Revision 2d481abb
Added by Katja Luther almost 10 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java | ||
|---|---|---|
| 34 | 34 |
public static ICdmDataSource cdm_test_local_faunaEu_mysql(){
|
| 35 | 35 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 36 | 36 |
String cdmServer = "127.0.0.1"; |
| 37 |
String cdmDB = "cdm_test_fauneu";
|
|
| 37 |
String cdmDB = "cdm_test"; |
|
| 38 | 38 |
String cdmUserName = "root"; |
| 39 | 39 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 40 | 40 |
} |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/FaunaEuropaeaActivator.java | ||
|---|---|---|
| 37 | 37 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaActivator.class); |
| 38 | 38 |
|
| 39 | 39 |
|
| 40 |
static final Source faunaEuropaeaSource = PesiSources.faunEu_pesi3(); |
|
| 40 |
static final Source faunaEuropaeaSource = PesiSources.mfn_faunEu_pesi3();
|
|
| 41 | 41 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_faunaEu_mysql(); |
| 42 | 42 |
|
| 43 | 43 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/IndexFungorumActivator.java | ||
|---|---|---|
| 41 | 41 |
|
| 42 | 42 |
//database validation status (create, update, validate ...) |
| 43 | 43 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
| 44 |
static final Source indexFungorumSource = PesiSources.PESI_IF(); |
|
| 44 |
static final Source indexFungorumSource = PesiSources.PESI3_IF();
|
|
| 45 | 45 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_erms(); |
| 46 | 46 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_indexFungorum(); |
| 47 | 47 |
static final UUID treeUuid = UUID.fromString("4bea48c3-eb10-41d1-b708-b5ee625ed243");
|
| ... | ... | |
| 51 | 51 |
|
| 52 | 52 |
static final int partitionSize = 2000; |
| 53 | 53 |
|
| 54 |
static final boolean doPesiExport = true;
|
|
| 54 |
static final boolean doPesiExport = false;
|
|
| 55 | 55 |
|
| 56 | 56 |
|
| 57 | 57 |
//NomeclaturalCode |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiDestinations.java | ||
|---|---|---|
| 61 | 61 |
String strServer = "pesiimport3"; //192.168.1.223 |
| 62 | 62 |
String strDB = "CDM_IF2PESI"; |
| 63 | 63 |
int port = 1433; |
| 64 |
String userName = "pesiexport";
|
|
| 64 |
String userName = "pesiExportFaunaEu";
|
|
| 65 | 65 |
return makeSource(dbms, strServer, strDB, port, userName, null); |
| 66 | 66 |
} |
| 67 | 67 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiSources.java | ||
|---|---|---|
| 37 | 37 |
// Fauna Europaea auf pesiimport3 |
| 38 | 38 |
String dbms = Source.SQL_SERVER_2008; |
| 39 | 39 |
String strServer = "pesiimport3"; |
| 40 |
String strDB = "MfN_FaunaEuropeae";
|
|
| 40 |
String strDB = "MfN_FaunaEuropaea";
|
|
| 41 | 41 |
int port = 1433; |
| 42 | 42 |
String userName = "pesiExportFaunaEu"; |
| 43 | 43 |
return ImportUtils.makeSource(dbms, strServer, strDB, port, userName, null); |
| ... | ... | |
| 93 | 93 |
return makeSource(dbms, strServer, strDB, port, userName, null); |
| 94 | 94 |
} |
| 95 | 95 |
|
| 96 |
public static Source PESI3_IF(){
|
|
| 97 |
// BerlinModel - Pesi-ERMS |
|
| 98 |
String dbms = Source.SQL_SERVER_2008; |
|
| 99 |
String strServer = "Pesiimport3"; |
|
| 100 |
String strDB = "IF_2014_06"; |
|
| 101 |
int port = 1433; |
|
| 102 |
String userName = "pesiExportFaunaEu"; |
|
| 103 |
return makeSource(dbms, strServer, strDB, port, userName, null); |
|
| 104 |
} |
|
| 105 |
|
|
| 96 | 106 |
public static Source PESI_IF(){
|
| 97 | 107 |
// BerlinModel - Pesi-IF |
| 98 | 108 |
String dbms = Source.SQL_SERVER_2008; |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaAdditionalTaxonDataImport.java | ||
|---|---|---|
| 37 | 37 |
public class FaunaEuropaeaAdditionalTaxonDataImport extends FaunaEuropaeaImportBase {
|
| 38 | 38 |
|
| 39 | 39 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaAdditionalTaxonDataImport.class); |
| 40 |
private static final String parentPluralString = "Synonyms"; |
|
| 40 |
// private static final String parentPluralString = "Synonyms";
|
|
| 41 | 41 |
private static final String pluralString = "InfraGenericEpithets"; |
| 42 |
private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database |
|
| 42 |
//private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database
|
|
| 43 | 43 |
|
| 44 | 44 |
/* (non-Javadoc) |
| 45 | 45 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaDistributionImport.java | ||
|---|---|---|
| 221 | 221 |
e.printStackTrace(); |
| 222 | 222 |
} |
| 223 | 223 |
} |
| 224 |
rs = null; |
|
| 224 | 225 |
} catch (SQLException e) {
|
| 225 | 226 |
logger.error("SQLException:" + e);
|
| 226 | 227 |
state.setUnsuccessfull(); |
| 227 | 228 |
} |
| 229 |
|
|
| 228 | 230 |
if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }
|
| 229 | 231 |
|
| 230 | 232 |
return; |
| ... | ... | |
| 238 | 240 |
List<TaxonBase> taxonList = prepareTaxaAndDistribution(getTaxonService().find(taxonUuids), fauEuTaxonMap, noDataUuid, state); |
| 239 | 241 |
|
| 240 | 242 |
getTaxonService().save(taxonList); |
| 243 |
taxonList = null; |
|
| 244 |
taxonUuids = null; |
|
| 245 |
fauEuTaxonMap = null; |
|
| 241 | 246 |
commitTransaction(txStatus); |
| 242 | 247 |
|
| 243 | 248 |
} |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaHeterotypicSynonymImport.java | ||
|---|---|---|
| 96 | 96 |
NameRelationship nameRelation = null; |
| 97 | 97 |
TaxonNameBase acceptedName = null; |
| 98 | 98 |
|
| 99 |
for (Synonym synonym : synonymList) {
|
|
| 99 |
for (TaxonBase synonym : synonymList) {
|
|
| 100 | 100 |
synonymName = synonym.getName(); |
| 101 | 101 |
if (synonymName.isGroupsBasionym()) {
|
| 102 | 102 |
nameRelations = synonymName.getNameRelations(); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaRefImport.java | ||
|---|---|---|
| 208 | 208 |
|
| 209 | 209 |
if ((i++ % limit) == 0) {
|
| 210 | 210 |
|
| 211 |
txStatus = startTransaction(); |
|
| 211 |
txStatus = startTransactionForImports();
|
|
| 212 | 212 |
references = new HashMap<Integer,Reference>(limit); |
| 213 | 213 |
authors = new HashMap<String,TeamOrPersonBase>(limit); |
| 214 | 214 |
|
| ... | ... | |
| 281 | 281 |
|
| 282 | 282 |
|
| 283 | 283 |
} |
| 284 |
rsRefs = null; |
|
| 284 | 285 |
if (references != null){
|
| 285 | 286 |
commitReferences(references, authors, referenceUuids, i, txStatus); |
| 286 | 287 |
references= null; |
| ... | ... | |
| 290 | 291 |
logger.error("SQLException:" + e);
|
| 291 | 292 |
state.setUnsuccessfull(); |
| 292 | 293 |
} |
| 294 |
references = null; |
|
| 295 |
authors = null; |
|
| 293 | 296 |
|
| 294 | 297 |
} |
| 295 | 298 |
|
| ... | ... | |
| 453 | 456 |
logger.error("SQLException:" + e);
|
| 454 | 457 |
state.setUnsuccessfull(); |
| 455 | 458 |
} |
| 459 |
taxonUuids = null; |
|
| 460 |
references = null; |
|
| 461 |
taxonList = null; |
|
| 462 |
fauEuTaxonMap = null; |
|
| 463 |
referenceIDs = null; |
|
| 464 |
referenceList = null; |
|
| 465 |
|
|
| 466 |
|
|
| 456 | 467 |
} |
| 457 | 468 |
|
| 458 | 469 |
private void commitTaxaReferenceRel(Set<UUID> taxonUuids, |
| ... | ... | |
| 492 | 503 |
Set<Taxon> acceptedTaxa = syn.getAcceptedTaxa(); |
| 493 | 504 |
if (acceptedTaxa.size() > 0) {
|
| 494 | 505 |
taxon = syn.getAcceptedTaxa().iterator().next(); |
| 506 |
logger.warn("Synonym (" + taxonBase.getUuid() + ") has accepted taxon" + taxon.getUuid());
|
|
| 495 | 507 |
} else {
|
| 496 | 508 |
// if (logger.isDebugEnabled()) {
|
| 497 |
logger.warn("Synonym (" + taxonBase.getUuid() + ") does not have accepted taxa");
|
|
| 509 |
logger.warn("Synonym (" + taxonBase.getUuid() + ") does not have accepted taxa");
|
|
| 498 | 510 |
// } |
| 499 | 511 |
} |
| 500 | 512 |
} else {
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaRelTaxonIncludeImport.java | ||
|---|---|---|
| 50 | 50 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaRelTaxonIncludeImport.class); |
| 51 | 51 |
//private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database |
| 52 | 52 |
//private static final String acceptedTaxonUUID = "E23E6295-836A-4332-BF72-7D29949C7C60"; //faunaEu_1_3 |
| 53 |
private static final String acceptedTaxonUUID = "BB9CDF6C-BBA3-4AC7-A3FD-648A14F518A0"; //for faunEu (2.4) |
|
| 53 |
//private static final String acceptedTaxonUUID = "bab7642e-f733-4a21-848d-a15250d2f4ed"; //for faunEu (2.4) |
|
| 54 |
private static final String acceptedTaxonUUID = "DADA6F44-B7B5-4C0A-9F32-980F54B02C36"; // for MfNFaunaEuropaea |
|
| 54 | 55 |
|
| 55 | 56 |
private Reference<?> sourceRef; |
| 56 | 57 |
private static String ALL_SYNONYM_FROM_CLAUSE = " FROM Taxon INNER JOIN Taxon AS Parent " + |
| ... | ... | |
| 108 | 109 |
|
| 109 | 110 |
Classification tree = getClassificationFor(state, sourceRef); |
| 110 | 111 |
commitTransaction(txStatus); |
| 111 |
/* |
|
| 112 |
logger.warn("Before processParentsChildren");
|
|
| 113 | 112 |
|
| 114 |
ProfilerController.memorySnapshot(); |
|
| 115 |
*/ |
|
| 116 |
if (state.getConfig().isDoTaxonomicallyIncluded()) {
|
|
| 113 |
logger.warn("Before processParentsChildren" + state.getConfig().isDoTaxonomicallyIncluded());
|
|
| 114 |
|
|
| 115 |
//ProfilerController.memorySnapshot(); |
|
| 116 |
|
|
| 117 |
if (state.getConfig().isDoTaxonomicallyIncluded()) {
|
|
| 117 | 118 |
processParentsChildren(state); |
| 118 | 119 |
} |
| 119 |
/* |
|
| 120 |
logger.warn("Before processMissappliedNames");
|
|
| 121 | 120 |
|
| 122 |
ProfilerController.memorySnapshot(); |
|
| 123 |
*/ |
|
| 121 |
logger.warn("Before processMissappliedNames" + state.getConfig().isDoMisappliedNames());
|
|
| 122 |
|
|
| 123 |
//ProfilerController.memorySnapshot(); |
|
| 124 |
|
|
| 124 | 125 |
if (state.getConfig().isDoMisappliedNames()) {
|
| 125 | 126 |
processMisappliedNames(state); |
| 126 | 127 |
} |
| ... | ... | |
| 138 | 139 |
logger.warn("End RelTaxon doInvoke");
|
| 139 | 140 |
ProfilerController.memorySnapshot(); |
| 140 | 141 |
*/ |
| 141 |
logger.info("End making taxa...");
|
|
| 142 |
logger.info("End making relationships......");
|
|
| 142 | 143 |
|
| 143 | 144 |
return; |
| 144 | 145 |
} |
| ... | ... | |
| 225 | 226 |
} |
| 226 | 227 |
} |
| 227 | 228 |
} |
| 228 |
|
|
| 229 |
rs = null; |
|
| 229 | 230 |
if (childParentMap != null){
|
| 230 | 231 |
logger.info("processParentsChildren... last commit");
|
| 231 | 232 |
createAndCommitParentChildRelationships( |
| ... | ... | |
| 237 | 238 |
logger.error("SQLException:" + e);
|
| 238 | 239 |
state.setUnsuccessfull(); |
| 239 | 240 |
} |
| 241 |
childParentMap = null; |
|
| 240 | 242 |
return; |
| 241 | 243 |
} |
| 242 | 244 |
|
| ... | ... | |
| 395 | 397 |
} |
| 396 | 398 |
|
| 397 | 399 |
storeSynonymRelationships(rs, count, state); |
| 398 |
|
|
| 400 |
rs = null; |
|
| 399 | 401 |
} catch (SQLException e) {
|
| 400 | 402 |
logger.error("SQLException:" + e);
|
| 401 | 403 |
state.setUnsuccessfull(); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaTaxonNameImport.java | ||
|---|---|---|
| 416 | 416 |
|
| 417 | 417 |
taxon = Taxon.NewInstance(zooName, auctReference); |
| 418 | 418 |
taxonBase = taxon; |
| 419 |
logger.info("Misapplied name created ("+ taxonId + ") " + autName);
|
|
| 419 |
//logger.info("Misapplied name created ("+ taxonId + ") " + autName);
|
|
| 420 | 420 |
if (logger.isDebugEnabled()) {
|
| 421 | 421 |
logger.debug("Misapplied name created (" + taxonId + ")");
|
| 422 | 422 |
} |
| ... | ... | |
| 485 | 485 |
} |
| 486 | 486 |
|
| 487 | 487 |
} |
| 488 |
rs = null; |
|
| 488 | 489 |
if (taxonMap != null){
|
| 489 | 490 |
commitTaxa(state, txStatus, taxonMap, fauEuTaxonMap, |
| 490 | 491 |
synonymSet); |
| ... | ... | |
| 496 | 497 |
logger.error("SQLException:" + e);
|
| 497 | 498 |
state.setUnsuccessfull(); |
| 498 | 499 |
} |
| 499 |
|
|
| 500 |
taxonMap = null; |
|
| 501 |
synonymSet = null; |
|
| 502 |
fauEuTaxonMap = null; |
|
| 500 | 503 |
return; |
| 501 | 504 |
} |
| 502 | 505 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaUsersImport.java | ||
|---|---|---|
| 19 | 19 |
import java.util.UUID; |
| 20 | 20 |
|
| 21 | 21 |
import org.apache.log4j.Logger; |
| 22 |
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken; |
|
| 23 |
import org.springframework.security.core.userdetails.UserDetails; |
|
| 22 | 24 |
import org.springframework.stereotype.Component; |
| 23 | 25 |
import org.springframework.transaction.TransactionStatus; |
| 26 |
import org.springframework.transaction.support.DefaultTransactionDefinition; |
|
| 24 | 27 |
|
| 25 | 28 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
| 26 | 29 |
import eu.etaxonomy.cdm.io.common.ImportHelper; |
| ... | ... | |
| 45 | 48 |
|
| 46 | 49 |
/* Interval for progress info message when retrieving taxa */ |
| 47 | 50 |
private int modCount = 10000; |
| 51 |
|
|
| 52 |
protected DefaultTransactionDefinition txDefinition = new DefaultTransactionDefinition(); |
|
| 48 | 53 |
|
| 49 | 54 |
/* (non-Javadoc) |
| 50 | 55 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
| ... | ... | |
| 81 | 86 |
logger.warn("Start User doInvoke");
|
| 82 | 87 |
ProfilerController.memorySnapshot(); |
| 83 | 88 |
*/ |
| 89 |
|
|
| 84 | 90 |
TransactionStatus txStatus = null; |
| 85 | 91 |
Map<String, AgentBase<?>> persons = null; |
| 86 |
Map<Integer, User> users= null; |
|
| 92 |
Map<String, User> users= null; |
|
| 93 |
Map<Integer, Reference> references = null; |
|
| 87 | 94 |
Map<Integer, UUID> userUuids = new HashMap<Integer, UUID>(); |
| 88 | 95 |
int limit = state.getConfig().getLimitSave(); |
| 89 |
|
|
| 96 |
//this.authenticate("admin", "00000");
|
|
| 97 |
|
|
| 90 | 98 |
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig(); |
| 91 | 99 |
Source source = fauEuConfig.getSource(); |
| 92 | 100 |
|
| ... | ... | |
| 117 | 125 |
} |
| 118 | 126 |
|
| 119 | 127 |
while (rsUser.next()){
|
| 120 |
int userId = rsUser.getInt("usr_id");
|
|
| 128 |
int refId = rsUser.getInt("usr_id");
|
|
| 121 | 129 |
String userTitle = rsUser.getString("usr_title");
|
| 122 | 130 |
String userFirstname = rsUser.getString("usr_firstname");
|
| 123 | 131 |
String userLastname = rsUser.getString("usr_lastname");
|
| ... | ... | |
| 136 | 144 |
if ((userTitle != null || userFirstname != null) && userLastname != null) {
|
| 137 | 145 |
userPerson += " " + userLastname; |
| 138 | 146 |
} |
| 139 |
|
|
| 147 |
this.authenticate("admin", "00000");
|
|
| 140 | 148 |
// build year |
| 141 | 149 |
String year = null; |
| 142 | 150 |
if (createdDate != null) {
|
| ... | ... | |
| 147 | 155 |
|
| 148 | 156 |
txStatus = startTransaction(); |
| 149 | 157 |
persons= new HashMap<String,AgentBase<?>>(limit); |
| 150 |
users = new HashMap<Integer,User>(limit); |
|
| 158 |
users = new HashMap<String,User>(limit); |
|
| 159 |
references = new HashMap<Integer, Reference>(limit); |
|
| 151 | 160 |
|
| 152 | 161 |
if(logger.isInfoEnabled()) {
|
| 153 | 162 |
logger.info("i = " + i + " - User import transaction started");
|
| ... | ... | |
| 156 | 165 |
|
| 157 | 166 |
AgentBase<?> person = null; |
| 158 | 167 |
User user = null; |
| 159 |
person= Person.NewTitledInstance(userTitle); |
|
| 168 |
Reference reference = null; |
|
| 169 |
person= Person.NewTitledInstance(userPerson); |
|
| 160 | 170 |
user = User.NewInstance(userPerson, userPwd); |
| 161 |
//reference.setTitle("" + refId); // This unique key is needed to get a hand on this Reference in PesiTaxonExport
|
|
| 162 |
//reference.setDatePublished(ImportHelper.getDatePublished(year)); |
|
| 171 |
reference = ReferenceFactory.newGeneric(); |
|
| 172 |
reference.setTitle("" + refId); // This unique key is needed to get a hand on this Reference in PesiTaxonExport
|
|
| 173 |
reference.setDatePublished(ImportHelper.getDatePublished(year)); |
|
| 174 |
|
|
| 163 | 175 |
|
| 164 | 176 |
if (!persons.containsKey(userPerson)) {
|
| 165 | 177 |
if (userPerson == null) {
|
| ... | ... | |
| 175 | 187 |
} else {
|
| 176 | 188 |
person = persons.get(userPerson); |
| 177 | 189 |
if (logger.isDebugEnabled()) {
|
| 178 |
logger.debug("Not imported user with duplicated user_id (" + userId +
|
|
| 190 |
logger.debug("Not imported user with duplicated ref_id (" + refId +
|
|
| 179 | 191 |
") " + userPerson); |
| 180 | 192 |
} |
| 181 | 193 |
} |
| 182 | 194 |
|
| 183 | 195 |
// set protected titleCache |
| 184 |
/*StringBuilder referenceTitleCache = new StringBuilder(user.getTitleCache() + ".");
|
|
| 196 |
StringBuilder referenceTitleCache = new StringBuilder(person.getTitleCache() + ".");
|
|
| 185 | 197 |
if (year != null) {
|
| 186 | 198 |
referenceTitleCache.append(" " + year);
|
| 187 | 199 |
} |
| 188 | 200 |
reference.setTitleCache(referenceTitleCache.toString(), true); |
| 189 | 201 |
|
| 190 |
reference.setAuthorTeam(author);*/
|
|
| 202 |
reference.setAuthorTeam((TeamOrPersonBase)person);
|
|
| 191 | 203 |
|
| 192 | 204 |
//ImportHelper.setOriginalSource(user, fauEuConfig.getSourceReference(), userId, namespace); |
| 193 |
ImportHelper.setOriginalSource(person, fauEuConfig.getSourceReference(), userId, namespace);
|
|
| 205 |
ImportHelper.setOriginalSource(person, fauEuConfig.getSourceReference(), refId, namespace);
|
|
| 194 | 206 |
|
| 195 | 207 |
|
| 196 | 208 |
// Store persons |
| 197 |
if (!users.containsKey(userId)) {
|
|
| 209 |
if (!users.containsKey(userPerson)) {
|
|
| 198 | 210 |
|
| 199 | 211 |
if (user == null) {
|
| 200 | 212 |
logger.warn("User is null");
|
| 201 | 213 |
} |
| 202 |
users.put(userId, user);
|
|
| 214 |
users.put(userPerson, user);
|
|
| 203 | 215 |
if (logger.isTraceEnabled()) {
|
| 204 |
logger.trace("Stored user (" + userTitle + ")");
|
|
| 216 |
logger.trace("Stored user (" + userPerson + ")");
|
|
| 205 | 217 |
} |
| 206 | 218 |
} else {
|
| 207 | 219 |
if (logger.isDebugEnabled()) {
|
| 208 |
logger.debug("Duplicated user(" + userId + ", " + userTitle+ ")");
|
|
| 220 |
logger.debug("Duplicated user(" + userPerson +")");
|
|
| 209 | 221 |
} |
| 210 | 222 |
//continue; |
| 211 | 223 |
} |
| 212 | 224 |
|
| 213 | 225 |
if (((i % limit) == 0 && i > 1 ) || i == count ) {
|
| 214 | 226 |
|
| 215 |
commitUsers(txStatus, persons, users, |
|
| 227 |
commitUsers(txStatus, persons, users, references,
|
|
| 216 | 228 |
userUuids, i); |
| 217 | 229 |
|
| 218 | 230 |
users = null; |
| ... | ... | |
| 221 | 233 |
|
| 222 | 234 |
} |
| 223 | 235 |
if (users != null){
|
| 224 |
commitUsers(txStatus, persons, users, userUuids, i); |
|
| 236 |
commitUsers(txStatus, persons, users, references, userUuids, i);
|
|
| 225 | 237 |
users = null; |
| 226 | 238 |
persons= null; |
| 227 | 239 |
} |
| ... | ... | |
| 240 | 252 |
|
| 241 | 253 |
private void commitUsers(TransactionStatus txStatus, |
| 242 | 254 |
Map<String, AgentBase<?>> persons, |
| 243 |
Map<Integer, User> users, |
|
| 255 |
Map<String, User> users, |
|
| 256 |
Map<Integer, Reference> references, |
|
| 244 | 257 |
Map<Integer, UUID> userUuids, int i) {
|
| 258 |
|
|
| 245 | 259 |
Map<UUID, AgentBase> userMap =getAgentService().save((Collection)persons.values()); |
| 246 |
logger.info("i = " + i + " - users saved");
|
|
| 247 |
|
|
| 260 |
logger.info("i = " + i + " - persons saved");
|
|
| 261 |
|
|
| 262 |
|
|
| 263 |
|
|
| 248 | 264 |
Iterator<Entry<UUID, AgentBase>> it = userMap.entrySet().iterator(); |
| 249 | 265 |
while (it.hasNext()){
|
| 250 | 266 |
AgentBase person = it.next().getValue(); |
| ... | ... | |
| 254 | 270 |
} |
| 255 | 271 |
|
| 256 | 272 |
getUserService().save((Collection)users.values()); |
| 273 |
logger.info("i = " + users.size() + " - users saved");
|
|
| 274 |
//getReferenceService().save(references.values()); |
|
| 275 |
//logger.info("i = " +references.size() + " - references saved");
|
|
| 257 | 276 |
commitTransaction(txStatus); |
| 258 | 277 |
} |
| 259 | 278 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumDistributionImport.java | ||
|---|---|---|
| 97 | 97 |
Integer id = rs.getInt("PreferredNameIFnumber");
|
| 98 | 98 |
Taxon taxon = state.getRelatedObject(NAMESPACE_SPECIES, String.valueOf(id), Taxon.class); |
| 99 | 99 |
Reference<?> ref = null; |
| 100 |
TaxonDescription description = getTaxonDescription(taxon, ref, false, true); |
|
| 100 |
if (taxon == null){
|
|
| 101 |
logger.debug("taxon is null for id " + id);
|
|
| 102 |
} else{
|
|
| 103 |
TaxonDescription description = getTaxonDescription(taxon, ref, false, true); |
|
| 101 | 104 |
|
| 102 |
//handle single distributions |
|
| 103 |
int count = rs.getMetaData().getColumnCount(); |
|
| 104 |
for (int i=1; i <= count; i++ ){
|
|
| 105 |
String colName = rs.getMetaData().getColumnName(i); |
|
| 106 |
//exclude non distribution columns |
|
| 107 |
if (! excludedColumns.contains(colName)){
|
|
| 108 |
String distributionValue = rs.getString(i); |
|
| 109 |
if (StringUtils.isNotBlank(distributionValue)){
|
|
| 110 |
//create distribution for existing occurrences |
|
| 111 |
if (! distributionValue.equals("X")){
|
|
| 112 |
logger.warn("Unexpected distribution value '" + distributionValue + "' for area " + colName);
|
|
| 105 |
//handle single distributions |
|
| 106 |
int count = rs.getMetaData().getColumnCount(); |
|
| 107 |
for (int i=1; i <= count; i++ ){
|
|
| 108 |
String colName = rs.getMetaData().getColumnName(i); |
|
| 109 |
//exclude non distribution columns |
|
| 110 |
if (! excludedColumns.contains(colName)){
|
|
| 111 |
String distributionValue = rs.getString(i); |
|
| 112 |
if (StringUtils.isNotBlank(distributionValue)){
|
|
| 113 |
//create distribution for existing occurrences |
|
| 114 |
if (! distributionValue.equals("X")){
|
|
| 115 |
logger.warn("Unexpected distribution value '" + distributionValue + "' for area " + colName);
|
|
| 116 |
} |
|
| 117 |
NamedArea area = state.getTransformer().getNamedAreaByKey(colName); |
|
| 118 |
Distribution distribution = Distribution.NewInstance(area, status); |
|
| 119 |
description.addElement(distribution); |
|
| 120 |
//no last action |
|
| 121 |
distribution.addMarker(Marker.NewInstance(noLastActionMarkerType, true)); |
|
| 113 | 122 |
} |
| 114 |
NamedArea area = state.getTransformer().getNamedAreaByKey(colName); |
|
| 115 |
Distribution distribution = Distribution.NewInstance(area, status); |
|
| 116 |
description.addElement(distribution); |
|
| 117 |
//no last action |
|
| 118 |
distribution.addMarker(Marker.NewInstance(noLastActionMarkerType, true)); |
|
| 123 |
|
|
| 119 | 124 |
} |
| 120 |
|
|
| 121 | 125 |
} |
| 126 |
getTaxonService().saveOrUpdate(taxon); |
|
| 122 | 127 |
} |
| 123 | 128 |
|
| 124 | 129 |
//save |
| 125 |
getTaxonService().saveOrUpdate(taxon); |
|
| 130 |
|
|
| 126 | 131 |
} |
| 127 | 132 |
|
| 128 | 133 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumGeneraImport.java | ||
|---|---|---|
| 53 | 53 |
|
| 54 | 54 |
@Override |
| 55 | 55 |
protected String getIdQuery() {
|
| 56 |
String result = " SELECT RECORD_NUMBER FROM " + getTableName() +
|
|
| 57 |
" ORDER BY PreferredName ";
|
|
| 56 |
String result = " SELECT [RECORD NUMBER] FROM " + getTableName() +
|
|
| 57 |
" ORDER BY [NAME OF FUNGUS] ";
|
|
| 58 | 58 |
return result; |
| 59 | 59 |
} |
| 60 | 60 |
|
| ... | ... | |
| 64 | 64 |
@Override |
| 65 | 65 |
protected String getRecordQuery(IndexFungorumImportConfigurator config) {
|
| 66 | 66 |
String strRecordQuery = |
| 67 |
" SELECT DISTINCT c.FamilyName, c.OrderName, c.SubclassName, c.ClassName, c.SubphylumName, c.PhylumName, c.KingdomName, g.* " +
|
|
| 68 |
" FROM tblGenera AS g LEFT OUTER JOIN dbo.[tblPESIfungi-Classification] AS c ON g.RECORD_NUMBER = c.PreferredNameFDCnumber " +
|
|
| 69 |
" WHERE ( g.RECORD_NUMBER IN (" + ID_LIST_TOKEN + ") )" +
|
|
| 67 |
" SELECT DISTINCT c.[Family name], c.[Order name], c.[Subclass name], c.[Class name], c.[Subphylum name], c.[Phylum name], c.[Kingdom name], g.* " +
|
|
| 68 |
" FROM tblGenera AS g LEFT OUTER JOIN dbo.[tblPESIfungi-Classification] AS c ON g.[RECORD NUMBER] = c.PreferredNameFDCnumber " +
|
|
| 69 |
" WHERE ( g.[RECORD NUMBER] IN (" + ID_LIST_TOKEN + ") )" +
|
|
| 70 | 70 |
""; |
| 71 | 71 |
return strRecordQuery; |
| 72 | 72 |
} |
| ... | ... | |
| 86 | 86 |
//TODO |
| 87 | 87 |
//DisplayName, NomRefCache |
| 88 | 88 |
|
| 89 |
Integer id = (Integer)rs.getObject("RECORD_NUMBER");
|
|
| 89 |
Double id = (Double)rs.getObject("RECORD NUMBER");
|
|
| 90 | 90 |
|
| 91 | 91 |
|
| 92 |
String preferredName = rs.getString("PreferredName");
|
|
| 92 |
String preferredName = rs.getString("NAME OF FUNGUS");
|
|
| 93 | 93 |
if (StringUtils.isBlank(preferredName)){
|
| 94 |
logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD_NUMBER" + CdmUtils.Nz(id));
|
|
| 94 |
logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD NUMBER" + id);
|
|
| 95 | 95 |
} |
| 96 | 96 |
|
| 97 | 97 |
Rank rank = Rank.GENUS(); |
| ... | ... | |
| 105 | 105 |
//author + publication |
| 106 | 106 |
makeAuthorAndPublication(state, rs, name); |
| 107 | 107 |
//source |
| 108 |
makeSource(state, taxon, id, NAMESPACE_GENERA ); |
|
| 109 |
|
|
| 108 |
//makeSource(state, taxon, id, NAMESPACE_GENERA ); |
|
| 109 |
if (id != null){
|
|
| 110 |
makeSource(state, taxon, id.intValue(), NAMESPACE_GENERA ); |
|
| 111 |
} else{
|
|
| 112 |
makeSource(state, taxon, null,NAMESPACE_GENERA); |
|
| 113 |
} |
|
| 110 | 114 |
getTaxonService().saveOrUpdate(taxon); |
| 111 | 115 |
} |
| 112 | 116 |
|
| ... | ... | |
| 123 | 127 |
|
| 124 | 128 |
private Taxon getParentTaxon(IndexFungorumImportState state, ResultSet rs) throws SQLException {
|
| 125 | 129 |
String parentName = getParentNameString(rs); |
| 126 |
|
|
| 130 |
if (parentName == null){
|
|
| 131 |
logger.warn("Parent name not found for: " + rs.getString("NAME OF FUNGUS"));
|
|
| 132 |
} |
|
| 127 | 133 |
Taxon taxon = state.getRelatedObject(NAMESPACE_SUPRAGENERIC_NAMES, parentName, Taxon.class); |
| 128 | 134 |
if (taxon == null){
|
| 129 |
logger.warn("Taxon not found for " + parentName);
|
|
| 135 |
logger.warn("Taxon not found for " + parentName + " name of fungus: " +rs.getString("NAME OF FUNGUS") );
|
|
| 130 | 136 |
} |
| 131 | 137 |
return taxon; |
| 132 | 138 |
} |
| 133 | 139 |
|
| 134 | 140 |
|
| 135 | 141 |
private String getParentNameString(ResultSet rs) throws SQLException {
|
| 136 |
String parentName = rs.getString("FamilyName");
|
|
| 142 |
String parentName = rs.getString("Family name");
|
|
| 143 |
if (parentName == null){
|
|
| 144 |
logger.warn(rs.getObject("NAME OF FUNGUS") + " has no family name. ");
|
|
| 145 |
return null; |
|
| 146 |
} |
|
| 137 | 147 |
if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
|
| 138 |
parentName = rs.getString("OrderName");
|
|
| 148 |
parentName = rs.getString("Order name");
|
|
| 139 | 149 |
if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
|
| 140 |
parentName = rs.getString("SubclassName");
|
|
| 150 |
parentName = rs.getString("Subclass name");
|
|
| 141 | 151 |
if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
|
| 142 |
parentName = rs.getString("ClassName");
|
|
| 152 |
parentName = rs.getString("Class name");
|
|
| 143 | 153 |
if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
|
| 144 |
parentName = rs.getString("SubphylumName");
|
|
| 154 |
parentName = rs.getString("Subphylum name");
|
|
| 145 | 155 |
if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){
|
| 146 |
parentName = rs.getString("PhylumName");
|
|
| 156 |
parentName = rs.getString("Phylum name");
|
|
| 147 | 157 |
if (parentName.equalsIgnoreCase(INCERTAE_SEDIS) || parentName.equalsIgnoreCase(FOSSIL_FUNGI) ){
|
| 148 |
parentName = rs.getString("KingdomName");
|
|
| 158 |
parentName = rs.getString("Kingdom name");
|
|
| 149 | 159 |
} |
| 150 | 160 |
} |
| 151 | 161 |
} |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumHigherClassificationImport.java | ||
|---|---|---|
| 21 | 21 |
import org.springframework.stereotype.Component; |
| 22 | 22 |
import org.springframework.transaction.TransactionStatus; |
| 23 | 23 |
|
| 24 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
|
| 24 | 25 |
import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer; |
| 25 | 26 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 26 | 27 |
import eu.etaxonomy.cdm.model.common.Marker; |
| ... | ... | |
| 31 | 32 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 32 | 33 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 33 | 34 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 35 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
|
| 34 | 36 |
|
| 35 | 37 |
|
| 36 | 38 |
/** |
| ... | ... | |
| 52 | 54 |
@Override |
| 53 | 55 |
protected String getRecordQuery(IndexFungorumImportConfigurator config) {
|
| 54 | 56 |
String strRecordQuery = |
| 55 |
" SELECT DISTINCT KingdomName, PhylumName, SubphylumName, ClassName, SubclassName, OrderName, FamilyName, g.PreferredName as GenusName, c.PreferredName as SpeciesName " +
|
|
| 57 |
" SELECT DISTINCT [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name], [Family name], g.[NAME OF FUNGUS] as GenusName, c.PreferredName as SpeciesName " +
|
|
| 56 | 58 |
" FROM [tblPESIfungi-Classification] c LEFT OUTER JOIN " + |
| 57 |
" tblGenera g ON c.PreferredNameFDCnumber = g.RECORD_NUMBER" +
|
|
| 59 |
" tblGenera g ON c.PreferredNameFDCnumber = g.[RECORD NUMBER]" +
|
|
| 58 | 60 |
// " WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";
|
| 59 |
" ORDER BY KingdomName, PhylumName, SubphylumName, ClassName, SubclassName, OrderName, FamilyName, GenusName, SpeciesName ";
|
|
| 61 |
" ORDER BY [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name], [Family name], GenusName, SpeciesName ";
|
|
| 60 | 62 |
return strRecordQuery; |
| 61 | 63 |
} |
| 62 | 64 |
|
| ... | ... | |
| 102 | 104 |
|
| 103 | 105 |
try {
|
| 104 | 106 |
while (rs.next()){
|
| 105 |
String kingdom = rs.getString("KingdomName");
|
|
| 106 |
String phylum = rs.getString("PhylumName");
|
|
| 107 |
String subphylum = rs.getString("SubphylumName");
|
|
| 108 |
String classname = rs.getString("ClassName");
|
|
| 109 |
String subclass = rs.getString("SubclassName");
|
|
| 110 |
String order = rs.getString("OrderName");
|
|
| 111 |
String family = rs.getString("FamilyName");
|
|
| 107 |
String kingdom = rs.getString("Kingdom name");
|
|
| 108 |
String phylum = rs.getString("Phylum name");
|
|
| 109 |
String subphylum = rs.getString("Subphylum name");
|
|
| 110 |
String classname = rs.getString("Class name");
|
|
| 111 |
String subclass = rs.getString("Subclass name");
|
|
| 112 |
String order = rs.getString("Order name");
|
|
| 113 |
String family = rs.getString("Family name");
|
|
| 112 | 114 |
// String genus = rs.getString("GenusName");
|
| 113 | 115 |
// String species = rs.getString("SpeciesName");
|
| 114 | 116 |
|
| ... | ... | |
| 132 | 134 |
Rank newRank = (lastKingdom.equals("Fungi") ? null : Rank.PHYLUM());
|
| 133 | 135 |
taxonPhylum = makeTaxon(state, phylum, newRank); |
| 134 | 136 |
if (taxonPhylum != null){
|
| 135 |
classification.addParentChild(higherTaxon, taxonPhylum, null, null); |
|
| 137 |
classification.addParentChild(higherTaxon, taxonPhylum, null, null, true);
|
|
| 136 | 138 |
} |
| 137 | 139 |
higherTaxon = isIncertisSedis(phylum) ? higherTaxon : taxonPhylum; |
| 138 | 140 |
lastPhylum = phylum; |
| ... | ... | |
| 143 | 145 |
Rank newRank = (lastKingdom.equals("Fungi") ? null : Rank.SUBPHYLUM());
|
| 144 | 146 |
taxonSubphylum = makeTaxon(state, subphylum, newRank); |
| 145 | 147 |
if (taxonSubphylum != null){
|
| 146 |
getClassification(state).addParentChild(higherTaxon,taxonSubphylum, null, null); |
|
| 148 |
getClassification(state).addParentChild(higherTaxon,taxonSubphylum, null, null,true);
|
|
| 147 | 149 |
} |
| 148 | 150 |
higherTaxon = isIncertisSedis(subphylum) ? higherTaxon : taxonSubphylum; |
| 149 | 151 |
lastSubphylum = subphylum; |
| ... | ... | |
| 152 | 154 |
} |
| 153 | 155 |
taxonClass = makeTaxon(state, classname, Rank.CLASS()); |
| 154 | 156 |
if (taxonClass != null){
|
| 155 |
getClassification(state).addParentChild(higherTaxon, taxonClass, null, null); |
|
| 157 |
getClassification(state).addParentChild(higherTaxon, taxonClass, null, null, true);
|
|
| 156 | 158 |
} |
| 157 | 159 |
higherTaxon = isIncertisSedis(classname) ? higherTaxon : taxonClass; |
| 158 | 160 |
lastClassname = classname; |
| ... | ... | |
| 161 | 163 |
} |
| 162 | 164 |
taxonSubclass = makeTaxon(state, subclass, Rank.SUBCLASS()); |
| 163 | 165 |
if (taxonSubclass != null){
|
| 164 |
getClassification(state).addParentChild(higherTaxon, taxonSubclass,null, null); |
|
| 166 |
getClassification(state).addParentChild(higherTaxon, taxonSubclass,null, null, true);
|
|
| 165 | 167 |
} |
| 166 | 168 |
higherTaxon = isIncertisSedis(subclass) ? higherTaxon : taxonSubclass; |
| 167 | 169 |
lastSubclass = subclass; |
| ... | ... | |
| 170 | 172 |
} |
| 171 | 173 |
taxonOrder = makeTaxon(state, order, Rank.ORDER()); |
| 172 | 174 |
if (taxonOrder != null){
|
| 173 |
getClassification(state).addParentChild(higherTaxon, taxonOrder, null, null); |
|
| 175 |
getClassification(state).addParentChild(higherTaxon, taxonOrder, null, null, true);
|
|
| 174 | 176 |
} |
| 175 | 177 |
higherTaxon = isIncertisSedis(order) ? higherTaxon : taxonOrder; |
| 176 | 178 |
lastOrder = order; |
| ... | ... | |
| 179 | 181 |
} |
| 180 | 182 |
taxonFamily = makeTaxon(state, family, Rank.FAMILY()); |
| 181 | 183 |
if (taxonFamily != null){
|
| 182 |
getClassification(state).addParentChild(higherTaxon, taxonFamily, null, null); |
|
| 184 |
try{
|
|
| 185 |
getClassification(state).addParentChild(higherTaxon, taxonFamily, null, null, true); |
|
| 186 |
}catch(IllegalStateException e){
|
|
| 187 |
if (e.getMessage().startsWith("The child taxon is already part of the tree")){
|
|
| 188 |
//TaxonNode node = getClassification(state).getNode(taxonFamily); |
|
| 189 |
logger.warn(e.getMessage() + taxonFamily.getTitleCache() + " " + higherTaxon.getTitleCache()); |
|
| 190 |
|
|
| 191 |
|
|
| 192 |
|
|
| 193 |
} |
|
| 194 |
|
|
| 195 |
} |
|
| 183 | 196 |
} |
| 184 | 197 |
higherTaxon = isIncertisSedis(family) ? higherTaxon : taxonFamily; |
| 185 | 198 |
lastFamily = family; |
| ... | ... | |
| 240 | 253 |
Taxon taxon = state.getRelatedObject(IndexFungorumSupraGeneraImport.NAMESPACE_SUPRAGENERIC_NAMES, uninomial, Taxon.class); |
| 241 | 254 |
if (taxon == null){
|
| 242 | 255 |
if (! newRank.equals(Rank.KINGDOM())){
|
| 243 |
logger.warn("Taxon not found for " + uninomial);
|
|
| 256 |
logger.warn("Taxon not found for uninomial " + uninomial);
|
|
| 244 | 257 |
} |
| 245 | 258 |
NonViralName<?> name = BotanicalName.NewInstance(newRank); |
| 246 | 259 |
name.setGenusOrUninomial(uninomial); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportBase.java | ||
|---|---|---|
| 283 | 283 |
boolean hasInReference = false; |
| 284 | 284 |
//publishing authors |
| 285 | 285 |
Team pubAuthor = null; |
| 286 |
String pubAuthorStr = rs.getString("PUBLISHING_AUTHORS");
|
|
| 286 |
String pubAuthorStr = rs.getString("PUBLISHING AUTHORS");
|
|
| 287 | 287 |
if (StringUtils.isNotBlank(pubAuthorStr)){
|
| 288 | 288 |
if (StringUtils.isNotBlank(authorStr)){
|
| 289 | 289 |
if (! pubAuthorStr.equals(authorStr)){
|
| ... | ... | |
| 345 | 345 |
ref.setVolume(volume); |
| 346 | 346 |
|
| 347 | 347 |
//year |
| 348 |
String yearOfPubl = rs.getString("YEAR_OF_PUBLICATION");
|
|
| 349 |
String yearOnPubl = rs.getString("YEAR_ON_PUBLICATION");
|
|
| 348 |
String yearOfPubl = rs.getString("YEAR OF PUBLICATION");
|
|
| 349 |
String yearOnPubl = rs.getString("YEAR ON PUBLICATION");
|
|
| 350 | 350 |
String year = null; |
| 351 | 351 |
if (StringUtils.isNotBlank(yearOfPubl)){
|
| 352 | 352 |
year = yearOfPubl.trim(); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSpeciesImport.java | ||
|---|---|---|
| 58 | 58 |
|
| 59 | 59 |
@Override |
| 60 | 60 |
protected String getIdQuery() {
|
| 61 |
String result = " SELECT RECORD_NUMBER FROM " + getTableName() +
|
|
| 61 |
String result = " SELECT PreferredNameIFnumber FROM " + getTableName() +
|
|
| 62 | 62 |
" ORDER BY PreferredName "; |
| 63 | 63 |
return result; |
| 64 | 64 |
} |
| ... | ... | |
| 72 | 72 |
@Override |
| 73 | 73 |
protected String getRecordQuery(IndexFungorumImportConfigurator config) {
|
| 74 | 74 |
String strRecordQuery = |
| 75 |
" SELECT DISTINCT distribution.PreferredNameFDCnumber, species.* , cl.PhylumName" +
|
|
| 76 |
" FROM tblPESIfungi AS distribution RIGHT OUTER JOIN dbo.[tblPESIfungi-IFdata] AS species ON distribution.PreferredNameIFnumber = species.RECORD_NUMBER " +
|
|
| 75 |
" SELECT DISTINCT distribution.PreferredNameFDCnumber, species.* , cl.[Phylum name]" +
|
|
| 76 |
" FROM tblPESIfungi AS distribution RIGHT OUTER JOIN dbo.[tblPESIfungi-IFdata] AS species ON distribution.PreferredNameIFnumber = species.PreferredNameIFnumber " +
|
|
| 77 | 77 |
" LEFT OUTER JOIN [tblPESIfungi-Classification] cl ON species.PreferredName = cl.PreferredName " + |
| 78 |
" WHERE ( species.RECORD_NUMBER IN (" + ID_LIST_TOKEN + ") )" +
|
|
| 78 |
" WHERE ( species.PreferredNameIFnumber IN (" + ID_LIST_TOKEN + ") )" +
|
|
| 79 | 79 |
""; |
| 80 | 80 |
return strRecordQuery; |
| 81 | 81 |
} |
| ... | ... | |
| 93 | 93 |
|
| 94 | 94 |
//DisplayName, NomRefCache -> don't use, created by Marc |
| 95 | 95 |
|
| 96 |
Integer id = (Integer)rs.getObject("RECORD_NUMBER");
|
|
| 97 |
String phylumName = rs.getString("PhylumName");
|
|
| 96 |
Integer id = (Integer)rs.getObject("PreferredNameIFnumber");
|
|
| 97 |
String phylumName = rs.getString("Phylum name");
|
|
| 98 | 98 |
|
| 99 | 99 |
String preferredName = rs.getString("PreferredName");
|
| 100 | 100 |
if (StringUtils.isBlank(preferredName)){
|
| 101 |
logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD_NUMBER" + CdmUtils.Nz(id));
|
|
| 101 |
logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD UMBER" + CdmUtils.Nz(id));
|
|
| 102 | 102 |
} |
| 103 | 103 |
|
| 104 | 104 |
Rank rank = Rank.SPECIES(); |
| ... | ... | |
| 108 | 108 |
|
| 109 | 109 |
Taxon taxon = Taxon.NewInstance(name, sourceReference); |
| 110 | 110 |
Taxon parent = getParentTaxon(state, rs); |
| 111 |
if (parent == null){
|
|
| 112 |
logger.warn("parent not found for name:" +preferredName);
|
|
| 113 |
} |
|
| 111 | 114 |
classification.addParentChild(parent, taxon, null, null); |
| 112 | 115 |
|
| 113 | 116 |
//author + publication |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSupraGeneraImport.java | ||
|---|---|---|
| 77 | 77 |
//TODO |
| 78 | 78 |
//DisplayName, NomRefCache |
| 79 | 79 |
|
| 80 |
Integer id = (Integer)rs.getObject("RECORD_NUMBER");
|
|
| 80 |
Double id = (Double)rs.getObject("RECORD NUMBER");
|
|
| 81 | 81 |
|
| 82 |
String supragenericNames = rs.getString("SupragenericNames");
|
|
| 83 |
String preferredName = rs.getString("PreferredName");
|
|
| 82 |
String supragenericNames = rs.getString("Suprageneric names");
|
|
| 83 |
//String preferredName = rs.getString("PreferredName");
|
|
| 84 | 84 |
Integer rankFk = rs.getInt("PESI_RankFk");
|
| 85 | 85 |
|
| 86 | 86 |
//name |
| 87 | 87 |
Rank rank = state.getTransformer().getRankByKey(String.valueOf(rankFk)); |
| 88 | 88 |
NonViralName<?> name = BotanicalName.NewInstance(rank); |
| 89 | 89 |
name.setGenusOrUninomial(supragenericNames); |
| 90 |
if (preferredName != null && !preferredName.equals(supragenericNames)){
|
|
| 91 |
logger.warn("Suprageneric names and preferredName is not equal. This case is not yet handled by IF import. I take SupragenericNames for import. RECORD_NUMBER" + CdmUtils.Nz(id));
|
|
| 92 |
} |
|
| 90 |
/*if (preferredName != null && !preferredName.equals(supragenericNames)){
|
|
| 91 |
logger.warn("Suprageneric names and preferredName is not equal. This case is not yet handled by IF import. I take SupragenericNames for import. RECORD NUMBER" +id);
|
|
| 92 |
}*/
|
|
| 93 | 93 |
|
| 94 | 94 |
//taxon |
| 95 | 95 |
Taxon taxon = Taxon.NewInstance(name, sourceReference); |
| 96 | 96 |
//author + nom.ref. |
| 97 | 97 |
makeAuthorAndPublication(state, rs, name); |
| 98 | 98 |
//source |
| 99 |
makeSource(state, taxon, id, NAMESPACE_SUPRAGENERIC_NAMES ); |
|
| 100 |
|
|
| 99 |
if (id != null){
|
|
| 100 |
makeSource(state, taxon, id.intValue(), NAMESPACE_SUPRAGENERIC_NAMES ); |
|
| 101 |
} else{
|
|
| 102 |
makeSource(state, taxon, null,NAMESPACE_SUPRAGENERIC_NAMES); |
|
| 103 |
} |
|
| 101 | 104 |
getTaxonService().saveOrUpdate(taxon); |
| 102 | 105 |
} |
| 103 | 106 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java | ||
|---|---|---|
| 341 | 341 |
addSourceSourceMapping, additionalSourceMapping, isImageGallery, element); |
| 342 | 342 |
} |
| 343 | 343 |
} |
| 344 |
descriptions = null; |
|
| 344 | 345 |
return success; |
| 345 | 346 |
} |
| 346 | 347 |
|
| ... | ... | |
| 834 | 835 |
private PesiExportMapping getNotesMapping() {
|
| 835 | 836 |
PesiExportMapping mapping = new PesiExportMapping(dbNoteTableName); |
| 836 | 837 |
|
| 837 |
mapping.addMapper(IdMapper.NewInstance("NoteId"));
|
|
| 838 |
//mapping.addMapper(IdMapper.NewInstance("NoteId"));
|
|
| 838 | 839 |
mapping.addMapper(DbTextDataMapper.NewInstance(Language.ENGLISH(), "Note_1")); |
| 839 | 840 |
//TODO |
| 840 | 841 |
mapping.addMapper(MethodMapper.NewInstance("Note_2", this, DescriptionElementBase.class));
|
| ... | ... | |
| 871 | 872 |
private PesiExportMapping getOccurrenceMapping() {
|
| 872 | 873 |
PesiExportMapping mapping = new PesiExportMapping(dbOccurrenceTableName); |
| 873 | 874 |
|
| 874 |
mapping.addMapper(IdMapper.NewInstance("OccurrenceId"));
|
|
| 875 |
//mapping.addMapper(IdMapper.NewInstance("OccurrenceId"));
|
|
| 875 | 876 |
mapping.addMapper(DbDescriptionElementTaxonMapper.NewInstance("taxonFk"));
|
| 876 | 877 |
mapping.addMapper(DbDescriptionElementTaxonMapper.NewInstance("TaxonFullNameCache", true, true, null));
|
| 877 | 878 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiSourceExport.java | ||
|---|---|---|
| 422 | 422 |
PesiExportMapping mapping = new PesiExportMapping(dbTableName); |
| 423 | 423 |
ExtensionType extensionType = null; |
| 424 | 424 |
|
| 425 |
mapping.addMapper(IdMapper.NewInstance("SourceId"));
|
|
| 425 |
// mapping.addMapper(IdMapper.NewInstance("SourceId"));
|
|
| 426 | 426 |
|
| 427 | 427 |
// IMIS_Id |
| 428 | 428 |
extensionType = (ExtensionType)getTermService().find(ErmsTransformer.IMIS_UUID); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 777 | 777 |
// Increment pageNumber |
| 778 | 778 |
pageNumber++; |
| 779 | 779 |
} |
| 780 |
|
|
| 780 |
taxonList = null; |
|
| 781 | 781 |
while ((taxonList = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", Rank.SUBSPECIES(), pageSize, pageNumber)).size() > 0) {
|
| 782 | 782 |
HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>(); |
| 783 | 783 |
|
| ... | ... | |
| 866 | 866 |
// Classification could not be determined directly from this TaxonNode |
| 867 | 867 |
// The stored classification from another TaxonNode is used. It's a simple, but not a failsafe fallback solution. |
| 868 | 868 |
if (taxonNodes.size() == 0) {
|
| 869 |
logger.error("Classification could not be determined directly from this Taxon: " + acceptedTaxon.getUuid() + " is misapplication? "+acceptedTaxon.isMisapplication()+ "). The classification of the last taxon is used");
|
|
| 869 |
//logger.error("Classification could not be determined directly from this Taxon: " + acceptedTaxon.getUuid() + " is misapplication? "+acceptedTaxon.isMisapplication()+ "). The classification of the last taxon is used");
|
|
| 870 | 870 |
|
| 871 | 871 |
} |
| 872 | 872 |
} |
| ... | ... | |
| 940 | 940 |
logger.error("This TaxonBase is not a Taxon even though it should be: " + taxonBase.getUuid() + " (" + taxonBase.getTitleCache() + ")");
|
| 941 | 941 |
} |
| 942 | 942 |
} |
| 943 |
taxonList = null; |
|
| 943 | 944 |
return inferredSynonymsDataToBeSaved; |
| 944 | 945 |
} |
| 945 | 946 |
|
| ... | ... | |
| 2524 | 2525 |
private PesiExportMapping getMapping() {
|
| 2525 | 2526 |
PesiExportMapping mapping = new PesiExportMapping(dbTableName); |
| 2526 | 2527 |
|
| 2527 |
mapping.addMapper(IdMapper.NewInstance("TaxonId"));
|
|
| 2528 |
//mapping.addMapper(IdMapper.NewInstance("TaxonId"));
|
|
| 2528 | 2529 |
mapping.addMapper(DbObjectMapper.NewInstance("sec", "sourceFk")); //OLD:mapping.addMapper(MethodMapper.NewInstance("SourceFK", this.getClass(), "getSourceFk", standardMethodParameter, PesiExportState.class));
|
| 2529 | 2530 |
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusFk", this.getClass(), "getTaxonStatusFk", standardMethodParameter, PesiExportState.class));
|
| 2530 | 2531 |
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusCache", this.getClass(), "getTaxonStatusCache", standardMethodParameter, PesiExportState.class));
|
Also available in: Unified diff
changes in Fauna Europeae Import and Index Fungorum Import and PESI Export