Revision 72eb64b9
Added by Andreas Müller over 12 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupDocumentImport.java | ||
|---|---|---|
| 60 | 60 |
import eu.etaxonomy.cdm.model.common.TermVocabulary; |
| 61 | 61 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| 62 | 62 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 63 |
import eu.etaxonomy.cdm.model.description.Distribution; |
|
| 63 | 64 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 65 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase; |
|
| 64 | 66 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 65 | 67 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 66 | 68 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| ... | ... | |
| 84 | 86 |
import eu.etaxonomy.cdm.model.reference.IJournal; |
| 85 | 87 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 86 | 88 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 89 |
import eu.etaxonomy.cdm.model.reference.ReferenceType; |
|
| 87 | 90 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 88 | 91 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| 89 | 92 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| ... | ... | |
| 101 | 104 |
*/ |
| 102 | 105 |
@Component |
| 103 | 106 |
public class MarkupDocumentImport extends MarkupImportBase implements ICdmIO<MarkupImportState> {
|
| 107 |
private static final String HABITAT = "habitat"; |
|
| 108 |
|
|
| 109 |
|
|
| 110 |
|
|
| 111 |
private static final String LIFE_CYCLE_PERIODS = "lifeCyclePeriods"; |
|
| 112 |
|
|
| 113 |
|
|
| 114 |
|
|
| 115 |
private static final String DISTRIBUTION_LOCALITY = "distributionLocality"; |
|
| 116 |
|
|
| 117 |
|
|
| 118 |
|
|
| 119 |
private static final String REFERENCE = "reference"; |
|
| 120 |
|
|
| 121 |
|
|
| 122 |
|
|
| 104 | 123 |
private static final Logger logger = Logger.getLogger(MarkupDocumentImport.class); |
| 105 | 124 |
|
| 106 | 125 |
|
| ... | ... | |
| 480 | 499 |
boolean hasTitle = false; |
| 481 | 500 |
boolean hasNomenclature = false; |
| 482 | 501 |
String taxonTitle = null; |
| 483 |
Extension writerExtension = null; |
|
| 484 |
|
|
| 485 |
|
|
| 502 |
|
|
| 486 | 503 |
while (reader.hasNext()){
|
| 487 | 504 |
XMLEvent next = readNoWhitespace(reader); |
| 488 | 505 |
if (next.isEndElement()){
|
| ... | ... | |
| 505 | 522 |
}else if(isEndingElement(next, KEY)){
|
| 506 | 523 |
//NOT YET IMPLEMENTED |
| 507 | 524 |
popUnimplemented(next.asEndElement()); |
| 508 |
}else if(isEndingElement(next, NOTES)){
|
|
| 509 |
//NOT YET IMPLEMENTED |
|
| 510 |
popUnimplemented(next.asEndElement()); |
|
| 511 | 525 |
}else if(isEndingElement(next, REFERENCES)){
|
| 512 | 526 |
//NOT YET IMPLEMENTED |
| 513 | 527 |
popUnimplemented(next.asEndElement()); |
| ... | ... | |
| 522 | 536 |
taxonTitle = handleTaxonTitle(state, reader, next); |
| 523 | 537 |
hasTitle = true; |
| 524 | 538 |
}else if(isStartingElement(next, WRITER)){
|
| 525 |
List<FootnoteDataHolder> footNotes = new ArrayList<FootnoteDataHolder>(); |
|
| 526 |
writerExtension = handleWriter(state, reader, next, footNotes);
|
|
| 527 |
taxon.addExtension(writerExtension);
|
|
| 539 |
|
|
| 540 |
WriterDataHolder writer = handleWriter(state, reader, next);
|
|
| 541 |
taxon.addExtension(writer.extension);
|
|
| 528 | 542 |
//TODO what if taxonTitle comes later |
| 529 |
if (StringUtils.isNotBlank(taxonTitle) && writerExtension != null){
|
|
| 530 |
String writer = writerExtension.getValue(); |
|
| 531 |
Reference sec = ReferenceFactory.newBookSection(); |
|
| 543 |
if (StringUtils.isNotBlank(taxonTitle) && writer.extension != null){
|
|
| 544 |
Reference<?> sec = ReferenceFactory.newBookSection(); |
|
| 532 | 545 |
sec.setTitle(taxonTitle); |
| 533 |
TeamOrPersonBase author = createAuthor(writer);
|
|
| 546 |
TeamOrPersonBase<?> author = createAuthor(writer.writer);
|
|
| 534 | 547 |
sec.setAuthorTeam(author); |
| 535 | 548 |
sec.setInReference(state.getConfig().getSourceReference()); |
| 536 | 549 |
taxon.setSec(sec); |
| 537 |
registerFootnotes(state, sec, footNotes);
|
|
| 550 |
registerFootnotes(state, sec, writer.footnotes);
|
|
| 538 | 551 |
}else{
|
| 539 | 552 |
String message = "No taxontitle exists for writer"; |
| 540 | 553 |
fireWarningEvent(message, next, 6); |
| ... | ... | |
| 550 | 563 |
}else if(isStartingElement(next, FEATURE)){
|
| 551 | 564 |
handleFeature(state, reader, next); |
| 552 | 565 |
}else if(isStartingElement(next, NOTES)){
|
| 553 |
handleNotYetImplementedElement(next); |
|
| 566 |
//TODO is this the correct way to handle notes? |
|
| 567 |
String note = handleNotes(state, reader, next); |
|
| 568 |
|
|
| 569 |
UUID notesUuid; |
|
| 570 |
try {
|
|
| 571 |
notesUuid = state.getTransformer().getFeatureUuid("notes");
|
|
| 572 |
Feature feature = getFeature(state, notesUuid, "Notes", "Notes", "note", null); |
|
| 573 |
TextData textData = TextData.NewInstance(feature); |
|
| 574 |
textData.putText(Language.DEFAULT(), note); |
|
| 575 |
TaxonDescription description = getTaxonDescription(taxon, false, true); |
|
| 576 |
description.addElement(textData); |
|
| 577 |
} catch (UndefinedTransformerMethodException e) {
|
|
| 578 |
String message = "getFeatureUuid method not yet implemented"; |
|
| 579 |
fireWarningEvent(message, next, 8); |
|
| 580 |
} |
|
| 554 | 581 |
}else if(isStartingElement(next, REFERENCES)){
|
| 555 | 582 |
handleNotYetImplementedElement(next); |
| 556 | 583 |
}else if(isStartingElement(next, FIGURE)){
|
| ... | ... | |
| 575 | 602 |
} |
| 576 | 603 |
|
| 577 | 604 |
|
| 605 |
private String handleNotes(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 606 |
checkNoAttributes(parentEvent); |
|
| 607 |
|
|
| 608 |
String text = ""; |
|
| 609 |
while (reader.hasNext()){
|
|
| 610 |
XMLEvent next = readNoWhitespace(reader); |
|
| 611 |
if(isMyEndingElement(next, parentEvent)){
|
|
| 612 |
return text; |
|
| 613 |
}else if (next.isEndElement()){
|
|
| 614 |
if (isEndingElement(next, HEADING)){
|
|
| 615 |
popUnimplemented(next.asEndElement()); |
|
| 616 |
}else if (isEndingElement(next, SUB_HEADING)){
|
|
| 617 |
popUnimplemented(next.asEndElement()); |
|
| 618 |
}else if (isEndingElement(next, WRITER)){
|
|
| 619 |
popUnimplemented(next.asEndElement()); |
|
| 620 |
}else if (isEndingElement(next, NUM)){
|
|
| 621 |
popUnimplemented(next.asEndElement()); |
|
| 622 |
}else {
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|
| 623 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 624 |
} |
|
| 625 |
}else if (next.isStartElement()){
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|
| 626 |
if (isStartingElement(next, HEADING)){
|
|
| 627 |
handleNotYetImplementedElement(next); |
|
| 628 |
}else if (isStartingElement(next, SUB_HEADING)){
|
|
| 629 |
handleNotYetImplementedElement(next); |
|
| 630 |
}else if (isStartingElement(next, WRITER)){
|
|
| 631 |
handleNotYetImplementedElement(next); |
|
| 632 |
}else if (isStartingElement(next, NUM)){
|
|
| 633 |
handleNotYetImplementedElement(next); |
|
| 634 |
}else if (isStartingElement(next, STRING)){
|
|
| 635 |
//TODO why multiple strings? |
|
| 636 |
text += handleString(state, reader, next); |
|
| 637 |
}else {
|
|
| 638 |
handleUnexpectedStartElement(next.asStartElement()); |
|
| 639 |
} |
|
| 640 |
}else {
|
|
| 641 |
handleUnexpectedElement(next); |
|
| 642 |
} |
|
| 643 |
} |
|
| 644 |
throw new IllegalStateException("<Notes> has no closing tag");
|
|
| 645 |
} |
|
| 646 |
|
|
| 647 |
|
|
| 578 | 648 |
/** |
| 579 | 649 |
* @param state |
| 580 | 650 |
* @param attributes |
| ... | ... | |
| 690 | 760 |
|
| 691 | 761 |
} |
| 692 | 762 |
|
| 693 |
private Extension handleWriter(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, List<FootnoteDataHolder> footNotes) throws XMLStreamException {
|
|
| 763 |
private WriterDataHolder handleWriter(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 694 | 764 |
String text = ""; |
| 695 | 765 |
checkNoAttributes(parentEvent); |
| 766 |
WriterDataHolder dataHolder = new WriterDataHolder(); |
|
| 767 |
List<FootnoteDataHolder> footnotes = new ArrayList<FootnoteDataHolder>(); |
|
| 696 | 768 |
|
| 697 | 769 |
//TODO handle attributes |
| 698 | 770 |
while (reader.hasNext()){
|
| 699 | 771 |
XMLEvent next = readNoWhitespace(reader); |
| 700 | 772 |
if (next.isEndElement()){
|
| 701 | 773 |
if (isMyEndingElement(next, parentEvent)){
|
| 774 |
text = CdmUtils.removeBrackets(text); |
|
| 702 | 775 |
if (checkMandatoryText(text, parentEvent)){
|
| 703 |
UUID uuidWriter = MarkupTransformer.uuidWriter; |
|
| 704 |
ExtensionType titleExtensionType = this.getExtensionType(state, uuidWriter, "Writer", "writer", "writer"); |
|
| 776 |
text = normalize(text); |
|
| 777 |
dataHolder.writer = text; |
|
| 778 |
dataHolder.footnotes = footnotes; |
|
| 779 |
|
|
| 780 |
//Extension |
|
| 781 |
UUID uuidWriterExtension = MarkupTransformer.uuidWriterExtension; |
|
| 782 |
ExtensionType writerExtensionType = this.getExtensionType(state, uuidWriterExtension, "Writer", "writer", "writer"); |
|
| 705 | 783 |
Extension extension = Extension.NewInstance(); |
| 706 |
extension.setType(titleExtensionType); |
|
| 707 |
extension.setValue(normalize(text)); |
|
| 708 |
return extension; |
|
| 784 |
extension.setType(writerExtensionType); |
|
| 785 |
extension.setValue(text); |
|
| 786 |
dataHolder.extension = extension; |
|
| 787 |
|
|
| 788 |
//Annotation |
|
| 789 |
UUID uuidWriterAnnotation = MarkupTransformer.uuidWriterAnnotation; |
|
| 790 |
AnnotationType writerAnnotationType = this.getAnnotationType(state, uuidWriterAnnotation, "Writer", "writer", "writer", null); |
|
| 791 |
Annotation annotation = Annotation.NewInstance(text, writerAnnotationType, Language.DEFAULT()); |
|
| 792 |
dataHolder.annotation = annotation; |
|
| 793 |
|
|
| 794 |
|
|
| 795 |
|
|
| 796 |
return dataHolder; |
|
| 709 | 797 |
}else{
|
| 710 | 798 |
return null; |
| 711 | 799 |
} |
| ... | ... | |
| 722 | 810 |
if(isStartingElement(next, FOOTNOTE_REF)){
|
| 723 | 811 |
FootnoteDataHolder footNote = handleFootnoteRef(state, reader, next); |
| 724 | 812 |
if (footNote.isRef()){
|
| 725 |
footNotes.add(footNote);
|
|
| 813 |
footnotes.add(footNote);
|
|
| 726 | 814 |
}else{
|
| 727 | 815 |
logger.warn ("Non ref footnotes not yet impelemnted");
|
| 728 | 816 |
} |
| ... | ... | |
| 1015 | 1103 |
popUnimplemented(next.asEndElement()); |
| 1016 | 1104 |
}else if (isEndingElement(next, COLLECTION)){
|
| 1017 | 1105 |
popUnimplemented(next.asEndElement()); |
| 1018 |
}else if (isEndingElement(next, REFERENCES)){
|
|
| 1019 |
popUnimplemented(next.asEndElement()); |
|
| 1020 | 1106 |
}else if (isEndingElement(next, BR)){
|
| 1021 | 1107 |
isTextMode = true; |
| 1022 | 1108 |
}else if (isHtml(next)){
|
| ... | ... | |
| 1030 | 1116 |
}else if (isStartingElement(next, COLLECTION)){
|
| 1031 | 1117 |
handleNotYetImplementedElement(next); |
| 1032 | 1118 |
}else if (isStartingElement(next, REFERENCES)){
|
| 1033 |
handleNotYetImplementedElement(next);
|
|
| 1119 |
text += " " + handleInLineReferences(state, reader, next) + " ";
|
|
| 1034 | 1120 |
}else if (isStartingElement(next, BR)){
|
| 1035 | 1121 |
text += "<br/>"; |
| 1036 | 1122 |
isTextMode = false; |
| ... | ... | |
| 1044 | 1130 |
String message = "footnoteString is not in text mode"; |
| 1045 | 1131 |
fireWarningEvent(message, next, 6); |
| 1046 | 1132 |
}else{
|
| 1047 |
text += next.asCharacters().getData();
|
|
| 1133 |
text += next.asCharacters().getData().trim(); //getCData(state, reader, next); does not work as we have inner tags like <references>
|
|
| 1048 | 1134 |
} |
| 1049 | 1135 |
}else {
|
| 1050 | 1136 |
handleUnexpectedEndElement(next.asEndElement()); |
| ... | ... | |
| 1055 | 1141 |
} |
| 1056 | 1142 |
|
| 1057 | 1143 |
|
| 1144 |
private String handleInLineReferences(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 1145 |
checkNoAttributes(parentEvent); |
|
| 1146 |
|
|
| 1147 |
boolean hasReference = false; |
|
| 1148 |
String text = ""; |
|
| 1149 |
while (reader.hasNext()){
|
|
| 1150 |
XMLEvent next = readNoWhitespace(reader); |
|
| 1151 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 1152 |
checkMandatoryElement(hasReference, parentEvent.asStartElement(), REFERENCE); |
|
| 1153 |
return text; |
|
| 1154 |
}else if(isStartingElement(next, REFERENCE)){
|
|
| 1155 |
text += handleInLineReference(state, reader, next); |
|
| 1156 |
hasReference = true; |
|
| 1157 |
}else{
|
|
| 1158 |
handleUnexpectedElement(next); |
|
| 1159 |
} |
|
| 1160 |
} |
|
| 1161 |
//TODO handle missing end element |
|
| 1162 |
throw new IllegalStateException("<References> has no closing tag");
|
|
| 1163 |
} |
|
| 1164 |
|
|
| 1165 |
|
|
| 1166 |
private String handleInLineReference(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 1167 |
checkNoAttributes(parentEvent); |
|
| 1168 |
|
|
| 1169 |
boolean hasRefPart = false; |
|
| 1170 |
Map<String, String> refMap = new HashMap<String, String>(); |
|
| 1171 |
while (reader.hasNext()){
|
|
| 1172 |
XMLEvent next = readNoWhitespace(reader); |
|
| 1173 |
if (isMyEndingElement(next, parentEvent)){
|
|
| 1174 |
checkMandatoryElement(hasRefPart, parentEvent.asStartElement(), REF_PART); |
|
| 1175 |
Reference<?> reference = createReference(state, refMap, next); |
|
| 1176 |
String result = "<ref uuid='%s'>%s</ref>"; |
|
| 1177 |
result = String.format(result, reference.getUuid(), reference.getTitleCache()); |
|
| 1178 |
return result; |
|
| 1179 |
}else if(isStartingElement(next, REF_PART)){
|
|
| 1180 |
handleRefPart(state, reader, next, refMap); |
|
| 1181 |
hasRefPart = true; |
|
| 1182 |
}else{
|
|
| 1183 |
handleUnexpectedElement(next); |
|
| 1184 |
} |
|
| 1185 |
} |
|
| 1186 |
//TODO handle missing end element |
|
| 1187 |
throw new IllegalStateException("<Reference> has no closing tag");
|
|
| 1188 |
} |
|
| 1189 |
|
|
| 1190 |
|
|
| 1058 | 1191 |
private void handleHomotypes(MarkupImportState state, XMLEventReader reader, StartElement parentEvent) throws XMLStreamException {
|
| 1059 | 1192 |
checkNoAttributes(parentEvent); |
| 1060 | 1193 |
|
| ... | ... | |
| 1084 | 1217 |
hasNom = true; |
| 1085 | 1218 |
}else if(isStartingElement(next, NAME_TYPE)){
|
| 1086 | 1219 |
state.setNameType(true); |
| 1087 |
handleNameType(state, reader, next); |
|
| 1220 |
handleNameType(state, reader, next, homotypicalGroup);
|
|
| 1088 | 1221 |
}else if(isStartingElement(next, SPECIMEN_TYPE)){
|
| 1089 | 1222 |
handleSpecimenType(state, reader, next, homotypicalGroup); |
| 1090 | 1223 |
}else if(isStartingElement(next, NOTES)){
|
| ... | ... | |
| 1102 | 1235 |
} |
| 1103 | 1236 |
|
| 1104 | 1237 |
|
| 1105 |
private void handleNameType(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 1238 |
private void handleNameType(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, HomotypicalGroup homotypicalGroup) throws XMLStreamException {
|
|
| 1106 | 1239 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
| 1107 | 1240 |
String typeStatus = getAndRemoveAttributeValue(attributes, TYPE_STATUS); |
| 1108 | 1241 |
checkNoAttributes(attributes, parentEvent); |
| ... | ... | |
| 1114 | 1247 |
String message = "Type status could not be recognized: %s"; |
| 1115 | 1248 |
message = String.format(message, typeStatus); |
| 1116 | 1249 |
fireWarningEvent(message, parentEvent, 4); |
| 1250 |
status = null; |
|
| 1117 | 1251 |
} |
| 1118 | 1252 |
|
| 1119 | 1253 |
boolean hasNom = false; |
| ... | ... | |
| 1122 | 1256 |
if (next.isEndElement()){
|
| 1123 | 1257 |
if (isMyEndingElement(next, parentEvent)){
|
| 1124 | 1258 |
checkMandatoryElement(hasNom, parentEvent.asStartElement(), NOM); |
| 1259 |
state.setNameType(false); |
|
| 1125 | 1260 |
return; |
| 1126 | 1261 |
}else{
|
| 1127 | 1262 |
if(isEndingElement(next, ACCEPTED_NAME)){
|
| ... | ... | |
| 1133 | 1268 |
} |
| 1134 | 1269 |
}else if (next.isStartElement()){
|
| 1135 | 1270 |
if(isStartingElement(next, NOM)){
|
| 1136 |
NonViralName name = handleNom(state, reader, next, null); |
|
| 1271 |
//TODO should we check if the type is always a species, is this a rule? |
|
| 1272 |
NonViralName<?> speciesName = handleNom(state, reader, next, null); |
|
| 1273 |
for (TaxonNameBase<?,?> name : homotypicalGroup.getTypifiedNames()){
|
|
| 1274 |
name.addNameTypeDesignation(speciesName, null, null, null, status, false, false, false, false); |
|
| 1275 |
} |
|
| 1137 | 1276 |
hasNom = true; |
| 1138 | 1277 |
}else if(isStartingElement(next, ACCEPTED_NAME)){
|
| 1139 | 1278 |
handleNotYetImplementedElement(next); |
| ... | ... | |
| 1397 | 1536 |
if ("locality".equalsIgnoreCase(classValue)){
|
| 1398 | 1537 |
isLocality = true; |
| 1399 | 1538 |
}else{
|
| 1400 |
try {
|
|
| 1401 |
areaLevel = state.getTransformer().getNamedAreaLevelByKey(classValue); |
|
| 1402 |
} catch (UndefinedTransformerMethodException e) {
|
|
| 1403 |
//do nothing |
|
| 1404 |
} |
|
| 1405 |
if (areaLevel == null){
|
|
| 1406 |
String message = "Named area level '%s' not yet implemented."; |
|
| 1407 |
message = String.format(message, classValue); |
|
| 1408 |
fireWarningEvent(message, parentEvent, 6); |
|
| 1409 |
} |
|
| 1539 |
areaLevel = makeNamedAreaLevel(state, classValue, parentEvent); |
|
| 1410 | 1540 |
} |
| 1411 | 1541 |
|
| 1412 | 1542 |
String text = ""; |
| ... | ... | |
| 1783 | 1913 |
if (isSynonym){
|
| 1784 | 1914 |
Rank defaultRank = Rank.SPECIES(); //can be any |
| 1785 | 1915 |
name = createNameByCode(state, defaultRank); |
| 1786 |
name.setHomotypicalGroup(homotypicalGroup); |
|
| 1916 |
if (homotypicalGroup != null){
|
|
| 1917 |
name.setHomotypicalGroup(homotypicalGroup); |
|
| 1918 |
} |
|
| 1787 | 1919 |
SynonymRelationshipType synonymType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(); |
| 1788 | 1920 |
if (taxon.getHomotypicGroup().equals(homotypicalGroup)){
|
| 1789 | 1921 |
synonymType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF(); |
| ... | ... | |
| 1865 | 1997 |
|
| 1866 | 1998 |
state.setCitation(true); |
| 1867 | 1999 |
boolean hasRefPart = false; |
| 1868 |
Reference reference = ReferenceFactory.newGeneric(); |
|
| 1869 | 2000 |
Map<String, String> refMap = new HashMap<String, String>(); |
| 1870 | 2001 |
while (reader.hasNext()){
|
| 1871 | 2002 |
XMLEvent next = readNoWhitespace(reader); |
| 1872 | 2003 |
if (isMyEndingElement(next, parentEvent)){
|
| 1873 | 2004 |
checkMandatoryElement(hasRefPart, parentEvent.asStartElement(), REF_PART); |
| 1874 |
reference = createReference(state, refMap, next); |
|
| 2005 |
Reference reference = createReference(state, refMap, next);
|
|
| 1875 | 2006 |
String microReference = refMap.get(DETAILS); |
| 1876 | 2007 |
doCitation(state, name, classValue, reference, microReference, parentEvent); |
| 1877 | 2008 |
state.setCitation(false); |
| ... | ... | |
| 1944 | 2075 |
reference = (Reference)article; |
| 1945 | 2076 |
|
| 1946 | 2077 |
}else{
|
| 2078 |
//TODO |
|
| 1947 | 2079 |
Reference bookOrPartOf = ReferenceFactory.newGeneric(); |
| 1948 | 2080 |
reference = bookOrPartOf; |
| 1949 | 2081 |
} |
| ... | ... | |
| 1953 | 2085 |
|
| 1954 | 2086 |
|
| 1955 | 2087 |
}else{
|
| 1956 |
reference = ReferenceFactory.newGeneric(); |
|
| 2088 |
if (volume != null || "journal".equalsIgnoreCase(type)){
|
|
| 2089 |
IArticle article = ReferenceFactory.newArticle(); |
|
| 2090 |
if (pubName != null){
|
|
| 2091 |
IJournal journal = ReferenceFactory.newJournal(); |
|
| 2092 |
journal.setTitle(pubName); |
|
| 2093 |
article.setInJournal(journal); |
|
| 2094 |
} |
|
| 2095 |
reference = (Reference)article; |
|
| 2096 |
|
|
| 2097 |
}else{
|
|
| 2098 |
Reference bookOrPartOf = ReferenceFactory.newGeneric(); |
|
| 2099 |
reference = bookOrPartOf; |
|
| 2100 |
} |
|
| 2101 |
|
|
| 1957 | 2102 |
//TODO type |
| 1958 | 2103 |
TeamOrPersonBase author = createAuthor(authorStr); |
| 1959 | 2104 |
reference.setAuthorTeam(author); |
| ... | ... | |
| 1966 | 2111 |
reference.setEditor(editors); |
| 1967 | 2112 |
|
| 1968 | 2113 |
if (pubName != null){
|
| 1969 |
Reference inReference = ReferenceFactory.newGeneric(); |
|
| 2114 |
Reference inReference; |
|
| 2115 |
if (reference.getType().equals(ReferenceType.Article)){
|
|
| 2116 |
inReference = ReferenceFactory.newJournal(); |
|
| 2117 |
}else{
|
|
| 2118 |
inReference = ReferenceFactory.newGeneric(); |
|
| 2119 |
} |
|
| 1970 | 2120 |
inReference.setTitle(pubName); |
| 1971 | 2121 |
reference.setInReference(inReference); |
| 1972 | 2122 |
} |
| ... | ... | |
| 2041 | 2191 |
if (isMyEndingElement(next, parentEvent)){
|
| 2042 | 2192 |
return; |
| 2043 | 2193 |
}else{
|
| 2044 |
if(isEndingElement(next, WRITER)){
|
|
| 2045 |
//NOT YET IMPLEMENTED |
|
| 2046 |
popUnimplemented(next.asEndElement()); |
|
| 2047 |
}else if(isEndingElement(next, DISTRIBUTION_LIST)){
|
|
| 2048 |
//NOT YET IMPLEMENTED |
|
| 2049 |
popUnimplemented(next.asEndElement()); |
|
| 2050 |
}else if(isEndingElement(next, HABITAT_LIST)){
|
|
| 2051 |
//NOT YET IMPLEMENTED |
|
| 2052 |
popUnimplemented(next.asEndElement()); |
|
| 2194 |
if(isEndingElement(next, DISTRIBUTION_LIST) || isEndingElement(next, HABITAT_LIST)){
|
|
| 2195 |
//only handle list elements |
|
| 2053 | 2196 |
}else if(isEndingElement(next, REFERENCES)){
|
| 2054 | 2197 |
//NOT YET IMPLEMENTED |
| 2055 | 2198 |
popUnimplemented(next.asEndElement()); |
| ... | ... | |
| 2070 | 2213 |
} |
| 2071 | 2214 |
} |
| 2072 | 2215 |
}else if(isStartingElement(next, WRITER)){
|
| 2073 |
handleNotYetImplementedElement(next); |
|
| 2216 |
WriterDataHolder writer = handleWriter(state, reader, next); |
|
| 2217 |
if (StringUtils.isNotBlank(writer.writer)){
|
|
| 2218 |
//TODO |
|
| 2219 |
Reference<?> ref = state.getConfig().getSourceReference(); |
|
| 2220 |
TaxonDescription description = getTaxonDescription(taxon, ref, false, true); |
|
| 2221 |
TextData featurePlaceholder = getFeaturePlaceholder(state, description, true); |
|
| 2222 |
featurePlaceholder.addAnnotation(writer.annotation); |
|
| 2223 |
registerFootnotes(state, featurePlaceholder, writer.footnotes); |
|
| 2224 |
}else{
|
|
| 2225 |
String message = "Writer element is empty"; |
|
| 2226 |
fireWarningEvent(message, next, 4); |
|
| 2227 |
} |
|
| 2228 |
}else if(isStartingElement(next, DISTRIBUTION_LOCALITY)){
|
|
| 2229 |
if (! feature.equals(Feature.DISTRIBUTION())){
|
|
| 2230 |
String message = "Distribution locality only allowed for feature of type 'distribution'"; |
|
| 2231 |
fireWarningEvent(message, next, 4); |
|
| 2232 |
} |
|
| 2233 |
handleDistributionLocality(state,reader, next); |
|
| 2074 | 2234 |
}else if(isStartingElement(next, DISTRIBUTION_LIST)){
|
| 2075 |
handleNotYetImplementedElement(next); |
|
| 2235 |
//only handle list elements |
|
| 2236 |
}else if(isStartingElement(next, HABITAT)){
|
|
| 2237 |
if (! (feature.equals(Feature.HABITAT())) || feature.equals(Feature.HABITAT_ECOLOGY()) || feature.equals(Feature.ECOLOGY()) ){
|
|
| 2238 |
String message = "Habitat only allowed for feature of type 'habitat','habitat ecology' or 'ecology'"; |
|
| 2239 |
fireWarningEvent(message, next, 4); |
|
| 2240 |
} |
|
| 2241 |
handleHabitat(state,reader, next); |
|
| 2076 | 2242 |
}else if(isStartingElement(next, HABITAT_LIST)){
|
| 2077 |
handleNotYetImplementedElement(next);
|
|
| 2243 |
//only handle list elements
|
|
| 2078 | 2244 |
}else if(isStartingElement(next, CHAR)){
|
| 2079 | 2245 |
TextData textData = handleChar (state,reader, next); |
| 2080 | 2246 |
taxonDescription.addElement(textData); |
| ... | ... | |
| 2130 | 2296 |
} |
| 2131 | 2297 |
|
| 2132 | 2298 |
|
| 2299 |
private void handleHabitat(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 2300 |
checkNoAttributes(parentEvent); |
|
| 2301 |
Taxon taxon = state.getCurrentTaxon(); |
|
| 2302 |
//TODO which ref to take? |
|
| 2303 |
Reference<?> ref = state.getConfig().getSourceReference(); |
|
| 2304 |
|
|
| 2305 |
String text = ""; |
|
| 2306 |
while (reader.hasNext()){
|
|
| 2307 |
XMLEvent next = readNoWhitespace(reader); |
|
| 2308 |
if(isMyEndingElement(next, parentEvent)){
|
|
| 2309 |
TaxonDescription description = getTaxonDescription(taxon, ref, false, true); |
|
| 2310 |
UUID uuidExtractedHabitat = MarkupTransformer.uuidExtractedHabitat; |
|
| 2311 |
Feature feature = getFeature(state, uuidExtractedHabitat, "Extracted Habitat", "An structured habitat that was extracted from a habitat text", "extr. habit.", null); |
|
| 2312 |
TextData habitat = TextData.NewInstance(feature); |
|
| 2313 |
habitat.putText(Language.DEFAULT(), text); |
|
| 2314 |
description.addElement(habitat); |
|
| 2315 |
|
|
| 2316 |
return; |
|
| 2317 |
}else if (next.isStartElement()){
|
|
| 2318 |
if (isStartingElement(next, ALTITUDE)){
|
|
| 2319 |
handleNotYetImplementedElement(next); |
|
| 2320 |
}else if (isStartingElement(next, LIFE_CYCLE_PERIODS)){
|
|
| 2321 |
handleNotYetImplementedElement(next); |
|
| 2322 |
}else {
|
|
| 2323 |
handleUnexpectedStartElement(next.asStartElement()); |
|
| 2324 |
} |
|
| 2325 |
} else if (next.isCharacters()){
|
|
| 2326 |
text += next.asCharacters().getData(); |
|
| 2327 |
}else {
|
|
| 2328 |
handleUnexpectedElement(next); |
|
| 2329 |
} |
|
| 2330 |
} |
|
| 2331 |
throw new IllegalStateException("<Habitat> has no closing tag");
|
|
| 2332 |
|
|
| 2333 |
|
|
| 2334 |
} |
|
| 2335 |
|
|
| 2336 |
|
|
| 2337 |
private void handleDistributionLocality(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 2338 |
String classValue =getClassOnlyAttribute(parentEvent); |
|
| 2339 |
|
|
| 2340 |
Taxon taxon = state.getCurrentTaxon(); |
|
| 2341 |
//TODO which ref to take? |
|
| 2342 |
Reference ref = state.getConfig().getSourceReference(); |
|
| 2343 |
|
|
| 2344 |
String text = ""; |
|
| 2345 |
while (reader.hasNext()){
|
|
| 2346 |
XMLEvent next = readNoWhitespace(reader); |
|
| 2347 |
if(isMyEndingElement(next, parentEvent)){
|
|
| 2348 |
if (StringUtils.isNotBlank(text)){
|
|
| 2349 |
TaxonDescription description = getTaxonDescription(taxon, ref, false, true); |
|
| 2350 |
NamedAreaLevel level = makeNamedAreaLevel(state, classValue, next); |
|
| 2351 |
NamedArea area = createArea(text, level, state); |
|
| 2352 |
|
|
| 2353 |
PresenceAbsenceTermBase<?> status = null; |
|
| 2354 |
Distribution distribution = Distribution.NewInstance(area, status); |
|
| 2355 |
description.addElement(distribution); |
|
| 2356 |
}else{
|
|
| 2357 |
String message = "Empty distribution locality"; |
|
| 2358 |
fireWarningEvent(message, next, 4); |
|
| 2359 |
} |
|
| 2360 |
return; |
|
| 2361 |
}else if (next.isStartElement()){
|
|
| 2362 |
if (isStartingElement(next, COORDINATES)){
|
|
| 2363 |
handleNotYetImplementedElement(next); |
|
| 2364 |
}else {
|
|
| 2365 |
handleUnexpectedStartElement(next.asStartElement()); |
|
| 2366 |
} |
|
| 2367 |
} else if (next.isCharacters()){
|
|
| 2368 |
text += next.asCharacters().getData(); |
|
| 2369 |
}else {
|
|
| 2370 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 2371 |
} |
|
| 2372 |
} |
|
| 2373 |
throw new IllegalStateException("<String> has no closing tag");
|
|
| 2374 |
} |
|
| 2375 |
|
|
| 2376 |
|
|
| 2377 |
/** |
|
| 2378 |
* @param state |
|
| 2379 |
* @param levelString |
|
| 2380 |
* @param next |
|
| 2381 |
* @return |
|
| 2382 |
*/ |
|
| 2383 |
private NamedAreaLevel makeNamedAreaLevel(MarkupImportState state, |
|
| 2384 |
String levelString, XMLEvent next) {
|
|
| 2385 |
NamedAreaLevel level; |
|
| 2386 |
try {
|
|
| 2387 |
level = state.getTransformer().getNamedAreaLevelByKey(levelString); |
|
| 2388 |
if (level == null){
|
|
| 2389 |
UUID levelUuid = state.getTransformer().getNamedAreaLevelUuid(levelString); |
|
| 2390 |
if (levelUuid == null){
|
|
| 2391 |
String message = "Unknown distribution locality class (named area level): %s. Create new level instead."; |
|
| 2392 |
message = String.format(message, levelString); |
|
| 2393 |
fireWarningEvent(message, next, 6); |
|
| 2394 |
} |
|
| 2395 |
level = getNamedAreaLevel(state, levelUuid, levelString, levelString, levelString, null); |
|
| 2396 |
} |
|
| 2397 |
} catch (UndefinedTransformerMethodException e) {
|
|
| 2398 |
throw new RuntimeException(e); |
|
| 2399 |
} |
|
| 2400 |
return level; |
|
| 2401 |
} |
|
| 2133 | 2402 |
|
| 2134 | 2403 |
|
| 2135 | 2404 |
private String handleHeading(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
| ... | ... | |
| 2222 | 2491 |
} |
| 2223 | 2492 |
|
| 2224 | 2493 |
protected static final List<String> htmlList = Arrays.asList( |
| 2225 |
"sub", "sup", "ol", "ul", "i", "b", "table", "br"); |
|
| 2494 |
"sub", "sup", "ol", "ul", "li", "i", "b", "table", "br");
|
|
| 2226 | 2495 |
|
| 2227 | 2496 |
|
| 2228 | 2497 |
private boolean isHtml(XMLEvent event) {
|
Also available in: Unified diff
Update on Markup import