Function InlineEditManager has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

var InlineEditManager = function()
{
    // values in the default config are dummy - just to illustrate the concept
    var config = {
        endpoint_save: '/save_message/',

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Function gather_muts_and_sites has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

    def gather_muts_and_sites(
        self, mutations: BaseQuery, sites: BaseQuery,
        show_progress=True, occurrences_in: List[MutationSource] = None, intersection=None
    ) -> MotifsData:
        """If occurrences_in is provided, the count of mutations will

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File manager.py has 322 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import re
from collections import namedtuple, defaultdict

from sqlalchemy import and_

Function init_nodes has 93 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function init_nodes(vis, nodes_data, created_nodes)
    {
        tooltip = init_tooltips()

        nodes = vis.selectAll('.node')

File __init__.py has 320 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import gc
import gzip
from abc import abstractmethod
from collections import defaultdict
from typing import List, Iterable

Function ProteinForm has 90 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var ProteinForm = (function ()
{
    var element
    var empty_indicator, no_results_indicator, waiting_indicator
    var result_ul, recent_value, protein_search

File basic_filter.py has 316 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import operator
from functools import lru_cache
from types import MethodType

from sqlalchemy.ext.associationproxy import AssociationProxyInstance

Function count_ptm has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

def count_ptm(
    counter, site_types: Iterable[models.SiteType] = tuple(), models=None,
    only_primary=False, site_mode='any',
    custom_filters=None,
    custom_joins=None

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Function MutationTable has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.

Open

var MutationTable = function ()
{
    var element
    var mutations
    var impact_importances = {}

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Function import_genome_proteome_mappings has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.

Open

def import_genome_proteome_mappings(
    proteins: Dict[str, Protein],
    mappings_dir='data/200616/all_variants/playground',
    mappings_file_pattern='annot_*.txt.gz',
    bdb_dir=''

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Function as_sqlalchemy has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.

Open

    def as_sqlalchemy(self, target):

        value = self.mapped_value

        if value is None:

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File assets.py has 305 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from flask_assets import Bundle
from abc import ABC, abstractmethod
from flask import Markup

Function ShortURL has 81 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var ShortURL = function()
{
    // values in the default config are dummy - just to illustrate the concept
    var config = {
        endpoint_get: '/get_shorthand_for_url_provided_in_get/',

MutationImporter has 27 functions (exceeds 20 allowed). Consider refactoring.

Open

class MutationImporter(BioImporter, MutationExporter):

    @abstract_property
    def name(self):
        """Name of the mutations importer"""

Function init_tinymce has 77 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function init_tinymce(config)
{
    var default_config = {
        selector: 'textarea',
        body_class: 'page-content',

Function Widgets has 73 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var Widgets = (function () {
    var form
    var select_sth_popover = {
        content: 'You should select at least one option',
        placement: 'top',

Function import_aminoacid_mutation_refseq_mappings has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

def import_aminoacid_mutation_refseq_mappings(
    proteins: Dict[str, Protein],
    mappings_dir='data/200616/all_variants/playground',
    mappings_file_pattern='annot_*.txt.gz',
    bdb_dir=''

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Function __init__ has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, domains):

        tracks = OrderedDict()

        grouped_domains = self.group_domains(domains)

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Function basic_auto_migrate_relational_db has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

def basic_auto_migrate_relational_db(app, bind: str):
    """Inspired by http://stackoverflow.com/questions/2103274/"""

    from sqlalchemy import Table
    from sqlalchemy import MetaData

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Function ForceManager has 72 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function ForceManager(config)
    {
        var force_affected_nodes = [];
        var force_affected_links = [];
        var force;