Showing 217 of 237 total issues
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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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Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
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 ) ) {
Function matcherFromTokens
has 48 lines of code (exceeds 25 allowed). Consider refactoring. Open
function matcherFromTokens( tokens ) {
var checkContext, matcher, j,
len = tokens.length,
leadingRelative = Expr.relative[ tokens[ 0 ].type ],
implicitRelative = leadingRelative || Expr.relative[ " " ],
Function select
has 48 lines of code (exceeds 25 allowed). Consider refactoring. Open
select = Sizzle.select = function( selector, context, results, seed ) {
var i, tokens, token, type, find,
compiled = typeof selector === "function" && selector,
match = !seed && tokenize( ( selector = compiled.selector || selector ) );