Revision f2be28b3
Added by Andreas Müller over 11 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImageImport.java | ||
|---|---|---|
| 18 | 18 |
import java.util.HashSet; |
| 19 | 19 |
import java.util.Map; |
| 20 | 20 |
import java.util.Set; |
| 21 |
import java.util.UUID; |
|
| 22 |
import java.util.regex.Matcher; |
|
| 23 |
import java.util.regex.Pattern; |
|
| 21 | 24 |
|
| 22 | 25 |
import org.apache.http.client.ClientProtocolException; |
| 23 | 26 |
import org.apache.log4j.Logger; |
| ... | ... | |
| 28 | 31 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
| 29 | 32 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 30 | 33 |
import eu.etaxonomy.cdm.io.globis.validation.GlobisImageImportValidator; |
| 34 |
import eu.etaxonomy.cdm.model.common.Annotation; |
|
| 31 | 35 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 32 | 36 |
import eu.etaxonomy.cdm.model.common.Language; |
| 37 |
import eu.etaxonomy.cdm.model.common.Marker; |
|
| 38 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
|
| 33 | 39 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 34 |
import eu.etaxonomy.cdm.model.description.SpecimenDescription; |
|
| 40 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
| 41 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
| 35 | 42 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 36 | 43 |
import eu.etaxonomy.cdm.model.media.Media; |
| 44 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
|
| 45 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
|
| 46 |
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent; |
|
| 37 | 47 |
import eu.etaxonomy.cdm.model.occurrence.Specimen; |
| 38 | 48 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 49 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
| 39 | 50 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 51 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 40 | 52 |
|
| 41 | 53 |
|
| 42 | 54 |
/** |
| ... | ... | |
| 49 | 61 |
private static final Logger logger = Logger.getLogger(GlobisImageImport.class); |
| 50 | 62 |
|
| 51 | 63 |
private int modCount = 10000; |
| 64 |
|
|
| 65 |
private UUID uuidArtNonSpecTaxMarkerType = UUID.fromString("be362085-0f5b-4314-96d1-78b9b129ef6d") ;
|
|
| 52 | 66 |
private static final String pluralString = "images"; |
| 53 | 67 |
private static final String dbTableName = "Einzelbilder"; |
| 54 |
private static final Class cdmTargetClass = Media |
|
| 55 |
.class; //not needed |
|
| 68 |
private static final Class cdmTargetClass = Media.class; //not needed |
|
| 56 | 69 |
|
| 57 | 70 |
private static final String IMAGE_NAMESPACE = "Einzelbilder"; |
| 71 |
private static UUID uuidGartRef = UUID.fromString("af85470f-6e54-4304-9d29-fd117cd56161");
|
|
| 58 | 72 |
|
| 59 | 73 |
public GlobisImageImport(){
|
| 60 | 74 |
super(pluralString, dbTableName, cdmTargetClass); |
| ... | ... | |
| 105 | 119 |
Map<String, Specimen> typeMap = (Map<String, Specimen>) partitioner.getObjectMap(GlobisSpecTaxImport.TYPE_NAMESPACE); |
| 106 | 120 |
|
| 107 | 121 |
Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE); |
| 108 |
// Map<String, DerivedUnit> ecoFactDerivedUnitMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE);
|
|
| 122 |
Map<String, ZoologicalName> specTaxNameMap = (Map<String, ZoologicalName>) partitioner.getObjectMap(GlobisSpecTaxImport.SPEC_TAX_NAMESPACE);
|
|
| 109 | 123 |
|
| 110 | 124 |
ResultSet rs = partitioner.getResultSet(); |
| 111 | 125 |
|
| 126 |
Reference<?> refGart = getReferenceService().find(uuidGartRef); |
|
| 127 |
|
|
| 128 |
|
|
| 112 | 129 |
try {
|
| 113 | 130 |
|
| 114 | 131 |
int i = 0; |
| 115 | 132 |
|
| 116 |
//for each reference
|
|
| 133 |
//for each record
|
|
| 117 | 134 |
while (rs.next()){
|
| 118 | 135 |
|
| 119 | 136 |
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
|
| 120 | 137 |
|
| 121 | 138 |
Integer bildID = rs.getInt("BildID");
|
| 122 |
|
|
| 123 | 139 |
Integer spectaxID = nullSafeInt(rs, "spectaxID"); |
| 124 |
|
|
| 125 | 140 |
Integer taxonID = nullSafeInt(rs, "SpecCurrspecID"); |
| 126 |
|
|
| 127 | 141 |
String copyright = rs.getString("copyright");
|
| 142 |
String specimenId = rs.getString("specimenID");
|
|
| 143 |
String bemerkungen = rs.getString("Bemerkungen");
|
|
| 144 |
String artNotSpecTax = rs.getString("Art non spectax");
|
|
| 145 |
String motiv = rs.getString("Motiv");
|
|
| 128 | 146 |
|
| 129 | 147 |
//ignore: |
| 130 | 148 |
// [file lab2], same as Dateiname04 but less data |
| 131 | 149 |
// Dateipfad |
| 150 |
|
|
| 132 | 151 |
Set<Media> recordMedia = new HashSet<Media>(); |
| 133 | 152 |
|
| 134 | 153 |
try {
|
| 135 | 154 |
|
| 136 |
//make image path |
|
| 137 |
String pathShort = rs.getString("Dateipfad_kurz");
|
|
| 138 |
String fileOS = rs.getString("file OS");
|
|
| 139 |
pathShort= pathShort.replace(fileOS, ""); |
|
| 140 |
String newPath = state.getConfig().getImageBaseUrl(); |
|
| 141 |
String path = pathShort.replace("image:Webversionen/", newPath);
|
|
| 142 |
|
|
| 143 |
Media singleMedia = makeMedia(state, rs, "file OS", "Legende 1", path, objectsToSave ); |
|
| 144 |
recordMedia.add(singleMedia); |
|
| 145 |
singleMedia = makeMedia(state, rs, "Dateinamen02", "Legende 2", path, objectsToSave ); |
|
| 146 |
recordMedia.add(singleMedia); |
|
| 147 |
singleMedia = makeMedia(state, rs, "Dateinamen03", "Legende 3", path, objectsToSave ); |
|
| 148 |
recordMedia.add(singleMedia); |
|
| 149 |
singleMedia = makeMedia(state, rs, "Dateinamen04", "Legende 4", path, objectsToSave ); |
|
| 150 |
recordMedia.add(singleMedia); |
|
| 151 |
|
|
| 152 |
if (spectaxID != null){
|
|
| 155 |
makeAllMedia(state, rs, recordMedia, objectsToSave); |
|
| 156 |
|
|
| 157 |
String title = null; |
|
| 158 |
|
|
| 159 |
Specimen specimen = null; |
|
| 160 |
if (spectaxID != null){
|
|
| 161 |
//try to find type specimen |
|
| 162 |
if (isNotBlank(motiv) && (motiv.startsWith("type specimen"))){
|
|
| 163 |
String collectionCode = transformCopyright2CollectionCode(copyright); |
|
| 164 |
String id = GlobisSpecTaxImport.getTypeId(spectaxID, collectionCode); |
|
| 165 |
specimen = typeMap.get(id); |
|
| 166 |
} |
|
| 167 |
|
|
| 168 |
//try to find specTaxName |
|
| 169 |
ZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID)); |
|
| 170 |
if (specTaxTaxonName != null){
|
|
| 171 |
title = " taxon name " + specTaxTaxonName.getTitleCache(); |
|
| 172 |
}else{
|
|
| 173 |
title = " spectaxID " + spectaxID; |
|
| 174 |
} |
|
| 175 |
}else{
|
|
| 176 |
title = " name " + getNameFromFileOs(rs) + (isBlank(specimenId)? "" : " (specimenId: " + specimenId + ")"); |
|
| 177 |
} |
|
| 178 |
|
|
| 179 |
//not type specimen |
|
| 180 |
if (specimen == null){
|
|
| 181 |
specimen = Specimen.NewInstance(); |
|
| 182 |
specimen.setTitleCache("Specimen for " + title );
|
|
| 153 | 183 |
String collectionCode = transformCopyright2CollectionCode(copyright); |
| 154 |
String id = GlobisSpecTaxImport.getTypeId(spectaxID, collectionCode); |
|
| 155 |
Specimen typeSpecimen = typeMap.get(id); |
|
| 156 |
if (typeSpecimen != null){
|
|
| 157 |
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(typeSpecimen); |
|
| 158 |
for (Media media: recordMedia){
|
|
| 159 |
facade.addDerivedUnitMedia(media); |
|
| 160 |
} |
|
| 161 |
}else{
|
|
| 162 |
//TODO |
|
| 163 |
} |
|
| 164 |
}else{
|
|
| 165 | 184 |
//TODO |
| 185 |
Collection collection = getCollection(collectionCode); |
|
| 186 |
specimen.setCollection(collection); |
|
| 166 | 187 |
} |
| 167 | 188 |
|
| 168 | 189 |
|
| 190 |
//source |
|
| 191 |
specimen.addSource(String.valueOf(bildID), IMAGE_NAMESPACE, state.getTransactionalSourceReference(), null); |
|
| 169 | 192 |
|
| 193 |
//GART id (specimenID) |
|
| 194 |
if (isNotBlank(specimenId)){
|
|
| 195 |
specimen.addSource(specimenId, "", refGart, null); |
|
| 196 |
} |
|
| 197 |
//bemerkungen |
|
| 198 |
if (isNotBlank(bemerkungen)){
|
|
| 199 |
Annotation annotation = Annotation.NewInstance(bemerkungen, null, null); |
|
| 200 |
specimen.addAnnotation(annotation); |
|
| 201 |
} |
|
| 202 |
//media |
|
| 203 |
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(specimen); |
|
| 204 |
for (Media media: recordMedia){
|
|
| 205 |
facade.addDerivedUnitMedia(media); |
|
| 206 |
} |
|
| 207 |
//art non spectax |
|
| 208 |
if (isNotBlank(artNotSpecTax)){
|
|
| 209 |
if (artNotSpecTax.equalsIgnoreCase("ja")){
|
|
| 210 |
MarkerType artNotSpecTaxMarker = getMarkerType(state, uuidArtNonSpecTaxMarkerType , "Art non spectax", "This marker is true if in the orginal data the 'Art non spectax' was 'ja'", null) ; |
|
| 211 |
specimen.addMarker(Marker.NewInstance(artNotSpecTaxMarker, true)); |
|
| 212 |
}else{
|
|
| 213 |
logger.warn(artNotSpecTax + " is not a valid value for 'Art non spectax' (BildID: " + bildID + ")" ); |
|
| 214 |
} |
|
| 215 |
} |
|
| 216 |
|
|
| 217 |
if (spectaxID != null){
|
|
| 218 |
|
|
| 219 |
//add to image gallery (discuss if this is also needed if taxon is already added to type specimen |
|
| 220 |
// Taxon taxon = taxonMap.get(String.valueOf(taxonID)); |
|
| 221 |
ZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID)); |
|
| 222 |
|
|
| 223 |
// |
|
| 224 |
// if (taxon == null){
|
|
| 225 |
//// taxon = specTaxMap.get(String.valueOf(spectaxID)); |
|
| 226 |
//// specTaxName = specTaxMap.g |
|
| 227 |
// } |
|
| 228 |
// if (taxon == null){
|
|
| 229 |
// logger.warn("No taxon available for specTaxID: " + spectaxID);
|
|
| 230 |
// }else{
|
|
| 231 |
// name = CdmBase.deproxy(taxon.getName(), ZoologicalName.class); |
|
| 232 |
// } |
|
| 233 |
|
|
| 234 |
//TODO FIXME |
|
| 235 |
|
|
| 236 |
if (specTaxTaxonName == null){
|
|
| 237 |
logger.warn("Name could not be found for spectaxID: " + spectaxID + " in BildID: " + bildID);
|
|
| 238 |
}else{
|
|
| 239 |
Taxon taxon = null; |
|
| 240 |
for (Taxon specTaxTaxon: specTaxTaxonName.getTaxa()){
|
|
| 241 |
taxon = specTaxTaxon; |
|
| 242 |
} |
|
| 243 |
if (taxon == null){
|
|
| 244 |
//FIXME |
|
| 245 |
Reference undefinedSec = null; |
|
| 246 |
taxon = Taxon.NewInstance(specTaxTaxonName, undefinedSec); |
|
| 247 |
} |
|
| 248 |
|
|
| 249 |
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(); |
|
| 250 |
determinationEvent.setTaxon(taxon); |
|
| 251 |
determinationEvent.setIdentifiedUnit(specimen); |
|
| 252 |
} |
|
| 253 |
|
|
| 254 |
|
|
| 255 |
|
|
| 256 |
|
|
| 257 |
// if (taxon != null){
|
|
| 258 |
// TaxonDescription taxonDescription = getTaxonDescription(taxon, true, true); |
|
| 259 |
// if (taxonDescription.getElements().size() == 0){
|
|
| 260 |
// TextData textData = TextData.NewInstance(Feature.IMAGE()); |
|
| 261 |
// taxonDescription.addElement(textData); |
|
| 262 |
// } |
|
| 263 |
// Set<DescriptionElementBase> elements = taxonDescription.getElements(); |
|
| 264 |
// TextData textData = CdmBase.deproxy(elements.iterator().next(), TextData.class); |
|
| 265 |
// for (Media media: recordMedia){
|
|
| 266 |
// textData.addMedia(media); |
|
| 267 |
// } |
|
| 268 |
// } |
|
| 269 |
} |
|
| 170 | 270 |
|
| 171 | 271 |
} catch (Exception e) {
|
| 172 | 272 |
logger.warn("Exception in Einzelbilder: bildID " + bildID + ". " + e.getMessage());
|
| ... | ... | |
| 184 | 284 |
return false; |
| 185 | 285 |
} |
| 186 | 286 |
} |
| 287 |
|
|
| 288 |
private Collection getCollection(String collectionCode) {
|
|
| 289 |
//TODO |
|
| 290 |
return null; |
|
| 291 |
} |
|
| 292 |
|
|
| 293 |
|
|
| 294 |
|
|
| 295 |
|
|
| 296 |
private String getNameFromFileOs(ResultSet rs) throws SQLException {
|
|
| 297 |
String fileOS = rs.getString("file OS");
|
|
| 298 |
Pattern pattern = Pattern.compile("(.+)(_...._..\\.jpg)");
|
|
| 299 |
Matcher matcher = pattern.matcher(fileOS); |
|
| 300 |
if (matcher.matches()){
|
|
| 301 |
String match = matcher.group(1); |
|
| 302 |
return match; |
|
| 303 |
}else{
|
|
| 304 |
logger.warn("FileOS does not match: " + fileOS);
|
|
| 305 |
return fileOS; |
|
| 306 |
} |
|
| 307 |
} |
|
| 308 |
|
|
| 309 |
|
|
| 310 |
|
|
| 311 |
|
|
| 312 |
private void makeAllMedia(GlobisImportState state, ResultSet rs, Set<Media> recordMedia, Set<Media> objectsToSave) throws SQLException{
|
|
| 313 |
//make image path |
|
| 314 |
String pathShort = rs.getString("Dateipfad_kurz");
|
|
| 315 |
String fileOS = rs.getString("file OS");
|
|
| 316 |
pathShort= pathShort.replace(fileOS, ""); |
|
| 317 |
String newPath = state.getConfig().getImageBaseUrl(); |
|
| 318 |
String path = pathShort.replace("image:Webversionen/", newPath);
|
|
| 319 |
|
|
| 320 |
Media singleMedia = makeMedia(state, rs, "file OS", "Legende 1", path, objectsToSave ); |
|
| 321 |
recordMedia.add(singleMedia); |
|
| 322 |
singleMedia = makeMedia(state, rs, "Dateinamen02", "Legende 2", path, objectsToSave ); |
|
| 323 |
recordMedia.add(singleMedia); |
|
| 324 |
singleMedia = makeMedia(state, rs, "Dateinamen03", "Legende 3", path, objectsToSave ); |
|
| 325 |
recordMedia.add(singleMedia); |
|
| 326 |
singleMedia = makeMedia(state, rs, "Dateinamen04", "Legende 4", path, objectsToSave ); |
|
| 327 |
recordMedia.add(singleMedia); |
|
| 328 |
|
|
| 329 |
} |
|
| 187 | 330 |
|
| 188 | 331 |
private Media makeMedia(GlobisImportState state, ResultSet rs, String fileNameAttr, String legendAttr, String path, Set<Media> objectsToSave) throws SQLException {
|
| 189 | 332 |
Media media = null; |
| ... | ... | |
| 191 | 334 |
String legend = rs.getString(legendAttr); |
| 192 | 335 |
Integer bildID = rs.getInt("BildID");
|
| 193 | 336 |
|
| 194 |
URI uri = URI.create(path+fileName); |
|
| 337 |
String uriStr = path+fileName; |
|
| 338 |
uriStr = uriStr.replace(" ", "%20");
|
|
| 339 |
|
|
| 340 |
URI uri = URI.create(uriStr); |
|
| 195 | 341 |
|
| 196 | 342 |
// Media media = ImageInfo.NewInstanceWithMetaData(uri, null); |
| 197 | 343 |
|
| ... | ... | |
| 283 | 429 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 284 | 430 |
try{
|
| 285 | 431 |
Set<String> currSpecIdSet = new HashSet<String>(); |
| 432 |
Set<String> specTaxIdSet = new HashSet<String>(); |
|
| 286 | 433 |
Set<String> typeIdSet = new HashSet<String>(); |
| 287 | 434 |
|
| 288 | 435 |
while (rs.next()){
|
| ... | ... | |
| 290 | 437 |
handleTypeKey(rs, typeIdSet, "spectaxID", "copyright"); |
| 291 | 438 |
} |
| 292 | 439 |
|
| 440 |
//specTax map |
|
| 441 |
nameSpace = GlobisSpecTaxImport.SPEC_TAX_NAMESPACE; |
|
| 442 |
cdmClass = TaxonBase.class; |
|
| 443 |
idSet = specTaxIdSet; |
|
| 444 |
Map<String, TaxonBase> specTaxMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 445 |
result.put(nameSpace, specTaxMap); |
|
| 446 |
|
|
| 293 | 447 |
//taxon map |
| 294 | 448 |
nameSpace = TAXON_NAMESPACE; |
| 295 | 449 |
cdmClass = Taxon.class; |
| ... | ... | |
| 297 | 451 |
Map<String, Taxon> taxonMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
| 298 | 452 |
result.put(nameSpace, taxonMap); |
| 299 | 453 |
|
| 454 |
|
|
| 300 | 455 |
//type map |
| 301 | 456 |
nameSpace = GlobisSpecTaxImport.TYPE_NAMESPACE; |
| 302 | 457 |
cdmClass = Specimen.class; |
| ... | ... | |
| 343 | 498 |
|
| 344 | 499 |
|
| 345 | 500 |
|
| 501 |
/* (non-Javadoc) |
|
| 502 |
* @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doInvoke(eu.etaxonomy.cdm.io.globis.GlobisImportState) |
|
| 503 |
*/ |
|
| 504 |
@Override |
|
| 505 |
protected void doInvoke(GlobisImportState state) {
|
|
| 506 |
Reference refGart = ReferenceFactory.newGeneric(); |
|
| 507 |
refGart.setTitleCache("GART");
|
|
| 508 |
refGart.setUuid(uuidGartRef); |
|
| 509 |
getReferenceService().saveOrUpdate(refGart); |
|
| 510 |
super.doInvoke(state); |
|
| 511 |
} |
|
| 512 |
|
|
| 513 |
|
|
| 514 |
|
|
| 515 |
|
|
| 346 | 516 |
|
| 347 | 517 |
} |
Also available in: Unified diff
latest globis