private File convertNWBtoGraphML(File nwbFile, ValidateNWBFile validator) {
try {
File graphml = getTempFile();
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(graphml)));
BufferedReader reader = new BufferedReader(new FileReader(nwbFile));
writeGraphMLHeader(out);
writeAttributes(out, validator);
printGraph(out, validator, reader);
out.println("</graph>");
out.println("</graphml>");
reader.close();
out.close();
return graphml;
} catch (FileNotFoundException e) {
guiBuilder.showError("File Not Found Exception", "Got an File Not Found Exception", e);
return null;
} catch (IOException ioe) {
guiBuilder.showError("IOException", "Got an IOException", ioe);
return null;
}
}
public Data[] execute() {
File inData, outData;
Data[] dm = null;
ValidateNWBFile validator;
guiBuilder = (GUIBuilderService) ciContext.getService(GUIBuilderService.class.getName());
logger = (LogService) ciContext.getService(LogService.class.getName());
Object inFile = data[0].getData();
String format = data[0].getFormat();
if (inFile instanceof File && format.equalsIgnoreCase(NWBFileProperty.NWB_MIME_TYPE)) {
inData = (File) inFile;
validator = new ValidateNWBFile();
try {
validator.validateNWBFormat(inData);
if (validator.getValidationResult()) {
outData = convertNWBtoGraphML(inData, validator);
if (outData != null) {
dm = new Data[] {new BasicData(outData, "file:text/graphml+xml")};
return dm;
} else {
guiBuilder.showError(
"Unable to Make a File Conversion",
"Fail to convert a file from NWB file format to GraphML file format.",
"");
return null;
}
} else {
guiBuilder.showError(
"Unable to Make a File Conversion",
"The input file has a bad NWB format. \n"
+ "Please review the latest NWB File Formate Specification at \n"
+ "http://nwb.slis.indiana.edu/software.html, and update your file.",
"");
return null;
}
} catch (FileNotFoundException e) {
guiBuilder.showError("File Not Found Exception", "Got an File Not Found Exception", e);
return null;
} catch (IOException ioe) {
guiBuilder.showError("IOException", "Got an IOException", ioe);
return null;
}
} else {
if (!(inFile instanceof File)) {
guiBuilder.showError(
"Unable to Make a File Conversion",
"Fail to convert a file from NWB format to GraphML format, because the input is not a file.",
"");
} else if (!(format.equalsIgnoreCase(NWBFileProperty.NWB_MIME_TYPE))) {
guiBuilder.showError(
"Unable to Make a File Conversion",
"Wrong input file type. Expecting "
+ NWBFileProperty.NWB_MIME_TYPE
+ ", but the input file type is "
+ format
+ ".",
"");
}
return null;
}
}