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src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js

Summary

Maintainability
F
1 wk
Test Coverage
F
48%

Function formatData has a Cognitive Complexity of 122 (exceeds 5 allowed). Consider refactoring.
Open

  static formatData(query, organism, rawData) {
    const formattedData = [];
    for (const rawDatum of rawData) {
      if ("halflives" in rawDatum && rawDatum.halflives) {
        const measurements = rawDatum.halflives;
Severity: Minor
Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js - About 2 days 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 getColDefs has 144 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [
      {
        headerName: "Half-life",
        headerComponentFramework: HtmlColumnHeader,
Severity: Major
Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js - About 5 hrs to fix

    Function formatData has 121 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      static formatData(query, organism, rawData) {
    const formattedData = [];
    for (const rawDatum of rawData) {
      if ("halflives" in rawDatum && rawDatum.halflives) {
        const measurements = rawDatum.halflives;
    Severity: Major
    Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js - About 4 hrs to fix

      File RnaHalfLifeDataTable.js has 365 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      import React, { Component } from "react";
import PropTypes from "prop-types";
import {
  upperCaseFirstLetter,
  isOrthoDbId,
      Severity: Minor
      Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js - About 4 hrs to fix

        Function getColDefs has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
        Open

          static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [
      {
        headerName: "Half-life",
        headerComponentFramework: HtmlColumnHeader,
        Severity: Minor
        Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.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 getSideBarDef has 31 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          static getSideBarDef() {
    return {
      toolPanels: [
        {
          id: "columns",
        Severity: Minor
        Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js - About 1 hr to fix

          Avoid deeply nested control flow statements.
          Open

                    } else if ("values" in measurement) {
            const cellLineValues = {};

            for (const value of measurement.values) {
              let cellLine;
          Severity: Major
          Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js - About 45 mins to fix

            Avoid deeply nested control flow statements.
            Open

                        if (organism != null) {
              formattedDatum[
                "taxonomicProximity"
              ] = DataTable.calcTaxonomicDistance(
                measurement.taxon_distance,
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js - About 45 mins to fix

              Similar blocks of code found in 5 locations. Consider refactoring.
              Open

                    {
        headerName: "Taxonomic similarity",
        headerComponentFramework: HtmlColumnHeader,
        headerComponentParams: {
          name: (
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 4 other locations - About 6 hrs to fix
              src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 225..254
              src/scenes/BiochemicalEntityDetails/Gene/ProteinModificationDataTable.js on lines 240..269
              src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js on lines 149..178
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 488..517

              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 168.

              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 3 locations. Consider refactoring.
              Open

                static getSideBarDef() {
    return {
      toolPanels: [
        {
          id: "columns",
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 2 other locations - About 4 hrs to fix
              src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 128..160
              src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 156..188

              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 127.

              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 7 locations. Consider refactoring.
              Open

                    {
        headerName: "Organism",
        field: "organism",
        filter: "textFilter",
        cellRenderer: function (params) {
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 6 other locations - About 1 hr to fix
              src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 206..224
              src/scenes/BiochemicalEntityDetails/Gene/ProteinModificationDataTable.js on lines 221..239
              src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js on lines 307..325
              src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js on lines 125..143
              src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 250..268
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 461..479

              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 72.

              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 7 locations. Consider refactoring.
              Open

                    {
        headerName: "Cell line",
        field: "cellLine",
        filter: "textFilter",
        cellRenderer: function (params) {
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 6 other locations - About 1 hr to fix
              src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 206..224
              src/scenes/BiochemicalEntityDetails/Gene/ProteinModificationDataTable.js on lines 221..239
              src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js on lines 258..276
              src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js on lines 125..143
              src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 250..268
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 461..479

              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 72.

              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

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

                            source: {
                id: "DOI: " + castToArray(measurement.reference)[0].doi,
                url:
                  "https://dx.doi.org/" +
                  castToArray(measurement.reference)[0].doi,
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 1 other location - About 1 hr to fix
              src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js on lines 148..153

              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 56.

              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

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

                              source: {
                  id: "DOI: " + castToArray(measurement.reference)[0].doi,
                  url:
                    "https://dx.doi.org/" +
                    castToArray(measurement.reference)[0].doi,
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 1 other location - About 1 hr to fix
              src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js on lines 69..74

              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 56.

              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 3 locations. Consider refactoring.
              Open

                static getColSortOrder() {
    return [
      { colId: "taxonomicProximity", sort: "asc" },
      { colId: "organism", sort: "asc" },
      // { colId: "cellLine", sort: "asc" },
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 2 other locations - About 45 mins to fix
              src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 285..292
              src/scenes/BiochemicalEntityDetails/Gene/ProteinModificationDataTable.js on lines 296..303

              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 50.

              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

                    {
        headerName: "UniProt id",
        field: "uniprotId",
        cellRenderer: function (params) {
          return (
              Severity: Minor
              Found in src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js and 1 other location - About 45 mins to fix
              src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 187..199

              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 50.

              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

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