Revision 76dce350
Added by Patrick Plitzner about 8 years ago
app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportConfigurator.java | ||
---|---|---|
36 | 36 |
@Override |
37 | 37 |
protected void makeIoClassList() { |
38 | 38 |
ioClassList = new Class[]{ |
39 |
// RedListGefaesspflanzenImportAuthor.class, |
|
40 |
// RedListGefaesspflanzenImportNames.class, |
|
41 |
RedListGefaesspflanzenImportTaxa.class, |
|
39 |
RedListGefaesspflanzenImportAuthor.class, |
|
40 |
RedListGefaesspflanzenImportNames.class, |
|
42 | 41 |
RedListGefaesspflanzenImportClassification.class, |
43 | 42 |
}; |
44 | 43 |
} |
app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
---|---|---|
31 | 31 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
32 | 32 |
import eu.etaxonomy.cdm.model.name.Rank; |
33 | 33 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
34 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
35 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
36 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
34 | 37 |
|
35 | 38 |
/** |
36 | 39 |
* |
... | ... | |
83 | 86 |
public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) { |
84 | 87 |
ResultSet rs = partitioner.getResultSet(); |
85 | 88 |
Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>(); |
89 |
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>(); |
|
86 | 90 |
try { |
87 | 91 |
while (rs.next()){ |
88 |
makeSingleName(state, rs, namesToSave);
|
|
92 |
makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave);
|
|
89 | 93 |
|
90 | 94 |
} |
91 | 95 |
} catch (SQLException e) { |
... | ... | |
93 | 97 |
} |
94 | 98 |
|
95 | 99 |
getNameService().saveOrUpdate(namesToSave); |
100 |
getTaxonService().saveOrUpdate(taxaToSave); |
|
96 | 101 |
return true; |
97 | 102 |
} |
98 | 103 |
|
99 |
private void makeSingleName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave)
|
|
104 |
private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
|
|
100 | 105 |
throws SQLException { |
101 | 106 |
long id = rs.getLong("NAMNR"); |
102 | 107 |
String taxNameString = rs.getString("TAXNAME"); |
108 |
String gueltString = rs.getString("GUELT"); |
|
103 | 109 |
String rangString = rs.getString("RANG"); |
104 | 110 |
String ep1String = rs.getString("EPI1"); |
105 | 111 |
String ep2String = rs.getString("EPI2"); |
... | ... | |
116 | 122 |
Rank rank = makeRank(state, rangString); |
117 | 123 |
if(rank==null){ |
118 | 124 |
logger.error("NAMNR: "+id+" Rank could not be resolved."); |
119 |
return; |
|
120 | 125 |
} |
121 | 126 |
BotanicalName name = BotanicalName.NewInstance(rank); |
122 | 127 |
|
... | ... | |
194 | 199 |
state.getNameMap().put(id, name.getUuid()); |
195 | 200 |
|
196 | 201 |
namesToSave.add(name); |
202 |
|
|
203 |
//---TAXON--- |
|
204 |
TaxonBase taxonBase = null; |
|
205 |
if(gueltString.equals("1")){ |
|
206 |
taxonBase = Taxon.NewInstance(name, null); |
|
207 |
} |
|
208 |
else if(gueltString.equals("x")){ |
|
209 |
taxonBase = Synonym.NewInstance(name, null); |
|
210 |
} |
|
211 |
else if(gueltString.equals("b")){ |
|
212 |
taxonBase = Synonym.NewInstance(name, null); |
|
213 |
} |
|
214 |
if(taxonBase==null){ |
|
215 |
logger.error("NAMNR: "+id+" Taxon for name "+name+" could not be created."); |
|
216 |
return; |
|
217 |
} |
|
218 |
|
|
219 |
taxaToSave.add(taxonBase); |
|
220 |
|
|
221 |
//id |
|
222 |
ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, Namespace.TAXON_NAMESPACE); |
|
223 |
state.getTaxonMap().put(id, taxonBase.getUuid()); |
|
197 | 224 |
} |
198 | 225 |
|
199 | 226 |
private Rank makeRank(RedListGefaesspflanzenImportState state, String rankStr) { |
app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportTaxa.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.redlist.gefaesspflanzen; |
|
11 |
|
|
12 |
import java.sql.ResultSet; |
|
13 |
import java.sql.SQLException; |
|
14 |
import java.util.HashMap; |
|
15 |
import java.util.HashSet; |
|
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.io.common.DbImportBase; |
|
23 |
import eu.etaxonomy.cdm.io.common.IPartitionedIO; |
|
24 |
import eu.etaxonomy.cdm.io.common.ImportHelper; |
|
25 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
|
26 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
27 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
|
28 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
29 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
30 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
31 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
32 |
|
|
33 |
/** |
|
34 |
* |
|
35 |
* @author pplitzner |
|
36 |
* @date Mar 1, 2016 |
|
37 |
* |
|
38 |
*/ |
|
39 |
|
|
40 |
@Component |
|
41 |
@SuppressWarnings("serial") |
|
42 |
public class RedListGefaesspflanzenImportTaxa extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> { |
|
43 |
|
|
44 |
private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportTaxa.class); |
|
45 |
|
|
46 |
private static final String tableName = "Rote Liste Gefäßpflanzen"; |
|
47 |
|
|
48 |
private static final String pluralString = "taxa"; |
|
49 |
|
|
50 |
public RedListGefaesspflanzenImportTaxa() { |
|
51 |
super(tableName, pluralString); |
|
52 |
} |
|
53 |
|
|
54 |
@Override |
|
55 |
protected String getIdQuery(RedListGefaesspflanzenImportState state) { |
|
56 |
return "SELECT NAMNR " |
|
57 |
+ "FROM V_TAXATLAS_D20_EXPORT t " |
|
58 |
+ " ORDER BY NAMNR"; |
|
59 |
} |
|
60 |
|
|
61 |
@Override |
|
62 |
protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) { |
|
63 |
String result = " SELECT * " |
|
64 |
+ " FROM V_TAXATLAS_D20_EXPORT t " |
|
65 |
+ " WHERE t.NAMNR IN (@IDSET)"; |
|
66 |
result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN); |
|
67 |
return result; |
|
68 |
} |
|
69 |
|
|
70 |
@Override |
|
71 |
protected void doInvoke(RedListGefaesspflanzenImportState state) { |
|
72 |
super.doInvoke(state); |
|
73 |
} |
|
74 |
|
|
75 |
@Override |
|
76 |
public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) { |
|
77 |
ResultSet rs = partitioner.getResultSet(); |
|
78 |
Set<TaxonBase> taxaToSave = new HashSet<>(); |
|
79 |
try { |
|
80 |
while (rs.next()){ |
|
81 |
makeSingleTaxon(state, rs, taxaToSave); |
|
82 |
|
|
83 |
} |
|
84 |
} catch (SQLException e) { |
|
85 |
e.printStackTrace(); |
|
86 |
} |
|
87 |
|
|
88 |
getTaxonService().saveOrUpdate(taxaToSave); |
|
89 |
return true; |
|
90 |
} |
|
91 |
|
|
92 |
private void makeSingleTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonBase> taxaToSave) |
|
93 |
throws SQLException { |
|
94 |
long id = rs.getLong("NAMNR"); |
|
95 |
String gueltString = rs.getString("GUELT"); |
|
96 |
|
|
97 |
// BotanicalName name = state.getRelatedObject(Namespace.NAME_NAMESPACE,String.valueOf(id), BotanicalName.class); |
|
98 |
BotanicalName name = BotanicalName.NewInstance(Rank.GENUS()); |
|
99 |
name.setGenusOrUninomial(String.valueOf(id)); |
|
100 |
|
|
101 |
TaxonBase taxonBase = null; |
|
102 |
if(gueltString.equals("1")){ |
|
103 |
taxonBase = Taxon.NewInstance(name, null); |
|
104 |
} |
|
105 |
else if(gueltString.equals("x")){ |
|
106 |
taxonBase = Synonym.NewInstance(name, null); |
|
107 |
} |
|
108 |
else if(gueltString.equals("b")){ |
|
109 |
taxonBase = Synonym.NewInstance(name, null); |
|
110 |
} |
|
111 |
if(taxonBase==null){ |
|
112 |
logger.error("NAMNR: "+id+" Taxon for name "+name+" could not be created."); |
|
113 |
return; |
|
114 |
} |
|
115 |
|
|
116 |
taxaToSave.add(taxonBase); |
|
117 |
|
|
118 |
//id |
|
119 |
ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, Namespace.TAXON_NAMESPACE); |
|
120 |
state.getTaxonMap().put(id, taxonBase.getUuid()); |
|
121 |
} |
|
122 |
|
|
123 |
@Override |
|
124 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, |
|
125 |
RedListGefaesspflanzenImportState state) { |
|
126 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
127 |
// Map<String, BotanicalName> nameMap = new HashMap<String, BotanicalName>(); |
|
128 |
// try { |
|
129 |
// while (rs.next()){ |
|
130 |
// long id = rs.getLong("NAMNR"); |
|
131 |
// nameMap.put(String.valueOf(id), (BotanicalName) getNameService().load(state.getNameMap().get(id))); |
|
132 |
// } |
|
133 |
// } catch (SQLException e) { |
|
134 |
// e.printStackTrace(); |
|
135 |
// } |
|
136 |
// result.put(Namespace.NAME_NAMESPACE, nameMap); |
|
137 |
|
|
138 |
return result; |
|
139 |
} |
|
140 |
|
|
141 |
@Override |
|
142 |
protected boolean doCheck(RedListGefaesspflanzenImportState state) { |
|
143 |
return false; |
|
144 |
} |
|
145 |
|
|
146 |
@Override |
|
147 |
protected boolean isIgnore(RedListGefaesspflanzenImportState state) { |
|
148 |
return false; |
|
149 |
} |
|
150 |
|
|
151 |
} |
Also available in: Unified diff
Unifiy name and taxon creation