moving to obg-reader

monarch-initiative · Jun 26, 2024 · da95f7c · da95f7c
1 parent 279a757
commit da95f7c
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/...ol-io/src/main/java/org/monarchinitiative/phenol/io/obographs/OboGraphDocumentLoader.java b/...ol-io/src/main/java/org/monarchinitiative/phenol/io/obographs/OboGraphDocumentLoader.java
@@ -13,6 +13,8 @@
  *
  * @author Jules Jacobsen <[email protected]>
  */
+// REMOVE(3.0.0)
+@Deprecated(forRemoval = true, since = "2.1.2")
 public class OboGraphDocumentLoader {
 
   private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

diff --git a/phenol-io/src/main/java/org/monarchinitiative/phenol/io/utils/OntologyLoadingRoutines.java b/phenol-io/src/main/java/org/monarchinitiative/phenol/io/utils/OntologyLoadingRoutines.java
@@ -1,10 +1,10 @@
 package org.monarchinitiative.phenol.io.utils;
 
+import org.geneontology.obographs.core.io.OgJsonReader;
 import org.geneontology.obographs.core.model.GraphDocument;
 import org.monarchinitiative.phenol.base.PhenolRuntimeException;
 import org.monarchinitiative.phenol.io.MinimalOntologyLoader;
 import org.monarchinitiative.phenol.io.OntologyLoader;
-import org.monarchinitiative.phenol.io.obographs.OboGraphDocumentLoader;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -41,7 +41,7 @@ public static GraphDocument loadGraphDocument(InputStream inputStream) {
         logger.debug("Looks like a JSON file...");
         try {
           bufferedStream.reset();
-          return OboGraphDocumentLoader.loadJson(bufferedStream);
+          return OgJsonReader.readInputStream(bufferedStream);
         } catch (Exception e) {
           throw new PhenolRuntimeException("Error loading JSON", e);
         }