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File AddonC.java has 404 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
Severity: Minor
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/addons/AddonC.java - About 5 hrs to fix

File MetadataDocument.java has 404 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*
 ***************************************************************************************************
 * Copyright (c) 2017 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify it under the terms of the
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-1_0_2/de/bund/bfr/knime/fsklab/nodes/MetadataDocument.java - About 5 hrs to fix

Method execute has 142 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    @Override
    protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec) throws Exception {

        ResultSet result;
        Bfrdb db;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/modelcatalogreader/ModelCatalogReaderNodeModel.java - About 5 hrs to fix

Method insertCondition has 142 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private Integer insertCondition(Integer condId, final Integer tempId, final Integer phId, final Integer awId, final String agentName, final String matrixName,
            final String combaseId, Integer matrixId, Integer agentId, final String agentDetail, final String matrixDetail, PmmXmlDoc misc, final String comment, final Integer qs, final Boolean checked, PmmXmlDoc lit,
            PmmTimeSeries ts) {

        String warnings = "";
Severity: Major
Found in de.bund.bfr.knime.pmm.bfrdbiface.lib/src/de/bund/bfr/knime/pmm/bfrdbiface/lib/Bfrdb.java - About 5 hrs to fix

File GoogleSheetImporterTest.java has 403 lines of code (exceeds 250 allowed). Consider refactoring.
Open

package metadata;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model.tests/src/metadata/GoogleSheetImporterTest.java - About 5 hrs to fix

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

  var colorKeywords_ = [
    "aliceblue", "antiquewhite", "aqua", "aquamarine", "azure", "beige",
    "bisque", "black", "blanchedalmond", "blue", "blueviolet", "brown",
    "burlywood", "cadetblue", "chartreuse", "chocolate", "coral", "cornflowerblue",
    "cornsilk", "crimson", "cyan", "darkblue", "darkcyan", "darkgoldenrod",
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/css/css.js and 1 other location - About 5 hrs to fix
de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/stylus/stylus.js on lines 740..740

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 148.

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

    this.$selection.on(
      'keyup.search input.search',
      '.select2-search--inline',
      function (evt) {
        // IE will trigger the `input` event when a placeholder is used on a
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/select2.full.js and 1 other location - About 5 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-lib/select2/4_0_3/debug/js/select2.js on lines 1961..1987

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 148.

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

    this.$selection.on(
      'keyup.search input.search',
      '.select2-search--inline',
      function (evt) {
        // IE will trigger the `input` event when a placeholder is used on a
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-lib/select2/4_0_3/debug/js/select2.js and 1 other location - About 5 hrs to fix
de.bund.bfr.knime.js/src/js/lib/select2.full.js on lines 2177..2203

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 148.

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

  var colorKeywords_ = ["aliceblue","antiquewhite","aqua","aquamarine","azure","beige","bisque","black","blanchedalmond","blue","blueviolet","brown","burlywood","cadetblue","chartreuse","chocolate","coral","cornflowerblue","cornsilk","crimson","cyan","darkblue","darkcyan","darkgoldenrod","darkgray","darkgreen","darkkhaki","darkmagenta","darkolivegreen","darkorange","darkorchid","darkred","darksalmon","darkseagreen","darkslateblue","darkslategray","darkturquoise","darkviolet","deeppink","deepskyblue","dimgray","dodgerblue","firebrick","floralwhite","forestgreen","fuchsia","gainsboro","ghostwhite","gold","goldenrod","gray","grey","green","greenyellow","honeydew","hotpink","indianred","indigo","ivory","khaki","lavender","lavenderblush","lawngreen","lemonchiffon","lightblue","lightcoral","lightcyan","lightgoldenrodyellow","lightgray","lightgreen","lightpink","lightsalmon","lightseagreen","lightskyblue","lightslategray","lightsteelblue","lightyellow","lime","limegreen","linen","magenta","maroon","mediumaquamarine","mediumblue","mediumorchid","mediumpurple","mediumseagreen","mediumslateblue","mediumspringgreen","mediumturquoise","mediumvioletred","midnightblue","mintcream","mistyrose","moccasin","navajowhite","navy","oldlace","olive","olivedrab","orange","orangered","orchid","palegoldenrod","palegreen","paleturquoise","palevioletred","papayawhip","peachpuff","peru","pink","plum","powderblue","purple","rebeccapurple","red","rosybrown","royalblue","saddlebrown","salmon","sandybrown","seagreen","seashell","sienna","silver","skyblue","slateblue","slategray","snow","springgreen","steelblue","tan","teal","thistle","tomato","turquoise","violet","wheat","white","whitesmoke","yellow","yellowgreen"];
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/stylus/stylus.js and 1 other location - About 5 hrs to fix
de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/css/css.js on lines 563..590

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 148.

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

Method loadSettings has 141 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public void loadSettings(NodeSettingsRO settings) {
        try {
            selectedIDs = XmlConverter.xmlToObject(
                    settings.getString(CFG_SELECTEDIDS),
                    new ArrayList<String>());
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/SettingsHelper.java - About 5 hrs to fix

Method createChart has 141 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private JFreeChart createChart(DataTableSpec spec, List<DataRow> rowList, DataTable table,
            List<String> usedParameters, String xUnits, boolean equidistantProcesses, boolean plotLines, boolean plotPoints) {
        LinkedList<XYDataset> dataSets = new LinkedList<XYDataset>();
        LinkedList<XYDataset> equiDataSets = new LinkedList<XYDataset>();
        int timeIndex = spec.findColumnIndex(AttributeUtilities.TIME + " [s]");
Severity: Major
Found in de.bund.bfr.knime.foodprocess.view/src/de/bund/bfr/knime/foodprocess/view/MyChartCreator.java - About 5 hrs to fix

Function token has 141 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        token: function (stream, state) {
            if (state.indentStack == null && stream.sol()) {
                // update indentation, but only if indentStack is empty
                state.indentation = stream.indentation();
            }
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/scheme/scheme.js - About 5 hrs to fix

Method setValueAt has 140 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    @Override
    public void setValueAt(Object aValue, int rowIndex, int columnIndex) {

      if (columnIndex == 1) {
        String stringValue = (String) aValue;
Severity: Major
Found in de.bund.bfr.knime.fsklab.nodes.common/src/de/bund/bfr/knime/fsklab/nodes/common/ui/MetaDataPane2.java - About 5 hrs to fix

File toastr.js has 400 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*
 * Toastr
 * Copyright 2012-2015
 * Authors: John Papa, Hans Fjällemark, and Tim Ferrell.
 * All Rights Reserved.
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/js-lib/toastr/2_1_3/debug/js/toastr.js - About 5 hrs to fix

Function initToolbar has 140 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    BootstrapTable.prototype.initToolbar = function () {
        var that = this,
            html = [],
            timeoutId = 0,
            $keepOpen,
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-lib/bootstrap-table/1_11_1/debug/js/bootstrap-table.js - About 5 hrs to fix

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

    public static String getModelName(Model model) {
        String name;

        final String modelType = model.getModelType();
        if (modelType.equalsIgnoreCase("genericModel")) {
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java and 2 other locations - About 5 hrs to fix
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java on lines 567..600
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java on lines 706..739

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 346.

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

    public static List<Parameter> getParameter(Model model) {
        List<Parameter> parameters;

        final String modelType = model.getModelType();
        if (modelType.equalsIgnoreCase("genericModel")) {
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java and 2 other locations - About 5 hrs to fix
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java on lines 670..703
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java on lines 706..739

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 346.

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

    public static String getModelId(Model model) {
        String name;

        final String modelType = model.getModelType();
        if (modelType.equalsIgnoreCase("genericModel")) {
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java and 2 other locations - About 5 hrs to fix
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java on lines 567..600
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java on lines 670..703

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 346.

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

Method flush16le has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
Open

    public void flush16le() throws UnsupportedEncodingException, FileNotFoundException, IOException, PmmException {
        StringBuffer buf = new StringBuffer();
        for (PmmTimeSeries candidate : buffer) {
            String organism = "";
            String matrix = "";
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/combaseio/lib/CombaseWriter.java - 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

Method doRestore has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
Open

    public static boolean doRestore(final MyDBTable myDB, final File scriptFile, final boolean silent, boolean doReconnect) {
        boolean result = true;
        if (scriptFile != null && scriptFile.exists()) {
            if (!silent) {
                int returnVal = JOptionPane.showConfirmDialog(DBKernel.mainFrame,
Severity: Minor
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/BackupMyDBI.java - 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

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