Exemplo n.º 1
0
 /**
  * Scans the given command-line options for a specific file option and returns the corresponding
  * file if it exists, {@code null} otherwise.
  *
  * @param args command-line options.
  * @param option a specific file option to look for.
  * @return a {@link File} object that corresponds to a desired command-line option, or {@code
  *     null} if it does not exist.
  */
 private File parseFileOption(SBProperties args, Option<File> option) {
   if (args.containsKey(option)) {
     File notesFile = new File(args.getProperty(option));
     if ((notesFile != null) && notesFile.exists() && notesFile.canRead()) {
       return notesFile;
     }
   }
   return null;
 }
Exemplo n.º 2
0
  /*
   * (non-Javadoc)
   * @see de.zbit.Launcher#commandLineMode(de.zbit.AppConf)
   */
  @Override
  public void commandLineMode(AppConf appConf) {
    SBProperties args = appConf.getCmdArgs();
    if (args.containsKey(LogOptions.LOG_FILE)) {
      LogUtil.addHandler(
          new ConsoleHandler() {

            /** Formatter */
            OneLineFormatter formatter = new OneLineFormatter(false, false, false);

            /*
             * (non-Javadoc)
             * @see java.util.logging.StreamHandler#flush()
             */
            @Override
            public synchronized void flush() {
              System.out.flush();
            }

            /*
             * (non-Javadoc)
             * @see
             * java.util.logging.ConsoleHandler#publish(java.util.logging.LogRecord)
             */
            @Override
            public void publish(LogRecord record) {
              if (record.getLevel().intValue() == Level.INFO.intValue()) {
                try {
                  String message = formatter.format(record);
                  System.out.write(message.getBytes());
                } catch (IOException exc) {
                  reportError(null, exc, ErrorManager.FORMAT_FAILURE);
                  return;
                }
              }
            }
          },
          getLogPackages());
    }
    BiGGDB bigg = null;
    Parameters parameters = new Parameters();
    parameters.annotateWithBiGG = args.getBooleanProperty(ModelPolisherOptions.ANNOTATE_WITH_BIGG);
    if (parameters.annotateWithBiGG) {
      try {
        // Connect to database and launch application:
        String passwd = args.getProperty(DBOptions.PASSWD);
        bigg =
            new BiGGDB(
                new PostgreSQLConnector(
                    args.getProperty(DBOptions.HOST),
                    args.getIntProperty(DBOptions.PORT),
                    args.getProperty(DBOptions.USER),
                    passwd != null ? passwd : "",
                    args.getProperty(DBOptions.DBNAME)));
      } catch (SQLException | ClassNotFoundException exc) {
        exc.printStackTrace();
      }
    }
    // Gives users the choice to pass an alternative model notes XHTML file to
    // the program.
    File modelNotesFile = parseFileOption(args, ModelPolisherOptions.MODEL_NOTES_FILE);
    File documentNotesFile = parseFileOption(args, ModelPolisherOptions.DOCUMENT_NOTES_FILE);
    String documentTitlePattern = null;
    if (args.containsKey(ModelPolisherOptions.DOCUMENT_TITLE_PATTERN)) {
      documentTitlePattern = args.getProperty(ModelPolisherOptions.DOCUMENT_TITLE_PATTERN);
    }
    double[] coefficients = null;
    if (args.containsKey(ModelPolisherOptions.FLUX_COEFFICIENTS)) {
      String c = args.getProperty(ModelPolisherOptions.FLUX_COEFFICIENTS);
      String coeff[] = c.substring(1, c.length() - 1).split(",");
      coefficients = new double[coeff.length];
      for (int i = 0; i < coeff.length; i++) {
        coefficients[i] = Double.parseDouble(coeff[i].trim());
      }
    }
    String fObj[] = null;
    if (args.containsKey(ModelPolisherOptions.FLUX_OBJECTIVES)) {
      String fObjectives = args.getProperty(ModelPolisherOptions.FLUX_OBJECTIVES);
      fObj = fObjectives.substring(1, fObjectives.length() - 1).split(":");
    }
    parameters.includeAnyURI = args.getBooleanProperty(ModelPolisherOptions.INCLUDE_ANY_URI);
    parameters.checkMassBalance = args.getBooleanProperty(ModelPolisherOptions.CHECK_MASS_BALANCE);
    parameters.compression =
        ModelPolisherOptions.Compression.valueOf(
            args.getProperty(ModelPolisherOptions.COMPRESSION_TYPE));
    parameters.documentNotesFile = documentNotesFile;
    parameters.documentTitlePattern = documentTitlePattern;
    parameters.fluxCoefficients = coefficients;
    parameters.fluxObjectives = fObj;
    parameters.modelNotesFile = modelNotesFile;
    parameters.omitGenericTerms = args.getBooleanProperty(ModelPolisherOptions.OMIT_GENERIC_TERMS);
    parameters.sbmlValidation = args.getBooleanProperty(ModelPolisherOptions.SBML_VALIDATION);
    // run polishing operations in background and parallel.
    try {
      batchProcess(
          bigg,
          new File(args.getProperty(IOOptions.INPUT)),
          new File(args.getProperty(IOOptions.OUTPUT)),
          parameters);
    } catch (SBMLException | XMLStreamException | IOException exc) {
      exc.printStackTrace();
    }
  }