Revision f104a204
Added by Andreas Müller almost 2 years ago
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaVernacularExport.java | ||
---|---|---|
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.dwca.out; |
|
11 |
|
|
12 |
import java.io.FileNotFoundException; |
|
13 |
import java.io.IOException; |
|
14 |
import java.io.PrintWriter; |
|
15 |
import java.io.UnsupportedEncodingException; |
|
16 |
import java.util.Set; |
|
17 |
|
|
18 |
import org.apache.commons.lang.StringUtils; |
|
19 |
import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger; |
|
20 |
|
|
21 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
22 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
|
23 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
24 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
25 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
26 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
27 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
|
28 |
|
|
29 |
/** |
|
30 |
* @author a.mueller |
|
31 |
* @since 18.04.2011 |
|
32 |
*/ |
|
33 |
public class DwcaVernacularExport extends DwcaDataExportBase { |
|
34 |
private static final long serialVersionUID = 3169086545830374918L; |
|
35 |
|
|
36 |
private static final Logger logger = LogManager.getLogger(DwcaVernacularExport.class); |
|
37 |
|
|
38 |
private static final String ROW_TYPE = "http://rs.gbif.org/terms/1.0/VernacularName"; |
|
39 |
protected static final String fileName = "vernacular.txt"; |
|
40 |
|
|
41 |
private DwcaMetaDataRecord metaRecord; |
|
42 |
|
|
43 |
/** |
|
44 |
* Constructor |
|
45 |
*/ |
|
46 |
public DwcaVernacularExport(DwcaTaxExportState state) { |
|
47 |
super(); |
|
48 |
this.ioName = this.getClass().getSimpleName(); |
|
49 |
metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, ROW_TYPE); |
|
50 |
state.addMetaRecord(metaRecord); |
|
51 |
file = DwcaTaxExportFile.VERNACULAR; |
|
52 |
} |
|
53 |
|
|
54 |
@Override |
|
55 |
protected void doInvoke(DwcaTaxExportState state){} |
|
56 |
|
|
57 |
/** |
|
58 |
* {@inheritDoc} |
|
59 |
*/ |
|
60 |
@Override |
|
61 |
protected void handleTaxonNode(DwcaTaxExportState state, TaxonNode node) |
|
62 |
throws IOException, FileNotFoundException, UnsupportedEncodingException { |
|
63 |
|
|
64 |
try { |
|
65 |
DwcaTaxExportConfigurator config = state.getConfig(); |
|
66 |
Taxon taxon = CdmBase.deproxy(node.getTaxon()); |
|
67 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
|
68 |
for (TaxonDescription description : descriptions){ |
|
69 |
for (DescriptionElementBase el : description.getElements()){ |
|
70 |
if (el.isInstanceOf(CommonTaxonName.class)){ |
|
71 |
DwcaVernacularRecord record = new DwcaVernacularRecord(metaRecord, config); |
|
72 |
CommonTaxonName commonTaxonName = CdmBase.deproxy(el, CommonTaxonName.class); |
|
73 |
if (! state.recordExists(file, commonTaxonName)){ |
|
74 |
handleCommonTaxonName(state, record, commonTaxonName, taxon, config); |
|
75 |
PrintWriter writer = createPrintWriter(state, file); |
|
76 |
record.write(state, writer); |
|
77 |
state.addExistingRecord(file, commonTaxonName); |
|
78 |
} |
|
79 |
}else if (el.getFeature().equals(Feature.COMMON_NAME())){ |
|
80 |
//TODO |
|
81 |
String message = "Vernacular name export for TextData not yet implemented"; |
|
82 |
state.getResult().addError(message, this, "doInvoke()"); |
|
83 |
logger.warn(message); |
|
84 |
} |
|
85 |
} |
|
86 |
} |
|
87 |
|
|
88 |
} catch (Exception e) { |
|
89 |
String message = "Unexpected exception: " + e.getMessage(); |
|
90 |
state.getResult().addException(e, message); |
|
91 |
}finally{ |
|
92 |
flushWriter(state, file); |
|
93 |
} |
|
94 |
} |
|
95 |
|
|
96 |
|
|
97 |
|
|
98 |
|
|
99 |
private void handleCommonTaxonName(DwcaTaxExportState state, DwcaVernacularRecord record, CommonTaxonName commonTaxonName, Taxon taxon, DwcaTaxExportConfigurator config) { |
|
100 |
record.setId(taxon.getId()); |
|
101 |
record.setUuid(taxon.getUuid()); |
|
102 |
if (StringUtils.isBlank(commonTaxonName.getName())){ |
|
103 |
String message = "'Name' is required field for vernacular name but does not exist for taxon " + getTaxonLogString(taxon); |
|
104 |
state.getResult().addWarning(message); |
|
105 |
}else{ |
|
106 |
record.setVernacularName(commonTaxonName.getName()); |
|
107 |
} |
|
108 |
//sources |
|
109 |
record.setSource(getSources(commonTaxonName, config)); |
|
110 |
record.setLanguage(commonTaxonName.getLanguage()); |
|
111 |
// does not exist in CDM |
|
112 |
record.setTemporal(null); |
|
113 |
|
|
114 |
handleArea(state, record, commonTaxonName.getArea(), taxon, false); |
|
115 |
} |
|
116 |
|
|
117 |
@Override |
|
118 |
protected boolean doCheck(DwcaTaxExportState state) { |
|
119 |
boolean result = true; |
|
120 |
logger.warn("No check implemented for " + this.ioName); |
|
121 |
return result; |
|
122 |
} |
|
123 |
|
|
124 |
@Override |
|
125 |
public boolean isIgnore(DwcaTaxExportState state) { |
|
126 |
return ! state.getConfig().isDoVernacularNames(); |
|
127 |
} |
|
128 |
} |
|
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.dwca.out; |
|
11 |
|
|
12 |
import java.io.FileNotFoundException; |
|
13 |
import java.io.IOException; |
|
14 |
import java.io.PrintWriter; |
|
15 |
import java.io.UnsupportedEncodingException; |
|
16 |
import java.util.Set; |
|
17 |
|
|
18 |
import org.apache.commons.lang.StringUtils; |
|
19 |
import org.apache.logging.log4j.LogManager; |
|
20 |
import org.apache.logging.log4j.Logger; |
|
21 |
|
|
22 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
23 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
|
24 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
25 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
26 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
27 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
28 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
|
29 |
|
|
30 |
/** |
|
31 |
* @author a.mueller |
|
32 |
* @since 18.04.2011 |
|
33 |
*/ |
|
34 |
public class DwcaVernacularExport extends DwcaDataExportBase { |
|
35 |
private static final long serialVersionUID = 3169086545830374918L; |
|
36 |
|
|
37 |
private static final Logger logger = LogManager.getLogger(DwcaVernacularExport.class); |
|
38 |
|
|
39 |
private static final String ROW_TYPE = "http://rs.gbif.org/terms/1.0/VernacularName"; |
|
40 |
protected static final String fileName = "vernacular.txt"; |
|
41 |
|
|
42 |
private DwcaMetaDataRecord metaRecord; |
|
43 |
|
|
44 |
/** |
|
45 |
* Constructor |
|
46 |
*/ |
|
47 |
public DwcaVernacularExport(DwcaTaxExportState state) { |
|
48 |
super(); |
|
49 |
this.ioName = this.getClass().getSimpleName(); |
|
50 |
metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, ROW_TYPE); |
|
51 |
state.addMetaRecord(metaRecord); |
|
52 |
file = DwcaTaxExportFile.VERNACULAR; |
|
53 |
} |
|
54 |
|
|
55 |
@Override |
|
56 |
protected void doInvoke(DwcaTaxExportState state){} |
|
57 |
|
|
58 |
@Override |
|
59 |
protected void handleTaxonNode(DwcaTaxExportState state, TaxonNode node) |
|
60 |
throws IOException, FileNotFoundException, UnsupportedEncodingException { |
|
61 |
|
|
62 |
try { |
|
63 |
DwcaTaxExportConfigurator config = state.getConfig(); |
|
64 |
Taxon taxon = CdmBase.deproxy(node.getTaxon()); |
|
65 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
|
66 |
for (TaxonDescription description : descriptions){ |
|
67 |
for (DescriptionElementBase el : description.getElements()){ |
|
68 |
if (el.isInstanceOf(CommonTaxonName.class)){ |
|
69 |
DwcaVernacularRecord record = new DwcaVernacularRecord(metaRecord, config); |
|
70 |
CommonTaxonName commonTaxonName = CdmBase.deproxy(el, CommonTaxonName.class); |
|
71 |
if (! state.recordExists(file, commonTaxonName)){ |
|
72 |
handleCommonTaxonName(state, record, commonTaxonName, taxon, config); |
|
73 |
PrintWriter writer = createPrintWriter(state, file); |
|
74 |
record.write(state, writer); |
|
75 |
state.addExistingRecord(file, commonTaxonName); |
|
76 |
} |
|
77 |
}else if (el.getFeature().equals(Feature.COMMON_NAME())){ |
|
78 |
//TODO |
|
79 |
String message = "Vernacular name export for TextData not yet implemented"; |
|
80 |
state.getResult().addError(message, this, "doInvoke()"); |
|
81 |
logger.warn(message); |
|
82 |
} |
|
83 |
} |
|
84 |
} |
|
85 |
|
|
86 |
} catch (Exception e) { |
|
87 |
String message = "Unexpected exception: " + e.getMessage(); |
|
88 |
state.getResult().addException(e, message); |
|
89 |
}finally{ |
|
90 |
flushWriter(state, file); |
|
91 |
} |
|
92 |
} |
|
93 |
|
|
94 |
|
|
95 |
|
|
96 |
|
|
97 |
private void handleCommonTaxonName(DwcaTaxExportState state, DwcaVernacularRecord record, CommonTaxonName commonTaxonName, Taxon taxon, DwcaTaxExportConfigurator config) { |
|
98 |
record.setId(taxon.getId()); |
|
99 |
record.setUuid(taxon.getUuid()); |
|
100 |
if (StringUtils.isBlank(commonTaxonName.getName())){ |
|
101 |
String message = "'Name' is required field for vernacular name but does not exist for taxon " + getTaxonLogString(taxon); |
|
102 |
state.getResult().addWarning(message); |
|
103 |
}else{ |
|
104 |
record.setVernacularName(commonTaxonName.getName()); |
|
105 |
} |
|
106 |
//sources |
|
107 |
record.setSource(getSources(commonTaxonName, config)); |
|
108 |
record.setLanguage(commonTaxonName.getLanguage()); |
|
109 |
// does not exist in CDM |
|
110 |
record.setTemporal(null); |
|
111 |
|
|
112 |
handleArea(state, record, commonTaxonName.getArea(), taxon, false); |
|
113 |
} |
|
114 |
|
|
115 |
@Override |
|
116 |
protected boolean doCheck(DwcaTaxExportState state) { |
|
117 |
boolean result = true; |
|
118 |
logger.warn("No check implemented for " + this.ioName); |
|
119 |
return result; |
|
120 |
} |
|
121 |
|
|
122 |
@Override |
|
123 |
public boolean isIgnore(DwcaTaxExportState state) { |
|
124 |
return ! state.getConfig().isDoVernacularNames(); |
|
125 |
} |
|
126 |
} |
Also available in: Unified diff
cleanup