Prevend highly ambigous genera without well defined parents to be mer…

…ged, see #1368

dao/src/main/java/life/catalogue/matching/TaxGroupAnalyzer.java

@@ -22,7 +22,7 @@
 
 public class TaxGroupAnalyzer {
   private static final Logger LOG = LoggerFactory.getLogger(TaxGroupAnalyzer.class);
-  final TaxGroupParser parser = TaxGroupParser.PARSER;
+  private static final TaxGroupParser parser = TaxGroupParser.PARSER;
   private static final Pattern YEAR_PATTERN = Pattern.compile("([12]\\d{3})");
   private static final Pattern BAS_COMB_PATTERN = Pattern.compile("\\(\\s*[A-Z].+\\)[^()]*[A-Z]");
   // map of suffix to groups, sorted by suffix length

webservice/src/main/java/life/catalogue/assembly/TreeMergeHandler.java

@@ -39,6 +39,7 @@ public class TreeMergeHandler extends TreeBaseHandler {
   private static final Set<Rank> LOW_RANKS = Set.of(Rank.FAMILY, Rank.SUBFAMILY, Rank.TRIBE, Rank.GENUS);
   private final MatchedParentStack parents;
   private final UsageMatcherGlobal matcher;
+  private final TaxGroupAnalyzer groupAnalyzer;
   private final UsageCache uCache;
   private final CacheLoader loader;
   private int counter = 0;  // all source usages
@@ -61,6 +62,7 @@ public class TreeMergeHandler extends TreeBaseHandler {
     this.vKey = DSID.root(sourceDatasetKey);
     this.matcher = matcher;
     uCache = matcher.getUCache();
+    groupAnalyzer = new TaxGroupAnalyzer();
 
     // figure out the lowest insertion point in the project/release
     // a) a target is given
@@ -320,14 +322,33 @@ public void acceptThrowsNoCatch(NameUsageBase nu) throws Exception {
 
     } else {
       // *** CREATE ***
-      if ( nu.isTaxon() && syncTaxa  ||  nu.isSynonym() && syncSynonyms) {
+      if ( nu.isTaxon() && syncTaxa && !isAmbiguousGenus(nu) ||  nu.isSynonym() && syncSynonyms) {
         sn = create(nu, parent);
       }
     }
 
     processEnd(sn, mod);
   }
 
+  /**
+   * Detects unqualified genus usages without authorship
+   * which are placed under no parents or Biota and similar parents which have no taxonomic group at all.
+   *
+   * These ambiguous genera often cause trouble as they match later on to pretty much anything alike
+   * and also adapt (wrong) authorships.
+   */
+  private boolean isAmbiguousGenus(NameUsageBase nu) {
+    if (nu.getRank() == Rank.GENUS) {
+      var psn = parents.matchedParentsOnlySN();
+      var group = groupAnalyzer.analyze(nu.toSimpleNameLink(), psn);
+      if (group == null || group.equals(TaxGroup.Eukaryotes)) {
+        LOG.info("Ignore canonical genus {} with vague parents: {}", nu.getLabel(), psn);
+        return true;
+      }
+    }
+    return false;
+  }
+
   public void acceptName(Name n) throws InterruptedException {
     try {
       acceptNameThrowsNoCatch(n);

webservice/src/main/java/life/catalogue/matching/MatchedParentStack.java

@@ -163,6 +163,13 @@ public LinkedList<MatchedUsage> matchedParentsOnly(String... excludeIDs) {
     return parents.stream().filter(u -> u.match != null && !exclusion.contains(u.match.getId())).collect(Collectors.toCollection(LinkedList::new));
   }
 
+  public List<SimpleNameCached> matchedParentsOnlySN() {
+    return parents.stream()
+      .filter(u -> u.match != null)
+      .map(u -> u.usage)
+      .collect(Collectors.toList());
+  }
+
   public MatchedUsage secondLast() {
     return parents.isEmpty() ? null : parents.get(parents.size()-2);
   }

webservice/src/test/java/life/catalogue/assembly/SectorSyncMergeIT.java

@@ -83,6 +83,7 @@ public class SectorSyncMergeIT extends SectorSyncTestBase {
   @Parameterized.Parameters
   public static Collection<Object[]> data() {
     return Arrays.asList(new Object[][] {
+      {"doryphora", List.of("worms", "wcvp", "3i", "coleo", "pbdb", "zoobank")},
       {"bolyeriidae", List.of("itis", "reptiledb", "uksi", "pbdb")},
       {"myosotis", List.of("taxref", "uksi", "pbdb", "bavaria")},
       {"tetralobus", List.of("wfo", "bouchard", "plazi")},

webservice/src/test/resources/txtree/doryphora/3i.txtree

@@ -0,0 +1,8 @@
+Auchenorrhyncha Duméril, 1805 [suborder]
+  Fulgoromorpha Evans, 1946 [infraorder]
+    Fulgoroidea Latreille, 1807 [superfamily]
+      Dictyopharidae Spinola, 1839 [family]
+        Dictyopharinae Spinola, 1839 [subfamily]
+          Dictyopharini Spinola, 1839 [tribe]
+            Doryphorina Melichar, 1912 [genus]
+              =Doryphora Melichar, 1912 [genus]

webservice/src/test/resources/txtree/doryphora/coleo.txtree

@@ -0,0 +1,8 @@
+Coleoptera [order]
+  Polyphaga [suborder]
+    Cucujiformia [series]
+      Chrysomeloidea Latreille, 1802 [superfamily]
+        Chrysomelidae Latreille, 1802 [family]
+          Chrysomelinae Latreille, 1802 [subfamily]
+            Chrysomelini Latreille, 1802 [tribe]
+              Doryphora Illiger, 1807 [genus]

webservice/src/test/resources/txtree/doryphora/coleo.yaml

@@ -0,0 +1,6 @@
+ranks:
+  - superfamily
+  - family
+  - subfamily
+  - genus
+  - species

webservice/src/test/resources/txtree/doryphora/expected.txtree

@@ -0,0 +1,34 @@
+Biota [unranked]
+  Animalia [kingdom]
+    Arthropoda [phylum]
+      Insecta [class]
+        Coleoptera [order]
+          Chrysomeloidea Latreille, 1802 [superfamily]
+            Chrysomelidae Latreille, 1802 [family]
+              Chrysomelinae Latreille, 1802 [subfamily]
+                Doryphora Illiger, 1807 [genus]
+        Hemiptera Linnaeus, 1758 [order]
+          Auchenorrhyncha Duméril, 1805 [suborder]
+            Fulgoromorpha Evans, 1946 [infraorder]
+              Fulgoroidea [superfamily]
+                Dictyopharidae Spinola, 1839 [family]
+                  Doryphorina Melichar, 1912 [genus]
+                    =Doryphora Melichar, 1912 [genus]
+        Lepidoptera [order]
+          Gelechioidea [superfamily]
+            Gelechiidae [family]
+              Anomologinae [subfamily]
+                Xystophora Wocke, 1876 [genus]
+                  =Doryphora Heinemann, 1870 [genus]
+          Zygaenoidea Latreille, 1809 [superfamily]
+            Limacodidae [family]
+              Doratifera (&Westwood),1841 Duncan [genus]
+                =Doryphora (&Westwood),1841 Duncan [genus]
+  Plantae [kingdom]
+    Pteridobiotina Britton & Brown [subkingdom]
+      Tracheophyta [phylum]
+        Magnoliopsida [class]
+          Laurales Juss. ex Bercht. & J.Presl [order]
+            Atherospermataceae R.Br. [family]
+              Doryphora Endl. [genus]
+                =Doratophora Lem. [genus]

webservice/src/test/resources/txtree/doryphora/pbdb.txtree

@@ -0,0 +1,10 @@
+Life [unranked]
+  Eukaryota (Chatton, 1925) [unranked]
+    Plantae (Haeckel, 1866) [kingdom]
+      Spermatophyta [phylum]
+        Angiospermae [class]
+          Mesangiosperms The Angiosperm Phylogeny Group, 2016 [unranked]
+            Magnoliid Jud, 2011 [unranked]
+              Laurales Jussieu, 1820 [order]
+                Atherospermataceae Brown, 1814 [family]
+                  Doryphora Endlicher, 1837 [genus]

webservice/src/test/resources/txtree/doryphora/project.txtree

@@ -0,0 +1,27 @@
+Biota [unranked]
+  Animalia [kingdom]
+    Arthropoda [phylum]
+      Insecta [class]
+        Coleoptera [order]
+          Chrysomeloidea Latreille, 1802 [superfamily]
+        Hemiptera Linnaeus, 1758 [order]
+          Auchenorrhyncha Duméril, 1805 [suborder]
+            Fulgoromorpha Evans, 1946 [infraorder]
+              Fulgoroidea [superfamily]
+                Dictyopharidae Spinola, 1839 [family]
+        Lepidoptera [order]
+          Gelechioidea [superfamily]
+            Gelechiidae [family]
+              Anomologinae [subfamily]
+                Xystophora Wocke, [1876] [genus]
+                  =Doryphora Heinemann, 1870 [genus]
+          Zygaenoidea Latreille, 1809 [superfamily]
+            Limacodidae [family]
+              Doratifera Duncan [& Westwood], 1841 [genus]
+                =Doryphora Duncan [& Westwood], 1841 [genus]
+  Plantae [kingdom]
+    Pteridobiotina Britton & Brown [subkingdom]
+      Tracheophyta [phylum]
+        Magnoliopsida [class]
+          Laurales Juss. ex Bercht. & J. Presl [order]
+            Atherospermataceae R. Br. [family]

webservice/src/test/resources/txtree/doryphora/readme.md

@@ -0,0 +1,3 @@
+Avoid adding canonical genus names to the root of the tree, e.g. Biota, which has no taxgroup context.
+Algae Doryphora from Bacillariophyceae, Chromista cannot be mapped to the project (we intentionally omitted the Chromista kingdom in this test)
+https://github.com/CatalogueOfLife/backend/issues/1368

webservice/src/test/resources/txtree/doryphora/wcvp.txtree

@@ -0,0 +1,3 @@
+Atherospermataceae [family]
+  Doryphora Endl. [genus]
+    =Doratophora Lem. [genus]

webservice/src/test/resources/txtree/doryphora/worms.txtree

@@ -0,0 +1,6 @@
+Biota [unranked]
+  Chromista [kingdom]
+    Heterokontophyta [phylum]
+      Bacillariophytina [subphylum]
+        Bacillariophyceae [class]
+          Doryphora [genus]

webservice/src/test/resources/txtree/doryphora/zoobank.txtree

@@ -0,0 +1 @@
+Doryphora Illiger, 1807 sensu Illiger 1807 [genus]