ref #5983 and ref #6410 parsing of hybrid formulas with missing name parts

[cdmlib.git] / cdmlib-model / src / main / java / eu / etaxonomy / cdm / strategy / parser / NonViralNameParserImpl.java

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java
index c9b2882eec682ea1d388792d2e7f7858bde4c3d6..4427f6c027b0c38452444057ed1278580e7a5b26 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java
@@ -909,8 +909,8 @@ public class NonViralNameParserImpl extends NonViralNameParserImplRegExBase impl
                        }
                     //hybrid formula
                         else if (hybridFormulaPattern.matcher(fullNameString).matches()){
-                                Set<HybridRelationship> existingRelations = new HashSet<HybridRelationship>();
-                                Set<HybridRelationship> notToBeDeleted = new HashSet<HybridRelationship>();
+                                Set<HybridRelationship> existingRelations = new HashSet<>();
+                                Set<HybridRelationship> notToBeDeleted = new HashSet<>();
 
                                 for ( HybridRelationship rel : nameToBeFilled.getHybridChildRelations()){
                                     existingRelations.add(rel);
@@ -928,10 +928,15 @@ public class NonViralNameParserImpl extends NonViralNameParserImplRegExBase impl
                                                 secondNameString += " " + str;
                                         }
                                 }
+                                firstNameString = firstNameString.trim();
+                                secondNameString = secondNameString.trim();
                                 nameToBeFilled.setHybridFormula(true);
                                 NomenclaturalCode code = nameToBeFilled.getNomenclaturalCode();
-                                INonViralName firstName = this.parseFullName(firstNameString.trim(), code, rank);
-                                INonViralName secondName = this.parseFullName(secondNameString.trim(), code, rank);
+                                INonViralName firstName = this.parseFullName(firstNameString, code, rank);
+                                if (secondNameString.matches(abbrevHybridSecondPart)){
+                                    secondNameString = extendSecondHybridPart(firstName, secondNameString);
+                                }
+                                INonViralName secondName = this.parseFullName(secondNameString, code, rank);
                                 HybridRelationship firstRel = nameToBeFilled.addHybridParent(firstName, HybridRelationshipType.FIRST_PARENT(), null);
                                 HybridRelationship second = nameToBeFilled.addHybridParent(secondName, HybridRelationshipType.SECOND_PARENT(), null);
                                 checkRelationExist(firstRel, existingRelations, notToBeDeleted);
@@ -941,7 +946,7 @@ public class NonViralNameParserImpl extends NonViralNameParserImplRegExBase impl
                                 Rank firstRank = firstName.getRank();
                                 Rank secondRank = secondName.getRank();
 
-                                if (firstRank == null || firstRank.isHigher(secondRank)){
+                                if (firstRank == null || (secondRank != null && firstRank.isHigher(secondRank))){
                                         newRank = secondRank;
                                 }else{
                                         newRank = firstRank;
@@ -996,6 +1001,27 @@ public class NonViralNameParserImpl extends NonViralNameParserImplRegExBase impl
        }
 
        /**
+     * @param firstName
+     * @param secondNameString
+     * @return
+     */
+    private String extendSecondHybridPart(INonViralName firstName, String secondNameString) {
+        //first letter of genus given
+        if (secondNameString.matches("^" + abbrevHybridGenus + ".*")){
+            if (StringUtils.isNotBlank(firstName.getGenusOrUninomial())){
+                if (secondNameString.substring(0,1).equals(firstName.getGenusOrUninomial().substring(0, 1))){
+                    secondNameString = secondNameString.replaceAll("^" + abbrevHybridGenus, firstName.getGenusOrUninomial() + " ");
+                }
+            }
+        }else if (secondNameString.matches(abbrevHybridSecondPartOnlyInfraSpecies)){
+            secondNameString = CdmUtils.concat(" " , firstName.getGenusOrUninomial(), firstName.getSpecificEpithet(), secondNameString);
+        }else if (true){  //there will be further alternatives in future maybe
+            secondNameString = CdmUtils.concat(" " , firstName.getGenusOrUninomial(), secondNameString);
+        }
+        return secondNameString;
+    }
+
+    /**
      * Checks if a hybrid relation exists in the Set of existing relations
      * and <BR>
      *  if it does not adds it to relations not to be deleted <BR>