|
1
|
/**
|
|
2
|
* Copyright (C) 2016 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.greece;
|
|
10
|
|
|
11
|
import java.util.Arrays;
|
|
12
|
import java.util.List;
|
|
13
|
import java.util.Map;
|
|
14
|
import java.util.Set;
|
|
15
|
|
|
16
|
import org.apache.log4j.Logger;
|
|
17
|
import org.springframework.stereotype.Component;
|
|
18
|
|
|
19
|
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
|
|
20
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
21
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
22
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
23
|
import eu.etaxonomy.cdm.model.description.TextData;
|
|
24
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
25
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
|
26
|
|
|
27
|
/**
|
|
28
|
* Import for the Flora Hellenica taxon comments.
|
|
29
|
*
|
|
30
|
* @author a.mueller
|
|
31
|
* @since 14.12.2016
|
|
32
|
*/
|
|
33
|
|
|
34
|
@Component
|
|
35
|
public class FloraHellenicaCommentsImport<CONFIG extends FloraHellenicaImportConfigurator>
|
|
36
|
extends FloraHellenicaImportBase<CONFIG>{
|
|
37
|
|
|
38
|
private static final long serialVersionUID = -3565782012921316901L;
|
|
39
|
private static final Logger logger = Logger.getLogger(FloraHellenicaCommentsImport.class);
|
|
40
|
|
|
41
|
private static final String TAXON = "Taxon";
|
|
42
|
private static final String UNIQUE_ID_ACCEPTED = "Unique ID of taxon name (Includes valid and excluded taxa IDs)";
|
|
43
|
private static final String COMMENT = "Comment";
|
|
44
|
|
|
45
|
|
|
46
|
private static List<String> expectedKeys= Arrays.asList(new String[]{
|
|
47
|
UNIQUE_ID_ACCEPTED,
|
|
48
|
TAXON,
|
|
49
|
COMMENT
|
|
50
|
});
|
|
51
|
|
|
52
|
@Override
|
|
53
|
protected String getWorksheetName(CONFIG config) {
|
|
54
|
return "comments";
|
|
55
|
}
|
|
56
|
|
|
57
|
/**
|
|
58
|
* {@inheritDoc}
|
|
59
|
*/
|
|
60
|
@Override
|
|
61
|
protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
|
|
62
|
|
|
63
|
String line = state.getCurrentLine() + ": ";
|
|
64
|
Map<String, String> record = state.getOriginalRecord();
|
|
65
|
|
|
66
|
Set<String> keys = record.keySet();
|
|
67
|
for (String key: keys) {
|
|
68
|
if (! expectedKeys.contains(key)){
|
|
69
|
logger.warn(line + "Unexpected Key: " + key);
|
|
70
|
}
|
|
71
|
}
|
|
72
|
|
|
73
|
String noStr = getValue(record, "Unique ID");
|
|
74
|
makeComment(state, line, record, noStr);
|
|
75
|
}
|
|
76
|
|
|
77
|
|
|
78
|
/**
|
|
79
|
* @param state
|
|
80
|
* @param line
|
|
81
|
* @param record
|
|
82
|
* @param noStr
|
|
83
|
* @return
|
|
84
|
*/
|
|
85
|
private void makeComment(SimpleExcelTaxonImportState<CONFIG> state, String line,
|
|
86
|
Map<String, String> record,
|
|
87
|
String noStr) {
|
|
88
|
|
|
89
|
Taxon acceptedTaxon = getAcceptedTaxon(record, state, UNIQUE_ID_ACCEPTED);
|
|
90
|
if (acceptedTaxon == null){
|
|
91
|
logger.warn(line + "Accepted not found: " + record.get(UNIQUE_ID_ACCEPTED));
|
|
92
|
return;
|
|
93
|
}
|
|
94
|
|
|
95
|
String commentStr = getValue(record, COMMENT);
|
|
96
|
|
|
97
|
TaxonDescription desc = getTaxonDescription(acceptedTaxon);
|
|
98
|
TextData comment = TextData.NewInstance(Feature.NOTES(), commentStr, Language.ENGLISH(), null);
|
|
99
|
desc.addElement(comment);
|
|
100
|
comment.addImportSource(noStr, getWorksheetName(state.getConfig()), getSourceCitation(state), null);
|
|
101
|
getTaxonService().saveOrUpdate(acceptedTaxon);
|
|
102
|
|
|
103
|
TaxonNode taxonNode = acceptedTaxon.getTaxonNodes().iterator().next();
|
|
104
|
if(taxonNode.isExcluded()){
|
|
105
|
taxonNode.putExcludedNote(Language.ENGLISH(), commentStr);
|
|
106
|
}
|
|
107
|
return ;
|
|
108
|
}
|
|
109
|
|
|
110
|
}
|