|
1
|
/**
|
|
2
|
* Copyright (C) 2009 EDIT
|
|
3
|
* European Distributed Institute of Taxonomy
|
|
4
|
* http://www.e-taxonomy.eu
|
|
5
|
*
|
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
|
8
|
*/
|
|
9
|
package eu.etaxonomy.cdm.io.dwca.in;
|
|
10
|
|
|
11
|
import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
|
|
12
|
import org.springframework.stereotype.Component;
|
|
13
|
|
|
14
|
import eu.etaxonomy.cdm.common.URI;
|
|
15
|
import eu.etaxonomy.cdm.io.stream.CsvStream;
|
|
16
|
import eu.etaxonomy.cdm.io.stream.IPartitionableConverter;
|
|
17
|
import eu.etaxonomy.cdm.io.stream.IReader;
|
|
18
|
import eu.etaxonomy.cdm.io.stream.StreamItem;
|
|
19
|
import eu.etaxonomy.cdm.io.stream.terms.TermUri;
|
|
20
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
21
|
|
|
22
|
/**
|
|
23
|
* @author a.mueller
|
|
24
|
*/
|
|
25
|
@Component
|
|
26
|
public class DwcaImport
|
|
27
|
extends DwcaDataImportBase<DwcaImportConfigurator, DwcaImportState>{
|
|
28
|
|
|
29
|
private static final long serialVersionUID = -4340782092317841321L;
|
|
30
|
private static final Logger logger = LogManager.getLogger(DwcaImport.class);
|
|
31
|
|
|
32
|
@Override
|
|
33
|
protected void doInvoke(DwcaImportState state) {
|
|
34
|
URI source = state.getConfig().getSource();
|
|
35
|
makeSourceRef(state);
|
|
36
|
|
|
37
|
DwcaZipToStreamConverter<DwcaImportState> dwcaStreamConverter = DwcaZipToStreamConverter.NewInstance(source);
|
|
38
|
IReader<CsvStream> zipEntryStream = dwcaStreamConverter.getEntriesStream(state);
|
|
39
|
while (zipEntryStream.hasNext()){
|
|
40
|
CsvStream csvStream = zipEntryStream.read();
|
|
41
|
try {
|
|
42
|
handleSingleRecord(state, csvStream);
|
|
43
|
} catch (Exception e) {
|
|
44
|
String message = "Exception (%s) occurred while handling zip entry %s";
|
|
45
|
message = String.format(message, e.getMessage(), csvStream.toString());
|
|
46
|
fireWarningEvent (message, csvStream.toString(), 14);
|
|
47
|
}
|
|
48
|
}
|
|
49
|
if (!state.getConfig().isKeepMappingForFurtherImports()){
|
|
50
|
state.finish();
|
|
51
|
}
|
|
52
|
return;
|
|
53
|
}
|
|
54
|
|
|
55
|
@Override
|
|
56
|
protected IPartitionableConverter<StreamItem,IReader<CdmBase>, String>
|
|
57
|
getConverter(TermUri namespace, DwcaImportState state) {
|
|
58
|
|
|
59
|
if (namespace.equals(TermUri.DWC_TAXON)){
|
|
60
|
if (state.getConfig().isDoTaxa() && ! state.isTaxaCreated()){
|
|
61
|
return new DwcTaxonStreamItem2CdmTaxonConverter<>(state);
|
|
62
|
}else{
|
|
63
|
return new DwcTaxonCsv2CdmTaxonRelationConverter(state);
|
|
64
|
}
|
|
65
|
}else if (namespace.equals(TermUri.GBIF_VERNACULAR_NAMES)){
|
|
66
|
return new GbifVernacularNameCsv2CdmConverter(state);
|
|
67
|
}else if (namespace.equals(TermUri.GBIF_DESCRIPTION)){
|
|
68
|
return new GbifDescriptionCsv2CdmConverter(state);
|
|
69
|
}else if (namespace.equals(TermUri.GBIF_DISTRIBUTION)){
|
|
70
|
return new GbifDistributionCsv2CdmConverter(state);
|
|
71
|
}else if (namespace.equals(TermUri.GBIF_REFERENCE)){
|
|
72
|
return new GbifReferenceCsv2CdmConverter(state);
|
|
73
|
}else if (namespace.equals(TermUri.GBIF_TYPES_AND_SPECIMEN)){
|
|
74
|
return new GbifTypesAndSpecimen2CdmConverter(state);
|
|
75
|
}else if (namespace.equals(TermUri.EOL_AGENT)){
|
|
76
|
return new EolAgent2CdmConverter(state);
|
|
77
|
}else{
|
|
78
|
String message = "No converter available for %s";
|
|
79
|
logger.error(String.format(message, namespace));
|
|
80
|
return null;
|
|
81
|
}
|
|
82
|
}
|
|
83
|
|
|
84
|
|
|
85
|
@Override
|
|
86
|
protected boolean doCheck(DwcaImportState state) {
|
|
87
|
return state.isCheck();
|
|
88
|
}
|
|
89
|
|
|
90
|
@Override
|
|
91
|
protected boolean isIgnore(DwcaImportState state) {
|
|
92
|
return false;
|
|
93
|
}
|
|
94
|
|
|
95
|
|
|
96
|
}
|