SiLeBAT/FSK-Lab

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Method createPanel has 88 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    @Override
    public JComponent createPanel(String assignments) {
        JPanel panel = new JPanel();
        JPanel topPanel = new JPanel();

Method runSnippet has 88 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  public final void runSnippet(final FskPortObject fskObj, final FskSimulation simulation,
      final ExecutionContext exec, NodeLogger logger, File imageFile,
      List<JoinRelationAdvanced> joinRelationList, String suffix) throws Exception {

    // Sets up working directory with resource files. This directory needs to be deleted.

Method updateMetaData has 88 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private static void updateMetaData(List<KnimeTuple> tuples, Map<KnimeTuple, List<KnimeTuple>> tupleCombinations) {
        Map<Integer, Set<String>> organisms = new LinkedHashMap<>();
        Map<Integer, Set<String>> matrices = new LinkedHashMap<>();
        Map<Integer, Set<String>> organismDetails = new LinkedHashMap<>();
        Map<Integer, Set<String>> matrixDetails = new LinkedHashMap<>();

Function token has 88 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    token: function (stream, state) {
      if (stream.sol()) {
        state.lineNumber++;
        state.inKeywordLine = false;
        if (state.inMultilineTable) {
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/codemirror-5.49.2/mode/gherkin/gherkin.js - About 3 hrs to fix

Function set has 88 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    set: function(models, options) {
      if (models == null) return;

      options = _.extend({}, setOptions, options);
      if (options.parse && !this._isModel(models)) {

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

  private JPanel createScriptPanel() {

    DefaultMutableTreeNode modelNode = new DefaultMutableTreeNode("Model scripts");
    buildNode(modelNode, this, 0);

de.bund.bfr.knime.fsklab.nodes/src/de/bund/bfr/knime/fsklab/v2_0/CombinedFskPortObject.java on lines 714..751

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 221.

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

  private JPanel createScriptPanel() {

    DefaultMutableTreeNode modelNode = new DefaultMutableTreeNode("Model scripts");
    buildNode(modelNode, this, 0);

de.bund.bfr.knime.fsklab.deprecatednodes/src-1_9_0/de/bund/bfr/knime/fsklab/v1_9/CombinedFskPortObject.java on lines 713..750

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 221.

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

FSKEditorJSConfig has 29 methods (exceeds 20 allowed). Consider refactoring.
Open

class FSKEditorJSConfig {

  private static final ObjectMapper MAPPER = FskPlugin.getDefault().MAPPER104;

  private static final String METADATA = "ModelMetaData";

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

  function updateParameterValues(simulationIndex) {

    // Disable parameter inputs for the default simulation.
    const isDisabled = simulationIndex == 0;
de.bund.bfr.knime.fsklab.deprecatednodes/js-src/de/bund/bfr/knime/fsklab/v1.9/simulator/jssimulator.js on lines 209..219

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 105.

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

  function updateParameterValues(simulationIndex) {

    // Disable parameter inputs for the default simulation.
    const isDisabled = simulationIndex == 0;
de.bund.bfr.knime.fsklab.deprecatednodes/js-src/de/bund/bfr/knime/fsklab/1.7.2/simulator/jssimulator.js on lines 196..206

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 105.

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

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

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

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

Refactorings

Further Reading

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

        if(joinerModelsData.thirdModel && joinerModelsData.thirdModel[0]){
            joinerModelsData.thirdModel[0] = fixModelMetadata(joinerModelsData.thirdModel[0]);
            joinerModelsData.thirdModelName = joinerModelsData.thirdModelName?joinerModelsData.thirdModelName.trim():joinerModelsData.thirdModelName;
            joinerModelsData.thirdModelName = escapeHtmlChars(joinerModelsData.thirdModelName);
        }
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 275..280
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 281..286
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 292..296

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 105.

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

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

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

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

Refactorings

Further Reading

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

        if(joinerModelsData.fourthModel && joinerModelsData.fourthModel[0]){
            joinerModelsData.fourthModel[0] = fixModelMetadata(joinerModelsData.fourthModel[0]);
            joinerModelsData.fourthModelName = joinerModelsData.fourthModelName?joinerModelsData.fourthModelName.trim():joinerModelsData.fourthModelName;
            joinerModelsData.fourthModelName = escapeHtmlChars(joinerModelsData.fourthModelName);
        }
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 275..280
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 281..286
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 287..291

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 105.

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 (!isValid) {
                O.input.$validationContainer.text(`required`);
                O.input.parents( '.form-group' ).addClass( 'has-error' );
                O.input.addClass( 'is-invalid' );
                O.input.$validationContainer.css("display", "block") ;
de.bund.bfr.knime.js/src/js/app/app.editable.mt.SelectForm.js on lines 161..169

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 105.

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

        onblurHandler(){
            let O = this;
            let closestForm = O.input.closest( "form" );
            let attr = closestForm.attr('no-immidiate-submit' );
            let can_emit_Event = typeof attr === typeof undefined || attr === false;
de.bund.bfr.knime.js/src/js/app/app.editable.mt.SelectForm.js on lines 132..141

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 105.

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

        onblurHandler(){
            let O = this;
            let closestForm = O.input.closest( "form" );
            let attr = closestForm.attr('no-immidiate-submit' );
            let can_emit_Event = typeof attr === typeof undefined || attr === false;
de.bund.bfr.knime.js/src/js/app/app.editable.mt.TextareaForm.js on lines 99..108

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 105.

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 (!isValid) {
                O.input.$validationContainer.text(`required`);
                O.input.parents( '.form-group' ).addClass( 'has-error' );
                O.input.addClass( 'is-invalid' );
                O.input.$validationContainer.css("display", "block") ;
de.bund.bfr.knime.js/src/js/app/app.editable.mt.TextareaForm.js on lines 128..135

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 105.

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

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

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

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

Refactorings

Further Reading

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

        if(joinerModelsData.firstModel && joinerModelsData.firstModel[0]){
            joinerModelsData.firstModel[0] = fixModelMetadata(joinerModelsData.firstModel[0]);
            joinerModelsData.firstModelName = joinerModelsData.firstModelName?joinerModelsData.firstModelName.trim():joinerModelsData.firstModelName;
            joinerModelsData.firstModelName = escapeHtmlChars(joinerModelsData.firstModelName);
            
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 281..286
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 287..291
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 292..296

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 105.

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

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

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

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

Refactorings

Further Reading

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

        if(joinerModelsData.secondModel && joinerModelsData.secondModel[0]){
            joinerModelsData.secondModel[0] = fixModelMetadata(joinerModelsData.secondModel[0]);
            joinerModelsData.secondModelName = joinerModelsData.secondModelName?joinerModelsData.secondModelName.trim():joinerModelsData.secondModelName;
            joinerModelsData.secondModelName = escapeHtmlChars(joinerModelsData.secondModelName);
            
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 275..280
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 287..291
de.bund.bfr.knime.fsklab.nodes/js-src/de/bund/bfr/knime/fsklab/v2.0/joiner/joiner.js on lines 292..296

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 105.

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

                case "from":
                    this.coords.p_gap = this.toFixed(this.coords.p_pointer - this.coords.p_from_fake);
                    this.$cache.s_from.addClass("state_hover");
                    this.$cache.s_from.addClass("type_last");
                    this.$cache.s_to.removeClass("type_last");
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js and 1 other location - About 3 hrs to fix
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 609..614

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 105.

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

                case "to":
                    this.coords.p_gap = this.toFixed(this.coords.p_pointer - this.coords.p_to_fake);
                    this.$cache.s_to.addClass("state_hover");
                    this.$cache.s_to.addClass("type_last");
                    this.$cache.s_from.removeClass("type_last");
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js and 1 other location - About 3 hrs to fix
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 603..608

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 105.

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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