Merge pull request #73 from DiSSCo/feature/add-chronometric-age

Add mapping for chronometricAge

src/main/java/eu/dissco/core/translator/domain/AgentRoleType.java

@@ -10,7 +10,8 @@ public enum AgentRoleType {
   CREATOR("creator"),
   IDENTIFIER("identifier"),
   GEOREFERENCER("georeferencer"),
-  RIGHTS_OWNER("rights-owner");
+  RIGHTS_OWNER("rights-owner"),
+  CHRONOMETRIC_AGE_DETERMINER("chronometric-age-determiner"),;
 
   private final String name;
 

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

@@ -1,5 +1,6 @@
 package eu.dissco.core.translator.terms;
 
+import static eu.dissco.core.translator.domain.AgentRoleType.CHRONOMETRIC_AGE_DETERMINER;
 import static eu.dissco.core.translator.domain.AgentRoleType.COLLECTOR;
 import static eu.dissco.core.translator.domain.AgentRoleType.CREATOR;
 import static eu.dissco.core.translator.domain.AgentRoleType.GEOREFERENCER;
@@ -25,6 +26,7 @@
 import eu.dissco.core.translator.exception.OrganisationException;
 import eu.dissco.core.translator.exception.UnknownPhysicalSpecimenIdType;
 import eu.dissco.core.translator.properties.FdoProperties;
+import eu.dissco.core.translator.schema.ChronometricAge;
 import eu.dissco.core.translator.schema.Citation;
 import eu.dissco.core.translator.schema.DigitalMedia;
 import eu.dissco.core.translator.schema.DigitalMedia.DctermsType;
@@ -102,6 +104,24 @@
 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.chronometric.ChronometricAgeConversionProtocol;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeDeterminedBy;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeDeterminedDate;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeID;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeProtocol;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeReferences;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeRemarks;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeUncertaintyInYears;
+import eu.dissco.core.translator.terms.specimen.chronometric.ChronometricAgeUncertaintyMethod;
+import eu.dissco.core.translator.terms.specimen.chronometric.EarliestChronometricAge;
+import eu.dissco.core.translator.terms.specimen.chronometric.EarliestChronometricAgeReferenceSystem;
+import eu.dissco.core.translator.terms.specimen.chronometric.LatestChronometricAge;
+import eu.dissco.core.translator.terms.specimen.chronometric.LatestChronometricAgeReferenceSystem;
+import eu.dissco.core.translator.terms.specimen.chronometric.MaterialDated;
+import eu.dissco.core.translator.terms.specimen.chronometric.MaterialDatedID;
+import eu.dissco.core.translator.terms.specimen.chronometric.MaterialDatedRelationship;
+import eu.dissco.core.translator.terms.specimen.chronometric.UncalibratedChronometricAge;
+import eu.dissco.core.translator.terms.specimen.chronometric.VerbatimChronometricAge;
 import eu.dissco.core.translator.terms.specimen.citation.BibliographicCitation;
 import eu.dissco.core.translator.terms.specimen.citation.CitationDescription;
 import eu.dissco.core.translator.terms.specimen.citation.Date;
@@ -260,6 +280,7 @@ public DigitalSpecimen assembleDigitalSpecimenTerm(JsonNode data, boolean dwc)
     ds.withOdsHasIdentifiers(assembleIdentifiers(data));
     ds.withOdsHasCitations(assembleSpecimenCitations(data, dwc));
     ds.withOdsHasEntityRelationships(assembleDigitalSpecimenEntityRelationships(ds));
+    ds.withOdsHasChronometricAges(assembleChronometricAges(data, dwc));
     setCalculatedFields(ds, data);
     return ds;
   }
@@ -281,6 +302,8 @@ private void setCalculatedFields(DigitalSpecimen ds, JsonNode data) {
 
   protected abstract List<Identification> assembleIdentifications(JsonNode data, boolean dwc);
 
+  protected abstract List<ChronometricAge> assembleChronometricAges(JsonNode data, boolean dwc);
+
   protected Citation createCitation(JsonNode data, boolean dwc) {
     var citation = new Citation()
         .withId(termMapper.retrieveTerm(new ReferenceIRI(), data, dwc))
@@ -397,6 +420,45 @@ private List<eu.dissco.core.translator.schema.Identifier> assembleIdentifiers(Js
     return identifiers;
   }
 
+  protected ChronometricAge createChronometricAge(JsonNode data, boolean dwc) {
+    var chronometricAge = new ChronometricAge()
+        .withChronoChronometricAgeConversionProtocol(
+            termMapper.retrieveTerm(new ChronometricAgeConversionProtocol(), data, dwc))
+        .withChronoChronometricAgeDeterminedDate(
+            termMapper.retrieveTerm(new ChronometricAgeDeterminedDate(), data, dwc))
+        .withChronoChronometricAgeID(termMapper.retrieveTerm(new ChronometricAgeID(), data, dwc))
+        .withChronoChronometricAgeReferences(
+            termMapper.retrieveTerm(new ChronometricAgeReferences(), data, dwc))
+        .withChronoChronometricAgeRemarks(
+            termMapper.retrieveTerm(new ChronometricAgeRemarks(), data, dwc))
+        .withChronoChronometricAgeUncertaintyInYears(
+            parseToInteger(new ChronometricAgeUncertaintyInYears(), data, dwc))
+        .withChronoChronometricAgeUncertaintyMethod(
+            termMapper.retrieveTerm(new ChronometricAgeUncertaintyMethod(), data, dwc))
+        .withChronoEarliestChronometricAge(parseToInteger(new EarliestChronometricAge(), data, dwc))
+        .withChronoEarliestChronometricAgeReferenceSystem(
+            termMapper.retrieveTerm(new EarliestChronometricAgeReferenceSystem(), data, dwc))
+        .withChronoLatestChronometricAge(parseToInteger(new LatestChronometricAge(), data, dwc))
+        .withChronoLatestChronometricAgeReferenceSystem(
+            termMapper.retrieveTerm(new LatestChronometricAgeReferenceSystem(), data, dwc))
+        .withChronoMaterialDated(termMapper.retrieveTerm(new MaterialDated(), data, dwc))
+        .withChronoMaterialDatedID(termMapper.retrieveTerm(new MaterialDatedID(), data, dwc))
+        .withChronoMaterialDatedRelationship(
+            termMapper.retrieveTerm(new MaterialDatedRelationship(), data, dwc))
+        .withChronoUncalibratedChronometricAge(
+            termMapper.retrieveTerm(new UncalibratedChronometricAge(), data, dwc))
+        .withChronoVerbatimChronometricAge(
+            termMapper.retrieveTerm(new VerbatimChronometricAge(), data, dwc))
+        .withChronoChronometricAgeProtocol(
+            termMapper.retrieveTerm(new ChronometricAgeProtocol(), data, dwc))
+        .withChronoVerbatimChronometricAge(
+            termMapper.retrieveTerm(new VerbatimChronometricAge(), data, dwc));
+    chronometricAge.setOdsHasAgents(addAgent(chronometricAge.getOdsHasAgents(),
+        termMapper.retrieveTerm(new ChronometricAgeDeterminedBy(), data, dwc), null,
+        CHRONOMETRIC_AGE_DETERMINER, SCHEMA_PERSON));
+    return chronometricAge;
+  }
+
   protected Identification createIdentification(JsonNode data, boolean dwc) {
     var taxonId = termMapper.retrieveTerm(new TaxonID(), data, dwc);
     var mappedTaxonIdentification = new TaxonIdentification()

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

@@ -6,6 +6,7 @@
 import eu.dissco.core.translator.component.OrganisationNameComponent;
 import eu.dissco.core.translator.component.SourceSystemComponent;
 import eu.dissco.core.translator.properties.FdoProperties;
+import eu.dissco.core.translator.schema.ChronometricAge;
 import eu.dissco.core.translator.schema.Citation;
 import eu.dissco.core.translator.schema.DigitalSpecimen;
 import eu.dissco.core.translator.schema.Identification;
@@ -82,6 +83,24 @@ protected List<Identification> assembleIdentifications(JsonNode data, boolean dw
     return identifications;
   }
 
+  @Override
+  protected List<ChronometricAge> assembleChronometricAges(JsonNode data, boolean dwc) {
+    var chronometricAges = new ArrayList<ChronometricAge>();
+    var iterateOverElements = true;
+    var count = 0;
+    while (iterateOverElements) {
+      var chronometricAgeNode = getSubJsonAbcd(data, count,
+          List.of("abcd-efg:earthScienceSpecimen:unitStratigraphicDetermination/radiometricDates/radiometricDate"));
+      if (!chronometricAgeNode.isEmpty()) {
+        chronometricAges.add(createChronometricAge(chronometricAgeNode, dwc));
+        count++;
+      } else {
+        iterateOverElements = false;
+      }
+    }
+    return chronometricAges;
+  }
+
   private ArrayList<Citation> getCitations(JsonNode data, boolean dwc, String subPath) {
     var citations = new ArrayList<Citation>();
     var iterateOverElements = true;

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

@@ -6,6 +6,7 @@
 import eu.dissco.core.translator.component.OrganisationNameComponent;
 import eu.dissco.core.translator.component.SourceSystemComponent;
 import eu.dissco.core.translator.properties.FdoProperties;
+import eu.dissco.core.translator.schema.ChronometricAge;
 import eu.dissco.core.translator.schema.Citation;
 import eu.dissco.core.translator.schema.DigitalSpecimen;
 import eu.dissco.core.translator.schema.Identification;
@@ -91,6 +92,20 @@ protected List<Identification> assembleIdentifications(JsonNode data, boolean dw
     }
     return mappedIdentifications;
   }
+
+  @Override
+  protected List<ChronometricAge> assembleChronometricAges(JsonNode data, boolean dwc) {
+    var mappedChrono = new ArrayList<ChronometricAge>();
+    if (data.get(EXTENSION) != null
+        && data.get(EXTENSION).get("http://rs.tdwg.org/chrono/terms/ChronometricAge") != null) {
+      var chronometricAges = data.get(EXTENSION).get("http://rs.tdwg.org/chrono/terms/ChronometricAge");
+      for (int i = 0; i < chronometricAges.size(); i++) {
+        var chronometricAge = chronometricAges.get(i);
+        mappedChrono.add(createChronometricAge(chronometricAge, dwc));
+      }
+    }
+    return mappedChrono;
+  }
 }
 
 

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

@@ -15,6 +15,7 @@ public abstract class Term {
   protected static final String ODS_PREFIX = "ods:";
   protected static final String DWC_PREFIX = "dwc:";
   protected static final String DCTERMS_PREFIX = "dcterms:";
+  protected static final String CHRONO_PREFIX = "chrono:";
   protected static final Pair<String, String> ABCD_NAMED_AREA_KEY =
       Pair.of(
           "abcd:gathering/namedAreas/namedArea/",

src/main/java/eu/dissco/core/translator/terms/specimen/chronometric/ChronometricAgeConversionProtocol.java

@@ -0,0 +1,22 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeConversionProtocol extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeConversionProtocol";
+
+  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/chronometric/ChronometricAgeDeterminedBy.java

@@ -0,0 +1,22 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeDeterminedBy extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeDeterminedBy";
+
+  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/chronometric/ChronometricAgeDeterminedDate.java

@@ -0,0 +1,28 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeDeterminedDate extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeDeterminedDate";
+  private final List<String> abcdTerms = List.of("analysisDateTime/exactDate/dateText",
+      "analysisDateTime/dateText");
+  private final List<String> dwcaTerms = List.of(TERM);
+
+  @Override
+  public String retrieveFromDWCA(JsonNode unit) {
+    return super.searchJsonForTerm(unit, dwcaTerms);
+  }
+
+  @Override
+  public String retrieveFromABCD(JsonNode unit) {
+    return super.searchJsonForTerm(unit, abcdTerms);
+  }
+
+  @Override
+  public String getTerm() {
+    return TERM;
+  }
+}

src/main/java/eu/dissco/core/translator/terms/specimen/chronometric/ChronometricAgeID.java

@@ -0,0 +1,22 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeID extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeID";
+
+  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/chronometric/ChronometricAgeProtocol.java

@@ -0,0 +1,28 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeProtocol extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeProtocol";
+
+  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> abcdTerms = List.of("radiometricDatingMethod");
+
+  @Override
+  public String retrieveFromDWCA(JsonNode unit) {
+    return super.searchJsonForTerm(unit, dwcaTerms);
+  }
+
+  @Override
+  public String retrieveFromABCD(JsonNode unit) {
+    return super.searchJsonForTerm(unit, abcdTerms);
+  }
+
+  @Override
+  public String getTerm() {
+    return TERM;
+  }
+}

src/main/java/eu/dissco/core/translator/terms/specimen/chronometric/ChronometricAgeReferences.java

@@ -0,0 +1,29 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeReferences extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeReferences";
+
+  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> abcdTerms = List.of("analysisReferences/uri",
+      "analysisReferences/titleCitation", "analysisReferences/citationDetail");
+
+  @Override
+  public String retrieveFromDWCA(JsonNode unit) {
+    return super.searchJsonForTerm(unit, dwcaTerms);
+  }
+
+  @Override
+  public String retrieveFromABCD(JsonNode unit) {
+    return super.searchJsonForTerm(unit, abcdTerms);
+  }
+
+  @Override
+  public String getTerm() {
+    return TERM;
+  }
+}

src/main/java/eu/dissco/core/translator/terms/specimen/chronometric/ChronometricAgeRemarks.java

@@ -0,0 +1,28 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeRemarks extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeRemarks";
+
+  private final List<String> dwcaTerms = List.of(TERM);
+  private final List<String> abcdTerms = List.of("datingComment");
+
+  @Override
+  public String retrieveFromDWCA(JsonNode unit) {
+    return super.searchJsonForTerm(unit, dwcaTerms);
+  }
+
+  @Override
+  public String retrieveFromABCD(JsonNode unit) {
+    return super.searchJsonForTerm(unit, abcdTerms);
+  }
+
+  @Override
+  public String getTerm() {
+    return TERM;
+  }
+}

src/main/java/eu/dissco/core/translator/terms/specimen/chronometric/ChronometricAgeUncertaintyInYears.java

@@ -0,0 +1,22 @@
+package eu.dissco.core.translator.terms.specimen.chronometric;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import eu.dissco.core.translator.terms.Term;
+import java.util.List;
+
+public class ChronometricAgeUncertaintyInYears extends Term {
+
+  public static final String TERM = CHRONO_PREFIX + "chronometricAgeUncertaintyInYears";
+
+  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;
+  }
+}