scout/adapter/mongo/clinvar.py
def case_to_clinVars(self, case_id):
        """Get all variants included in clinvar submissions for a case

        Args:
            case_id(str): a case _id

        Returns:
            submission_variants(dict): keys are variant ids and values are variant submission objects

        """
        query = dict(case_id=case_id, csv_type='variant')
        clinvar_objs = list(self.clinvar_collection.find(query))
        submitted_vars = {}
        for clinvar in clinvar_objs:
            submitted_vars[clinvar.get('local_id')] = clinvar

        return submitted_vars
def case_to_clinVars(self, case_id):
        query = dict(case_id=case_id, csv_type='variant')
        clinvar_objs = list(self.clinvar_collection.find(query))
        submitted_vars = {}
        for clinvar in clinvar_objs:
            submitted_vars[clinvar.get('local_id')] = clinvar

        return submitted_vars
def case_to_clinVars ( self , case_id ) : query = dict ( case_id = case_id , csv_type = 'variant' ) clinvar_objs = list ( self . clinvar_collection . find ( query ) ) submitted_vars = { } for clinvar in clinvar_objs : submitted_vars [ clinvar . get ( 'local_id' ) ] = clinvar return submitted_vars
Get all variants included in clinvar submissions for a case

        Args:
            case_id(str): a case _id

        Returns:
            submission_variants(dict): keys are variant ids and values are variant submission objects
Get all variants included in clinvar submissions for a case