\r
import java.net.MalformedURLException;\r
import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.Arrays;\r
-import java.util.HashMap;\r
import java.util.HashSet;\r
-import java.util.List;\r
import java.util.Map;\r
import java.util.Set;\r
import java.util.UUID;\r
-import java.util.regex.Matcher;\r
-import java.util.regex.Pattern;\r
\r
import javax.xml.stream.Location;\r
import javax.xml.stream.XMLEventReader;\r
import org.apache.commons.lang.StringUtils;\r
import org.apache.log4j.Logger;\r
\r
-import eu.etaxonomy.cdm.common.CdmUtils;\r
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
-import eu.etaxonomy.cdm.model.common.AnnotatableEntity;\r
-import eu.etaxonomy.cdm.model.common.Annotation;\r
-import eu.etaxonomy.cdm.model.common.AnnotationType;\r
-import eu.etaxonomy.cdm.model.common.CdmBase;\r
-import eu.etaxonomy.cdm.model.common.Extension;\r
import eu.etaxonomy.cdm.model.common.ExtensionType;\r
import eu.etaxonomy.cdm.model.common.Language;\r
import eu.etaxonomy.cdm.model.common.OriginalSourceType;\r
import eu.etaxonomy.cdm.model.description.Feature;\r
import eu.etaxonomy.cdm.model.description.PolytomousKey;\r
import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;\r
-import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;\r
-import eu.etaxonomy.cdm.model.description.PresenceTerm;\r
import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
import eu.etaxonomy.cdm.model.description.TextData;\r
-import eu.etaxonomy.cdm.model.location.NamedArea;\r
-import eu.etaxonomy.cdm.model.location.NamedAreaLevel;\r
-import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;\r
-import eu.etaxonomy.cdm.model.media.Media;\r
import eu.etaxonomy.cdm.model.name.CultivarPlantName;\r
import eu.etaxonomy.cdm.model.name.NonViralName;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
import eu.etaxonomy.cdm.model.taxon.Classification;\r
* \r
*/\r
public class MarkupDocumentImportNoComponent extends MarkupImportBase {\r
+ @SuppressWarnings("unused")\r
private static final Logger logger = Logger.getLogger(MarkupDocumentImportNoComponent.class);\r
-\r
-\r
+ \r
private MarkupKeyImport keyImport;\r
+\r
+ private MarkupModsImport modsImport;\r
+ private MarkupFeatureImport featureImport;\r
private MarkupSpecimenImport specimenImport;\r
- \r
private MarkupNomenclatureImport nomenclatureImport;\r
- \r
+\r
public MarkupDocumentImportNoComponent(MarkupDocumentImport docImport) {\r
super(docImport);\r
- keyImport = new MarkupKeyImport(docImport);\r
- specimenImport = new MarkupSpecimenImport(docImport);\r
- nomenclatureImport = new MarkupNomenclatureImport(docImport, keyImport, specimenImport);\r
+ this.keyImport = new MarkupKeyImport(docImport);\r
+ this.specimenImport = new MarkupSpecimenImport(docImport);\r
+ this.nomenclatureImport = new MarkupNomenclatureImport(docImport, specimenImport);\r
+ this.modsImport = new MarkupModsImport(docImport);\r
+ this.featureImport = new MarkupFeatureImport(docImport, specimenImport, nomenclatureImport);\r
}\r
\r
public void doInvoke(MarkupImportState state) throws XMLStreamException { \r
message = String.format(message, baseUrl);\r
fireWarningEvent(message, next, 8);\r
}\r
- } else if (isStartingElement(next, MODS)){\r
- handleNotYetImplementedElement(next);\r
+ } else if (isStartingElement(next, MODS)){ \r
+ modsImport.handleMods(state, reader, next);\r
} else {\r
handleUnexpectedElement(next);\r
}\r
}\r
Rank thisRank = taxon.getName().getRank();\r
Rank lastRank = lastTaxon.getName().getRank();\r
+ if (lastRank == null){\r
+ String message = "Last rank was null. Can't create tree correctly";\r
+ fireWarningEvent(message, makeLocationStr(dataLocation), 12);\r
+ }\r
if (lastTaxon.getTaxonNodes().size() > 0) {\r
TaxonNode lastNode = lastTaxon.getTaxonNodes().iterator().next();\r
if (thisRank == null){\r
tree.addChildTaxon(taxon, null, null);\r
}\r
} else if (thisRank.isHigher(lastRank)) {\r
- doTaxonRelation(state, taxon, lastNode.getParent().getTaxon(), dataLocation);\r
+ TaxonNode parent = lastNode.getParent();\r
+ if (parent != null){\r
+ doTaxonRelation(state, taxon, parent.getTaxon(), dataLocation);\r
+ }else{\r
+ String warning = "No parent available for lastNode. Classification can not be build correctly. Maybe the rank was missing for the lastNode";\r
+ fireWarningEvent(warning, makeLocationStr(dataLocation), 16);\r
+ //TODO what to do in this case (haven't spend time to think about yet\r
+ }\r
// TaxonNode parentNode = handleTaxonRelation(state, taxon,\r
// lastNode.getParent().getTaxon());\r
// parentNode.addChildTaxon(taxon, null, null, null);\r
nomenclatureImport.handleNomenclature(state, reader, next);\r
hasNomenclature = true;\r
} else if (isStartingElement(next, FEATURE)) {\r
- handleFeature(state, reader, next);\r
+ featureImport.handleFeature(state, reader, next);\r
} else if (isStartingElement(next, NOTES)) {\r
// TODO is this the correct way to handle notes?\r
String note = handleNotes(state, reader, next);\r
desc.addElement(textData);\r
}\r
textData = (TextData)desc.getElements().iterator().next();\r
- makeFeatureFigureRef(state, reader, desc, false, textData, next);\r
+ featureImport.makeFeatureFigureRef(state, reader, desc, false, textData, next);\r
} else if (isStartingElement(next, FIGURE)) {\r
- handleFigure(state, reader, next);\r
+ handleFigure(state, reader, next, specimenImport, nomenclatureImport);\r
} else if (isStartingElement(next, FOOTNOTE)) {\r
- FootnoteDataHolder footnote = handleFootnote(state, reader, next);\r
+ FootnoteDataHolder footnote = handleFootnote(state, reader, next, specimenImport, nomenclatureImport);\r
if (footnote.isRef()) {\r
String message = "Ref footnote not implemented here";\r
fireWarningEvent(message, next, 4);\r
WriterDataHolder writer = handleWriter(state, reader, next);\r
taxon.addExtension(writer.extension);\r
// TODO what if taxonTitle comes later\r
- if (StringUtils.isNotBlank(taxonTitle)\r
- && writer.extension != null) {\r
+ if (StringUtils.isNotBlank(taxonTitle) && writer.extension != null) {\r
Reference<?> sec = ReferenceFactory.newBookSection();\r
sec.setTitle(taxonTitle);\r
TeamOrPersonBase<?> author = createAuthor(writer.writer);\r
- sec.setAuthorTeam(author);\r
- sec.setInReference(state.getConfig()\r
- .getSourceReference());\r
+ sec.setAuthorship(author);\r
+ sec.setInReference(state.getConfig().getSourceReference());\r
taxon.setSec(sec);\r
registerFootnotes(state, sec, writer.footnotes);\r
} else {\r
\r
}\r
\r
- private WriterDataHolder handleWriter(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- String text = "";\r
- checkNoAttributes(parentEvent);\r
- WriterDataHolder dataHolder = new WriterDataHolder();\r
- List<FootnoteDataHolder> footnotes = new ArrayList<FootnoteDataHolder>();\r
-\r
- // TODO handle attributes\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- text = CdmUtils.removeBrackets(text);\r
- if (checkMandatoryText(text, parentEvent)) {\r
- text = normalize(text);\r
- dataHolder.writer = text;\r
- dataHolder.footnotes = footnotes;\r
-\r
- // Extension\r
- UUID uuidWriterExtension = MarkupTransformer.uuidWriterExtension;\r
- ExtensionType writerExtensionType = this\r
- .getExtensionType(state, uuidWriterExtension,\r
- "Writer", "writer", "writer");\r
- Extension extension = Extension.NewInstance();\r
- extension.setType(writerExtensionType);\r
- extension.setValue(text);\r
- dataHolder.extension = extension;\r
-\r
- // Annotation\r
- UUID uuidWriterAnnotation = MarkupTransformer.uuidWriterAnnotation;\r
- AnnotationType writerAnnotationType = this.getAnnotationType(state, uuidWriterAnnotation, "Writer", "writer", "writer", null);\r
- Annotation annotation = Annotation.NewInstance(text, writerAnnotationType, getDefaultLanguage(state));\r
- dataHolder.annotation = annotation;\r
-\r
- return dataHolder;\r
- } else {\r
- return null;\r
- }\r
- } else if (isStartingElement(next, FOOTNOTE_REF)) {\r
- FootnoteDataHolder footNote = handleFootnoteRef(state, reader, next);\r
- if (footNote.isRef()) {\r
- footnotes.add(footNote);\r
- } else {\r
- logger.warn("Non ref footnotes not yet impelemnted");\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
-\r
- } else {\r
- handleUnexpectedElement(next);\r
- state.setUnsuccessfull();\r
- }\r
- }\r
- throw new IllegalStateException("<writer> has no end tag");\r
- }\r
-\r
- private void registerFootnotes(MarkupImportState state, AnnotatableEntity entity, List<FootnoteDataHolder> footnotes) {\r
- for (FootnoteDataHolder footNote : footnotes) {\r
- registerFootnoteDemand(state, entity, footNote);\r
- }\r
- }\r
-\r
- private void registerGivenFootnote(MarkupImportState state, FootnoteDataHolder footnote) {\r
- state.registerFootnote(footnote);\r
- Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.id);\r
- if (demands != null) {\r
- for (AnnotatableEntity entity : demands) {\r
- attachFootnote(state, entity, footnote);\r
- }\r
- }\r
- }\r
-\r
- private void registerGivenFigure(MarkupImportState state, XMLEvent next, String id, Media figure) {\r
- state.registerFigure(id, figure);\r
- Set<AnnotatableEntity> demands = state.getFigureDemands(id);\r
- if (demands != null) {\r
- for (AnnotatableEntity entity : demands) {\r
- attachFigure(state, next, entity, figure);\r
- }\r
- }\r
- save(figure, state);\r
- }\r
-\r
- private void registerFootnoteDemand(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {\r
- FootnoteDataHolder existingFootnote = state.getFootnote(footnote.ref);\r
- if (existingFootnote != null) {\r
- attachFootnote(state, entity, existingFootnote);\r
- } else {\r
- Set<AnnotatableEntity> demands = state.getFootnoteDemands(footnote.ref);\r
- if (demands == null) {\r
- demands = new HashSet<AnnotatableEntity>();\r
- state.putFootnoteDemands(footnote.ref, demands);\r
- }\r
- demands.add(entity);\r
- }\r
- }\r
-\r
- private void registerFigureDemand(MarkupImportState state, XMLEvent next, AnnotatableEntity entity, String figureRef) {\r
- Media existingFigure = state.getFigure(figureRef);\r
- if (existingFigure != null) {\r
- attachFigure(state, next, entity, existingFigure);\r
- } else {\r
- Set<AnnotatableEntity> demands = state.getFigureDemands(figureRef);\r
- if (demands == null) {\r
- demands = new HashSet<AnnotatableEntity>();\r
- state.putFigureDemands(figureRef, demands);\r
- }\r
- demands.add(entity);\r
- }\r
- }\r
-\r
- private void attachFootnote(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote) {\r
- AnnotationType annotationType = this.getAnnotationType(state, MarkupTransformer.uuidFootnote, "Footnote", "An e-flora footnote", "fn", null);\r
- Annotation annotation = Annotation.NewInstance(footnote.string, annotationType, getDefaultLanguage(state));\r
- // TODO transient objects\r
- entity.addAnnotation(annotation);\r
- save(entity, state);\r
- }\r
-\r
- private void attachFigure(MarkupImportState state, XMLEvent next, AnnotatableEntity entity, Media figure) {\r
- // IdentifiableEntity<?> toSave;\r
- if (entity.isInstanceOf(TextData.class)) {\r
- TextData deb = CdmBase.deproxy(entity, TextData.class);\r
- deb.addMedia(figure);\r
- // toSave = ((TaxonDescription)deb.getInDescription()).getTaxon();\r
- } else if (entity.isInstanceOf(SpecimenOrObservationBase.class)) {\r
- String message = "figures for specimen should be handled as Textdata";\r
- fireWarningEvent(message, next, 4);\r
- // toSave = ime;\r
- } else if (entity.isInstanceOf(IdentifiableMediaEntity.class)) {\r
- IdentifiableMediaEntity<?> ime = CdmBase.deproxy(entity, IdentifiableMediaEntity.class);\r
- ime.addMedia(figure);\r
- // toSave = ime;\r
- } else {\r
- String message = "Unsupported entity to attach media: %s";\r
- message = String.format(message, entity.getClass().getName());\r
- // toSave = null;\r
- }\r
- save(entity, state);\r
- }\r
-\r
- private Media handleFigure(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- // FigureDataHolder result = new FigureDataHolder();\r
-\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String id = getAndRemoveAttributeValue(attributes, ID);\r
- String type = getAndRemoveAttributeValue(attributes, TYPE);\r
- String urlAttr = getAndRemoveAttributeValue(attributes, URL);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- String urlString = null;\r
- String legendString = null;\r
- String titleString = null;\r
- String numString = null;\r
- String text = null;\r
- if (isNotBlank(urlAttr)){\r
- urlString = CdmUtils.Nz(state.getBaseMediaUrl()) + urlAttr;\r
- }\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- if (isNotBlank(text)){\r
- fireWarningEvent("Text not yet handled for figures: " + text, next, 4);\r
- }\r
- Media media = makeFigure(state, id, type, urlString, legendString, titleString, numString, next);\r
- return media;\r
- } else if (isStartingElement(next, FIGURE_LEGEND)) {\r
- // TODO same as figure string ?\r
- legendString = handleFootnoteString(state, reader, next);\r
- } else if (isStartingElement(next, FIGURE_TITLE)) {\r
- titleString = getCData(state, reader, next);\r
- } else if (isStartingElement(next, URL)) {\r
- String localUrl = getCData(state, reader, next);\r
- String url = CdmUtils.Nz(state.getBaseMediaUrl()) + localUrl;\r
- if (isBlank(urlString)){\r
- urlString = url;\r
- }\r
- if (! url.equals(urlString)){\r
- String message = "URL attribute and URL element differ. Attribute: %s, Element: %s";\r
- fireWarningEvent(String.format(message, urlString, url), next, 2);\r
- }\r
- } else if (isStartingElement(next, NUM)) {\r
- numString = getCData(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- text += CdmUtils.concat("", text, next.asCharacters().getData());\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- throw new IllegalStateException("<figure> has no end tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param id\r
- * @param type\r
- * @param urlString\r
- * @param legendString\r
- * @param titleString\r
- * @param numString\r
- * @param next\r
- */\r
- private Media makeFigure(MarkupImportState state, String id, String type, String urlString, \r
- String legendString, String titleString, String numString, XMLEvent next) {\r
- Media media = null;\r
- boolean isFigure = false;\r
- try {\r
- //TODO maybe everything is a figure as it is all taken from a book\r
- if ("lineart".equals(type)) {\r
- isFigure = true;\r
-// media = Figure.NewInstance(url.toURI(), null, null, null);\r
- } else if (type == null || "photo".equals(type)\r
- || "signature".equals(type)\r
- || "others".equals(type)) {\r
- //TODO\r
- } else {\r
- String message = "Unknown figure type '%s'";\r
- message = String.format(message, type);\r
- fireWarningEvent(message, next, 2);\r
- }\r
- media = docImport.getImageMedia(urlString, docImport.getReadMediaData(), isFigure);\r
- \r
- if (media != null){\r
- // title\r
- if (StringUtils.isNotBlank(titleString)) {\r
- media.putTitle(getDefaultLanguage(state), titleString);\r
- }\r
- // legend\r
- if (StringUtils.isNotBlank(legendString)) {\r
- media.putDescription(getDefaultLanguage(state), legendString);\r
- }\r
- if (StringUtils.isNotBlank(numString)) {\r
- // TODO use concrete source (e.g. DAPHNIPHYLLACEAE in FM\r
- // vol.13)\r
- Reference<?> citation = state.getConfig().getSourceReference();\r
- media.addImportSource( numString, "num", citation, null);\r
- // TODO name used in source if available\r
- }\r
- // TODO which citation\r
- if (StringUtils.isNotBlank(id)) {\r
- media.addImportSource(id, null, state.getConfig().getSourceReference(), null);\r
- } else {\r
- String message = "Figure id should never be empty or null";\r
- fireWarningEvent(message, next, 6);\r
- }\r
-\r
- // text\r
- // do nothing\r
- registerGivenFigure(state, next, id, media);\r
- \r
- }else{\r
- String message = "No media found: ";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- } catch (MalformedURLException e) {\r
- String message = "Media uri has incorrect syntax: %s";\r
- message = String.format(message, urlString);\r
- fireWarningEvent(message, next, 4);\r
-// } catch (URISyntaxException e) {\r
-// String message = "Media uri has incorrect syntax: %s";\r
-// message = String.format(message, urlString);\r
-// fireWarningEvent(message, next, 4);\r
- }\r
-\r
- return media;\r
- }\r
-\r
- private FigureDataHolder handleFigureRef(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent)\r
- throws XMLStreamException {\r
- FigureDataHolder result = new FigureDataHolder();\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- result.ref = getAndRemoveAttributeValue(attributes, REF);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- // text is not handled, needed only for debugging purposes\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else if (isStartingElement(next, NUM)) {\r
- String num = getCData(state, reader, next);\r
- result.num = num; // num is not handled during import\r
- } else if (isStartingElement(next, FIGURE_PART)) {\r
- result.figurePart = getCData(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- throw new IllegalStateException("<figureRef> has no end tag");\r
- }\r
-\r
- private FootnoteDataHolder handleFootnote(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- FootnoteDataHolder result = new FootnoteDataHolder();\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- result.id = getAndRemoveAttributeValue(attributes, ID);\r
- // result.ref = getAndRemoveAttributeValue(attributes, REF);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isStartingElement(next, FOOTNOTE_STRING)) {\r
- String string = handleFootnoteString(state, reader, next);\r
- result.string = string;\r
- } else if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- private FootnoteDataHolder handleFootnoteRef(MarkupImportState state,\r
- XMLEventReader reader, XMLEvent parentEvent)\r
- throws XMLStreamException {\r
- FootnoteDataHolder result = new FootnoteDataHolder();\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- result.ref = getAndRemoveAttributeValue(attributes, REF);\r
- checkNoAttributes(attributes, parentEvent);\r
-\r
- // text is not handled, needed only for debugging purposes\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- // if (isStartingElement(next, FOOTNOTE_STRING)){\r
- // String string = handleFootnoteString(state, reader, next);\r
- // result.string = string;\r
- // }else\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
-\r
- } else {\r
- fireUnexpectedEvent(next, 0);\r
- }\r
- }\r
- return result;\r
- }\r
-\r
-\r
-\r
- private String handleFootnoteString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- boolean isTextMode = true;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return text;\r
- } else if (next.isEndElement()) {\r
- if (isEndingElement(next, FULL_NAME)) {\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, BR)) {\r
- isTextMode = true;\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, FULL_NAME)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, GATHERING)) {\r
- text += specimenImport.handleInLineGathering(state, reader, next);\r
- } else if (isStartingElement(next, REFERENCES)) {\r
- text += " " + handleInLineReferences(state, reader, next)+ " ";\r
- } else if (isStartingElement(next, BR)) {\r
- text += "<br/>";\r
- isTextMode = false;\r
- } else if (isStartingElement(next, NOMENCLATURE)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- if (!isTextMode) {\r
- String message = "footnoteString is not in text mode";\r
- fireWarningEvent(message, next, 6);\r
- } else {\r
- text += next.asCharacters().getData().trim(); \r
- // getCData(state, reader, next); does not work as we have inner tags like <references>\r
- }\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("<footnoteString> has no closing tag");\r
-\r
- }\r
-\r
- private String handleInLineReferences(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- boolean hasReference = false;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- checkMandatoryElement(hasReference, parentEvent.asStartElement(), REFERENCE);\r
- return text;\r
- } else if (isStartingElement(next, REFERENCE)) {\r
- text += handleInLineReference(state, reader, next);\r
- hasReference = true;\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<References> has no closing tag");\r
- }\r
-\r
- private String handleInLineReference(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {\r
- Reference<?> reference = nomenclatureImport.handleReference(state, reader, parentEvent);\r
- String result = "<cdm:ref uuid='%s'>%s</ref>";\r
- result = String.format(result, reference.getUuid(), reference.getTitleCache());\r
- save(reference, state);\r
- return result;\r
- }\r
-\r
-\r
- private void handleFeature(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- Map<String, Attribute> attrs = getAttributes(parentEvent);\r
- Boolean isFreetext = getAndRemoveBooleanAttributeValue(parentEvent, attrs, IS_FREETEXT, false);\r
- String classValue =getAndRemoveRequiredAttributeValue(parentEvent, attrs, CLASS);\r
- checkNoAttributes(attrs, parentEvent);\r
- \r
- \r
- Feature feature = makeFeature(classValue, state, parentEvent, null);\r
- Taxon taxon = state.getCurrentTaxon();\r
- TaxonDescription taxonDescription = getTaxonDescription(taxon, state.getConfig().getSourceReference(), NO_IMAGE_GALLERY, CREATE_NEW);\r
- // TextData figureHolderTextData = null; //for use with one TextData for\r
- // all figure only\r
-\r
- boolean isDescription = feature.equals(Feature.DESCRIPTION());\r
- DescriptionElementBase lastDescriptionElement = null;\r
- \r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- state.putFeatureToGeneralSorterList(feature);\r
- return;\r
- } else if (isEndingElement(next, DISTRIBUTION_LIST) || isEndingElement(next, HABITAT_LIST)) { \r
- // only handle list elements\r
- } else if (isStartingElement(next, HEADING)) {\r
- makeFeatureHeading(state, reader, classValue, feature, next);\r
- } else if (isStartingElement(next, WRITER)) {\r
- makeFeatureWriter(state, reader, feature, taxon, next);\r
-// } else if (isStartingElement(next, DISTRIBUTION_LOCALITY)) {\r
-// if (!feature.equals(Feature.DISTRIBUTION())) {\r
-// String message = "Distribution locality only allowed for feature of type 'distribution'";\r
-// fireWarningEvent(message, next, 4);\r
-// }\r
-// handleDistributionLocality(state, reader, next);\r
- } else if (isStartingElement(next, DISTRIBUTION_LIST) || isStartingElement(next, HABITAT_LIST)) {\r
- // only handle single list elements\r
- } else if (isStartingElement(next, HABITAT)) {\r
- if (!(feature.equals(Feature.HABITAT())\r
- || feature.equals(Feature.HABITAT_ECOLOGY()) \r
- || feature.equals(Feature.ECOLOGY()))) {\r
- String message = "Habitat only allowed for feature of type 'habitat','habitat ecology' or 'ecology'";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- handleHabitat(state, reader, next);\r
- } else if (isStartingElement(next, CHAR)) {\r
- List<TextData> textDataList = handleChar(state, reader, next, null);\r
- for (TextData textData : textDataList){\r
- taxonDescription.addElement(textData);\r
- }\r
- } else if (isStartingElement(next, STRING)) {\r
- lastDescriptionElement = makeFeatureString(state, reader,feature, taxonDescription, lastDescriptionElement,next, isFreetext);\r
- } else if (isStartingElement(next, FIGURE_REF)) {\r
- lastDescriptionElement = makeFeatureFigureRef(state, reader, taxonDescription, isDescription, lastDescriptionElement, next);\r
- } else if (isStartingElement(next, REFERENCES)) {\r
- // TODO details/microcitation ??\r
-\r
- List<Reference<?>> refs = handleReferences(state, reader, next);\r
- if (!refs.isEmpty()) {\r
- // TODO\r
- Reference<?> descriptionRef = state.getConfig().getSourceReference();\r
- TaxonDescription description = getTaxonDescription(taxon, descriptionRef, false, true);\r
- TextData featurePlaceholder = docImport.getFeaturePlaceholder(state, description, feature, true);\r
- for (Reference<?> citation : refs) {\r
- featurePlaceholder.addSource(OriginalSourceType.PrimaryTaxonomicSource,\r
- null, null, citation, null);\r
- }\r
- } else {\r
- String message = "No reference found in references";\r
- fireWarningEvent(message, next, 6);\r
- }\r
- } else if (isStartingElement(next, NUM)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, NUM)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<Feature> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param taxonDescription\r
- * @param isDescription\r
- * @param lastDescriptionElement\r
- * @param next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private DescriptionElementBase makeFeatureFigureRef(MarkupImportState state, XMLEventReader reader,TaxonDescription taxonDescription, \r
- boolean isDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next) throws XMLStreamException {\r
- FigureDataHolder figureHolder = handleFigureRef(state, reader, next);\r
- Feature figureFeature = getFeature(state, MarkupTransformer.uuidFigures, "Figures", "Figures", "Fig.",null);\r
- if (isDescription) {\r
- TextData figureHolderTextData = null;\r
- // if (figureHolderTextData == null){\r
- figureHolderTextData = TextData.NewInstance(figureFeature);\r
- if (StringUtils.isNotBlank(figureHolder.num)) {\r
- String annotationText = "<num>" + figureHolder.num.trim() + "</num>";\r
- Annotation annotation = Annotation.NewInstance(annotationText, AnnotationType.TECHNICAL(), getDefaultLanguage(state));\r
- figureHolderTextData.addAnnotation(annotation);\r
- }\r
- if (StringUtils.isNotBlank(figureHolder.figurePart)) {\r
- String annotationText = "<figurePart>"+ figureHolder.figurePart.trim() + "</figurePart>";\r
- Annotation annotation = Annotation.NewInstance(annotationText,AnnotationType.EDITORIAL(), getDefaultLanguage(state));\r
- figureHolderTextData.addAnnotation(annotation);\r
- }\r
- // if (StringUtils.isNotBlank(figureText)){\r
- // figureHolderTextData.putText(language, figureText);\r
- // }\r
- taxonDescription.addElement(figureHolderTextData);\r
- // }\r
- registerFigureDemand(state, next, figureHolderTextData, figureHolder.ref);\r
- } else {\r
- if (lastDescriptionElement == null) {\r
- String message = "No description element created yet that can be referred by figure. Create new TextData instead";\r
- fireWarningEvent(message, next, 4);\r
- lastDescriptionElement = TextData.NewInstance(figureFeature);\r
- taxonDescription.addElement(lastDescriptionElement);\r
- }\r
- registerFigureDemand(state, next, lastDescriptionElement, figureHolder.ref);\r
- }\r
- return lastDescriptionElement;\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param feature\r
- * @param taxonDescription\r
- * @param lastDescriptionElement\r
- * @param distributionList \r
- * @param next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private DescriptionElementBase makeFeatureString(MarkupImportState state,XMLEventReader reader, Feature feature, \r
- TaxonDescription taxonDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next, Boolean isFreetext) throws XMLStreamException {\r
- \r
- //for specimen only\r
- if (feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.MATERIALS_EXAMINED())){\r
- \r
- \r
- List<DescriptionElementBase> specimens = specimenImport.handleMaterialsExamined(state, reader, next, feature);\r
- for (DescriptionElementBase specimen : specimens){\r
- taxonDescription.addElement(specimen);\r
- lastDescriptionElement = specimen;\r
- }\r
- state.setCurrentCollector(null);\r
- \r
- return lastDescriptionElement;\r
- }else{\r
- \r
- //others\r
- Map<String, String> subheadingMap = handleString(state, reader, next, feature);\r
- for (String subheading : subheadingMap.keySet()) {\r
- Feature subheadingFeature = feature;\r
- if (StringUtils.isNotBlank(subheading) && subheadingMap.size() > 1) {\r
- subheadingFeature = makeFeature(subheading, state, next, null);\r
- }\r
- if (feature.equals(Feature.COMMON_NAME()) && (isFreetext == null || !isFreetext)){\r
- List<DescriptionElementBase> commonNames = makeVernacular(state, subheading, subheadingMap.get(subheading));\r
- for (DescriptionElementBase commonName : commonNames){\r
- taxonDescription.addElement(commonName);\r
- lastDescriptionElement = commonName;\r
- }\r
- }else {\r
- TextData textData = TextData.NewInstance(subheadingFeature);\r
- textData.putText(getDefaultLanguage(state), subheadingMap.get(subheading));\r
- taxonDescription.addElement(textData);\r
- lastDescriptionElement = textData;\r
- // TODO how to handle figures when these data are split in\r
- // subheadings\r
- }\r
- }\r
- return lastDescriptionElement;\r
- }\r
- }\r
-\r
- private List<DescriptionElementBase> makeVernacular(MarkupImportState state, String subheading, String commonNameString) throws XMLStreamException {\r
- List<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>();\r
- String[] splits = commonNameString.split(",");\r
- for (String split : splits){\r
- split = split.trim();\r
- if (! split.matches(".*\\(.*\\)\\.?")){\r
- fireWarningEvent("Common name string '"+split+"' does not match given pattern", state.getReader().peek(), 4);\r
- }\r
- \r
- String name = split.replaceAll("\\(.*\\)", "").replace(".", "").trim();\r
- String languageStr = split.replaceFirst(".*\\(", "").replaceAll("\\)\\.?", "").trim();\r
- \r
- Language language = null;\r
- if (StringUtils.isNotBlank(languageStr)){\r
- try {\r
- UUID langUuid = state.getTransformer().getLanguageUuid(languageStr);\r
- TermVocabulary<?> voc = null;\r
- language = getLanguage(state, langUuid, languageStr, languageStr, null, voc);\r
- if (language == null){\r
- logger.warn("Language " + languageStr + " not recognized by transformer");\r
- }\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- }\r
- NamedArea area = null;\r
- CommonTaxonName commonTaxonName = CommonTaxonName.NewInstance(name, language, area);\r
- result.add(commonTaxonName);\r
- }\r
- \r
- return result;\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param feature\r
- * @param taxon\r
- * @param next\r
- * @throws XMLStreamException\r
- */\r
- private void makeFeatureWriter(MarkupImportState state,XMLEventReader reader, Feature feature, Taxon taxon, XMLEvent next) throws XMLStreamException {\r
- WriterDataHolder writer = handleWriter(state, reader, next);\r
- if (isNotBlank(writer.writer)) {\r
- // TODO\r
- Reference<?> ref = state.getConfig().getSourceReference();\r
- TaxonDescription description = getTaxonDescription(taxon, ref,\r
- false, true);\r
- TextData featurePlaceholder = docImport.getFeaturePlaceholder(state,\r
- description, feature, true);\r
- featurePlaceholder.addAnnotation(writer.annotation);\r
- registerFootnotes(state, featurePlaceholder, writer.footnotes);\r
- } else {\r
- String message = "Writer element is empty";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param classValue\r
- * @param feature\r
- * @param next\r
- * @throws XMLStreamException\r
- */\r
- private void makeFeatureHeading(MarkupImportState state, XMLEventReader reader, String classValue, Feature feature, XMLEvent next) throws XMLStreamException {\r
- String heading = handleHeading(state, reader, next);\r
- if (StringUtils.isNotBlank(heading)) {\r
- if (!heading.equalsIgnoreCase(classValue)) {\r
- try {\r
- if (!feature.equals(state.getTransformer().getFeatureByKey(\r
- heading))) {\r
- UUID headerFeatureUuid = state.getTransformer()\r
- .getFeatureUuid(heading);\r
- if (!feature.getUuid().equals(headerFeatureUuid)) {\r
- String message = "Feature heading '%s' differs from feature class '%s' and can not be transformed to feature";\r
- message = String.format(message, heading,\r
- classValue);\r
- fireWarningEvent(message, next, 1);\r
- }\r
- }\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- } else {\r
- // do nothing\r
- }\r
- }\r
- }\r
-\r
- private List<Reference<?>> handleReferences(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- // attributes\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String bibliography = getAndRemoveAttributeValue(attributes,\r
- BIBLIOGRAPHY);\r
- String serialsAbbreviations = getAndRemoveAttributeValue(attributes,\r
- SERIALS_ABBREVIATIONS);\r
- if (isNotBlank(bibliography) || isNotBlank(serialsAbbreviations)) {\r
- String message = "Attributes not yet implemented for <references>";\r
- fireWarningEvent(message, parentEvent, 4);\r
- }\r
-\r
- List<Reference<?>> result = new ArrayList<Reference<?>>();\r
-\r
- // elements\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (next.isEndElement()) {\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return result;\r
- } else {\r
- if (isEndingElement(next, HEADING)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, WRITER)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, FOOTNOTE)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, STRING)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else if (isEndingElement(next, REF_NUM)) {\r
- // NOT YET IMPLEMENTED\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, HEADING)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, SUB_HEADING)) {\r
- String subheading = getCData(state, reader, next).trim();\r
- String excludePattern = "(i?)(References?|Literature):?";\r
- if (!subheading.matches(excludePattern)) {\r
- fireNotYetImplementedElement(next.getLocation(), next.asStartElement().getName(), 0);\r
- }\r
- } else if (isStartingElement(next, WRITER)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, STRING)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, REF_NUM)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, REFERENCE)) {\r
- Reference<?> ref = nomenclatureImport.handleReference(state, reader, next);\r
- result.add(ref);\r
- } else {\r
- handleUnexpectedStartElement(next);\r
- }\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<References> has no closing tag");\r
- }\r
-\r
- private void handleHabitat(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
- Taxon taxon = state.getCurrentTaxon();\r
- // TODO which ref to take?\r
- Reference<?> ref = state.getConfig().getSourceReference();\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- TaxonDescription description = getTaxonDescription(taxon, ref,\r
- false, true);\r
- UUID uuidExtractedHabitat = MarkupTransformer.uuidExtractedHabitat;\r
- Feature feature = getFeature(\r
- state,\r
- uuidExtractedHabitat,\r
- "Extracted Habitat",\r
- "An structured habitat that was extracted from a habitat text",\r
- "extr. habit.", null);\r
- TextData habitat = TextData.NewInstance(feature);\r
- habitat.putText(getDefaultLanguage(state), text);\r
- description.addElement(habitat);\r
-\r
- return;\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, ALTITUDE)) {\r
- text = text.trim() + getTaggedCData(state, reader, next);\r
- } else if (isStartingElement(next, LIFE_CYCLE_PERIODS)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<Habitat> has no closing tag");\r
- }\r
-\r
- private String getTaggedCData(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- String text = getXmlTag(parentEvent);\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- text += getXmlTag(next);\r
- return text;\r
- } else if (next.isStartElement()) {\r
- text += getTaggedCData(state, reader, next);\r
- } else if (next.isEndElement()) {\r
- text += getTaggedCData(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("Some tag has no closing tag");\r
- }\r
-\r
- private String handleDistributionLocality(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String classValue = getAndRemoveRequiredAttributeValue(parentEvent, attributes, CLASS);\r
- String statusValue =getAndRemoveAttributeValue(attributes, STATUS);\r
- String frequencyValue =getAndRemoveAttributeValue(attributes, FREQUENCY);\r
- \r
-\r
- Taxon taxon = state.getCurrentTaxon();\r
- // TODO which ref to take?\r
- Reference<?> ref = state.getConfig().getSourceReference();\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- if (StringUtils.isNotBlank(text)) {\r
- String label = CdmUtils.removeTrailingDot(normalize(text));\r
- TaxonDescription description = getTaxonDescription(taxon, ref, false, true);\r
- NamedAreaLevel level = makeNamedAreaLevel(state,classValue, next);\r
- \r
- //status\r
- PresenceAbsenceTermBase<?> status = null;\r
- if (isNotBlank(statusValue)){\r
- try {\r
- status = state.getTransformer().getPresenceTermByKey(statusValue);\r
- if (status == null){\r
- //TODO\r
- String message = "The presence/absence status '%s' could not be transformed to an CDM status"; \r
- fireWarningEvent(String.format(message, statusValue), next, 4);\r
- }\r
- } catch (UndefinedTransformerMethodException e) {\r
- throw new RuntimeException(e);\r
- }\r
- }else{\r
- status = PresenceTerm.PRESENT();\r
- }\r
- //frequency\r
- if (isNotBlank(frequencyValue)){\r
- String message = "The frequency attribute is currently not yet available in CDM";\r
- fireWarningEvent(message, parentEvent, 6);\r
- }\r
- \r
- NamedArea higherArea = null;\r
- List<NamedArea> areas = new ArrayList<NamedArea>(); \r
- \r
- String patSingleArea = "([^,\\(]{3,})";\r
- String patSeparator = "(,|\\sand\\s)";\r
- String hierarchiePattern = String.format("%s\\((%s(%s%s)*)\\)",patSingleArea, patSingleArea, patSeparator, patSingleArea);\r
- Pattern patHierarchie = Pattern.compile(hierarchiePattern, Pattern.CASE_INSENSITIVE);\r
- Matcher matcher = patHierarchie.matcher(label); \r
- if (matcher.matches()){\r
- String higherAreaStr = matcher.group(1).trim();\r
- higherArea = makeArea(state, higherAreaStr, level);\r
- String[] innerAreas = matcher.group(2).split(patSeparator);\r
- for (String innerArea : innerAreas){\r
- if (isNotBlank(innerArea)){\r
- NamedArea singleArea = makeArea(state, innerArea.trim(), level);\r
- areas.add(singleArea);\r
- NamedArea partOf = singleArea.getPartOf();\r
-// if (partOf == null){\r
-// singleArea.setPartOf(higherArea);\r
-// }\r
- }\r
- }\r
- }else{\r
- NamedArea singleArea = makeArea(state, label, level);\r
- areas.add(singleArea);\r
- }\r
- \r
- for (NamedArea area : areas){\r
- //create distribution\r
- Distribution distribution = Distribution.NewInstance(area,status);\r
- description.addElement(distribution);\r
- }\r
- } else {\r
- String message = "Empty distribution locality";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- return text;\r
- } else if (isStartingElement(next, COORDINATES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, COORDINATES)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<DistributionLocality> has no closing tag");\r
- } \r
-\r
- private String handleHeading(MarkupImportState state,XMLEventReader reader, XMLEvent parentEvent)throws XMLStreamException {\r
- checkNoAttributes(parentEvent);\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return text;\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, FOOTNOTE)) {\r
- handleNotYetImplementedElement(next);\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- text += next.asCharacters().getData();\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("<String> has no closing tag");\r
-\r
- }\r
-\r
- /**\r
- * Handle string\r
- * @param state\r
- * @param reader\r
- * @param parentEvent\r
- * @param feature only needed for distributionLocalities\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private Map<String, String> handleString(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Feature feature)throws XMLStreamException {\r
- // attributes\r
- String classValue = getClassOnlyAttribute(parentEvent, false);\r
- if (StringUtils.isNotBlank(classValue)) {\r
- String message = "class attribute for <string> not yet implemented";\r
- fireWarningEvent(message, parentEvent, 2);\r
- }\r
-\r
- // subheadings\r
- Map<String, String> subHeadingMap = new HashMap<String, String>();\r
- String currentSubheading = null;\r
-\r
- boolean isTextMode = true;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- putCurrentSubheading(subHeadingMap, currentSubheading, text);\r
- return subHeadingMap;\r
- } else if (isStartingElement(next, BR)) {\r
- text += "<br/>";\r
- isTextMode = false;\r
- } else if (isEndingElement(next, BR)) {\r
- isTextMode = true;\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else if (isStartingElement(next, SUB_HEADING)) {\r
- text = putCurrentSubheading(subHeadingMap,currentSubheading, text);\r
- // TODO footnotes\r
- currentSubheading = getCData(state, reader, next).trim();\r
- } else if (isStartingElement(next, DISTRIBUTION_LOCALITY)) {\r
- if (feature != null && !feature.equals(Feature.DISTRIBUTION())) {\r
- String message = "Distribution locality only allowed for feature of type 'distribution'";\r
- fireWarningEvent(message, next, 4);\r
- }\r
- text += handleDistributionLocality(state, reader, next);\r
- } else if (next.isCharacters()) {\r
- if (! isTextMode) {\r
- String message = "String is not in text mode";\r
- fireWarningEvent(message, next, 6);\r
- } else {\r
- text += next.asCharacters().getData();\r
- }\r
- } else if (isStartingElement(next, HEADING)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, VERNACULAR_NAMES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, HEADING)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, QUOTE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, QUOTE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, DEDICATION)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, DEDICATION)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, TAXONTYPE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, TAXONTYPE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FULL_NAME)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FULL_NAME)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- }else if (isStartingElement(next, REFERENCES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, REFERENCES)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, GATHERING)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, GATHERING)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, ANNOTATION)) {\r
- //TODO //TODO test handleSimpleAnnotation\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, ANNOTATION)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, HABITAT)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, HABITAT)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FIGURE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FIGURE_REF)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FIGURE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FIGURE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FOOTNOTE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FOOTNOTE_REF)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, FOOTNOTE)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, WRITER)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, WRITER)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, DATES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, DATES)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<String> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param subHeadingMap\r
- * @param currentSubheading\r
- * @param text\r
- * @return\r
- */\r
- private String putCurrentSubheading(Map<String, String> subHeadingMap, String currentSubheading, String text) {\r
- if (StringUtils.isNotBlank(text)) {\r
- text = removeStartingMinus(text);\r
- subHeadingMap.put(currentSubheading, text.trim());\r
- }\r
- return "";\r
- }\r
-\r
- private String removeStartingMinus(String string) {\r
- string = replaceStart(string, "-");\r
- string = replaceStart(string, "\u002d");\r
- string = replaceStart(string, "\u2013");\r
- string = replaceStart(string, "\u2014");\r
- string = replaceStart(string, "--");\r
- return string;\r
- }\r
- \r
- /**\r
- * @param value\r
- * @param replacementString\r
- */\r
- private String replaceStart(String value, String replacementString) {\r
- if (value.startsWith(replacementString) ){\r
- value = value.substring(replacementString.length()).trim();\r
- }\r
- while (value.startsWith("-") || value.startsWith("\u2014") ){\r
- value = value.substring("-".length()).trim();\r
- }\r
- return value;\r
- }\r
- \r
- private String getXmlTag(XMLEvent event) {\r
- String result;\r
- if (event.isStartElement()) {\r
- result = "<" + event.asStartElement().getName().getLocalPart()\r
- + ">";\r
- } else if (event.isEndElement()) {\r
- result = "</" + event.asEndElement().getName().getLocalPart() + ">";\r
- } else {\r
- String message = "Only start or end elements are allowed as Html tags";\r
- throw new IllegalStateException(message);\r
- }\r
- return result;\r
- }\r
-\r
- protected static final List<String> htmlList = Arrays.asList("sub", "sup",\r
- "ol", "ul", "li", "i", "b", "table", "br","tr","td");\r
-\r
- private boolean isHtml(XMLEvent event) {\r
- if (event.isStartElement()) {\r
- String tag = event.asStartElement().getName().getLocalPart();\r
- return htmlList.contains(tag);\r
- } else if (event.isEndElement()) {\r
- String tag = event.asEndElement().getName().getLocalPart();\r
- return htmlList.contains(tag);\r
- } else {\r
- return false;\r
- }\r
-\r
- }\r
-\r
- /**\r
- * Handle the char or subchar element. As \r
- * @param state the import state\r
- * @param reader \r
- * @param parentEvent\r
- * @param parentFeature in case of subchars we need to attache the newly created feature to a parent feature, should be <code>null</code>\r
- * for top level chars. \r
- * @return List of TextData. Not a single one as the recursive TextData will also be returned\r
- * @throws XMLStreamException\r
- */\r
- private List<TextData> handleChar(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, Feature parentFeature) throws XMLStreamException {\r
- List<TextData> result = new ArrayList<TextData>();\r
- String classValue = getClassOnlyAttribute(parentEvent);\r
- Feature feature = makeFeature(classValue, state, parentEvent, parentFeature);\r
-\r
- boolean isTextMode = true;\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- state.putFeatureToCharSorterList(feature);\r
- TextData textData = TextData.NewInstance(feature);\r
- textData.putText(getDefaultLanguage(state), text);\r
- result.add(textData);\r
- return result;\r
- } else if (isStartingElement(next, FIGURE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FOOTNOTE_REF)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, BR)) {\r
- text += "<br/>";\r
- isTextMode = false;\r
- } else if (isEndingElement(next, BR)) {\r
- isTextMode = true;\r
- } else if (isHtml(next)) {\r
- text += getXmlTag(next);\r
- } else if (next.isStartElement()) {\r
- if (isStartingElement(next, ANNOTATION)) {\r
- handleNotYetImplementedElement(next); //TODO test handleSimpleAnnotation\r
- } else if (isStartingElement(next, ITALICS)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, BOLD)) {\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, FIGURE)) {\r
- handleFigure(state, reader, next);\r
- } else if (isStartingElement(next, SUB_CHAR)) {\r
- List<TextData> textData = handleChar(state, reader, next, feature);\r
- result.addAll(textData);\r
- } else if (isStartingElement(next, FOOTNOTE)) {\r
- FootnoteDataHolder footnote = handleFootnote(state, reader, next);\r
- if (footnote.isRef()) {\r
- String message = "Ref footnote not implemented here";\r
- fireWarningEvent(message, next, 4);\r
- } else {\r
- registerGivenFootnote(state, footnote);\r
- }\r
- } else {\r
- handleUnexpectedStartElement(next.asStartElement());\r
- }\r
- } else if (next.isCharacters()) {\r
- if (!isTextMode) {\r
- String message = "String is not in text mode";\r
- fireWarningEvent(message, next, 6);\r
- } else {\r
- text += next.asCharacters().getData();\r
- }\r
- } else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
- }\r
- }\r
- throw new IllegalStateException("RefPart has no closing tag");\r
- }\r
-\r
- /**\r
- * @param classValue\r
- * @param state\r
- * @param parentEvent\r
- * @param parentFeature \r
- * @return\r
- * @throws UndefinedTransformerMethodException\r
- */\r
- private Feature makeFeature(String classValue, MarkupImportState state, XMLEvent parentEvent, Feature parentFeature) {\r
- UUID uuid;\r
- try {\r
- String featureText = StringUtils.capitalize(classValue);\r
- if (parentFeature != null){\r
- featureText = "<%s>" + featureText;\r
- featureText = String.format(featureText, parentFeature.getTitleCache());\r
- classValue = "<%s>" + classValue;\r
- classValue = String.format(classValue, parentFeature.getTitleCache());\r
- }\r
-\r
- \r
- Feature feature = state.getTransformer().getFeatureByKey(classValue);\r
- if (feature != null) {\r
- return feature;\r
- }\r
- uuid = state.getTransformer().getFeatureUuid(classValue);\r
- if (uuid == null) {\r
- uuid = state.getFeatureUuid(classValue);\r
- } \r
- if (uuid == null) {\r
- // TODO\r
- String message = "Uuid is not defined for '%s'";\r
- message = String.format(message, classValue);\r
- fireWarningEvent(message, parentEvent, 8);\r
- uuid = UUID.randomUUID();\r
- state.putFeatureUuid(classValue, uuid);\r
- }\r
-\r
- // TODO eFlora vocabulary\r
- TermVocabulary<Feature> voc = null;\r
- feature = getFeature(state, uuid, featureText, featureText, classValue, voc);\r
- if (parentFeature != null){\r
- parentFeature.addIncludes(feature);\r
- save(parentFeature, state);\r
- }\r
- save(feature, state);\r
- \r
- if (feature == null) {\r
- throw new NullPointerException(classValue + " not recognized as a feature");\r
- }\r
-// state.putFeatureToCurrentList(feature);\r
- return feature;\r
- } catch (Exception e) {\r
- String message = "Could not create feature for %s: %s";\r
- message = String.format(message, classValue, e.getMessage());\r
- fireWarningEvent(message, parentEvent, 4);\r
- e.printStackTrace();\r
- return Feature.UNKNOWN();\r
- }\r
- }\r
-\r
-\r
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff