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de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java

Summary

Maintainability
D
2 days
Test Coverage

Method execute has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.
Open

    @Override
    protected BufferedDataTable[] execute(final BufferedDataTable[] inData,
            final ExecutionContext exec) throws Exception {
        KnimeRelationReader reader = new KnimeRelationReader(
                SchemaFactory.createDataSchema(), inData[0]);

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method execute has 105 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    @Override
    protected BufferedDataTable[] execute(final BufferedDataTable[] inData,
            final ExecutionContext exec) throws Exception {
        KnimeRelationReader reader = new KnimeRelationReader(
                SchemaFactory.createDataSchema(), inData[0]);

Refactor this method to reduce its Cognitive Complexity from 38 to the 15 allowed.
Open

    protected BufferedDataTable[] execute(final BufferedDataTable[] inData,

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

Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation.
Open

    protected void loadInternals(final File internDir,

There are several reasons for a method not to have a method body:

  • It is an unintentional omission, and should be fixed to prevent an unexpected behavior in production.
  • It is not yet, or never will be, supported. In this case an UnsupportedOperationException should be thrown.
  • The method is an intentionally-blank override. In this case a nested comment should explain the reason for the blank override.

Noncompliant Code Example

public void doSomething() {
}

public void doSomethingElse() {
}

Compliant Solution

@Override
public void doSomething() {
  // Do nothing because of X and Y.
}

@Override
public void doSomethingElse() {
  throw new UnsupportedOperationException();
}

Exceptions

Default (no-argument) constructors are ignored when there are other constructors in the class, as are empty methods in abstract classes.

public abstract class Animal {
  void speak() {  // default implementation ignored
  }
}

Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation.
Open

    protected void saveInternals(final File internDir,

There are several reasons for a method not to have a method body:

  • It is an unintentional omission, and should be fixed to prevent an unexpected behavior in production.
  • It is not yet, or never will be, supported. In this case an UnsupportedOperationException should be thrown.
  • The method is an intentionally-blank override. In this case a nested comment should explain the reason for the blank override.

Noncompliant Code Example

public void doSomething() {
}

public void doSomethingElse() {
}

Compliant Solution

@Override
public void doSomething() {
  // Do nothing because of X and Y.
}

@Override
public void doSomethingElse() {
  throw new UnsupportedOperationException();
}

Exceptions

Default (no-argument) constructors are ignored when there are other constructors in the class, as are empty methods in abstract classes.

public abstract class Animal {
  void speak() {  // default implementation ignored
  }
}

Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation.
Open

    protected void reset() {

There are several reasons for a method not to have a method body:

  • It is an unintentional omission, and should be fixed to prevent an unexpected behavior in production.
  • It is not yet, or never will be, supported. In this case an UnsupportedOperationException should be thrown.
  • The method is an intentionally-blank override. In this case a nested comment should explain the reason for the blank override.

Noncompliant Code Example

public void doSomething() {
}

public void doSomethingElse() {
}

Compliant Solution

@Override
public void doSomething() {
  // Do nothing because of X and Y.
}

@Override
public void doSomethingElse() {
  throw new UnsupportedOperationException();
}

Exceptions

Default (no-argument) constructors are ignored when there are other constructors in the class, as are empty methods in abstract classes.

public abstract class Animal {
  void speak() {  // default implementation ignored
  }
}

Add a nested comment explaining why this method is empty, throw an UnsupportedOperationException or complete the implementation.
Open

    protected void validateSettings(final NodeSettingsRO settings)

There are several reasons for a method not to have a method body:

  • It is an unintentional omission, and should be fixed to prevent an unexpected behavior in production.
  • It is not yet, or never will be, supported. In this case an UnsupportedOperationException should be thrown.
  • The method is an intentionally-blank override. In this case a nested comment should explain the reason for the blank override.

Noncompliant Code Example

public void doSomething() {
}

public void doSomethingElse() {
}

Compliant Solution

@Override
public void doSomething() {
  // Do nothing because of X and Y.
}

@Override
public void doSomethingElse() {
  throw new UnsupportedOperationException();
}

Exceptions

Default (no-argument) constructors are ignored when there are other constructors in the class, as are empty methods in abstract classes.

public abstract class Animal {
  void speak() {  // default implementation ignored
  }
}

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

            if (set.getAgents().containsKey(id)) {
                PmmXmlDoc agentXml = new PmmXmlDoc();
                AgentXml agent = set.getAgents().get(id);

                if (agent != null) {
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 117..128

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 74.

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 (set.getMatrices().containsKey(id)) {
                PmmXmlDoc matrixXml = new PmmXmlDoc();
                MatrixXml matrix = set.getMatrices().get(id);

                if (matrix != null) {
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 95..106

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 74.

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 5 locations. Consider refactoring.
Open

            if (set.getQualityScores().containsKey(id)) {
                PmmXmlDoc infoXml = tuple
                        .getPmmXml(TimeSeriesSchema.ATT_MDINFO);

                ((MdInfoXml) infoXml.get(0)).qualityScore = set
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 108..115
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 130..138
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 140..148
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 160..168

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 62.

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 5 locations. Consider refactoring.
Open

            if (set.getMatrixDetails().containsKey(id)) {
                PmmXmlDoc matrixXml = tuple
                        .getPmmXml(TimeSeriesSchema.ATT_MATRIX);

                ((MatrixXml) matrixXml.get(0)).detail = set.getMatrixDetails()
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 108..115
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 140..148
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 150..158
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 160..168

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 62.

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 5 locations. Consider refactoring.
Open

            if (set.getChecks().containsKey(id)) {
                PmmXmlDoc infoXml = tuple
                        .getPmmXml(TimeSeriesSchema.ATT_MDINFO);

                ((MdInfoXml) infoXml.get(0))
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 108..115
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 130..138
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 140..148
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 150..158

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 62.

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 5 locations. Consider refactoring.
Open

            if (set.getComments().containsKey(id)) {
                PmmXmlDoc infoXml = tuple
                        .getPmmXml(TimeSeriesSchema.ATT_MDINFO);

                ((MdInfoXml) infoXml.get(0)).comment = set.getComments().get(
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 108..115
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 130..138
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 150..158
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 160..168

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 62.

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 5 locations. Consider refactoring.
Open

            if (set.getAgentDetails().containsKey(id)) {
                PmmXmlDoc agentXml = tuple
                        .getPmmXml(TimeSeriesSchema.ATT_AGENT);

                ((AgentXml) agentXml.get(0)).detail = set.getAgentDetails().get(id);
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 130..138
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 140..148
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 150..158
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 160..168

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 62.

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 (set.getTimeSeries().containsKey(id)) {
                PmmXmlDoc timeSeriesXml = new PmmXmlDoc();

                timeSeriesXml.getElementSet().addAll(
                        set.getTimeSeries().get(id));
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 178..183

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

            if (set.getReferences().containsKey(id)) {
                PmmXmlDoc refXml = new PmmXmlDoc();

                refXml.getElementSet().addAll(set.getReferences().get(id));
                tuple.setValue(TimeSeriesSchema.ATT_LITMD, refXml);
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeModel.java on lines 170..176

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

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

            if (combaseID != null) {
                id = combaseID + " (" + condID + ")";
            } else {
                id = condID + "";
            }
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/microbialdataedit/MicrobialDataEditNodeDialog.java on lines 245..249

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 44.

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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