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src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js

Summary

Maintainability
F
5 days
Test Coverage
C
75%

Function formatData has a Cognitive Complexity of 81 (exceeds 5 allowed). Consider refactoring.
Open

  static formatData(query, organism, rawData) {
    const formattedData = [];
    for (const metabolite of rawData) {
      if ("concentrations" in metabolite && metabolite.concentrations) {
        for (const metConc of metabolite["concentrations"]) {
Severity: Minor
Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js - About 1 day 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 169 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [
      {
        headerName: "Concentration",
        field: "value",
Severity: Major
Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js - About 6 hrs to fix

    File ConcentrationDataTable.js has 385 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 Tooltip from "@material-ui/core/Tooltip";
    Severity: Minor
    Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.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 metabolite of rawData) {
      if ("concentrations" in metabolite && metabolite.concentrations) {
        for (const metConc of metabolite["concentrations"]) {
      Severity: Major
      Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js - About 4 hrs to fix

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

          static getColDefs(query, organism, formattedData, taxonomicRanks) {
    const colDefs = [
      {
        headerName: "Concentration",
        field: "value",
        Severity: Minor
        Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.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 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/Metabolite/ConcentrationDataTable.js - About 1 hr to fix

          Avoid deeply nested control flow statements.
          Open

                      if (metConc.reference.namespace === "doi") {
              conc.source = {
                id: "DOI: " + metConc.reference.id,
                url: "https://dx.doi.org/" + metConc.reference.id,
              };
          Severity: Major
          Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js - About 45 mins to fix

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

              static getSideBarDef() {
    return {
      toolPanels: [
        {
          id: "columns",
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 2 other locations - About 4 hrs to fix
            src/scenes/BiochemicalEntityDetails/Gene/ProteinAbundanceDataTable.js on lines 128..160
            src/scenes/BiochemicalEntityDetails/Gene/RnaHalfLifeDataTable.js on lines 184..216

            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/Metabolite/ConcentrationDataTable.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/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

                      if (conc.growthPhase && conc.growthPhase.indexOf(" phase") >= 0) {
            conc.growthPhase = conc.growthPhase.split(" phase")[0];
          }
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 1 other location - About 1 hr to fix
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 112..114

            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 58.

            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

                      if (conc.growthPhase && conc.growthPhase.indexOf(" Phase") >= 0) {
            conc.growthPhase = conc.growthPhase.split(" Phase")[0];
          }
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 1 other location - About 1 hr to fix
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 109..111

            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 58.

            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: "Concentration",
        field: "value",
        cellRenderer: "numericCellRenderer",
        type: "numericColumn",
            Severity: Minor
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 1 other location - About 50 mins to fix
            src/scenes/BiochemicalEntityDetails/Gene/RnaModificationDataTable.js on lines 94..104

            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

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

                        if (metConc.reference.namespace === "doi") {
              conc.source = {
                id: "DOI: " + metConc.reference.id,
                url: "https://dx.doi.org/" + metConc.reference.id,
              };
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 3 other locations - About 45 mins to fix
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 121..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 126..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 131..145

            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 4 locations. Consider refactoring.
            Open

                        } else if (metConc.reference.namespace === "ecmdb") {
              conc.source = {
                id: "ECMDB: " + metConc.reference.id,
                url: "http://ecmdb.ca/compounds/" + metConc.reference.id,
              };
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 3 other locations - About 45 mins to fix
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 116..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 126..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 131..145

            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 4 locations. Consider refactoring.
            Open

                        } else if (
              metConc.reference.namespace === "pubmed" &&
              metConc.reference.id
            ) {
              conc.source = {
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 3 other locations - About 45 mins to fix
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 116..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 121..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 126..145

            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 4 locations. Consider refactoring.
            Open

                        } else if (metConc.reference.namespace === "ymdb") {
              conc.source = {
                id: "YMDB: " + metConc.reference.id,
                url: "http://www.ymdb.ca/compounds/" + metConc.reference.id,
              };
            Severity: Major
            Found in src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js and 3 other locations - About 45 mins to fix
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 116..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 121..145
            src/scenes/BiochemicalEntityDetails/Metabolite/ConcentrationDataTable.js on lines 131..145

            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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