ipr.util¶

VERBOSE_ERROR_CODE¶

VERBOSE_ERROR_CODE = (logging.INFO + logging.DEBUG) // 2

logger¶

logger = logging.getLogger('ipr')

LOG_LEVELS¶

LOG_LEVELS = {
    'info': logging.INFO,
    'debug': logging.DEBUG,
    'warn': logging.WARN,
    'error': logging.ERROR,
    'verbose': VERBOSE_ERROR_CODE,

create_variant_name()¶

Given an IPR variant row, create the variant representation to be used as the name of the variant

def create_variant_name(variant: IprVariant) -> str:

Args

• variant (IprVariant)

Returns

• str

create_variant_name_tuple()¶

Given an IPR variant row, create the variant representation to be used as the name of the variant

def create_variant_name_tuple(variant: IprVariant) -> Tuple[str, str]:

Args

• variant (IprVariant)

Returns

• Tuple[str, str]

find_variant()¶

Find a variant in a list of variants by its key and type

def find_variant(all_variants: List[IprVariant], variant_type: str, variant_key: str) -> IprVariant:

Args

• all_variants (List[IprVariant])
• variant_type (str)
• variant_key (str)

Returns

• IprVariant

generate_ontology_preference_key()¶

Generate a tuple key for comparing preferred ontology terms.

def generate_ontology_preference_key(record: Dict, sources_sort: Dict[str, int] = {}) -> Tuple:

Args

• record (Dict)
• sources_sort (Dict[str, int])

Returns

• Tuple

get_preferred_drug_representation()¶

Given a Drug record, follow its linked records to find the preferred representation by following alias, deprecating, and cross reference links

def get_preferred_drug_representation(graphkb_conn: GraphKBConnection, drug_record_id: str) -> Dict:

Args

• graphkb_conn (GraphKBConnection)
• drug_record_id (str)

Returns

• Dict

get_preferred_gene_name()¶

Given some Feature record ID return the preferred gene name

def get_preferred_gene_name(graphkb_conn: GraphKBConnection, record_id: str) -> str:

Args

• graphkb_conn (GraphKBConnection)
• record_id (str)

Returns

• str

pandas_falsy()¶

Check if a field is python falsy or pandas null

def pandas_falsy(field):

Args

• field