/**
* @param bigg
* @param input
* @param output
* @param parameters
* @throws IOException
* @throws XMLStreamException
*/
public void batchProcess(BiGGDB bigg, File input, File output, Parameters parameters)
throws IOException, XMLStreamException {
// We test if non-existing path denotes a file or directory by checking if
// it contains at least one period in its name. If so, we assume it is a
// file.
if (!output.exists()
&& (output.getName().lastIndexOf('.') < 0)
&& !(input.isFile() && input.getName().equals(output.getName()))) {
logger.info(MessageFormat.format("Creating directory {0}.", output.getAbsolutePath()));
output.mkdir();
}
if (input.isFile()) {
boolean jsonFile = SBFileFilter.hasFileType(input, SBFileFilter.FileType.JSON_FILES);
boolean matFile = SBFileFilter.hasFileType(input, SBFileFilter.FileType.MAT_FILES);
if (SBFileFilter.isSBMLFile(input) || matFile || jsonFile) {
if (output.isDirectory()) {
String fName = input.getName();
if (matFile || jsonFile) {
fName = FileTools.removeFileExtension(fName) + ".xml";
}
output = new File(Utils.ensureSlash(output.getAbsolutePath()) + fName);
}
polish(bigg, input, output, parameters);
}
} else {
if (!output.isDirectory()) {
throw new IOException(
MessageFormat.format("Cannot write to file {0}.", output.getAbsolutePath()));
}
for (File file : input.listFiles()) {
File target = new File(Utils.ensureSlash(output.getAbsolutePath()) + file.getName());
batchProcess(bigg, file, target, parameters);
}
}
}
