justaddcoffee/kg-emerging-viruses

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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
Severity: Minor
Found in kg_covid_19/transform_utils/pharmgkb/pharmgkb.py - About 4 hrs to fix

    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,
    Severity: Major
    Found in docs/_static/jquery-3.5.1.js - About 4 hrs to fix

      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,
      Severity: Major
      Found in docs/_static/jquery-3.5.1.js - About 3 hrs to fix

        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,
        Severity: Major
        Found in docs/_static/jquery-3.5.1.js - About 3 hrs to fix

          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.
          Severity: Minor
          Found in kg_covid_19/transform_utils/scibite_cord/scibite_cord.py - About 3 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 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")
          Severity: Minor
          Found in kg_covid_19/transform_utils/pharmgkb/pharmgkb.py - About 3 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 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
          Severity: Major
          Found in docs/_static/jquery-3.5.1.js - About 3 hrs to fix

            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";
            
            
            Severity: Major
            Found in docs/_static/jquery-3.5.1.js - About 3 hrs to fix

              Function send has 77 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                          send: function( headers, complete ) {
                              var i,
                                  xhr = options.xhr();
              
                              xhr.open(
              Severity: Major
              Found in docs/_static/jquery-3.5.1.js - About 3 hrs to fix

                File intact.py has 295 lines of code (exceeds 250 allowed). Consider refactoring.
                Open

                """Transform IntAct PPI data."""
                
                import fnmatch
                import logging
                import os
                Severity: Minor
                Found in kg_covid_19/transform_utils/intact/intact.py - About 3 hrs to fix

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

                    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.
                    Severity: Minor
                    Found in kg_covid_19/transform_utils/scibite_cord/scibite_cord.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 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,
                    Severity: Major
                    Found in docs/_static/language_data.js - About 2 hrs to fix

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

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

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

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

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

                                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
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