public static HashMap<Long, UUID> readSCTIDtoUUIDMapInfo(File snomedLocation)
throws ClassNotFoundException, IOException {
File snomedJbinFile = null;
if (snomedLocation.isDirectory()) {
for (File f : snomedLocation.listFiles()) {
if (f.isFile() && f.getName().toLowerCase().endsWith(".jbin")) {
snomedJbinFile = f;
break;
}
}
} else {
snomedJbinFile = snomedLocation;
}
if (snomedJbinFile == null) {
throw new IOException("Couldn't find sct data file in " + snomedLocation);
}
UUID sctIDType = IsaacMetadataAuxiliaryBinding.SNOMED_INTEGER_ID.getPrimodialUuid();
// Read in the SCT data
HashMap<Long, UUID> sctConcepts = new HashMap<>();
ConsoleUtil.println("Reading " + snomedJbinFile.getName());
DataInputStream in = new DataInputStream(new FileInputStream(snomedJbinFile));
while (in.available() > 0) {
if (sctConcepts.size() % 1000 == 0) {
ConsoleUtil.showProgress();
}
TtkConceptChronicle concept = new TtkConceptChronicle(in);
if (concept.getConceptAttributes() != null
&& concept.getConceptAttributes().getAdditionalIdComponents() != null) {
for (TtkIdentifier id : concept.getConceptAttributes().getAdditionalIdComponents()) {
if (sctIDType.equals(id.getAuthorityUuid())) {
// Store these by SCTID, because there is no reliable way to generate a UUID from a
// SCTID.
sctConcepts.put(
Long.parseLong(id.getDenotation().toString()), concept.getPrimordialUuid());
break;
}
}
}
}
in.close();
ConsoleUtil.println("Read UUIDs from SCT file - read " + sctConcepts.size() + " concepts");
return sctConcepts;
}
@Override
public void execute() throws MojoExecutionException {
ConverterUUID.disableUUIDMap_ =
((createDebugUUIDMap == null || createDebugUUIDMap.length() == 0)
? false
: Boolean.parseBoolean(createDebugUUIDMap));
if (ConverterUUID.disableUUIDMap_) {
ConsoleUtil.println(
"The UUID Debug map is disabled - this also prevents duplicate ID detection");
}
// Set up the output
if (!outputDirectory.exists()) {
outputDirectory.mkdirs();
}
checkSkipListSupport();
}
