Merge pull request #59 from DiSSCo/feature/add-additional-terms

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/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");
 

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

@@ -0,0 +1,22 @@
+package eu.dissco.core.translator.terms.specimen.identification;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class IdentifiedById extends Term {
+
+  public static final String TERM = DWC_PREFIX + "identifiedById";
+
+  private final List<String> dwcaTerms = List.of(TERM);
+
+  @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/identification/TypeDesignatedBy.java

@@ -5,6 +5,7 @@
 import java.util.List;
 
 public class TypeDesignatedBy extends Term {
+
   public static final String TERM = "typeDesignatedBy";
 
   private final List<String> abcdTerms = List.of("verifier/fullName/value");

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

@@ -5,6 +5,7 @@
 import java.util.List;
 
 public class AcceptedNameUsage extends Term {
+
   public static final String TERM = DWC_PREFIX + "acceptedNameUsage";
 
   private final List<String> dwcaTerms = List.of(TERM);

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

@@ -5,6 +5,7 @@
 import java.util.List;
 
 public class AcceptedNameUsageId extends Term {
+
   public static final String TERM = DWC_PREFIX + "acceptedNameUsageId";
 
   private final List<String> dwcaTerms = List.of(TERM);

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

@@ -5,6 +5,7 @@
 import java.util.List;
 
 public class CultivarEpithet extends Term {
+
   public static final String TERM = DWC_PREFIX + "cultivarEpithet";
 
   private final List<String> dwcaTerms = List.of(TERM);

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

@@ -5,6 +5,7 @@
 import java.util.List;
 
 public class GenericName extends Term {
+
   public static final String TERM = DWC_PREFIX + "genericName";
 
   private final List<String> dwcaTerms = List.of(TERM);

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

@@ -5,6 +5,7 @@
 import java.util.List;
 
 public class OriginalNameUsage extends Term {
+
   public static final String TERM = DWC_PREFIX + "originalNameUsage";
 
   private final List<String> dwcaTerms = List.of(TERM);

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

@@ -8,7 +8,7 @@
 public class ScientificName extends AbstractTaxonomy {
 
   public static final String TERM = DWC_PREFIX + "scientificName";
-  private final List<String> dwcaTerms = List.of("dwc:scientificName");
+  private final List<String> dwcaTerms = List.of(TERM);
   private final List<String> abcdTerms = List.of(
       "result/taxonIdentified/scientificName/fullScientificNameString",
       "result/mineralRockIdentified/classifiedName/fullScientificNameString",

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

@@ -0,0 +1,21 @@
+package eu.dissco.core.translator.terms.specimen.identification.taxonomy;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ScientificNameId extends Term {
+
+  public static final String TERM = DWC_PREFIX + "scientificNameID";
+  private final List<String> dwcaTerms = List.of(TERM);
+
+  @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/identification/taxonomy/Subtribe.java

@@ -19,6 +19,7 @@ public String retrieveFromDWCA(JsonNode unit) {
   public String retrieveFromABCD(JsonNode unit) {
     return super.searchABCDSplitTerms(unit, abcdSplitTerms);
   }
+
   @Override
   public String getTerm() {
     return TERM;

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

@@ -19,6 +19,7 @@ public String retrieveFromDWCA(JsonNode unit) {
   public String retrieveFromABCD(JsonNode unit) {
     return super.searchABCDSplitTerms(unit, abcdSplitTerms);
   }
+
   @Override
   public String getTerm() {
     return TERM;

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

@@ -7,7 +7,7 @@ public class TaxonRank extends AbstractTaxonomy {
 
   public static final String TERM = DWC_PREFIX + "taxonRank";
 
-  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> dwcaTerms = List.of(TERM, VerbatimTaxonRank.TERM);
   private final List<String> abcdTerms = List.of(
       "result/taxonIdentified/scientificName/nameAtomised/botanical/rank");
 

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

@@ -19,6 +19,7 @@ public String retrieveFromDWCA(JsonNode unit) {
   public String retrieveFromABCD(JsonNode unit) {
     return super.searchABCDSplitTerms(unit, abcdSplitTerms);
   }
+
   @Override
   public String getTerm() {
     return TERM;

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

@@ -0,0 +1,28 @@
+package eu.dissco.core.translator.terms.specimen.identification.taxonomy;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import java.util.List;
+
+public class VerbatimTaxonRank extends AbstractTaxonomy {
+
+  public static final String TERM = DWC_PREFIX + "verbatimTaxonRank";
+
+  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> abcdTerms = List.of(
+      "result/taxonIdentified/scientificName/nameAtomised/botanical/rank");
+
+  @Override
+  public String retrieveFromDWCA(JsonNode unit) {
+    return super.searchJsonForTerm(unit, dwcaTerms);
+  }
+
+  @Override
+  public String retrieveFromABCD(JsonNode unit) {
+    return searchJsonForTerm(unit, abcdTerms);
+  }
+
+  @Override
+  public String getTerm() {
+    return TERM;
+  }
+}

src/main/java/eu/dissco/core/translator/terms/specimen/location/Locality.java

@@ -8,7 +8,7 @@ public class Locality extends Term {
 
   public static final String TERM = DWC_PREFIX + "locality";
 
-  private final List<String> dwcaTerms = List.of(TERM, "dwc:verbatimLocality");
+  private final List<String> dwcaTerms = List.of(TERM, VerbatimLocality.TERM);
   private final List<String> abcdTerms = List.of("abcd:gathering/localityText/value");
 
   @Override

src/main/java/eu/dissco/core/translator/terms/specimen/location/LocationId.java

@@ -0,0 +1,22 @@
+package eu.dissco.core.translator.terms.specimen.location;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class LocationId extends Term {
+
+  public static final String TERM = DWC_PREFIX + "locationID";
+
+  private final List<String> dwcaTerms = List.of(TERM);
+
+  @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/location/MaximumDepthInMeters.java

@@ -8,9 +8,10 @@ public class MaximumDepthInMeters extends Term {
 
   public static final String TERM = DWC_PREFIX + "maximumDepthInMeters";
 
-  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> dwcaTerms = List.of(TERM, VerbatimDepth.TERM);
   private final List<String> abcdTerms = List.of(
-      "abcd:gathering/depth/measurementOrFactAtomised/upperValue/value");
+      "abcd:gathering/depth/measurementOrFactAtomised/upperValue/value",
+      "abcd:gathering/depth/measurementOrFactText/value");
 
   @Override
   public String retrieveFromDWCA(JsonNode unit) {

src/main/java/eu/dissco/core/translator/terms/specimen/location/MaximumElevationInMeters.java

@@ -8,9 +8,10 @@ public class MaximumElevationInMeters extends Term {
 
   public static final String TERM = DWC_PREFIX + "maximumElevationInMeters";
 
-  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> dwcaTerms = List.of(TERM, VerbatimElevation.TERM);
   private final List<String> abcdTerms = List.of(
-      "abcd:gathering/altitude/measurementOrFactAtomised/upperValue/value", "abcd:gathering/altitude/measurementOrFactText/value");
+      "abcd:gathering/altitude/measurementOrFactAtomised/upperValue/value",
+      "abcd:gathering/altitude/measurementOrFactText/value");
 
   @Override
   public String retrieveFromDWCA(JsonNode unit) {

src/main/java/eu/dissco/core/translator/terms/specimen/location/MinimumDepthInMeters.java

@@ -8,9 +8,10 @@ public class MinimumDepthInMeters extends Term {
 
   public static final String TERM = DWC_PREFIX + "minimumDepthInMeters";
 
-  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> dwcaTerms = List.of(TERM, VerbatimDepth.TERM);
   private final List<String> abcdTerms = List.of(
-      "abcd:gathering/depth/measurementOrFactAtomised/lowerValue/value");
+      "abcd:gathering/depth/measurementOrFactAtomised/lowerValue/value",
+      "abcd:gathering/depth/measurementOrFactText/value");
 
   @Override
   public String retrieveFromDWCA(JsonNode unit) {