Showing 217 of 237 total issues
File pharmgkb.py
has 338 lines of code (exceeds 250 allowed). Consider refactoring. Open
"""Transform for PharmGKB drug to drug target data."""
import logging
import os
import re
Function then
has 102 lines of code (exceeds 25 allowed). Consider refactoring. Open
then: function( onFulfilled, onRejected, onProgress ) {
var maxDepth = 0;
function resolve( depth, deferred, handler, special ) {
return function() {
var that = this,
Function Animation
has 96 lines of code (exceeds 25 allowed). Consider refactoring. Open
function Animation( elem, properties, options ) {
var result,
stopped,
index = 0,
length = Animation.prefilters.length,
Function trigger
has 96 lines of code (exceeds 25 allowed). Consider refactoring. Open
trigger: function( event, data, elem, onlyHandlers ) {
var i, cur, tmp, bubbleType, ontype, handle, special, lastElement,
eventPath = [ elem || document ],
type = hasOwn.call( event, "type" ) ? event.type : event,
Function parse_annotation_doc
has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring. Open
def parse_annotation_doc(self, node_handle, edge_handle, doc: Dict) -> None:
"""Parse a JSON document corresponding to a publication.
Args:
node_handle: File handle for nodes.csv.
- Read upRead up
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 23 (exceeds 5 allowed). Consider refactoring. Open
def run(self, data_file: Optional[str] = None):
"""Run the transformation."""
rel_zip_file_name = os.path.join(self.input_base_dir, "relationships.zip")
relationship_file_name = "relationships.tsv"
gene_mapping_zip_file = os.path.join(self.input_base_dir, "pharmgkb_genes.zip")
- Read upRead up
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 Sizzle
has 81 lines of code (exceeds 25 allowed). Consider refactoring. Open
function Sizzle( selector, context, results, seed ) {
var m, i, elem, nid, match, groups, newSelector,
newContext = context && context.ownerDocument,
// nodeType defaults to 9, since context defaults to document
Function CHILD
has 81 lines of code (exceeds 25 allowed). Consider refactoring. Open
"CHILD": function( type, what, _argument, first, last ) {
var simple = type.slice( 0, 3 ) !== "nth",
forward = type.slice( -4 ) !== "last",
ofType = what === "of-type";
Function send
has 77 lines of code (exceeds 25 allowed). Consider refactoring. Open
send: function( headers, complete ) {
var i,
xhr = options.xhr();
xhr.open(
File intact.py
has 295 lines of code (exceeds 250 allowed). Consider refactoring. Open
"""Transform IntAct PPI data."""
import fnmatch
import logging
import os
Function performTermsSearch
has 74 lines of code (exceeds 25 allowed). Consider refactoring. Open
performTermsSearch : function(searchterms, excluded, terms, titleterms) {
var docnames = this._index.docnames;
var filenames = this._index.filenames;
var titles = this._index.titles;
Function contract_uri
has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring. Open
def contract_uri(self, iri) -> str:
"""Contract a given IRI.
Contract a given IRI, with special parsing and transformations
depending on the nature of the IRI.
- Read upRead up
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 splitChars
has 72 lines of code (exceeds 25 allowed). Consider refactoring. Open
var splitChars = (function() {
var result = {};
var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
Function matcherFromGroupMatchers
has 72 lines of code (exceeds 25 allowed). Consider refactoring. Open
function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
var bySet = setMatchers.length > 0,
byElement = elementMatchers.length > 0,
superMatcher = function( seed, context, xml, results, outermost ) {
var elem, j, matcher,
Function add
has 72 lines of code (exceeds 25 allowed). Consider refactoring. Open
add: function( elem, types, handler, data, selector ) {
var handleObjIn, eventHandle, tmp,
events, t, handleObj,
special, handlers, type, namespaces, origType,
Function setMatcher
has 70 lines of code (exceeds 25 allowed). Consider refactoring. Open
function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
if ( postFilter && !postFilter[ expando ] ) {
postFilter = setMatcher( postFilter );
}
if ( postFinder && !postFinder[ expando ] ) {
Function done
has 70 lines of code (exceeds 25 allowed). Consider refactoring. Open
function done( status, nativeStatusText, responses, headers ) {
var isSuccess, success, error, response, modified,
statusText = nativeStatusText;
// Ignore repeat invocations
Function resolve
has 69 lines of code (exceeds 25 allowed). Consider refactoring. Open
function resolve( depth, deferred, handler, special ) {
return function() {
var that = this,
args = arguments,
mightThrow = function() {
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,
- Read upRead up
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
Consider simplifying this complex logical expression. Open
if ( forward && useCache ) {
// Seek `elem` from a previously-cached index
// ...in a gzip-friendly way