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src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js

Summary

Maintainability
D
3 days
Test Coverage
F
23%

Function getColDefs has 102 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [
      {
        headerName: "Modifications",
        field: "numModifications",
Severity: Major
Found in src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js - About 4 hrs to fix

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

      formatData(query, organism, rawData) {
    const formattedData = [];
    for (const rawDatum of rawData) {
      if ("modifications" in rawDatum && rawDatum.modifications) {
        for (const measurement of rawDatum.modifications) {
    Severity: Minor
    Found in src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.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 formatData has 29 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

      formatData(query, organism, rawData) {
    const formattedData = [];
    for (const rawDatum of rawData) {
      if ("modifications" in rawDatum && rawDatum.modifications) {
        for (const measurement of rawDatum.modifications) {
    Severity: Minor
    Found in src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js - About 1 hr to fix

      Function getColDefs has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
      Open

        static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [
      {
        headerName: "Modifications",
        field: "numModifications",
      Severity: Minor
      Found in src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.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

      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/RnaModificationDataTable.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/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

        render() {
    return (
      <DataTable
        id="rna-modifications"
        title="RNA modifications"
      Severity: Major
      Found in src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js and 2 other locations - About 4 hrs to fix
      src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 294..310
      src/scenes/BiochemicalEntityDetails/Gene/ProteinModificationDataTable.js on lines 305..321

      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 128.

      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

        static getSideBarDef() {
    return {
      toolPanels: [
        {
          id: "columns",
      Severity: Major
      Found in src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js and 1 other location - About 2 hrs to fix
      src/scenes/BiochemicalEntityDetails/Gene/ProteinModificationDataTable.js on lines 141..163

      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 87.

      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/RnaModificationDataTable.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/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 2 locations. Consider refactoring.
      Open

            {
        headerName: "Modifications",
        field: "numModifications",
        cellRenderer: "numericCellRenderer",
        type: "numericColumn",
      Severity: Minor
      Found in src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js and 1 other location - About 50 mins to fix
      src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 192..202

      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 51.

      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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