Revision 02153b5c
Added by Andreas Müller over 11 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisCurrentSpeciesImport.java | ||
|---|---|---|
| 304 | 304 |
} |
| 305 | 305 |
|
| 306 | 306 |
private void handleCommonNames(GlobisImportState state, ResultSet rs, Taxon species) throws SQLException {
|
| 307 |
String commonNamesStr = rs.getString("vernacularnames");
|
|
| 308 |
if (isBlank(commonNamesStr)){
|
|
| 309 |
return; |
|
| 310 |
} |
|
| 311 |
String[] commonNamesSplit = commonNamesStr.split(";");
|
|
| 312 |
for (String commonNameStr : commonNamesSplit){
|
|
| 313 |
if (isBlank(commonNameStr)){
|
|
| 314 |
continue; |
|
| 315 |
} |
|
| 316 |
Language language = null; //TODO |
|
| 317 |
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameStr, language); |
|
| 318 |
TaxonDescription desc = getTaxonDescription(species, state.getTransactionalSourceReference(), false, true); |
|
| 319 |
desc.addElement(commonName); |
|
| 320 |
} |
|
| 307 |
//DON't use, use seperate common name tables instead |
|
| 308 |
|
|
| 309 |
// String commonNamesStr = rs.getString("vernacularnames");
|
|
| 310 |
// if (isBlank(commonNamesStr)){
|
|
| 311 |
// return; |
|
| 312 |
// } |
|
| 313 |
// String[] commonNamesSplit = commonNamesStr.split(";");
|
|
| 314 |
// for (String commonNameStr : commonNamesSplit){
|
|
| 315 |
// if (isBlank(commonNameStr)){
|
|
| 316 |
// continue; |
|
| 317 |
// } |
|
| 318 |
// Language language = null; //TODO |
|
| 319 |
// CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameStr, language); |
|
| 320 |
// TaxonDescription desc = getTaxonDescription(species, state.getTransactionalSourceReference(), false, true); |
|
| 321 |
// desc.addElement(commonName); |
|
| 322 |
// } |
|
| 321 | 323 |
} |
| 322 | 324 |
|
| 323 | 325 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImageImport.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.globis; |
| 11 | 11 |
|
| 12 |
import java.net.MalformedURLException; |
|
| 13 |
import java.net.URI; |
|
| 12 | 14 |
import java.sql.ResultSet; |
| 13 | 15 |
import java.sql.SQLException; |
| 14 | 16 |
import java.util.HashMap; |
| ... | ... | |
| 20 | 22 |
import org.apache.log4j.Logger; |
| 21 | 23 |
import org.springframework.stereotype.Component; |
| 22 | 24 |
|
| 25 |
import eu.etaxonomy.cdm.common.media.ImageInfo; |
|
| 23 | 26 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
| 24 | 27 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 25 | 28 |
import eu.etaxonomy.cdm.io.globis.validation.GlobisCurrentSpeciesImportValidator; |
| ... | ... | |
| 97 | 100 |
public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {
|
| 98 | 101 |
boolean success = true; |
| 99 | 102 |
|
| 100 |
Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>();
|
|
| 103 |
Set<Media> objectsToSave = new HashSet<Media>();
|
|
| 101 | 104 |
|
| 102 |
Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 105 |
// Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);
|
|
| 103 | 106 |
// Map<String, DerivedUnit> ecoFactDerivedUnitMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE); |
| 104 | 107 |
|
| 105 | 108 |
ResultSet rs = partitioner.getResultSet(); |
| 106 |
|
|
| 107 |
Classification classification = getClassification(state); |
|
| 108 | 109 |
|
| 109 | 110 |
try {
|
| 110 | 111 |
|
| ... | ... | |
| 115 | 116 |
|
| 116 | 117 |
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
|
| 117 | 118 |
|
| 118 |
Integer taxonId = rs.getInt("IDcurrentspec");
|
|
| 119 |
Integer bildID = rs.getInt("BildID");
|
|
| 120 |
|
|
| 121 |
Integer spectaxID = nullSafeInt(rs, "spectaxID"); |
|
| 119 | 122 |
|
| 123 |
//ignore: [file lab2], same as Dateiname04 but less data |
|
| 120 | 124 |
|
| 121 |
//TODO |
|
| 122 |
//String dtSpcJahr, |
|
| 123 |
//dtSpcFamakt,dtSpcSubfamakt,dtSpcTribakt, |
|
| 124 |
//fiSpcLiteratur, fiSpcspcgrptax, dtSpcCountries,vernacularnames |
|
| 125 | 125 |
|
| 126 |
try {
|
|
| 126 |
|
|
| 127 |
try {
|
|
| 127 | 128 |
|
| 128 |
//source ref
|
|
| 129 |
//source ref
|
|
| 129 | 130 |
Reference<?> sourceRef = state.getTransactionalSourceReference(); |
| 130 |
Taxon nextHigherTaxon = null; |
|
| 131 | 131 |
|
| 132 |
Taxon species = createObject(rs, state); |
|
| 132 |
//make image path |
|
| 133 |
String pathShort = rs.getString("Dateipfad_kurz");
|
|
| 134 |
String fileOS = rs.getString("file OS");
|
|
| 135 |
pathShort.replace(fileOS, ""); |
|
| 136 |
//TODO move to config |
|
| 137 |
String newPath = "http://globis-images.insects-online.de/images/"; |
|
| 138 |
String path = pathShort.replace("image:Webversionen", newPath);
|
|
| 139 |
|
|
| 133 | 140 |
|
| 134 |
//subgenus |
|
| 135 |
String subGenusStr = rs.getString("dtSpcSubgenakt");
|
|
| 136 |
String subGenusAuthorStr = rs.getString("dtSpcSubgenaktauthor");
|
|
| 137 |
boolean hasSubgenus = StringUtils.isNotBlank(subGenusStr) || StringUtils.isNotBlank(subGenusAuthorStr); |
|
| 138 |
if (hasSubgenus){
|
|
| 139 |
Taxon subGenus = getTaxon(state, rs, subGenusStr, Rank.SUBGENUS(), subGenusAuthorStr, taxonMap); |
|
| 140 |
classification.addParentChild(subGenus, species, sourceRef, null); |
|
| 141 |
nextHigherTaxon = getParent(subGenus, classification); |
|
| 142 |
} |
|
| 143 | 141 |
|
| 144 |
//genus |
|
| 145 |
String genusStr = rs.getString("dtSpcGenusakt");
|
|
| 146 |
String genusAuthorStr = rs.getString("dtSpcGenusaktauthor");
|
|
| 147 |
Taxon genus = getTaxon(state, rs, genusStr, Rank.GENUS(), genusAuthorStr, taxonMap); |
|
| 148 |
if (nextHigherTaxon != null){
|
|
| 149 |
if (! compareTaxa(genus, nextHigherTaxon)){
|
|
| 150 |
logger.warn("Current genus and parent of subgenus are not equal: " + taxonId);
|
|
| 151 |
} |
|
| 152 |
}else{
|
|
| 153 |
classification.addParentChild(genus, species, sourceRef, null); |
|
| 154 |
nextHigherTaxon = getParent(genus, classification); |
|
| 155 |
} |
|
| 142 |
Media media1 = makeMedia(state, rs, "file OS", "Legende 1", path ); |
|
| 143 |
Media media2 = makeMedia(state, rs, "Dateiname02", "Legende 2", path ); |
|
| 144 |
Media media3 = makeMedia(state, rs, "Dateiname03", "Legende 3", path ); |
|
| 145 |
Media media4 = makeMedia(state, rs, "Dateiname04", "Legende 4", path ); |
|
| 146 |
|
|
| 156 | 147 |
|
| 157 |
this.doIdCreatedUpdatedNotes(state, species, rs, taxonId, REFERENCE_NAMESPACE); |
|
| 148 |
//TODO |
|
| 149 |
this.doIdCreatedUpdatedNotes(state, media1, rs, bildID, IMAGE_NAMESPACE); |
|
| 158 | 150 |
|
| 159 |
objectsToSave.add(species);
|
|
| 151 |
save(objectsToSave, media1);
|
|
| 160 | 152 |
|
| 153 |
|
|
| 161 | 154 |
|
| 162 | 155 |
} catch (Exception e) {
|
| 163 |
logger.warn("Exception in current_species: IDcurrentspec " + taxonId + ". " + e.getMessage());
|
|
| 156 |
logger.warn("Exception in Einzelbilder: bildID " + bildID + ". " + e.getMessage());
|
|
| 164 | 157 |
// e.printStackTrace(); |
| 165 | 158 |
} |
| 166 | 159 |
|
| ... | ... | |
| 169 | 162 |
// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
|
| 170 | 163 |
|
| 171 | 164 |
logger.warn(pluralString + " to save: " + objectsToSave.size()); |
| 172 |
getTaxonService().save(objectsToSave);
|
|
| 165 |
getMediaService().save(objectsToSave);
|
|
| 173 | 166 |
|
| 174 | 167 |
return success; |
| 175 | 168 |
} catch (SQLException e) {
|
| ... | ... | |
| 178 | 171 |
} |
| 179 | 172 |
} |
| 180 | 173 |
|
| 181 |
/** |
|
| 182 |
* Compares 2 taxa, returns true of both taxa look similar |
|
| 183 |
* @param genus |
|
| 184 |
* @param nextHigherTaxon |
|
| 185 |
* @return |
|
| 186 |
*/ |
|
| 187 |
private boolean compareTaxa(Taxon taxon1, Taxon taxon2) {
|
|
| 188 |
ZoologicalName name1 = CdmBase.deproxy(taxon1.getName(), ZoologicalName.class); |
|
| 189 |
ZoologicalName name2 = CdmBase.deproxy(taxon2.getName(), ZoologicalName.class); |
|
| 190 |
if (!name1.getRank().equals(name2.getRank())){
|
|
| 191 |
return false; |
|
| 192 |
} |
|
| 193 |
if (! name1.getTitleCache().equals(name2.getTitleCache())){
|
|
| 194 |
return false; |
|
| 174 |
private void save(Set<Media> objectsToSave, Media media) {
|
|
| 175 |
if (media != null){
|
|
| 176 |
objectsToSave.add(media); |
|
| 195 | 177 |
} |
| 196 |
return true; |
|
| 197 | 178 |
} |
| 198 | 179 |
|
| 199 | 180 |
|
| 200 | 181 |
|
| 201 | 182 |
|
| 202 |
private Taxon getParent(Taxon subgenus, Classification classification) {
|
|
| 203 |
for (TaxonNode node : subgenus.getTaxonNodes()){
|
|
| 204 |
if (node.getClassification().equals(classification)){
|
|
| 205 |
return node.getParent().getTaxon(); |
|
| 206 |
} |
|
| 183 |
private Media makeMedia(GlobisImportState state, ResultSet rs, String fileNameAttr, String legendAttr, String path) throws SQLException {
|
|
| 184 |
Media media = null; |
|
| 185 |
String fileName = rs.getString(fileNameAttr); |
|
| 186 |
String legend = rs.getString(legendAttr); |
|
| 187 |
|
|
| 188 |
URI uri = URI.create(path+fileName); |
|
| 189 |
|
|
| 190 |
// Media media = ImageInfo.NewInstanceWithMetaData(uri, null); |
|
| 191 |
|
|
| 192 |
try {
|
|
| 193 |
media = this.getImageMedia(uri.toString(), true, false); |
|
| 194 |
media.putTitle(Language.ENGLISH(), legend); |
|
| 195 |
} catch (MalformedURLException e) {
|
|
| 196 |
e.printStackTrace(); |
|
| 207 | 197 |
} |
| 208 |
return null; |
|
| 198 |
|
|
| 199 |
return media; |
|
| 209 | 200 |
} |
| 210 | 201 |
|
| 211 | 202 |
|
| ... | ... | |
| 225 | 216 |
} |
| 226 | 217 |
|
| 227 | 218 |
|
| 228 |
//fast and dirty is enough here |
|
| 229 |
private Classification classification; |
|
| 230 |
|
|
| 231 |
private Classification getClassification(GlobisImportState state) {
|
|
| 232 |
if (this.classification == null){
|
|
| 233 |
String name = state.getConfig().getClassificationName(); |
|
| 234 |
Reference<?> reference = state.getTransactionalSourceReference(); |
|
| 235 |
this.classification = Classification.NewInstance(name, reference, Language.DEFAULT()); |
|
| 236 |
classification.setUuid(state.getConfig().getClassificationUuid()); |
|
| 237 |
getClassificationService().save(classification); |
|
| 238 |
} |
|
| 239 |
return this.classification; |
|
| 240 |
|
|
| 241 |
} |
|
| 242 |
|
|
| 243 |
private INonViralNameParser parser = NonViralNameParserImpl.NewInstance(); |
|
| 244 |
|
|
| 245 | 219 |
|
| 246 |
/* (non-Javadoc) |
|
| 247 |
* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase) |
|
| 248 |
*/ |
|
| 249 |
public Taxon createObject(ResultSet rs, GlobisImportState state) |
|
| 250 |
throws SQLException {
|
|
| 251 |
String speciesEpi = rs.getString("dtSpcSpcakt");
|
|
| 252 |
String subGenusEpi = rs.getString("dtSpcSubgenakt");
|
|
| 253 |
String genusEpi = rs.getString("dtSpcGenusakt");
|
|
| 254 |
String author = rs.getString("dtSpcAutor");
|
|
| 255 |
|
|
| 256 |
|
|
| 257 |
ZoologicalName zooName = ZoologicalName.NewInstance(Rank.SPECIES()); |
|
| 258 |
zooName.setSpecificEpithet(speciesEpi); |
|
| 259 |
if (StringUtils.isNotBlank(subGenusEpi)){
|
|
| 260 |
zooName.setInfraSpecificEpithet(subGenusEpi); |
|
| 261 |
} |
|
| 262 |
zooName.setGenusOrUninomial(genusEpi); |
|
| 263 |
handleAuthorAndYear(author, zooName); |
|
| 264 |
|
|
| 265 |
Taxon taxon = Taxon.NewInstance(zooName, state.getTransactionalSourceReference()); |
|
| 266 |
|
|
| 267 |
return taxon; |
|
| 268 |
} |
|
| 269 | 220 |
|
| 270 | 221 |
|
| 271 | 222 |
/* (non-Javadoc) |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisReferenceImport.java | ||
|---|---|---|
| 20 | 20 |
import org.apache.log4j.Logger; |
| 21 | 21 |
import org.springframework.stereotype.Component; |
| 22 | 22 |
|
| 23 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
|
| 24 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType; |
|
| 25 |
import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportState; |
|
| 26 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport; |
|
| 27 | 23 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
| 28 | 24 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
| 29 | 25 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 30 |
import eu.etaxonomy.cdm.io.common.mapping.DbIgnoreMapper; |
|
| 31 |
import eu.etaxonomy.cdm.io.common.mapping.DbImportExtensionMapper; |
|
| 32 |
import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping; |
|
| 33 |
import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectCreationMapper; |
|
| 34 |
import eu.etaxonomy.cdm.io.common.mapping.DbImportStringMapper; |
|
| 35 |
import eu.etaxonomy.cdm.io.common.mapping.DbNotYetImplementedMapper; |
|
| 36 | 26 |
import eu.etaxonomy.cdm.io.common.mapping.IMappingImport; |
| 37 | 27 |
import eu.etaxonomy.cdm.io.globis.validation.GlobisReferenceImportValidator; |
| 38 | 28 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 39 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
| 40 |
import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
|
| 41 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
| 42 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
| 43 | 29 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 44 | 30 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 45 | 31 |
import eu.etaxonomy.cdm.model.reference.ReferenceType; |
| 46 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 47 | 32 |
|
| 48 | 33 |
|
| 49 | 34 |
/** |
| ... | ... | |
| 212 | 197 |
*/ |
| 213 | 198 |
public Reference<?> createObject(ResultSet rs, GlobisImportState state) |
| 214 | 199 |
throws SQLException {
|
| 200 |
String refJournal = rs.getString("RefJournal");
|
|
| 201 |
boolean isInJournal =isNotBlank(refJournal); |
|
| 202 |
String refBookTitle = rs.getString("RefBookTitle");
|
|
| 203 |
boolean isInBook =isNotBlank(refBookTitle); |
|
| 204 |
|
|
| 205 |
|
|
| 206 |
|
|
| 215 | 207 |
Reference<?> ref; |
| 216 | 208 |
String refType = rs.getString("RefType");
|
| 217 | 209 |
if (refType == null){
|
| 218 |
ref = ReferenceFactory.newGeneric(); |
|
| 210 |
if (isInJournal && ! isInBook){
|
|
| 211 |
ref = ReferenceFactory.newArticle(); |
|
| 212 |
}else{
|
|
| 213 |
ref = ReferenceFactory.newGeneric(); |
|
| 214 |
} |
|
| 219 | 215 |
}else if (refType.equals("book")){
|
| 220 | 216 |
ref = ReferenceFactory.newBook(); |
| 221 | 217 |
}else if (refType.equals("paper in journal")){
|
| ... | ... | |
| 226 | 222 |
ref = ReferenceFactory.newArticle(); |
| 227 | 223 |
}else if (refType.equals("paper in book")){
|
| 228 | 224 |
ref = ReferenceFactory.newBookSection(); |
| 229 |
}else if (refType.equals("paper in journalwebsite")){
|
|
| 225 |
}else if (refType.matches("paper in journal.*website.*")){
|
|
| 230 | 226 |
ref = ReferenceFactory.newArticle(); |
| 231 | 227 |
}else{
|
| 232 | 228 |
logger.warn("Unknown reference type: " + refType);
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.java | ||
|---|---|---|
| 148 | 148 |
}else if (specSystaxRank.equals("synonym")){
|
| 149 | 149 |
Synonym synonym = getSynonym(state, rs); |
| 150 | 150 |
if (acceptedTaxon == null){
|
| 151 |
//TODO |
|
| 152 |
logger.warn("Accepted taxon (" + acceptedTaxonId + ") not found for synonym "+ specTaxId);
|
|
| 151 |
if (acceptedTaxonId == null){
|
|
| 152 |
logger.warn("Synonym has no accepted taxon defined. SpecTaxId: "+ specTaxId);
|
|
| 153 |
}else{
|
|
| 154 |
logger.warn("Accepted taxon (" + acceptedTaxonId + ") not found for synonym "+ specTaxId);
|
|
| 155 |
} |
|
| 153 | 156 |
}else{
|
| 154 | 157 |
acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF()); |
| 155 | 158 |
thisTaxon = synonym; |
| ... | ... | |
| 200 | 203 |
|
| 201 | 204 |
private void handleTypeInformation(GlobisImportState state, ResultSet rs, ZoologicalName name, Integer specTaxId) throws SQLException {
|
| 202 | 205 |
|
| 203 |
String specTypeDepositoriesStr = rs.getString("SpecTypeDepository");
|
|
| 204 |
String countryString = rs.getString("SpecTypeCountry");
|
|
| 205 | 206 |
|
| 206 |
if (! hasTypeInformation(specTypeDepositoriesStr, countryString)){
|
|
| 207 |
if (! hasTypeInformation(rs)){
|
|
| 207 | 208 |
return; |
| 208 | 209 |
} |
| 209 | 210 |
|
| 210 |
FieldObservation fieldObservation = makeTypeFieldObservation(state, countryString);
|
|
| 211 |
FieldObservation fieldObservation = makeTypeFieldObservation(state, rs);
|
|
| 211 | 212 |
|
| 213 |
//typeDepository |
|
| 214 |
String specTypeDepositoriesStr = rs.getString("SpecTypeDepository");
|
|
| 212 | 215 |
String[] specTypeDepositories; |
| 213 | 216 |
if (isNotBlank(specTypeDepositoriesStr) ){
|
| 214 |
specTypeDepositories = specTypeDepositoriesStr.split(";");
|
|
| 217 |
specTypeDepositories = specTypeDepositoriesStr.trim().split(";");
|
|
| 215 | 218 |
}else{
|
| 216 | 219 |
specTypeDepositories = new String[0]; |
| 217 | 220 |
} |
| 218 |
//TODO different issues |
|
| 221 |
|
|
| 222 |
//TODO several issues |
|
| 219 | 223 |
if (specTypeDepositories.length == 0){
|
| 220 |
logger.warn("SpecTax has type information but no SpecTypeDepository. specTaxId: " + specTaxId);
|
|
| 224 |
Specimen specimen = makeSingleTypeSpecimen(fieldObservation); |
|
| 225 |
makeTypeDesignation(name, rs, specimen); |
|
| 221 | 226 |
} |
| 222 | 227 |
for (String specTypeDepositoryStr : specTypeDepositories){
|
| 223 | 228 |
specTypeDepositoryStr = specTypeDepositoryStr.trim(); |
| ... | ... | |
| 227 | 232 |
|
| 228 | 233 |
if (specTypeDepositoryStr.equals("??")){
|
| 229 | 234 |
//unknown |
| 230 |
//TODO |
|
| 231 | 235 |
specimen.setTitleCache("??", true);
|
| 232 | 236 |
}else{
|
| 233 | 237 |
specTypeDepositoryStr = makeAdditionalSpecimenInformation( |
| 234 |
specTypeDepositoryStr, specimen); |
|
| 238 |
specTypeDepositoryStr, specimen, specTaxId);
|
|
| 235 | 239 |
|
| 236 |
makeCollection(specTypeDepositoryStr, specimen); |
|
| 240 |
makeCollection(specTypeDepositoryStr, specimen, specTaxId);
|
|
| 237 | 241 |
} |
| 238 | 242 |
|
| 239 | 243 |
//type Designation |
| ... | ... | |
| 246 | 250 |
|
| 247 | 251 |
|
| 248 | 252 |
|
| 249 |
private boolean hasTypeInformation(String specTypeDepositoriesStr, String countryString) {
|
|
| 253 |
private boolean hasTypeInformation(ResultSet rs) throws SQLException {
|
|
| 254 |
String specTypeDepositoriesStr = rs.getString("SpecTypeDepository");
|
|
| 255 |
String countryString = rs.getString("SpecTypeCountry");
|
|
| 256 |
String specType = rs.getString("SpecType");
|
|
| 250 | 257 |
boolean result = false; |
| 251 |
result |= isNotBlank(specTypeDepositoriesStr) || isNotBlank(countryString); |
|
| 258 |
result |= isNotBlank(specTypeDepositoriesStr) || isNotBlank(countryString) |
|
| 259 |
|| isNotBlank(specType); |
|
| 252 | 260 |
return result; |
| 253 | 261 |
} |
| 254 | 262 |
|
| ... | ... | |
| 257 | 265 |
/** |
| 258 | 266 |
* @param specTypeDepositoryStr |
| 259 | 267 |
* @param specimen |
| 268 |
* @param specTaxId |
|
| 260 | 269 |
*/ |
| 261 |
protected void makeCollection(String specTypeDepositoryStr, Specimen specimen) {
|
|
| 270 |
protected void makeCollection(String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
|
|
| 262 | 271 |
//TODO deduplicate |
| 263 | 272 |
Map<String, Collection> collectionMap = new HashMap<String, Collection>(); |
| 264 | 273 |
|
| 265 | 274 |
|
| 266 | 275 |
//Collection |
| 267 |
String[] split = specTypeDepositoryStr.split(",");
|
|
| 268 |
if (split.length != 2){
|
|
| 269 |
if (split.length == 1 && split[0].startsWith("coll.")){
|
|
| 270 |
Collection collection = Collection.NewInstance(); |
|
| 271 |
collection.setName(split[0]); |
|
| 272 |
}else{
|
|
| 273 |
logger.warn("Split size is not 2: " + specTypeDepositoryStr);
|
|
| 274 |
} |
|
| 275 |
|
|
| 276 |
specTypeDepositoryStr = specTypeDepositoryStr.replace("Washington, D.C.", "Washington@ D.C.");
|
|
| 277 |
|
|
| 278 |
if (specTypeDepositoryStr.equals("BMNH, London and/or MNHN, Paris")){
|
|
| 279 |
//TODO deduplicate |
|
| 280 |
Collection collection = Collection.NewInstance(); |
|
| 281 |
collection.setName(specTypeDepositoryStr); |
|
| 282 |
specimen.setCollection(collection); |
|
| 283 |
}else if (specTypeDepositoryStr.equals("coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov, Moscow")){
|
|
| 284 |
Collection collection = Collection.NewInstance(); |
|
| 285 |
collection.setName("coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov");
|
|
| 286 |
collection.setTownOrLocation("Moscow");
|
|
| 287 |
specimen.setCollection(collection); |
|
| 288 |
}else if (specTypeDepositoryStr.matches("coll. R. E. Parrott?, Port Hope, Ontario")){
|
|
| 289 |
//TODO deduplicate |
|
| 290 |
Collection collection = Collection.NewInstance(); |
|
| 291 |
collection.setName("coll. R. E. Parrott");
|
|
| 292 |
collection.setTownOrLocation("Port Hope, Ontario");
|
|
| 293 |
specimen.setCollection(collection); |
|
| 276 | 294 |
}else{
|
| 277 |
String collectionStr = split[0]; |
|
| 278 |
String location = split[1]; |
|
| 279 | 295 |
|
| 280 |
|
|
| 281 |
Collection collection = collectionMap.get(collectionStr); |
|
| 282 |
if (collection == null){
|
|
| 283 |
collection = Collection.NewInstance(); |
|
| 284 |
collection.setCode(collectionStr); |
|
| 285 |
collection.setTownOrLocation(split[1]); |
|
| 286 |
}else if (CdmUtils.nullSafeEqual(location, collection.getTownOrLocation())){
|
|
| 287 |
String message = "Location (%s) is not equal to location (%s) of existing collection"; |
|
| 288 |
logger.warn(String.format(message, location, collection.getTownOrLocation(), collection.getCode())); |
|
| 296 |
String[] split = specTypeDepositoryStr.split(",");
|
|
| 297 |
if (split.length != 2){
|
|
| 298 |
if (split.length == 1 && split[0].startsWith("coll.")){
|
|
| 299 |
Collection collection = Collection.NewInstance(); |
|
| 300 |
collection.setName(split[0]); |
|
| 301 |
specimen.setCollection(collection); |
|
| 302 |
}else{
|
|
| 303 |
logger.warn("Split size is not 2: " + specTypeDepositoryStr + " (specTaxID:" + specTaxId + ")");
|
|
| 304 |
} |
|
| 305 |
|
|
| 306 |
}else{
|
|
| 307 |
String collectionStr = split[0]; |
|
| 308 |
String location = split[1].replace("Washington@ D.C.", "Washington, D.C.");
|
|
| 309 |
|
|
| 310 |
Collection collection = collectionMap.get(collectionStr); |
|
| 311 |
if (collection == null){
|
|
| 312 |
collection = Collection.NewInstance(); |
|
| 313 |
collection.setCode(collectionStr); |
|
| 314 |
collection.setTownOrLocation(split[1]); |
|
| 315 |
}else if (CdmUtils.nullSafeEqual(location, collection.getTownOrLocation())){
|
|
| 316 |
String message = "Location (%s) is not equal to location (%s) of existing collection"; |
|
| 317 |
logger.warn(String.format(message, location, collection.getTownOrLocation(), collection.getCode())); |
|
| 318 |
} |
|
| 319 |
|
|
| 320 |
specimen.setCollection(collection); |
|
| 321 |
|
|
| 289 | 322 |
} |
| 290 |
|
|
| 291 |
specimen.setCollection(collection); |
|
| 292 |
|
|
| 293 | 323 |
} |
| 294 | 324 |
} |
| 295 | 325 |
|
| ... | ... | |
| 300 | 330 |
* @param specTypeDepositoriesStr |
| 301 | 331 |
* @param specTypeDepositoryStr |
| 302 | 332 |
* @param specimen |
| 333 |
* @param specTaxId |
|
| 303 | 334 |
* @return |
| 304 | 335 |
*/ |
| 305 |
protected String makeAdditionalSpecimenInformation( String specTypeDepositoryStr, |
|
| 306 |
Specimen specimen) {
|
|
| 336 |
protected String makeAdditionalSpecimenInformation( String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
|
|
| 307 | 337 |
//doubful |
| 308 | 338 |
if (specTypeDepositoryStr.endsWith("?")){
|
| 309 | 339 |
Marker.NewInstance(specimen, true, MarkerType.IS_DOUBTFUL()); |
| ... | ... | |
| 321 | 351 |
brackets = brackets.replace("[m]", "\u2642");
|
| 322 | 352 |
brackets = brackets.replace("[ff]", "\u2640\u2640");
|
| 323 | 353 |
brackets = brackets.replace("[f]", "\u2640");
|
| 354 |
brackets = brackets.replace("[m/f]", "\u26a5");
|
|
| 324 | 355 |
|
| 325 | 356 |
if (brackets.contains("[") || brackets.contains("]")){
|
| 326 |
logger.warn ("There are still '[', ']' in the bracket part: " + brackets);
|
|
| 357 |
logger.warn ("There are still '[', ']' in the bracket part: " + brackets + "; specTaxId: " + specTaxId);
|
|
| 327 | 358 |
} |
| 328 | 359 |
|
| 329 | 360 |
//TODO replace mm/ff by Unicode male |
| ... | ... | |
| 358 | 389 |
* @throws SQLException |
| 359 | 390 |
*/ |
| 360 | 391 |
protected FieldObservation makeTypeFieldObservation(GlobisImportState state, |
| 361 |
String countryString) throws SQLException {
|
|
| 392 |
ResultSet rs) throws SQLException {
|
|
| 393 |
|
|
| 394 |
String countryString = rs.getString("SpecTypeCountry");
|
|
| 362 | 395 |
|
| 363 | 396 |
DerivedUnitType unitType = DerivedUnitType.Specimen; |
| 364 | 397 |
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(unitType); |
| ... | ... | |
| 401 | 434 |
return SpecimenTypeDesignationStatus.HOLOTYPE(); |
| 402 | 435 |
}else if (specType.matches("Neotype")){
|
| 403 | 436 |
return SpecimenTypeDesignationStatus.NEOTYPE(); |
| 404 |
}else if (specType.matches("Syntype(\\(s\\))?")){
|
|
| 437 |
}else if (specType.matches("Syntype(\\(s\\))?") || specType.matches("Syntype.*Syntype\\(s\\)\\s*") ){
|
|
| 405 | 438 |
return SpecimenTypeDesignationStatus.SYNTYPE(); |
| 406 | 439 |
}else if (specType.matches("Lectotype")){
|
| 407 | 440 |
return SpecimenTypeDesignationStatus.LECTOTYPE(); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisTransformer.java | ||
|---|---|---|
| 221 | 221 |
}else if (area.equals("Gambia")){return WaterbodyOrCountry.GAMBIAREPUBLICOFTHE();
|
| 222 | 222 |
}else if (area.equals("Dominica")){return WaterbodyOrCountry.DOMINICACOMMONWEALTHOF();
|
| 223 | 223 |
}else if (area.equals("Liechtenstein")){return WaterbodyOrCountry.LIECHTENSTEINPRINCIPALITYOF();
|
| 224 |
}else if (area.matches("B(y)?elarus")){return WaterbodyOrCountry.BELARUS();
|
|
| 225 |
|
|
| 224 | 226 |
|
| 225 |
|
|
| 226 | 227 |
|
| 227 | 228 |
|
| 228 | 229 |
|
Also available in: Unified diff
update Globis import