Add Fury instance and mapdb serializer with tests

api/src/main/java/life/catalogue/common/fury/FuryFactory.java

@@ -0,0 +1,190 @@
+package life.catalogue.common.fury;
+
+import life.catalogue.api.model.*;
+import life.catalogue.api.search.NameUsageWrapper;
+import life.catalogue.api.search.SimpleDecision;
+import life.catalogue.api.vocab.*;
+import life.catalogue.api.vocab.terms.*;
+import life.catalogue.coldp.ColdpTerm;
+import life.catalogue.common.date.FuzzyDate;
+
+import org.gbif.dwc.terms.BibTexTerm;
+import org.gbif.dwc.terms.TermFactory;
+import org.gbif.dwc.terms.UnknownTerm;
+import org.gbif.nameparser.api.*;
+
+import java.net.URI;
+import java.time.LocalDate;
+import java.time.LocalDateTime;
+import java.util.*;
+
+import org.apache.fury.Fury;
+import org.apache.fury.ThreadLocalFury;
+import org.apache.fury.ThreadSafeFury;
+
+import de.undercouch.citeproc.csl.CSLType;
+import it.unimi.dsi.fastutil.ints.IntOpenHashSet;
+import it.unimi.dsi.fastutil.ints.IntSet;
+import it.unimi.dsi.fastutil.objects.ObjectArrayList;
+
+
+/**
+ * Creates a thread safe fury instance with pre registered API classes
+ */
+public class FuryFactory {
+
+  public static final ThreadSafeFury FURY = new ThreadLocalFury(classLoader -> {
+    Fury f = Fury.builder()
+      .withLanguage(org.apache.fury.config.Language.JAVA)
+      .withClassLoader(classLoader)
+      .requireClassRegistration(false) // some non public class like JumboEnumSet cannot be registered
+      .build();
+    return configure(f);
+  });
+
+  public static Fury configure(Fury fury) {
+    // clb core
+    fury.register(Agent.class);
+    fury.register(Authorship.class);
+    fury.register(BareName.class);
+    fury.register(Citation.class);
+    fury.register(Classification.class);
+    fury.register(Coordinate.class);
+    fury.register(DOI.class);
+    fury.register(Dataset.class);
+    fury.register(DatasetImport.class);
+    fury.register(Distribution.class);
+    fury.register(EditorialDecision.Mode.class);
+    fury.register(EditorialDecision.class);
+    fury.register(Identifier.class);
+    fury.register(IndexName.class);
+    fury.register(Media.class);
+    fury.register(Name.class);
+    fury.register(NameRelation.class);
+    fury.register(NameUsageWrapper.class);
+    fury.register(Page.class);
+    fury.register(ParsedName.State.class);
+    fury.register(ParsedName.class);
+    fury.register(ParsedNameUsage.class);
+    fury.register(Reference.class);
+    fury.register(Sector.Mode.class);
+    fury.register(Sector.class);
+    fury.register(SimpleDecision.class);
+    fury.register(SimpleName.class);
+    fury.register(SpeciesEstimate.class);
+    fury.register(SpeciesInteraction.class);
+    fury.register(Synonym.class);
+    fury.register(TaxGroup.class);
+    fury.register(Taxon.class);
+    fury.register(TaxonConceptRelation.class);
+    fury.register(TaxonProperty.class);
+    fury.register(Treatment.class);
+    fury.register(TypeMaterial.class);
+    fury.register(VerbatimRecord.class);
+    fury.register(VernacularName.class);
+
+    // search
+    fury.register(NameUsageWrapper.class);
+    fury.register(SimpleDecision.class);
+
+    // CSL classes & enums
+    fury.register(CslData.class);
+    fury.register(CslDate.class);
+    fury.register(CslName.class);
+    fury.register(CslName[].class);
+    fury.register(CSLType.class);
+    fury.register(int[][].class);
+    fury.register(String[].class);
+
+    // date/time
+    fury.register(FuzzyDate.class);
+    fury.register(LocalDate.class);
+    fury.register(LocalDateTime.class);
+
+    // java & commons
+    fury.register(int[].class);
+    fury.register(URI.class);
+    fury.register(UUID.class);
+    registerCollectionClasses(fury);
+
+    // areas
+    fury.register(Area.class);
+    fury.register(AreaImpl.class);
+    fury.register(LonghurstArea.class);
+    fury.register(TdwgArea.class);
+
+    // enums
+    fury.register(Country.class);
+    fury.register(DataFormat.class);
+    fury.register(DatasetOrigin.class);
+    fury.register(Setting.class);
+    fury.register(DatasetType.class);
+    fury.register(DistributionStatus.class);
+    fury.register(EnumMap.class);
+    fury.register(EnumSet.class);
+    fury.register(EstimateType.class);
+    fury.register(Frequency.class);
+    fury.register(Gender.class);
+    fury.register(Gazetteer.class);
+    fury.register(GeoTime.class);
+    fury.register(GeoTimeType.class);
+    fury.register(ImportState.class);
+    fury.register(Issue.class);
+    fury.register(JobStatus.class);
+    fury.register(License.class);
+    fury.register(Environment.class);
+    fury.register(MatchType.class);
+    fury.register(MediaType.class);
+    fury.register(NamePart.class);
+    fury.register(NameType.class);
+    fury.register(NomCode.class);
+    fury.register(NomRelType.class);
+    fury.register(NomStatus.class);
+    fury.register(Origin.class);
+    fury.register(Rank.class);
+    fury.register(Sex.class);
+    fury.register(SpeciesInteractionType.class);
+    fury.register(TaxonomicStatus.class);
+    fury.register(TaxonConceptRelType.class);
+    fury.register(TreatmentFormat.class);
+    fury.register(TypeStatus.class);
+    fury.register(InfoGroup.class);
+
+    // term enums
+    TermFactory.instance().registerTermEnum(BiboOntTerm.class);
+    TermFactory.instance().registerTermEnum(ColdpTerm.class);
+    TermFactory.instance().registerTermEnum(EolDocumentTerm.class);
+    TermFactory.instance().registerTermEnum(EolReferenceTerm.class);
+    TermFactory.instance().registerTermEnum(InatTerm.class);
+    TermFactory.instance().registerTermEnum(TxtTreeTerm.class);
+    TermFactory.instance().registerTermEnum(WfoTerm.class);
+    for (Class<?> cl : TermFactory.instance().listRegisteredTermEnums()) {
+      fury.register(cl);
+    }
+    fury.register(UnknownTerm.class);
+    fury.register(BibTexTerm.class);
+    return fury;
+  }
+
+  public static void registerCollectionClasses(Fury fury) {
+    fury.register(ArrayList.class);
+    fury.register(HashMap.class);
+    fury.register(HashSet.class);
+    fury.register(EnumMap.class);
+    fury.register(EnumSet.class);
+    fury.register(LinkedHashMap.class);
+    fury.register(LinkedList.class);
+    fury.register(Collections.emptyList().getClass());
+    // private class, special registration
+    try {
+      Class clazz = Class.forName("java.util.Arrays$ArrayList");
+      fury.register(clazz);
+    } catch (ClassNotFoundException e) {
+      throw new RuntimeException(e);
+    }
+    // fastutils
+    fury.register(IntSet.class);
+    fury.register(IntOpenHashSet.class);
+    fury.register(ObjectArrayList.class);
+  }
+}

api/src/main/java/life/catalogue/common/fury/MapDbSerializer.java

@@ -0,0 +1,55 @@
+package life.catalogue.common.fury;
+
+import com.esotericsoftware.kryo.Kryo;
+import com.esotericsoftware.kryo.io.Input;
+import com.esotericsoftware.kryo.io.Output;
+import com.esotericsoftware.kryo.util.Pool;
+
+import org.apache.commons.lang3.NotImplementedException;
+import org.mapdb.DataIO;
+import org.mapdb.DataInput2;
+import org.mapdb.DataOutput2;
+import org.mapdb.serializer.GroupSerializerObjectArray;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+
+/**
+ * A mapDB serializer that uses fury under the hood to quickly serialize objects into the mapdb data output/input.
+ *
+ * @param <T> the class to serialize
+ */
+public class MapDbSerializer<T> extends GroupSerializerObjectArray<T> {
+  private final Class<T> clazz;
+
+  public MapDbSerializer(Class<T> clazz) {
+    this.clazz = clazz;
+  }
+
+  @Override
+  public void serialize(DataOutput2 out, T value) throws IOException {
+    byte[] bytes = FuryFactory.FURY.serializeJavaObject(value);
+    DataIO.packInt(out, bytes.length);
+    out.write(bytes);
+  }
+
+  @Override
+  public T deserialize(DataInput2 in, int available) throws IOException {
+    if (available == 0) return null;
+    int size = DataIO.unpackInt(in);
+    byte[] ret = new byte[size];
+    in.readFully(ret);
+    return FuryFactory.FURY.deserializeJavaObject(ret, clazz);
+  }
+
+  @Override
+  public boolean isTrusted() {
+    return true;
+  }
+
+  @Override
+  public int compare(T first, T second) {
+    throw new NotImplementedException("compare should not be needed for our mapdb use");
+  }
+
+}