datacatalog.linkedstores.file package

Submodules

datacatalog.linkedstores.file.schemas module

datacatalog.linkedstores.file.schemas.get_schemas()

Get JSON schemas for FileDocument

Returns:Object and document JSON schema that define the store Return type:JSONSchemaCollection

datacatalog.linkedstores.file.store module

class datacatalog.linkedstores.file.store.FileDocument(inheritance=True, **kwargs)

Bases: datacatalog.linkedstores.basestore.heritableschema.HeritableDocumentSchema

Defines experiment-linked metadata for a file

class datacatalog.linkedstores.file.store.FileRecord(value, *args, **kwargs)

Bases: datacatalog.extensible.ExtensibleAttrDict

New document for FileStore with schema enforcement

PARAMS = [('level', False, 'level', 'Unknown'), ('storage_system', False, 'storage_system', 'data-sd2e-community')]

set_token(value)

class datacatalog.linkedstores.file.store.FileStore(mongodb, agave=None, config={}, session=None, **kwargs)

Bases: datacatalog.linkedstores.basestore.agaveclient.AgaveClient, datacatalog.linkedstores.basestore.store.LinkedStore

Manage storage and retrieval of FileDocuments

LINK_FIELDS = ['child_of', 'derived_from', 'derived_using', 'generated_by']

add_update_document(document_dict, uuid=None, token=None, strategy='merge')

classmethod generate_string_id(document_dict)

classmethod generate_string_id_v2_0(document_dict)

get_typeduuid(payload, binary=False)

index(filename, storage_system=None, token=None, **kwargs)

Capture a skeleton metadata entry for a file

Parameters:

• filename (str) – Agave-canonical absolute path to the target
• storage_system (str, optional) – Agave storage system for the target

Returns:

A LinkedStore document containing file details

Return type:

dict

exception datacatalog.linkedstores.file.store.FileUpdateFailure

Bases: datacatalog.linkedstores.basestore.exceptions.CatalogUpdateFailure

class datacatalog.linkedstores.file.store.StoreInterface(mongodb, agave=None, config={}, session=None, **kwargs)

Bases: datacatalog.linkedstores.file.store.FileStore