Revision ad3ad9e0
Added by Andreas Kohlbecker over 12 years ago
- ID ad3ad9e0f0560d0bb782836297c4ffe39b2625c8
- Parent 55d84577
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java | ||
|---|---|---|
| 109 | 109 |
private Map<String,String> locations = new HashMap<String,String>(); |
| 110 | 110 |
private Map<String,List<CdmBase>> mediaObject_ListCdmBase = new HashMap<String,List<CdmBase>>(); |
| 111 | 111 |
private Map<String,String> mediaObject_Role = new HashMap<String,String>(); |
| 112 |
private Map<String,Reference> publications = new HashMap<String,Reference>();
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|
| 112 |
private Map<String,Reference<?>> publications = new HashMap<String,Reference<?>>();
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|
| 113 | 113 |
private Map<String,State> states = new HashMap<String,State>(); |
| 114 | 114 |
private Map<String,TaxonDescription> taxonDescriptions = new HashMap<String,TaxonDescription>(); |
| 115 |
private Map<String,NonViralName> taxonNameBases = new HashMap<String,NonViralName>();
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|
| 115 |
private Map<String,NonViralName<?>> taxonNameBases = new HashMap<String,NonViralName<?>>();
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|
| 116 | 116 |
private Map<String,MeasurementUnit> units = new HashMap<String,MeasurementUnit>(); |
| 117 | 117 |
private Map<String,TaxonNode> taxonNodes = new HashMap<String,TaxonNode>(); |
| 118 | 118 |
private Map<String,NamedArea> namedAreas = new HashMap<String,NamedArea>(); |
| ... | ... | |
| 120 | 120 |
private Map<String,Modifier> modifiers = new HashMap<String,Modifier>(); |
| 121 | 121 |
|
| 122 | 122 |
private Set<MarkerType> markerTypes = new HashSet<MarkerType>(); |
| 123 |
private Set<TermVocabulary> vocabularies = new HashSet<TermVocabulary>();
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|
| 123 |
private Set<TermVocabulary<?>> vocabularies = new HashSet<TermVocabulary<?>>();
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|
| 124 | 124 |
|
| 125 | 125 |
private Set<Feature> descriptiveConcepts = new HashSet<Feature>(); |
| 126 | 126 |
private Set<AnnotationType> annotationTypes = new HashSet<AnnotationType>(); |
| 127 | 127 |
// private Set<Feature> featureSet = new HashSet<Feature>(); |
| 128 |
private Set<Reference> sources = new HashSet<Reference>();
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|
| 129 |
private Reference sec = ReferenceFactory.newDatabase(); |
|
| 130 |
private Reference sourceReference = null; |
|
| 128 |
private Set<Reference<?>> sources = new HashSet<Reference<?>>();
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|
| 129 |
private Reference<?> sec = ReferenceFactory.newDatabase();
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|
| 130 |
private Reference<?> sourceReference = null;
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|
| 131 | 131 |
|
| 132 | 132 |
private Language datasetLanguage = null; |
| 133 | 133 |
private WorkingSet workingSet = null; |
| ... | ... | |
| 177 | 177 |
// <TechnicalMetadata created="2006-04-20T10:00:00"> |
| 178 | 178 |
importTechnicalMetadata(root, sddNamespace, sddConfig); |
| 179 | 179 |
List<Element> elDatasets = root.getChildren("Dataset",sddNamespace);
|
| 180 |
int i = 0; |
|
| 180 |
// int i = 0;
|
|
| 181 | 181 |
|
| 182 | 182 |
//for each Dataset |
| 183 | 183 |
logger.info("start Dataset ...");
|
| ... | ... | |
| 389 | 389 |
if (StringUtils.isNotBlank(ref)) {
|
| 390 | 390 |
if (ve instanceof TaxonDescription) {
|
| 391 | 391 |
TaxonDescription td = (TaxonDescription) ve; |
| 392 |
if (td.getDescriptionSources().size() > 0) {
|
|
| 393 |
this.associateImageWithCdmBase(ref,(Reference) td.getDescriptionSources().toArray()[0]);
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|
| 392 |
if (td.getSources().size() > 0) {
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|
| 393 |
this.associateImageWithCdmBase(ref, td.getSources().iterator().next().getCitation());
|
|
| 394 | 394 |
} else {
|
| 395 |
Reference descriptionSource = ReferenceFactory.newGeneric(); |
|
| 395 |
Reference<?> descriptionSource = ReferenceFactory.newGeneric();
|
|
| 396 | 396 |
sources.add(descriptionSource); |
| 397 |
td.addDescriptionSource(descriptionSource);
|
|
| 397 |
td.addSource(null, null, descriptionSource, null);
|
|
| 398 | 398 |
this.associateImageWithCdmBase(ref,descriptionSource); |
| 399 | 399 |
} |
| 400 | 400 |
} else {
|
| ... | ... | |
| 618 | 618 |
location.setAnnotationType(annotationType); |
| 619 | 619 |
(publication).addAnnotation(location); |
| 620 | 620 |
} |
| 621 |
td.addDescriptionSource(publication);
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|
| 621 |
td.addSource(null, null,publication, null);
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|
| 622 | 622 |
} |
| 623 | 623 |
} |
| 624 | 624 |
logger.info("end makeTaxonDescriptions ...");
|
| ... | ... | |
| 632 | 632 |
} |
| 633 | 633 |
saveFeatures(); |
| 634 | 634 |
|
| 635 |
for (Reference publication : publications.values()){
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|
| 635 |
for (Reference<?> publication : publications.values()){
|
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| 636 | 636 |
getReferenceService().save(publication); |
| 637 | 637 |
} |
| 638 | 638 |
|
| 639 |
for (Reference source : sources){
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|
| 639 |
for (Reference<?> source : sources){
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|
| 640 | 640 |
getReferenceService().save(source); |
| 641 | 641 |
} |
| 642 | 642 |
|
| ... | ... | |
| 659 | 659 |
* |
| 660 | 660 |
*/ |
| 661 | 661 |
private void saveVocabularies() {
|
| 662 |
for (TermVocabulary vocabulary : vocabularies ){
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|
| 662 |
for (TermVocabulary<?> vocabulary : vocabularies ){
|
|
| 663 | 663 |
getVocabularyService().save(vocabulary); |
| 664 | 664 |
} |
| 665 | 665 |
|
| ... | ... | |
| 749 | 749 |
Element elSpecimens = elDataset.getChild("Specimens",sddNamespace);
|
| 750 | 750 |
if (elSpecimens != null){
|
| 751 | 751 |
List<Element> listSpecimens = elSpecimens.getChildren("Specimen", sddNamespace);
|
| 752 |
int j = 0; |
|
| 753 | 752 |
for (Element elSpecimen : listSpecimens) {
|
| 754 | 753 |
String id = elSpecimen.getAttributeValue("id");
|
| 755 | 754 |
Specimen specimen = null; |
| ... | ... | |
| 881 | 880 |
String id = elTaxonName.getAttributeValue("id");
|
| 882 | 881 |
String uri = elTaxonName.getAttributeValue("uri");
|
| 883 | 882 |
|
| 884 |
NonViralName tnb = null; |
|
| 883 |
NonViralName<?> tnb = null;
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|
| 885 | 884 |
if (!id.equals("")) {
|
| 886 | 885 |
tnb = NonViralName.NewInstance(null); |
| 887 | 886 |
IdentifiableSource source = null; |
| ... | ... | |
| 1188 | 1187 |
*/ |
| 1189 | 1188 |
private Taxon handleCDNoScope(Namespace sddNamespace, SDDImportState cdmState, Element elCodedDescription ) {
|
| 1190 | 1189 |
Taxon taxon = null; |
| 1191 |
NonViralName nonViralName = NonViralName.NewInstance(null); |
|
| 1190 |
NonViralName<?> nonViralName = NonViralName.NewInstance(null);
|
|
| 1192 | 1191 |
String id = new String("" + taxonNamesCount);
|
| 1193 | 1192 |
IdentifiableSource source = IdentifiableSource.NewInstance(id, "TaxonName"); |
| 1194 | 1193 |
importRepresentation(elCodedDescription, sddNamespace, nonViralName, id, cdmState); |
| ... | ... | |
| 1225 | 1224 |
Taxon taxon = null; |
| 1226 | 1225 |
Element elTaxonName = elScope.getChild("TaxonName", sddNamespace);
|
| 1227 | 1226 |
String ref = elTaxonName.getAttributeValue("ref");
|
| 1228 |
NonViralName nonViralName = taxonNameBases.get(ref); |
|
| 1227 |
NonViralName<?> nonViralName = taxonNameBases.get(ref);
|
|
| 1229 | 1228 |
|
| 1230 | 1229 |
if(cdmState.getConfig().isDoMatchTaxa()){
|
| 1231 | 1230 |
taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache()); |
| ... | ... | |
| 1508 | 1507 |
try {
|
| 1509 | 1508 |
|
| 1510 | 1509 |
String idP = elPublication.getAttributeValue("id");
|
| 1511 |
Reference publication = ReferenceFactory.newArticle(); |
|
| 1510 |
Reference<?> publication = ReferenceFactory.newArticle();
|
|
| 1512 | 1511 |
importRepresentation(elPublication, sddNamespace, publication, idP, cdmState); |
| 1513 | 1512 |
|
| 1514 | 1513 |
publications.put(idP,publication); |
| ... | ... | |
| 1585 | 1584 |
if (lcb != null) {
|
| 1586 | 1585 |
for (int k = 0; k < lcb.size(); k++) {
|
| 1587 | 1586 |
if (lcb.get(k) instanceof DefinedTermBase) {
|
| 1588 |
DefinedTermBase dtb = (DefinedTermBase) lcb.get(k);
|
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| 1587 |
DefinedTermBase<?> dtb = (DefinedTermBase<?>) lcb.get(k);
|
|
| 1589 | 1588 |
// if (lcb.get(0) instanceof DefinedTermBase) {
|
| 1590 | 1589 |
// DefinedTermBase dtb = (DefinedTermBase) lcb.get(0); |
| 1591 | 1590 |
// if (dtb!=null) {
|
| ... | ... | |
| 1598 | 1597 |
// } |
| 1599 | 1598 |
// } |
| 1600 | 1599 |
} else if (lcb.get(k) instanceof Reference) {
|
| 1601 |
Reference rb = (Reference) lcb.get(k);
|
|
| 1600 |
Reference<?> rb = (Reference<?>) lcb.get(k);
|
|
| 1602 | 1601 |
//} else if (lcb.get(0) instanceof Reference) {
|
| 1603 | 1602 |
//Reference rb = (Reference) lcb.get(0); |
| 1604 | 1603 |
// rb.setTitleCache(label); |
| ... | ... | |
| 1859 | 1858 |
Classification classification = Classification.NewInstance(label); |
| 1860 | 1859 |
importRepresentation(elTaxonHierarchy, sddNamespace, classification, "", cdmState); |
| 1861 | 1860 |
|
| 1862 |
Set<TaxonNode> root = classification.getChildNodes(); |
|
| 1863 | 1861 |
Element elNodes = elTaxonHierarchy.getChild("Nodes", sddNamespace); // There can be only one <Nodes> block for TaxonHierarchies
|
| 1864 | 1862 |
List<Element> listNodes = elNodes.getChildren("Node", sddNamespace);
|
| 1865 | 1863 |
|
| 1866 | 1864 |
for (Element elNode : listNodes){
|
| 1867 | 1865 |
String idN = elNode.getAttributeValue("id");
|
| 1868 |
TaxonNameBase tnb = null; |
|
| 1866 |
TaxonNameBase<?,?> tnb = null;
|
|
| 1869 | 1867 |
if (!idN.equals("")) {
|
| 1870 | 1868 |
Element elTaxonName = elNode.getChild("TaxonName", sddNamespace);
|
| 1871 | 1869 |
String refTN = elTaxonName.getAttributeValue("ref");
|
Also available in: Unified diff
Merging r13295 through r13325 from trunk