import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
-import eu.etaxonomy.cdm.api.service.dto.CondensedDistribution;
+import eu.etaxonomy.cdm.api.service.geo.IDistributionService;
+import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetComparator;
+import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetContainer;
import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetFormatter;
-import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager;
import eu.etaxonomy.cdm.common.CdmUtils;
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
import eu.etaxonomy.cdm.compare.name.TypeComparator;
import eu.etaxonomy.cdm.compare.taxon.HomotypicGroupTaxonComparator;
-import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
+import eu.etaxonomy.cdm.format.description.CategoricalDataFormatter;
+import eu.etaxonomy.cdm.format.description.QuantitativeDataFormatter;
+import eu.etaxonomy.cdm.format.description.distribution.CondensedDistribution;
import eu.etaxonomy.cdm.format.reference.OriginalSourceFormatter;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.common.CdmExportBase;
import eu.etaxonomy.cdm.model.common.Identifier;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.common.LanguageString;
+import eu.etaxonomy.cdm.model.description.CategoricalData;
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
import eu.etaxonomy.cdm.model.description.DescriptionBase;
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
import eu.etaxonomy.cdm.model.description.Distribution;
import eu.etaxonomy.cdm.model.description.Feature;
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
+import eu.etaxonomy.cdm.model.description.QuantitativeData;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.description.TaxonInteraction;
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
-import eu.etaxonomy.cdm.model.term.DefinedTerm;
+import eu.etaxonomy.cdm.model.term.IdentifierType;
+import eu.etaxonomy.cdm.model.term.TermTree;
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDtoByRankAndNameComparator;
import eu.etaxonomy.cdm.strategy.cache.HTMLTagRules;
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
/**
+ * The export exporting a classification or a taxonomic subtree into CDM light.
+ *
* @author k.luther
* @since 15.03.2017
*/
extends CdmExportBase<CdmLightExportConfigurator, CdmLightExportState, IExportTransformer, File>{
private static final long serialVersionUID = 2518643632756927053L;
- private static final String STD_TEAM_CONCATINATION = ", ";
- private static final String FINAL_TEAM_CONCATINATION = " & ";
-
- private static final String IPNI_NAME_IDENTIFIER = "Ipni Name Identifier";
- private static final String TROPICOS_NAME_IDENTIFIER = "Tropicos Name Identifier";
- private static final String WFO_NAME_IDENTIFIER = "WFO Name Identifier";
@Autowired
- IEditGeoService geoService;
+ private IDistributionService distributionService;
public CdmLightClassificationExport() {
- super();
this.ioName = this.getClass().getSimpleName();
}
if (state.getRootId() != null) {
List<TaxonNodeDto> childrenOfRoot = state.getNodeChildrenMap().get(state.getRootId());
- Comparator<TaxonNodeDto> comp = state.getConfig().getComparator();
+ Comparator<TaxonNodeDto> comp = state.getConfig().getTaxonNodeComparator();
if (comp == null) {
comp = new TaxonNodeDtoByRankAndNameComparator();
}
private void setOrderIndex(CdmLightExportState state, OrderHelper order) {
- // String sortIndex = StringUtils.isBlank(sort_index)?
- // String.valueOf(order.getOrderIndex()): sort_index+ "_"
- // +String.valueOf(order.getOrderIndex());
-
if (order.getTaxonUuid() != null
&& state.getProcessor().hasRecord(CdmLightExportTable.TAXON, order.getTaxonUuid().toString())) {
String[] csvLine = state.getProcessor().getRecord(CdmLightExportTable.TAXON,
if (children == null) {
return null;
}
- Comparator<TaxonNodeDto> comp = state.getConfig().getComparator();
+ Comparator<TaxonNodeDto> comp = state.getConfig().getTaxonNodeComparator();
if (comp == null) {
comp = new TaxonNodeDtoByRankAndNameComparator();
}
state.getNodeChildrenMap().put(root.getUuid(), childNodes);
// add root to node map
-
}
TaxonNodeDto rootDto = new TaxonNodeDto(root);
UUID parentUuid = root.getParent() != null ? root.getParent().getUuid()
List<TaxonNodeDto> rootList = new ArrayList<>();
rootList.add(rootDto);
state.getNodeChildrenMap().put(parentUuid, rootList);
-
}
if (root.hasTaxon()) {
handleTaxon(state, root);
-
}
} catch (Exception e) {
state.getResult().addException(e, "An unexpected error occurred when handling taxonNode "
"handleTaxon");
state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
} else {
- Taxon taxon = HibernateProxyHelper.deproxy(taxonNode.getTaxon(), Taxon.class);
+ Taxon taxon = CdmBase.deproxy(taxonNode.getTaxon());
try {
+ //accepted name
TaxonName name = taxon.getName();
handleName(state, name, taxon, true);
+
+ //homotypic group / synonyms
HomotypicalGroup homotypicGroup = taxon.getHomotypicGroup();
int index = 0;
int homotypicGroupIndex = 0;
homotypicGroupIndex++;
}
+ //pro parte synonyms
index = 0;
for (Taxon tax : taxon.getAllProParteSynonyms()) {
handleProPartePartialMisapplied(state, tax, taxon, true, false, index);
index++;
}
-
+ //misapplications
for (Taxon tax : taxon.getAllMisappliedNames()) {
handleProPartePartialMisapplied(state, tax, taxon, false, true, index);
index++;
}
+ //taxon table
CdmLightExportTable table = CdmLightExportTable.TAXON;
String[] csvLine = new String[table.getSize()];
csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
Taxon parent = (taxonNode.getParent() == null) ? null : taxonNode.getParent().getTaxon();
csvLine[table.getIndex(CdmLightExportTable.PARENT_FK)] = getId(state, parent);
+
+ //secundum reference
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, taxon.getSec());
if (taxon.getSec() != null && taxon.getSec().getDatePublished() != null
&& taxon.getSec().getDatePublished().getFreeText() != null) {
handleReference(state, taxon.getSec());
}
}
+ //secundum subname
+ TaxonName subName = taxon.getSecSource() == null? null : taxon.getSecSource().getNameUsedInSource();
+ if (subName != null) {
+ csvLine[table.getIndex(CdmLightExportTable.SEC_SUBNAME_FK)] = getId(state, subName);
+ if (!state.getNameStore().containsKey((subName.getId()))) {
+ handleName(state, subName, null);
+ }
+ csvLine[table.getIndex(CdmLightExportTable.SEC_SUBNAME)] = subName.getNameCache();
+ csvLine[table.getIndex(CdmLightExportTable.SEC_SUBNAME_AUTHORS)] = subName.getAuthorshipCache();
+ }
+
csvLine[table.getIndex(CdmLightExportTable.APPENDED_PHRASE)] = taxon.getAppendedPhrase();
csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_ID)] = getId(state,
taxonNode.getClassification());
csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_TITLE)] = taxonNode.getClassification()
.getTitleCache();
-
csvLine[table.getIndex(CdmLightExportTable.PUBLISHED)] = taxon.isPublish() ? "1" : "0";
+
+ //taxon node
+ csvLine[table.getIndex(CdmLightExportTable.INCLUDED)] = taxonNode.getStatus() == null ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.DOUBTFUL)] = taxonNode.isDoubtful() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.UNPLACED)] = taxonNode.isUnplaced() ? "1" : "0";
csvLine[table.getIndex(CdmLightExportTable.EXCLUDED)] = taxonNode.isExcluded() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.EXCLUDED_EXACT)] = taxonNode.isExcludedExact() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.EXCLUDED_GEO)] = taxonNode.isGeographicallyExcluded() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.EXCLUDED_TAX)] = taxonNode.isTaxonomicallyExcluded() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.EXCLUDED_NOM)] = taxonNode.isNomenclaturallyExcluded() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.UNCERTAIN_APPLICATION)] = taxonNode.isUncertainApplication() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.UNRESOLVED)] = taxonNode.isUnresolved() ? "1" : "0";
+ csvLine[table.getIndex(CdmLightExportTable.PLACEMENT_STATUS)] = taxonNode.getStatus() == null ? null : taxonNode.getStatus().getLabel();
Map<Language, LanguageString> notesMap = taxonNode.getStatusNote();
String statusNotes = "";
if (!notesMap.isEmpty() && notesMap.size() == 1) {
statusNotes = notesMap.values().iterator().next().getText();
}
}
- csvLine[table.getIndex(CdmLightExportTable.STATUS_NOTES)] = statusNotes;
+ csvLine[table.getIndex(CdmLightExportTable.PLACEMENT_NOTES)] = statusNotes;
- csvLine[table.getIndex(CdmLightExportTable.UNPLACED)] = taxonNode.isUnplaced() ? "1" : "0";
- csvLine[table.getIndex(CdmLightExportTable.DOUBTFUL)] = taxonNode.isDoubtful() ? "1" : "0";
+ if (taxonNode.getSource() != null) {
+ csvLine[table.getIndex(CdmLightExportTable.PLACEMENT_REF_FK)] = getId(state, taxonNode.getSource().getCitation());
+ String sourceStr = OriginalSourceFormatter.INSTANCE.format(taxonNode.getSource());
+ csvLine[table.getIndex(CdmLightExportTable.PLACEMENT_REFERENCE)] = sourceStr;
+ }
+
+ //process taxon line
state.getProcessor().put(table, taxon, csvLine);
+
+ //descriptions
handleDescriptions(state, taxon);
} catch (Exception e) {
state.getResult().addException(e,
state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
}
}
-
- taxonNode.removeNullValueFromChildren();
-
} catch (Exception e) {
state.getResult().addException(e, "An unexpected error occurred when handling the taxon node of "
+ cdmBaseStr(taxonNode.getTaxon()) + ", titleCache:"+ taxonNode.getTaxon().getTitleCache()+": " + e.getMessage());
}
private void handleDescriptions(CdmLightExportState state, CdmBase cdmBase) {
+ if (!state.getConfig().isDoFactualData()) {
+ return;
+ }
String titleCache = null;
try {
} else {
state.getProcessor().put(table, textData, csvLine);
}
+ }else if (element instanceof CategoricalData) {
+ //use formater
+ CategoricalData categoricalData = (CategoricalData)element;
+ String cache = CategoricalDataFormatter.NewInstance(null).format(categoricalData);
+ csvLine = new String[table.getSize()];
+ csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
+ if (cdmBase instanceof Taxon) {
+ csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
+ } else if (cdmBase instanceof TaxonName) {
+ csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
+ }
+ csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = cache;
+ csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = categoricalData.getFeature().getLabel();
+ state.getProcessor().put(table, categoricalData, csvLine);
+ }else if (element instanceof QuantitativeData) {
+ QuantitativeData quantitativeData = (QuantitativeData) element;
+ String cache = QuantitativeDataFormatter.NewInstance(null).format(quantitativeData);
+ csvLine = new String[table.getSize()];
+ csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
+ if (cdmBase instanceof Taxon) {
+ csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
+ } else if (cdmBase instanceof TaxonName) {
+ csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
+ }
+ csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = cache;
+ csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = quantitativeData.getFeature().getLabel();
+ state.getProcessor().put(table, quantitativeData, csvLine);
}
} catch (Exception e) {
state.getResult().addException(e, "An unexpected error occurred when handling single simple fact "
for (DescriptionElementSource source : sources) {
if (!(source.getType().equals(OriginalSourceType.Import)
- && state.getConfig().isFilterImportSources())) {
+ && state.getConfig().isExcludeImportSources())) {
String[] csvLine = new String[table.getSize()];
Reference ref = source.getCitation();
if ((ref == null) && (source.getNameUsedInSource() == null)) {
}
state.getProcessor().put(table, source, csvLine);
}
-
}
} catch (Exception e) {
state.getResult().addException(e, "An unexpected error occurred when handling single source "
+ cdmBaseStr(element) + ": " + e.getMessage());
}
-
}
private void handleDistributionFacts(CdmLightExportState state, Taxon taxon,
if(state.getConfig().isCreateCondensedDistributionString()){
List<Language> langs = new ArrayList<>();
langs.add(Language.ENGLISH());
+ TermTree<NamedArea> areaTree = null; //TODO
- CondensedDistribution conDis = geoService.getCondensedDistribution(
+ CondensedDistribution conDis = distributionService.getCondensedDistribution(
//TODO add CondensedDistributionConfiguration to export configuration
- distributions, true, null, state.getConfig().getCondensedDistributionRecipe().toConfiguration(), langs);
+ distributions, areaTree, true, null, state.getConfig().getCondensedDistributionConfiguration(), langs);
CdmLightExportTable tableCondensed =
CdmLightExportTable.SIMPLE_FACT;
String[] csvLine = new String[tableCondensed.getSize()];
}
/**
- * Handles Misapplied names (including pro parte and partial as well as pro
+ * Handles misapplied names (including pro parte and partial as well as pro
* parte and partial synonyms
- *
- * @param state
- * @param rel
*/
private void handleProPartePartialMisapplied(CdmLightExportState state, Taxon taxon, Taxon accepted, boolean isProParte, boolean isMisapplied, int index) {
try {
csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_REF)] = name.getFullTitleCache();
} else {
List<TaggedText> taggedFullTitleCache = name.getTaggedFullTitle();
+ List<TaggedText> taggedName = name.getTaggedName();
+
String fullTitleWithHtml = createNameWithItalics(taggedFullTitleCache);
// TODO: adapt the tropicos titlecache creation
csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_REF)] = fullTitleWithHtml.trim();
NomenclaturalSource nomenclaturalSource = name.getNomenclaturalSource();
if (nomenclaturalSource != null &&nomenclaturalSource.getNameUsedInSource() != null){
handleName(state, nomenclaturalSource.getNameUsedInSource(), null);
- csvLine[table.getIndex(CdmLightExportTable.NAME_USED_IN_SOURCE)] = getId(state, nomenclaturalSource.getNameUsedInSource());
+ csvLine[table.getIndex(CdmLightExportTable.NAME_USED_IN_SOURCE_FK)] = getId(state, nomenclaturalSource.getNameUsedInSource());
}
if (nomRef != null) {
textualTypeDesignations.add((TextualTypeDesignation) typeDesignation);
}
} else if (typeDesignation.isInstanceOf(SpecimenTypeDesignation.class)) {
+ SpecimenTypeDesignation specimenType = HibernateProxyHelper.deproxy(typeDesignation, SpecimenTypeDesignation.class);
+ specimenTypeDesignations.add(specimenType);
+ handleSpecimenType(state, specimenType);
- specimenTypeDesignations.add(HibernateProxyHelper.deproxy(typeDesignation, SpecimenTypeDesignation.class));
}else if (typeDesignation instanceof NameTypeDesignation){
specimenTypeDesignations.add(HibernateProxyHelper.deproxy(typeDesignation, NameTypeDesignation.class));
}
}
- TypeDesignationSetManager manager = new TypeDesignationSetManager(specimenTypeDesignations, name);
+ TypeDesignationSetContainer manager = new TypeDesignationSetContainer(specimenTypeDesignations, name, TypeDesignationSetComparator.ORDER_BY.TYPE_STATUS);
HTMLTagRules rules = new HTMLTagRules();
rules.addRule(TagEnum.name, "i");
- String test = manager.print(false, false, false, rules);;
csvLine[table.getIndex(CdmLightExportTable.TYPE_SPECIMEN)] = manager.print(false, false, false, rules);
StringBuilder stringbuilder = new StringBuilder();
synonymsInGroup = acceptedTaxon.getSynonymsInGroup(group, comparator);
}
- synonymsInGroup.stream().forEach(synonym -> typifiedNames.add(HibernateProxyHelper.deproxy(synonym.getName(), TaxonName.class)));
+ synonymsInGroup.stream().forEach(synonym -> typifiedNames.add(HibernateProxyHelper.deproxy(synonym.getName())));
}else{
typifiedNames.addAll(group.getTypifiedNames());
}
}
+ private void handleSpecimenType_(CdmLightExportState state, SpecimenTypeDesignation specimenType) {
+ if (specimenType.getTypeSpecimen() != null){
+ DerivedUnit specimen = specimenType.getTypeSpecimen();
+ if(specimen != null && !state.getSpecimenStore().contains( specimen.getUuid())){
+ handleSpecimen(state, specimen);
+ }
+ }
+ CdmLightExportTable table = CdmLightExportTable.TYPE_DESIGNATION;
+ String[] csvLine = new String[table.getSize()];
+ //TYPE_ID, SPECIMEN_FK, TYPE_VERBATIM_CITATION, TYPE_STATUS, TYPE_DESIGNATED_BY_STRING, TYPE_DESIGNATED_BY_REF_FK};
+ //Specimen_Fk und den Typusangaben (Art des Typus [holo, lecto, etc.], Quelle, Designation-Quelle, +
+ Set<TaxonName> typifiedNames = specimenType.getTypifiedNames();
+ for (TaxonName name: typifiedNames){
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_STATUS)] = specimenType.getTypeStatus() != null? specimenType.getTypeStatus().getDescription(): "";
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_ID)] = getId(state, specimenType);
+ csvLine[table.getIndex(CdmLightExportTable.TYPIFIED_NAME_FK)] = getId(state, name);
+ csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, specimenType.getTypeSpecimen());
+ if (specimenType.getSources() != null && !specimenType.getSources().isEmpty()){
+ String sourceString = "";
+ int index = 0;
+ for (IdentifiableSource source: specimenType.getSources()){
+ if (source.getCitation()!= null){
+ sourceString = sourceString.concat(source.getCitation().getCitation());
+ }
+ index++;
+ if (index != specimenType.getSources().size()){
+ sourceString.concat(", ");
+ }
+ }
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_INFORMATION_REF_STRING)] = sourceString;
+ }
+ if (specimenType.getDesignationSource() != null && specimenType.getDesignationSource().getCitation() != null && !state.getReferenceStore().contains(specimenType.getDesignationSource().getCitation().getUuid())){
+ handleReference(state, specimenType.getDesignationSource().getCitation());
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_REF_FK)] = specimenType.getDesignationSource() != null ? getId(state, specimenType.getDesignationSource().getCitation()): "";
+ }
+
+ state.getProcessor().put(table, specimenType, csvLine);
+ }
+ }
+
+
+ /**
+ * @param specimenType
+ */
+ private void handleSpecimenType(CdmLightExportState state, SpecimenTypeDesignation specimenType) {
+ if (specimenType.getTypeSpecimen() != null){
+ DerivedUnit specimen = specimenType.getTypeSpecimen();
+ if(specimen != null && !state.getSpecimenStore().contains( specimen.getUuid())){
+ handleSpecimen(state, specimen);
+ }
+ }
+ CdmLightExportTable table = CdmLightExportTable.TYPE_DESIGNATION;
+ String[] csvLine = new String[table.getSize()];
+
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_STATUS)] = specimenType.getTypeStatus() != null? specimenType.getTypeStatus().getDescription(): "";
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_ID)] = getId(state, specimenType);
+ csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, specimenType.getTypeSpecimen());
+ if (specimenType.getSources() != null && !specimenType.getSources().isEmpty()){
+ String sourceString = "";
+ int index = 0;
+ List<IdentifiableSource> sources = new ArrayList<>(specimenType.getSources());
+ Comparator<IdentifiableSource> compareByYear = new Comparator<IdentifiableSource>() {
+ @Override
+ public int compare(IdentifiableSource o1, IdentifiableSource o2) {
+ if (o1 == o2){
+ return 0;
+ }
+ if (o1.getCitation() == null && o2.getCitation() != null){
+ return -1;
+ }
+ if (o2.getCitation() == null && o1.getCitation() != null){
+ return 1;
+ }
+ if (o1.getCitation().equals(o2.getCitation())){
+ return 0;
+ }
+ if (o1.getCitation().getDatePublished() == null && o2.getCitation().getDatePublished() != null){
+ return -1;
+ }
+ if (o1.getCitation().getDatePublished() != null && o2.getCitation().getDatePublished() == null){
+ return 1;
+ }
+ if (o1.getCitation().getDatePublished().getYear() == null && o2.getCitation().getDatePublished().getYear() != null){
+ return -1;
+ }
+ if (o1.getCitation().getDatePublished().getYear() != null && o2.getCitation().getDatePublished().getYear() == null){
+ return 1;
+ }
+ return o1.getCitation().getDatePublished().getYear().compareTo(o2.getCitation().getDatePublished().getYear());
+ }
+ };
+ Collections.sort(sources, compareByYear);
+ for (IdentifiableSource source: sources){
+ if (source.getCitation()!= null){
+ sourceString = sourceString.concat(source.getCitation().getCitation());
+ handleReference(state, source.getCitation());
+ }
+ index++;
+ if (index <= specimenType.getSources().size()){
+ sourceString = sourceString.concat("; ");
+ }
+ }
+
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_INFORMATION_REF_STRING)] = sourceString;
+ if (sources.get(0).getCitation() != null ){
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_INFORMATION_REF_FK)] = getId(state, sources.get(0).getCitation());
+ }
+ }
+ if (specimenType.getDesignationSource() != null && specimenType.getDesignationSource().getCitation() != null && !state.getReferenceStore().contains(specimenType.getDesignationSource().getCitation().getUuid())){
+ handleReference(state, specimenType.getDesignationSource().getCitation());
+ csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_REF_FK)] = specimenType.getDesignationSource() != null ? getId(state, specimenType.getDesignationSource().getCitation()): "";
+ }
+
+
+ Set<TaxonName> typifiedNames = specimenType.getTypifiedNames();
+
+ if (typifiedNames.size() > 1){
+ state.getResult().addWarning("Please check the specimen type "
+ + cdmBaseStr(specimenType) + " there are more then one typified name.");
+ }
+ if (typifiedNames.iterator().hasNext()){
+ TaxonName name = typifiedNames.iterator().next();
+ csvLine[table.getIndex(CdmLightExportTable.TYPIFIED_NAME_FK)] = getId(state, name);
+ }
+ state.getProcessor().put(table, specimenType, csvLine);
+ }
+
private String createNameWithItalics(List<TaggedText> taggedName) {
String fullTitleWithHtml = "";
if (!state.getNameStore().containsKey(name2.getId())) {
handleName(state, name2, null);
}
-
+ csvLine = new String[table.getSize()];
csvLine[table.getIndex(CdmLightExportTable.NAME_REL_TYPE)] = type.getLabel();
csvLine[table.getIndex(CdmLightExportTable.NAME1_FK)] = getId(state, name);
csvLine[table.getIndex(CdmLightExportTable.NAME2_FK)] = getId(state, name2);
- state.getProcessor().put(table, name, csvLine);
+ state.getProcessor().put(table, rel.getUuid().toString(), csvLine);
}
rels = name.getRelationsToThisName();
csvLine = new String[table.getSize()];
for (NameRelationship rel : rels) {
- NameRelationshipType type = rel.getType();
TaxonName name2 = rel.getFromName();
- name2 = HibernateProxyHelper.deproxy(name2, TaxonName.class);
+ name2 = HibernateProxyHelper.deproxy(name2);
if (!state.getNameStore().containsKey(name2.getId())) {
handleName(state, name2, null);
}
-
-
}
}
TaxonName name = (TaxonName)cdmBase;
try{
- Set<String> IPNIidentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_IPNI());
- Set<String> tropicosIdentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_TROPICOS());
- Set<String> WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
- if (!IPNIidentifiers.isEmpty()) {
- csvLine = new String[table.getSize()];
- csvLine[table.getIndex(CdmLightExportTable.FK)] = getId(state, name);
- csvLine[table.getIndex(CdmLightExportTable.REF_TABLE)] = "ScientificName";
- csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = IPNI_NAME_IDENTIFIER;
- csvLine[table.getIndex(CdmLightExportTable.EXTERNAL_NAME_IDENTIFIER)] = extractIdentifier(
- IPNIidentifiers);
- state.getProcessor().put(table, name.getUuid() + ", " + IPNI_NAME_IDENTIFIER, csvLine);
- }
- if (!tropicosIdentifiers.isEmpty()) {
- csvLine = new String[table.getSize()];
- csvLine[table.getIndex(CdmLightExportTable.FK)] = getId(state, name);
- csvLine[table.getIndex(CdmLightExportTable.REF_TABLE)] = "ScientificName";
- csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = name.getUuid() + ", " + IPNI_NAME_IDENTIFIER;
- csvLine[table.getIndex(CdmLightExportTable.EXTERNAL_NAME_IDENTIFIER)] = extractIdentifier(
- tropicosIdentifiers);
- state.getProcessor().put(table, name.getUuid() + ", " + IPNI_NAME_IDENTIFIER, csvLine);
+ List<Identifier> identifiers = name.getIdentifiers();
+
+ //first check which kind of identifiers are available and then sort and create table entries
+ Map<IdentifierType, Set<Identifier>> identifierTypes = new HashMap<>();
+ for (Identifier identifier: identifiers){
+ IdentifierType type = identifier.getType();
+ if (identifierTypes.containsKey(type)){
+ identifierTypes.get(type).add(identifier);
+ }else{
+ Set<Identifier> tempList = new HashSet<>();
+ tempList.add(identifier);
+ identifierTypes.put(type, tempList);
+ }
}
- if (!WFOIdentifiers.isEmpty()) {
+
+ for (IdentifierType type:identifierTypes.keySet()){
+ Set<Identifier> identifiersByType = identifierTypes.get(type);
csvLine = new String[table.getSize()];
csvLine[table.getIndex(CdmLightExportTable.FK)] = getId(state, name);
csvLine[table.getIndex(CdmLightExportTable.REF_TABLE)] = "ScientificName";
- csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = WFO_NAME_IDENTIFIER;
+ csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = type.getLabel();
csvLine[table.getIndex(CdmLightExportTable.EXTERNAL_NAME_IDENTIFIER)] = extractIdentifier(
- WFOIdentifiers);
- state.getProcessor().put(table, name.getUuid() + ", " + WFO_NAME_IDENTIFIER, csvLine);
+ identifiersByType);
+ state.getProcessor().put(table, name.getUuid() + ", " + type.getLabel(), csvLine);
}
+
+
+// Set<String> IPNIidentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_IPNI());
+// Set<String> tropicosIdentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_TROPICOS());
+// Set<String> WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
+// if (!IPNIidentifiers.isEmpty()) {
+// csvLine = new String[table.getSize()];
+// csvLine[table.getIndex(CdmLightExportTable.FK)] = getId(state, name);
+// csvLine[table.getIndex(CdmLightExportTable.REF_TABLE)] = "ScientificName";
+// csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = IPNI_NAME_IDENTIFIER;
+// csvLine[table.getIndex(CdmLightExportTable.EXTERNAL_NAME_IDENTIFIER)] = extractIdentifier(
+// IPNIidentifiers);
+// state.getProcessor().put(table, name.getUuid() + ", " + IPNI_NAME_IDENTIFIER, csvLine);
+// }
+// if (!tropicosIdentifiers.isEmpty()) {
+// csvLine = new String[table.getSize()];
+// csvLine[table.getIndex(CdmLightExportTable.FK)] = getId(state, name);
+// csvLine[table.getIndex(CdmLightExportTable.REF_TABLE)] = "ScientificName";
+// csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = TROPICOS_NAME_IDENTIFIER;
+// csvLine[table.getIndex(CdmLightExportTable.EXTERNAL_NAME_IDENTIFIER)] = extractIdentifier(
+// tropicosIdentifiers);
+// state.getProcessor().put(table, name.getUuid() + ", " + IPNI_NAME_IDENTIFIER, csvLine);
+// }
+// if (!WFOIdentifiers.isEmpty()) {
+// csvLine = new String[table.getSize()];
+// csvLine[table.getIndex(CdmLightExportTable.FK)] = getId(state, name);
+// csvLine[table.getIndex(CdmLightExportTable.REF_TABLE)] = "ScientificName";
+// csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = WFO_NAME_IDENTIFIER;
+// csvLine[table.getIndex(CdmLightExportTable.EXTERNAL_NAME_IDENTIFIER)] = extractIdentifier(
+// WFOIdentifiers);
+// state.getProcessor().put(table, name.getUuid() + ", " + WFO_NAME_IDENTIFIER, csvLine);
+// }
}catch(Exception e){
state.getResult().addWarning("Please check the identifiers for "
+ cdmBaseStr(cdmBase) + " maybe there is an empty identifier");
}
}
- private String extractIdentifier(Set<String> identifierSet) {
+ private String extractIdentifier(Set<Identifier> identifierSet) {
String identifierString = "";
- for (String identifier : identifierSet) {
+ for (Identifier identifier : identifierSet) {
if (!StringUtils.isBlank(identifierString)) {
identifierString += ", ";
}
- identifierString += identifier;
+ identifierString += identifier.getIdentifier();
}
return identifierString;
}
if (group.equals(acceptedTaxon.getHomotypicGroup())){
typifiedNames.add(acceptedTaxon.getName());
}
- synonymsInGroup.stream().forEach(synonym -> typifiedNames.add(HibernateProxyHelper.deproxy(synonym.getName(), TaxonName.class)));
+ synonymsInGroup.stream().forEach(synonym -> typifiedNames.add(CdmBase.deproxy(synonym.getName())));
}
Set<NameRelationship> related = name.getNameRelations();
List<NameRelationship> relatedList = new ArrayList<>(related);
- Collections.sort(relatedList, new Comparator<NameRelationship>() {
- @Override
- public int compare(NameRelationship nr1, NameRelationship nr2) {
- return nr1.getType().compareTo(nr2.getType());
- }
-
- });
+ Collections.sort(relatedList, (nr1, nr2)-> {
+ return nr1.getType().compareTo(nr2.getType());});
List<NameRelationship> nonNames = new ArrayList<>();
List<NameRelationship> otherRelationships = new ArrayList<>();
// alle Homonyme und inverse blocking names
if (rel.getType().equals(NameRelationshipType.LATER_HOMONYM())
|| rel.getType().equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())
- || (rel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR()))){
+ || (rel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR()))
+ || (rel.getType().equals(NameRelationshipType.UNSPECIFIC_NON()))
+ || (rel.getType().equals(NameRelationshipType.AVOIDS_HOMONYM_OF()))
+ ){
nonNames.add(rel);
}else if (!rel.getType().isBasionymRelation()){
otherRelationships.add(rel);
}
}
+ if (state.getConfig().isShowInverseNameRelationsInHomotypicGroup()) {
+ if (rel.getToName().equals(name)){
+ // alle Homonyme und inverse blocking names
+// if (rel.getType().equals(NameRelationshipType.LATER_HOMONYM())
+// || rel.getType().equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())
+// || (rel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR()))
+// || (rel.getType().equals(NameRelationshipType.UNSPECIFIC_NON()))
+// || (rel.getType().equals(NameRelationshipType.AVOIDS_HOMONYM_OF()))
+// ){
+// nonNames.add(rel);
+// }else if (!rel.getType().isBasionymRelation()){
+ otherRelationships.add(rel);
+// }
+ }
+ }
}
String nonRelNames = "";
TaxonName relatedName = null;
if (relName.getFromName().equals(name)){
relatedName = relName.getToName();
- nonRelNames += label + relatedName.getTitleCache() + " ";
+ if (state.getConfig().isAddHTML()){
+ nonRelNames += label + createNameWithItalics(relatedName.getTaggedName())+ " ";
+ }else{
+ nonRelNames += label + relatedName.getTitleCache();
+ }
}
// else{
// label = relName.getType().getInverseLabel() + " ";
// relatedName = relName.getFromName();
// nonRelNames += label + relatedName.getTitleCache() + " ";
// }
-
-
}
- relNames.trim();
+ nonRelNames.trim();
if (nonNames.size() > 0){
+ nonRelNames = StringUtils.strip(nonRelNames, null);
nonRelNames += "] ";
}
+ //other relationships
if (otherRelationships.size() > 0){
relNames += " [";
}
if (rel.getFromName().equals(name)){
label = rel.getType().getLabel() + " ";
relatedName = rel.getToName();
- relNames += label + relatedName.getTitleCache() + " ";
+ if (state.getConfig().isAddHTML()){
+ relNames += label + createNameWithItalics(relatedName.getTaggedName())+ " ";
+ }else{
+ relNames += label + relatedName.getTitleCache();
+ }
+ }
+ else {
+ label = rel.getType().getInverseLabel() + " ";
+ relatedName = rel.getFromName();
+ if (state.getConfig().isAddHTML()){
+ relNames += label + createNameWithItalics(relatedName.getTaggedName())+ " ";
+ }else{
+ relNames += label + relatedName.getTitleCache();
+ }
}
-// else {
-// label = rel.getType().getInverseLabel() + " ";
-// relatedName = rel.getFromName();
-// }
-
}
relNames.trim();
if (otherRelationships.size() > 0){
+ relNames = StringUtils.stripEnd(relNames, null);
relNames += "] ";
}
+
String synonymSign = "";
if (index > 0){
if (name.isInvalid()){
}else{
synonymSign = "\u2261 ";
}
+ }else{
+ if (name.isInvalid() ){
+ synonymSign = "\u2212 ";
+ }else{
+ synonymSign = "\u003D ";
+ }
}
boolean isAccepted = false;
if (taxonBases.size() == 1){
taxonBase = HibernateProxyHelper.deproxy(taxonBases.iterator().next());
+
if (taxonBase.getSec() != null){
sec = OriginalSourceFormatter.INSTANCE_WITH_YEAR_BRACKETS.format(taxonBase.getSecSource());
}
typifiedNamesWithoutAccepted += synonymSign + doubtful + nameString + nonRelNames + relNames;
typifiedNamesWithoutAcceptedWithSec += synonymSign + doubtful + nameString + sec + nonRelNames + relNames;
}else{
- sec = "";
+// sec = "";
if (!(((Taxon)taxonBase).isProparteSynonym() || ((Taxon)taxonBase).isMisapplication())){
isAccepted = true;
+ }else {
+ synonymSign = "\u003D ";
+ }
+
+ }
+ if (taxonBase.getAppendedPhrase() != null){
+ if (state.getConfig().isAddHTML()){
+ String taxonString = createNameWithItalics(taxonBase.getTaggedTitle()) ;
+ taxonString = taxonString.replace("sec "+sec, "");
+ String nameCacheWithItalics = createNameWithItalics(name.getTaggedName());
+ nameString = nameString.replace(nameCacheWithItalics, taxonString);
}
}
}else{
}else{
doubtful = "";
}
- if (tb instanceof Synonym){
+ if (tb instanceof Synonym ){
+ if (!((Synonym)tb).getAcceptedTaxon().equals(acceptedTaxon)) {
+ continue;
+ }
if (StringUtils.isNotBlank(sec)){
sec = " syn. sec. " + sec + " ";
}else {
if (!(((Taxon)tb).isProparteSynonym() || ((Taxon)tb).isMisapplication())){
isAccepted = true;
break;
+ }else {
+ synonymSign = "\u003D ";
}
-
}
}
if (!isAccepted){
List<TaggedText> list = new ArrayList<>();
if (!designationList.isEmpty()) {
- TypeDesignationSetManager manager = new TypeDesignationSetManager(group);
- list.addAll(new TypeDesignationSetFormatter(false, false, false).toTaggedText(manager));
+ TypeDesignationSetContainer manager = new TypeDesignationSetContainer(group);
+ list.addAll(new TypeDesignationSetFormatter(true, false, false).toTaggedText(manager));
}
String typeTextDesignations = "";
//The typeDesignationManager does not handle the textual typeDesignations
typeTextDesignations = typeTextDesignations + typeDesStateRefs +"; ";
+ }else if (typeDes instanceof SpecimenTypeDesignation){
+ DerivedUnit specimen = ((SpecimenTypeDesignation)typeDes).getTypeSpecimen();
+ if(specimen != null && !state.getSpecimenStore().contains( specimen.getUuid())){
+ handleSpecimen(state, specimen);
+ }
}
}
if (typeTextDesignations.equals("; ")) {
StringBuffer homotypicalGroupTypeDesignationString = new StringBuffer();
for (TaggedText text : list) {
- if (text != null && text.getText() != null
- && (text.getText().equals("Type:") || text.getText().equals("NameType:") || (text.getType().equals(TagEnum.name) && !isHomotypicGroup))) {
+ if (text == null || text.getText() == null){
+ continue; //just in case
+ }
+ if ((text.getText().equalsIgnoreCase("Type:") //should not happen anymore
+ || text.getText().equalsIgnoreCase("Nametype:") //should not happen anymore
+ || (text.getType().equals(TagEnum.name) && !isHomotypicGroup))) {
// do nothing
- } else if (text.getType().equals(TagEnum.reference)) {
+ }else if (text.getType().equals(TagEnum.reference)) {
homotypicalGroupTypeDesignationString.append(text.getText());
}else if (text.getType().equals(TagEnum.name)){
if (!isSpecimenTypeDesignation){
homotypicalGroupTypeDesignationString
- .append("<i>"+text.getText()+"</i> ");
+ .append("<i>"+text.getText()+"</i> ");
}
}else if (text.getType().equals(TagEnum.typeDesignation) ) {
if(isSpecimenTypeDesignation){
typeDesignations += ".";
typeDesignations = typeDesignations.replace("..", ".");
typeDesignations = typeDesignations.replace(". .", ".");
+ typeDesignations = typeDesignations.replace("; \u2261", " \u2261 ");
if (typeDesignations.trim().equals(".")) {
typeDesignations = null;
} else if (authorship instanceof Team) {
Team authorTeam = (Team)authorship;
- fullAuthorship = authorTeam.getCacheStrategy().getTitleCache(authorTeam);
+ fullAuthorship = authorTeam.cacheStrategy().getTitleCache(authorTeam);
}
return fullAuthorship;
}
csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_IMAGE_URIS)] = extractMediaURIs(state,
specimen.getDescriptions(), Feature.IMAGE());
if (specimen instanceof DerivedUnit) {
- DerivedUnit derivedUnit = (DerivedUnit) specimen;
+ DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(specimen, DerivedUnit.class);
if (derivedUnit.getCollection() != null) {
csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = derivedUnit.getCollection()
.getCode();
}
}
} else {
- state.getResult().addError("The specimen with uuid " + specimen.getUuid()
- + " is not an DerivedUnit. Could not be exported.");
+ state.getResult().addWarning("The specimen with uuid " + specimen.getUuid()
+ + " is not an DerivedUnit.");
}
}
BGBM BDI Projects / cdmlib.git / blobdiff