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ref #8162 adapt cdmlip to new term package structure
[cdmlib.git] / cdmlib-persistence / src / main / java / eu / etaxonomy / cdm / database / data / FullCoverageDataGenerator.java
diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java
index 13350f795f94c9c7b5a7b4763dd8b2d069f989bd..169b58939f9946f165d8f7b6ce680e73013687a9 100644 (file)
--- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java
+++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java
@@ -22,7 +22,6 @@ import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
 import eu.etaxonomy.cdm.model.common.Annotation;
 import eu.etaxonomy.cdm.model.common.CdmBase;
 import eu.etaxonomy.cdm.model.common.Credit;
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
 import eu.etaxonomy.cdm.model.common.EventBase;
 import eu.etaxonomy.cdm.model.common.Extension;
 import eu.etaxonomy.cdm.model.common.ExtensionType;
@@ -38,13 +37,12 @@ import eu.etaxonomy.cdm.model.common.LanguageString;
 import eu.etaxonomy.cdm.model.common.Marker;
 import eu.etaxonomy.cdm.model.common.MarkerType;
 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
-import eu.etaxonomy.cdm.model.common.Representation;
-import eu.etaxonomy.cdm.model.common.TermType;
-import eu.etaxonomy.cdm.model.common.TermVocabulary;
+import eu.etaxonomy.cdm.model.common.TimePeriod;
 import eu.etaxonomy.cdm.model.common.User;
 import eu.etaxonomy.cdm.model.description.CategoricalData;
 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
+import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
 import eu.etaxonomy.cdm.model.description.Distribution;
 import eu.etaxonomy.cdm.model.description.Feature;
 import eu.etaxonomy.cdm.model.description.FeatureNode;
@@ -68,12 +66,13 @@ import eu.etaxonomy.cdm.model.description.TaxonInteraction;
 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
 import eu.etaxonomy.cdm.model.description.TextData;
 import eu.etaxonomy.cdm.model.description.TextFormat;
-import eu.etaxonomy.cdm.model.description.WorkingSet;
 import eu.etaxonomy.cdm.model.location.Country;
 import eu.etaxonomy.cdm.model.location.NamedArea;
 import eu.etaxonomy.cdm.model.location.Point;
 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
 import eu.etaxonomy.cdm.model.media.AudioFile;
+import eu.etaxonomy.cdm.model.media.ExternalLink;
+import eu.etaxonomy.cdm.model.media.ExternalLinkType;
 import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
 import eu.etaxonomy.cdm.model.media.ImageFile;
 import eu.etaxonomy.cdm.model.media.Media;
@@ -103,6 +102,7 @@ import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.Registration;
 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
 import eu.etaxonomy.cdm.model.name.TaxonName;
@@ -126,8 +126,13 @@ import eu.etaxonomy.cdm.model.taxon.Synonym;
 import eu.etaxonomy.cdm.model.taxon.SynonymType;
 import eu.etaxonomy.cdm.model.taxon.Taxon;
 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
+import eu.etaxonomy.cdm.model.term.DefinedTerm;
+import eu.etaxonomy.cdm.model.term.Representation;
+import eu.etaxonomy.cdm.model.term.TermType;
+import eu.etaxonomy.cdm.model.term.TermVocabulary;
 import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
 
 /**
@@ -142,7 +147,7 @@ import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
  * depend on general parameter than concrete data values.
  *
  * @author a.mueller
- * @created 3013-12-02
+ * @since 3013-12-02
  *
  *
  */
@@ -150,7 +155,7 @@ public class FullCoverageDataGenerator {
 
 
        public void fillWithData(Session session){
-               List<CdmBase> cdmBases = new ArrayList<CdmBase>();
+               List<CdmBase> cdmBases = new ArrayList<>();
 
                createAgents(cdmBases);
 
@@ -220,8 +225,8 @@ public class FullCoverageDataGenerator {
        private void createAgents(List<CdmBase> cdmBases) {
                //Person
                Person person = Person.NewTitledInstance("Person Title");
-               person.setFirstname("first name");
-               person.setLastname("last name");
+               person.setGivenName("first name");
+               person.setFamilyName("last name");
                person.setLifespan(TimePeriodParser.parseString("1905-1995"));
                person.setPrefix("prefix");
                person.setSuffix("suffix");
@@ -385,6 +390,9 @@ public class FullCoverageDataGenerator {
                Reference ref = ReferenceFactory.newArticle();
                DescriptionElementSource source = textData.addSource(OriginalSourceType.Import, "22", "taxon description table", ref, "detail");
                source.setNameUsedInSource(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()));
+               ExternalLink link = ExternalLink.NewInstance(ExternalLinkType.WebSite,
+                       URI.create("http://wwww.abd.de"), "Somehow useful link", 445);
+               source.addLink(link);
                handleAnnotatableEntity(source);
 
                taxonDescription.addDescriptionSource(ref);
@@ -422,11 +430,20 @@ public class FullCoverageDataGenerator {
                cdmBases.add(leaveLengthNode);
 
 
-               WorkingSet workingSet = WorkingSet.NewInstance();
-               workingSet.addDescription(taxonDescription);
-               workingSet.setLabel("My Workingset");
-               workingSet.getDescriptiveSystem();
-               handleAnnotatableEntity(workingSet);
+               //DescriptiveDataSet
+               DescriptiveDataSet descriptiveDataSet = DescriptiveDataSet.NewInstance();
+               descriptiveDataSet.addDescription(taxonDescription);
+               descriptiveDataSet.setLabel("My Descriptive Dataset");
+               descriptiveDataSet.getDescriptiveSystem();
+               handleAnnotatableEntity(descriptiveDataSet);
+               descriptiveDataSet.addGeoFilterArea(Country.GERMANY());
+               Classification classification = Classification.NewInstance("DescriptiveDataSet subtree classification");
+               Taxon subTreeTaxon = getTaxon();
+        TaxonNode subtree = classification.addChildTaxon(subTreeTaxon, null, null);
+               descriptiveDataSet.addTaxonSubtree(subtree);
+
+               cdmBases.add(classification);
+               cdmBases.add(subtree);
 
 
                //polytomous keys
@@ -495,7 +512,7 @@ public class FullCoverageDataGenerator {
                media.addRepresentation(mediaRepresentation);
 
                media.putTitle(Language.ENGLISH(), "Media title");
-               media.setMediaCreated(DateTime.now());
+               media.setMediaCreated(TimePeriod.NewInstance(DateTime.now()));
                media.putDescription(Language.ENGLISH(), "Media description");
                handleIdentifiableEntity(media);
 
@@ -647,10 +664,14 @@ public class FullCoverageDataGenerator {
                classification.addGeoScope(Country.GERMANY());
                classification.putDescription(Language.ENGLISH(), "An interesting classification");
 
-
                TaxonNode node = classification.addChildTaxon(taxon, sec,"22");
                handleIdentifiableEntity(classification);
                handleAnnotatableEntity(node);
+               node.putExcludedNote(Language.DEFAULT(), "Excluded note");
+               DefinedTerm agentRelationType = DefinedTerm.NewTaxonNodeAgentRelationTypeInstance(null, "agentRelation", "ar");
+               Person agent = Person.NewTitledInstance("Related agent");
+               TaxonNodeAgentRelation agentRelation = node.addAgentRelation(agentRelationType, agent);
+               handleAnnotatableEntity(agentRelation);
 
                Taxon childTaxon = Taxon.NewInstance(synName, sec);
                node.addChildTaxon(childTaxon, sec, "44");
@@ -661,6 +682,7 @@ public class FullCoverageDataGenerator {
                cdmBases.add(concept);
                cdmBases.add(childTaxon);
                cdmBases.add(classification);
+               cdmBases.add(agentRelationType);
 
 
        }
@@ -674,7 +696,7 @@ public class FullCoverageDataGenerator {
                reference.setAuthorship(author);
                reference.setTitle("ref title");
                reference.setAbbrevTitle("abbrev title");
-               reference.setDatePublished(TimePeriodParser.parseString("1999"));
+               reference.setDatePublished(TimePeriodParser.parseStringVerbatim("1999"));
                reference.setEdition("edition");
                reference.setEditor("editor");
                Institution institution = Institution.NewInstance();
@@ -787,7 +809,7 @@ public class FullCoverageDataGenerator {
                DefinedTerm kindOfUnit = DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null);
                cdmBases.add(kindOfUnit);
                fieldUnit.setKindOfUnit(kindOfUnit);
-               fieldUnit.setIndividualCount(3);
+               fieldUnit.setIndividualCount("3");
                fieldUnit.putDefinition(Language.ENGLISH(), "definition");
                fieldUnit.setPublish(true);
                handleIdentifiableEntity(fieldUnit);
@@ -863,11 +885,24 @@ public class FullCoverageDataGenerator {
                viralName.setAcronym("acronym");
                handleIdentifiableEntity(viralName);
 
-
+               //Registration
+               Registration registration = Registration.NewInstance("registration identifier",
+                       "specificIdentifier", speciesZooName, null);
+               registration.addTypeDesignation(specimenDesig);
+               registration.setRegistrationDate(DateTime.now());
+               Registration blockingRegistration = Registration.NewInstance();
+               registration.addBlockedBy(blockingRegistration);
+               registration.setInstitution(Institution.NewInstance());
+               User submitter = User.NewInstance("submitter", "12345");
+               registration.setSubmitter(submitter);
+               handleAnnotatableEntity(registration);;
+
+               cdmBases.add(submitter);
                cdmBases.add(bacName);
                cdmBases.add(botName);
                cdmBases.add(viralName);
                cdmBases.add(zooName);
+               cdmBases.add(botName2);
        }
 
        private void handleEventBase(EventBase event){