|
1
|
package eu.etaxonomy.cdm.io.taxonx2013;
|
|
2
|
|
|
3
|
import eu.etaxonomy.cdm.common.URI;
|
|
4
|
import java.util.Map;
|
|
5
|
|
|
6
|
import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
|
|
7
|
import org.w3c.dom.Document;
|
|
8
|
import org.w3c.dom.Node;
|
|
9
|
import org.w3c.dom.NodeList;
|
|
10
|
|
|
11
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
12
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
13
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
|
14
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
15
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
|
16
|
|
|
17
|
public class TaxonXXMLFieldGetter {
|
|
18
|
|
|
19
|
private static final Logger logger = LogManager.getLogger(TaxonXXMLFieldGetter.class);
|
|
20
|
private final Document doc;
|
|
21
|
|
|
22
|
|
|
23
|
private final NomenclaturalCode nomenclaturalCode;
|
|
24
|
private Classification classification;
|
|
25
|
private final TaxonXImport importer;
|
|
26
|
private final TaxonXImportState taxonXstate;
|
|
27
|
private TaxonXModsExtractor modsextractor;
|
|
28
|
private TaxonXTreatmentExtractor treatmentextractor ;
|
|
29
|
|
|
30
|
public TaxonXXMLFieldGetter(TaxonXDataHolder dataholder, String prefix,Document document, TaxonXImport taxonXImport,
|
|
31
|
TaxonXImportState taxonXstate, Classification classif, Map<String,Feature> featuresMap){
|
|
32
|
this.doc = document;
|
|
33
|
this.importer = taxonXImport;
|
|
34
|
this.nomenclaturalCode = taxonXstate.getConfig().getNomenclaturalCode();
|
|
35
|
this.classification = classif;
|
|
36
|
logger.info("CLASSIFICATION "+classification);
|
|
37
|
this.taxonXstate=taxonXstate;
|
|
38
|
modsextractor = new TaxonXModsExtractor(importer);
|
|
39
|
Reference originalSourceUrl =taxonXstate.getConfig().getOriginalSourceURL();
|
|
40
|
treatmentextractor = new TaxonXTreatmentExtractor(nomenclaturalCode,classification,importer, taxonXstate,featuresMap,originalSourceUrl );
|
|
41
|
}
|
|
42
|
|
|
43
|
|
|
44
|
/**
|
|
45
|
* parse the Mods from the TaxonX file
|
|
46
|
*
|
|
47
|
*@return the created Reference object
|
|
48
|
**/
|
|
49
|
public Reference parseMods(){
|
|
50
|
// System.out.println("PARSEMODS");
|
|
51
|
//taxonx
|
|
52
|
Node root = doc.getFirstChild();
|
|
53
|
|
|
54
|
|
|
55
|
//taxonHeader, taxonBody
|
|
56
|
NodeList nodes = root.getChildNodes();
|
|
57
|
Reference ref = null;
|
|
58
|
for (int i=0; i< nodes.getLength();i++) {
|
|
59
|
// System.out.println(nodes.item(i).getNodeName());
|
|
60
|
if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxheader")){
|
|
61
|
NodeList nodes2 = nodes.item(i).getChildNodes();
|
|
62
|
for (int j=0; j< nodes2.getLength();j++){
|
|
63
|
if (nodes2.item(j).getNodeName().equalsIgnoreCase("mods:mods")){
|
|
64
|
ref = modsextractor.extractMods(nodes2.item(j));
|
|
65
|
importer.getReferenceService().saveOrUpdate(ref);
|
|
66
|
}
|
|
67
|
}
|
|
68
|
}
|
|
69
|
}
|
|
70
|
if (ref!=null) {
|
|
71
|
taxonXstate.getConfig().setClassificationName(ref.getCitation());
|
|
72
|
} else {
|
|
73
|
taxonXstate.getConfig().setClassificationName("no reference title");
|
|
74
|
}
|
|
75
|
ref=CdmBase.deproxy(ref, Reference.class);
|
|
76
|
return ref;
|
|
77
|
}
|
|
78
|
|
|
79
|
|
|
80
|
/**
|
|
81
|
* Foreach treatment section, launches the treatment "extractor"
|
|
82
|
* @param ref : the current reference, extracted from the mods
|
|
83
|
* @param sourcename: the URI of the TaxonX document
|
|
84
|
*/
|
|
85
|
public void parseTreatment(Reference ref, URI sourceName){
|
|
86
|
System.out.println("PARSETREATMENT "+ref);
|
|
87
|
//taxonx
|
|
88
|
Node root = doc.getFirstChild();
|
|
89
|
//taxonHeader, taxonBody
|
|
90
|
NodeList nodes = root.getChildNodes();
|
|
91
|
|
|
92
|
for ( int i=0; i< nodes.getLength();i++) {
|
|
93
|
// System.out.println(nodes.item(i).getNodeName());
|
|
94
|
if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxBody")){
|
|
95
|
NodeList nodes2 = nodes.item(i).getChildNodes();
|
|
96
|
for (int j=0; j< nodes2.getLength();j++){
|
|
97
|
if (nodes2.item(j).getNodeName().equalsIgnoreCase("tax:treatment")){
|
|
98
|
try {
|
|
99
|
treatmentextractor.extractTreatment(nodes2.item(j), ref,sourceName);
|
|
100
|
} catch (Exception e) {
|
|
101
|
logger.error("Unhandled exception occurred in treatment. Treatment not fully imported.");
|
|
102
|
e.printStackTrace();
|
|
103
|
}
|
|
104
|
}
|
|
105
|
}
|
|
106
|
}
|
|
107
|
}
|
|
108
|
}
|
|
109
|
|
|
110
|
|
|
111
|
|
|
112
|
/**
|
|
113
|
* updates the classification in the treatment extractor
|
|
114
|
* @param classification2
|
|
115
|
*/
|
|
116
|
public void updateClassification(Classification classification2) {
|
|
117
|
//System.out.println("UPDATECLASSIFICATIONS "+classification2);
|
|
118
|
classification=classification2;
|
|
119
|
if (treatmentextractor != null) {
|
|
120
|
treatmentextractor.updateClassification(classification);
|
|
121
|
}
|
|
122
|
|
|
123
|
}
|
|
124
|
|
|
125
|
|
|
126
|
/**
|
|
127
|
* @return
|
|
128
|
*/
|
|
129
|
public Map<String,Feature> getFeaturesUsed() {
|
|
130
|
return treatmentextractor.getFeaturesUsed();
|
|
131
|
}
|
|
132
|
|
|
133
|
|
|
134
|
}
|