Sign upLogin

justaddcoffee/kg-emerging-viruses

View on GitHub
Star

Showing 237 of 237 total issues

Function matcherFromTokens has 48 lines of code (exceeds 25 allowed). Consider refactoring.
Open

function matcherFromTokens( tokens ) {
    var checkContext, matcher, j,
        len = tokens.length,
        leadingRelative = Expr.relative[ tokens[ 0 ].type ],
        implicitRelative = leadingRelative || Expr.relative[ " " ],
Severity: Minor
Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

    Function select has 48 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

    select = Sizzle.select = function( selector, context, results, seed ) {
    var i, tokens, token, type, find,
        compiled = typeof selector === "function" && selector,
        match = !seed && tokenize( ( selector = compiled.selector || selector ) );
    Severity: Minor
    Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

      Function highlightText has 48 lines of code (exceeds 25 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 1 hr to fix

        Function make_id_mapping_file has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
        Open

            def make_id_mapping_file(
        self,
        map_file: str,
        sep: str = "\t",
        pharmgkb_id_col: str = "PharmGKB Accession Id",
        Severity: Minor
        Found in kg_covid_19/transform_utils/pharmgkb/pharmgkb.py - About 1 hr 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 gpi_to_gene_node_data has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
        Open

            def gpi_to_gene_node_data(self, rec: dict) -> list:
        """Return node that can be passed to write_node_edge_item().

        Uses a parsed gpi entry.
        :param rec: record from gpi iterator
        Severity: Minor
        Found in kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py - About 1 hr 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_experiment_info has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
        Open

            def parse_experiment_info(self, xmldoc: minidom.Document) -> Dict[int, str]:
        """Extract info about experiment from miXML doc.

        :param self: IntAct instance
        :param xmldoc: a minidom object containing a miXML doc
        Severity: Minor
        Found in kg_covid_19/transform_utils/intact/intact.py - About 1 hr 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 addCombinator has 47 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

        function addCombinator( matcher, combinator, base ) {
    var dir = combinator.dir,
        skip = combinator.next,
        key = skip || dir,
        checkNonElements = base && key === "parentNode",
        Severity: Minor
        Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

          Function tokenize has 46 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

          tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
    var matched, match, tokens, type,
        soFar, groups, preFilters,
        cached = tokenCache[ selector + " " ];
          Severity: Minor
          Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

            Function val has 45 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                val: function( value ) {
        var hooks, ret, valueIsFunction,
            elem = this[ 0 ];

        if ( !arguments.length ) {
            Severity: Minor
            Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

              Function data has 44 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  data: function( key, value ) {
        var i, name, data,
            elem = this[ 0 ],
            attrs = elem && elem.attributes;
              Severity: Minor
              Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

                Function leverageNative has 44 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                function leverageNative( el, type, expectSync ) {

    // Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add
    if ( !expectSync ) {
        if ( dataPriv.get( el, type ) === undefined ) {
                Severity: Minor
                Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

                  Similar blocks of code found in 2 locations. Consider refactoring.
                  Open

                      each(obj, function(value, index, list) {
      var computed = iterator ? iterator.call(context, value, index, list) : value;
      computed < result.computed && (result = {value : value, computed : computed});
    });
                  Severity: Major
                  Found in docs/_static/underscore-1.3.1.js and 1 other location - About 1 hr to fix
                  docs/_static/underscore-1.3.1.js on lines 230..233

                  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 70.

                  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

                  Further Reading

                  Function download_from_yaml has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
                  Open

                  def download_from_yaml(
    yaml_file: str, output_dir: str, ignore_cache: bool = False
) -> None:
    """
    Download files specified in an input yaml.
                  Severity: Minor
                  Found in kg_covid_19/utils/download_utils.py - About 1 hr 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

                  Similar blocks of code found in 2 locations. Consider refactoring.
                  Open

                      each(obj, function(value, index, list) {
      var computed = iterator ? iterator.call(context, value, index, list) : value;
      computed >= result.computed && (result = {value : value, computed : computed});
    });
                  Severity: Major
                  Found in docs/_static/underscore-1.3.1.js and 1 other location - About 1 hr to fix
                  docs/_static/underscore-1.3.1.js on lines 242..245

                  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 70.

                  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

                  Further Reading

                  Function interaction_to_edge has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def interaction_to_edge(
        self, interaction: minidom.Element, nodes_dict: dict, exp_dict: dict
    ) -> list:
        """Parse an interaction to an edge."""
        edges: List[list] = []
                  Severity: Minor
                  Found in kg_covid_19/transform_utils/intact/intact.py - About 1 hr 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 extend has 43 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                  jQuery.extend = jQuery.fn.extend = function() {
    var options, name, src, copy, copyIsArray, clone,
        target = arguments[ 0 ] || {},
        i = 1,
        length = arguments.length,
                  Severity: Minor
                  Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix

                    Consider simplifying this complex logical expression.
                    Open

                    if (!jQuery.browser) {
  jQuery.uaMatch = function(ua) {
    ua = ua.toLowerCase();

    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
                    Severity: Critical
                    Found in docs/_static/doctools.js - About 1 hr to fix

                      Similar blocks of code found in 2 locations. Consider refactoring.
                      Open

                              for (var w in terms) {
          if (w.match(word) && !terms[word]) {
            _o.push({files: terms[w], score: Scorer.partialTerm})
          }
        }
                      Severity: Major
                      Found in docs/_static/searchtools.js and 1 other location - About 1 hr to fix
                      docs/_static/searchtools.js on lines 410..414

                      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 68.

                      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

                      Further Reading

                      Similar blocks of code found in 2 locations. Consider refactoring.
                      Open

                              for (var w in titleterms) {
          if (w.match(word) && !titleterms[word]) {
              _o.push({files: titleterms[w], score: Scorer.partialTitle})
          }
        }
                      Severity: Major
                      Found in docs/_static/searchtools.js and 1 other location - About 1 hr to fix
                      docs/_static/searchtools.js on lines 405..409

                      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 68.

                      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

                      Further Reading

                      Function access has 41 lines of code (exceeds 25 allowed). Consider refactoring.
                      Open

                      var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
    var i = 0,
        len = elems.length,
        bulk = key == null;
                      Severity: Minor
                      Found in docs/_static/jquery-3.5.1.js - About 1 hr to fix
                        Severity
                        Category
                        Status
                        Source
                        Language