private static boolean retainTerm(LoomTerm term) {
if (termRetainer.isEmpty()) {
// There are no term labels to compare.
return termRetainer.add(term);
}
LoomTerm retainedTerm = termRetainer.get(0);
if (retainedTerm.matchLabel(term)) {
return termRetainer.add(term);
}
return false;
}
/**
* Construct an ontology {@link LoomTerm}, by reading a line of text that contains: label type
* ontologyID virtualOntologyID.
*
* @throws IOException
*/
private static LoomTerm readTerm() throws IOException {
LoomTerm iTerm = null;
String iLine = iReader.readLine();
while (iLine != null) {
log.trace("iLine = " + iLine);
// Skip blank or comment lines
if (iLine.length() == 0 || iLine.startsWith("#")) {
iLine = iReader.readLine();
continue;
}
iTerm = new LoomTerm();
iTerm.parseTerm(iLine, delimiter);
break;
}
return iTerm;
}
/**
* @param args args[0] may contain a file path for input, which can be used when calling this
* class from a shell script.
*/
public static void main(String[] args) {
try {
// Configure input file(s).
if (args.length > 0) {
iFileName = args[0];
}
createInputStream(iFileName);
// Configure output file(s).
if (args.length > 1) {
oFileName = args[1];
}
if (oFileName != null) {
// Create the first of N output files.
createOutputStream(oFileName);
}
log.trace("iFileName = " + iFileName);
// Populate an array of term labels to be ignored. These are used in
// processMatchingTerms().
skipLabels.add("none");
skipLabels.add("other");
skipLabels.add("unidentified");
skipLabels.add("unknown");
skipLabels.add("unspecified");
// The label 'all' is often poorly used in ontologies, so
// it's vague and often generates poor matches in LOOM.
skipLabels.add("all");
// The label 'chair' has been found to match 'chairman'
// or 'chairperson' erroneously.
skipLabels.add("chair");
// Skip matches between 'cell' and 'cellulartelephone'
cellphone[0] = "cellulartelephone";
cellphone[1] = "cell";
/*
* Process sorted terms. The algorithm reads N consecutive lines
* that have matching labels and reports all their matching terms.
*/
boolean retain = true;
while (retain) {
LoomTerm iTerm = readTerm();
if (iTerm == null) {
// At the EOF for the terms to be processed.
break;
}
log.trace("iTerm = " + iTerm.toString());
// Retain this term if it's label matches a retained term.
retain = retainTerm(iTerm);
if (!retain) {
// This iTerm doesn't match any retained terms, so
// process and clear the terms already retained.
processMatchingTerms();
// Start a new retention set.
retain = retainTerm(iTerm);
}
log.trace("retain = " + retain);
}
// Process any remaining set of retained terms (at EOF).
processMatchingTerms();
} catch (Exception e) {
log.fatal(e.toString());
e.printStackTrace();
System.exit(1);
}
}
private static void processMatchingTerms() throws Exception {
// Report all the matches between terms.
LoomTerm term1 = null;
LoomTerm term2 = null;
while (!termRetainer.isEmpty()) {
term1 = termRetainer.remove(0);
Iterator<LoomTerm> itr = termRetainer.iterator();
while (itr.hasNext()) {
term2 = itr.next();
// Don't report any matches within an ontology.
if (term1.matchOntID(term2)) {
log.trace("Skipping terms, same ontology:");
log.trace("... {}", term1.toString());
log.trace("... {}", term2.toString());
continue;
}
// Detect any exact match for term URI.
if (term1.matchURL(term2)) {
// This is handled by the UriMatchMappings process
log.trace("Skipping terms, same URL:");
log.trace("... {}", term1.toString());
log.trace("... {}", term2.toString());
continue;
}
// Don't report matches between synonyms.
if (term1.isSkosAltLabel() && term2.isSkosAltLabel()) {
log.trace("Skipping terms, both altLabel:");
log.trace("... {}", term1.toString());
log.trace("... {}", term2.toString());
continue;
}
// Ignore some term labels.
if (skipLabels(term1, term2) || skipCellPhone(term1, term2)) {
log.trace("Skipping terms, a label is problematic:");
log.trace("... {}", term1.toString());
log.trace("... {}", term2.toString());
continue;
}
createLoomMappings(term1, term2);
}
}
// Should not be necessary, but just to be sure!
termRetainer.clear();
// Do we need a new output file?
if (oFileName != null && oMapCount > oMapCountMax) {
createOutputStream(oFileName);
oMapCount = 0;
}
}
