package eu.etaxonomy.cdm.io.cuba;
+import java.net.URI;
import java.util.UUID;
import org.apache.log4j.Logger;
import org.springframework.stereotype.Component;
import org.springframework.transaction.TransactionStatus;
+import eu.etaxonomy.cdm.common.DOI;
import eu.etaxonomy.cdm.io.common.CdmImportBase;
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
+import eu.etaxonomy.cdm.model.agent.Person;
+import eu.etaxonomy.cdm.model.agent.Team;
import eu.etaxonomy.cdm.model.common.TermType;
import eu.etaxonomy.cdm.model.common.TermVocabulary;
+import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
import eu.etaxonomy.cdm.model.location.NamedAreaType;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
+import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
+
/**
* @author a.mueller
try {
makeAreas(state);
makePresenceAbsenceTerms(state);
+ makeAlternativeFloras(state);
} catch (UndefinedTransformerMethodException e) {
e.printStackTrace();
}
/**
* @param state
*/
- private void makePresenceAbsenceTerms(CubaImportState state) {
+ private void makeAlternativeFloras(CubaImportState state) {
+
+ //FRC
+ Reference<?> refFRC = ReferenceFactory.newBook();
+ refFRC.setUuid(CubaTransformer.uuidRefFRC);
+ refFRC.setTitle("Flora de la República de Cuba");
+ getReferenceService().save(refFRC);
+
+ //A&S
+ Reference<?> refAS = ReferenceFactory.newArticle();
+ refAS.setUuid(CubaTransformer.uuidRefAS);
+ refAS.setTitle("Catalogue of seed plants of the West Indies");
+ Person acevedo = Person.NewInstance();
+ acevedo.setFirstname("Pedro");
+ acevedo.setLastname("Acevedo-Rodríguez");
+ Person strong = Person.NewInstance();
+ strong.setFirstname("Mark T.");
+ strong.setLastname("Strong");
+ Team asTeam = Team.NewInstance();
+ asTeam.addTeamMember(acevedo);
+ asTeam.addTeamMember(strong);
+ refAS.setAuthorship(asTeam);
+ refAS.setDatePublished(TimePeriodParser.parseString("2012-01-01"));
+ refAS.setVolume("98");
+ refAS.setPages("i-xxv, 1-1192");
+ refAS.setIssn("0081-024X");
+ refAS.setDoi(DOI.fromString("10.5479/si.0081024X.98.1"));
+ refAS.setUri(URI.create("http://hdl.handle.net/10088/17551"));
+ String abstracct = "The catalogue enumerates all taxa of Gymnosperms, Dicotyledons, and Monocotyledons occurring in the West Indies archipelago excluding the islands off the coast of Venezuela (Netherlands Antilles, Venezuelan Antilles, Tobago, and Trinidad). For each accepted taxon, nomenclature (including synonyms described from the West Indies and their references to publication), distribution in the West Indies (including endemic, native, or exotic status), common names, and a numerical listing of literature records are given. Type specimen citations are provided for accepted names and synonyms of Cyperaceae, Sapindaceae, and some selected genera in several families including the Apocynaceae (Plumeria), Aquifoliaceae (Ilex), and Santalaceae (Dendrophthora). More than 30,000 names were treated comprising 208 families, 2,033 genera, and 12,279 taxa, which includes exotic and commonly cultivated plants. The total number of indigenous taxa was approximately 10,470 of which 71% (7,446 taxa) are endemic to the archipelago or part of it. Fifteen new names, 37 combinations, and 7 lectotypifications are validated. A searchable website of this catalogue, maintained and continuously updated at the Smithsonian Institution, is available at http://botany.si.edu/antilles/WestIndies/.";
+ refAS.setReferenceAbstract(abstracct);
+ Reference<?> refASIn = ReferenceFactory.newJournal();
+ refAS.setInReference(refASIn);
+ getReferenceService().save(refAS);
+
+ //FC
+ Reference<?> refFC = ReferenceFactory.newBook();
+ refFC.setUuid(CubaTransformer.uuidRefFC);
+ refFC.setTitle("Flora de Cuba");
+ Person leon = Person.NewTitledInstance("León");
+ Person alain = Person.NewTitledInstance("Alain");
+ Team fcTeam = Team.NewInstance();
+ fcTeam.addTeamMember(leon);
+ fcTeam.addTeamMember(alain);
+ refAS.setAuthorship(fcTeam);
+ getReferenceService().save(refFC);
+
+ }
+
+ /**
+ * @param state
+ * @throws UndefinedTransformerMethodException
+ */
+ private void makePresenceAbsenceTerms(CubaImportState state) throws UndefinedTransformerMethodException {
TransactionStatus tx = startTransaction();
+
+ IInputTransformer transformer = state.getTransformer();
+
+ //vocabulary
+ UUID cubaStatusVocabularyUuid = UUID.fromString("e74bba61-551b-4f59-af83-a1a770e4b0ae");
+ String label = "Flora of Cuba Distribution Status";
+ String abbrev = null;
+ boolean isOrdered = true;
+ PresenceAbsenceTerm anyTerm = PresenceAbsenceTerm.PRESENT(); //just any
+ TermVocabulary<PresenceAbsenceTerm> cubaStatusVocabualary = getVocabulary(TermType.PresenceAbsenceTerm, cubaStatusVocabularyUuid, label, label, abbrev, null, isOrdered, anyTerm);
+
+ final boolean PRESENT = false;
+
+ //doubtfully endemic
+ UUID doubtfullyEndemicUuid = transformer.getPresenceTermUuid("?E");
+ this.getPresenceTerm(state, doubtfullyEndemicUuid, "doubtfully endemic", "doubtfully endemic", "?E", false);
+
+ //indigenous
+ UUID indigenousUuid = transformer.getPresenceTermUuid("+");
+ this.getPresenceTerm(state, indigenousUuid, "indigenous", "Indigenous", "+", false);
+ UUID indigenousDoubtfulUuid = transformer.getPresenceTermUuid("?");
+ this.getPresenceTerm(state, indigenousDoubtfulUuid, "indigenous, doubtfully present", "indigenous, doubtfully present", "?", false);
+ UUID nonNativeDoubtfulNaturalizedUuid = transformer.getPresenceTermUuid("P");
+ this.getPresenceTerm(state, nonNativeDoubtfulNaturalizedUuid, "non-native and doubtfully naturalised", "non-native and doubtfully naturalised", "P", false);
+ UUID casualUuid = transformer.getPresenceTermUuid("A");
+ this.getPresenceTerm(state, casualUuid, "adventive (casual) alien", "adventive (casual) alien", "A", false);
+
+ //occasionally cultivated
+ label = "occasionally cultivated";
+ abbrev = "(C)";
+ UUID occasionallyCultivatedUuid = transformer.getPresenceTermUuid(abbrev);
+ getPresenceTerm(state, occasionallyCultivatedUuid, label, label, abbrev, PRESENT, cubaStatusVocabualary);
+
+ //doubtfully present
+ UUID doubtfullyIndigenousUuid = transformer.getPresenceTermUuid("D");
+ this.getPresenceTerm(state, doubtfullyIndigenousUuid, "indigenous?", "Indigenous?", "D", false);
+ UUID doubtfullyIndigenousDoubtfulUuid = transformer.getPresenceTermUuid("??");
+ this.getPresenceTerm(state, doubtfullyIndigenousDoubtfulUuid, "?indigenous?", "doubfully indigenous, (und) doubtfully present", "??", false);
+
+ UUID doubtfullyNaturalisedUuid = transformer.getPresenceTermUuid("?N");
+ this.getPresenceTerm(state, doubtfullyNaturalisedUuid, "?non-native and doubtfully naturalised", "non-native and doubtfully naturalised, doubtfully present", "?N", false);
+ UUID doubtfullyNonNativeUuid = transformer.getPresenceTermUuid("?P");
+ this.getPresenceTerm(state, doubtfullyNonNativeUuid, "?adventive (casual) alien ", "adventive (casual) alien, doubtfully present", "?P", false);
+
+ //reported in error
+ boolean isAbsent = true;
+ UUID endemicErrorUuid = transformer.getPresenceTermUuid("-E");
+ this.getPresenceTerm(state, endemicErrorUuid, "endemic, reported in error", "endemic, reported in error", "-E", isAbsent);
+ UUID naturalizedErrorUuid = transformer.getPresenceTermUuid("-N");
+ this.getPresenceTerm(state, naturalizedErrorUuid, "naturalised, reported in error", "naturalised, reported in error", "-N", isAbsent);
+ UUID nonNativeErrorUuid = transformer.getPresenceTermUuid("-P");
+ this.getPresenceTerm(state, nonNativeErrorUuid, "non-native and doubtfully naturalised, reported in error", "non-native and doubtfully naturalised, reported in error", "-P", isAbsent);
+ UUID casualErrorUuid = transformer.getPresenceTermUuid("-A");
+ this.getPresenceTerm(state, casualErrorUuid, "adventive alien , reported in error", "adventive alien , reported in error", "-A", isAbsent);
+
commitTransaction(tx);
}
//Pinar del Río PR
label = "Pinar del Río";
- abbrev = "PR";
+ abbrev = "PR*";
UUID uuid = transformer.getNamedAreaUuid(abbrev);
NamedArea area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
westernCuba.addIncludes(area);
- //Habana Hab
- label = "Habana"; //including Ciudad de la Habana, Mayabeque, Artemisa
- abbrev = "Hab";
+// //Habana Hab
+// label = "Habana"; //including Ciudad de la Habana, Mayabeque, Artemisa
+// abbrev = "HAB";
+// uuid = transformer.getNamedAreaUuid(abbrev);
+// NamedArea habana = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
+// westernCuba.addIncludes(habana);
+
+ //Ciudad de la Habana
+ label = "Ciudad de la Habana";
+ abbrev = "Hab*";
uuid = transformer.getNamedAreaUuid(abbrev);
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
westernCuba.addIncludes(area);
+ //Ciudad de la Habana
+ label = "Mayabeque";
+ abbrev = "May";
+ uuid = transformer.getNamedAreaUuid(abbrev);
+ area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
+ westernCuba.addIncludes(area);
+ //Ciudad de la Habana
+ label = "Artemisa";
+ abbrev = "Art";
+ uuid = transformer.getNamedAreaUuid(abbrev);
+ area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
+ westernCuba.addIncludes(area);
+
//Matanzas Mat
label = "Matanzas";
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
eastCuba.addIncludes(area);
- //Surrounding
- //Española Esp
+ //other Greater Antilles (Cuba, Española, Jamaica, Puerto Rico)
+ level = null;
+ //Española Esp (=Haiti + Dominican Republic)
label = "Española";
abbrev = "Esp";
uuid = transformer.getNamedAreaUuid(abbrev);
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
//Jamaica Ja
+ level = NamedAreaLevel.COUNTRY();
label = "Jamaica";
abbrev = "Ja";
uuid = transformer.getNamedAreaUuid(abbrev);
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
//Puerto Rico PR
- label = "Puerto Rico"; //Greater Antilles
+ level = NamedAreaLevel.COUNTRY();
+ label = "Puerto Rico";
abbrev = "PR";
uuid = transformer.getNamedAreaUuid(abbrev);
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
- //Smaller Antilles Men
- label = "Smaller Antilles";
+ //Lesser Antilles Men
+ level = null;
+ label = "Lesser Antilles";
abbrev = "Men";
uuid = transformer.getNamedAreaUuid(abbrev);
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
//Cayman Islands
- label = "Cayman Islands"; //[Trinidad, Tobago, Curaçao, Margarita, ABC Isl. = S. America];
+ label = "Cayman Islands"; //[Trinidad, Tobago, Curaçao, Margarita, ABC Isl. => S. America];
abbrev = "Cay";
uuid = transformer.getNamedAreaUuid(abbrev);
area = getNamedArea(state, uuid, label, label, abbrev, areaType, level, cubaAreasVocabualary, matchMode);
@Override
protected boolean isIgnore(CubaImportState state) {
- return ! state.getConfig().isDoTaxa();
+ return ! state.getConfig().isDoVocabularies();
}
BGBM BDI Projects / cdmlib-apps.git / blobdiff