import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeCacheStrategy;
import eu.etaxonomy.cdm.common.CdmUtils;
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
+import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
import eu.etaxonomy.cdm.model.common.Annotation;
import eu.etaxonomy.cdm.model.common.AnnotationType;
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
import eu.etaxonomy.cdm.model.name.INonViralName;
-import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.occurrence.Collection;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
String destroyed = getAndRemoveAttributeValue(attributes, DESTROYED);
String lost = getAndRemoveAttributeValue(attributes, LOST);
checkNoAttributes(attributes, parentEvent);
- if (StringUtils.isNotEmpty(typeStatus)) {
+ if (isNotBlank(typeStatus)) {
// TODO
// currently not needed
fireWarningEvent("Type status not yet used", parentEvent, 4);
- } else if (StringUtils.isNotEmpty(notSeen)) {
- handleNotYetImplementedAttribute(attributes, NOT_SEEN);
- } else if (StringUtils.isNotEmpty(unknown)) {
- handleNotYetImplementedAttribute(attributes, UNKNOWN);
- } else if (StringUtils.isNotEmpty(notFound)) {
- handleNotYetImplementedAttribute(attributes, NOT_FOUND);
- } else if (StringUtils.isNotEmpty(destroyed)) {
- handleNotYetImplementedAttribute(attributes, DESTROYED);
- } else if (StringUtils.isNotEmpty(lost)) {
- handleNotYetImplementedAttribute(attributes, LOST);
+ }
+ if (isNotBlank(notSeen)) {
+ handleNotYetImplementedAttribute(attributes, NOT_SEEN, parentEvent);
+ }
+ if (isNotBlank(unknown)) {
+ handleNotYetImplementedAttribute(attributes, UNKNOWN, parentEvent);
+ }
+ if (isNotBlank(notFound)) {
+ handleNotYetImplementedAttribute(attributes, NOT_FOUND, parentEvent);
+ }
+ if (isNotBlank(destroyed)) {
+ handleNotYetImplementedAttribute(attributes, DESTROYED, parentEvent);
+ }
+ if (isNotBlank(lost)) {
+ handleNotYetImplementedAttribute(attributes, LOST, parentEvent);
}
INonViralName firstName = null;
- Set<TaxonNameBase> names = homotypicalGroup.getTypifiedNames();
+ Set<TaxonName> names = homotypicalGroup.getTypifiedNames();
if (names.isEmpty()) {
String message = "There is no name in a homotypical group. Can't create the specimen type";
fireWarningEvent(message, parentEvent, 8);
} else {
- firstName = CdmBase.deproxy(names.iterator().next(),NonViralName.class);
+ firstName = CdmBase.deproxy(names.iterator().next());
}
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
+ state.setFirstSpecimenInFacade(true);
String text = "";
state.resetCollectionAndType();
state.setSpecimenType(true);
}
state.setSpecimenType(false);
state.resetCollectionAndType();
+ state.setFirstSpecimenInFacade(false);
return;
} else if (isStartingElement(next, FULL_TYPE)) {
handleAmbigousManually(state, reader, next.asStartElement());
private void makeSpecimenType(MarkupImportState state, DerivedUnitFacade facade, String text, String collectionAndType,
INonViralName name, XMLEvent parentEvent) {
text = text.trim();
- if (isPunctuation(text)){
+ if (isBlank(text) || isPunctuation(text)){
//do nothing
}else{
String message = "Text '%s' not handled for <SpecimenType>";
collectionAndType = collectionAndType.substring(1, collectionAndType.length() - 1);
}
- String[] split = collectionAndType.split("[;,]");
- for (String str : split) {
- str = str.trim();
- boolean addToAllNamesInGroup = true;
- TypeInfo typeInfo = makeSpecimenTypeTypeInfo(str, parentEvent);
- SpecimenTypeDesignationStatus typeStatus = typeInfo.status;
- Collection collection = this.getCollection(state, typeInfo.collectionString);
-
- // TODO improve cache strategy handling
- DerivedUnit typeSpecimen = facade.addDuplicate(collection, null, null, null, null);
- typeSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());
- name.addSpecimenTypeDesignation(typeSpecimen, typeStatus, null, null, null, false, addToAllNamesInGroup);
+ String[] splitsSemi = collectionAndType.split("[;]");
+ for (String splitSemi : splitsSemi) {
+ String[] splitKomma = splitSemi.split("[,]");
+ TypeInfo lastTypeInfo = null;
+ for (String str : splitKomma) {
+ str = str.trim();
+ boolean addToAllNamesInGroup = true;
+ TypeInfo typeInfo = makeSpecimenTypeTypeInfo(state, str, lastTypeInfo, parentEvent);
+ SpecimenTypeDesignationStatus typeStatus = typeInfo.status;
+ Collection collection = this.getCollection(state, typeInfo.collectionString);
+
+ // TODO improve cache strategy handling
+ DerivedUnit typeSpecimen;
+ if (state.isFirstSpecimenInFacade()){
+ state.setFirstSpecimenInFacade(false);
+ typeSpecimen = facade.innerDerivedUnit();
+ typeSpecimen.setCollection(collection);
+ }else{
+ typeSpecimen = facade.addDuplicate(collection, null, null, null, null);
+ }
+ typeSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());
+ name.addSpecimenTypeDesignation(typeSpecimen, typeStatus,
+ null, null, null, typeInfo.notDesignated, addToAllNamesInGroup);
+ handleNotSeen(state, typeSpecimen, typeInfo);
+ lastTypeInfo = typeInfo;
+ }
}
}
-
}
- private Pattern fotgTypePattern = null;
+ /**
+ * @param state
+ * @param typeSpecimen
+ * @param typeInfo
+ */
+ private void handleNotSeen(MarkupImportState state, DerivedUnit typeSpecimen, TypeInfo typeInfo) {
+ if (typeInfo.notSeen){
+ String text = "n.v. for " + state.getConfig().getSourceReference().getAbbrevTitleCache();
+ typeSpecimen.addAnnotation(Annotation.NewInstance(text, AnnotationType.EDITORIAL(), getDefaultLanguage(state)));
+ if(state.getConfig().getSpecimenNotSeenMarkerTypeUuid() != null){
+ UUID uuidNotSeenMarker = state.getConfig().getSpecimenNotSeenMarkerTypeUuid();
+ String markerTypeNotSeenLabel = state.getConfig().getSpecimenNotSeenMarkerTypeLabel();
+ markerTypeNotSeenLabel = markerTypeNotSeenLabel == null ? "Not seen" : markerTypeNotSeenLabel;
+ MarkerType notSeenMarkerType = getMarkerType(state, uuidNotSeenMarker, markerTypeNotSeenLabel, markerTypeNotSeenLabel, null, null);
+ Marker marker = Marker.NewInstance(notSeenMarkerType, true);
+ typeSpecimen.addMarker(marker);
+ }
+ }
+ }
+
+
+ private Pattern fotgTypePattern = null;
/**
* Implemented for Flora of the Guyanas this may include duplicated code from similar places
* @param state
Matcher matcher = fotgTypePattern.matcher(collectionAndType);
if (matcher.matches()){
+ fireWarningEvent("Try to synchronize type handling (at least creation) with standard type handling. E.g. use TypeInfo and according algorithms", parentEvent, 2);
if (collectionAndType.matches(notDesignatedRE)){
SpecimenTypeDesignation desig = SpecimenTypeDesignation.NewInstance();
desig.setNotDesignated(true);
*/
private void handleSpecimenTypeAddInfo(MarkupImportState state, boolean notSeen, boolean destroyed,
boolean presumedDestroyed, SpecimenTypeDesignation desig) {
- if (notSeen){
- UUID uuidNotSeenMarker = MarkupTransformer.uuidNotSeen;
+ DerivedUnit specimen = desig.getTypeSpecimen();
+ AnnotatableEntity annotEntity = specimen != null ? specimen : desig;
+
+ if (notSeen){
+ UUID uuidNotSeenMarker = MarkupTransformer.uuidMarkerNotSeen;
MarkerType notSeenMarkerType = getMarkerType(state, uuidNotSeenMarker, "Not seen", "Not seen", null, null);
Marker marker = Marker.NewInstance(notSeenMarkerType, true);
- desig.addMarker(marker);
+ annotEntity.addMarker(marker);
fireWarningEvent("not seen not yet implemented", "handleSpecimenTypeAddInfo", 4);
}
if (destroyed){
- UUID uuidDestroyedMarker = MarkupTransformer.uuidDestroyed;
+ UUID uuidDestroyedMarker = MarkupTransformer.uuidMarkerDestroyed;
MarkerType destroyedMarkerType = getMarkerType(state, uuidDestroyedMarker, "Destroyed", "Destroyed", null, null);
Marker marker = Marker.NewInstance(destroyedMarkerType, true);
- desig.addMarker(marker);
+ annotEntity.addMarker(marker);
fireWarningEvent("'destroyed' not yet fully implemented", "handleSpecimenTypeAddInfo", 4);
}
if (presumedDestroyed){
Annotation annotation = Annotation.NewInstance("presumably destroyed", Language.ENGLISH());
annotation.setAnnotationType(AnnotationType.EDITORIAL());
- desig.addAnnotation(annotation);
+ annotEntity.addAnnotation(annotation);
}
}
- private TypeInfo makeSpecimenTypeTypeInfo(String originalString, XMLEvent event) {
+ private TypeInfo makeSpecimenTypeTypeInfo(MarkupImportState state, String originalString, TypeInfo lastTypeInfo, XMLEvent event) {
TypeInfo result = new TypeInfo();
- String[] split = originalString.split("\\s+");
if ("not designated".equals(originalString)){
result.notDesignated = true;
return result;
}
+ List<String> knownCollections = state.getConfig().getKnownCollections();
+ for (String knownCollection:knownCollections){
+ if (originalString.contains(knownCollection)){
+ result.collectionString = knownCollection;
+ originalString = originalString.replace(knownCollection, "").trim();
+ break;
+ }
+ }
+ String[] split = originalString.split("(?<!not)\\s+");
+
+ String unrecognizedTypeParts = null;
for (String str : split) {
+ //holo/lecto/iso ...
if (str.matches(SpecimenTypeParser.typeTypePattern)) {
SpecimenTypeDesignationStatus status;
try {
fireWarningEvent(String.format(message, str), event, 4);
status = null;
}
+ if (result.status != null){
+ String message = "More than 1 status string found: " + originalString;
+ fireWarningEvent(message, event, 4);
+ }
result.status = status;
} else if (str.matches(SpecimenTypeParser.collectionPattern)) {
- result.collectionString = str;
- } else {
- String message = "Type part '%s' could not be recognized";
- fireWarningEvent(String.format(message, str), event, 2);
+ if (result.collectionString != null){
+ String message = "More than 1 collection string found: " + originalString;
+ fireWarningEvent(message, event, 4);
+ }
+ result.collectionString = str;
+ } else if (str.matches(SpecimenTypeParser.notSeen)) {
+ if (result.notSeen){
+ String message = "More than 1 'not seen' string found: " + originalString;
+ fireWarningEvent(message, event, 4);
+ }
+ result.notSeen = true;
+ } else {
+ unrecognizedTypeParts = CdmUtils.concat(" ", unrecognizedTypeParts, str);
+ }
+ if (result.status == null && lastTypeInfo != null && lastTypeInfo.status != null){
+ result.status = lastTypeInfo.status;
}
}
-
+ if(isNotBlank(unrecognizedTypeParts)){
+ String message = "Type parts '%s' could not be recognized";
+ fireWarningEvent(String.format(message, unrecognizedTypeParts), event, 2);
+ }
return result;
}
}else if (isStartingElement(next, COLLECTOR)) {
hasCollector = true;
String collectorStr = getCData(state, reader, next);
- TeamOrPersonBase<?> collector = createCollector(collectorStr);
+ TeamOrPersonBase<?> collector = createCollector(state, collectorStr);
facade.setCollector(collector);
state.setCurrentCollector(collector);
} else if (isStartingElement(next, ALTERNATIVE_COLLECTOR)) {
Rank defaultRank = Rank.SPECIES(); // can be any
INonViralName nvn = createNameByCode(state, defaultRank);
handleFullName(state, reader, nvn, next);
- TaxonNameBase<?,?> name = TaxonNameBase.castAndDeproxy(nvn);
+ TaxonName name = TaxonName.castAndDeproxy(nvn);
DeterminationEvent.NewInstance(name, facade.innerDerivedUnit() != null ? facade.innerDerivedUnit() : facade.innerFieldUnit());
} else if (isStartingElement(next, DATES)) {
TimePeriod timePeriod = handleDates(state, reader, next);
return result;
} else if (isStartingElement(next, FULL_DATE)) {
String fullDate = getCData(state, reader, next, true);
+ if (fullDate.endsWith(".")){
+ fullDate = fullDate.substring(0, fullDate.length()-1);
+ }
result = TimePeriodParser.parseString(fullDate);
if (result.getFreeText() != null){
fireWarningEvent(String.format(parseMessage, FULL_DATE, fullDate), parent, 1);
String classValue = getClassOnlyAttribute(parentEvent);
boolean isLocality = false;
NamedAreaLevel areaLevel = null;
- if ("locality".equalsIgnoreCase(classValue)) {
+ if ("locality".equalsIgnoreCase(classValue)||state.getConfig().isIgnoreLocalityClass()) {
isLocality = true;
} else {
areaLevel = makeNamedAreaLevel(state, classValue, parentEvent);
XMLEvent next = readNoWhitespace(reader);
if (isMyEndingElement(next, parentEvent)) {
if (StringUtils.isNotBlank(text)) {
- text = normalize(text);
+ text = normalize(text);text = removeTrailingPunctuation(text);
if (isLocality) {
facade.setLocality(text, getDefaultLanguage(state));
} else {
- private TeamOrPersonBase<?> createCollector(String collectorStr) {
- return createAuthor(collectorStr);
+ /**
+ * @param text
+ * @return
+ */
+ private String removeTrailingPunctuation(String text) {
+ while (isPunctuation(text.substring(text.length()-1))){
+ text = text.substring(0, text.length()-1).trim();
+ }
+ return text;
+ }
+
+
+ private TeamOrPersonBase<?> createCollector(MarkupImportState state, String collectorStr) {
+ return createAuthor(state, collectorStr);
}
specimen = facade.innerFieldUnit();
}
IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance();
+ individualsAssociation.addPrimaryTaxonomicSource(state.getConfig().getSourceReference());
individualsAssociation.setAssociatedSpecimenOrObservation(specimen);
result.add(individualsAssociation);
} else if (isStartingElement(next, GATHERING_GROUP)) {
}
if (td == null){
TaxonDescription desc = TaxonDescription.NewInstance(state.getCurrentTaxon());
+ desc.addPrimaryTaxonomicSource(state.getConfig().getSourceReference(), null);
desc.addGeoScope(area);
if (doubtful != null){
desc.addMarker(Marker.NewInstance(MarkerType.IS_DOUBTFUL(), doubtful));
specimen = facade.innerFieldUnit();
}
IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance();
+ individualsAssociation.addPrimaryTaxonomicSource(state.getConfig().getSourceReference());
individualsAssociation.setAssociatedSpecimenOrObservation(specimen);
result.add(individualsAssociation);
BGBM BDI Projects / cdmlib.git / blobdiff