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wurmlab/sequenceserver

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Showing 16,957 of 16,957 total issues

Class has too many lines. [220/150]
Open

  class Routes < Sinatra::Base
    # See
    # http://www.sinatrarb.com/configuration.html
    configure do
      # We don't need Rack::MethodOverride. Let's avoid the overhead.
Severity: Minor
Found in lib/sequenceserver/routes.rb by rubocop

Class has too many lines. [214/150]
Open

  class MAKEBLASTDB
    extend Forwardable
    GUESS_SAMPLE_SIZE = 1_048_576
 
    def_delegators SequenceServer, :config, :sys
Severity: Minor
Found in lib/sequenceserver/makeblastdb.rb by rubocop

Class has too many lines. [195/150]
Open

    class Report < Report
      def initialize(job)
        super do
          @querydb = job.databases
        end
Severity: Minor
Found in lib/sequenceserver/blast/report.rb by rubocop

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

        _.each(
            this.hit_arr,
            _.bind(function (id, index) {
                this.chordsHide = [];
                this.layoutHide = [];
Severity: Major
Found in public/js/circos.js and 1 other location - About 1 day to fix
public/js/circos.js on lines 484..512

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

        _.each(
            this.query_arr,
            _.bind(function (id, index) {
                this.chordsHide = [];
                this.layoutHide = [];
Severity: Major
Found in public/js/circos.js and 1 other location - About 1 day to fix
public/js/circos.js on lines 513..541

Function Track has a Cognitive Complexity of 61 (exceeds 5 allowed). Consider refactoring.
Open

circosJS.Track = function() {
    this.build = function(instance, conf, data) {
        this.dispatch = d3.dispatch('mouseover', 'mouseout');
        this.loadData(data, instance);
        this.conf = this.processConf(conf, this.defaultConf, this.meta, instance, this);
Severity: Minor
Found in public/js/circosjs.js - About 1 day to fix

Function HSP has 220 lines of code (exceeds 25 allowed). Consider refactoring.
Open

export default function HSP(props) {
  const hsp = props.hsp;
  const hspRef = createRef();
  const printing = useDetectPrint();
  const [chars, setChars] = useState(0)
Severity: Major
Found in public/js/hsp.js - About 1 day to fix

    Function Track has 215 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

    circosJS.Track = function() {
        this.build = function(instance, conf, data) {
            this.dispatch = d3.dispatch('mouseover', 'mouseout');
            this.loadData(data, instance);
            this.conf = this.processConf(conf, this.defaultConf, this.meta, instance, this);
    Severity: Major
    Found in public/js/circosjs.js - About 1 day to fix

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

          this.x = (function(_this) {
              return function(d, layout, conf) {
                  var angle, height, r;
                  height = _this.ratio(d.value, conf.cmin, conf.cmax, conf.outerRadius - conf.innerRadius, false, conf.logscale);
                  if (conf.direction === 'in') {
      Severity: Major
      Found in public/js/circosjs.js and 1 other location - About 1 day to fix
      public/js/circosjs.js on lines 721..733

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

          this.ratio = function(value, min, max, scope, reverse, logScale) {
              var fraction, scaleLogBase, x;
              scaleLogBase = logScale ? 2.3 : 1;
              if (min === max || (value === min && !reverse) || (value === max && reverse)) {
                  return 0;
      Severity: Major
      Found in public/js/circosjs.js and 1 other location - About 1 day to fix
      public/js/circosjs.js on lines 601..616

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

          this.ratio = function(value, min, max, scope, reverse, logScale) {
              var fraction, scaleLogBase, x;
              scaleLogBase = logScale ? 2.3 : 1;
              if (min === max || (value === min && !reverse) || (value === max && reverse)) {
                  return 0;
      Severity: Major
      Found in public/js/circosjs.js and 1 other location - About 1 day to fix
      public/js/circosjs.js on lines 734..749

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

          this.y = (function(_this) {
              return function(d, layout, conf) {
                  var angle, height, r;
                  height = _this.ratio(d.value, conf.cmin, conf.cmax, conf.outerRadius - conf.innerRadius, false, conf.logscale);
                  if (conf.direction === 'in') {
      Severity: Major
      Found in public/js/circosjs.js and 1 other location - About 1 day to fix
      public/js/circosjs.js on lines 708..720

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

          this.getSource = (function(_this) {
              return function(d, layout) {
                  var block, endAngle, result, startAngle;
                  d = d.source;
                  block = layout.blocks[d.id];
      Severity: Major
      Found in public/js/circosjs.js and 1 other location - About 1 day to fix
      public/js/circosjs.js on lines 448..462

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

          this.getTarget = (function(_this) {
              return function(d, layout) {
                  var block, endAngle, result, startAngle;
                  d = d.target;
                  block = layout.blocks[d.id];
      Severity: Major
      Found in public/js/circosjs.js and 1 other location - About 1 day to fix
      public/js/circosjs.js on lines 433..447

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

                          {
                              !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                                  <a href={'download/' + this.props.data.search_id + '.std_tsv'}>
                                      <div className="relative flex flex-col items-center group">
                                          <div className="flex items-center w-full">
      Severity: Major
      Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
      public/js/sidebar.js on lines 337..356
      public/js/sidebar.js on lines 357..373
      public/js/sidebar.js on lines 374..390

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

                          {
                              !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                                  <a href={'download/' + this.props.data.search_id + '.full_tsv'}>
                                      <div className="relative flex flex-col items-center group">
                                          <div className="flex items-center w-full">
      Severity: Major
      Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
      public/js/sidebar.js on lines 317..336
      public/js/sidebar.js on lines 357..373
      public/js/sidebar.js on lines 374..390

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

                          {
                              !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                                  <a href={'download/' + this.props.data.search_id + '.xml'}>
                                      <div className="relative flex flex-col items-center group">
                                          <div className="flex items-center w-full">
      Severity: Major
      Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
      public/js/sidebar.js on lines 317..336
      public/js/sidebar.js on lines 337..356
      public/js/sidebar.js on lines 374..390

      Similar blocks of code found in 4 locations. Consider refactoring.
      Open

                          {
                              !this.props.data.imported_xml && <li className="hover:bg-gray-200 mb-1">
                                  <a href={'download/' + this.props.data.search_id + '.pairwise'}>
                                      <div className="relative flex flex-col items-center group">
                                          <div className="flex items-center w-full">
      Severity: Major
      Found in public/js/sidebar.js and 3 other locations - About 7 hrs to fix
      public/js/sidebar.js on lines 317..336
      public/js/sidebar.js on lines 337..356
      public/js/sidebar.js on lines 357..373

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

              $('.circos').tooltip({
                  position: {
                      my: 'left+3 bottom-3',
                      at: 'right bottom',
                      using: function(position, feedback) {
      Severity: Major
      Found in public/js/circos.js and 1 other location - About 6 hrs to fix
      public/js/jquery_world.js on lines 49..71

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

          $(document).tooltip({
              position: {
                  my: 'center bottom-20',
                  at: 'center top',
                  using: function( position, feedback ) {
      Severity: Major
      Found in public/js/jquery_world.js and 1 other location - About 6 hrs to fix
      public/js/circos.js on lines 569..591
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