Use OgJsonReader instead of OboGraphDocumentLoader. Add a depreca…

…tion note.
monarch-initiative · Jun 28, 2024 · bf3489a · bf3489a
1 parent a793737
commit bf3489a
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Showing 2 changed files with 4 additions and 3 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
@@ -11,9 +11,12 @@
 /**
  * Loads an ontology using the obograph library.
  *
+ * @deprecated use {@link org.geneontology.obographs.core.io.OgJsonReader} instead of <code>OboGraphDocumentLoader</code>.
+ * {@code OboGraphDocumentLoader} will be removed in <em>3.0.0</em>.
  * @author Jules Jacobsen <[email protected]>
  */
 // REMOVE(3.0.0)
+// Removing this class will remove the last use of `com.fasterxml.jackson` package in `phenol-io`.
 @Deprecated(forRemoval = true, since = "2.1.2")
 public class OboGraphDocumentLoader {
 

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
@@ -5,7 +5,6 @@
 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;
 
@@ -42,8 +41,7 @@ public static GraphDocument loadGraphDocument(InputStream inputStream) {
         logger.debug("Looks like a JSON file...");
         try {
           bufferedStream.reset();
-//          return OgJsonReader.readInputStream(bufferedStream);
-          return OboGraphDocumentLoader.loadJson(bufferedStream);
+          return OgJsonReader.readInputStream(bufferedStream);
         } catch (Exception e) {
           throw new PhenolRuntimeException("Error loading JSON", e);
         }