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10 package eu.etaxonomy.cdm.io.sdd;
11
12 import java.io.File;
13 import java.io.FileOutputStream;
14 import java.io.OutputStreamWriter;
15 import java.io.PrintWriter;
16 import java.util.HashSet;
17 import java.util.List;
18 import java.util.Set;
19
20 import org.apache.log4j.Logger;
21 import org.springframework.stereotype.Component;
22 import org.springframework.transaction.TransactionStatus;
23
24 import eu.etaxonomy.cdm.io.common.CdmExportBase;
25 import eu.etaxonomy.cdm.io.common.ICdmExport;
26 import eu.etaxonomy.cdm.io.common.IExportConfigurator;
27 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
28 import eu.etaxonomy.cdm.model.agent.AgentBase;
29 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
30 import eu.etaxonomy.cdm.model.common.RelationshipBase;
31 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
32 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
33 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
34 import eu.etaxonomy.cdm.model.taxon.Synonym;
35 import eu.etaxonomy.cdm.model.taxon.Taxon;
36 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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42
43 @Component("sddCdmExporter")
44 public class SDDCdmExporter extends CdmExportBase<SDDExportConfigurator, SDDExportState> implements ICdmExport<SDDExportConfigurator, SDDExportState> {
45
46
47
48 private static final Logger logger = Logger.getLogger(SDDCdmExporter.class);
49 private SDDDocumentBuilder sddDocumentBuilder = null;
50
51 private String ioName = null;
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56
57 public SDDCdmExporter() {
58 super();
59 this.ioName = this.getClass().getSimpleName();
60 }
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70 @Override
71 protected boolean doInvoke(SDDExportState state){
72
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75 SDDExportConfigurator sddExpConfig = state.getConfig();
76
77 String dbname = sddExpConfig.getSource() != null ? sddExpConfig.getSource().getName() : "unknown";
78 String fileName = sddExpConfig.getDestinationNameString();
79 logger.info("Serializing DB " + dbname + " to file " + fileName);
80 logger.debug("DbSchemaValidation = " + sddExpConfig.getDbSchemaValidation());
81
82 TransactionStatus txStatus = startTransaction(true);
83 SDDDataSet dataSet = new SDDDataSet();
84 List<Taxon> taxa = null;
85 List<DefinedTermBase> terms = null;
86
87
88
89 try {
90 logger.info("Retrieving data from DB");
91
92 retrieveData(sddExpConfig, dataSet);
93
94 } catch (Exception e) {
95 logger.error("Error retrieving data");
96 e.printStackTrace();
97 }
98
99 logger.info("All data retrieved");
100
101 try {
102 sddDocumentBuilder = new SDDDocumentBuilder();
103 File f = new File(fileName);
104
105 FileOutputStream fos = new FileOutputStream(f);
106 PrintWriter writer = new PrintWriter(new OutputStreamWriter(fos, "UTF8"), true);
107 sddDocumentBuilder.marshal(dataSet, f);
108
109
110
111 logger.info("XML file written");
112 logger.info("Filename is: " + fileName);
113
114 } catch (Exception e) {
115 logger.error("Marshalling error");
116 e.printStackTrace();
117 }
118 commitTransaction(txStatus);
119
120 return true;
121
122 }
123
124
125 private void retrieveData (IExportConfigurator config, SDDDataSet sddDataSet) {
126
127 SDDExportConfigurator sddExpConfig = (SDDExportConfigurator)config;
128 final int MAX_ROWS = 50000;
129 int numberOfRows = sddExpConfig.getMaxRows();
130
131
132
133 int agentRows = numberOfRows;
134 int definedTermBaseRows = numberOfRows;
135 int referenceBaseRows = numberOfRows;
136 int taxonNameBaseRows = numberOfRows;
137 int taxonBaseRows = numberOfRows;
138 int relationshipRows = numberOfRows;
139 int occurrencesRows = numberOfRows;
140 int mediaRows = numberOfRows;
141 int featureDataRows = numberOfRows;
142 int languageDataRows = numberOfRows;
143 int termVocabularyRows = numberOfRows;
144 int homotypicalGroupRows = numberOfRows;
145
146 if (sddExpConfig.isDoTermVocabularies() == true) {
147 if (termVocabularyRows == 0) { termVocabularyRows = MAX_ROWS; }
148 logger.info("# TermVocabulary");
149 sddDataSet.setTermVocabularies((List)getVocabularyService().list(null,MAX_ROWS, 0,null,null));;
150 }
151
152 if (sddExpConfig.isDoLanguageData() == true) {
153 if (languageDataRows == 0) { languageDataRows = MAX_ROWS; }
154 logger.info("# Representation, Language String");
155 sddDataSet.setLanguageData(getTermService().getAllRepresentations(MAX_ROWS, 0));
156 sddDataSet.addLanguageData(getTermService().getAllLanguageStrings(MAX_ROWS, 0));
157 }
158
159 if (sddExpConfig.isDoTerms() == true) {
160 if (definedTermBaseRows == 0) { definedTermBaseRows = getTermService().count(DefinedTermBase.class); }
161 logger.info("# DefinedTermBase: " + definedTermBaseRows);
162 sddDataSet.setTerms(getTermService().list(null,definedTermBaseRows, 0,null,null));
163 }
164
165 if (sddExpConfig.isDoAuthors() == true) {
166 if (agentRows == 0) { agentRows = getAgentService().count(AgentBase.class); }
167 logger.info("# Agents: " + agentRows);
168
169 sddDataSet.setAgents(getAgentService().list(null,agentRows, 0,null,null));
170 }
171
172 if (sddExpConfig.getDoReferences() != IImportConfigurator.DO_REFERENCES.NONE) {
173 if (referenceBaseRows == 0) { referenceBaseRows = getReferenceService().count(ReferenceBase.class); }
174 logger.info("# ReferenceBase: " + referenceBaseRows);
175 sddDataSet.setReferences(getReferenceService().list(null,referenceBaseRows, 0,null,null));
176 }
177
178 if (sddExpConfig.isDoTaxonNames() == true) {
179 if (taxonNameBaseRows == 0) { taxonNameBaseRows = getNameService().count(TaxonNameBase.class); }
180 logger.info("# TaxonNameBase: " + taxonNameBaseRows);
181
182 sddDataSet.setTaxonomicNames(getNameService().list(null,taxonNameBaseRows, 0,null,null));
183 }
184
185 if (sddExpConfig.isDoHomotypicalGroups() == true) {
186 if (homotypicalGroupRows == 0) { homotypicalGroupRows = MAX_ROWS; }
187 logger.info("# Homotypical Groups");
188 sddDataSet.setHomotypicalGroups(getNameService().getAllHomotypicalGroups(homotypicalGroupRows, 0));
189 }
190
191 if (sddExpConfig.isDoTaxa() == true) {
192 if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); }
193 logger.info("# TaxonBase: " + taxonBaseRows);
194
195
196 List<TaxonBase> tb = getTaxonService().list(null,taxonBaseRows, 0,null,null);
197 for (TaxonBase taxonBase : tb) {
198 if (taxonBase instanceof Taxon) {
199 sddDataSet.addTaxon((Taxon)taxonBase);
200 } else if (taxonBase instanceof Synonym) {
201 sddDataSet.addSynonym((Synonym)taxonBase);
202 } else {
203 logger.error("entry of wrong type: " + taxonBase.toString());
204 }
205 }
206 }
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214
215
216 if (sddExpConfig.isDoRelTaxa() == true) {
217 if (relationshipRows == 0) { relationshipRows = MAX_ROWS; }
218 logger.info("# Relationships");
219 List<RelationshipBase> relationList = getTaxonService().getAllRelationships(relationshipRows, 0);
220 Set<RelationshipBase> relationSet = new HashSet<RelationshipBase>(relationList);
221 sddDataSet.setRelationships(relationSet);
222 }
223
224 if (sddExpConfig.isDoReferencedEntities() == true) {
225 logger.info("# Referenced Entities");
226 sddDataSet.setReferencedEntities(getNameService().getAllNomenclaturalStatus(MAX_ROWS, 0));
227 sddDataSet.addReferencedEntities(getNameService().getAllTypeDesignations(MAX_ROWS, 0));
228 }
229
230 if (sddExpConfig.isDoOccurrence() == true) {
231 if (occurrencesRows == 0) { occurrencesRows = getOccurrenceService().count(SpecimenOrObservationBase.class); }
232 logger.info("# SpecimenOrObservationBase: " + occurrencesRows);
233 sddDataSet.setOccurrences(getOccurrenceService().list(null,occurrencesRows,0, null,null));
234 }
235
236 if (sddExpConfig.isDoMedia() == true) {
237 if (mediaRows == 0) { mediaRows = MAX_ROWS; }
238 logger.info("# Media");
239 sddDataSet.setMedia(getMediaService().list(null,mediaRows, 0,null,null));
240
241
242 }
243
244 if (sddExpConfig.isDoFeatureData() == true) {
245 if (featureDataRows == 0) { featureDataRows = MAX_ROWS; }
246 logger.info("# Feature Tree, Feature Node");
247 sddDataSet.setFeatureData(getFeatureTreeService().getFeatureNodesAll());
248 sddDataSet.addFeatureData(getFeatureTreeService().list(null,null,null,null,null));
249 }
250 }
251
252
253 @Override
254 protected boolean doCheck(SDDExportState state) {
255 boolean result = true;
256 logger.warn("No check implemented for Jaxb export");
257 return result;
258 }
259
260
261 @Override
262 protected boolean isIgnore(SDDExportState state) {
263 return false;
264 }
265
266 }