Revision 67426b79
Added by Andreas Müller over 3 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiDestinations.java | ||
|---|---|---|
| 23 | 23 |
|
| 24 | 24 |
public static Source pesi_test_local_CDM_EM2PESI(){
|
| 25 | 25 |
String dbms = Source.SQL_SERVER_2008; |
| 26 |
String strServer = "localhost";
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|
| 26 |
String strServer = "pesiimport3";
|
|
| 27 | 27 |
String strDB = "CDM_EM2PESI"; |
| 28 | 28 |
int port = 1433; |
| 29 |
String userName = "pesiexport";// "pesiexport3";
|
|
| 29 |
String userName = "pesi2019";// "pesiexport3";
|
|
| 30 | 30 |
return makeSource(dbms, strServer, strDB, port, userName, null); |
| 31 | 31 |
} |
| 32 | 32 |
|
| 33 |
public static Source pesi_test_local_CDM_EM2PESI_tmp(){
|
|
| 33 |
public static Source pesi_test_local_CDM_EM2PESI_2(){
|
|
| 34 | 34 |
String dbms = Source.SQL_SERVER_2008; |
| 35 |
String strServer = "localhost";
|
|
| 36 |
String strDB = "CDMTMP_EM2PESI";
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|
| 35 |
String strServer = "pesiimport3";
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| 36 |
String strDB = "CDM_EM2PESI_2";
|
|
| 37 | 37 |
int port = 1433; |
| 38 |
String userName = "pesiexport";
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| 38 |
String userName = "pesi2019";
|
|
| 39 | 39 |
return makeSource(dbms, strServer, strDB, port, userName, null); |
| 40 | 40 |
} |
| 41 | 41 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivatorEM.java | ||
|---|---|---|
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.Source; |
| 20 | 20 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportConfigurator; |
| 21 | 21 |
import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer; |
| 22 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 23 | 22 |
|
| 24 | 23 |
/** |
| 25 | 24 |
* @author a.mueller |
| ... | ... | |
| 30 | 29 |
@SuppressWarnings("unused")
|
| 31 | 30 |
private static final Logger logger = Logger.getLogger(PesiExportActivatorEM.class); |
| 32 | 31 |
|
| 33 |
static final ICdmDataSource cdmSource = CdmDestinations.test_cdm_pesi_euroMed(); |
|
| 32 |
// static final ICdmDataSource cdmSource = CdmDestinations.test_cdm_pesi_euroMed(); |
|
| 33 |
static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql_euromed(); |
|
| 34 | 34 |
|
| 35 | 35 |
//database validation status (create, update, validate ...) |
| 36 | 36 |
static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_EM2PESI(); |
| 37 |
// static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_FE2PESI(); |
|
| 38 |
// static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI(); |
|
| 39 |
|
|
| 40 |
//Taxon names can't be mapped to their CDM ids as PESI Taxon table mainly holds taxa and there IDs. We ad nameIdStart to the TaxonName id to get a unique id |
|
| 41 |
static final int nameIdStart = 10000000; |
|
| 42 |
static final IdType idType = IdType.CDM_ID_WITH_EXCEPTIONS; |
|
| 43 |
|
|
| 44 |
static final int partitionSize = 1000; |
|
| 45 |
|
|
| 46 |
//check - export |
|
| 47 |
static final CHECK check = CHECK.EXPORT_WITHOUT_CHECK; |
|
| 48 |
|
|
| 49 |
//NomenclaturalCode |
|
| 50 |
static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP; |
|
| 51 |
|
|
| 52 |
static final boolean deleteAll = true; |
|
| 53 |
|
|
| 37 |
// static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_EM2PESI_2(); |
|
| 54 | 38 |
|
| 55 | 39 |
// ****************** ALL ***************************************** |
| 56 | 40 |
|
| 57 |
//references |
|
| 58 |
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 41 |
boolean deleteAll = false; |
|
| 42 |
DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
|
| 43 |
boolean doTaxa = true; |
|
| 44 |
boolean doTaxaPhase1 = true; //better do not use, Phase1 is needed in Phase3 |
|
| 45 |
boolean doPureNames = true; |
|
| 46 |
boolean doTreeIndex = true; |
|
| 47 |
boolean doParentAndBiota = true; |
|
| 48 |
boolean doInferredSynonyms = false; //no inferred synonyms in E+M |
|
| 49 |
boolean doRelTaxa = true; |
|
| 50 |
boolean doAdditionalTaxonSource = true; |
|
| 51 |
boolean doDescriptions = true; |
|
| 52 |
boolean doEcologyAndLink = true; |
|
| 59 | 53 |
|
| 60 |
//taxa |
|
| 61 |
static final boolean doTaxa = true; |
|
| 62 |
static final boolean doPureNames = true; |
|
| 63 |
static final boolean doTreeIndex = true; |
|
| 64 |
static final boolean doParentAndBiota = true; |
|
| 65 |
static final boolean doRank = true; |
|
| 66 |
static final boolean doInferredSynonyms = false; //no inferred synonyms in E+M |
|
| 67 |
static final boolean doRelTaxa = true; |
|
| 68 |
static final boolean doDescriptions = true; |
|
| 54 |
// ************************ NONE **************************************** // |
|
| 69 | 55 |
|
| 70 |
static final boolean doNotes = true; |
|
| 71 |
static final boolean doNoteSources = true; |
|
| 72 |
static final boolean doAdditionalTaxonSource = true; |
|
| 73 |
static final boolean doOccurrence = true; |
|
| 74 |
static final boolean doOccurrenceSource = true; |
|
| 75 |
static final boolean doImage = true; |
|
| 56 |
// boolean deleteAll = false; |
|
| 57 |
// DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
|
| 58 |
// boolean doTaxa = false; |
|
| 59 |
// boolean doPureNames = false; |
|
| 60 |
// boolean doTreeIndex = false; |
|
| 61 |
// boolean doParentAndBiota = false; |
|
| 62 |
// boolean doInferredSynonyms = false; //no inferred synonyms in E+M |
|
| 63 |
// boolean doRelTaxa = false; |
|
| 64 |
// boolean doAdditionalTaxonSource = false; |
|
| 65 |
// boolean doDescriptions = false; |
|
| 66 |
// boolean doEcologyAndLink = false; |
|
| 76 | 67 |
|
| 77 | 68 |
|
| 78 |
// ************************ NONE **************************************** // |
|
| 69 |
//check - export |
|
| 70 |
static final CHECK check = CHECK.EXPORT_WITHOUT_CHECK; |
|
| 79 | 71 |
|
| 80 |
// //references |
|
| 81 |
// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE; |
|
| 82 |
// |
|
| 83 |
// //taxa |
|
| 84 |
// static final boolean doTaxa = false; |
|
| 85 |
// static final boolean doPureNames = false; |
|
| 86 |
// static final boolean doRelTaxa = false; |
|
| 87 |
// static final boolean doNotes = false; |
|
| 88 |
// static final boolean doNoteSources = false; |
|
| 89 |
// static final boolean doAdditionalTaxonSource = false; |
|
| 90 |
// static final boolean doOccurrence = false; |
|
| 91 |
// static final boolean doOccurrenceSource = false; |
|
| 92 |
// static final boolean doImage = false; |
|
| 93 |
// static final boolean doTreeIndex = false; |
|
| 94 |
// static final boolean doRank = true; |
|
| 95 |
// static final boolean doInferredSynonyms = true; |
|
| 72 |
//Taxon names can't be mapped to their CDM ids as PESI Taxon table mainly holds taxa and there IDs. We ad nameIdStart to the TaxonName id to get a unique id |
|
| 73 |
static final int nameIdStart = 10000000; |
|
| 74 |
static final IdType idType = IdType.CDM_ID_WITH_EXCEPTIONS; |
|
| 96 | 75 |
|
| 76 |
static final int partitionSize = 1000; |
|
| 97 | 77 |
|
| 98 | 78 |
public boolean doExport(ICdmDataSource source){
|
| 99 |
System.out.println("Start export to PESI ("+ pesiDestination.getDatabase() + ") ...");
|
|
| 79 |
System.out.println("Start export from " + source.getDatabase() + " to PESI ("+ pesiDestination.getDatabase() + ") ...");
|
|
| 100 | 80 |
|
| 101 | 81 |
//make PESI Source |
| 102 | 82 |
Source destination = pesiDestination; |
| ... | ... | |
| 106 | 86 |
|
| 107 | 87 |
config.setDoTaxa(doTaxa); |
| 108 | 88 |
config.setDoPureNames(doPureNames); |
| 89 |
config.setDoTaxaPhase1(doTaxaPhase1); |
|
| 109 | 90 |
config.setDoRelTaxa(doRelTaxa); |
| 110 |
config.setDoOccurrence(doOccurrence); |
|
| 111 | 91 |
config.setDoReferences(doReferences); |
| 112 |
config.setDoImages(doImage); |
|
| 113 |
config.setDoNotes(doNotes); |
|
| 114 |
config.setDoNoteSources(doNoteSources); |
|
| 115 |
config.setDoOccurrenceSource(doOccurrenceSource); |
|
| 116 | 92 |
config.setDoTreeIndex(doTreeIndex); |
| 117 |
config.setDoTreeIndex(doParentAndBiota);
|
|
| 93 |
config.setDoParentAndBiota(doParentAndBiota);
|
|
| 118 | 94 |
config.setDoInferredSynonyms(doInferredSynonyms); |
| 119 | 95 |
config.setDoDescription(doDescriptions); |
| 96 |
config.setDoAdditionalTaxonSource(doAdditionalTaxonSource); |
|
| 97 |
config.setDoEcologyAndLink(doEcologyAndLink); |
|
| 120 | 98 |
|
| 121 | 99 |
config.setCheck(check); |
| 122 | 100 |
config.setLimitSave(partitionSize); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportBase.java | ||
|---|---|---|
| 643 | 643 |
} |
| 644 | 644 |
|
| 645 | 645 |
// return all sources with a PESI reference |
| 646 |
private static Set<IdentifiableSource> filterPesiSources(Set<? extends IdentifiableSource> sources) {
|
|
| 646 |
protected static Set<IdentifiableSource> filterPesiSources(Set<? extends IdentifiableSource> sources) {
|
|
| 647 | 647 |
Set<IdentifiableSource> result = new HashSet<>(); |
| 648 | 648 |
for (IdentifiableSource source : sources){
|
| 649 | 649 |
Reference ref = source.getCitation(); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportConfigurator.java | ||
|---|---|---|
| 45 | 45 |
private boolean doParentAndBiota = true; |
| 46 | 46 |
private boolean doInferredSynonyms = true; |
| 47 | 47 |
private boolean doPureNames = true; |
| 48 |
private boolean doTaxaPhase1 = true; |
|
| 48 | 49 |
private boolean doDescription = true; |
| 49 | 50 |
private boolean doEcologyAndLink = true; |
| 50 | 51 |
|
| ... | ... | |
| 197 | 198 |
this.doPureNames = doPureNames; |
| 198 | 199 |
} |
| 199 | 200 |
|
| 200 |
public boolean isDoDescription() {
|
|
| 201 |
public boolean isDoTaxaPhase1() {
|
|
| 202 |
return doTaxaPhase1; |
|
| 203 |
} |
|
| 204 |
public void setDoTaxaPhase1(boolean doTaxaPhase1) {
|
|
| 205 |
this.doTaxaPhase1 = doTaxaPhase1; |
|
| 206 |
} |
|
| 207 |
|
|
| 208 |
public boolean isDoDescription() {
|
|
| 201 | 209 |
return doDescription; |
| 202 | 210 |
} |
| 203 | 211 |
public void setDoDescription(boolean doDescription) {
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiSourceExport.java | ||
|---|---|---|
| 11 | 11 |
import java.sql.SQLException; |
| 12 | 12 |
import java.util.ArrayList; |
| 13 | 13 |
import java.util.EnumSet; |
| 14 |
import java.util.HashSet; |
|
| 15 | 14 |
import java.util.List; |
| 16 | 15 |
import java.util.Set; |
| 17 | 16 |
|
| ... | ... | |
| 35 | 34 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
| 36 | 35 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 37 | 36 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 38 |
import eu.etaxonomy.cdm.model.reference.ReferenceType; |
|
| 39 | 37 |
|
| 40 | 38 |
/** |
| 41 | 39 |
* The export class for {@link eu.etaxonomy.cdm.model.reference.Reference References}.<p>
|
| ... | ... | |
| 299 | 297 |
String result = null; |
| 300 | 298 |
|
| 301 | 299 |
try {
|
| 302 |
if (reference != null) {
|
|
| 303 |
Set<IdentifiableSource> sourceAll = reference.getSources(); |
|
| 304 |
Set<IdentifiableSource> sourceCandidates = filterOriginalPesiDbSources(sourceAll);
|
|
| 305 |
|
|
| 306 |
if (sourceCandidates.size() == 1) {
|
|
| 307 |
result = sourceCandidates.iterator().next().getIdInSource(); |
|
| 308 |
} else if (sourceCandidates.size() > 1) {
|
|
| 309 |
logger.warn("Reference for RefIdInSource has multiple IdentifiableSources which are candidates for a PESI originalDbSource. RefIdInSource can't be determined correctly and will be left out: " + reference.getUuid() + " (" + reference.getTitleCache() + ")");
|
|
| 310 |
int count = 1; |
|
| 311 |
// for (IdentifiableSource source : sources) {
|
|
| 312 |
// result += source.getIdInSource(); |
|
| 313 |
// if (count < sources.size()) {
|
|
| 314 |
// result += "; "; |
|
| 315 |
// } |
|
| 316 |
// count++; |
|
| 317 |
// } |
|
| 318 |
} |
|
| 319 |
} |
|
| 300 |
if (reference != null) {
|
|
| 301 |
Set<IdentifiableSource> sourceAll = reference.getSources();
|
|
| 302 |
Set<IdentifiableSource> sourceCandidates = filterPesiSources(sourceAll);
|
|
| 303 |
|
|
| 304 |
if (sourceCandidates.size() == 1) {
|
|
| 305 |
result = sourceCandidates.iterator().next().getIdInSource();
|
|
| 306 |
} else if (sourceCandidates.size() > 1) {
|
|
| 307 |
logger.warn("Reference for RefIdInSource has multiple IdentifiableSources which are candidates for a PESI originalDbSource. RefIdInSource can't be determined correctly and will be left out: " + reference.getUuid() + " (" + reference.getTitleCache() + ")");
|
|
| 308 |
int count = 1;
|
|
| 309 |
// for (IdentifiableSource source : sources) {
|
|
| 310 |
// result += source.getIdInSource();
|
|
| 311 |
// if (count < sources.size()) {
|
|
| 312 |
// result += "; ";
|
|
| 313 |
// }
|
|
| 314 |
// count++;
|
|
| 315 |
// }
|
|
| 316 |
}
|
|
| 317 |
}
|
|
| 320 | 318 |
} catch (Exception e) {
|
| 321 | 319 |
e.printStackTrace(); |
| 322 | 320 |
} |
| ... | ... | |
| 324 | 322 |
return result; |
| 325 | 323 |
} |
| 326 | 324 |
|
| 327 |
private static Set<IdentifiableSource> filterOriginalPesiDbSources( |
|
| 328 |
Set<IdentifiableSource> sourceAll) {
|
|
| 329 |
Set<IdentifiableSource> sourceCandidates = new HashSet<>(); |
|
| 330 |
for (IdentifiableSource source : sourceAll){
|
|
| 331 |
if (isOriginalPesiDbSource(source)){
|
|
| 332 |
sourceCandidates.add(source); |
|
| 333 |
} |
|
| 334 |
} |
|
| 335 |
return sourceCandidates; |
|
| 336 |
} |
|
| 337 |
|
|
| 338 |
private static boolean isOriginalPesiDbSource(IdentifiableSource source) {
|
|
| 339 |
return (source.getCitation() != null) && |
|
| 340 |
source.getCitation().getType().equals(ReferenceType.Database); |
|
| 341 |
} |
|
| 325 |
// private static Set<IdentifiableSource> filterOriginalPesiDbSources(
|
|
| 326 |
// Set<IdentifiableSource> sourceAll) {
|
|
| 327 |
// Set<IdentifiableSource> sourceCandidates = new HashSet<>();
|
|
| 328 |
// for (IdentifiableSource source : sourceAll){
|
|
| 329 |
// if (isOriginalPesiDbSource(source)){
|
|
| 330 |
// sourceCandidates.add(source);
|
|
| 331 |
// }
|
|
| 332 |
// }
|
|
| 333 |
// return sourceCandidates;
|
|
| 334 |
// }
|
|
| 335 |
// |
|
| 336 |
// private static boolean isOriginalPesiDbSource(IdentifiableSource source) {
|
|
| 337 |
// return (source.getCitation() != null) &&
|
|
| 338 |
// source.getCitation().getType().equals(ReferenceType.Database);
|
|
| 339 |
// }
|
|
| 342 | 340 |
|
| 343 | 341 |
/** |
| 344 | 342 |
* Returns the <code>OriginalDB</code> attribute. |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 34 | 34 |
|
| 35 | 35 |
import eu.etaxonomy.cdm.api.service.TaxonServiceImpl; |
| 36 | 36 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 37 |
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer; |
|
| 38 | 37 |
import eu.etaxonomy.cdm.io.common.Source; |
| 39 | 38 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 40 | 39 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbConstantMapper; |
| ... | ... | |
| 104 | 103 |
|
| 105 | 104 |
private static final String pluralString = "Taxa"; |
| 106 | 105 |
private static final String parentPluralString = "Taxa"; |
| 106 |
private static final String pluralStringNames = "Names"; |
|
| 107 | 107 |
|
| 108 | 108 |
private PreparedStatement parentTaxonFk_TreeIndex_KingdomFkStmt; |
| 109 | 109 |
private PreparedStatement parentTaxonFkStmt; |
| 110 | 110 |
private PreparedStatement rankTypeExpertsUpdateStmt; |
| 111 | 111 |
private PreparedStatement rankUpdateStmt; |
| 112 | 112 |
private Integer kingdomFk; |
| 113 |
private AnnotationType treeIndexAnnotationType; |
|
| 113 |
|
|
| 114 | 114 |
private static ExtensionType lastActionExtensionType; |
| 115 | 115 |
private static ExtensionType lastActionDateExtensionType; |
| 116 | 116 |
private static ExtensionType expertNameExtensionType; |
| 117 | 117 |
private static ExtensionType speciesExpertNameExtensionType; |
| 118 | 118 |
private static ExtensionType cacheCitationExtensionType; |
| 119 |
|
|
| 119 | 120 |
public static TaxonNameDefaultCacheStrategy zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance(); |
| 120 | 121 |
public static TaxonNameDefaultCacheStrategy nonViralNameStrategy = TaxonNameDefaultCacheStrategy.NewInstance(); |
| 121 | 122 |
private static int currentTaxonId; |
| 122 | 123 |
|
| 123 |
protected AnnotationType getTreeIndexAnnotationType() {
|
|
| 124 |
return treeIndexAnnotationType; |
|
| 125 |
} |
|
| 126 |
|
|
| 127 |
protected void setTreeIndexAnnotationType(AnnotationType treeIndexAnnotationType) {
|
|
| 128 |
this.treeIndexAnnotationType = treeIndexAnnotationType; |
|
| 129 |
} |
|
| 130 |
|
|
| 131 | 124 |
enum NamePosition {
|
| 132 | 125 |
beginning, |
| 133 | 126 |
end, |
| ... | ... | |
| 247 | 240 |
} |
| 248 | 241 |
|
| 249 | 242 |
private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping additionalSourceMapping){
|
| 250 |
int count = 0; |
|
| 243 |
if (!state.getConfig().isDoTaxaPhase1()){
|
|
| 244 |
return true; |
|
| 245 |
} |
|
| 246 |
int count = 0; |
|
| 251 | 247 |
int pastCount = 0; |
| 252 | 248 |
boolean success = true; |
| 253 | 249 |
// Get the limit for objects to save within a single transaction. |
| ... | ... | |
| 294 | 290 |
}else{
|
| 295 | 291 |
logger.warn("Kingdom taxon is not of class Taxon but " + taxon.getClass().getSimpleName() + ": " + nvn.getGenusOrUninomial());
|
| 296 | 292 |
} |
| 293 |
}else if (taxon.getUuid().equals(PesiTransformer.uuidTaxonValuelessEuroMed)){
|
|
| 294 |
String treeIndex = ((Taxon)taxon).getTaxonNodes().iterator().next().treeIndex(); |
|
| 295 |
Integer kingdomId = PesiTransformer.pesiKingdomMap.get("Plantae");
|
|
| 296 |
state.getTreeIndexKingdomMap().put(treeIndex, kingdomId); |
|
| 297 | 297 |
} |
| 298 | 298 |
}catch(NullPointerException e){
|
| 299 | 299 |
logger.error(nvn.getTitleCache() + " has no Rank!"); |
| ... | ... | |
| 425 | 425 |
for (TaxonNode node : taxon.getTaxonNodes()){
|
| 426 | 426 |
doCount(count++, modCount, pluralString); |
| 427 | 427 |
TaxonNode parentNode = node.getParent(); |
| 428 |
if (parentNode != null && parentNode.getTaxon() != null){ //new root node handling requires has root taxon with taxon == null
|
|
| 428 |
if (parentNode != null && isPesiTaxon(parentNode.getTaxon())){//exclude root taxa and unpublished parents (relevant for "Valueless" parent for E+M Rubus taxa). Usually a parent should not be unpublished
|
|
| 429 | 429 |
int childId = state.getDbId( taxon); |
| 430 | 430 |
int parentId = state.getDbId(parentNode.getTaxon()); |
| 431 | 431 |
success &= invokeParentTaxonFk(parentId, childId); |
| ... | ... | |
| 555 | 555 |
return success; |
| 556 | 556 |
} |
| 557 | 557 |
|
| 558 |
private static Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxonBase,PesiExportState state) {
|
|
| 558 |
private static Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxonBase, PesiExportState state) {
|
|
| 559 | 559 |
Taxon taxon; |
| 560 | 560 |
if (taxonBase instanceof Synonym){
|
| 561 | 561 |
taxon = ((Synonym) taxonBase).getAcceptedTaxon(); |
| ... | ... | |
| 584 | 584 |
if(matcher.find()) {
|
| 585 | 585 |
String treeIndexKingdom = matcher.group(0); |
| 586 | 586 |
kingdomID = state.getTreeIndexKingdomMap().get(treeIndexKingdom); |
| 587 |
}else{
|
|
| 587 |
} |
|
| 588 |
if (kingdomID == null){
|
|
| 588 | 589 |
pattern = Pattern.compile("#t[0-9]+#([0-9]+#){2}");
|
| 589 | 590 |
matcher = pattern.matcher(treeIndex); |
| 590 | 591 |
if(matcher.find()) {
|
| ... | ... | |
| 901 | 902 |
List<TaxonName> list; |
| 902 | 903 |
while ((list = getNextPureNamePartition(null, limit, partitionCount++)) != null ) {
|
| 903 | 904 |
|
| 904 |
logger.info("Fetched " + list.size() + " names without taxa. Exporting...");
|
|
| 905 |
logger.debug("Fetched " + list.size() + pluralStringNames + " without taxa. Exporting...");
|
|
| 905 | 906 |
for (TaxonName taxonName : list) {
|
| 906 | 907 |
doCount(count++, modCount, pluralString); |
| 907 | 908 |
success &= mapping.invoke(taxonName); |
| ... | ... | |
| 914 | 915 |
// Commit transaction |
| 915 | 916 |
commitTransaction(txStatus); |
| 916 | 917 |
logger.debug("Committed transaction.");
|
| 917 |
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
|
|
| 918 |
logger.info("Exported " + (count - pastCount) + " " + pluralStringNames + ". Total: " + count + ". Partition: " + partitionCount);
|
|
| 918 | 919 |
pastCount = count; |
| 919 | 920 |
|
| 920 | 921 |
// Start transaction |
| 921 | 922 |
txStatus = startTransaction(true); |
| 922 |
logger.info("Started new transaction for PureNames. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
| 923 |
logger.debug("Started new transaction for PureNames. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
| 923 | 924 |
} |
| 924 |
logger.info("No " + pluralString + " left to fetch.");
|
|
| 925 |
logger.debug("No " + pluralString + " left to fetch.");
|
|
| 925 | 926 |
|
| 926 | 927 |
// Commit transaction |
| 927 | 928 |
commitTransaction(txStatus); |
| ... | ... | |
| 1172 | 1173 |
* @return Whether the delete operation was successful or not. |
| 1173 | 1174 |
*/ |
| 1174 | 1175 |
protected boolean doDelete(PesiExportState state) {
|
| 1175 |
PesiExportConfigurator pesiConfig = state.getConfig();
|
|
| 1176 |
|
|
| 1177 |
String sql;
|
|
| 1178 |
Source destination = pesiConfig.getDestination();
|
|
| 1176 |
if (!state.getConfig().isDoTaxaPhase1()){
|
|
| 1177 |
return true; |
|
| 1178 |
}
|
|
| 1179 |
Source destination = state.getConfig().getDestination();
|
|
| 1179 | 1180 |
|
| 1180 |
// Clear Taxon |
|
| 1181 |
sql = "DELETE FROM " + dbTableName; |
|
| 1182 |
destination.update(sql); |
|
| 1181 |
String[] tables = new String[]{"AdditionalTaxonSource","CommonNameSource","CommonName",
|
|
| 1182 |
"Image","NoteSource","Note","OccurrenceSource","Occurrence","RelTaxon","Taxon"}; |
|
| 1183 | 1183 |
|
| 1184 |
//TODO due to foreign keys we should also delete all tables linking to Taxon table |
|
| 1184 |
for(String table : tables){
|
|
| 1185 |
String sql = "DELETE FROM " + table; |
|
| 1186 |
destination.update(sql); |
|
| 1187 |
} |
|
| 1185 | 1188 |
|
| 1186 | 1189 |
return true; |
| 1187 | 1190 |
} |
| ... | ... | |
| 1217 | 1220 |
return result; |
| 1218 | 1221 |
} |
| 1219 | 1222 |
|
| 1220 |
private static String getRankCache(TaxonName taxonName, PesiExportState state) {
|
|
| 1223 |
@SuppressWarnings("unused")
|
|
| 1224 |
private static String getRankCache(TaxonName taxonName, PesiExportState state) {
|
|
| 1221 | 1225 |
List<TaxonNode> nodes = getTaxonNodes(taxonName); |
| 1222 |
Integer kingdomId = findKingdomIdFromTreeIndex(nodes.iterator().next().getTaxon(), state); |
|
| 1226 |
Integer kingdomId; |
|
| 1227 |
if (nodes == null||nodes.isEmpty()){
|
|
| 1228 |
kingdomId = getKingdomFk(taxonName); |
|
| 1229 |
}else{
|
|
| 1230 |
kingdomId = findKingdomIdFromTreeIndex(nodes.iterator().next().getTaxon(), state); |
|
| 1231 |
} |
|
| 1223 | 1232 |
return getRankCache(taxonName, kingdomId, state); |
| 1224 | 1233 |
} |
| 1225 | 1234 |
|
| 1226 |
|
|
| 1227 |
/** |
|
| 1228 |
* Returns the <code>RankCache</code> attribute. |
|
| 1229 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
| 1230 |
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
| 1231 |
* @param state |
|
| 1232 |
* @return The <code>RankCache</code> attribute. |
|
| 1233 |
* @see MethodMapper |
|
| 1234 |
*/ |
|
| 1235 | 1235 |
private static String getRankCache(TaxonName taxonName, Integer kingdomFk, PesiExportState state) {
|
| 1236 | 1236 |
if (Rank.DOMAIN().equals(taxonName.getRank())){
|
| 1237 | 1237 |
return state.getTransformer().getCacheByRankAndKingdom(Rank.DOMAIN(), null); |
| ... | ... | |
| 1255 | 1255 |
}else{
|
| 1256 | 1256 |
taxon = CdmBase.deproxy(tb, Synonym.class).getAcceptedTaxon(); |
| 1257 | 1257 |
} |
| 1258 |
if (taxon != null){
|
|
| 1258 |
if (isPesiTaxon(taxon)){
|
|
| 1259 | 1259 |
for (TaxonNode node : taxon.getTaxonNodes()){
|
| 1260 | 1260 |
result.add(node); |
| 1261 | 1261 |
} |
| ... | ... | |
| 1264 | 1264 |
return result; |
| 1265 | 1265 |
} |
| 1266 | 1266 |
|
| 1267 |
// @SuppressWarnings("unused") //used by pure name mapper and by getRankFk
|
|
| 1268 |
private static Integer getKingdomFk(TaxonName taxonName){
|
|
| 1269 |
EnumSet<PesiSource> origin = getSources(taxonName); |
|
| 1270 |
if (origin.size() == 1 && origin.contains(PesiSource.EM)){
|
|
| 1271 |
//maybe simply replace by |
|
| 1272 |
//return PesiTransformer.KINGDOM_PLANTAE; |
|
| 1273 |
return PesiTransformer.nomenclaturalCode2Kingdom(taxonName.getNameType()); |
|
| 1274 |
}else{
|
|
| 1275 |
logger.warn("getKingdomFk not yet implemented for non-EuroMed pure names");
|
|
| 1276 |
return null; |
|
| 1277 |
} |
|
| 1278 |
} |
|
| 1279 |
|
|
| 1280 |
/** |
|
| 1281 |
* Returns the rankFk for the taxon name based on the names nomenclatural code. |
|
| 1282 |
* You may not use this method for kingdoms other then Animalia, Plantae and Bacteria. |
|
| 1283 |
*/ |
|
| 1284 |
@SuppressWarnings("unused") //used by pure name mapper
|
|
| 1285 |
private static Integer getRankFk(TaxonName taxonName) {
|
|
| 1286 |
EnumSet<PesiSource> origin = getSources(taxonName); |
|
| 1287 |
if (origin.size() == 1 && origin.contains(PesiSource.EM)){
|
|
| 1288 |
return getRankFk(taxonName, getKingdomFk(taxonName)); |
|
| 1289 |
}else{
|
|
| 1290 |
logger.warn("getRankFk not yet implemented for non-EuroMed pure names");
|
|
| 1291 |
return null; |
|
| 1292 |
} |
|
| 1293 |
} |
|
| 1294 |
|
|
| 1267 | 1295 |
/** |
| 1268 | 1296 |
* Returns the <code>DisplayName</code> attribute. |
| 1269 | 1297 |
* @param taxon The {@link TaxonBase Taxon}.
|
| ... | ... | |
| 1470 | 1498 |
/** |
| 1471 | 1499 |
* Returns the nomenclatural reference which is the reference |
| 1472 | 1500 |
* including the detail (microreference). |
| 1473 |
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
| 1474 |
* @return The <code>AuthorString</code> attribute. |
|
| 1501 |
* @param taxonName The {@link TaxonName taxon name}.
|
|
| 1475 | 1502 |
* @see MethodMapper |
| 1476 | 1503 |
*/ |
| 1477 | 1504 |
@SuppressWarnings("unused")
|
| ... | ... | |
| 1690 | 1717 |
* @return The <code>TypeDesignationStatusFk</code> attribute. |
| 1691 | 1718 |
* @see MethodMapper |
| 1692 | 1719 |
*/ |
| 1693 |
@SuppressWarnings("unused")
|
|
| 1720 |
//TODO seems not to be used
|
|
| 1694 | 1721 |
private static Integer getTypeDesignationStatusFk(TaxonName taxonName) {
|
| 1695 | 1722 |
Integer result = null; |
| 1696 | 1723 |
|
| 1697 | 1724 |
try {
|
| 1698 |
if (taxonName != null) {
|
|
| 1699 |
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations(); |
|
| 1700 |
if (typeDesignations.size() == 1) {
|
|
| 1701 |
Object obj = typeDesignations.iterator().next().getTypeStatus(); |
|
| 1702 |
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class); |
|
| 1703 |
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusId(designationStatus); |
|
| 1704 |
} else if (typeDesignations.size() > 1) {
|
|
| 1705 |
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1706 |
} |
|
| 1707 |
} |
|
| 1708 |
|
|
| 1725 |
if (taxonName != null) {
|
|
| 1726 |
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations(); |
|
| 1727 |
if (typeDesignations.size() == 1) {
|
|
| 1728 |
Object obj = typeDesignations.iterator().next().getTypeStatus(); |
|
| 1729 |
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class); |
|
| 1730 |
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusId(designationStatus); |
|
| 1731 |
} else if (typeDesignations.size() > 1) {
|
|
| 1732 |
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1733 |
} |
|
| 1734 |
} |
|
| 1709 | 1735 |
} catch (Exception e) {
|
| 1710 | 1736 |
e.printStackTrace(); |
| 1711 | 1737 |
} |
| ... | ... | |
| 1718 | 1744 |
* @return The <code>TypeDesignationStatusCache</code> attribute. |
| 1719 | 1745 |
* @see MethodMapper |
| 1720 | 1746 |
*/ |
| 1721 |
@SuppressWarnings("unused")
|
|
| 1747 |
//TODO seems not to be used
|
|
| 1722 | 1748 |
private static String getTypeDesignationStatusCache(TaxonName taxonName) {
|
| 1723 | 1749 |
String result = null; |
| 1724 | 1750 |
|
| 1725 | 1751 |
try {
|
| 1726 |
if (taxonName != null) {
|
|
| 1727 |
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations(); |
|
| 1728 |
if (typeDesignations.size() == 1) {
|
|
| 1729 |
Object obj = typeDesignations.iterator().next().getTypeStatus(); |
|
| 1730 |
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class); |
|
| 1731 |
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusCache(designationStatus); |
|
| 1732 |
} else if (typeDesignations.size() > 1) {
|
|
| 1733 |
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1734 |
} |
|
| 1735 |
} |
|
| 1736 |
|
|
| 1752 |
if (taxonName != null) {
|
|
| 1753 |
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations(); |
|
| 1754 |
if (typeDesignations.size() == 1) {
|
|
| 1755 |
Object obj = typeDesignations.iterator().next().getTypeStatus(); |
|
| 1756 |
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class); |
|
| 1757 |
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusCache(designationStatus); |
|
| 1758 |
} else if (typeDesignations.size() > 1) {
|
|
| 1759 |
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1760 |
} |
|
| 1761 |
} |
|
| 1737 | 1762 |
} catch (Exception e) {
|
| 1738 | 1763 |
e.printStackTrace(); |
| 1739 | 1764 |
} |
| ... | ... | |
| 1803 | 1828 |
Reference ref = source.getCitation(); |
| 1804 | 1829 |
UUID refUuid = ref.getUuid(); |
| 1805 | 1830 |
String idInSource = source.getIdInSource(); |
| 1806 |
if (refUuid.equals(BerlinModelTransformer.uuidSourceRefEuroMed)){
|
|
| 1831 |
if (refUuid.equals(PesiTransformer.uuidSourceRefEuroMed)){
|
|
| 1807 | 1832 |
result = idInSource != null ? ("NameId: " + source.getIdInSource()) : null;
|
| 1808 | 1833 |
}else if (refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)){
|
| 1809 | 1834 |
result = idInSource != null ? ("TAX_ID: " + source.getIdInSource()) : null;
|
| ... | ... | |
| 1993 | 2018 |
* @return The <code>LastAction</code> attribute. |
| 1994 | 2019 |
* @see MethodMapper |
| 1995 | 2020 |
*/ |
| 1996 |
@SuppressWarnings("unused")
|
|
| 2021 |
//TODO still in use?
|
|
| 1997 | 2022 |
private static String getLastAction(IdentifiableEntity<?> identEntity) {
|
| 1998 | 2023 |
String result = null; |
| 1999 | 2024 |
try {
|
| 2000 |
Set<Extension> extensions = identEntity.getExtensions(); |
|
| 2001 |
for (Extension extension : extensions) {
|
|
| 2002 |
if (extension.getType().equals(lastActionExtensionType)) {
|
|
| 2003 |
result = extension.getValue(); |
|
| 2004 |
} |
|
| 2005 |
} |
|
| 2025 |
Set<Extension> extensions = identEntity.getExtensions();
|
|
| 2026 |
for (Extension extension : extensions) {
|
|
| 2027 |
if (extension.getType().equals(lastActionExtensionType)) {
|
|
| 2028 |
result = extension.getValue();
|
|
| 2029 |
}
|
|
| 2030 |
}
|
|
| 2006 | 2031 |
} catch (Exception e) {
|
| 2007 | 2032 |
e.printStackTrace(); |
| 2008 | 2033 |
} |
| ... | ... | |
| 2015 | 2040 |
* @return The <code>LastActionDate</code> attribute. |
| 2016 | 2041 |
* @see MethodMapper |
| 2017 | 2042 |
*/ |
| 2018 |
@SuppressWarnings({ "unused" })
|
|
| 2043 |
//TODO still in use?
|
|
| 2019 | 2044 |
private static DateTime getLastActionDate(IdentifiableEntity<?> identEntity) {
|
| 2020 | 2045 |
DateTime result = null; |
| 2021 | 2046 |
try {
|
| ... | ... | |
| 2041 | 2066 |
* @return The <code>ExpertName</code> attribute. |
| 2042 | 2067 |
* @see MethodMapper |
| 2043 | 2068 |
*/ |
| 2044 |
@SuppressWarnings("unused")
|
|
| 2069 |
@SuppressWarnings("unused") //for some reason it is also called by getCacheCitation
|
|
| 2045 | 2070 |
private static String getExpertName(TaxonBase<?> taxonName) {
|
| 2046 |
String result = null;
|
|
| 2071 |
String result = null;
|
|
| 2047 | 2072 |
try {
|
| 2048 |
Set<Extension> extensions = taxonName.getExtensions(); |
|
| 2049 |
for (Extension extension : extensions) {
|
|
| 2050 |
if (extension.getType().equals(expertNameExtensionType)) {
|
|
| 2051 |
result = extension.getValue(); |
|
| 2052 |
} |
|
| 2053 |
} |
|
| 2073 |
if(expertNameExtensionType!=null){ //some databases do not have this extension type
|
|
| 2074 |
Set<Extension> extensions = taxonName.getExtensions(); |
|
| 2075 |
for (Extension extension : extensions) {
|
|
| 2076 |
if (extension.getType().equals(expertNameExtensionType)) {
|
|
| 2077 |
result = extension.getValue(); |
|
| 2078 |
} |
|
| 2079 |
} |
|
| 2080 |
} |
|
| 2054 | 2081 |
} catch (Exception e) {
|
| 2055 | 2082 |
e.printStackTrace(); |
| 2056 | 2083 |
} |
| ... | ... | |
| 2075 | 2102 |
* @return The <code>SpeciesExpertName</code> attribute. |
| 2076 | 2103 |
* @see MethodMapper |
| 2077 | 2104 |
*/ |
| 2078 |
@SuppressWarnings("unused")
|
|
| 2105 |
//TODO still in use?
|
|
| 2079 | 2106 |
private static String getSpeciesExpertName(TaxonBase<?> taxonName) {
|
| 2080 | 2107 |
String result = null; |
| 2081 | 2108 |
try {
|
| 2082 |
Set<Extension> extensions = taxonName.getExtensions(); |
|
| 2083 |
for (Extension extension : extensions) {
|
|
| 2084 |
if (extension.getType().equals(speciesExpertNameExtensionType)) {
|
|
| 2085 |
result = extension.getValue(); |
|
| 2086 |
} |
|
| 2087 |
} |
|
| 2109 |
Set<Extension> extensions = taxonName.getExtensions();
|
|
| 2110 |
for (Extension extension : extensions) {
|
|
| 2111 |
if (extension.getType().equals(speciesExpertNameExtensionType)) {
|
|
| 2112 |
result = extension.getValue();
|
|
| 2113 |
}
|
|
| 2114 |
}
|
|
| 2088 | 2115 |
} catch (Exception e) {
|
| 2089 | 2116 |
e.printStackTrace(); |
| 2090 | 2117 |
} |
| ... | ... | |
| 2132 | 2159 |
return PesiTransformer.taxonRelation2RelTaxonQualifierFk(relationship); |
| 2133 | 2160 |
} |
| 2134 | 2161 |
|
| 2135 |
@SuppressWarnings("unused")
|
|
| 2162 |
//TODO still in use?
|
|
| 2136 | 2163 |
private static String getSynonymTypeCache(Synonym synonym, PesiExportState state) {
|
| 2137 | 2164 |
String result = null; |
| 2138 | 2165 |
NomenclaturalCode code = null; |
| ... | ... | |
| 2208 | 2235 |
mapping.addMapper(MethodMapper.NewInstance("KingdomFk", this, TaxonName.class));
|
| 2209 | 2236 |
mapping.addMapper(MethodMapper.NewInstance("RankFk", this, TaxonName.class));
|
| 2210 | 2237 |
mapping.addMapper(MethodMapper.NewInstance("RankCache", this, TaxonName.class, PesiExportState.class));
|
| 2211 |
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusFk", Types.INTEGER , PesiTransformer.T_STATUS_UNACCEPTED));
|
|
| 2212 |
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusCache", Types.VARCHAR , state.getTransformer().getTaxonStatusCacheByKey( PesiTransformer.T_STATUS_UNACCEPTED)));
|
|
| 2238 |
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusFk", Types.INTEGER, PesiTransformer.T_STATUS_UNACCEPTED));
|
|
| 2239 |
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusCache", Types.VARCHAR, state.getTransformer().getTaxonStatusCacheByKey( PesiTransformer.T_STATUS_UNACCEPTED)));
|
|
| 2213 | 2240 |
mapping.addMapper(DbStringMapper.NewInstance("AuthorshipCache", "AuthorString").setBlankToNull(true));
|
| 2214 | 2241 |
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this, TaxonName.class));
|
| 2215 | 2242 |
mapping.addMapper(MethodMapper.NewInstance("GUID", this, TaxonName.class));
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java | ||
|---|---|---|
| 74 | 74 |
public static final UUID uuidSourceRefIndexFungorum = UUID.fromString("8de25d27-7d40-47f4-af3b-59d64935a843");
|
| 75 | 75 |
public static final UUID uuidSourceRefAuct = UUID.fromString("5f79f96c-c100-4cd8-b78e-2b2dacf09a23");
|
| 76 | 76 |
|
| 77 |
public static final UUID uuidTaxonValuelessEuroMed = UUID.fromString("f0a9322b-a57e-447b-9a75-a909f2f2a994");
|
|
| 78 |
|
|
| 77 | 79 |
public static final String SOURCE_STR_EM = "E+M"; |
| 78 | 80 |
public static final String SOURCE_STR_FE = "FaEu"; |
| 79 | 81 |
public static final String SOURCE_STR_IF = "IF"; |
Also available in: Unified diff
ref #2717 adapt PesiExport to EuroMed requirements and adapt PesiExportActivatorEM