/**
* @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);
}
}
}
/**
* @param bigg
* @param input
* @param output
* @param parameters
* @throws XMLStreamException
* @throws IOException
*/
public void polish(BiGGDB bigg, File input, File output, Parameters parameters)
throws XMLStreamException, IOException {
long time = System.currentTimeMillis();
logger.info(MessageFormat.format("Reading input file {0}.", input.getAbsolutePath()));
SBMLDocument doc = null;
if (SBFileFilter.hasFileType(input, SBFileFilter.FileType.MAT_FILES)) {
doc = COBRAparser.read(input, parameters.omitGenericTerms);
} else if (SBFileFilter.hasFileType(input, SBFileFilter.FileType.JSON_FILES)) {
doc = JSONparser.read(input);
} else {
doc = SBMLReader.read(input, new UpdateListener());
}
if (!doc.isSetLevelAndVersion()
|| (doc.getLevelAndVersion().compareTo(ValuePair.of(3, 1)) < 0)) {
logger.info("Trying to convert the model to Level 3 Version 2.");
org.sbml.jsbml.util.SBMLtools.setLevelAndVersion(doc, 3, 1);
}
SBMLPolisher polisher = new SBMLPolisher();
polisher.setCheckMassBalance(parameters.checkMassBalance);
polisher.setOmitGenericTerms(parameters.omitGenericTerms);
if (parameters.includeAnyURI != null) {
polisher.setIncludeAnyURI(parameters.includeAnyURI.booleanValue());
}
if (parameters.documentTitlePattern != null) {
polisher.setDocumentTitlePattern(parameters.documentTitlePattern);
}
polisher.setFluxCoefficients(parameters.fluxCoefficients);
polisher.setFluxObjectives(parameters.fluxObjectives);
doc = polisher.polish(doc);
if (parameters.annotateWithBiGG) {
BiGGAnnotation annotation = new BiGGAnnotation(bigg, polisher);
if (parameters.documentNotesFile != null) {
annotation.setDocumentNotesFile(parameters.documentNotesFile);
}
if (parameters.modelNotesFile != null) {
annotation.setModelNotesFile(parameters.modelNotesFile);
}
doc = annotation.annotate(doc);
}
// <?xml-stylesheet type="text/xsl"
// href="/Users/draeger/Documents/workspace/BioNetView/resources/edu/ucsd/sbrg/bigg/bigg_sbml.xsl"?>
logger.info(MessageFormat.format("Writing output file {0}", output.getAbsolutePath()));
TidySBMLWriter.write(
doc, output, getClass().getSimpleName(), getVersionNumber(), ' ', (short) 2);
// SBMLWriter.write(doc, sbmlFile, ' ', (short) 2);
if (parameters.compression != Compression.NONE) {
String fileExtension = parameters.compression.getFileExtension();
String archive = output.getAbsolutePath() + "." + fileExtension;
logger.info(MessageFormat.format("Packing archive file {0}", archive));
switch (parameters.compression) {
case ZIP:
ZIPUtils.ZIPcompress(
new String[] {output.getAbsolutePath()}, archive, "SBML Archive", true);
break;
case GZIP:
ZIPUtils.GZip(output.getAbsolutePath(), archive);
break;
default:
break;
}
if ((parameters.sbmlValidation != null) && parameters.sbmlValidation) {
validate(archive);
}
}
time = System.currentTimeMillis() - time;
Calendar calendar = Calendar.getInstance();
calendar.setTimeInMillis(time);
logger.info(MessageFormat.format("Done ({0,time, ssss} s).", calendar.getTime()));
}
/* (non-Javadoc)
* @see de.zbit.kegg.gui.TranslatorGraphLayerPanel#getOutputFileFilterForRealDocument()
*/
@Override
protected List<FileFilter> getOutputFileFilterForRealDocument() {
List<FileFilter> ff = new LinkedList<FileFilter>();
ff.add(SBFileFilter.createSBGNFileFilter());
return ff;
}