extract

genie.extract

This module contains all the functions that extract data from Synapse

Attributes

logger = logging.getLogger(__name__) module-attribute

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

Functions

get_center_input_files(syn, synid, center, process='main', downloadFile=True)

Walks through each center's input directory to get a list of tuples of center files

PARAMETER	DESCRIPTION
syn	Synapse connection TYPE: Synapse
synid	Synapse Id of a folder TYPE: str
center	GENIE center name TYPE: str
process	Process type include "main", "mutation". Defaults to "main". TYPE: str DEFAULT: 'main'
downloadFile	Downloads the file. Defaults to True. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
list	List of Synapse entities TYPE: List[List[Entity]]

_map_name_to_filetype(name)

Maps file name to filetype

PARAMETER	DESCRIPTION
name	File name TYPE: str

RETURNS	DESCRIPTION
str	filetype TYPE: str

get_file_mapping(syn, synid)

Get mapping between Synapse entity name and Synapse ids of all entities in a folder

PARAMETER	DESCRIPTION
syn	Synapse connection TYPE: Synapse
synid	Synapse Id of folder TYPE: str

RETURNS	DESCRIPTION
dict	mapping between Synapse Entity name and Id TYPE: dict

get_public_to_consortium_synid_mapping(syn, release_synid)

Gets the mapping between potential public release names and the consortium release folder

PARAMETER	DESCRIPTION
syn	Synapse connection TYPE: Synapse
release_synid	Release folder fileview TYPE: str

RETURNS	DESCRIPTION
dict	Mapping between potential public release and consortium release synapse id TYPE: dict

get_syntabledf(syn, query_string)

Get dataframe from Synapse Table query

PARAMETER	DESCRIPTION
syn	Synapse connection TYPE: Synapse
query_string	Table query TYPE: str

RETURNS	DESCRIPTION
DataFrame	pd.DataFrame: Query results in a dataframe

_get_synid_database_mappingdf(syn, project_id)

Get database to synapse id mapping dataframe

PARAMETER	DESCRIPTION
syn	Synapse object
project_id	Synapse Project ID with a 'dbMapping' annotation.

RETURNS	DESCRIPTION
	database to synapse id mapping dataframe

getDatabaseSynId(syn, tableName, project_id=None, databaseToSynIdMappingDf=None)

Get database synapse id from database to synapse id mapping table

PARAMETER	DESCRIPTION
syn	Synapse object
project_id	Synapse Project ID with a database mapping table. DEFAULT: None
tableName	Name of synapse table
databaseToSynIdMappingDf	Avoid calling rest call to download table if the mapping table is already downloaded DEFAULT: None

RETURNS	DESCRIPTION
str	Synapse id of wanted database

_get_database_mapping_config(syn, synid)

Gets Synapse database to Table mapping in dict

PARAMETER	DESCRIPTION
syn	Synapse connection TYPE: Synapse
synid	Synapse id of database mapping table TYPE: str

RETURNS	DESCRIPTION
dict	{'databasename': 'synid'} TYPE: dict

get_genie_config(syn, project_id)

Get configurations needed for the GENIE codebase

PARAMETER	DESCRIPTION
syn	Synapse connection TYPE: Synapse
project_id	Synapse project id TYPE: str

RETURNS	DESCRIPTION
dict	GENIE table type/name to Synapse Id TYPE: dict

_get_oncotreelink(syn, genie_config, oncotree_link=None)

Gets oncotree link unless a link is specified by the user

PARAMETER	DESCRIPTION
syn	Synapse connection TYPE: Synapse
genie_config	database name to synid mapping TYPE: dict
oncotree_link	link to oncotree. Default is None TYPE: str DEFAULT: None

RETURNS	DESCRIPTION
str	oncotree link TYPE: str