Consortium to Public

genie.consortium_to_public

Converts consortium release files to public release files

Attributes

logger = logging.getLogger(__name__) module-attribute

stdout_handler = logging.StreamHandler(stream=(sys.stdout)) module-attribute

DEPRECATED_PUBLIC_RELEASE_FILES = ['data_fusions.txt', 'meta_fusions.txt'] module-attribute

Functions

_copyRecursive(syn, entity, destinationId, mapping=None, skipCopyAnnotations=False, **kwargs)

NOTE: This is a copy of the function found here: https://github.com/Sage-Bionetworks/synapsePythonClient/blob/develop/synapseutils/copy_functions.py#L409 This was copied because there is a restriction that doesn't allow for copying entities with access requirements

Recursively copies synapse entites, but does not copy the wikis

PARAMETER	DESCRIPTION
syn	A Synapse object with user's login TYPE: Synapse
entity	A synapse entity ID TYPE: str
destinationId	Synapse ID of a folder/project that the copied entity is being copied to TYPE: str
mapping	A mapping of the old entities to the new entities TYPE: Dict[str, str] DEFAULT: None
skipCopyAnnotations	Skips copying the annotations Default is False TYPE: bool DEFAULT: False

RETURNS	DESCRIPTION
Dict[str, str]	a mapping between the original and copied entity: {'syn1234':'syn33455'}

commonVariantFilter(mafDf)

This filter returns variants to keep

PARAMETER	DESCRIPTION
mafDf	Maf dataframe

consortiumToPublic(syn, processingDate, genie_version, releaseId, databaseSynIdMappingDf, publicReleaseCutOff=365)