
PasswordChangeRequired
to request that the client provide a new password before authentication is allowed to complete. In this case, the application must overridechange_password()
to handle the password change request.This method may be called multiple times with different passwords provided by the client. Applications may wish to limit the number of attempts which are allowed. This can be done by having
password_auth_supported()
begin returning False after the maximum number of attempts is exceeded.If blocking operations need to be performed to determine the validity of the password, this method may be defined as a coroutine.
By default, this method returns False for all passwords.
- Parameters:
username (str) – The user being authenticated
password (str) – The password sent by the client
- Returns:
A bool indicating if the specified password is valid for the user being authenticated
- Raises:
PasswordChangeRequired
if the password provided is expired and needs to be changed
- class biothings.hub.HubSSHServerSession(name, shell)[source]
Bases:
SSHServerSession
- break_received(msec)[source]
The client has sent a break
This method is called when the client requests that the server perform a break operation on the terminal. If the break is performed, this method should return True. Otherwise, it should return False.
By default, this method returns False indicating that no break was performed.
- Parameters:
msec (int) – The duration of the break in milliseconds
- Returns:
A bool to indicate if the break operation was performed or not
- connection_made(chan)[source]
Called when a channel is opened successfully
This method is called when a channel is opened successfully. The channel parameter should be stored if needed for later use.
- Parameters:
chan (
SSHServerChannel
) – The channel which was successfully opened.
- data_received(data, datatype)[source]
Called when data is received on the channel
This method is called when data is received on the channel. If an encoding was specified when the channel was created, the data will be delivered as a string after decoding with the requested encoding. Otherwise, the data will be delivered as bytes.
- Parameters:
data (str or bytes) – The data received on the channel
datatype – The extended data type of the data, from extended data types
- eof_received()[source]
Called when EOF is received on the channel
This method is called when an end-of-file indication is received on the channel, after which no more data will be received. If this method returns True, the channel remains half open and data may still be sent. Otherwise, the channel is automatically closed after this method returns. This is the default behavior for classes derived directly from
SSHSession
, but not when using the higher-level streams API. Because input is buffered in that case, streaming sessions enable half-open channels to allow applications to respond to input read after an end-of-file indication is received.
- exec_requested(command)[source]
The client has requested to execute a command
This method should be implemented by the application to perform whatever processing is required when a client makes a request to execute a command. It should return True to accept the request, or False to reject it.
If the application returns True, the
session_started()
method will be called once the channel is fully open. No output should be sent until this method is called.By default this method returns False to reject all requests.
- Parameters:
command (str) – The command the client has requested to execute
- Returns:
A bool indicating if the exec request was allowed or not
- session_started()[source]
Called when the session is started
This method is called when a session has started up. For client and server sessions, this will be called once a shell, exec, or subsystem request has been successfully completed. For TCP and UNIX domain socket sessions, it will be called immediately after the connection is opened.
- shell_requested()[source]
The client has requested a shell
This method should be implemented by the application to perform whatever processing is required when a client makes a request to open an interactive shell. It should return True to accept the request, or False to reject it.
If the application returns True, the
session_started()
method will be called once the channel is fully open. No output should be sent until this method is called.By default this method returns False to reject all requests.
- Returns:
A bool indicating if the shell request was allowed or not
- soft_eof_received()[source]
The client has sent a soft EOF
This method is called by the line editor when the client send a soft EOF (Ctrl-D on an empty input line).
By default, soft EOF will trigger an EOF to an outstanding read call but still allow additional input to be received from the client after that.
- class biothings.hub.HubServer(source_list, features=None, name='BioThings Hub', managers_custom_args=None, api_config=None, reloader_config=None, dataupload_config=None, websocket_config=None, autohub_config=None)[source]
Bases:
object
Helper to setup and instantiate common managers usually used in a hub (eg. dumper manager, uploader manager, etc…) “source_list” is either:
a list of string corresponding to paths to datasources modules
a package containing sub-folders with datasources modules
Specific managers can be retrieved adjusting “features” parameter, where each feature corresponds to one or more managers. Parameter defaults to all possible available. Managers are configured/init in the same order as the list, so if a manager (eg. job_manager) is required by all others, it must be the first in the list. “managers_custom_args” is an optional dict used to pass specific arguments while init managers:
will set poll schedule to check upload every 5min (instead of default 10s) “reloader_config”, “dataupload_config”, “autohub_config” and “websocket_config” can be used to customize reloader, dataupload and websocket. If None, default config is used. If explicitely False, feature is deactivated.
- DEFAULT_API_CONFIG = {}
- DEFAULT_AUTOHUB_CONFIG = {'es_host': None, 'indexer_factory': None, 'validator_class': None, 'version_urls': []}
- DEFAULT_DATAUPLOAD_CONFIG = {'upload_root': '.biothings_hub/archive/dataupload'}
- DEFAULT_FEATURES = ['config', 'job', 'dump', 'upload', 'dataplugin', 'source', 'build', 'auto_archive', 'diff', 'index', 'snapshot', 'auto_snapshot_cleaner', 'release', 'inspect', 'sync', 'api', 'terminal', 'reloader', 'dataupload', 'ws', 'readonly', 'upgrade', 'autohub', 'hooks']
- DEFAULT_MANAGERS_ARGS = {'upload': {'poll_schedule': '* * * * * */10'}}
- DEFAULT_RELOADER_CONFIG = {'folders': None, 'managers': ['source_manager', 'assistant_manager'], 'reload_func': None}
- DEFAULT_WEBSOCKET_CONFIG = {}
- add_api_endpoint(endpoint_name, command_name, method, **kwargs)[source]
Add an API endpoint to expose command named “command_name” using HTTP method “method”. **kwargs are used to specify more arguments for EndpointDefinition
- configure_extra_commands()[source]
Same as configure_commands() but commands are not exposed publicly in the shell (they are shortcuts or commands for API endpoints, supporting commands, etc…)
- configure_hooks_feature()[source]
Ingest user-defined commands into hub namespace, giving access to all pre-defined commands (commands, extra_commands). This method prepare the hooks but the ingestion is done later when all commands are defined
- configure_readonly_api_endpoints()[source]
Assuming read-write API endpoints have previously been defined (self.api_endpoints set) extract commands and their endpoint definitions only when method is GET. That is, for any given API definition honoring REST principle for HTTP verbs, generate endpoints only for which actions are read-only actions.
- configure_readonly_feature()[source]
Define then expose read-only Hub API endpoints so Hub can be accessed without any risk of modifying data
- configure_upgrade_feature()[source]
Allows a Hub to check for new versions (new commits to apply on running branch) and apply them on current code base
- quick_index(datasource_name, doc_type, indexer_env, subsource=None, index_name=None, **kwargs)[source]
Intention for datasource developers to quickly create an index to test their datasources. Automatically create temporary build config, build collection Then call the index method with the temporary build collection’s name
- async biothings.hub.start_ssh_server(loop, name, passwords, keys=['bin/ssh_host_key'], shell=None, host='', port=8022)[source]
- biothings.hub.status(managers)[source]
Return a global hub status (number or sources, documents, etc…) according to available managers
Modules
- biothings.hub.api
EndpointDefinition
create_handlers()
generate_api_routes()
generate_endpoint_for_callable()
generate_endpoint_for_composite_command()
generate_endpoint_for_display()
generate_handler()
start_api()
- biothings.hub.api.managers
- 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.autoupdate
- biothings.hub.autoupdate.dumper
BiothingsDumper
BiothingsDumper.AUTO_UPLOAD
BiothingsDumper.AWS_ACCESS_KEY_ID
BiothingsDumper.AWS_SECRET_ACCESS_KEY
BiothingsDumper.SRC_NAME
BiothingsDumper.SRC_ROOT_FOLDER
BiothingsDumper.TARGET_BACKEND
BiothingsDumper.VERSION_URL
BiothingsDumper.anonymous_download()
BiothingsDumper.auth_download()
BiothingsDumper.base_url
BiothingsDumper.check_compat()
BiothingsDumper.choose_best_version()
BiothingsDumper.compare_remote_local()
BiothingsDumper.create_todump_list()
BiothingsDumper.download()
BiothingsDumper.find_update_path()
BiothingsDumper.get_target_backend()
BiothingsDumper.info()
BiothingsDumper.load_remote_json()
BiothingsDumper.post_dump()
BiothingsDumper.prepare_client()
BiothingsDumper.remote_is_better()
BiothingsDumper.reset_target_backend()
BiothingsDumper.target_backend
BiothingsDumper.versions()
- biothings.hub.autoupdate.uploader
BiothingsUploader
BiothingsUploader.AUTO_PURGE_INDEX
BiothingsUploader.SYNCER_FUNC
BiothingsUploader.TARGET_BACKEND
BiothingsUploader.apply_diff()
BiothingsUploader.clean_archived_collections()
BiothingsUploader.get_snapshot_repository_config()
BiothingsUploader.load()
BiothingsUploader.name
BiothingsUploader.restore_snapshot()
BiothingsUploader.syncer_func
BiothingsUploader.target_backend
BiothingsUploader.update_data()
- biothings.hub.autoupdate.dumper
- biothings.hub.databuild
- biothings.hub.databuild.backend
- biothings.hub.databuild.buildconfig
AutoBuildConfig
AutoBuildConfig.BUILD_TYPES
AutoBuildConfig.RELEASE_TO_BUILD
AutoBuildConfig.RELEASE_TYPES
AutoBuildConfig.export()
AutoBuildConfig.should_diff_new_build()
AutoBuildConfig.should_install_new_diff()
AutoBuildConfig.should_install_new_release()
AutoBuildConfig.should_install_new_snapshot()
AutoBuildConfig.should_publish_new_diff()
AutoBuildConfig.should_publish_new_snapshot()
AutoBuildConfig.should_snapshot_new_build()
AutoBuildConfigError
test()
- biothings.hub.databuild.builder
BuilderException
BuilderManager
BuilderManager.archive_merge()
BuilderManager.build_config_info()
BuilderManager.build_info()
BuilderManager.clean_stale_status()
BuilderManager.clean_temp_collections()
BuilderManager.configure()
BuilderManager.create_build_configuration()
BuilderManager.delete_build_configuration()
BuilderManager.delete_merge()
BuilderManager.delete_merged_data()
BuilderManager.find_builder_classes()
BuilderManager.get_builder()
BuilderManager.get_builder_class()
BuilderManager.get_query_for_list_merge()
BuilderManager.list_merge()
BuilderManager.list_sources()
BuilderManager.merge()
BuilderManager.poll()
BuilderManager.register_builder()
BuilderManager.resolve_builder_class()
BuilderManager.save_mapping()
BuilderManager.setup_log()
BuilderManager.source_backend
BuilderManager.target_backend
BuilderManager.trigger_merge()
BuilderManager.update_build_configuration()
BuilderManager.upsert_build_conf()
BuilderManager.whatsnew()
DataBuilder
DataBuilder.build_config
DataBuilder.check_ready()
DataBuilder.clean_old_collections()
DataBuilder.document_cleaner()
DataBuilder.generate_document_query()
DataBuilder.get_build_version()
DataBuilder.get_custom_metadata()
DataBuilder.get_mapper_for_source()
DataBuilder.get_mapping()
DataBuilder.get_pinfo()
DataBuilder.get_predicates()
DataBuilder.get_root_document_sources()
DataBuilder.get_stats()
DataBuilder.get_target_name()
DataBuilder.init_mapper()
DataBuilder.init_state()
DataBuilder.keep_archive
DataBuilder.logger
DataBuilder.merge()
DataBuilder.merge_source()
DataBuilder.merge_sources()
DataBuilder.post_merge()
DataBuilder.prepare()
DataBuilder.register_status()
DataBuilder.resolve_sources()
DataBuilder.setup()
DataBuilder.setup_log()
DataBuilder.source_backend
DataBuilder.store_metadata()
DataBuilder.target_backend
DataBuilder.unprepare()
DataBuilder.update_src_meta_stats()
LinkDataBuilder
ResumeException
fix_batch_duplicates()
merger_worker()
pending()
set_pending_to_build()
- biothings.hub.databuild.differ
BaseDiffer
ColdHotDiffer
ColdHotJsonDiffer
ColdHotJsonDifferBase
ColdHotSelfContainedJsonDiffer
DiffReportRendererBase
DiffReportTxt
DifferException
DifferManager
DifferManager.build_diff_report()
DifferManager.clean_stale_status()
DifferManager.configure()
DifferManager.diff()
DifferManager.diff_info()
DifferManager.diff_report()
DifferManager.get_pinfo()
DifferManager.get_predicates()
DifferManager.poll()
DifferManager.rebuild_diff_file_list()
DifferManager.register_differ()
DifferManager.setup_log()
DifferManager.trigger_diff()
JsonDiffer
SelfContainedJsonDiffer
diff_worker_count()
diff_worker_new_vs_old()
diff_worker_old_vs_new()
reduce_diffs()
set_pending_to_diff()
- biothings.hub.databuild.mapper
- biothings.hub.databuild.prebuilder
- biothings.hub.databuild.syncer
BaseSyncer
ESColdHotJsonDiffSelfContainedSyncer
ESColdHotJsonDiffSyncer
ESJsonDiffSelfContainedSyncer
ESJsonDiffSyncer
MongoJsonDiffSelfContainedSyncer
MongoJsonDiffSyncer
SyncerException
SyncerManager
ThrottledESColdHotJsonDiffSelfContainedSyncer
ThrottledESColdHotJsonDiffSyncer
ThrottledESJsonDiffSelfContainedSyncer
ThrottledESJsonDiffSyncer
ThrottlerSyncer
sync_es_coldhot_jsondiff_worker()
sync_es_for_update()
sync_es_jsondiff_worker()
sync_mongo_jsondiff_worker()
- biothings.hub.dataexport
- biothings.hub.dataindex
- biothings.hub.dataindex.idcache
- biothings.hub.dataindex.indexer_cleanup
- biothings.hub.dataindex.indexer_payload
- biothings.hub.dataindex.indexer
ColdHotIndexer
DynamicIndexerFactory
IndexManager
IndexManager.DEFAULT_INDEXER
IndexManager.clean_stale_status()
IndexManager.cleanup()
IndexManager.configure()
IndexManager.get_indexes_by_name()
IndexManager.get_pinfo()
IndexManager.get_predicates()
IndexManager.index()
IndexManager.index_info()
IndexManager.update_metadata()
IndexManager.validate_mapping()
Indexer
IndexerCumulativeResult
IndexerException
IndexerStepResult
MainIndexStep
PostIndexStep
PreIndexStep
ProcessInfo
Step
- biothings.hub.dataindex.indexer_registrar
- biothings.hub.dataindex.indexer_schedule
- biothings.hub.dataindex.indexer_task
- biothings.hub.dataindex.snapshooter
Bucket
CloudStorage
CumulativeResult
ProcessInfo
RenderedStr
RepositoryConfig
SnapshotEnv
SnapshotManager
SnapshotManager.clean_stale_status()
SnapshotManager.cleanup()
SnapshotManager.configure()
SnapshotManager.delete_snapshots()
SnapshotManager.list_snapshots()
SnapshotManager.pending_snapshot()
SnapshotManager.poll()
SnapshotManager.snapshot()
SnapshotManager.snapshot_a_build()
SnapshotManager.snapshot_info()
StepResult
TemplateStr
- biothings.hub.dataindex.snapshot_cleanup
- biothings.hub.dataindex.snapshot_registrar
- biothings.hub.dataindex.snapshot_repo
- biothings.hub.dataindex.snapshot_task
- biothings.hub.datainspect
- biothings.hub.dataload
- biothings.hub.dataload.dumper
APIDumper
BaseDumper
BaseDumper.ARCHIVE
BaseDumper.AUTO_UPLOAD
BaseDumper.MAX_PARALLEL_DUMP
BaseDumper.SCHEDULE
BaseDumper.SLEEP_BETWEEN_DOWNLOAD
BaseDumper.SRC_NAME
BaseDumper.SRC_ROOT_FOLDER
BaseDumper.SUFFIX_ATTR
BaseDumper.client
BaseDumper.create_todump_list()
BaseDumper.current_data_folder
BaseDumper.current_release
BaseDumper.do_dump()
BaseDumper.download()
BaseDumper.dump()
BaseDumper.get_pinfo()
BaseDumper.get_predicates()
BaseDumper.init_state()
BaseDumper.logger
BaseDumper.mark_success()
BaseDumper.need_prepare()
BaseDumper.new_data_folder
BaseDumper.post_download()
BaseDumper.post_dump()
BaseDumper.post_dump_delete_files()
BaseDumper.prepare()
BaseDumper.prepare_client()
BaseDumper.prepare_local_folders()
BaseDumper.prepare_src_dump()
BaseDumper.register_status()
BaseDumper.release_client()
BaseDumper.remote_is_better()
BaseDumper.setup_log()
BaseDumper.src_doc
BaseDumper.src_dump
BaseDumper.to_delete
BaseDumper.unprepare()
DockerContainerDumper
DockerContainerDumper.CONTAINER_NAME
DockerContainerDumper.DATA_PATH
DockerContainerDumper.DOCKER_CLIENT_URL
DockerContainerDumper.DOCKER_IMAGE
DockerContainerDumper.DUMP_COMMAND
DockerContainerDumper.GET_VERSION_CMD
DockerContainerDumper.KEEP_CONTAINER
DockerContainerDumper.MAX_PARALLEL_DUMP
DockerContainerDumper.ORIGINAL_CONTAINER_STATUS
DockerContainerDumper.TIMEOUT
DockerContainerDumper.create_todump_list()
DockerContainerDumper.delete_or_restore_container()
DockerContainerDumper.download()
DockerContainerDumper.generate_remote_file()
DockerContainerDumper.get_remote_file()
DockerContainerDumper.get_remote_lastmodified()
DockerContainerDumper.need_prepare()
DockerContainerDumper.post_dump()
DockerContainerDumper.prepare_client()
DockerContainerDumper.prepare_dumper_params()
DockerContainerDumper.prepare_local_folders()
DockerContainerDumper.prepare_remote_container()
DockerContainerDumper.release_client()
DockerContainerDumper.remote_is_better()
DockerContainerDumper.set_data_path()
DockerContainerDumper.set_dump_command()
DockerContainerDumper.set_get_version_cmd()
DockerContainerDumper.set_keep_container()
DockerContainerDumper.set_release()
DockerContainerDumper.source_config
DockerContainerException
DummyDumper
DumperException
DumperManager
DumperManager.SOURCE_CLASS
DumperManager.call()
DumperManager.clean_stale_status()
DumperManager.create_and_call()
DumperManager.create_and_dump()
DumperManager.create_instance()
DumperManager.dump_all()
DumperManager.dump_info()
DumperManager.dump_src()
DumperManager.get_schedule()
DumperManager.get_source_ids()
DumperManager.mark_success()
DumperManager.register_classes()
DumperManager.schedule_all()
DumperManager.source_info()
FTPDumper
FilesystemDumper
GitDumper
GoogleDriveDumper
HTTPDumper
LastModifiedBaseDumper
LastModifiedFTPDumper
LastModifiedFTPDumper.RELEASE_FORMAT
LastModifiedFTPDumper.download()
LastModifiedFTPDumper.get_client_for_url()
LastModifiedFTPDumper.get_remote_file()
LastModifiedFTPDumper.prepare_client()
LastModifiedFTPDumper.release_client()
LastModifiedFTPDumper.remote_is_better()
LastModifiedFTPDumper.set_release()
LastModifiedHTTPDumper
ManualDumper
WgetDumper
- biothings.hub.dataload.source
- biothings.hub.dataload.storage
- biothings.hub.dataload.sync
- biothings.hub.dataload.uploader
BaseSourceUploader
BaseSourceUploader.check_ready()
BaseSourceUploader.clean_archived_collections()
BaseSourceUploader.config
BaseSourceUploader.create()
BaseSourceUploader.fullname
BaseSourceUploader.generate_doc_src_master()
BaseSourceUploader.get_current_and_new_master()
BaseSourceUploader.get_mapping()
BaseSourceUploader.get_pinfo()
BaseSourceUploader.get_predicates()
BaseSourceUploader.init_state()
BaseSourceUploader.keep_archive
BaseSourceUploader.load()
BaseSourceUploader.load_data()
BaseSourceUploader.main_source
BaseSourceUploader.make_temp_collection()
BaseSourceUploader.name
BaseSourceUploader.post_update_data()
BaseSourceUploader.prepare()
BaseSourceUploader.prepare_src_dump()
BaseSourceUploader.regex_name
BaseSourceUploader.register_status()
BaseSourceUploader.save_doc_src_master()
BaseSourceUploader.setup_log()
BaseSourceUploader.storage_class
BaseSourceUploader.switch_collection()
BaseSourceUploader.unprepare()
BaseSourceUploader.update_data()
BaseSourceUploader.update_master()
DummySourceUploader
IgnoreDuplicatedSourceUploader
MergerSourceUploader
NoBatchIgnoreDuplicatedSourceUploader
NoDataSourceUploader
ParallelizedSourceUploader
ResourceError
ResourceNotReady
UploaderManager
UploaderManager.SOURCE_CLASS
UploaderManager.clean_stale_status()
UploaderManager.create_and_load()
UploaderManager.create_and_update_master()
UploaderManager.create_instance()
UploaderManager.filter_class()
UploaderManager.get_source_ids()
UploaderManager.poll()
UploaderManager.register_classes()
UploaderManager.source_info()
UploaderManager.update_source_meta()
UploaderManager.upload_all()
UploaderManager.upload_info()
UploaderManager.upload_src()
set_pending_to_upload()
- biothings.hub.dataload.validator
- biothings.hub.dataload.dumper
- biothings.hub.dataplugin
- biothings.hub.dataplugin.assistant
AdvancedPluginLoader
AssistantException
AssistantManager
AssistantManager.configure()
AssistantManager.create_instance()
AssistantManager.export()
AssistantManager.export_dumper()
AssistantManager.export_mapping()
AssistantManager.export_uploader()
AssistantManager.load()
AssistantManager.load_plugin()
AssistantManager.register_classes()
AssistantManager.register_url()
AssistantManager.setup_log()
AssistantManager.submit()
AssistantManager.unregister_url()
AssistantManager.update_plugin_name()
AssistedDumper
AssistedUploader
BaseAssistant
BaseAssistant.can_handle()
BaseAssistant.data_plugin_manager
BaseAssistant.dumper_manager
BaseAssistant.handle()
BaseAssistant.keylookup
BaseAssistant.load_plugin()
BaseAssistant.loader
BaseAssistant.loaders
BaseAssistant.plugin_name
BaseAssistant.plugin_type
BaseAssistant.register_loader()
BaseAssistant.setup_log()
BaseAssistant.uploader_manager
BasePluginLoader
GithubAssistant
LoaderException
LocalAssistant
ManifestBasedPluginLoader
ManifestBasedPluginLoader.can_load_plugin()
ManifestBasedPluginLoader.dumper_registry
ManifestBasedPluginLoader.get_code_for_mod_name()
ManifestBasedPluginLoader.get_dumper_dynamic_class()
ManifestBasedPluginLoader.get_uploader_dynamic_class()
ManifestBasedPluginLoader.get_uploader_dynamic_classes()
ManifestBasedPluginLoader.interpret_manifest()
ManifestBasedPluginLoader.load_plugin()
ManifestBasedPluginLoader.loader_type
- biothings.hub.dataplugin.manager
- biothings.hub.dataplugin.assistant
- biothings.hub.datarelease
set_pending_to_publish()
set_pending_to_release_note()
- biothings.hub.datarelease.publisher
BasePublisher
BasePublisher.category
BasePublisher.clean_stale_status()
BasePublisher.collection
BasePublisher.create_bucket()
BasePublisher.get_pinfo()
BasePublisher.get_pre_post_previous_result()
BasePublisher.get_predicates()
BasePublisher.get_release_note_filename()
BasePublisher.load_build()
BasePublisher.publish_release_notes()
BasePublisher.register_status()
BasePublisher.run_pre_post()
BasePublisher.setup()
BasePublisher.setup_log()
BasePublisher.step_archive()
BasePublisher.step_upload()
BasePublisher.step_upload_s3()
BasePublisher.template_out_conf()
BasePublisher.trigger_release_note()
DiffPublisher
PublisherException
ReleaseManager
ReleaseManager.DEFAULT_DIFF_PUBLISHER_CLASS
ReleaseManager.DEFAULT_SNAPSHOT_PUBLISHER_CLASS
ReleaseManager.build_release_note()
ReleaseManager.clean_stale_status()
ReleaseManager.collection
ReleaseManager.configure()
ReleaseManager.create_release_note()
ReleaseManager.create_release_note_from_build()
ReleaseManager.get_pinfo()
ReleaseManager.get_predicates()
ReleaseManager.get_release_note()
ReleaseManager.load_build()
ReleaseManager.poll()
ReleaseManager.publish()
ReleaseManager.publish_build()
ReleaseManager.publish_diff()
ReleaseManager.publish_snapshot()
ReleaseManager.register_status()
ReleaseManager.release_info()
ReleaseManager.reset_synced()
ReleaseManager.setup()
ReleaseManager.setup_log()
SnapshotPublisher
- biothings.hub.datarelease.releasenote
ReleaseNoteSource
ReleaseNoteSrcBuildReader
ReleaseNoteSrcBuildReader.attach_cold_src_build_reader()
ReleaseNoteSrcBuildReader.build_id
ReleaseNoteSrcBuildReader.build_stats
ReleaseNoteSrcBuildReader.build_version
ReleaseNoteSrcBuildReader.cold_collection_name
ReleaseNoteSrcBuildReader.datasource_mapping
ReleaseNoteSrcBuildReader.datasource_stats
ReleaseNoteSrcBuildReader.datasource_versions
ReleaseNoteSrcBuildReader.has_cold_collection()
ReleaseNoteSrcBuildReaderAdapter
ReleaseNoteTxt
- biothings.hub.datatransform
- biothings.hub.standalone
AutoHubFeature
AutoHubFeature.DEFAULT_DUMPER_CLASS
AutoHubFeature.DEFAULT_UPLOADER_CLASS
AutoHubFeature.DEFAULT_VALIDATOR_CLASS
AutoHubFeature.configure()
AutoHubFeature.configure_auto_release()
AutoHubFeature.extract()
AutoHubFeature.get_class_name()
AutoHubFeature.get_folder_name()
AutoHubFeature.install()
AutoHubFeature.list_biothings()
AutoHubServer
Commands
- biothings.hub.commands
am
api
apply()
archive()
backend()
backup()
bm
build()
build_config_info()
build_save_mapping()
builds()
check()
command()
commands()
config()
create_api()
create_build_conf()
create_release_note()
delete_api()
delete_build_conf()
diff()
diff_info()
dim
dm
download()
dpm
dump()
dump_all()
dump_info()
dump_plugin()
export_command_documents()
export_plugin()
expose()
g
get_apis()
get_release_note()
help()
im
index()
index_cleanup()
index_config
index_info()
indexes_by_name()
info()
inspect()
install()
ism
jm
job_info()
jsondiff()
list()
loop
lsmerge()
merge()
pending
pqueue
publish()
publish_diff()
publish_snapshot()
quick_index()
register_url()
release_info()
report()
reset_backend()
reset_synced()
resetconf()
restart()
restore()
rm
rmmerge()
sch()
schedule()
setconf()
sm
snapshot()
snapshot_cleanup()
snapshot_config
snapshot_info()
source_info()
source_reset()
source_save_mapping()
sources()
ssm
start_api()
status()
stop()
stop_api()
sym
sync()
top()
tqueue
um
unregister_url()
update_build_conf()
update_metadata()
update_source_meta()
upgrade()
upload()
upload_all()
upload_info()
validate_mapping()
versions()
whatsnew()