add homonym annotation; related to #161

globalbioticinteractions · Apr 5, 2024 · 41c5a7f · 41c5a7f
1 parent 466394f
commit 41c5a7f
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Showing 4 changed files with 12 additions and 2 deletions.
diff --git a/nomer-taxon-resolver/src/main/java/org/eol/globi/taxon/DiscoverLifeUtil.java b/nomer-taxon-resolver/src/main/java/org/eol/globi/taxon/DiscoverLifeUtil.java
@@ -161,7 +161,7 @@ public static void emitNameRelatedToFocalTaxon(
             Taxon focalTaxon,
             Map<String, String> relatedTaxonMap,
             Taxon relatedTaxon) {
-        boolean relatedNameIsHomonym = isHomonym(relatedTaxonMap);
+        boolean relatedNameIsHomonym = isHomonym(relatedTaxonMap) || (relatedTaxon.getStatus() != null && NameType.HOMONYM_OF.name().equals(relatedTaxon.getStatus().getName()));
         if (relatedNameIsHomonym) {
             listener.foundTaxonForTerm(
                     null,

diff --git a/nomer-taxon-resolver/src/main/java/org/eol/globi/taxon/DiscoverLifeUtil2.java b/nomer-taxon-resolver/src/main/java/org/eol/globi/taxon/DiscoverLifeUtil2.java
@@ -6,9 +6,11 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.eol.globi.data.CharsetConstant;
+import org.eol.globi.domain.NameType;
 import org.eol.globi.domain.PropertyAndValueDictionary;
 import org.eol.globi.domain.Taxon;
 import org.eol.globi.domain.TaxonImpl;
+import org.eol.globi.domain.TermImpl;
 import org.eol.globi.service.TaxonUtil;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
@@ -268,6 +270,13 @@ public static Taxon parse(String name) {
             }
 
         }
+
+        if (matched != null) {
+            NameType status = StringUtils.contains(name, "_sic") ? NameType.TRANSLATES_TO : NameType.SYNONYM_OF;
+            status = StringUtils.contains(name, "_homonym") ? NameType.HOMONYM_OF : status;
+            matched.setStatus(new TermImpl(status.name(), status.name()));
+        }
+
         return matched;
     }
 }
diff --git a/nomer-taxon-resolver/src/test/java/org/eol/globi/taxon/DiscoverLifeUtil2IntegrationTest.java b/nomer-taxon-resolver/src/test/java/org/eol/globi/taxon/DiscoverLifeUtil2IntegrationTest.java
@@ -35,7 +35,7 @@ public void foundTaxonForTerm(Long requestId, Term providedTerm, NameType nameTy
                 counter.incrementAndGet();
             }
         });
-        assertThat(counter.get(), Is.is(48503));
+        assertThat(counter.get(), Is.is(48518));
     }
 
 }
diff --git a/nomer-taxon-resolver/src/test/java/org/eol/globi/taxon/DiscoverLifeUtil2Test.java b/nomer-taxon-resolver/src/test/java/org/eol/globi/taxon/DiscoverLifeUtil2Test.java
@@ -53,6 +53,7 @@ public void parseRelatedNames() throws ParserConfigurationException, XPathExpres
         Taxon lastTaxon = taxons.get(taxons.size() - 1);
         assertThat(lastTaxon.getName(), is("Andrena (Holandrena) cressonii"));
         assertThat(lastTaxon.getAuthorship(), is("Robertson, 1891"));
+        assertThat(lastTaxon.getStatus().getName(), is(NameType.SYNONYM_OF.name()));
     }
 
     @Test