Try to merge redundant accepted genera within the same family, see #273

checklistbank-cli/src/main/java/org/gbif/checklistbank/neo/UsageDao.java

@@ -422,7 +422,7 @@ private static void storeEnum(Node n, String property, Enum value) {
     }
   }
 
-  private Rank readRank(Node n) {
+  public Rank readRank(Node n) {
     return readEnum(n, NeoProperties.RANK, Rank.class, Rank.UNRANKED);
   }
 

checklistbank-cli/src/main/java/org/gbif/checklistbank/nub/NubBuilder.java

@@ -1080,10 +1080,12 @@ private NubUsage processSourceUsage(SrcUsage u, Origin origin, NubUsage parent)
     )) {
 
       if (!match.isMatch() || (
-              fromCurrentSource(match.usage) && currSrc.supragenericHomonymSource &&
-                      !IGNORABLE_ORIGINS.contains(origin) && !IGNORABLE_ORIGINS.contains(match.usage.origin)
-      )) {
-
+               currSrc.supragenericHomonymSource
+            && fromCurrentSource(match.usage)
+            && (u.rank.isSuprageneric() || !sameFamily(parent, match.usage))
+            && !IGNORABLE_ORIGINS.contains(origin) && !IGNORABLE_ORIGINS.contains(match.usage.origin)
+          )
+      ) {
         // remember if we had a doubtful match
         NubUsage doubtful = match.doubtfulUsage;
         // persistent new nub usage if there wasnt any yet
@@ -1151,6 +1153,16 @@ private NubUsage processSourceUsage(SrcUsage u, Origin origin, NubUsage parent)
     return match.usage;
   }
 
+  private boolean sameFamily(NubUsage u1, NubUsage u2) {
+    Node f1 = family(u1);
+    Node f2 = family(u2);
+    return Objects.equals(f1, f2);
+  }
+
+  private Node family(NubUsage u) {
+    return u.rank == Rank.FAMILY ? u.node : db.parent(u.node, Rank.FAMILY);
+  }
+
   private void delete(NubUsage nub) {
     for (int sourceId : nub.sourceIds) {
       src2NubKey.remove(sourceId);

checklistbank-cli/src/main/java/org/gbif/checklistbank/nub/NubDb.java

@@ -134,8 +134,21 @@ public Node parent(Node child) {
   }
 
   /**
-   * @return the parent (or accepted) nodes for a given node.
+   * @return the parent (or accepted) nub usage for a given node that has the matching rank. Will be null if nothing found.
    */
+  public Node parent(Node n, Rank rank) {
+    for (Node pn : parents(n)) {
+      Rank pr = dao.readRank(pn);
+      if (pr == rank){
+        return pn;
+      }
+    }
+    return null;
+  }
+
+    /**
+     * @return the parent (or accepted) nodes for a given node.
+     */
   public List<Node> parents(Node n) {
     return Iterables.asList(Traversals.PARENTS
         .relationships(RelType.SYNONYM_OF, Direction.OUTGOING)
@@ -413,6 +426,25 @@ public NubUsageMatch findNubUsage(UUID currSource, ParsedName pn, @Nullable Rank
       return NubUsageMatch.snap(synonym);
     }
 
+    // all canonical, one with the same parent?
+    if (currNubParent != null && checked.size() >= 2) {
+      NubUsage sibling = null;
+      for (NubUsage u : checked) {
+        if (parent(u.node).equals(currNubParent.node)) {
+          if (sibling == null){
+            sibling = u;
+          } else {
+            // multiple found!
+            sibling = null;
+            break;
+          }
+        }
+      }
+      if (sibling != null) {
+        return NubUsageMatch.match(sibling);
+      }
+    }
+
     // try to do better authorship matching, remove canonical matches
     if (qualifiedName) {
       iter = checked.iterator();
@@ -454,8 +486,10 @@ public NubUsageMatch findNubUsage(UUID currSource, ParsedName pn, @Nullable Rank
     if (curr != null) {
       curr.issues.add(NameUsageIssue.HOMONYM);
       curr.addRemark("Homonym known in other sources: " + pn.getScientificName());
-      LOG.warn("{} ambigous homonyms encountered for {} in source {}, picking largest taxon", checked.size(), pn.getScientificName(), currSource);
+      LOG.warn("{} ambiguous homonyms encountered for {} in source {}, picking largest taxon", checked.size(), pn.getScientificName(), currSource);
       return NubUsageMatch.snap(curr);
+    } else if (checked.isEmpty()) {
+      return NubUsageMatch.empty();
     }
 
     throw new IgnoreSourceUsageException("homonym " + pn.getScientificName(), pn.getScientificName());

checklistbank-cli/src/test/java/org/gbif/checklistbank/nub/NubBuilderIT.java

@@ -2171,6 +2171,18 @@ public void redundantHyla() throws Exception {
     assertTree("184 185.txt");
   }
 
+  /**
+   * https://github.com/gbif/checklistbank/issues/273
+   */
+  @Test
+  public void implicitGenera() throws Exception {
+    ClasspathSourceList src = ClasspathSourceList.source(neoRepo.cfg, 186);
+    src.setSourceRank(186, Rank.KINGDOM);
+    src.setSupragenericHomonymSource(186);
+    build(src);
+    assertTree("186.txt");
+  }
+
   /**
    * For profiling memory usage of nub builds
    */

checklistbank-cli/src/test/resources/nub-sources/dataset186.txt

@@ -0,0 +1,33 @@
+1			UNRANKED	ACCEPTED		Biota	
+2	1		KINGDOM	ACCEPTED		Animalia	
+3	2		PHYLUM	ACCEPTED		Chordata	
+4	3		SUBPHYLUM	ACCEPTED		Vertebrata	
+5	4		INFRAPHYLUM	ACCEPTED		Gnathostomata	
+6	5		UNRANKED	ACCEPTED		Osteichthyes	
+7	6		UNRANKED	ACCEPTED		Sarcopterygii	
+8	7		UNRANKED	ACCEPTED		Tetrapoda	
+9	8		CLASS	ACCEPTED		Amphibia	
+10	9		ORDER	ACCEPTED		Anura	
+11	10		FAMILY	ACCEPTED		Hylidae Rafinesque, 1815	
+12	11		GENUS	ACCEPTED		Hyla	
+20	12		SPECIES	ACCEPTED		Hyla imitator (Barbour & Dunn, 1921)	
+21	12		SPECIES	ACCEPTED		Hyla nicefori (Cochran & Goin, 1970)	
+13	11		SUBFAMILY	ACCEPTED		Hylinae Rafinesque, 1815	
+14	13		GENUS	ACCEPTED		Hyla Laurenti, 1768	
+22	14		SPECIES	ACCEPTED		Hyla annectans (Jerdon, 1870)	
+23	14		SPECIES	ACCEPTED		Hyla arborea (Linnaeus, 1758)	
+24	14		SPECIES	ACCEPTED		Hyla chinensis Günther, 1858	
+25	14		SPECIES	ACCEPTED		Hyla hallowellii Thompson, 1912	
+30	10		SUPERFAMILY	ACCEPTED		Brachycephaloidea Günther, 1858	
+31	30		FAMILY	ACCEPTED		Brachycephalidae Günther, 1858	
+32	31		GENUS	ACCEPTED		Brachycephalus Fitzinger, 1826	
+37	32		SPECIES	ACCEPTED		Brachycephalus germanicus Döring, 2023	
+33	31		GENUS	ACCEPTED		Ischnocnema Reinhardt & Lütken, 1862	
+34	33		SPECIES	ACCEPTED		Ischnocnema alpina Döring, 2023	
+35	31		GENUS	ACCEPTED		Ischnocnema	
+36	35		SPECIES	ACCEPTED		Ischnocnema vulgaris Döring, 2023	
+40	10		FAMILY	ACCEPTED		Inventedidae Döring, 2023	
+41	40		GENUS	ACCEPTED		Inventeda Döring, 2023	
+42	41		SPECIES	ACCEPTED		Inventeda pulchra Döring, 2023	
+43	40		GENUS	ACCEPTED		Ischnocnema	
+44	43		SPECIES	ACCEPTED		Ischnocnema viatrix Döring, 2023	

checklistbank-cli/src/test/resources/trees/184 185.txt

@@ -3,14 +3,13 @@ Animalia [kingdom]
     Amphibia [class]
       Anura [order]
         Hylidae [family]
-          Hyla [genus]
-            Hyla imitator (Barbour & Dunn, 1921) [species]
-            Hyla nicefori (Cochran & Goin, 1970) [species]
           Hyla Laurenti, 1768 [genus]
             Hyla annectans (Jerdon, 1870) [species]
             Hyla arborea (Linnaeus, 1758) [species]
             Hyla chinensis Günther, 1858 [species]
             Hyla hallowellii Thompson, 1912 [species]
+            Hyla imitator (Barbour & Dunn, 1921) [species]
+            Hyla nicefori (Cochran & Goin, 1970) [species]
 Archaea [kingdom]
 Bacteria [kingdom]
 Chromista [kingdom]

checklistbank-cli/src/test/resources/trees/186.txt

@@ -0,0 +1,31 @@
+Animalia [kingdom]
+  Chordata [phylum]
+    Amphibia [class]
+      Anura [order]
+        Brachycephalidae [family]
+          Brachycephalus Fitzinger, 1826 [genus]
+            Brachycephalus germanicus Döring, 2023 [species]
+          Ischnocnema Reinhardt & Lütken, 1862 [genus]
+            Ischnocnema alpina Döring, 2023 [species]
+            Ischnocnema vulgaris Döring, 2023 [species]
+        Hylidae [family]
+          Hyla Laurenti, 1768 [genus]
+            Hyla annectans (Jerdon, 1870) [species]
+            Hyla arborea (Linnaeus, 1758) [species]
+            Hyla chinensis Günther, 1858 [species]
+            Hyla hallowellii Thompson, 1912 [species]
+            Hyla imitator (Barbour & Dunn, 1921) [species]
+            Hyla nicefori (Cochran & Goin, 1970) [species]
+        Inventedidae [family]
+          Inventeda Döring, 2023 [genus]
+            Inventeda pulchra Döring, 2023 [species]
+          Ischnocnema [genus]
+            Ischnocnema viatrix Döring, 2023 [species]
+Archaea [kingdom]
+Bacteria [kingdom]
+Chromista [kingdom]
+Fungi [kingdom]
+Plantae [kingdom]
+Protozoa [kingdom]
+Viruses [kingdom]
+incertae sedis [kingdom]