justaddcoffee/kg-emerging-viruses

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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,
Severity: Minor
Found in kg_covid_19/transform_utils/pharmgkb/pharmgkb.py - About 2 hrs to fix

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
Severity: Critical
Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix

    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 && [],
    Severity: Major
    Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix

      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"
              )
      Severity: Minor
      Found in kg_covid_19/transform_utils/ttd/ttd.py - About 2 hrs to fix

      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
      Severity: Minor
      Found in kg_covid_19/transform_utils/ontology/ontology_transform.py - About 2 hrs to fix

      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
      Severity: Minor
      Found in kg_covid_19/transform_utils/string_ppi/string_ppi.py - About 2 hrs to fix

      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 );
      
      
      Severity: Major
      Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix

        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
        Severity: Major
        Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix

          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);
          Severity: Minor
          Found in docs/_static/doctools.js - About 2 hrs to fix

          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>');
          Severity: Major
          Found in docs/_static/searchtools.js - About 2 hrs to fix

            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`.
              Severity: Major
              Found in docs/_static/underscore-1.3.1.js - About 2 hrs to fix

                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 ) {
                Severity: Major
                Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix

                  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
                  Severity: Minor
                  Found in kg_covid_19/make_holdouts.py - About 2 hrs to fix

                    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.
                    
                    
                    Severity: Minor
                    Found in kg_covid_19/transform_utils/chembl/chembl_transform.py - About 2 hrs to fix

                    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.
                    Severity: Minor
                    Found in kg_covid_19/transform_utils/drug_central/drug_central.py - About 2 hrs to fix

                    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,
                    Severity: Major
                    Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix

                      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;
                      Severity: Major
                      Found in docs/_static/searchtools.js - About 2 hrs to fix

                        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,
                        Severity: Major
                        Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix

                          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 ) ) {
                          Severity: Critical
                          Found in docs/_static/jquery-3.5.1.js - About 2 hrs to fix
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