Merge pull request #464 from monarch-initiative/enhancement/aspect

Enhancement/aspect

phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/constants/hpo/HpoSubOntologyRootTermIds.java

@@ -25,5 +25,7 @@ public final class HpoSubOntologyRootTermIds {
   /** {@link TermId} of sub ontology "mode of inheritance" (<code>HP:0000005</code>). */
   public static final TermId MODE_OF_INHERITANCE = TermId.of("HP:0000005");
 
+  /** {@link TermId} of sub ontology Past medical history (<code>HP:0032443</code>). */
+  public static final TermId PAST_MEDICAL_HISTORY = TermId.of("HP:0032443");
   private HpoSubOntologyRootTermIds(){}
 }

phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/io/hpo/Aspect.java

@@ -1,16 +1,39 @@
 package org.monarchinitiative.phenol.annotations.io.hpo;
 
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Optional;
 
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoClinicalModifierTermIds.CLINICAL_COURSE;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoModeOfInheritanceTermIds.INHERITANCE_ROOT;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoSubOntologyRootTermIds.*;
+
 /**
  * An enum for aspect column of {@link HpoAnnotationLine}.
  */
 public enum Aspect {
 
-  P,
-  I,
-  C,
-  M;
+  P(PHENOTYPIC_ABNORMALITY),
+  I(INHERITANCE_ROOT),
+  C(CLINICAL_COURSE),
+  M(CLINICAL_MODIFIER),
+  H(PAST_MEDICAL_HISTORY);
+
+  private final TermId termId;
+  private static final Map<TermId, Aspect> BY_TERMID = new HashMap<>();
+
+
+  static {
+    for (Aspect e: values()) {
+      BY_TERMID.put(e.termId, e);
+    }
+  }
+
+  Aspect(TermId termId) {
+    this.termId = termId;
+  }
 
   public static Optional<Aspect> parse(String aspect) {
     switch (aspect.toUpperCase()) {
@@ -22,8 +45,15 @@ public static Optional<Aspect> parse(String aspect) {
         return Optional.of(Aspect.C);
       case "M":
         return Optional.of(Aspect.M);
+      case "H":
+        return Optional.of(Aspect.H);
       default:
         return Optional.empty();
     }
   }
+
+  public static Optional<Aspect> fromTermId(TermId termId) {
+    return Optional.ofNullable(BY_TERMID.get(termId));
+  }
+
 }

phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/io/hpo/AspectTest.java

@@ -0,0 +1,24 @@
+package org.monarchinitiative.phenol.annotations.io.hpo;
+
+import org.junit.jupiter.api.Test;
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import static org.hamcrest.MatcherAssert.*;
+import static org.hamcrest.Matchers.*;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoClinicalModifierTermIds.CLINICAL_COURSE;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoModeOfInheritanceTermIds.INHERITANCE_ROOT;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoSubOntologyRootTermIds.*;
+
+public class AspectTest {
+
+  @Test
+  public void test_aspect_from_termId() {
+    assertThat(Aspect.fromTermId(PHENOTYPIC_ABNORMALITY).get(), equalTo(Aspect.P));
+    assertThat(Aspect.fromTermId(INHERITANCE_ROOT).get(), equalTo(Aspect.I));
+    assertThat(Aspect.fromTermId(CLINICAL_COURSE).get(), equalTo(Aspect.C));
+    assertThat(Aspect.fromTermId(CLINICAL_MODIFIER).get(), equalTo(Aspect.M));
+    assertThat(Aspect.fromTermId(PAST_MEDICAL_HISTORY).get(), equalTo(Aspect.H));
+    assertThat(Aspect.fromTermId(TermId.of("HP:0000000")).isEmpty(), equalTo(true));
+    assertThat(Aspect.H.toString(), equalTo("H"));
+  }
+}