Showing 237 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.
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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 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")
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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 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.
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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 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,
Similar blocks of code found in 2 locations. Consider refactoring. Open
if (re.test(w)) {
var fp = re.exec(w);
stem = fp[1];
suffix = fp[2];
re = new RegExp(mgr0);
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 92.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Similar blocks of code found in 2 locations. Consider refactoring. Open
if (re.test(w)) {
var fp = re.exec(w);
stem = fp[1];
suffix = fp[2];
re = new RegExp(mgr0);
- Read upRead up
Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 92.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
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() {