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

  private static KnimeTuple mergeTuples(final KnimeTuple dataTuple, final KnimeTuple m1Tuple,
      final KnimeTuple m2Tuple) {

    final KnimeTuple tuple = new KnimeTuple(SchemaFactory.createM12DataSchema());
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/sbmlreader/SBMLReaderNodeModel.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 201..248

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 580.

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

  public static KnimeTuple mergeTuples(KnimeTuple dataTuple, KnimeTuple m1Tuple, KnimeTuple m2Tuple) {

    KnimeTuple tuple = new KnimeTuple(SchemaFactory.createM12DataSchema());

    tuple.setValue(TimeSeriesSchema.ATT_CONDID, dataTuple.getInt(TimeSeriesSchema.ATT_CONDID));
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/sbmlreader/SBMLReaderNodeModel.java on lines 245..293

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 580.

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

  Results.prototype.append = function (data) {
    this.hideLoading();

    var $options = [];
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/select2.full.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/js-lib/select2/4_0_3/debug/js/select2.js on lines 834..860

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 225.

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

  Results.prototype.append = function (data) {
    this.hideLoading();

    var $options = [];
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 1 day to fix
de.bund.bfr.knime.js/src/js/lib/select2.full.js on lines 912..938

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 225.

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

File WriterNodeModel.java has 562 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: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/writer/WriterNodeModel.java - About 1 day to fix

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

  Observable.prototype.trigger = function (event) {
    var slice = Array.prototype.slice;
    var params = slice.call(arguments, 1);

    this.listeners = this.listeners || {};
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 1 day to fix
de.bund.bfr.knime.js/src/js/lib/select2.full.js on lines 625..651

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 224.

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

  Observable.prototype.trigger = function (event) {
    var slice = Array.prototype.slice;
    var params = slice.call(arguments, 1);

    this.listeners = this.listeners || {};
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/select2.full.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/js-lib/select2/4_0_3/debug/js/select2.js on lines 621..647

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 224.

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

Function compile has 236 lines of code (exceeds 25 allowed). Consider refactoring.
Open

function compile(schema, root, localRefs, baseId) {
  /* jshint validthis: true, evil: true */
  /* eslint no-shadow: 0 */
  var self = this
    , opts = this._opts
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/js-src/de/bund/bfr/knime/fsklab/nodes/joiner/emfbundle/ajv.min.js - About 1 day to fix

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

    @Override
    @SuppressWarnings("unchecked")
    public FskPortObject loadPortObject(PortObjectZipInputStream in, PortObjectSpec spec,
        ExecutionMonitor exec) throws IOException, CanceledExecutionException {
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/FskPortObject.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.fsklab.nodes/src/de/bund/bfr/knime/fsklab/v2_0/FskPortObject.java on lines 381..467

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 576.

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

    @Override
    @SuppressWarnings("unchecked")
    public FskPortObject loadPortObject(PortObjectZipInputStream in, PortObjectSpec spec,
        ExecutionMonitor exec) throws IOException, CanceledExecutionException {
Severity: Major
Found in de.bund.bfr.knime.fsklab.nodes/src/de/bund/bfr/knime/fsklab/v2_0/FskPortObject.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/FskPortObject.java on lines 385..471

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 576.

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 computeSecondary has a Cognitive Complexity of 60 (exceeds 5 allowed). Consider refactoring.
Open

    public static List<KnimeTuple> computeSecondary(List<KnimeTuple> tuples) {
        Set<String> idSet = new LinkedHashSet<>();
        Map<String, String> formulaMap = new LinkedHashMap<>();
        Map<String, PmmXmlDoc> paramMap = new LinkedHashMap<>();
        Map<String, String> depVarMap = new LinkedHashMap<>();
Severity: Minor
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/QualityMeasurementComputation.java - 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

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

            for(index in paramsPrim){
                indep = paramsPrim[index];
            
                // convention #1: do not exchange a secondary formula dependent
                // convention #2: if a parameter has no mininmum or maximum but a value, it shall not be dynamic
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/pmm-plotter.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/pmm-plotter.js on lines 715..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 223.

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(index in paramsPrim){
                    indep = paramsPrim[index];
                    // convention #1: do not exchange a secondary formula dependent
                    // convention #2: if a parameter has no mininmum or maximum but a value, it shall not be dynamic
                    // convention #3: a parameter with "isStart"-Flag shall have a fixed value
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/pmm-plotter.js and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/pmm-plotter.js on lines 850..877

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 223.

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

    private class TimeStepDialog extends JDialog implements ActionListener,
            TextListener {

        private static final long serialVersionUID = 1L;
Severity: Major
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartSamplePanel.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/timeseriescreator/TimeSeriesCreatorNodeDialog.java on lines 1034..1133

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 571.

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

    private class TimeStepDialog extends JDialog implements ActionListener, TextListener {

        private static final long serialVersionUID = 1L;

        private boolean approved;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/timeseriescreator/TimeSeriesCreatorNodeDialog.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartSamplePanel.java on lines 285..388

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 571.

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

File ProcessParametersImpl.java has 556 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*
 * XML Type:  ProcessParameters
 * Namespace: http://www.bfr.bund.de/PCML-1_0
 * Java type: de.bund.bfr.pcml10.ProcessParameters
 *
Severity: Major
Found in de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/impl/ProcessParametersImpl.java - About 1 day to fix

SettingsHelper has 64 methods (exceeds 20 allowed). Consider refactoring.
Open

public class SettingsHelper {

    private static final String CFG_SELECTEDIDS = "SelectedIDs";
    private static final String CFG_PARAMXVALUES = "ParamXValues";
    private static final String CFG_TIMEVALUES = "TimeValues";
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/SettingsHelper.java - About 1 day to fix

MyDBTable has 64 methods (exceeds 20 allowed). Consider refactoring.
Open

public class MyDBTable extends DBTable implements RowSorterListener, KeyListener, ListSelectionListener, MouseListener  {
    
    /**
     * 
     */
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/gui/dbtable/MyDBTable.java - About 1 day to fix

Method execute has 233 lines of code (exceeds 25 allowed). Consider refactoring.
Open

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

        db = null;
        /*
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/estimatedmodelwriter/EstimatedModelWriterNodeModel.java - About 1 day to fix

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

package de.bund.bfr.knime.pmm.fskx;

import java.io.Serializable;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/src/de/bund/bfr/knime/pmm/fskx/FskMetaData.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.fsklab.metadata.model/src/de/bund/bfr/knime/fsklab/nodes/FskMetaData.java on lines 1..157

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 568.

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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