/**
* 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;
}
/*
* (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();
}
}
