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de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java

Summary

Maintainability
F
1 wk
Test Coverage

File FSMRUtils.java has 927 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: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 2 days to fix

Method createTupleFromTemplate has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.
Open

  public static KnimeTuple createTupleFromTemplate(FSMRTemplate template) {
    KnimeTuple tuple = new KnimeTuple(new OpenFSMRSchema());
    
    SimpleDateFormat sdf = new SimpleDateFormat("dd/MM/yyyy");
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 4 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 createTupleFromTemplate has 103 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  public static KnimeTuple createTupleFromTemplate(FSMRTemplate template) {
    KnimeTuple tuple = new KnimeTuple(new OpenFSMRSchema());
    
    SimpleDateFormat sdf = new SimpleDateFormat("dd/MM/yyyy");
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 4 hrs to fix

Method setMetaDataFromAnnotation has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.
Open

  void setMetaDataFromAnnotation(final Annotation annotation) {
    Metadata metadata = new MetadataAnnotation(annotation).getMetadata();

    if (metadata.isSetGivenName())
      template.setCreator(metadata.getGivenName());
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.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

Method setMetaDataFromAnnotation has 43 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  void setMetaDataFromAnnotation(final Annotation annotation) {
    Metadata metadata = new MetadataAnnotation(annotation).getMetadata();

    if (metadata.isSetGivenName())
      template.setCreator(metadata.getGivenName());
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 1 hr to fix

Method setIndependentVariableData has 39 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  @Override
  void setIndependentVariableData() {

    // Declare list of variables
    List<VariableData> variables = new LinkedList<>();
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 1 hr to fix

Method setIndependentVariableData has 36 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  @Override
  void setIndependentVariableData() {

    // Declare sets to hold data
    List<VariableData> variableList = new LinkedList<>();
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 1 hr to fix

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

  @Override
  void setDependentVariableData() {

    Model model = doc.getModel();
    ModelRule rule = new ModelRule((AssignmentRule) model.getRule(0));
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.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

Method setIndependentVariableData has 34 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  @Override
  void setIndependentVariableData() {

    List<VariableData> variables = new LinkedList<>();
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 1 hr to fix

Method setMetadata has 32 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  @Override
  void setMetadata() {
    ResultComponent rc = doc.getResultComponent();

    // Creator
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 1 hr to fix

Method setMetadata has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  @Override
  void setMetadata() {
    ResultComponent rc = doc.getResultComponent();

    // Creator
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.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

Method processDependentVariable has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

  static VariableData processDependentVariable(final Model model, final List<Limits> limits) {

    VariableData var = new VariableData();

    Species species = model.getSpecies(0);
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java - About 35 mins 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 40 to the 15 allowed.
Open

  public static KnimeTuple createTupleFromTemplate(FSMRTemplate template) {
Severity: Critical
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.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 "dimensionless" 3 times.
Open

      if (!unitId.equals("dimensionless") && DBUnits.getDBUnits().containsKey(var.unit)) {
Severity: Critical
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.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.

Define a constant instead of duplicating this literal " is not a valid date" 4 times.
Open

        System.err.println(createdDateAsString + " is not a valid date");
Severity: Critical
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.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

    {
      // Gets name of dependent variable from the model rule (1)
      Model model = primModelDoc.getModel();
      ModelRule rule = new ModelRule((AssignmentRule) model.getRule(0));
      String depName = rule.getVariable();
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 804..817

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 100.

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

    {
      // Gets name of dependent variable from the model rule (2)
      Model model = secModelDoc.getModel();
      ModelRule rule2 = new ModelRule((AssignmentRule) model.getRule(0));
      String depName = rule2.getVariable();
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 788..801

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 100.

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 5 locations. Consider refactoring.
Open

    for (int i = 0; i < variableList.size(); i++) {
      VariableData var = variableList.get(i);
      varsArray[i] = var.var;
      unitsArray[i] = var.unit;
      minsArray[i] = var.min;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 4 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 690..696
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 957..963
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1080..1086
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1215..1221

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 90.

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 5 locations. Consider refactoring.
Open

    for (int i = 0; i < variables.size(); i++) {
      VariableData var = variables.get(i);
      varsArray[i] = var.var;
      unitsArray[i] = var.unit;
      minsArray[i] = var.min;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 4 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 690..696
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 825..831
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 957..963
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1215..1221

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 90.

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 5 locations. Consider refactoring.
Open

    for (int i = 0; i < variables.size(); i++) {
      VariableData var = variables.get(i);
      varsArray[i] = var.var;
      unitsArray[i] = var.unit;
      minsArray[i] = var.min;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 4 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 690..696
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 825..831
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 957..963
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1080..1086

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 90.

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 5 locations. Consider refactoring.
Open

    for (int i = 0; i < variables.size(); i++) {
      VariableData var = variables.get(i);
      varsArray[i] = var.var;
      unitsArray[i] = var.unit;
      minsArray[i] = var.min;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 4 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 825..831
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 957..963
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1080..1086
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1215..1221

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 90.

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 5 locations. Consider refactoring.
Open

    for (int i = 0; i < variables.size(); i++) {
      VariableData var = variables.get(i);
      varsArray[i] = var.var;
      unitsArray[i] = var.unit;
      minsArray[i] = var.min;
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 4 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 690..696
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 825..831
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1080..1086
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1215..1221

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 90.

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

    {
      ModelRule rule = new ModelRule((AssignmentRule) secModel.getRule(0));
      String depName = rule.getVariable();

      List<Parameter> params = secModel.getListOfParameters().filterList(nonConstantFilter).stream()
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 926..936

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 90.

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

    {
      ModelRule rule = new ModelRule((AssignmentRule) primModel.getRule(0));
      String depName = rule.getVariable();

      List<Parameter> params = primModel.getListOfParameters().filterList(nonConstantFilter)
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 939..949

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 90.

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 3 locations. Consider refactoring.
Open

  @Override
  void setDependentVariableData() {
    VariableData var = processDependentVariable(primDoc.getModel(), primModelLimits);
    template.setDependentVariable(var.var);
    template.setDependentVariableUnit(var.unit);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 2 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 658..669
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 768..779

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 85.

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 3 locations. Consider refactoring.
Open

  @Override
  void setDependentVariableData() {
    VariableData var = processDependentVariable(doc.getModel(), limits);
    template.setDependentVariable(var.var);
    template.setDependentVariableUnit(var.unit);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 2 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 768..779
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1155..1166

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 85.

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 3 locations. Consider refactoring.
Open

  @Override
  void setDependentVariableData() {
    VariableData var = processDependentVariable(primModelDoc.getModel(), primModelLimits);
    template.setDependentVariable(var.var);
    template.setDependentVariableUnit(var.unit);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 2 other locations - About 1 hr to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 658..669
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 1155..1166

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 85.

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 (rc.isSetCreatedDate()) {
      String dateAsString = rc.getCreatedDate();
      try {
        Date date = dateFormat.parse(dateAsString);
        template.setCreatedDate(date);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 3 other locations - About 55 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 353..363
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 365..375
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 527..536

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 66.

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 (metadata.isSetCreatedDate()) {
      String createdDateAsString = metadata.getCreatedDate();

      try {
        Date createdDate = dateFormat.parse(createdDateAsString);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 3 other locations - About 55 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 365..375
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 515..524
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 527..536

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 66.

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 (rc.isSetModifiedDate()) {
      String dateAsString = rc.getModifiedDate();
      try {
        Date date = dateFormat.parse(dateAsString);
        template.setModifiedDate(date);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 3 other locations - About 55 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 353..363
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 365..375
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 515..524

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 66.

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 (metadata.isSetModifiedDate()) {
      String modifiedDateAsString = metadata.getModifiedDate();

      try {
        Date modifiedDate = dateFormat.parse(modifiedDateAsString);
Severity: Major
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 3 other locations - About 55 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 353..363
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 515..524
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 527..536

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 66.

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

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

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

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

Refactorings

Further Reading

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

    if (template.isSetIndependentVariablesMins()) {
      String formattedMins = Arrays.stream(template.getIndependentVariablesMins())
          .mapToObj(d -> Double.isNaN(d) ? "?" : Double.toString(d)).collect(Collectors.joining("||"));
      tuple.setValue(OpenFSMRSchema.ATT_INDEPENDENT_VARIABLE_MINS, formattedMins);
    }
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 55 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 236..240

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 64.

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

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

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

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

Refactorings

Further Reading

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

    if (template.isSetIndependentVariablesMaxs()) {
      String formattedMaxs = Arrays.stream(template.getIndependentVariablesMaxs())
          .mapToObj(d -> Double.isNaN(d) ? "?" : Double.toString(d)).collect(Collectors.joining("||"));
      tuple.setValue(OpenFSMRSchema.ATT_INDEPENDENT_VARIABLE_MAXS, formattedMaxs);
    }
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 55 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 230..234

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 64.

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

    for (Limits lim : limits) {
      if (lim.getVar().equals(param.getId())) {
        var.min = lim.getMin();
        var.max = lim.getMax();
        break;
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 414..420

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 50.

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

    for (Limits lim : limits) {
      if (lim.getVar().equals(species.getId())) {
        var.min = lim.getMin();
        var.max = lim.getMax();
        break;
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 440..446

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 50.

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

  void setOrganismDataFromSpecies(final Species species) {
    PMFSpecies pmfSpecies = SBMLFactory.createPMFSpecies(species);

    if (species.isSetName())
      template.setOrganismName(species.getName());
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 304..311

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 48.

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

  void setMatrixDataFromCompartment(final Compartment compartment) {
    PMFCompartment pmfCompartment = SBMLFactory.createPMFCompartment(compartment);

    if (compartment.isSetName())
      template.setMatrixName(compartment.getName());
Severity: Minor
Found in de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java and 1 other location - About 40 mins to fix
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/FSMRUtils.java on lines 295..302

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 48.

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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