Revision 43b37ce4
Added by Andreas Müller over 12 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupDocumentImport.java | ||
|---|---|---|
| 334 | 334 |
// "Start", 16); |
| 335 | 335 |
|
| 336 | 336 |
} |
| 337 |
|
|
| 337 |
|
|
| 338 | 338 |
return; |
| 339 | 339 |
|
| 340 | 340 |
} |
| ... | ... | |
| 421 | 421 |
|
| 422 | 422 |
} |
| 423 | 423 |
|
| 424 |
private void handleTreatment(MarkupImportState state, |
|
| 425 |
XMLEventReader reader, XMLEvent parentEvent) |
|
| 426 |
throws XMLStreamException {
|
|
| 424 |
private void handleTreatment(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 427 | 425 |
checkNoAttributes(parentEvent); |
| 428 | 426 |
Taxon lastTaxon = null; |
| 429 | 427 |
while (reader.hasNext()) {
|
| 430 | 428 |
XMLEvent next = readNoWhitespace(reader); |
| 431 | 429 |
if (isStartingElement(next, TAXON)) {
|
| 432 |
Taxon thisTaxon = handleTaxon(state, reader, |
|
| 433 |
next.asStartElement()); |
|
| 434 |
doTaxonRelation(state, thisTaxon, lastTaxon, |
|
| 435 |
parentEvent.getLocation()); |
|
| 430 |
Taxon thisTaxon = handleTaxon(state, reader, next.asStartElement()); |
|
| 431 |
doTaxonRelation(state, thisTaxon, lastTaxon, parentEvent.getLocation()); |
|
| 436 | 432 |
lastTaxon = thisTaxon; |
| 437 | 433 |
// TODO for imports spanning multiple documents ?? Still needed? |
| 438 | 434 |
state.getConfig().setLastTaxonUuid(lastTaxon.getUuid()); |
| 439 | 435 |
} else if (isMyEndingElement(next, parentEvent)) {
|
| 436 |
Set<PolytomousKeyNode> keyNodesToSave = state.getPolytomousKeyNodesToSave(); |
|
| 437 |
//better save the key then the nodes |
|
| 438 |
Set<PolytomousKey> keySet = new HashSet<PolytomousKey>(); |
|
| 439 |
for (PolytomousKeyNode node : keyNodesToSave){
|
|
| 440 |
PolytomousKey key = node.getKey(); |
|
| 441 |
keySet.add(key); |
|
| 442 |
} |
|
| 443 |
save(keySet, state); |
|
| 444 |
// save(keyNodesToSave, state); |
|
| 445 |
|
|
| 440 | 446 |
return; |
| 441 | 447 |
} else {
|
| 442 |
fireSchemaConflictEventExpectedStartTag(TAXON, reader); |
|
| 443 |
state.setUnsuccessfull(); |
|
| 448 |
handleUnexpectedElement(next); |
|
| 444 | 449 |
} |
| 445 | 450 |
} |
| 446 | 451 |
return; |
| ... | ... | |
| 513 | 518 |
|
| 514 | 519 |
private Classification createNewClassification(MarkupImportState state) {
|
| 515 | 520 |
Classification result; |
| 516 |
result = Classification.NewInstance(state.getConfig() |
|
| 517 |
.getClassificationTitle()); |
|
| 521 |
result = Classification.NewInstance(state.getConfig().getClassificationTitle()); |
|
| 518 | 522 |
state.putTree(null, result); |
| 519 | 523 |
return result; |
| 520 | 524 |
} |
| ... | ... | |
| 534 | 538 |
XMLEvent next = readNoWhitespace(reader); |
| 535 | 539 |
if (next.isEndElement()) {
|
| 536 | 540 |
if (isMyEndingElement(next, parentEvent)) {
|
| 537 |
|
|
| 538 | 541 |
checkMandatoryElement(hasTitle, parentEvent, TAXONTITLE); |
| 539 |
checkMandatoryElement(hasNomenclature, parentEvent, |
|
| 540 |
NOMENCLATURE); |
|
| 541 |
handleUnexpectedAttributes(parentEvent.getLocation(), |
|
| 542 |
attributes); |
|
| 543 |
|
|
| 542 |
checkMandatoryElement(hasNomenclature, parentEvent, NOMENCLATURE); |
|
| 543 |
handleUnexpectedAttributes(parentEvent.getLocation(),attributes); |
|
| 544 |
|
|
| 545 |
makeKeyNodes(state, parentEvent); |
|
| 544 | 546 |
state.setCurrentTaxon(null); |
| 547 |
state.setCurrentTaxonNum(null); |
|
| 545 | 548 |
save(taxon, state); |
| 546 | 549 |
return taxon; |
| 547 | 550 |
} else {
|
| ... | ... | |
| 614 | 617 |
handleUnexpectedElement(next); |
| 615 | 618 |
} |
| 616 | 619 |
} |
| 617 |
// TODO handle missing end element |
|
| 618 |
throw new IllegalStateException("Taxon has no closing tag");
|
|
| 620 |
throw new IllegalStateException("<Taxon> has no closing tag");
|
|
| 621 |
} |
|
| 622 |
|
|
| 623 |
private void makeKeyNodes(MarkupImportState state, XMLEvent event) {
|
|
| 624 |
Taxon taxon = state.getCurrentTaxon(); |
|
| 625 |
String num = state.getCurrentTaxonNum(); |
|
| 626 |
|
|
| 627 |
String nameString = CdmBase.deproxy(taxon.getName(), NonViralName.class).getNameCache(); |
|
| 628 |
|
|
| 629 |
//try to find matching lead nodes |
|
| 630 |
UnmatchedLeadsKey leadsKey = UnmatchedLeadsKey.NewInstance(num, nameString); |
|
| 631 |
Set<PolytomousKeyNode> matchingNodes = handleMatchingNodes(state, taxon, leadsKey); |
|
| 632 |
//same without using the num |
|
| 633 |
if (num != null){
|
|
| 634 |
UnmatchedLeadsKey noNumLeadsKey = UnmatchedLeadsKey.NewInstance("", nameString);
|
|
| 635 |
//TODO inform about differences |
|
| 636 |
handleMatchingNodes(state, taxon, noNumLeadsKey); |
|
| 637 |
} |
|
| 638 |
if (matchingNodes.isEmpty() && num != null){
|
|
| 639 |
String message = "Taxon has num in taxontitle but no matching nodes exist: %s, Key: %s"; |
|
| 640 |
message = String.format(message, num, leadsKey.toString()); |
|
| 641 |
fireWarningEvent(message, event, 1); |
|
| 642 |
} |
|
| 643 |
|
|
| 644 |
} |
|
| 645 |
|
|
| 646 |
private Set<PolytomousKeyNode> handleMatchingNodes(MarkupImportState state, Taxon taxon, UnmatchedLeadsKey leadsKey) {
|
|
| 647 |
Set<PolytomousKeyNode> matchingNodes = state.getUnmatchedLeads().getNodes(leadsKey); |
|
| 648 |
for (PolytomousKeyNode matchingNode : matchingNodes){
|
|
| 649 |
state.getUnmatchedLeads().removeNode(leadsKey, matchingNode); |
|
| 650 |
matchingNode.setTaxon(taxon); |
|
| 651 |
state.getPolytomousKeyNodesToSave().add(matchingNode); |
|
| 652 |
} |
|
| 653 |
return matchingNodes; |
|
| 619 | 654 |
} |
| 620 | 655 |
|
| 621 | 656 |
private void handleKey(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
| ... | ... | |
| 643 | 678 |
popUnimplemented(next.asEndElement()); |
| 644 | 679 |
} else if (next.isStartElement()) {
|
| 645 | 680 |
if (isStartingElement(next, KEY_TITLE)) {
|
| 646 |
String keyTitle = getCData(state, reader, next); |
|
| 647 |
if (isNotBlank(keyTitle)){
|
|
| 648 |
key.setTitleCache(keyTitle, true); |
|
| 649 |
} |
|
| 681 |
handleKeyTitle(state, reader, next); |
|
| 650 | 682 |
} else if (isStartingElement(next, KEYNOTES)) {
|
| 651 | 683 |
//TODO |
| 652 | 684 |
handleNotYetImplementedElement(next); |
| ... | ... | |
| 669 | 701 |
|
| 670 | 702 |
} |
| 671 | 703 |
|
| 672 |
private void handleCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode parentNode) throws XMLStreamException {
|
|
| 673 |
// attributes |
|
| 674 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
|
| 675 |
//TODO |
|
| 676 |
String num = getAndRemoveRequiredAttributeValue(parentEvent, attributes, NUM); |
|
| 704 |
/** |
|
| 705 |
* @param state |
|
| 706 |
* @param reader |
|
| 707 |
* @param key |
|
| 708 |
* @param next |
|
| 709 |
* @throws XMLStreamException |
|
| 710 |
*/ |
|
| 711 |
private void handleKeyTitle(MarkupImportState state, XMLEventReader reader, XMLEvent next) throws XMLStreamException {
|
|
| 712 |
PolytomousKey key = state.getCurrentKey(); |
|
| 713 |
String keyTitle = getCData(state, reader, next); |
|
| 714 |
String standardTitles = "(?i)(Key\\sto\\sthe\\s(genera|species|varieties|forms))"; |
|
| 677 | 715 |
|
| 716 |
if (isNotBlank(keyTitle) ){
|
|
| 717 |
if (!state.getConfig().isReplaceStandardKeyTitles() || ! keyTitle.matches(standardTitles)){
|
|
| 718 |
key.setTitleCache(keyTitle, true); |
|
| 719 |
} |
|
| 720 |
} |
|
| 721 |
} |
|
| 722 |
|
|
| 723 |
private void handleCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode parentNode) throws XMLStreamException {
|
|
| 724 |
String num = getOnlyAttribute(parentEvent, NUM, true); |
|
| 725 |
List<PolytomousKeyNode> childList = new ArrayList<PolytomousKeyNode>(); |
|
| 678 | 726 |
|
| 679 | 727 |
while (reader.hasNext()) {
|
| 680 | 728 |
XMLEvent next = readNoWhitespace(reader); |
| 681 | 729 |
if (isMyEndingElement(next, parentEvent)) {
|
| 730 |
completeCouplet(state, parentEvent, parentNode, num, childList); |
|
| 682 | 731 |
return; |
| 683 | 732 |
} else if (isEndingElement(next, KEYNOTES)){
|
| 684 | 733 |
popUnimplemented(next.asEndElement()); |
| 685 | 734 |
} else if (isStartingElement(next, QUESTION)) {
|
| 686 |
handleQuestion(state, reader, next, parentNode, num);
|
|
| 735 |
handleQuestion(state, reader, next, childList);
|
|
| 687 | 736 |
} else if (isStartingElement(next, KEYNOTES)) {
|
| 688 | 737 |
//TODO |
| 689 | 738 |
handleNotYetImplementedElement(next); |
| ... | ... | |
| 694 | 743 |
throw new IllegalStateException("<couplet> has no closing tag");
|
| 695 | 744 |
} |
| 696 | 745 |
|
| 697 |
private void handleQuestion(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode parentNode, String coupletNum) throws XMLStreamException {
|
|
| 746 |
/** |
|
| 747 |
* @param state |
|
| 748 |
* @param parentEvent |
|
| 749 |
* @param parentNode |
|
| 750 |
* @param num |
|
| 751 |
* @param childList |
|
| 752 |
*/ |
|
| 753 |
private void completeCouplet(MarkupImportState state, XMLEvent parentEvent, |
|
| 754 |
PolytomousKeyNode parentNode, String num, |
|
| 755 |
List<PolytomousKeyNode> childList) {
|
|
| 756 |
if (parentNode != null){
|
|
| 757 |
for (PolytomousKeyNode childNode : childList){
|
|
| 758 |
parentNode.addChild(childNode); |
|
| 759 |
} |
|
| 760 |
}else if (isNotBlank(num)){
|
|
| 761 |
UnmatchedLeadsKey unmatchedKey = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num); |
|
| 762 |
Set<PolytomousKeyNode> nodes = state.getUnmatchedLeads().getNodes(unmatchedKey); |
|
| 763 |
for(PolytomousKeyNode nodeToMatch: nodes){
|
|
| 764 |
for (PolytomousKeyNode childNode : childList){
|
|
| 765 |
nodeToMatch.addChild(childNode); |
|
| 766 |
} |
|
| 767 |
state.getUnmatchedLeads().removeNode(unmatchedKey, nodeToMatch); |
|
| 768 |
} |
|
| 769 |
}else{
|
|
| 770 |
String message = "Parent num could not be matched. Please check if num (%s) is correct"; |
|
| 771 |
message = String.format(message, num); |
|
| 772 |
fireWarningEvent(message, parentEvent, 6); |
|
| 773 |
} |
|
| 774 |
} |
|
| 775 |
|
|
| 776 |
private void handleQuestion(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, List<PolytomousKeyNode> nodesList) throws XMLStreamException {
|
|
| 698 | 777 |
// attributes |
| 699 | 778 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
| 700 | 779 |
//needed only for data lineage |
| 701 | 780 |
String questionNum = getAndRemoveRequiredAttributeValue(parentEvent, attributes, NUM); |
| 702 | 781 |
|
| 703 |
PolytomousKeyNode node = PolytomousKeyNode.NewInstance(); |
|
| 704 |
if (parentNode != null){
|
|
| 705 |
parentNode.addChild(node); |
|
| 706 |
}else if (isNotBlank(coupletNum)){
|
|
| 707 |
|
|
| 708 |
}else{
|
|
| 709 |
String message = "Parent num could not be determined. Please check if num (%s) is correct"; |
|
| 710 |
message = String.format(message, coupletNum); |
|
| 711 |
fireWarningEvent(message, parentEvent, 6); |
|
| 712 |
} |
|
| 782 |
PolytomousKeyNode myNode = PolytomousKeyNode.NewInstance(); |
|
| 783 |
myNode.setKey(state.getCurrentKey()); //to avoid NPE while computing num in PolytomousKeyNode in case this node is not matched correctly with a parent |
|
| 784 |
nodesList.add(myNode); |
|
| 713 | 785 |
|
| 714 | 786 |
while (reader.hasNext()) {
|
| 715 | 787 |
XMLEvent next = readNoWhitespace(reader); |
| 716 | 788 |
if (isMyEndingElement(next, parentEvent)) {
|
| 717 | 789 |
return; |
| 718 | 790 |
} else if (isEndingElement(next, TO_KEY)){
|
| 791 |
//TODO |
|
| 719 | 792 |
popUnimplemented(next.asEndElement()); |
| 720 | 793 |
} else if (isEndingElement(next, KEYNOTES)){
|
| 794 |
//TODO |
|
| 721 | 795 |
popUnimplemented(next.asEndElement()); |
| 722 | 796 |
|
| 723 | 797 |
} else if (isStartingElement(next, TEXT)) {
|
| 724 | 798 |
String text = getCData(state, reader, next); |
| 725 | 799 |
KeyStatement statement = KeyStatement.NewInstance(text); |
| 726 |
node.setStatement(statement);
|
|
| 800 |
myNode.setStatement(statement);
|
|
| 727 | 801 |
} else if (isStartingElement(next, COUPLET)) {
|
| 728 | 802 |
//TODO test |
| 729 |
handleCouplet(state, reader, next, node);
|
|
| 803 |
handleCouplet(state, reader, next, myNode);
|
|
| 730 | 804 |
} else if (isStartingElement(next, TO_COUPLET)) {
|
| 731 |
handleToCouplet(state, reader, next, node);
|
|
| 805 |
handleToCouplet(state, reader, next, myNode);
|
|
| 732 | 806 |
} else if (isStartingElement(next, TO_TAXON)) {
|
| 733 |
handleToTaxon(state, reader, next, node);
|
|
| 807 |
handleToTaxon(state, reader, next, myNode);
|
|
| 734 | 808 |
} else if (isStartingElement(next, TO_KEY)) {
|
| 735 | 809 |
//TODO |
| 736 | 810 |
handleNotYetImplementedElement(next); |
| ... | ... | |
| 742 | 816 |
} |
| 743 | 817 |
} |
| 744 | 818 |
throw new IllegalStateException("<question> has no closing tag");
|
| 745 |
|
|
| 746 | 819 |
} |
| 747 | 820 |
|
| 748 | 821 |
private void handleToCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent next, PolytomousKeyNode node) throws XMLStreamException {
|
| ... | ... | |
| 883 | 956 |
* @return |
| 884 | 957 |
* @throws XMLStreamException |
| 885 | 958 |
*/ |
| 886 |
private String makeNotesString(MarkupImportState state, XMLEventReader reader, String text, XMLEvent next) |
|
| 887 |
throws XMLStreamException {
|
|
| 959 |
private String makeNotesString(MarkupImportState state, XMLEventReader reader, String text, XMLEvent next) throws XMLStreamException {
|
|
| 888 | 960 |
Map<String, String> stringMap = handleString(state, reader, next); |
| 889 | 961 |
if (stringMap.size() == 0){
|
| 890 | 962 |
String message = "No text available in <notes>"; |
| ... | ... | |
| 973 | 1045 |
return nc; |
| 974 | 1046 |
} |
| 975 | 1047 |
|
| 976 |
private String handleTaxonTitle(MarkupImportState state, |
|
| 977 |
XMLEventReader reader, XMLEvent parentEvent) |
|
| 978 |
throws XMLStreamException {
|
|
| 1048 |
private String handleTaxonTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
|
|
| 1049 |
//attributes |
|
| 979 | 1050 |
String text = ""; |
| 980 | 1051 |
Map<String, Attribute> attributes = getAttributes(parentEvent); |
| 981 | 1052 |
String rankAttr = getAndRemoveAttributeValue(attributes, RANK); |
| 982 | 1053 |
Rank rank = makeRank(state, rankAttr, false); |
| 983 |
// TODO |
|
| 984 |
// String numAttr = getAndRemoveAttributeValue(attributes, NUM); |
|
| 985 |
handleNotYetImplementedAttribute(attributes, NUM); |
|
| 1054 |
String num = getAndRemoveAttributeValue(attributes, NUM); |
|
| 1055 |
state.setCurrentTaxonNum(num); |
|
| 986 | 1056 |
checkNoAttributes(attributes, parentEvent); |
| 987 | 1057 |
|
| 988 | 1058 |
// TODO handle attributes |
| ... | ... | |
| 995 | 1065 |
if (checkMandatoryText(text, parentEvent)) {
|
| 996 | 1066 |
titleText = normalize(text); |
| 997 | 1067 |
UUID uuidTitle = MarkupTransformer.uuidTaxonTitle; |
| 998 |
ExtensionType titleExtension = this.getExtensionType( |
|
| 999 |
state, uuidTitle, "Taxon Title ", |
|
| 1000 |
"taxon title", "title"); |
|
| 1068 |
ExtensionType titleExtension = this.getExtensionType(state, uuidTitle, "Taxon Title ","taxon title", "title"); |
|
| 1001 | 1069 |
taxon.addExtension(titleText, titleExtension); |
| 1002 | 1070 |
} |
| 1003 | 1071 |
taxon.getName().setRank(rank); |
| ... | ... | |
| 1658 | 1726 |
handleNotYetImplementedAttribute(attributes, LOST); |
| 1659 | 1727 |
} |
| 1660 | 1728 |
|
| 1661 |
NonViralName firstName = null; |
|
| 1729 |
NonViralName<?> firstName = null;
|
|
| 1662 | 1730 |
Set<TaxonNameBase> names = homotypicalGroup.getTypifiedNames(); |
| 1663 | 1731 |
if (names.isEmpty()) {
|
| 1664 | 1732 |
String message = "There is no name in a homotypical group. Can't create the specimen type"; |
| ... | ... | |
| 1733 | 1801 |
} |
| 1734 | 1802 |
} |
| 1735 | 1803 |
// TODO handle missing end element |
| 1736 |
throw new IllegalStateException("Specimen type has no closing tag"); // TODO
|
|
| 1737 |
// Auto-generated |
|
| 1738 |
// method |
|
| 1739 |
// stub |
|
| 1740 |
|
|
| 1804 |
throw new IllegalStateException("Specimen type has no closing tag");
|
|
| 1741 | 1805 |
} |
| 1742 | 1806 |
|
| 1743 | 1807 |
private void makeSpecimenType(MarkupImportState state, |
| ... | ... | |
| 1761 | 1825 |
DerivedUnitBase typeSpecimen = facade.addDuplicate(collection, |
| 1762 | 1826 |
null, null, null, null); |
| 1763 | 1827 |
typeSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy()); |
| 1764 |
name.addSpecimenTypeDesignation((Specimen) typeSpecimen, |
|
| 1765 |
typeStatus, null, null, null, false, addToAllNamesInGroup); |
|
| 1828 |
name.addSpecimenTypeDesignation((Specimen) typeSpecimen, typeStatus, null, null, null, false, addToAllNamesInGroup); |
|
| 1766 | 1829 |
} |
| 1767 |
|
|
| 1768 | 1830 |
} |
| 1769 | 1831 |
|
| 1770 | 1832 |
private Collection createCollection(String code) {
|
| ... | ... | |
| 1803 | 1865 |
return result; |
| 1804 | 1866 |
} |
| 1805 | 1867 |
|
| 1806 |
private void handleCollection(MarkupImportState state, |
|
| 1807 |
XMLEventReader reader, XMLEvent parentEvent, |
|
| 1808 |
HomotypicalGroup homotypicalGroup, DerivedUnitFacade facade) |
|
| 1868 |
|
|
| 1869 |
private void handleCollection(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, HomotypicalGroup homotypicalGroup, DerivedUnitFacade facade) |
|
| 1809 | 1870 |
throws XMLStreamException {
|
| 1810 | 1871 |
checkNoAttributes(parentEvent); |
| 1811 | 1872 |
boolean hasCollector = false; |
| ... | ... | |
| 1955 | 2016 |
|
| 1956 | 2017 |
} |
| 1957 | 2018 |
|
| 1958 |
private NamedArea createArea(String text, NamedAreaLevel areaLevel, |
|
| 1959 |
MarkupImportState state) {
|
|
| 2019 |
private NamedArea createArea(String text, NamedAreaLevel areaLevel, MarkupImportState state) {
|
|
| 1960 | 2020 |
NamedArea area = NamedArea.NewInstance(text, text, null); |
| 1961 | 2021 |
area.setLevel(areaLevel); |
| 1962 | 2022 |
save(area, state); |
| ... | ... | |
| 2629 | 2689 |
TextData textData = handleChar(state, reader, next); |
| 2630 | 2690 |
taxonDescription.addElement(textData); |
| 2631 | 2691 |
} else if (isStartingElement(next, STRING)) {
|
| 2632 |
lastDescriptionElement = makeFeatureString(state, reader, |
|
| 2633 |
feature, taxonDescription, lastDescriptionElement,next); |
|
| 2692 |
lastDescriptionElement = makeFeatureString(state, reader,feature, taxonDescription, lastDescriptionElement,next); |
|
| 2634 | 2693 |
} else if (isStartingElement(next, FIGURE_REF)) {
|
| 2635 |
lastDescriptionElement = makeFeatureFigureRef(state, reader, taxonDescription, isDescription, |
|
| 2636 |
lastDescriptionElement, next); |
|
| 2694 |
lastDescriptionElement = makeFeatureFigureRef(state, reader, taxonDescription, isDescription, lastDescriptionElement, next); |
|
| 2637 | 2695 |
} else if (isStartingElement(next, REFERENCES)) {
|
| 2638 | 2696 |
// TODO details/microcitation ?? |
| 2639 | 2697 |
|
| ... | ... | |
| 2727 | 2785 |
* @return |
| 2728 | 2786 |
* @throws XMLStreamException |
| 2729 | 2787 |
*/ |
| 2730 |
private DescriptionElementBase makeFeatureString(MarkupImportState state, |
|
| 2731 |
XMLEventReader reader, Feature feature, |
|
| 2732 |
TaxonDescription taxonDescription, |
|
| 2733 |
DescriptionElementBase lastDescriptionElement, XMLEvent next) |
|
| 2788 |
private DescriptionElementBase makeFeatureString(MarkupImportState state,XMLEventReader reader, Feature feature, |
|
| 2789 |
TaxonDescription taxonDescription, DescriptionElementBase lastDescriptionElement, XMLEvent next) |
|
| 2734 | 2790 |
throws XMLStreamException {
|
| 2735 | 2791 |
Map<String, String> subheadingMap = handleString(state, reader, next); |
| 2736 | 2792 |
for (String subheading : subheadingMap.keySet()) {
|
| ... | ... | |
| 3066 | 3122 |
while (reader.hasNext()) {
|
| 3067 | 3123 |
XMLEvent next = readNoWhitespace(reader); |
| 3068 | 3124 |
if (isMyEndingElement(next, parentEvent)) {
|
| 3069 |
if (StringUtils.isNotBlank(text)) {
|
|
| 3070 |
subHeadingMap.put(currentSubheading, text.trim()); |
|
| 3071 |
} |
|
| 3125 |
putCurrentSubheading(subHeadingMap, currentSubheading, text); |
|
| 3072 | 3126 |
return subHeadingMap; |
| 3127 |
} else if (isStartingElement(next, BR)) {
|
|
| 3128 |
text += "<br/>"; |
|
| 3129 |
isTextMode = false; |
|
| 3130 |
} else if (isEndingElement(next, BR)) {
|
|
| 3131 |
isTextMode = true; |
|
| 3073 | 3132 |
} else if (isHtml(next)) {
|
| 3074 | 3133 |
text += getXmlTag(next); |
| 3075 |
} else if (next.isEndElement()) {
|
|
| 3076 |
if (isEndingElement(next, ANNOTATION)) {
|
|
| 3077 |
popUnimplemented(next.asEndElement()); |
|
| 3078 |
} else if (isEndingElement(next, BR)) {
|
|
| 3079 |
isTextMode = true; |
|
| 3080 |
} else {
|
|
| 3081 |
handleUnexpectedEndElement(next.asEndElement()); |
|
| 3082 |
} |
|
| 3083 |
} else if (next.isStartElement()) {
|
|
| 3084 |
if (isStartingElement(next, SUB_HEADING)) {
|
|
| 3085 |
if (StringUtils.isNotBlank(text)) {
|
|
| 3086 |
subHeadingMap.put(currentSubheading, text.trim()); |
|
| 3087 |
text = ""; // reset |
|
| 3088 |
} |
|
| 3089 |
// TODO footnotes |
|
| 3090 |
currentSubheading = getCData(state, reader, next).trim(); |
|
| 3091 |
} else if (isStartingElement(next, ANNOTATION)) {
|
|
| 3092 |
handleNotYetImplementedElement(next); |
|
| 3093 |
} else if (isStartingElement(next, BR)) {
|
|
| 3094 |
text += "<br/>"; |
|
| 3095 |
isTextMode = false; |
|
| 3096 |
} else {
|
|
| 3097 |
handleUnexpectedStartElement(next.asStartElement()); |
|
| 3098 |
} |
|
| 3134 |
} else if (isStartingElement(next, SUB_HEADING)) {
|
|
| 3135 |
text = putCurrentSubheading(subHeadingMap,currentSubheading, text); |
|
| 3136 |
// TODO footnotes |
|
| 3137 |
currentSubheading = getCData(state, reader, next).trim(); |
|
| 3099 | 3138 |
} else if (next.isCharacters()) {
|
| 3100 | 3139 |
if (!isTextMode) {
|
| 3101 | 3140 |
String message = "String is not in text mode"; |
| ... | ... | |
| 3103 | 3142 |
} else {
|
| 3104 | 3143 |
text += next.asCharacters().getData(); |
| 3105 | 3144 |
} |
| 3145 |
} else if (isStartingElement(next, COLLECTION)) {
|
|
| 3146 |
//TODO |
|
| 3147 |
handleNotYetImplementedElement(next); |
|
| 3148 |
} else if (isEndingElement(next, COLLECTION)) {
|
|
| 3149 |
//TODO |
|
| 3150 |
popUnimplemented(next.asEndElement()); |
|
| 3151 |
} else if (isStartingElement(next, ANNOTATION)) {
|
|
| 3152 |
//TODO |
|
| 3153 |
handleNotYetImplementedElement(next); |
|
| 3154 |
} else if (isEndingElement(next, ANNOTATION)) {
|
|
| 3155 |
//TODO |
|
| 3156 |
popUnimplemented(next.asEndElement()); |
|
| 3106 | 3157 |
} else {
|
| 3107 |
handleUnexpectedEndElement(next.asEndElement());
|
|
| 3158 |
handleUnexpectedElement(next);
|
|
| 3108 | 3159 |
} |
| 3109 | 3160 |
} |
| 3110 | 3161 |
throw new IllegalStateException("<String> has no closing tag");
|
| 3162 |
} |
|
| 3111 | 3163 |
|
| 3164 |
/** |
|
| 3165 |
* @param subHeadingMap |
|
| 3166 |
* @param currentSubheading |
|
| 3167 |
* @param text |
|
| 3168 |
* @return |
|
| 3169 |
*/ |
|
| 3170 |
private String putCurrentSubheading(Map<String, String> subHeadingMap, String currentSubheading, String text) {
|
|
| 3171 |
if (StringUtils.isNotBlank(text)) {
|
|
| 3172 |
text = removeStartingMinus(text); |
|
| 3173 |
subHeadingMap.put(currentSubheading, text.trim()); |
|
| 3174 |
} |
|
| 3175 |
return ""; |
|
| 3112 | 3176 |
} |
| 3113 | 3177 |
|
| 3178 |
private String removeStartingMinus(String string) {
|
|
| 3179 |
string = replaceStart(string, "-"); |
|
| 3180 |
string = replaceStart(string, "\u002d"); |
|
| 3181 |
string = replaceStart(string, "\u2013"); |
|
| 3182 |
string = replaceStart(string, "\u2014"); |
|
| 3183 |
string = replaceStart(string, "--"); |
|
| 3184 |
return string; |
|
| 3185 |
} |
|
| 3186 |
|
|
| 3187 |
/** |
|
| 3188 |
* @param value |
|
| 3189 |
* @param replacementString |
|
| 3190 |
*/ |
|
| 3191 |
private String replaceStart(String value, String replacementString) {
|
|
| 3192 |
if (value.startsWith(replacementString) ){
|
|
| 3193 |
value = value.substring(replacementString.length()).trim(); |
|
| 3194 |
} |
|
| 3195 |
while (value.startsWith("-") || value.startsWith("\u2014") ){
|
|
| 3196 |
value = value.substring("-".length()).trim();
|
|
| 3197 |
} |
|
| 3198 |
return value; |
|
| 3199 |
} |
|
| 3200 |
|
|
| 3114 | 3201 |
private String getXmlTag(XMLEvent event) {
|
| 3115 | 3202 |
String result; |
| 3116 | 3203 |
if (event.isStartElement()) {
|
Also available in: Unified diff
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