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src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js

Summary

Maintainability
F
1 wk
Test Coverage
B
82%

Function getColDefs has 277 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [];

    // k_cat column
    let hasKcat = false;
Severity: Major
Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 1 day to fix

    File RateConstantsDataTable.js has 571 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    import React, { Component } from "react";
import PropTypes from "prop-types";
import { upperCaseFirstLetter } from "~/utils/utils";
import DataTable from "../DataTable/DataTable";
import { HtmlColumnHeader } from "../HtmlColumnHeader";
    Severity: Major
    Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 1 day to fix

      Function getColDefs has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.
      Open

        static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [];

    // k_cat column
    let hasKcat = false;
      Severity: Minor
      Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 5 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 93 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

        static getSideBarDef(query, organism, formattedData) {
    const sideBar = {
      toolPanels: [
        {
          id: "columns",
      Severity: Major
      Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 3 hrs to fix

        Function formatData has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
        Open

          static formatData(query, organism, rawData) {
    const formattedData = [];

    for (const datum of rawData) {
      let enzymeName = null;
        Severity: Minor
        Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - 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 formatData has 52 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

          static formatData(query, organism, rawData) {
    const formattedData = [];

    for (const datum of rawData) {
      let enzymeName = null;
        Severity: Major
        Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 2 hrs to fix

          Function getColSortOrder has 37 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

            static getColSortOrder(query, organism, formattedData) {
    const sortOrder = [
      { colId: "taxonomicProximity", sort: "asc" },
      { colId: "organism", sort: "asc" },
    ];
          Severity: Minor
          Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 1 hr to fix

            Function getColSortOrder has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
            Open

              static getColSortOrder(query, organism, formattedData) {
    const sortOrder = [
      { colId: "taxonomicProximity", sort: "asc" },
      { colId: "organism", sort: "asc" },
    ];
            Severity: Minor
            Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - 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 getSideBarDef has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
            Open

              static getSideBarDef(query, organism, formattedData) {
    const sideBar = {
      toolPanels: [
        {
          id: "columns",
            Severity: Minor
            Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - 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 cellRenderer has 26 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                  cellRenderer: function (params) {
        const subunits = params.value;
        if (subunits != null) {
          return (
            '<ul class="comma-separated-list">' +
            Severity: Minor
            Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 1 hr to fix

              Function getKiValues has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                static getKiValues(parameters) {
    const kis = {};
    for (const parameter of parameters) {
      if (parameter.type === 261 || parameter.sbo_type === 261) {
        if (parameter.value != null) {
              Severity: Minor
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 35 mins 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 getKcatValues has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                static getKcatValues(parameters) {
    for (const parameter of parameters) {
      if (
        parameter.type === 25 ||
        parameter.sbo_type === 25 ||
              Severity: Minor
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 35 mins 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 getKmValues has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

                static getKmValues(parameters) {
    const kms = {};
    for (const parameter of parameters) {
      if (parameter.type === 27 || parameter.sbo_type === 27) {
        if (parameter.value != null) {
              Severity: Minor
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js - About 35 mins 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

                  for (const kmMet of kmMets) {
      colDefs.push({
        headerName: "K_M " + kmMet + " value",
        headerComponentFramework: HtmlColumnHeader,
        headerComponentParams: {
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js and 1 other location - About 1 day to fix
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 366..397

              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 213.

              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 (const kiMet of kiMets) {
      colDefs.push({
        headerName: "K_I " + kiMet + " value",
        headerComponentFramework: HtmlColumnHeader,
        headerComponentParams: {
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js and 1 other location - About 1 day to fix
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 323..354

              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 213.

              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 5 locations. Consider refactoring.
              Open

                  colDefs.push({
      headerName: "Taxonomic similarity",
      headerComponentFramework: HtmlColumnHeader,
      headerComponentParams: {
        name: (
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.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/RnaHalfLifeDataTable.js on lines 277..306
              src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js on lines 149..178

              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 2 locations. Consider refactoring.
              Open

                static getKmValues(parameters) {
    const kms = {};
    for (const parameter of parameters) {
      if (parameter.type === 27 || parameter.sbo_type === 27) {
        if (parameter.value != null) {
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js and 1 other location - About 6 hrs to fix
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 138..156

              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 167.

              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

                static getKiValues(parameters) {
    const kis = {};
    for (const parameter of parameters) {
      if (parameter.type === 261 || parameter.sbo_type === 261) {
        if (parameter.value != null) {
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js and 1 other location - About 6 hrs to fix
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 118..136

              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 167.

              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 (const kiMet of kiMets) {
      sideBar["toolPanels"].push({
        id: "stats-ki-" + kiMet,
        labelDefault: (
          <span>
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js and 1 other location - About 3 hrs to fix
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 217..232

              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 103.

              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 (const kmMet of kmMets) {
      sideBar["toolPanels"].push({
        id: "stats-km-" + kmMet,
        labelDefault: (
          <span>
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js and 1 other location - About 3 hrs to fix
              src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.js on lines 244..259

              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 103.

              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

                  colDefs.push({
      headerName: "Organism",
      field: "organism",
      filter: "textFilter",
      cellRenderer: function (params) {
              Severity: Major
              Found in src/scenes/BiochemicalEntityDetails/Reaction/RateConstantsDataTable.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/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

              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

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