SiLeBAT/FSK-Lab

View on GitHub
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/WriterUtils.java

Summary

Maintainability
F
1 wk
Test Coverage

File WriterUtils.java has 879 lines of code (exceeds 250 allowed). Consider refactoring.
Open

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

import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.HashMap;

Method parse has 92 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        private static TwoStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, int modelNum,
                String mdName, Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

Method parse has 74 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        private static ManualSecondaryModel parse(KnimeTuple tuple, boolean isPMFX, String mdName, int mdNum,
                Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

Method createUnitFromDB has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    public static PMFUnitDefinition createUnitFromDB(String unit) throws XMLStreamException {
        if (!DBUnits.getDBUnits().containsKey(unit)) {
            return null;
        }

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 parse has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

        private static ManualSecondaryModel parse(KnimeTuple tuple, boolean isPMFX, String mdName, int mdNum,
                Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

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 parse has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

        private static TwoStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, int modelNum,
                String mdName, Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

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 parse has 55 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        private static OneStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, String mdName,
                int mdNum, Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

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

    public static PMFUnitDefinition createUnitFromDB(String unit) throws XMLStreamException {
        if (!DBUnits.getDBUnits().containsKey(unit)) {
            return null;
        }

Method parse has 33 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        private static TwoStepSecondaryModel parse(List<KnimeTuple> tuples, boolean isPMFX, int modelNum, String mdName,
                Metadata metadata, String notes) {
            /**
             * <ol>
             * <li>Create n SBMLDocument for primary models</li>

Method write has 33 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    public static void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
            boolean splitModels, String notes, ExecutionContext exec, ModelType modelType) throws Exception {

        Parser parser;

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

        private static ManualTertiaryModel parse(List<KnimeTuple> tupleList, boolean isPMFX, String mdName,
                int modelNum, Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

Method write has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            // Group tuples according to its secondary model

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 write has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            List<ManualTertiaryModel> tms = new LinkedList<>();

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 write has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring.
Open

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            // Group tuples according to its secondary model

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 write has 9 arguments (exceeds 4 allowed). Consider refactoring.
Open

    public static void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
            boolean splitModels, String notes, ExecutionContext exec, ModelType modelType) throws Exception {

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

        private static OneStepSecondaryModel parse(List<KnimeTuple> tuples, boolean isPMFX, String mdName, int modelNum,
                Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? ".pmf" : ".sbml";
            KnimeTuple firstTuple = tuples.get(0);

Method write has 26 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            // Group tuples according to its secondary model

Method write has 26 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            // Group tuples according to its secondary model

Method write has 26 lines of code (exceeds 25 allowed). Consider refactoring.
Open

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            List<ManualTertiaryModel> tms = new LinkedList<>();

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception;

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has 8 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

Method write has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            List<TwoStepTertiaryModel> tms = new LinkedList<>();

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 parse has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

        private static TwoStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, int modelNum,
                String mdName, Metadata metadata, String notes) {

Method parse has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

        private static ManualSecondaryModel parse(KnimeTuple tuple, boolean isPMFX, String mdName, int mdNum,
                Metadata metadata, String notes) {

Method parse has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

        private static OneStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, String mdName,
                int mdNum, Metadata metadata, String notes) {

Method parse has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

        private static ManualTertiaryModel parse(List<KnimeTuple> tupleList, boolean isPMFX, String mdName,
                int modelNum, Metadata metadata, String notes) {

Method parse has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

        private static OneStepSecondaryModel parse(List<KnimeTuple> tuples, boolean isPMFX, String mdName, int modelNum,
                Metadata metadata, String notes) {

Method parse has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

        private static OneStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, String mdName,
                int mdNum, Metadata metadata, String notes) {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

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 parse has 6 arguments (exceeds 4 allowed). Consider refactoring.
Open

        private static TwoStepSecondaryModel parse(List<KnimeTuple> tuples, boolean isPMFX, int modelNum, String mdName,
                Metadata metadata, String notes) {

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

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            List<OneStepTertiaryModel> tms = new LinkedList<>();

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

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            List<ManualSecondaryModel> sms = new LinkedList<>();

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 paramXml2Coefficient has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    public static PMFCoefficient paramXml2Coefficient(ParamXml paramXml) {
        String name = paramXml.name;
        double value = (paramXml.value == null) ? 0.0 : paramXml.value;
        String unit = (paramXml.unit == null) ? "dimensionless" : PMFUtil.createId(paramXml.unit);
        Double P = paramXml.P;

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

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            final String modelExtension = isPMFX ? "pmf" : "sbml";

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

        private static TwoStepSecondaryModel parse(List<KnimeTuple> tuples, boolean isPMFX, int modelNum, String mdName,
                Metadata metadata, String notes) {
            /**
             * <ol>
             * <li>Create n SBMLDocument for primary models</li>

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 17 to the 15 allowed.
Open

        private static ManualSecondaryModel parse(KnimeTuple tuple, boolean isPMFX, String mdName, int mdNum,

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

Refactor this method to reduce its Cognitive Complexity from 17 to the 15 allowed.
Open

        private static TwoStepTertiaryModel parse(List<List<KnimeTuple>> tupleList, boolean isPMFX, int modelNum,

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

Refactor this method to reduce its Cognitive Complexity from 17 to the 15 allowed.
Open

    public static PMFUnitDefinition createUnitFromDB(String unit) throws XMLStreamException {

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 "%s_%s.%s" 3 times.
Open

            String tertDocName = String.format("%s_%s.%s", mdName, modelNum, modelExtension);

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 "%s_%d.%s" 5 times.
Open

                String sbmlDocName = String.format("%s_%d.%s", mdName, pms.size(), modelExtension);

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 ".pmfx" 15 times.
Open

            Path path = Paths.get(dir, mdName + (isPMFX ? ".pmfx" : ".pmf"));

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 "metadata" 9 times.
Open

                    sbmlDoc.getModel().getAnnotation().getNonRDFannotation().getChildElement("metadata", "")

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 "%s.%s" 3 times.
Open

                String sbmlDocName = String.format("%s.%s", sbmlDoc.getModel().getId(), modelExtension);

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

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            // Group tuples according to its secondary model
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/WriterUtils.java on lines 486..520

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 281.

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

        @Override
        public void write(List<KnimeTuple> tuples, boolean isPMFX, String dir, String mdName, Metadata metadata,
                boolean splitModels, String notes, ExecutionContext exec) throws Exception {

            // Group tuples according to its secondary model
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/WriterUtils.java on lines 589..623

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 281.

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 (IndepXml indepXml : indepXmls) {
                // Creates SBML parameter
                // model.addParameter(new SecIndep(indepXml).getParam());
                SecIndep secIndep = new SecIndep(indepXml.name, indepXml.description, indepXml.unit);
                model.addParameter(secIndep.getParam());
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/Model2Parser.java on lines 114..123

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 82.

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

            for (ParamXml paramXml : constXmls) {
                // Creates SBML parameter
                PMFCoefficient coefficient = WriterUtils.paramXml2Coefficient(paramXml);
                model.addParameter(coefficient.getParameter());
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/Model1Parser.java on lines 141..151
de.bund.bfr.knime.pmm.nodes/src/de/bund/bfr/knime/pmm/common/writer/Model2Parser.java on lines 126..136

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

There are no issues that match your filters.

Category
Status