WIP - Checkpoint commit for Index generation for IUCN and ID lookups …

…for WoRMS #5

Switch to using opencsv
#1321

matching-ws/src/main/java/life/catalogue/matching/DatasetIndex.java

@@ -57,6 +57,7 @@ public class DatasetIndex {
   final static NameUsageMatch NO_MATCH = NameUsageMatch.builder()
     .diagnostics(
       Diagnostics.builder()
+        .confidence(100)
         .matchType(MatchType.NONE)
         .build())
     .build();

matching-ws/src/main/java/life/catalogue/matching/NameUsageMatch.java

@@ -7,12 +7,8 @@
 import java.util.Optional;
 import io.swagger.v3.oas.annotations.media.Schema;
 
-import life.catalogue.api.vocab.TaxonomicStatus;
-
 import lombok.Builder;
 import lombok.Data;
-import lombok.NoArgsConstructor;
-
 import org.gbif.nameparser.api.Rank;
 
 /**
@@ -41,6 +37,8 @@ public class NameUsageMatch implements LinneanClassification {
   List<Status> additionalStatus = new ArrayList<>();
 
   private String nameFor(Rank rank) {
+    if (classification == null)
+      return null;
     return getClassification().stream()
         .filter(c -> c.getRank().equals(rank))
         .findFirst()
@@ -49,6 +47,8 @@ private String nameFor(Rank rank) {
   }
 
   private String keyFor(Rank rank) {
+    if (classification == null)
+      return null;
     return getClassification().stream()
         .filter(c -> c.getRank().equals(rank))
         .findFirst()
@@ -57,8 +57,11 @@ private String keyFor(Rank rank) {
   }
 
   private void setNameFor(String value, Rank rank) {
+    if (classification == null) {
+      this.classification = new ArrayList<>();
+    }
     Optional<RankedName> name =
-        this.getClassification().stream().filter(c -> c.getRank().equals(rank)).findFirst();
+        this.classification.stream().filter(c -> c.getRank().equals(rank)).findFirst();
     if (name.isPresent()) {
       name.get().setName(value);
       name.get().setCanonicalName(value);
@@ -67,7 +70,7 @@ private void setNameFor(String value, Rank rank) {
       newRank.setRank(rank);
       newRank.setName(value);
       newRank.setCanonicalName(value);
-      this.getClassification().add(newRank);
+      this.classification.add(newRank);
     }
   }
 

matching-ws/src/test/java/life/catalogue/matching/NameUsageBuilder.java

@@ -37,7 +37,7 @@ public static NameUsageMatch newNameUsageMatch(
       String subgenusKey,
       String speciesKey) {
 
-    NameUsageMatch m = NameUsageMatch.builder().build();
+    NameUsageMatch m = NameUsageMatch.builder().diagnostics(Diagnostics.builder().build()).build();
     m.setUsage(new RankedName());
     m.getUsage().setKey(usageKey);
     m.getUsage().setName(scientificName);