Sign upLogin

SiLeBAT/FSK-Lab

View on GitHub
Star

Showing 14,752 of 14,752 total issues

Similar blocks of code found in 5 locations. Consider refactoring.
Open

/*
 * An XML document type.
 * Localname: ProcessChain
 * Namespace: http://www.bfr.bund.de/PCML-1_0
 * Java type: de.bund.bfr.pcml10.ProcessChainDocument
Severity: Major
Found in de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/impl/ProcessChainDocumentImpl.java and 4 other locations - About 1 day to fix
de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/impl/AgentRecipeDocumentImpl.java on lines 1..293
de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/impl/InlineTableDocumentImpl.java on lines 1..293
de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/impl/MatrixRecipeDocumentImpl.java on lines 1..293
de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/impl/ProcessChainDataDocumentImpl.java on lines 1..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 757.

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 doLayout has a Cognitive Complexity of 78 (exceeds 5 allowed). Consider refactoring.
Open

    public void doLayout(final Collection<NodeContainer> nodes) {

        int X_STRETCH = 100;
        int Y_STRETCH = 120;
Severity: Minor
Found in de.bund.bfr.knime.foodprocess/src/de/bund/bfr/knime/foodprocess/ui/LayoutManager.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

Method loadFSKPortObject has a Cognitive Complexity of 78 (exceeds 5 allowed). Consider refactoring.
Open

    @SuppressWarnings("unchecked")
    public FskPortObject loadFSKPortObject(PortObjectZipInputStream in, PortObjectSpec spec,
        ExecutionMonitor exec) throws IOException, CanceledExecutionException {

      String modelScript = "";
Severity: Minor
Found in de.bund.bfr.knime.fsklab.nodes/src/de/bund/bfr/knime/fsklab/v2_0/CombinedFskPortObject.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

File MetadataPackage.java has 681 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/**
 */
package metadata;

import org.eclipse.emf.ecore.EAttribute;
Severity: Major
Found in de.bund.bfr.knime.fsklab.metadata.model/gen/metadata/MetadataPackage.java - About 1 day to fix

Method run has a Cognitive Complexity of 77 (exceeds 5 allowed). Consider refactoring.
Open

          public void run() {
            try {
                MyLogger.handleMessage("Importing PEX-File: " + filename);
                  if (progress != null) {
                      progress.setVisible(true);
Severity: Minor
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/imports/custom/MyProzessXMLImporter.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 3 locations. Consider refactoring.
Open

                if (o.to_shadow && (is_to_min || is_to_max)) {
                    to_min = this.convertToPercent(is_to_min ? o.to_min : o.min);
                    to_max = this.convertToPercent(is_to_max ? o.to_max : o.max) - to_min;
                    to_min = this.toFixed(to_min - (this.coords.p_handle / 100 * to_min));
                    to_max = this.toFixed(to_max - (this.coords.p_handle / 100 * to_max));
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js and 2 other locations - About 1 day to fix
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 1600..1612
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 1614..1626

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 278.

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

                if (o.from_shadow && (is_from_min || is_from_max)) {
                    from_min = this.convertToPercent(is_from_min ? o.from_min : o.min);
                    from_max = this.convertToPercent(is_from_max ? o.from_max : o.max) - from_min;
                    from_min = this.toFixed(from_min - (this.coords.p_handle / 100 * from_min));
                    from_max = this.toFixed(from_max - (this.coords.p_handle / 100 * from_max));
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js and 2 other locations - About 1 day to fix
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 1614..1626
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 1628..1640

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 278.

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

                if (o.from_shadow && (is_from_min || is_from_max)) {
                    from_min = this.convertToPercent(is_from_min ? o.from_min : o.min);
                    from_max = this.convertToPercent(is_from_max ? o.from_max : o.max) - from_min;
                    from_min = this.toFixed(from_min - (this.coords.p_handle / 100 * from_min));
                    from_max = this.toFixed(from_max - (this.coords.p_handle / 100 * from_max));
Severity: Major
Found in de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js and 2 other locations - About 1 day to fix
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 1600..1612
de.bund.bfr.knime.js/src/js/lib/ion.rangeSlider.js on lines 1628..1640

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 278.

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 getPlausibilityRow has a Cognitive Complexity of 76 (exceeds 5 allowed). Consider refactoring.
Open

    public static Vector<String[]> getPlausibilityRow(MyDBTable table, MyTable myT, int row, String idField) {
        String tablename = myT.getTablename();
        Vector<String[]> result = new Vector<>();
        String idConf;
        if (idField.equalsIgnoreCase("ID")) {
Severity: Minor
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/PlausibilityChecker.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

Method optimize has a Cognitive Complexity of 76 (exceeds 5 allowed). Consider refactoring.
Open

    public void optimize(AtomicInteger progress, int nParameterSpace,
            int nLevenberg, boolean stopWhenSuccessful) {
        List<Double> paramMin = new ArrayList<>();
        List<Integer> paramStepCount = new ArrayList<>();
        List<Double> paramStepSize = new ArrayList<>();
Severity: Minor
Found in de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/math/ParameterOptimizer.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

/*
 * An XML document type.
 * Localname: Matrix
 * Namespace: http://www.bfr.bund.de/PCML-1_0
 * Java type: de.bund.bfr.pcml10.MatrixDocument
Severity: Major
Found in de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/MatrixDocument.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/AgentDocument.java on lines 1..259

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 732.

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

/*
 * An XML document type.
 * Localname: Agent
 * Namespace: http://www.bfr.bund.de/PCML-1_0
 * Java type: de.bund.bfr.pcml10.AgentDocument
Severity: Major
Found in de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/AgentDocument.java and 1 other location - About 1 day to fix
de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/MatrixDocument.java on lines 1..259

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 732.

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 TableReader.java has 665 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: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/predictorview/TableReader.java - About 1 day to fix

File UpdateChecker.java has 665 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: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/UpdateChecker.java - About 1 day to fix

Method fillHashtable has a Cognitive Complexity of 75 (exceeds 5 allowed). Consider refactoring.
Open

    LinkedHashMap<Object, String> fillHashtable(final MyTable theTable, final String startDelim, final String delimiter, final String endDelim, final boolean goDeeper,
            final boolean forceUpdate, HashSet<MyTable> alreadyUsed) {
        if (theTable == null) {
            return null;
        }
Severity: Minor
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/MyDBI.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

File OutportDocumentImpl.java has 662 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*
 * An XML document type.
 * Localname: Outport
 * Namespace: http://www.bfr.bund.de/PCML-1_0
 * Java type: de.bund.bfr.pcml10.OutportDocument
Severity: Major
Found in de.bund.bfr.knime.foodprocess.pcml/lib/src/de/bund/bfr/pcml10/impl/OutportDocumentImpl.java - About 1 day to fix

Method doImport has 295 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public String doImport(final String filename, final JProgressBar progress, final boolean showResults) {
        Runnable runnable = new Runnable() {
            public void run() {
                try {
                    if (progress != null) {
Severity: Major
Found in org.hsh.bfr.db/src/org/hsh/bfr/db/imports/GeneralXLSImporter.java - About 1 day to fix

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

    if ($.fn.mousewheel) {
      this.$results.on('mousewheel', function (e) {
        var top = self.$results.scrollTop();

        var bottom = self.$results.get(0).scrollHeight - top + e.deltaY;
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 1276..1299

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 271.

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

    "studySample": [{
        "id": "sampleName",
        "label": "Name",
        "type": "text",
        "description": "An unambiguous ID given to the samples used in the assay",
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/js-src/de/bund/bfr/knime/fsklab/1.7.2/editor/editor_data.js and 2 other locations - About 1 day to fix
de.bund.bfr.knime.js/js-lib/bfr/fskapp/editor_data_1.0.0.js on lines 570..629
de.bund.bfr.knime.js/js-lib/bfr/fskmetadata_1.0.0.js on lines 561..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 271.

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

    "studySample": [{
        "id": "sampleName",
        "label": "Name",
        "type": "text",
        "description": "An unambiguous ID given to the samples used in the assay",
Severity: Major
Found in de.bund.bfr.knime.js/js-lib/bfr/fskmetadata_1.0.0.js and 2 other locations - About 1 day to fix
de.bund.bfr.knime.fsklab.deprecatednodes/js-src/de/bund/bfr/knime/fsklab/1.7.2/editor/editor_data.js on lines 561..620
de.bund.bfr.knime.js/js-lib/bfr/fskapp/editor_data_1.0.0.js on lines 570..629

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 271.

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

Severity
Category
Status
Source
Language