SiLeBAT/FSK-Lab

              ObjectInputStream ois = new ObjectInputStream(in);

Close

Connections, streams, files, and other classes that implement the Closeable interface or its super-interface, AutoCloseable, needs to be closed after use. Further, that close call must be made in a finally block otherwise an exception could keep the call from being made. Preferably, when class implements AutoCloseable, resource should be created using "try-with-resources" pattern and will be closed automatically.

Failure to properly close resources will result in a resource leak which could bring first the application and then perhaps the box the application is on to their knees.

Noncompliant Code Example

private void readTheFile() throws IOException {
  Path path = Paths.get(this.fileName);
  BufferedReader reader = Files.newBufferedReader(path, this.charset);
  // ...
  reader.close();  // Noncompliant
  // ...
  Files.lines("input.txt").forEach(System.out::println); // Noncompliant: The stream needs to be closed
}

private void doSomething() {
  OutputStream stream = null;
  try {
    for (String property : propertyList) {
      stream = new FileOutputStream("myfile.txt");  // Noncompliant
      // ...
    }
  } catch (Exception e) {
    // ...
  } finally {
    stream.close();  // Multiple streams were opened. Only the last is closed.
  }
}

Compliant Solution

private void readTheFile(String fileName) throws IOException {
    Path path = Paths.get(fileName);
    try (BufferedReader reader = Files.newBufferedReader(path, StandardCharsets.UTF_8)) {
      reader.readLine();
      // ...
    }
    // ..
    try (Stream<String> input = Files.lines("input.txt"))  {
      input.forEach(System.out::println);
    }
}

private void doSomething() {
  OutputStream stream = null;
  try {
    stream = new FileOutputStream("myfile.txt");
    for (String property : propertyList) {
      // ...
    }
  } catch (Exception e) {
    // ...
  } finally {
    stream.close();
  }
}

Exceptions

Instances of the following classes are ignored by this rule because close has no effect:

• java.io.ByteArrayOutputStream
• java.io.ByteArrayInputStream
• java.io.CharArrayReader
• java.io.CharArrayWriter
• java.io.StringReader
• java.io.StringWriter

Java 7 introduced the try-with-resources statement, which implicitly closes Closeables. All resources opened in a try-with-resources statement are ignored by this rule.

try (BufferedReader br = new BufferedReader(new FileReader(fileName))) {
  //...
}
catch ( ... ) {
  //...
}

See

• MITRE, CWE-459 - Incomplete Cleanup
• MITRE, CWE-772 - Missing Release of Resource after Effective Lifetime
• CERT, FIO04-J. - Release resources when they are no longer needed
• CERT, FIO42-C. - Close files when they are no longer needed
• Try With Resources

  protected void reset() {

Close

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
  }
}

        public FskPortObject loadPortObject(PortObjectZipInputStream in, PortObjectSpec spec, ExecutionMonitor exec)

Close

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

• Cognitive Complexity

        out.putNextEntry(new ZipEntry("modelType" + level));

Close

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.

                field.setHorizontalAlignment(JTextField.RIGHT);

Close

In the interest of code clarity, static members of a base class should never be accessed using a derived type's name. Doing so is confusing and could create the illusion that two different static members exist.

Noncompliant Code Example

class Parent {
  public static int counter;
}

class Child extends Parent {
  public Child() {
    Child.counter++;  // Noncompliant
  }
}

Compliant Solution

class Parent {
  public static int counter;
}

class Child extends Parent {
  public Child() {
    Parent.counter++;
  }
}

  protected void useCurrentValueAsDefault() {}

Close

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
  }
}

  public void saveToNodeSettings(NodeSettingsWO settings) {}

Close

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
  }
}

      final Path workspacePath = FileUtil.createTempFile("workspace", ".r").toPath();

Close

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.

    exposureModel("Exposure model"),

Close

Shared coding conventions allow teams to collaborate efficiently. This rule checks that all constant names match a provided regular expression.

Noncompliant Code Example

With the default regular expression ^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$:

public class MyClass {
  public static final int first = 1;
}

public enum MyEnum {
  first;
}

Compliant Solution

public class MyClass {
  public static final int FIRST = 1;
}

public enum MyEnum {
  FIRST;
}

    FileUtils.writeStringToFile(rPackagesFile, packageInfoList, "UTF-8");

Close

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.

            Path workspacePath = FileUtil.createTempFile("workspace", ".r").toPath();

Close

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.

      String modelType = metadataNode.get("modelType").asText("genericModel");

Close

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.

    filePrefix = filePrefix + normalizeName(fskObj) + System.getProperty("file.separator");

Close

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.

  public void saveCurrentValue(NodeSettingsWO content) {

Close

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
  }
}

            ObjectOutputStream oos = new ObjectOutputStream(out);

Close

Connections, streams, files, and other classes that implement the Closeable interface or its super-interface, AutoCloseable, needs to be closed after use. Further, that close call must be made in a finally block otherwise an exception could keep the call from being made. Preferably, when class implements AutoCloseable, resource should be created using "try-with-resources" pattern and will be closed automatically.

Failure to properly close resources will result in a resource leak which could bring first the application and then perhaps the box the application is on to their knees.

Noncompliant Code Example

private void readTheFile() throws IOException {
  Path path = Paths.get(this.fileName);
  BufferedReader reader = Files.newBufferedReader(path, this.charset);
  // ...
  reader.close();  // Noncompliant
  // ...
  Files.lines("input.txt").forEach(System.out::println); // Noncompliant: The stream needs to be closed
}

private void doSomething() {
  OutputStream stream = null;
  try {
    for (String property : propertyList) {
      stream = new FileOutputStream("myfile.txt");  // Noncompliant
      // ...
    }
  } catch (Exception e) {
    // ...
  } finally {
    stream.close();  // Multiple streams were opened. Only the last is closed.
  }
}

Compliant Solution

private void readTheFile(String fileName) throws IOException {
    Path path = Paths.get(fileName);
    try (BufferedReader reader = Files.newBufferedReader(path, StandardCharsets.UTF_8)) {
      reader.readLine();
      // ...
    }
    // ..
    try (Stream<String> input = Files.lines("input.txt"))  {
      input.forEach(System.out::println);
    }
}

private void doSomething() {
  OutputStream stream = null;
  try {
    stream = new FileOutputStream("myfile.txt");
    for (String property : propertyList) {
      // ...
    }
  } catch (Exception e) {
    // ...
  } finally {
    stream.close();
  }
}

Exceptions

Instances of the following classes are ignored by this rule because close has no effect:

• java.io.ByteArrayOutputStream
• java.io.ByteArrayInputStream
• java.io.CharArrayReader
• java.io.CharArrayWriter
• java.io.StringReader
• java.io.StringWriter

Java 7 introduced the try-with-resources statement, which implicitly closes Closeables. All resources opened in a try-with-resources statement are ignored by this rule.

try (BufferedReader br = new BufferedReader(new FileReader(fileName))) {
  //...
}
catch ( ... ) {
  //...
}

See

• MITRE, CWE-459 - Incomplete Cleanup
• MITRE, CWE-772 - Missing Release of Resource after Effective Lifetime
• CERT, FIO04-J. - Release resources when they are no longer needed
• CERT, FIO42-C. - Close files when they are no longer needed
• Try With Resources

          targetName = normalizeName(portObject) + "/" + sbmlModelDoc.getModel().getId() + ".sbml";

Close

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.

          ObjectOutputStream oos = new ObjectOutputStream(out);

Close

Connections, streams, files, and other classes that implement the Closeable interface or its super-interface, AutoCloseable, needs to be closed after use. Further, that close call must be made in a finally block otherwise an exception could keep the call from being made. Preferably, when class implements AutoCloseable, resource should be created using "try-with-resources" pattern and will be closed automatically.

Failure to properly close resources will result in a resource leak which could bring first the application and then perhaps the box the application is on to their knees.

Noncompliant Code Example

private void readTheFile() throws IOException {
  Path path = Paths.get(this.fileName);
  BufferedReader reader = Files.newBufferedReader(path, this.charset);
  // ...
  reader.close();  // Noncompliant
  // ...
  Files.lines("input.txt").forEach(System.out::println); // Noncompliant: The stream needs to be closed
}

private void doSomething() {
  OutputStream stream = null;
  try {
    for (String property : propertyList) {
      stream = new FileOutputStream("myfile.txt");  // Noncompliant
      // ...
    }
  } catch (Exception e) {
    // ...
  } finally {
    stream.close();  // Multiple streams were opened. Only the last is closed.
  }
}

Compliant Solution

private void readTheFile(String fileName) throws IOException {
    Path path = Paths.get(fileName);
    try (BufferedReader reader = Files.newBufferedReader(path, StandardCharsets.UTF_8)) {
      reader.readLine();
      // ...
    }
    // ..
    try (Stream<String> input = Files.lines("input.txt"))  {
      input.forEach(System.out::println);
    }
}

private void doSomething() {
  OutputStream stream = null;
  try {
    stream = new FileOutputStream("myfile.txt");
    for (String property : propertyList) {
      // ...
    }
  } catch (Exception e) {
    // ...
  } finally {
    stream.close();
  }
}

Exceptions

Instances of the following classes are ignored by this rule because close has no effect:

• java.io.ByteArrayOutputStream
• java.io.ByteArrayInputStream
• java.io.CharArrayReader
• java.io.CharArrayWriter
• java.io.StringReader
• java.io.StringWriter

Java 7 introduced the try-with-resources statement, which implicitly closes Closeables. All resources opened in a try-with-resources statement are ignored by this rule.

try (BufferedReader br = new BufferedReader(new FileReader(fileName))) {
  //...
}
catch ( ... ) {
  //...
}

See

• MITRE, CWE-459 - Incomplete Cleanup
• MITRE, CWE-772 - Missing Release of Resource after Effective Lifetime
• CERT, FIO04-J. - Release resources when they are no longer needed
• CERT, FIO42-C. - Close files when they are no longer needed
• Try With Resources

  protected void useCurrentValueAsDefault() {}

Close

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
  }
}

  void convertToKnimeDataTable(FskPortObject fskObj, ExecutionContext exec) throws Exception {

Close

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
  }
}

    public FskPortObject loadPortObject(PortObjectZipInputStream in, PortObjectSpec spec,

Close

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

• Cognitive Complexity