/**
* Checks if the two entries represent the same publication.
*
* @param one BibtexEntry
* @param two BibtexEntry
* @return boolean
*/
public static boolean isDuplicate(BibtexEntry one, BibtexEntry two) {
// First check if they are of the same type - a necessary condition:
if (one.getType() != two.getType()) {
return false;
}
// The check if they have the same required fields:
String[] fields = one.getType().getRequiredFields().toArray(new String[0]);
double[] req;
if (fields == null) {
req = new double[] {0., 0.};
} else {
req = DuplicateCheck.compareFieldSet(fields, one, two);
}
if (Math.abs(req[0] - DuplicateCheck.duplicateThreshold) > DuplicateCheck.doubtRange) {
// Far from the threshold value, so we base our decision on the req. fields only
return req[0] >= DuplicateCheck.duplicateThreshold;
}
// Close to the threshold value, so we take a look at the optional fields, if any:
fields = one.getType().getOptionalFields().toArray(new String[0]);
if (fields != null) {
double[] opt = DuplicateCheck.compareFieldSet(fields, one, two);
double totValue =
((DuplicateCheck.reqWeight * req[0] * req[1]) + (opt[0] * opt[1]))
/ ((req[1] * DuplicateCheck.reqWeight) + opt[1]);
return totValue >= DuplicateCheck.duplicateThreshold;
}
return req[0] >= DuplicateCheck.duplicateThreshold;
}
private static double correlateStrings(String s1, String s2, boolean truncate) {
int minLength = Math.min(s1.length(), s2.length());
if (truncate && (minLength == 1)) {
return s1.charAt(0) == s2.charAt(0) ? 1.0 : 0.0;
} else if ((s1.length() == 1) && (s2.length() == 1)) {
return s1.equals(s2) ? 1.0 : 0.0;
} else if (minLength == 0) {
return s1.isEmpty() && s2.isEmpty() ? 1.0 : 0;
}
// Convert strings to numbers and harmonize length in a method dependent on truncate:
if (truncate) {
// Harmonize length by truncation:
if (s1.length() > minLength) {
s1 = s1.substring(0, minLength);
}
if (s2.length() > minLength) {
s2 = s2.substring(0, minLength);
}
}
double[] n1 = DuplicateCheck.numberizeString(s1);
double[] n2 = DuplicateCheck.numberizeString(s2);
// If truncation is disabled, harmonize length by interpolation:
if (!truncate) {
if (n1.length < n2.length) {
n1 = DuplicateCheck.stretchArray(n1, n2.length);
} else if (n2.length < n1.length) {
n2 = DuplicateCheck.stretchArray(n2, n1.length);
}
}
return DuplicateCheck.corrCoef(n1, n2);
}
private static int compareSingleField(String field, BibtexEntry one, BibtexEntry two) {
String s1 = one.getField(field);
String s2 = two.getField(field);
if (s1 == null) {
if (s2 == null) {
return EMPTY_IN_BOTH;
}
return EMPTY_IN_ONE;
} else if (s2 == null) {
return EMPTY_IN_TWO;
}
if (field.equals("author") || field.equals("editor")) {
// Specific for name fields.
// Harmonise case:
String auth1 =
AuthorList.fixAuthor_lastNameOnlyCommas(s1, false).replaceAll(" and ", " ").toLowerCase();
String auth2 =
AuthorList.fixAuthor_lastNameOnlyCommas(s2, false).replaceAll(" and ", " ").toLowerCase();
double similarity = DuplicateCheck.correlateByWords(auth1, auth2, false);
if (similarity > 0.8) {
return EQUAL;
}
return NOT_EQUAL;
} else if (field.equals("pages")) {
// Pages can be given with a variety of delimiters, "-", "--", " - ", " -- ".
// We do a replace to harmonize these to a simple "-":
// After this, a simple test for equality should be enough:
s1 = s1.replaceAll("[- ]+", "-");
s2 = s2.replaceAll("[- ]+", "-");
if (s1.equals(s2)) {
return EQUAL;
}
return NOT_EQUAL;
} else if (field.equals("journal")) {
// We do not attempt to harmonize abbreviation state of the journal names,
// but we remove periods from the names in case they are abbreviated with
// and without dots:
s1 = s1.replaceAll("\\.", "").toLowerCase();
s2 = s2.replaceAll("\\.", "").toLowerCase();
double similarity = DuplicateCheck.correlateByWords(s1, s2, true);
if (similarity > 0.8) {
return EQUAL;
}
return NOT_EQUAL;
} else {
s1 = s1.toLowerCase();
s2 = s2.toLowerCase();
double similarity = DuplicateCheck.correlateByWords(s1, s2, false);
if (similarity > 0.8) {
return EQUAL;
}
return NOT_EQUAL;
}
}
/**
* Goes through all entries in the given database, and if at least one of them is a duplicate of
* the given entry, as per Util.isDuplicate(BibtexEntry, BibtexEntry), the duplicate is returned.
* The search is terminated when the first duplicate is found.
*
* @param database The database to search.
* @param entry The entry of which we are looking for duplicates.
* @return The first duplicate entry found. null if no duplicates are found.
*/
public static BibtexEntry containsDuplicate(BibtexDatabase database, BibtexEntry entry) {
for (BibtexEntry other : database.getEntries()) {
if (DuplicateCheck.isDuplicate(entry, other)) {
return other; // Duplicate found.
}
}
return null; // No duplicate found.
}
/**
* Compare two strings on the basis of word-by-word correlation analysis.
*
* @param s1 The first string
* @param s2 The second string
* @param truncate if true, always truncate the longer of two words to be compared to harmonize
* their length. If false, use interpolation to harmonize the strings.
* @return a value in the interval [0, 1] indicating the degree of match.
*/
static double correlateByWords(String s1, String s2, boolean truncate) {
String[] w1 = s1.split("\\s");
String[] w2 = s2.split("\\s");
int n = Math.min(w1.length, w2.length);
int misses = 0;
for (int i = 0; i < n; i++) {
double corr = DuplicateCheck.correlateStrings(w1[i], w2[i], truncate);
if (corr < 0.75) {
misses++;
}
}
double missRate = (double) misses / (double) n;
return 1 - missRate;
}
public EntryDeleteChange(BibtexEntry memEntry, BibtexEntry tmpEntry) {
super("Deleted entry");
this.memEntry = memEntry;
this.tmpEntry = tmpEntry;
// Compare the deleted entry in memory with the one in the tmpfile. The
// entry could have been removed in memory.
double matchWithTmp = DuplicateCheck.compareEntriesStrictly(memEntry, tmpEntry);
// Check if it has been modified locally, since last tempfile was saved.
boolean isModifiedLocally = !(matchWithTmp > 1);
// Util.pr("Modified entry: "+memEntry.getCiteKey()+"\n Modified locally: "+isModifiedLocally
// +" Modifications agree: "+modificationsAgree);
PreviewPanel pp =
new PreviewPanel(
null, memEntry, null, new MetaData(), Globals.prefs.get(JabRefPreferences.PREVIEW_0));
sp = new JScrollPane(pp);
}
private static double[] compareFieldSet(String[] fields, BibtexEntry one, BibtexEntry two) {
double res = 0;
double totWeights = 0.;
for (String field : fields) {
double weight;
if (DuplicateCheck.fieldWeights.containsKey(field)) {
weight = DuplicateCheck.fieldWeights.get(field);
} else {
weight = 1.0;
}
totWeights += weight;
int result = DuplicateCheck.compareSingleField(field, one, two);
if (result == EQUAL) {
res += weight;
} else if (result == EMPTY_IN_BOTH) {
totWeights -= weight;
}
}
if (totWeights > 0) {
return new double[] {res / totWeights, totWeights};
}
return new double[] {0.5, 0.0};
}