scout/build/acmg.py
def build_evaluation(variant_specific, variant_id, user_id, user_name,
                     institute_id, case_id, classification, criteria):
    """Build a evaluation object ready to be inserted to database

    Args:
        variant_specific(str): md5 string for the specific variant
        variant_id(str): md5 string for the common variant
        user_id(str)
        user_name(str)
        institute_id(str)
        case_id(str)
        classification(str): The ACMG classification
        criteria(list(dict)): A list of dictionaries with ACMG criterias

    Returns:
        evaluation_obj(dict): Correctly formatted evaluation object

    """
    criteria = criteria or []
    evaluation_obj = dict(
        variant_specific = variant_specific,
        variant_id = variant_id,
        institute_id = institute_id,
        case_id = case_id,
        classification = classification,
        user_id = user_id,
        user_name = user_name,
        created_at = datetime.datetime.now(),
    )
    criteria_objs = []
    for info in criteria:
        criteria_obj = {}
        # This allways has to exist
        # We might want to check if the term is valid here...
        criteria_obj['term'] = info['term']
        if 'comment' in info:
            criteria_obj['comment'] = info['comment']
        if 'links' in info:
            criteria_obj['links'] = info['links']
        criteria_objs.append(criteria_obj)

    evaluation_obj['criteria'] = criteria_objs

    return evaluation_obj
def build_evaluation(variant_specific, variant_id, user_id, user_name,
                     institute_id, case_id, classification, criteria):
    """Build a evaluation object ready to be inserted to database

    Args:
        variant_specific(str): md5 string for the specific variant
        variant_id(str): md5 string for the common variant
        user_id(str)
        user_name(str)
        institute_id(str)
        case_id(str)
        classification(str): The ACMG classification
        criteria(list(dict)): A list of dictionaries with ACMG criterias

    Returns:
        evaluation_obj(dict): Correctly formatted evaluation object

    """
    criteria = criteria or []
    evaluation_obj = dict(
        variant_specific = variant_specific,
        variant_id = variant_id,
        institute_id = institute_id,
        case_id = case_id,
        classification = classification,
        user_id = user_id,
        user_name = user_name,
        created_at = datetime.datetime.now(),
    )
    criteria_objs = []
    for info in criteria:
        criteria_obj = {}
        # This allways has to exist
        # We might want to check if the term is valid here...
        criteria_obj['term'] = info['term']
        if 'comment' in info:
            criteria_obj['comment'] = info['comment']
        if 'links' in info:
            criteria_obj['links'] = info['links']
        criteria_objs.append(criteria_obj)

    evaluation_obj['criteria'] = criteria_objs

    return evaluation_obj
Build a evaluation object ready to be inserted to database

    Args:
        variant_specific(str): md5 string for the specific variant
        variant_id(str): md5 string for the common variant
        user_id(str)
        user_name(str)
        institute_id(str)
        case_id(str)
        classification(str): The ACMG classification
        criteria(list(dict)): A list of dictionaries with ACMG criterias

    Returns:
        evaluation_obj(dict): Correctly formatted evaluation object