Function make_preferred_drug_id has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

Open

    def make_preferred_drug_id(
        self,
        pharmgkb_id: str,
        drug_id_map: dict,
        preferred_ids: dict,

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Consider simplifying this complex logical expression.

Open

                        if ( forward && useCache ) {

                            // Seek `elem` from a previously-cached index

                            // ...in a gzip-friendly way

Function superMatcher has 65 lines of code (exceeds 25 allowed). Consider refactoring.

Open

        superMatcher = function( seed, context, xml, results, outermost ) {
            var elem, j, matcher,
                matchedCount = 0,
                i = "0",
                unmatched = seed && [],

Function run has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, data_file: Optional[str] = None):
        """Run the transformation."""
        ttd_file_name = os.path.join(
            self.input_base_dir, "P1-01-TTD_target_download.txt"
        )

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Function parse has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def parse(self, name: str, data_file: str, source: str) -> None:
        """Process the data_file.

        Args:
            name: Name of the ontology

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Function run has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self, data_file: Optional[str] = None) -> None:
        """Perform transformations to process protein-protein interactions.

        Args:
            data_file: data file to parse

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Function domManip has 60 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function domManip( collection, args, callback, ignored ) {

    // Flatten any nested arrays
    args = flat( args );

Function ajaxConvert has 59 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function ajaxConvert( s, response, jqXHR, isSuccess ) {
    var conv2, current, conv, tmp, prev,
        converters = {},

        // Work with a copy of dataTypes in case we need to modify it for conversion

Function highlightText has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

jQuery.fn.highlightText = function(text, className) {
  function highlight(node, addItems) {
    if (node.nodeType === 3) {
      var val = node.nodeValue;
      var pos = val.toLowerCase().indexOf(text);

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Function displayNextItem has 56 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    function displayNextItem() {
      // results left, load the summary and display it
      if (results.length) {
        var item = results.pop();
        var listItem = $('<li style="display:none"></li>');

File sars_cov_2_gene_annot.py has 258 lines of code (exceeds 250 allowed). Consider refactoring.

Open

"""Transform for SARS-CoV-2 gene annotation data."""

import logging
import os
from typing import Generator, List, Optional, TextIO

Function eq has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  function eq(a, b, stack) {
    // Identical objects are equal. `0 === -0`, but they aren't identical.
    // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
    if (a === b) return a !== 0 || 1 / a == 1 / b;
    // A strict comparison is necessary because `null == undefined`.

Function init has 54 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    init = jQuery.fn.init = function( selector, context, root ) {
        var match, elem;

        // HANDLE: $(""), $(null), $(undefined), $(false)
        if ( !selector ) {

File make_holdouts.py has 254 lines of code (exceeds 250 allowed). Consider refactoring.

Open

"""Functions for producing holdouts for graph ML."""

import logging
import os
import random

Function run has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def run(
        self, data_file: Optional[str] = None, chembl_data_files: Optional[dict] = None
    ) -> None:
        """Call method and perform needed transformations.

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Function run has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def run(
        self, data_file: Optional[str] = None, species: str = "Homo sapiens"
    ) -> None:
        """
        Call method and perform transformations.

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Function remove has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    remove: function( elem, types, handler, selector, mappedTypes ) {

        var j, origCount, tmp,
            events, t, handleObj,
            special, handlers, type, namespaces, origType,

Function performObjectSearch has 52 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  performObjectSearch : function(object, otherterms) {
    var filenames = this._index.filenames;
    var docnames = this._index.docnames;
    var objects = this._index.objects;
    var objnames = this._index.objnames;

Function buildFragment has 51 lines of code (exceeds 25 allowed). Consider refactoring.

Open

function buildFragment( elems, context, scripts, selection, ignored ) {
    var elem, tmp, tag, wrap, attached, j,
        fragment = context.createDocumentFragment(),
        nodes = [],
        i = 0,

Consider simplifying this complex logical expression.

Open

                if ( ( mappedTypes || origType === handleObj.origType ) &&
                    ( !handler || handler.guid === handleObj.guid ) &&
                    ( !tmp || tmp.test( handleObj.namespace ) ) &&
                    ( !selector || selector === handleObj.selector ||
                        selector === "**" && handleObj.selector ) ) {