Merge pull request #466 from monarch-initiative/enhancement/obg-reader

Moving to obg-reader

phenol-io/src/main/java/org/monarchinitiative/phenol/io/obographs/OboGraphDocumentLoader.java

@@ -11,8 +11,13 @@
 /**
  * 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 <j.jacobsen@qmul.ac.uk>
  */
+// 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 {
 
   private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

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);
         }

phenol-io/src/test/java/org/monarchinitiative/phenol/io/MinimalOntologyLoaderTest.java

@@ -30,15 +30,15 @@ public class LoadHpo {
     @Test
     public void metaInfoIsCorrect() {
       Map<String, String> metaInfo = hpo.getMetaInfo();
-      assertThat(metaInfo, hasEntry("release", "2021-06-08"));
-      assertThat(metaInfo, hasEntry("data-version", "http://purl.obolibrary.org/obo/hp/releases/2021-06-08/hp.json"));
+      assertThat(metaInfo, hasEntry("release", "2024-06-25"));
+      assertThat(metaInfo, hasEntry("data-version", "http://purl.obolibrary.org/obo/hp/releases/2024-06-25/hp.json"));
     }
 
     @Test
     public void versionIsParsed() {
       Optional<String> version = hpo.version();
       assertThat(version.isPresent(), equalTo(true));
-      assertThat(version.get(), equalTo("2021-06-08"));
+      assertThat(version.get(), equalTo("2024-06-25"));
     }
 
     @Test
@@ -48,9 +48,9 @@ public void rootTerm() {
 
     @Test
     public void testTheNumberOfParsedTermIds() {
-      assertThat(hpo.allTermIdsStream().count(), equalTo(381L));
-      assertThat(hpo.nonObsoleteTermIdsStream().count(), equalTo(280L));
-      assertThat(hpo.obsoleteTermIdsStream().count(), equalTo(381L - 280L));
+      assertThat(hpo.allTermIdsStream().count(), equalTo(637L));
+      assertThat(hpo.nonObsoleteTermIdsStream().count(), equalTo(533L));
+      assertThat(hpo.obsoleteTermIdsStream().count(), equalTo(637L - 533L));
     }
 
     @Test

phenol-io/src/test/java/org/monarchinitiative/phenol/io/OntologyLoaderHpoTest.java

@@ -42,13 +42,13 @@ public void testParseHpoToy() {
   @Test
   public void testMetadata() {
     Map<String, String> metaInfo = hpo.getMetaInfo();
-    assertThat(metaInfo, hasEntry("release", "2021-06-08"));
-    assertThat(metaInfo, hasEntry("data-version", "http://purl.obolibrary.org/obo/hp/releases/2021-06-08/hp.json"));
+    assertThat(metaInfo, hasEntry("release", "2024-06-25"));
+    assertThat(metaInfo, hasEntry("data-version", "http://purl.obolibrary.org/obo/hp/releases/2024-06-25/hp.json"));
   }
 
   @Test
   public void testGetRightNumberOfTerms() {
-    assertEquals(280, hpo.nonObsoleteTermIdCount());
+    assertEquals(533, hpo.nonObsoleteTermIdCount());
   }
 
   @Test
@@ -123,6 +123,6 @@ public void testArachnodactyly() {
   public void ontologyHasVersion() {
     Optional<String> version = hpo.version();
     assertThat(version.isPresent(), equalTo(true));
-    assertThat(version.get(), equalTo("2021-06-08"));
+    assertThat(version.get(), equalTo("2024-06-25"));
   }
 }

phenol-io/src/test/java/org/monarchinitiative/phenol/io/OntologyLoaderTest.java

@@ -18,11 +18,6 @@
 import org.jgrapht.graph.DefaultDirectedGraph;
 import org.junit.jupiter.api.Test;
 
-/**
- * A testcase that tests the codes of loading a dummy ontology built from ncit.owl.
- *
- * @author <a href="mailto:HyeongSikKim@lbl.gov">HyeongSik Kim</a>
- */
 public class OntologyLoaderTest {
 
   @Test

phenol-io/src/test/resources/README.md

@@ -12,7 +12,7 @@ etc.).
 ```shell
 module load robot/1.8.3
 
-HPO=https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2022-10-05/hp.obo
+HPO=https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-06-25/hp.obo
 wget $HPO
 robot extract --input hp.obo --method BOT --term HP:0001166  convert --output arachnodactyly.hp.obo
 robot extract --input hp.obo --method TOP --term HP:0012823  convert --output clinical-modifier.hp.obo
@@ -43,4 +43,24 @@ robot merge --input arachnodactyly.hp.obo \
 rm *.obo
 ```
 
-This was followed by replacing the top-level `meta` element with the value we see in the file.
+This was followed by few extra steps:
+
+- replace the top-level `meta` element with the value we see in the full HP JSON file
+- insert the following node as the 1st position of the `nodes` list:
+  ```json
+  {
+    "id" : "http://purl.obolibrary.org/obo/HP_0034334",
+    "lbl" : "allelic_requirement",
+    "type" : "PROPERTY",
+    "propertyType" : "ANNOTATION",
+    "meta" : {
+      "basicPropertyValues" : [ {
+       "pred" : "http://purl.org/dc/elements/1.1/date",
+       "val" : "2022-09-04T11:14:13Z"
+      }, {
+       "pred" : "http://purl.org/dc/terms/creator",
+       "val" : "https://orcid.org/0000-0002-0736-9199"
+      } ]
+    }
+  }
+  ```