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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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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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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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,

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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