1 |
bab4ff0b
|
Andreas Müller
|
/**
|
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;
|
11 |
|
|
|
12 |
|
|
import java.sql.ResultSet;
|
13 |
|
|
import java.sql.SQLException;
|
14 |
|
|
import java.sql.Timestamp;
|
15 |
|
|
import java.util.HashMap;
|
16 |
|
|
import java.util.HashSet;
|
17 |
|
|
import java.util.Map;
|
18 |
|
|
import java.util.Set;
|
19 |
|
|
import java.util.UUID;
|
20 |
|
|
|
21 |
|
|
import org.apache.log4j.Logger;
|
22 |
|
|
import org.joda.time.DateTime;
|
23 |
|
|
|
24 |
|
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
25 |
|
|
import eu.etaxonomy.cdm.io.common.CdmImportBase;
|
26 |
|
|
import eu.etaxonomy.cdm.io.common.ICdmIO;
|
27 |
|
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
|
28 |
|
|
import eu.etaxonomy.cdm.io.common.IPartitionedIO;
|
29 |
|
|
import eu.etaxonomy.cdm.io.common.ImportHelper;
|
30 |
|
|
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
|
31 |
|
|
import eu.etaxonomy.cdm.io.common.Source;
|
32 |
|
|
import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
|
33 |
|
|
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
|
34 |
|
|
import eu.etaxonomy.cdm.model.common.Annotation;
|
35 |
|
|
import eu.etaxonomy.cdm.model.common.AnnotationType;
|
36 |
|
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
37 |
|
|
import eu.etaxonomy.cdm.model.common.ExtensionType;
|
38 |
|
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
39 |
|
|
import eu.etaxonomy.cdm.model.common.Language;
|
40 |
|
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
41 |
|
|
import eu.etaxonomy.cdm.model.common.User;
|
42 |
|
|
|
43 |
|
|
/**
|
44 |
|
|
* @author a.mueller
|
45 |
|
|
* @created 27.08.2012
|
46 |
|
|
* @version 1.0
|
47 |
|
|
*/
|
48 |
|
|
public abstract class RoteListeDbImportBase<CDM_BASE extends CdmBase> extends CdmImportBase<RoteListeDbImportConfigurator, RoteListeDbImportState> implements ICdmIO<RoteListeDbImportState>, IPartitionedIO<RoteListeDbImportState> {
|
49 |
|
|
private static final Logger logger = Logger.getLogger(RoteListeDbImportBase.class);
|
50 |
|
|
|
51 |
|
|
|
52 |
|
|
private String pluralString;
|
53 |
|
|
private String dbTableName;
|
54 |
|
|
//TODO needed?
|
55 |
|
|
private Class cdmTargetClass;
|
56 |
|
|
|
57 |
|
|
|
58 |
|
|
|
59 |
|
|
|
60 |
|
|
/**
|
61 |
|
|
* @param dbTableName
|
62 |
|
|
* @param dbTableName2
|
63 |
|
|
*/
|
64 |
|
|
public RoteListeDbImportBase(String pluralString, String dbTableName, Class cdmTargetClass) {
|
65 |
|
|
this.pluralString = pluralString;
|
66 |
|
|
this.dbTableName = dbTableName;
|
67 |
|
|
this.cdmTargetClass = cdmTargetClass;
|
68 |
|
|
}
|
69 |
|
|
|
70 |
|
|
protected void doInvoke(RoteListeDbImportState state){
|
71 |
|
|
logger.info("start make " + getPluralString() + " ...");
|
72 |
|
|
RoteListeDbImportConfigurator config = state.getConfig();
|
73 |
|
|
Source source = config.getSource();
|
74 |
|
|
|
75 |
|
|
String strIdQuery = getIdQuery();
|
76 |
|
|
String strRecordQuery = getRecordQuery(config);
|
77 |
|
|
|
78 |
|
|
int recordsPerTransaction = config.getRecordsPerTransaction();
|
79 |
|
|
try{
|
80 |
|
|
ResultSetPartitioner partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery, strRecordQuery, recordsPerTransaction);
|
81 |
|
|
while (partitioner.nextPartition()){
|
82 |
|
|
partitioner.doPartition(this, state);
|
83 |
|
|
}
|
84 |
|
|
} catch (SQLException e) {
|
85 |
|
|
logger.error("SQLException:" + e);
|
86 |
|
|
state.setUnsuccessfull();
|
87 |
|
|
return;
|
88 |
|
|
}
|
89 |
|
|
|
90 |
|
|
logger.info("end make " + getPluralString() + " ... " + getSuccessString(true));
|
91 |
|
|
return;
|
92 |
|
|
}
|
93 |
|
|
|
94 |
|
|
public boolean doPartition(ResultSetPartitioner partitioner, RoteListeDbImportState state) {
|
95 |
|
|
boolean success = true ;
|
96 |
|
|
Set objectsToSave = new HashSet();
|
97 |
|
|
|
98 |
|
|
DbImportMapping<?, ?> mapping = getMapping();
|
99 |
|
|
mapping.initialize(state, cdmTargetClass);
|
100 |
|
|
|
101 |
|
|
ResultSet rs = partitioner.getResultSet();
|
102 |
|
|
try{
|
103 |
|
|
while (rs.next()){
|
104 |
|
|
success &= mapping.invoke(rs,objectsToSave);
|
105 |
|
|
}
|
106 |
|
|
} catch (SQLException e) {
|
107 |
|
|
logger.error("SQLException:" + e);
|
108 |
|
|
return false;
|
109 |
|
|
}
|
110 |
|
|
|
111 |
|
|
partitioner.startDoSave();
|
112 |
|
|
getCommonService().save(objectsToSave);
|
113 |
|
|
return success;
|
114 |
|
|
}
|
115 |
|
|
|
116 |
|
|
|
117 |
|
|
|
118 |
|
|
/**
|
119 |
|
|
* @return
|
120 |
|
|
*/
|
121 |
|
|
protected abstract DbImportMapping<?, ?> getMapping();
|
122 |
|
|
|
123 |
|
|
/**
|
124 |
|
|
* @return
|
125 |
|
|
*/
|
126 |
|
|
protected abstract String getRecordQuery(RoteListeDbImportConfigurator config);
|
127 |
|
|
|
128 |
|
|
/**
|
129 |
|
|
* @return
|
130 |
|
|
*/
|
131 |
|
|
protected String getIdQuery(){
|
132 |
|
|
String result = " SELECT id FROM " + getTableName();
|
133 |
|
|
return result;
|
134 |
|
|
}
|
135 |
|
|
|
136 |
|
|
/* (non-Javadoc)
|
137 |
|
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getPluralString()
|
138 |
|
|
*/
|
139 |
|
|
public String getPluralString(){
|
140 |
|
|
return pluralString;
|
141 |
|
|
}
|
142 |
|
|
|
143 |
|
|
/**
|
144 |
|
|
* @return
|
145 |
|
|
*/
|
146 |
|
|
protected String getTableName(){
|
147 |
|
|
return this.dbTableName;
|
148 |
|
|
}
|
149 |
|
|
|
150 |
|
|
protected boolean doIdCreatedUpdatedNotes(RoteListeDbImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace)
|
151 |
|
|
throws SQLException{
|
152 |
|
|
boolean success = true;
|
153 |
|
|
//id
|
154 |
|
|
success &= ImportHelper.setOriginalSource(identifiableEntity, state.getConfig().getSourceReference(), id, namespace);
|
155 |
|
|
//createdUpdateNotes
|
156 |
|
|
success &= doCreatedUpdatedNotes(state, identifiableEntity, rs, namespace);
|
157 |
|
|
return success;
|
158 |
|
|
}
|
159 |
|
|
|
160 |
|
|
|
161 |
|
|
protected boolean doCreatedUpdatedNotes(RoteListeDbImportState state, AnnotatableEntity annotatableEntity, ResultSet rs, String namespace)
|
162 |
|
|
throws SQLException{
|
163 |
|
|
|
164 |
|
|
RoteListeDbImportConfigurator config = state.getConfig();
|
165 |
|
|
Object createdWhen = rs.getObject("Created_When");
|
166 |
|
|
String createdWho = rs.getString("Created_Who");
|
167 |
|
|
Object updatedWhen = null;
|
168 |
|
|
String updatedWho = null;
|
169 |
|
|
try {
|
170 |
|
|
updatedWhen = rs.getObject("Updated_When");
|
171 |
|
|
updatedWho = rs.getString("Updated_who");
|
172 |
|
|
} catch (SQLException e) {
|
173 |
|
|
//Table "Name" has no updated when/who
|
174 |
|
|
}
|
175 |
|
|
String notes = rs.getString("notes");
|
176 |
|
|
|
177 |
|
|
boolean success = true;
|
178 |
|
|
|
179 |
|
|
//Created When, Who, Updated When Who
|
180 |
|
|
if (config.getEditor() == null || config.getEditor().equals(EDITOR.NO_EDITORS)){
|
181 |
|
|
//do nothing
|
182 |
|
|
}else if (config.getEditor().equals(EDITOR.EDITOR_AS_ANNOTATION)){
|
183 |
|
|
String createdAnnotationString = "Berlin Model record was created By: " + String.valueOf(createdWho) + " (" + String.valueOf(createdWhen) + ") ";
|
184 |
|
|
if (updatedWhen != null && updatedWho != null){
|
185 |
|
|
createdAnnotationString += " and updated By: " + String.valueOf(updatedWho) + " (" + String.valueOf(updatedWhen) + ")";
|
186 |
|
|
}
|
187 |
|
|
Annotation annotation = Annotation.NewInstance(createdAnnotationString, Language.DEFAULT());
|
188 |
|
|
annotation.setCommentator(config.getCommentator());
|
189 |
|
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
190 |
|
|
annotatableEntity.addAnnotation(annotation);
|
191 |
|
|
}else if (config.getEditor().equals(EDITOR.EDITOR_AS_EDITOR)){
|
192 |
|
|
User creator = getUser(createdWho, state);
|
193 |
|
|
User updator = getUser(updatedWho, state);
|
194 |
|
|
DateTime created = getDateTime(createdWhen);
|
195 |
|
|
DateTime updated = getDateTime(updatedWhen);
|
196 |
|
|
annotatableEntity.setCreatedBy(creator);
|
197 |
|
|
annotatableEntity.setUpdatedBy(updator);
|
198 |
|
|
annotatableEntity.setCreated(created);
|
199 |
|
|
annotatableEntity.setUpdated(updated);
|
200 |
|
|
}else {
|
201 |
|
|
logger.warn("Editor type not yet implemented: " + config.getEditor());
|
202 |
|
|
}
|
203 |
|
|
|
204 |
|
|
|
205 |
|
|
//notes
|
206 |
|
|
if (CdmUtils.isNotEmpty(notes)){
|
207 |
|
|
String notesString = String.valueOf(notes);
|
208 |
|
|
if (notesString.length() > 65530 ){
|
209 |
|
|
notesString = notesString.substring(0, 65530) + "...";
|
210 |
|
|
logger.warn("Notes string is longer than 65530 and was truncated: " + annotatableEntity);
|
211 |
|
|
}
|
212 |
|
|
Annotation notesAnnotation = Annotation.NewInstance(notesString, null);
|
213 |
|
|
//notesAnnotation.setAnnotationType(AnnotationType.EDITORIAL());
|
214 |
|
|
//notes.setCommentator(bmiConfig.getCommentator());
|
215 |
|
|
annotatableEntity.addAnnotation(notesAnnotation);
|
216 |
|
|
}
|
217 |
|
|
return success;
|
218 |
|
|
}
|
219 |
|
|
|
220 |
|
|
|
221 |
|
|
private User getUser(String createdWho, RoteListeDbImportState state) {
|
222 |
|
|
//not relevant here, for users see ERMS import
|
223 |
|
|
return null;
|
224 |
|
|
}
|
225 |
|
|
|
226 |
|
|
private DateTime getDateTime(Object timeString){
|
227 |
|
|
if (timeString == null){
|
228 |
|
|
return null;
|
229 |
|
|
}
|
230 |
|
|
DateTime dateTime = null;
|
231 |
|
|
if (timeString instanceof Timestamp){
|
232 |
|
|
Timestamp timestamp = (Timestamp)timeString;
|
233 |
|
|
dateTime = new DateTime(timestamp);
|
234 |
|
|
}else{
|
235 |
|
|
logger.warn("time ("+timeString+") is not a timestamp. Datetime set to current date. ");
|
236 |
|
|
dateTime = new DateTime();
|
237 |
|
|
}
|
238 |
|
|
return dateTime;
|
239 |
|
|
}
|
240 |
|
|
|
241 |
|
|
|
242 |
|
|
/**
|
243 |
|
|
* Returns a map that holds all values of a ResultSet. This is needed if a value needs to
|
244 |
|
|
* be accessed twice
|
245 |
|
|
* @param rs
|
246 |
|
|
* @return
|
247 |
|
|
* @throws SQLException
|
248 |
|
|
*/
|
249 |
|
|
protected Map<String, Object> getValueMap(ResultSet rs) throws SQLException{
|
250 |
|
|
try{
|
251 |
|
|
Map<String, Object> valueMap = new HashMap<String, Object>();
|
252 |
|
|
int colCount = rs.getMetaData().getColumnCount();
|
253 |
|
|
for (int c = 0; c < colCount ; c++){
|
254 |
|
|
Object value = rs.getObject(c+1);
|
255 |
|
|
String label = rs.getMetaData().getColumnLabel(c+1).toLowerCase();
|
256 |
|
|
if (value != null && ! CdmUtils.Nz(value.toString()).trim().equals("")){
|
257 |
|
|
valueMap.put(label, value);
|
258 |
|
|
}
|
259 |
|
|
}
|
260 |
|
|
return valueMap;
|
261 |
|
|
}catch(SQLException e){
|
262 |
|
|
throw e;
|
263 |
|
|
}
|
264 |
|
|
}
|
265 |
|
|
|
266 |
|
|
protected ExtensionType getExtensionType(UUID uuid, String label, String text, String labelAbbrev){
|
267 |
|
|
ExtensionType extensionType = (ExtensionType)getTermService().find(uuid);
|
268 |
|
|
if (extensionType == null){
|
269 |
|
|
extensionType = ExtensionType.NewInstance(text, label, labelAbbrev);
|
270 |
|
|
extensionType.setUuid(uuid);
|
271 |
|
|
getTermService().save(extensionType);
|
272 |
|
|
}
|
273 |
|
|
return extensionType;
|
274 |
|
|
}
|
275 |
|
|
|
276 |
|
|
protected MarkerType getMarkerType(UUID uuid, String label, String text, String labelAbbrev){
|
277 |
|
|
MarkerType markerType = (MarkerType)getTermService().find(uuid);
|
278 |
|
|
if (markerType == null){
|
279 |
|
|
markerType = MarkerType.NewInstance(label, text, labelAbbrev);
|
280 |
|
|
markerType.setUuid(uuid);
|
281 |
|
|
getTermService().save(markerType);
|
282 |
|
|
}
|
283 |
|
|
return markerType;
|
284 |
|
|
}
|
285 |
|
|
|
286 |
|
|
|
287 |
|
|
/**
|
288 |
|
|
* Reads a foreign key field from the result set and adds its value to the idSet.
|
289 |
|
|
* @param rs
|
290 |
|
|
* @param teamIdSet
|
291 |
|
|
* @throws SQLException
|
292 |
|
|
*/
|
293 |
|
|
protected void handleForeignKey(ResultSet rs, Set<String> idSet, String attributeName)
|
294 |
|
|
throws SQLException {
|
295 |
|
|
Object idObj = rs.getObject(attributeName);
|
296 |
|
|
if (idObj != null){
|
297 |
|
|
String id = String.valueOf(idObj);
|
298 |
|
|
idSet.add(id);
|
299 |
|
|
}
|
300 |
|
|
}
|
301 |
|
|
|
302 |
|
|
/**
|
303 |
|
|
* Returns true if i is a multiple of recordsPerTransaction
|
304 |
|
|
* @param i
|
305 |
|
|
* @param recordsPerTransaction
|
306 |
|
|
* @return
|
307 |
|
|
*/
|
308 |
|
|
protected boolean loopNeedsHandling(int i, int recordsPerLoop) {
|
309 |
|
|
startTransaction();
|
310 |
|
|
return (i % recordsPerLoop) == 0;
|
311 |
|
|
}
|
312 |
|
|
|
313 |
|
|
protected void doLogPerLoop(int count, int recordsPerLog, String pluralString){
|
314 |
|
|
if ((count % recordsPerLog ) == 0 && count!= 0 ){ logger.info(pluralString + " handled: " + (count));}
|
315 |
|
|
}
|
316 |
|
|
|
317 |
|
|
|
318 |
|
|
|
319 |
|
|
|
320 |
|
|
}
|