|
1
|
/**
|
|
2
|
* Copyright (C) 2007 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
|
|
|
10
|
package eu.etaxonomy.cdm.io;
|
|
11
|
|
|
12
|
import java.net.URI;
|
|
13
|
import java.net.URISyntaxException;
|
|
14
|
import java.util.HashSet;
|
|
15
|
import java.util.List;
|
|
16
|
import java.util.Map;
|
|
17
|
import java.util.Set;
|
|
18
|
|
|
19
|
import org.apache.log4j.Logger;
|
|
20
|
import org.springframework.stereotype.Component;
|
|
21
|
|
|
22
|
import eu.etaxonomy.cdm.app.images.AbstractImageImporter;
|
|
23
|
import eu.etaxonomy.cdm.app.images.ImageImportState;
|
|
24
|
import eu.etaxonomy.cdm.common.ExcelUtils;
|
|
25
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
26
|
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
|
|
27
|
import eu.etaxonomy.cdm.model.description.TextData;
|
|
28
|
import eu.etaxonomy.cdm.model.media.Media;
|
|
29
|
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
|
|
30
|
import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
|
|
31
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
|
32
|
|
|
33
|
/**
|
|
34
|
* @author n.hoffmann
|
|
35
|
* @since 19.11.2008
|
|
36
|
*/
|
|
37
|
@Component
|
|
38
|
public class PalmaeProtologueImport extends AbstractImageImporter {
|
|
39
|
private static final long serialVersionUID = -7178567387220714414L;
|
|
40
|
|
|
41
|
private static final Logger logger = Logger.getLogger(PalmaeProtologueImport.class);
|
|
42
|
|
|
43
|
public static final String SPECIES = "Species";
|
|
44
|
public static final String TAXONID = "Taxon ID";
|
|
45
|
public static final String LINK_PROTO = "Link proto";
|
|
46
|
|
|
47
|
@Override
|
|
48
|
protected void invokeImageImport(ImageImportState state) {
|
|
49
|
|
|
50
|
List<Map<String, String>> contents;
|
|
51
|
try {
|
|
52
|
contents = ExcelUtils.parseXLS(state.getConfig().getSource());
|
|
53
|
} catch (/*FileNotFound*/Exception e) {
|
|
54
|
logger.error("FileNotFound: " + state.getConfig().getSource().toString());
|
|
55
|
state.setUnsuccessfull();
|
|
56
|
return;
|
|
57
|
}
|
|
58
|
|
|
59
|
Set<TaxonName> taxonNameStore = new HashSet<>();
|
|
60
|
|
|
61
|
int count = 0;
|
|
62
|
|
|
63
|
for (Map<String, String> row : contents){
|
|
64
|
count++;
|
|
65
|
|
|
66
|
TaxonName taxonNameBase = null;
|
|
67
|
String species = null;
|
|
68
|
String taxonId = null;
|
|
69
|
String linkProto = null;
|
|
70
|
try{
|
|
71
|
species = row.get(PalmaeProtologueImport.SPECIES).trim();
|
|
72
|
taxonId = row.get(PalmaeProtologueImport.TAXONID);
|
|
73
|
linkProto= row.get(PalmaeProtologueImport.LINK_PROTO).trim();
|
|
74
|
taxonNameBase = getCommonService().getSourcedObjectByIdInSource(TaxonName.class, "palm_tn_" + taxonId.replace(".0", ""), "TaxonName");
|
|
75
|
}catch (Exception e){
|
|
76
|
logger.error("The row has errors: rowNumber: " +count + ", content: " + row, e);
|
|
77
|
}
|
|
78
|
|
|
79
|
if(taxonNameBase == null){
|
|
80
|
logger.warn("no taxon with this name found: " + species + ", idInSource: " + taxonId);
|
|
81
|
}else{
|
|
82
|
|
|
83
|
URI uri;
|
|
84
|
try {
|
|
85
|
uri = new URI(linkProto);
|
|
86
|
MediaRepresentationPart representationPart = MediaRepresentationPart.NewInstance(uri, 0);
|
|
87
|
MediaRepresentation representation = MediaRepresentation.NewInstance("text/html", null);
|
|
88
|
representation.addRepresentationPart(representationPart);
|
|
89
|
|
|
90
|
Media media = Media.NewInstance();
|
|
91
|
media.addRepresentation(representation);
|
|
92
|
|
|
93
|
TaxonNameDescription description = TaxonNameDescription.NewInstance();
|
|
94
|
TextData protolog = TextData.NewInstance(Feature.PROTOLOGUE());
|
|
95
|
protolog.addMedia(media);
|
|
96
|
description.addElement(protolog);
|
|
97
|
taxonNameBase.addDescription(description);
|
|
98
|
} catch (URISyntaxException e) {
|
|
99
|
String message= "URISyntaxException when trying to convert: " + linkProto;
|
|
100
|
logger.error(message);
|
|
101
|
e.printStackTrace();
|
|
102
|
}
|
|
103
|
|
|
104
|
taxonNameStore.add(taxonNameBase);
|
|
105
|
if(count % 50 == 0){
|
|
106
|
logger.info(count + " protologues processed.");
|
|
107
|
}
|
|
108
|
}
|
|
109
|
}
|
|
110
|
|
|
111
|
getNameService().save(taxonNameStore);
|
|
112
|
logger.info(count + " protologues imported to CDM store.");
|
|
113
|
|
|
114
|
return;
|
|
115
|
}
|
|
116
|
|
|
117
|
}
|