List comprehensions produce different types

Hi @northwestwitch ! I found a strange thing in scout/server/blueprints/cases/controllers.py.

The function looks like this (cropped)

def case(store, institute_obj, case_obj):
    """Preprocess a single case."""
    case_obj['individual_ids'] = []
    for individual in case_obj['individuals']:
        try:
            sex = int(individual.get('sex', 0))
        except ValueError as err:
            sex = 0
        individual['sex_human'] = SEX_MAP[sex]
        individual['phenotype_human'] = PHENOTYPE_MAP.get(individual['phenotype'])
        case_obj['individual_ids'].append(individual['individual_id'])

    case_obj['assignees'] = [store.user(user_email) for user_email in
                             case_obj.get('assignees', [])]
    suspects = [store.variant(variant_id) or variant_id for variant_id in
                case_obj.get('suspects', [])]
    causatives = [store.variant(variant_id) or variant_id for variant_id in
                  case_obj.get('causatives', [])]

When creating suspects and causatives above it says

store.variant(variant_id) or variant_id

This means that we either get a list with variants (dictionaries) or variant_ids (strings) or a mix of those. The problem arises later in the code when the result is sent to the function variants_filter_by_field in scout/server/blueprints/variants/controllers.py. That one looks like:

def variants_filter_by_field(store, variants, field, case_obj, institute_obj):
    """Given a list of variant objects return only those that have a key specified
      ....
    """
    filtered_variants = []
    # Check if the variants have information if "field"
    for var in variants:
        if var.get(field):
            # Add more details to the variant
            if var['category'] == 'snv':
                var_object = variant(store, institute_obj, case_obj, var['_id'])
            else:
                var_object = sv_variant(store, institute_obj['_id'], case_obj['display_name'], var['_id'])

            filtered_variants.append(var_object['variant'])

    return filtered_variants

It loops over variants and expects them to be dictionaries since it does .get. This fails when the objects are strings.

Could you fix?

[northwestwitch]

I’ll try to fix it today!

[northwestwitch]

Fixed!