Function mutations_affecting_ptm_sites has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def mutations_affecting_ptm_sites(f, sources):

    header = [
        'gene',
        'refseq',

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Function tsv_file_iterator has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def tsv_file_iterator(
    filename, file_header=None, file_opener=open, mode='r',
    skip=None, limit=None, sep='\t'
):
    data_lines_count = count_lines_tsv(filename, file_opener=file_opener, mode=mode)

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Function cache_decorator has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def cache_decorator(cache: Cache) -> Callable:
    """Create a decorator caching results of the function calls.

    The cache is specific to the function name and provided arguments.

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Function htmlwidget has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

Open

def htmlwidget(interactive_plot, args):
    knitr_output = htmlwidgets.knit_print_htmlwidget(interactive_plot, standalone=False)
    html = list(knitr_output)[0].replace('<!--html_preserve-->', '').replace('<!--/html_preserve-->', '')
    deps = base.attr(knitr_output, 'knit_meta')
    javascript = ''

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Function Progress has 47 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function Progress()
{
    var url;
    var progress_span, progress_bar;
    var state_failure, state_progress, state_pending;

Function multilinePlaceholderPolyfill has 47 lines of code (exceeds 25 allowed). Consider refactoring.

Open

var multilinePlaceholderPolyfill = (function()
{
    // allows to use multiline placeholders if textarea is given as field,
    // or imitates normal placeholders if an input is given as field
    var field

Function init has 45 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        init: function(data)
        {
            update_object(config, data)
            var box = $(data.box)
            input = box.find('input')

Function create_nodes has 45 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function create_nodes(data)
    {
        groups = data.kinase_groups;

        central_node = createProteinNode(data.protein);

Function SearchBar has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

Open

var SearchBar = function ()
{
    var input
    var results_div
    var current_query

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Function saveMessage has 43 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function saveMessage(editable_box)
    {
        $.ajax({
            url: config.endpoint_save,
            type: 'POST',

Function checkbox_list has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function checkbox_list(uls)
    {
        function block(ul)
        {
            ul.popover('show');

Function prepareSites has 41 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function prepareSites(sites, standalone_kinases)
    {
        var cloned_kinases = []

        function parse(site)

Function _setZoomAndMove has 40 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function _setZoomAndMove(new_zoom, new_pos, stop_callback, skip_animation, center_view)
    {
        new_pos = trim_position(new_pos, new_zoom)

        var styles = scalableElem.style;

Function initTable has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

function initTable($table, query, additional_columns)
{
    var initial_query = query

    function detailFormatter(index, row, $element)

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Function resolve_import_order has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def resolve_import_order(self):
        # make a copy of importers list
        unordered = self.importers[:]

        ordered = []

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Function ProteinForm has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

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

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Function divide_muts_by_sites has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

def divide_muts_by_sites(mutations, sites):
    """Aggregates mutations that are within +/-7 positions from sites by site"""
    from collections import defaultdict
    muts_by_site = defaultdict(list)

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Function best_uniprot_entry has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def best_uniprot_entry(self) -> UniprotEntry:
        if self.external_references:
            entries = self.external_references.uniprot_entries
            if not entries:
                return None

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Function joined_query has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

def joined_query(query, required_joins, limit_to=None):
    already_joined = set()
    for joins in required_joins:
        for join in joins:
            if limit_to and join not in limit_to:

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Function select_filters has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

def select_filters(filters, models):
    """Selects filters which are applicable to at least one of given models."""
    selected = set()
    tables = [model.__table__ for model in models]

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