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de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java

Summary

Maintainability
F
1 wk
Test Coverage

File ReaderUtils.java has 540 lines of code (exceeds 250 allowed). Consider refactoring.
Open

package de.bund.bfr.knime.pmm.common.reader;

import java.io.File;
import java.util.Arrays;
import java.util.HashMap;

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

  public static KnimeTuple mergeTuples(KnimeTuple dataTuple, KnimeTuple m1Tuple, KnimeTuple m2Tuple) {

    KnimeTuple tuple = new KnimeTuple(SchemaFactory.createM12DataSchema());

    tuple.setValue(TimeSeriesSchema.ATT_CONDID, dataTuple.getInt(TimeSeriesSchema.ATT_CONDID));

Method parseMiscs has 30 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  public static PmmXmlDoc parseMiscs(Map<String, Double> miscs) {
    PmmXmlDoc cell = new PmmXmlDoc();

    if (miscs != null) {
      // First misc item has id -1 and the rest of items have negative

Method parse has 28 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private static KnimeTuple parse(PrimaryModelWData pm) {
      // Add cells to the row
      KnimeTuple row = new KnimeTuple(SchemaFactory.createM1DataSchema());

      // time series cells

Method parse has 28 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    private static KnimeTuple parse(PrimaryModelWOData pm) {
      // Add cells to the row
      KnimeTuple row = new KnimeTuple(SchemaFactory.createM1DataSchema());

      // time series cells

Method parseMiscs has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  public static PmmXmlDoc parseMiscs(Map<String, Double> miscs) {
    PmmXmlDoc cell = new PmmXmlDoc();

    if (miscs != null) {
      // First misc item has id -1 and the rest of items have negative

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

Add a default case to this switch.
Open

        switch (name) {

The requirement for a final default clause is defensive programming. The clause should either take appropriate action, or contain a suitable comment as to why no action is taken.

Noncompliant Code Example

switch (param) {  //missing default clause
  case 0:
    doSomething();
    break;
  case 1:
    doSomethingElse();
    break;
}

switch (param) {
  default: // default clause should be the last one
    error();
    break;
  case 0:
    doSomething();
    break;
  case 1:
    doSomethingElse();
    break;
}

Compliant Solution

switch (param) {
  case 0:
    doSomething();
    break;
  case 1:
    doSomethingElse();
    break;
  default:
    error();
    break;
}

Exceptions

If the switch parameter is an Enum and if all the constants of this enum are used in the case statements, then no default clause is expected.

Example:

public enum Day {
    SUNDAY, MONDAY
}
...
switch(day) {
  case SUNDAY:
    doSomething();
    break;
  case MONDAY:
    doSomethingElse();
    break;
}

See

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

  private static class PrimaryModelWDataReader implements Reader {

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 392..462

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 582.

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

  private static class PrimaryModelWODataReader implements Reader {

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 321..390

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 582.

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

  public static KnimeTuple mergeTuples(KnimeTuple dataTuple, KnimeTuple m1Tuple, KnimeTuple m2Tuple) {

    KnimeTuple tuple = new KnimeTuple(SchemaFactory.createM12DataSchema());

    tuple.setValue(TimeSeriesSchema.ATT_CONDID, dataTuple.getInt(TimeSeriesSchema.ATT_CONDID));
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/sbmlreader/SBMLReaderNodeModel.java on lines 245..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 580.

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

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
      DataTableSpec modelSpec = SchemaFactory.createM12DataSchema().createSpec();
      BufferedDataContainer modelContainer = exec.createDataContainer(modelSpec);
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 466..495
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 612..640
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 664..693
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 723..752

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 168.

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

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
      DataTableSpec modelSpec = SchemaFactory.createM12DataSchema().createSpec();
      BufferedDataContainer modelContainer = exec.createDataContainer(modelSpec);
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 466..495
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 522..551
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 612..640
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 664..693

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 168.

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

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
      DataTableSpec modelSpec = SchemaFactory.createM12DataSchema().createSpec();
      BufferedDataContainer modelContainer = exec.createDataContainer(modelSpec);
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 522..551
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 612..640
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 664..693
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 723..752

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 168.

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

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
      DataTableSpec modelSpec = SchemaFactory.createM12DataSchema().createSpec();
      BufferedDataContainer modelContainer = exec.createDataContainer(modelSpec);
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 466..495
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 522..551
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 612..640
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 723..752

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 168.

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

    public BufferedDataContainer[] read(File file, boolean isPMFX, ExecutionContext exec)
        throws Exception {
      // Creates table spec and container
      DataTableSpec modelSpec = SchemaFactory.createM12DataSchema().createSpec();
      BufferedDataContainer modelContainer = exec.createDataContainer(modelSpec);
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 466..495
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 522..551
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 664..693
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 723..752

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 168.

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

  static {
    READERS.put(ModelType.EXPERIMENTAL_DATA, new ExperimentalDataReader());
    READERS.put(ModelType.PRIMARY_MODEL_WDATA, new PrimaryModelWDataReader());
    READERS.put(ModelType.PRIMARY_MODEL_WODATA, new PrimaryModelWODataReader());
    READERS.put(ModelType.TWO_STEP_SECONDARY_MODEL, new TwoStepSecondaryModelReader());
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/openfsmr/OpenFSMRConverterNodeModel.java on lines 93..103

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 112.

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

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

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

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

Refactorings

Further Reading

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

          case "Temperature":
            categories = Arrays.asList(Categories.getTempCategory().getName());
            description = name;
            unit = Categories.getTempCategory().getStandardUnit();
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 119..124

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

          case "aw":
            categories = Arrays.asList(Categories.getAwCategory().getName());
            description = name;
            unit = Categories.getAwCategory().getStandardUnit();
            cell.add(new MiscXml(-3, name, description, value, categories, unit));
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/reader/ReaderUtils.java on lines 103..109

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

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