SiLeBAT/FSK-Lab

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

                            if (points != null) {
                                for (int i = 0; i < points[0].length; i++) {
                                    if (isValid(points[0][i])) {
                                        usedMinX = Math.min(usedMinX,
                                                points[0][i]);
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartCreator.java on lines 244..251

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 96.

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

                result.add(new String[]{
                        "SELECT " + idConf + " FROM " + DBKernel.delimitL(tablename) +
                        " WHERE " + DBKernel.delimitL("Inkubationszeit") + " IS NOT NULL AND " + DBKernel.delimitL("IZ_Einheit") + " IS NULL" +
                                " OR " + DBKernel.delimitL("Inkubationszeit") + " IS NULL AND " + DBKernel.delimitL("IZ_Einheit") + " IS NOT NULL",
                        GuiMessages.getString("Bei Dateneingabe in \"Inkubationszeit\" muss Dateneingabe in \"IZ_Einheit\" erfolgen; " +
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java and 2 other locations - About 1 hr to fix
org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java on lines 262..268
org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java on lines 269..275

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 96.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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

    static {
        CLASSIF = new HashMap<>();

        CLASSIF.put(Parameter.Classification.input, de.bund.bfr.metadata.swagger.Parameter.ClassificationEnum.INPUT);
        CLASSIF.put(Parameter.Classification.output, de.bund.bfr.metadata.swagger.Parameter.ClassificationEnum.OUTPUT);
de.bund.bfr.knime.fsklab.metadata.model/src/metadata/SwaggerUtil.java on lines 520..529

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 96.

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 (points != null) {
                            for (int i = 0; i < points[0].length; i++) {
                                if (isValid(points[0][i])) {
                                    usedMinX = Math.min(usedMinX, points[0][i]);
                                    usedMaxX = Math.max(usedMaxX, points[0][i]);
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartCreator.java on lines 228..237

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 96.

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

                result.add(new String[]{
                        "SELECT " + idConf + " FROM " + DBKernel.delimitL(tablename) +
                        " WHERE " + DBKernel.delimitL("Symptomdauer") + " IS NOT NULL AND " + DBKernel.delimitL("SD_Einheit") + " IS NULL" +
                                " OR " + DBKernel.delimitL("Symptomdauer") + " IS NULL AND " + DBKernel.delimitL("SD_Einheit") + " IS NOT NULL",
                        GuiMessages.getString("Bei Dateneingabe in \"Symptomdauer\" muss Dateneingabe in \"SD_Einheit\" erfolgen; " +
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java and 2 other locations - About 1 hr to fix
org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java on lines 255..261
org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java on lines 269..275

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 96.

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

                result.add(new String[]{
                        "SELECT " + idConf + " FROM " + DBKernel.delimitL(tablename) +
                        " WHERE " + DBKernel.delimitL("Infektionsdosis") + " IS NOT NULL AND " + DBKernel.delimitL("ID_Einheit") + " IS NULL" +
                                " OR " + DBKernel.delimitL("Infektionsdosis") + " IS NULL AND " + DBKernel.delimitL("ID_Einheit") + " IS NOT NULL",
                        GuiMessages.getString("Bei Dateneingabe in \"Infektionsdosis\" muss Dateneingabe in \"ID_Einheit\" erfolgen; " +
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java and 2 other locations - About 1 hr to fix
org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java on lines 255..261
org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.java on lines 262..268

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 96.

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) 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 the Free Software Foundation, either version 3 of the
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/sbmlreader/SBMLReaderNodeFactory.java on lines 1..65

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 96.

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) 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 the Free Software Foundation, either version 3 of the
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/numl/NuMLReaderNodeFactory.java on lines 1..76

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 96.

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 (String id : idsToPaint) {
            Plotable plotable = plotables.get(id);

            if (plotable != null && plotable.getType() == Plotable.BOTH) {
                try {
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartCreator.java on lines 369..382

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 96.

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 (String id : idsToPaint) {
            Plotable plotable = plotables.get(id);

            if (plotable != null && plotable.getType() == Plotable.FUNCTION) {
                try {
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/ChartCreator.java on lines 403..416

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 96.

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 saveSettings has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    public void saveSettings(Config cM) {
        int[] iarr;
        String[] narr;
        if (forMatrices) {
            iarr = new int[lmat.size()];

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 getNArr has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    public String[] getNArr() {
        String[] narr;
        if (forMatrices) {
            narr = new String[lmat.size()];
            for (int i=0;i<lmat.size();i++) {

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 getIArr has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    public int[] getIArr() {
        int[] iarr;
        if (forMatrices) {
            iarr = new int[lmat.size()];
            for (int i=0;i<lmat.size();i++) {

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 setSetting has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    public void setSetting( final FoodProcessSetting fps ) {        
        int i;
        Double val;
        
        nameField.setText(fps.getProcessName());

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 getSetting has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    public AgentsSetting getSetting() throws InvalidSettingsException {        
        AgentsSetting as;

        as = new AgentsSetting();
        

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 calculateWeightedMean has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    private static Double calculateWeightedMean(Double sum, final Double newVal, final Double partVol, final Double totalVol,
            final String defaultValue) {
        // hier erstmal trivial ohne grosse Mischerei...
        if (defaultValue != null && !defaultValue.isEmpty()) {
            try{sum = Double.parseDouble(defaultValue);}catch(Exception e){}

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 setModelId has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    public static void setModelId(Model model, String id) {

        final String modelType = model.getModelType();
        if (modelType.equalsIgnoreCase("genericModel")) {
            ((GenericModel) model).getGeneralInformation().setIdentifier(id);

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 equals has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

  @Override
  public boolean equals(Object obj) {
    if (this == obj)
      return true;
    if (obj == null || getClass() != obj.getClass())

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 eIsSet has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    @Override
    public boolean eIsSet(int featureID) {
        switch (featureID) {
            case MetadataPackage.DIETARY_ASSESSMENT_METHOD__COLLECTION_TOOL:
                return COLLECTION_TOOL_EDEFAULT == null ? collectionTool != null : !COLLECTION_TOOL_EDEFAULT.equals(collectionTool);

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 execute has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.
Open

    @Override
    protected BufferedDataTable[] execute(final BufferedDataTable[] inData, final ExecutionContext exec)
            throws Exception {
        XLSReader xlsReader = new XLSReader();
        List<KnimeTuple> tuples = new ArrayList<>(xlsReader

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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