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de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java

Summary

Maintainability
D
2 days
Test Coverage

Method createSbmlDocument has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
Open

  private static SBMLDocument createSbmlDocument(final FskMetaData template) {

    // Creates SBMLDocument for the primary model
    final SBMLDocument sbmlDocument = new SBMLDocument(TableReader.LEVEL, TableReader.VERSION);
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java - About 3 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 createSbmlDocument has 92 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  private static SBMLDocument createSbmlDocument(final FskMetaData template) {

    // Creates SBMLDocument for the primary model
    final SBMLDocument sbmlDocument = new SBMLDocument(TableReader.LEVEL, TableReader.VERSION);
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java - About 3 hrs to fix

File FskxWriterNodeModel.java has 282 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 the Free Software Foundation, either version 3 of the
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java - About 2 hrs to fix

Method execute has 50 lines of code (exceeds 25 allowed). Consider refactoring.
Open

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

    FskPortObject portObject = (FskPortObject) inData[0];
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java - About 2 hrs to fix

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

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

    FskPortObject portObject = (FskPortObject) inData[0];
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java - About 1 hr 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

Refactor this method to reduce its Cognitive Complexity from 29 to the 15 allowed.
Open

  private static SBMLDocument createSbmlDocument(final FskMetaData template) {
Severity: Critical
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java by sonar-java

Cognitive Complexity is a measure of how hard the control flow of a method is to understand. Methods with high Cognitive Complexity will be difficult to maintain.

See

Define a constant instead of duplicating this literal "pmmlab" 3 times.
Open

      XMLNode nameNode = new XMLNode(new XMLTriple(FORMULA_TAG, null, "pmmlab"));
Severity: Critical
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java by sonar-java

Duplicated string literals make the process of refactoring error-prone, since you must be sure to update all occurrences.

On the other hand, constants can be referenced from many places, but only need to be updated in a single place.

Noncompliant Code Example

With the default threshold of 3:

public void run() {
  prepare("action1");                              // Noncompliant - "action1" is duplicated 3 times
  execute("action1");
  release("action1");
}

@SuppressWarning("all")                            // Compliant - annotations are excluded
private void method1() { /* ... */ }
@SuppressWarning("all")
private void method2() { /* ... */ }

public String method3(String a) {
  System.out.println("'" + a + "'");               // Compliant - literal "'" has less than 5 characters and is excluded
  return "";                                       // Compliant - literal "" has less than 5 characters and is excluded
}

Compliant Solution

private static final String ACTION_1 = "action1";  // Compliant

public void run() {
  prepare(ACTION_1);                               // Compliant
  execute(ACTION_1);
  release(ACTION_1);
}

Exceptions

To prevent generating some false-positives, literals having less than 5 characters are excluded.

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

    public static void addNamespaces(SBMLDocument doc) {
      doc.addDeclaredNamespace("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
      doc.addDeclaredNamespace("xmlns:pmml", "http://www.dmg.org/PMML-4_2");
      doc.addDeclaredNamespace("xmlns:pmf",
          "http://sourceforge.net/projects/microbialmodelingexchange/files/PMF-ML");
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/TableReader.java on lines 86..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 84.

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

      try {
        double min = Double.parseDouble(v.min);
        double max = Double.parseDouble(v.max);
        LimitsConstraint lc = new LimitsConstraint(param.getId(), min, max);
        if (lc.getConstraint() != null) {
Severity: Major
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.fsklab.deprecatednodes/src-1_0_2/de/bund/bfr/knime/fsklab/nodes/MetadataDocument.java on lines 216..225

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 80.

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 static File createScriptFile(String script) throws IOException {
    File f = FileUtil.createTempFile("script", ".r");
    try (FileWriter fw = new FileWriter(f)) {
      fw.write(script);
    }
Severity: Minor
Found in de.bund.bfr.knime.fsklab.deprecatednodes/src-prerakip/de/bund/bfr/knime/pmm/fskx/writer/FskxWriterNodeModel.java and 1 other location - About 30 mins to fix
de.bund.bfr.knime.fsklab.deprecatednodes/src-1_0_2/de/bund/bfr/knime/fsklab/nodes/writer/FskxWriterNodeModel.java on lines 140..147

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 42.

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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