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

      if (data.children && data.children.length > 0) {
        // Clone the data object if there are children
        // This is required as we modify the object to remove any non-matches
        var match = $.extend(true, {}, data);
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/select2.full.js and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-lib/select2/4_0_3/debug/js/select2.js on lines 4841..4865

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 185.

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

      if (data.children && data.children.length > 0) {
        // Clone the data object if there are children
        // This is required as we modify the object to remove any non-matches
        var match = $.extend(true, {}, data);
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 7 hrs to fix
de.bund.bfr.knime.js/src/js/lib/select2.full.js on lines 5139..5163

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 185.

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 (!o.axis || o.axis !== "x") {
                if (event.pageY - $(document).scrollTop() < o.scrollSensitivity) {
                    scrolled = $(document).scrollTop($(document).scrollTop() - o.scrollSpeed);
                } else if ($(window).height() - (event.pageY - $(document).scrollTop()) < o.scrollSensitivity) {
                    scrolled = $(document).scrollTop($(document).scrollTop() + o.scrollSpeed);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js on lines 2519..2525

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 185.

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 ( overLeft < 0 ) {
                newOverRight = position.left + myOffset + atOffset + offset + data.collisionWidth - outerWidth - withinOffset;
                if ( newOverRight < 0 || newOverRight < abs( overLeft ) ) {
                    position.left += myOffset + atOffset + offset;
                }
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js on lines 1483..1493

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 185.

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 ( overTop < 0 ) {
                newOverBottom = position.top + myOffset + atOffset + offset + data.collisionHeight - outerHeight - withinOffset;
                if ( newOverBottom < 0 || newOverBottom < abs( overTop ) ) {
                    position.top += myOffset + atOffset + offset;
                }
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js on lines 1449..1459

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 185.

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 (!o.axis || o.axis !== "y") {
                if (event.pageX - $(document).scrollLeft() < o.scrollSensitivity) {
                    scrolled = $(document).scrollLeft($(document).scrollLeft() - o.scrollSpeed);
                } else if ($(window).width() - (event.pageX - $(document).scrollLeft()) < o.scrollSensitivity) {
                    scrolled = $(document).scrollLeft($(document).scrollLeft() + o.scrollSpeed);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.pmm.nodes/js-src/de/bund/bfr/knime/pmm/js/modelplotter/jquery-ui.js on lines 2511..2517

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 185.

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 DoseResponseSheetImporter.java has 479 lines of code (exceeds 250 allowed). Consider refactoring.
Open

package metadata.swagger;

import java.math.BigDecimal;
import java.util.HashMap;
Severity: Minor
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/swagger/DoseResponseSheetImporter.java - About 7 hrs to fix

File PmmTimeSeries.java has 479 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.pmm.common/src/de/bund/bfr/knime/pmm/common/PmmTimeSeries.java - About 7 hrs to fix

Method look4ParentNode has a Cognitive Complexity of 48 (exceeds 5 allowed). Consider refactoring.
Open

    private DefaultMutableTreeNode look4ParentNode(final LinkedHashMap<String, DefaultMutableTreeNode> myCodes, final String code, final int[] cutSystem) {
        DefaultMutableTreeNode result = null;
        String key;
        if (cutSystem == null) {
            for (int i=code.length()-1;i>=0;i--) {
Severity: Minor
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/gui/dbtree/MyDBTreeModel.java - About 7 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 getFunctionSamplePointsErrors has a Cognitive Complexity of 48 (exceeds 5 allowed). Consider refactoring.
Open

    public double[][] getFunctionSamplePointsErrors(String paramX,
            String paramY, String unitX, String unitY, String transformX,
            String transformY, double minX, double maxX, double minY,
            double maxY, Map<String, Integer> choice) throws ConvertException {
        if (function == null) {
Severity: Minor
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/Plotable.java - About 7 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

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

                                else if(c=="w"){
                                        c=look(stream, 1);
                                        if(c=="("){
                                                eatSuffix(stream, 2);
                                                return tokenChain(stream,state,[")"],"bracket");}
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/perl/perl.js and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/perl/perl.js on lines 555..620

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 183.

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

                                else if(c=="q"){
                                        c=look(stream, 1);
                                        if(c=="("){
                                                eatSuffix(stream, 2);
                                                return tokenChain(stream,state,[")"],"string");}
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/perl/perl.js and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/perl/perl.js on lines 572..620

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 183.

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

Study has 52 methods (exceeds 20 allowed). Consider refactoring.
Open

@javax.annotation.Generated(value = "io.swagger.codegen.languages.JavaClientCodegen", date = "2019-07-02T16:22:48.194+02:00")
public class Study {
  @SerializedName("identifier")
  private String identifier = null;
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/gen/de/bund/bfr/metadata/swagger/Study.java - About 7 hrs to fix

SettingsHelper has 52 methods (exceeds 20 allowed). Consider refactoring.
Open

public class SettingsHelper {

    protected static final String CFG_SELECTEDIDS = "SelectedIDs";
    protected static final String CFG_COLORS = "Colors";
    protected static final String CFG_SHAPES = "Shapes";
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/primarymodelviewandselect/SettingsHelper.java - About 7 hrs to fix

EmReaderUi has 52 methods (exceeds 20 allowed). Consider refactoring.
Open

public class EmReaderUi extends JPanel {
    /**
     * 
     */
    private static final long serialVersionUID = -7838365860944621209L;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/estimatedmodelreader/EmReaderUi.java - About 7 hrs to fix

Method initComponents has 183 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private void initComponents() {
        // JFormDesigner - Component initialization - DO NOT MODIFY  //GEN-BEGIN:initComponents
        panel1 = new JPanel();
        label1 = new JLabel();
        agensIDField = new JTextField();
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/timeseriesreader/MdReaderUi.java - About 7 hrs to fix

Method doImport has 183 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        public String doImport(final String filename, final JProgressBar progress, final boolean showResults) {
            errorMessage = "";
          Runnable runnable = new Runnable() {
          public void run() {
            try {
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/imports/custom/MyProzessXMLImporter.java - About 7 hrs to fix

Similar blocks of code found in 2 locations. 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
 * GNU General Public License as published by the Free Software Foundation, either version 3 of the
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/pmfwriter/PMFWriterNodeSettings.java and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/pmfwriter/fsk/NodeSettings.java on lines 1..90

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 449.

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

/*******************************************************************************
 * 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
 * GNU General Public License as published by the Free Software Foundation, either version 3 of the
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/pmfwriter/fsk/NodeSettings.java and 1 other location - About 7 hrs to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/pmfwriter/PMFWriterNodeSettings.java on lines 1..96

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 449.

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 13 locations. Consider refactoring.
Open

    public Reference retrieveReference(Row row) {

        // Check mandatory properties and throw exception if missing
        if (row.getCell(L).getCellType() != Cell.CELL_TYPE_STRING) {
            throw new IllegalArgumentException("Missing Is reference description?");
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerConsumptionSheetImporter.java and 12 other locations - About 7 hrs to fix
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerDataModelSheetImporter.java on lines 510..577
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerDoseResponseSheetImporter.java on lines 462..529
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerExposureSheetImporter.java on lines 538..605
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerGenericSheetImporter.java on lines 537..604
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerHealthModelSheetImporter.java on lines 461..528
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerOtherModelSheetImporter.java on lines 530..597
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerPredictiveModelSheetImporter.java on lines 523..590
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerProcessModelSheetImporter.java on lines 528..595
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerQraModelSheetImporter.java on lines 543..610
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerRiskModelSheetImporter.java on lines 540..607
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerSheetImporter.java on lines 245..312
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerToxicologicalSheetImporter.java on lines 461..528

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 448.

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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