- Add preferredPrefix in rdf2json

- Change curie logic linker pass 1
EBISPOT · Aug 19, 2024 · d3da8e0 · d3da8e0
1 parent 931c002
commit d3da8e0
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/dataload/linker/src/main/java/LinkerPass1.java b/dataload/linker/src/main/java/LinkerPass1.java
@@ -178,7 +178,8 @@ public static LinkerPass1Result run(String inputJsonFilename) throws IOException
 					if(curieObject.has("value")) {
 						String curieValue = curieObject.get("value").getAsString();
 						if(!curieValue.contains(":")) {
-							curieValue = entry.getValue().definingOntologyIds.iterator().next().toUpperCase() + ":" + curieValue;
+							var definingOntologyId = entry.getValue().definingOntologyIds.iterator().next();
+							curieValue = entry.getValue().ontologyIdToDefinitions.get(definingOntologyId).curie.getAsJsonObject().get("value").getAsString();
 							curieObject.addProperty("value", curieValue);
 							result.iriToDefinitions.put(entry.getKey(), definitions);
 						}

diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
@@ -31,6 +31,9 @@ public static void annotateShortForms(OntologyGraph graph) {
 			if(c.uri == null)
 				continue;
 
+			if (preferredPrefix == null || preferredPrefix.isEmpty()) {
+				preferredPrefix = graph.config.get("id").toString().toUpperCase();
+			}
 
 			String shortForm = extractShortForm(graph, ontologyBaseUris, preferredPrefix, c.uri);
 			String curie = shortForm.replaceFirst("_", ":");