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Update curie formation logic #767

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Oct 25, 2024
Merged

Update curie formation logic #767

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24 changes: 22 additions & 2 deletions dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package uk.ac.ebi.rdf2json.annotators;

import java.util.Set;
import java.util.regex.Pattern;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -39,16 +40,35 @@ public static void annotateShortForms(OntologyGraph graph) {

/*
CURIEs are formed by following rules:
If there is only one underscore "_" AND the characters before the underscore are PreferredPrefix then replace the underscore with colon ":"
If there is only one underscore "_" AND the characters after the underscore are numbers then replace the underscore with colon ":"
If there is only one underscore "_" and the characters after the underscore are not just numbers then just keep the curie same as shortform
If there are multiple underscore but has only digits after the last underscore then the code replaces the last underscore with a colon
*/
String curie;
// Pattern for: single underscore, prefix matches preferredPrefix
String preferredPrefixPattern = "^(?:" + Pattern.quote(preferredPrefix) + ")_([^_]+)$";
// Pattern for: single underscore, suffix is all digits
String singleUnderscoreDigitsPattern = "^[^_]+_(\\d+)$";
// Pattern for: multiple underscores, suffix is all digits
String multipleUnderscoresDigitsPattern = "^(.*)_(\\d+)$";
if (shortForm.matches(preferredPrefixPattern)) {
curie = shortForm.replaceFirst("_", ":");
} else if (shortForm.matches(singleUnderscoreDigitsPattern)) {
curie = shortForm.replaceFirst("_", ":");
} else if (shortForm.matches(multipleUnderscoresDigitsPattern)) {
// Multiple underscores, suffix is digits
// Replace the last underscore with a colon
curie = shortForm.replaceFirst("_(?=\\d+$)", ":");
} else {
// No transformation needed
curie = shortForm;
}

String curie = shortForm.replaceFirst("_(\\d+)$", ":$1");
c.properties.addProperty("shortForm", PropertyValueLiteral.fromString(shortForm));
c.properties.addProperty("curie", PropertyValueLiteral.fromString(curie));
}
}
}
long endTime3 = System.nanoTime();
logger.info("annotate short forms: {}", ((endTime3 - startTime3) / 1000 / 1000 / 1000));
}
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