Function Network has 1152 lines of code (exceeds 25 allowed). Consider refactoring.

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var Network = function ()
{
    // data variables
    var sites
    var groups

Function Network has a Cognitive Complexity of 204 (exceeds 5 allowed). Consider refactoring.

Open

var Network = function ()
{
    // data variables
    var sites
    var groups

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File network.js has 1167 lines of code (exceeds 250 allowed). Consider refactoring.

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function prepareSVG(element)
{
    return d3
        .select(element)
        .append('svg')

File protein_data.py has 888 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from collections import defaultdict, namedtuple
from pathlib import Path
from typing import Callable, Type
from warnings import warn

Function Tracks has 423 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var Tracks = function ()
{
    var scale = 1.0
    var scrollArea, scalableArea, scalableElem, tracks
    var needle_plot

File mutations.py has 862 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from abc import ABCMeta, abstractmethod
from collections import UserList, OrderedDict
from functools import lru_cache
from typing import Type, Iterable, Mapping, List, Dict, TYPE_CHECKING

File enrichment.py has 832 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import operator
import random
from collections import namedtuple, Counter, defaultdict
from functools import reduce, partial
from statistics import median, mean

File cms.py has 756 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import re
from os import path
from functools import wraps
from pathlib import Path

File search.py has 682 lines of code (exceeds 250 allowed). Consider refactoring.

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import pickle
from collections import defaultdict
from urllib.parse import unquote

from flask import make_response, redirect, abort

Function Tracks has a Cognitive Complexity of 72 (exceeds 5 allowed). Consider refactoring.

Open

var Tracks = function ()
{
    var scale = 1.0
    var scrollArea, scalableArea, scalableElem, tracks
    var needle_plot

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File clinvar.py has 535 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import re
from collections import defaultdict
from typing import Mapping, Iterable, Dict, TextIO, Union, NamedTuple
from xml.etree import ElementTree

File manage.py has 516 lines of code (exceeds 250 allowed). Consider refactoring.

Open

#!/usr/bin/env python3
import argparse
from contextlib import contextmanager
from typing import Mapping, Text

Function AsyncFiltersHandler has 203 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var AsyncFiltersHandler = function()
{
    var config;
    var form;
    var current_state_checksum;

Function Tooltip has 203 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var Tooltip = function()
{
    var body = d3.select('body').node()

    // internals

Function import_disease_associations has a Cognitive Complexity of 48 (exceeds 5 allowed). Consider refactoring.

Open

    def import_disease_associations(self):
        """Add disease association details to the already imported mutation-disease associations"""
        from tqdm import tqdm
        import gzip

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Function Zoom has 160 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var Zoom = function(css_zoom)
{
    var svg;
    var min;
    var max;

File tracks.js has 426 lines of code (exceeds 250 allowed). Consider refactoring.

Open

var Tracks = function ()
{
    var scale = 1.0
    var scrollArea, scalableArea, scalableElem, tracks
    var needle_plot

Function Tooltip has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring.

Open

var Tooltip = function()
{
    var body = d3.select('body').node()

    // internals

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Function export_genomic_coordinates_of_ptm has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring.

Open

    def export_genomic_coordinates_of_ptm(
        self, export_path=None, path=None,
        only_primary_isoforms=False, only_confirmed_mutations=True
    ):
        path = self.choose_path(path)

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File infections.py has 417 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from abc import abstractmethod
from datetime import datetime
from functools import partial
from typing import List, Iterable, Union
from math import log2