Package org.sbml.jsbml

Examples of org.sbml.jsbml.SBMLDocument.checkConsistency()

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  @Test public void checkConsistency() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v4/BIOMD0000000228.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);

    int nbErrors = doc.checkConsistency();

    System.out.println("Found " + nbErrors + " errors on Biomodels 228 with the unit checking turned off.");
   
    // assertTrue(nbErrors > 0); // not sure what is happening with this model and the online validator !!!
    assertTrue(nbErrors == 0); // sometimes there is an error, sometimes no errors !
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    SBMLDocument doc = new SBMLReader().readSBML(fileName);
   
    doc.setConsistencyChecks(SBMLValidator.CHECK_CATEGORY.UNITS_CONSISTENCY, true);
   
    int nbErrors = doc.checkConsistency();

    int numRealErrors = doc.getErrorLog().getNumFailsWithSeverity(SEVERITY.ERROR);
      if (numRealErrors > 0) {
        System.out.println("# Found " + numRealErrors + " VALIDATION ERRORS !!!");
      }
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  @Test public void checkConsistency228() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v4/BIOMD0000000228.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
    try {
      int nbErrors = doc.checkConsistency();

      System.out.println("Found " + nbErrors + " errors on Biomodels 228 with the unit checking turned off.");

    } catch (Exception e) {
      e.printStackTrace();
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  @Test public void checkConsistency025() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v1/BIOMD0000000025.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
    try {
      int nbErrors = doc.checkConsistency();

      System.out.println("Found " + nbErrors + " errors on Biomodels 025 with the unit checking turned off.");

    } catch (Exception e) {
      e.printStackTrace();
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      print("\nFurther consistency checking and validation aborted.\n");
      System.exit(1);
    }
    else
    {
      long errors = document.checkConsistency();
      long size   = new File(filename).length();

      println("            filename: " + filename);
      println("           file size: " + size);
      println("      read time (ms): " + (stop - start));
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  @Test public void checkConsistency() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v4/BIOMD0000000228.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);

    int nbErrors = doc.checkConsistency();

    System.out.println("Found " + nbErrors + " errors on Biomodels 228 with the unit checking turned off.");
   
    // assertTrue(nbErrors > 0); // not sure what is happening with this model and the online validator !!!
    assertTrue(nbErrors == 0); // sometimes there is an error, sometimes no errors !
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    SBMLDocument doc = new SBMLReader().readSBML(fileName);
   
    doc.setConsistencyChecks(SBMLValidator.CHECK_CATEGORY.UNITS_CONSISTENCY, true);
   
    int nbErrors = doc.checkConsistency();

    System.out.println("Found " + nbErrors + " errors on Biomodels 025 with the unit checking turned on.");
    assertTrue(nbErrors > 0);
   
    assertTrue(doc.getErrorLog().getNumFailsWithSeverity(SEVERITY.ERROR) == 0);
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  @Test public void checkConsistency228() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v4/BIOMD0000000228.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
    try {
      int nbErrors = doc.checkConsistency();

      System.out.println("Found " + nbErrors + " errors on Biomodels 228 with the unit checking turned off.");

    } catch (Exception e) {
      e.printStackTrace();
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  @Test public void checkConsistency025() throws IOException, XMLStreamException {
    String fileName = DATA_FOLDER + "/l2v1/BIOMD0000000025.xml";
   
    SBMLDocument doc = new SBMLReader().readSBML(fileName);
    try {
      int nbErrors = doc.checkConsistency();

      System.out.println("Found " + nbErrors + " errors on Biomodels 025 with the unit checking turned off.");

    } catch (Exception e) {
      e.printStackTrace();
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      print("\nFurther consistency checking and validation aborted.\n");
      System.exit(1);
    }
    else
    {
      long errors = document.checkConsistency();
      long size   = new File(filename).length();

      println("            filename: " + filename);
      println("           file size: " + size);
      println("      read time (ms): " + (stop - start));
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