Feature/add additional terms

pom.xml

@@ -6,7 +6,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.2.4</version>
+    <version>3.2.5</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
   <groupId>eu.dissco.core</groupId>

src/main/java/eu/dissco/core/translator/terms/BaseDigitalObjectDirector.java

@@ -46,11 +46,13 @@
 import eu.dissco.core.translator.terms.specimen.PhysicalSpecimenIdType;
 import eu.dissco.core.translator.terms.specimen.Preparations;
 import eu.dissco.core.translator.terms.specimen.RecordedBy;
+import eu.dissco.core.translator.terms.specimen.RecordedById;
 import eu.dissco.core.translator.terms.specimen.RightsHolder;
 import eu.dissco.core.translator.terms.specimen.SpecimenName;
 import eu.dissco.core.translator.terms.specimen.TopicDiscipline;
 import eu.dissco.core.translator.terms.specimen.TopicDomain;
 import eu.dissco.core.translator.terms.specimen.TopicOrigin;
+import eu.dissco.core.translator.terms.specimen.VerbatimLabel;
 import eu.dissco.core.translator.terms.specimen.citation.BibliographicCitation;
 import eu.dissco.core.translator.terms.specimen.citation.CitationRemarks;
 import eu.dissco.core.translator.terms.specimen.citation.Date;
@@ -83,6 +85,7 @@
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.Phylum;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.ScientificName;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.ScientificNameAuthorship;
+import eu.dissco.core.translator.terms.specimen.identification.taxonomy.ScientificNameId;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.SpecificEpithet;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.Subfamily;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.Subgenus;
@@ -93,6 +96,7 @@
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.TaxonRemarks;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.TaxonomicStatus;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.Tribe;
+import eu.dissco.core.translator.terms.specimen.identification.taxonomy.VerbatimTaxonRank;
 import eu.dissco.core.translator.terms.specimen.identification.taxonomy.VernacularName;
 import eu.dissco.core.translator.terms.specimen.location.Continent;
 import eu.dissco.core.translator.terms.specimen.location.Country;
@@ -103,6 +107,7 @@
 import eu.dissco.core.translator.terms.specimen.location.IslandGroup;
 import eu.dissco.core.translator.terms.specimen.location.Locality;
 import eu.dissco.core.translator.terms.specimen.location.LocationAccordingTo;
+import eu.dissco.core.translator.terms.specimen.location.LocationId;
 import eu.dissco.core.translator.terms.specimen.location.LocationRemarks;
 import eu.dissco.core.translator.terms.specimen.location.MaximumDepthInMeters;
 import eu.dissco.core.translator.terms.specimen.location.MaximumDistanceAboveSurfaceInMeters;
@@ -112,6 +117,9 @@
 import eu.dissco.core.translator.terms.specimen.location.MinimumElevationInMeters;
 import eu.dissco.core.translator.terms.specimen.location.Municipality;
 import eu.dissco.core.translator.terms.specimen.location.StateProvince;
+import eu.dissco.core.translator.terms.specimen.location.VerbatimDepth;
+import eu.dissco.core.translator.terms.specimen.location.VerbatimElevation;
+import eu.dissco.core.translator.terms.specimen.location.VerbatimLocality;
 import eu.dissco.core.translator.terms.specimen.location.VerticalDatum;
 import eu.dissco.core.translator.terms.specimen.location.WaterBody;
 import eu.dissco.core.translator.terms.specimen.location.georeference.CoordinatePrecision;
@@ -128,8 +136,14 @@
 import eu.dissco.core.translator.terms.specimen.location.georeference.GeoreferencedBy;
 import eu.dissco.core.translator.terms.specimen.location.georeference.GeoreferencedDate;
 import eu.dissco.core.translator.terms.specimen.location.georeference.PointRadiusSpatialFit;
+import eu.dissco.core.translator.terms.specimen.location.georeference.VerbatimCoordinateSystem;
+import eu.dissco.core.translator.terms.specimen.location.georeference.VerbatimCoordinates;
+import eu.dissco.core.translator.terms.specimen.location.georeference.VerbatimLatitude;
+import eu.dissco.core.translator.terms.specimen.location.georeference.VerbatimLongitude;
+import eu.dissco.core.translator.terms.specimen.location.georeference.VerbatimSRS;
 import eu.dissco.core.translator.terms.specimen.occurence.Behavior;
 import eu.dissco.core.translator.terms.specimen.occurence.Caste;
+import eu.dissco.core.translator.terms.specimen.occurence.Day;
 import eu.dissco.core.translator.terms.specimen.occurence.DegreeOfEstablishment;
 import eu.dissco.core.translator.terms.specimen.occurence.EstablishmentMeans;
 import eu.dissco.core.translator.terms.specimen.occurence.EventDate;
@@ -139,18 +153,22 @@
 import eu.dissco.core.translator.terms.specimen.occurence.GeoreferenceVerificationStatus;
 import eu.dissco.core.translator.terms.specimen.occurence.Habitat;
 import eu.dissco.core.translator.terms.specimen.occurence.LifeStage;
+import eu.dissco.core.translator.terms.specimen.occurence.Month;
 import eu.dissco.core.translator.terms.specimen.occurence.OccurrenceAssertions;
 import eu.dissco.core.translator.terms.specimen.occurence.OccurrenceRemarks;
 import eu.dissco.core.translator.terms.specimen.occurence.OccurrenceStatus;
 import eu.dissco.core.translator.terms.specimen.occurence.OrganismQuantity;
 import eu.dissco.core.translator.terms.specimen.occurence.OrganismQuantityType;
 import eu.dissco.core.translator.terms.specimen.occurence.Pathway;
+import eu.dissco.core.translator.terms.specimen.occurence.RecordNumber;
 import eu.dissco.core.translator.terms.specimen.occurence.ReproductiveCondition;
 import eu.dissco.core.translator.terms.specimen.occurence.SampleSizeUnit;
 import eu.dissco.core.translator.terms.specimen.occurence.SampleSizeValue;
 import eu.dissco.core.translator.terms.specimen.occurence.SamplingProtocol;
 import eu.dissco.core.translator.terms.specimen.occurence.Sex;
+import eu.dissco.core.translator.terms.specimen.occurence.VerbatimEventDate;
 import eu.dissco.core.translator.terms.specimen.occurence.Vitality;
+import eu.dissco.core.translator.terms.specimen.occurence.Year;
 import eu.dissco.core.translator.terms.specimen.stratigraphy.biostratigraphic.HighestBiostratigraphicZone;
 import eu.dissco.core.translator.terms.specimen.stratigraphy.biostratigraphic.LowestBiostratigraphicZone;
 import eu.dissco.core.translator.terms.specimen.stratigraphy.chronostratigraphic.EarliestAgeOrLowestStage;
@@ -256,12 +274,14 @@ private DigitalSpecimen assembleDigitalSpecimenTerms(JsonNode data, boolean dwc)
         .withDwcInstitutionName(
             getInstitutionName(organisationId))
         .withDwcRecordedBy(termMapper.retrieveTerm(new RecordedBy(), data, dwc))
+        .withDwcRecordedById(termMapper.retrieveTerm(new RecordedById(), data, dwc))
         .withDwcBasisOfRecord(termMapper.retrieveTerm(new BasisOfRecord(), data, dwc))
         .withDctermsAccessRights(termMapper.retrieveTerm(new AccessRights(), data, dwc))
         .withDctermsRightsHolder(termMapper.retrieveTerm(new RightsHolder(), data, dwc))
         .withDwcDatasetName(termMapper.retrieveTerm(new DatasetName(), data, dwc))
         .withDwcDisposition(termMapper.retrieveTerm(new Disposition(), data, dwc))
         .withDwcInformationWithheld(termMapper.retrieveTerm(new InformationWithheld(), data, dwc))
+        .withDwcVerbatimLabel(termMapper.retrieveTerm(new VerbatimLabel(), data, dwc))
         .withDwcDataGeneralizations(termMapper.retrieveTerm(new DataGeneralizations(), data, dwc));
   }
 
@@ -273,7 +293,8 @@ private String getInstitutionName(String organisationId) throws OrganisationExce
       var wikidataId = organisationId.replace("https://www.wikidata.org/wiki/", "");
       return institutionNameComponent.getWikiDataName(wikidataId);
     } else {
-      throw new OrganisationException(organisationId + " is not a valid ror or wikidata identifier");
+      throw new OrganisationException(
+          organisationId + " is not a valid ror or wikidata identifier");
     }
   }
 
@@ -324,12 +345,14 @@ protected Identifications createIdentification(JsonNode data, boolean dwc) {
         .withDwcTaxonID(termMapper.retrieveTerm(new TaxonId(), data, dwc))
         .withDwcKingdom(termMapper.retrieveTerm(new Kingdom(), data, dwc))
         .withDwcTaxonRank(termMapper.retrieveTerm(new TaxonRank(), data, dwc))
+        .withDwcVerbatimTaxonRank(termMapper.retrieveTerm(new VerbatimTaxonRank(), data, dwc))
         .withDwcGenus(termMapper.retrieveTerm(new Genus(), data, dwc))
         .withDwcSubgenus(termMapper.retrieveTerm(new Subgenus(), data, dwc))
         .withDwcOrder(termMapper.retrieveTerm(new Order(), data, dwc))
         .withDwcScientificName(termMapper.retrieveTerm(new ScientificName(), data, dwc))
         .withDwcScientificNameAuthorship(
             termMapper.retrieveTerm(new ScientificNameAuthorship(), data, dwc))
+        .withDwcScientificNameId(termMapper.retrieveTerm(new ScientificNameId(), data, dwc))
         .withDwcNamePublishedInYear(termMapper.retrieveTerm(new NamePublishedInYear(), data, dwc))
         .withDwcClass(termMapper.retrieveTerm(new Class(), data, dwc))
         .withDwcFamily(termMapper.retrieveTerm(new Family(), data, dwc))
@@ -373,8 +396,14 @@ private List<Occurrences> assembleOccurrenceTerms(JsonNode data,
     var georeference = new Georeference()
         .withDwcDecimalLatitude(
             parseToDouble(new DecimalLatitude(), data, dwc))
+        .withDwcVerbatimLatitude(termMapper.retrieveTerm(new VerbatimLatitude(), data, dwc))
         .withDwcDecimalLongitude(parseToDouble(new DecimalLongitude(), data, dwc))
+        .withDwcVerbatimLongitude(termMapper.retrieveTerm(new VerbatimLongitude(), data, dwc))
         .withDwcGeodeticDatum(termMapper.retrieveTerm(new GeodeticDatum(), data, dwc))
+        .withDwcVerbatimCoordinates(termMapper.retrieveTerm(new VerbatimCoordinates(), data, dwc))
+        .withDwcVerbatimCoordinateSystem(
+            termMapper.retrieveTerm(new VerbatimCoordinateSystem(), data, dwc))
+        .withDwcVerbatimSRS(termMapper.retrieveTerm(new VerbatimSRS(), data, dwc))
         .withDwcGeoreferenceProtocol(termMapper.retrieveTerm(new GeoreferenceProtocol(), data, dwc))
         .withDwcCoordinatePrecision(parseToDouble(new CoordinatePrecision(), data, dwc))
         .withDwcCoordinateUncertaintyInMeters(
@@ -419,6 +448,7 @@ private List<Occurrences> assembleOccurrenceTerms(JsonNode data,
         .withDwcGroup(termMapper.retrieveTerm(new Group(), data, dwc))
         .withDwcMember(termMapper.retrieveTerm(new Member(), data, dwc));
     var location = new eu.dissco.core.translator.schema.Location()
+        .withDwcLocationID(termMapper.retrieveTerm(new LocationId(), data, dwc))
         .withDwcContinent(termMapper.retrieveTerm(new Continent(), data, dwc))
         .withDwcCountry(termMapper.retrieveTerm(new Country(), data, dwc))
         .withDwcCountryCode(termMapper.retrieveTerm(new CountryCode(), data, dwc))
@@ -427,6 +457,7 @@ private List<Occurrences> assembleOccurrenceTerms(JsonNode data,
         .withDwcIslandGroup(termMapper.retrieveTerm(new IslandGroup(), data, dwc))
         .withDwcMunicipality(termMapper.retrieveTerm(new Municipality(), data, dwc))
         .withDwcLocality(termMapper.retrieveTerm(new Locality(), data, dwc))
+        .withDwcVerbatimLocality(termMapper.retrieveTerm(new VerbatimLocality(), data, dwc))
         .withDwcStateProvince(termMapper.retrieveTerm(new StateProvince(), data, dwc))
         .withDwcWaterBody(termMapper.retrieveTerm(new WaterBody(), data, dwc))
         .withDwcHigherGeography(termMapper.retrieveTerm(new HigherGeography(), data, dwc))
@@ -438,6 +469,8 @@ private List<Occurrences> assembleOccurrenceTerms(JsonNode data,
         .withDwcMinimumDistanceAboveSurfaceInMeters(
             parseToDouble(new MinimumDistanceAboveSurfaceInMeters(), data, dwc))
         .withDwcMinimumElevationInMeters(parseToDouble(new MinimumElevationInMeters(), data, dwc))
+        .withDwcVerbatimDepth(termMapper.retrieveTerm(new VerbatimDepth(), data, dwc))
+        .withDwcVerbatimElevation(termMapper.retrieveTerm(new VerbatimElevation(), data, dwc))
         .withDwcVerticalDatum(termMapper.retrieveTerm(new VerticalDatum(), data, dwc))
         .withDwcLocationAccordingTo(termMapper.retrieveTerm(new LocationAccordingTo(), data, dwc))
         .withDwcLocationRemarks(termMapper.retrieveTerm(new LocationRemarks(), data, dwc))
@@ -447,13 +480,18 @@ private List<Occurrences> assembleOccurrenceTerms(JsonNode data,
     var occurrence = new eu.dissco.core.translator.schema.Occurrences()
         .withDwcFieldNumber(termMapper.retrieveTerm(new FieldNumber(), data, dwc))
         .withDwcEventDate(termMapper.retrieveTerm(new EventDate(), data, dwc))
+        .withDwcVerbatimEventDate(termMapper.retrieveTerm(new VerbatimEventDate(), data, dwc))
+        .withDwcYear(parseToInteger(new Year(), data, dwc))
+        .withDwcMonth(parseToInteger(new Month(), data, dwc))
+        .withDwcDay(parseToInteger(new Day(), data, dwc))
         .withDwcSex(termMapper.retrieveTerm(new Sex(), data, dwc))
         .withDwcOrganismQuantity(termMapper.retrieveTerm(new OrganismQuantity(), data, dwc))
         .withDwcOrganismQuantityType(termMapper.retrieveTerm(new OrganismQuantityType(), data, dwc))
         .withDwcSamplingProtocol(termMapper.retrieveTerm(new SamplingProtocol(), data, dwc))
         .withDwcLifeStage(termMapper.retrieveTerm(new LifeStage(), data, dwc))
         .withDwcEventRemarks(termMapper.retrieveTerm(new EventRemark(), data, dwc))
         .withDwcFieldNumber(termMapper.retrieveTerm(new FieldNumber(), data, dwc))
+        .withDwcRecordNumber(termMapper.retrieveTerm(new RecordNumber(), data, dwc))
         .withDwcFieldNotes(termMapper.retrieveTerm(new FieldNotes(), data, dwc))
         .withDwcHabitat(termMapper.retrieveTerm(new Habitat(), data, dwc))
         .withDwcReproductiveCondition(

src/main/java/eu/dissco/core/translator/terms/BiocaseDigitalObjectDirector.java

@@ -73,7 +73,8 @@ protected List<Identifications> assembleIdentifications(JsonNode data, boolean d
         iterateOverElements = false;
       }
     }
-    if (identifications.size() == 1 && identifications.get(0).getDwcIdentificationVerificationStatus() == null){
+    if (identifications.size() == 1
+        && identifications.get(0).getDwcIdentificationVerificationStatus() == null) {
       //If there is only one identification, and it doesn't have a verification status, set it to true
       identifications.get(0).setDwcIdentificationVerificationStatus(Boolean.TRUE);
     }

src/main/java/eu/dissco/core/translator/terms/License.java

@@ -9,7 +9,7 @@ public class License extends Term {
 
   public static final String TERM = DCTERMS_PREFIX + "license";
 
-// Fall back to dc terms rights if no license is present
+  // Fall back to dc terms rights if no license is present
   private final List<String> dwcaTerms = List.of(TERM, "dc:license", "eml:license",
       "dcterms:rights", "dc:rights");
   private final List<String> abcdUnitTerms = List.of(

src/main/java/eu/dissco/core/translator/terms/Term.java

@@ -1,9 +1,9 @@
 package eu.dissco.core.translator.terms;
 
 
-import eu.dissco.core.translator.schema.Identifications;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dissco.core.translator.schema.Identifications;
 import java.util.List;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang3.tuple.Pair;

src/main/java/eu/dissco/core/translator/terms/specimen/PhysicalSpecimenId.java

@@ -8,7 +8,8 @@ public class PhysicalSpecimenId extends Term {
 
   public static final String TERM = ODS_PREFIX + "physicalSpecimenId";
 
-  private final List<String> dwcaTerms = List.of("dwc:occurrenceID", "dwc:catalogNumber");
+  private final List<String> dwcaTerms = List.of("dwc:occurrenceID", "dwc:catalogNumber",
+      "dwc:materialSampleID", "dwc:materialEntityID");
   private final List<String> abcdTerms = List.of("abcd:unitGUID", "abcd:unitID");
 
   @Override

src/main/java/eu/dissco/core/translator/terms/specimen/Preparations.java

@@ -8,7 +8,8 @@ public class Preparations extends Term {
 
   public static final String TERM = DWC_PREFIX + "preparations";
   private final List<String> dwcaTerms = List.of("dwc:preparations");
-  private final List<String> abcdTerms = List.of("abcd:kindOfUnit/0/value", "abcd:specimenUnit/preparations/preparation/0/preparationType/value");
+  private final List<String> abcdTerms = List.of("abcd:kindOfUnit/0/value",
+      "abcd:specimenUnit/preparations/preparation/0/preparationType/value");
 
   @Override
   public String retrieveFromDWCA(JsonNode unit) {

src/main/java/eu/dissco/core/translator/terms/specimen/RecordedById.java

@@ -0,0 +1,22 @@
+package eu.dissco.core.translator.terms.specimen;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class RecordedById extends Term {
+
+  public static final String TERM = DWC_PREFIX + "recordedByID";
+
+  private final List<String> dwcaTerms = List.of("dwc:recordedByID");
+
+  @Override
+  public String retrieveFromDWCA(JsonNode unit) {
+    return super.searchJsonForTerm(unit, dwcaTerms);
+  }
+
+  @Override
+  public String getTerm() {
+    return TERM;
+  }
+}

src/main/java/eu/dissco/core/translator/terms/specimen/SpecimenName.java

@@ -11,7 +11,16 @@ public String calculate(DigitalSpecimen ds) {
     var acceptedIdentification = retrieveAcceptedIdentification(ds);
     if (acceptedIdentification != null && acceptedIdentification.getTaxonIdentifications() != null
         && !acceptedIdentification.getTaxonIdentifications().isEmpty()) {
-      return acceptedIdentification.getTaxonIdentifications().get(0).getDwcScientificName();
+      if (acceptedIdentification.getTaxonIdentifications().get(0)
+          .getDwcScientificName() != null) {
+        return acceptedIdentification.getTaxonIdentifications().get(0)
+            .getDwcScientificName();
+      }
+      if (acceptedIdentification.getTaxonIdentifications().get(0)
+          .getDwcVernacularName() != null) {
+        return acceptedIdentification.getTaxonIdentifications().get(0)
+            .getDwcVernacularName();
+      }
     }
     return null;
   }

src/main/java/eu/dissco/core/translator/terms/specimen/VerbatimLabel.java

@@ -0,0 +1,28 @@
+package eu.dissco.core.translator.terms.specimen;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class VerbatimLabel extends Term {
+
+  public static final String TERM = DWC_PREFIX + "verbatimLabel";
+  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> abcdUnitTerms = List.of(
+      "abcd:specimenUnit/marks/mark/0/markText/value");
+
+  @Override
+  public String retrieveFromDWCA(JsonNode unit) {
+    return super.searchJsonForTerm(unit, dwcaTerms);
+  }
+
+  @Override
+  public String retrieveFromABCD(JsonNode unit) {
+    return searchJsonForTerm(unit, abcdUnitTerms);
+  }
+
+  @Override
+  public String getTerm() {
+    return TERM;
+  }
+}

src/main/java/eu/dissco/core/translator/terms/specimen/identification/AbcdTypeInformation.java

@@ -39,8 +39,10 @@ private boolean isNameMatch(Identifications identification, JsonNode node) {
     }
   }
 
-  private void setAdditionalIdentificationInfo(Identifications identification, JsonNode typeDesignationNodes) {
-    identification.setTypeDesignatedBy(new TypeDesignatedBy().retrieveFromABCD(typeDesignationNodes));
+  private void setAdditionalIdentificationInfo(Identifications identification,
+      JsonNode typeDesignationNodes) {
+    identification.setTypeDesignatedBy(
+        new TypeDesignatedBy().retrieveFromABCD(typeDesignationNodes));
     identification.setDwcTypeStatus(new TypeStatus().retrieveFromABCD(typeDesignationNodes));
   }
 

src/main/java/eu/dissco/core/translator/terms/specimen/identification/IdentificationVerificationStatus.java

@@ -15,7 +15,7 @@ public class IdentificationVerificationStatus extends Term {
   @Override
   public String retrieveFromDWCA(JsonNode unit) {
     var result = super.searchJsonForTerm(unit, dwcaTerms);
-    if (result != null){
+    if (result != null) {
       if (result.equals("1")) {
         return Boolean.TRUE.toString();
       } else {

src/main/java/eu/dissco/core/translator/terms/specimen/identification/IdentifiedBy.java

@@ -8,7 +8,7 @@ public class IdentifiedBy extends Term {
 
   public static final String TERM = DWC_PREFIX + "identifiedBy";
 
-  private final List<String> dwcaTerms = List.of(TERM, "dwc:identifiedByID");
+  private final List<String> dwcaTerms = List.of(TERM);
 
   private final List<String> abcdTerms = List.of("identifiers/identifier/0/personName/fullName");