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; |
|
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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; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
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import eu.etaxonomy.cdm.model.description.TextData; |
| 36 | 43 |
import eu.etaxonomy.cdm.model.media.Media; |
| 44 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
|
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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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 |
|
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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 |
|
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.class; //not needed |
|
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private static final Class cdmTargetClass = Media.class; //not needed |
|
| 56 | 69 |
|
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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 |
|
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Reference<?> refGart = getReferenceService().find(uuidGartRef); |
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|
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|
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try {
|
| 113 | 130 |
|
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int i = 0; |
| 115 | 132 |
|
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//for each reference
|
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//for each record
|
|
| 117 | 134 |
while (rs.next()){
|
| 118 | 135 |
|
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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");
|
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String specimenId = rs.getString("specimenID");
|
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String bemerkungen = rs.getString("Bemerkungen");
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String artNotSpecTax = rs.getString("Art non spectax");
|
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String motiv = rs.getString("Motiv");
|
|
| 128 | 146 |
|
| 129 | 147 |
//ignore: |
| 130 | 148 |
// [file lab2], same as Dateiname04 but less data |
| 131 | 149 |
// Dateipfad |
| 150 |
|
|
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Set<Media> recordMedia = new HashSet<Media>(); |
| 133 | 152 |
|
| 134 | 153 |
try {
|
| 135 | 154 |
|
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//make image path |
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String pathShort = rs.getString("Dateipfad_kurz");
|
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String fileOS = rs.getString("file OS");
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pathShort= pathShort.replace(fileOS, ""); |
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String newPath = state.getConfig().getImageBaseUrl(); |
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String path = pathShort.replace("image:Webversionen/", newPath);
|
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|
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Media singleMedia = makeMedia(state, rs, "file OS", "Legende 1", path, objectsToSave ); |
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recordMedia.add(singleMedia); |
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singleMedia = makeMedia(state, rs, "Dateinamen02", "Legende 2", path, objectsToSave ); |
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recordMedia.add(singleMedia); |
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singleMedia = makeMedia(state, rs, "Dateinamen03", "Legende 3", path, objectsToSave ); |
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recordMedia.add(singleMedia); |
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singleMedia = makeMedia(state, rs, "Dateinamen04", "Legende 4", path, objectsToSave ); |
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recordMedia.add(singleMedia); |
|
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|
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if (spectaxID != null){
|
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makeAllMedia(state, rs, recordMedia, objectsToSave); |
|
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|
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String title = null; |
|
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|
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Specimen specimen = null; |
|
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if (spectaxID != null){
|
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//try to find type specimen |
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if (isNotBlank(motiv) && (motiv.startsWith("type specimen"))){
|
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String collectionCode = transformCopyright2CollectionCode(copyright); |
|
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String id = GlobisSpecTaxImport.getTypeId(spectaxID, collectionCode); |
|
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specimen = typeMap.get(id); |
|
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} |
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|
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//try to find specTaxName |
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ZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID)); |
|
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if (specTaxTaxonName != null){
|
|
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title = " taxon name " + specTaxTaxonName.getTitleCache(); |
|
| 172 |
}else{
|
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title = " spectaxID " + spectaxID; |
|
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} |
|
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}else{
|
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title = " name " + getNameFromFileOs(rs) + (isBlank(specimenId)? "" : " (specimenId: " + specimenId + ")"); |
|
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} |
|
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|
|
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//not type specimen |
|
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if (specimen == null){
|
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specimen = Specimen.NewInstance(); |
|
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specimen.setTitleCache("Specimen for " + title );
|
|
| 153 | 183 |
String collectionCode = transformCopyright2CollectionCode(copyright); |
| 154 |
String id = GlobisSpecTaxImport.getTypeId(spectaxID, collectionCode); |
|
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Specimen typeSpecimen = typeMap.get(id); |
|
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if (typeSpecimen != null){
|
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(typeSpecimen); |
|
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for (Media media: recordMedia){
|
|
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facade.addDerivedUnitMedia(media); |
|
| 160 |
} |
|
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}else{
|
|
| 162 |
//TODO |
|
| 163 |
} |
|
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}else{
|
|
| 165 | 184 |
//TODO |
| 185 |
Collection collection = getCollection(collectionCode); |
|
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specimen.setCollection(collection); |
|
| 166 | 187 |
} |
| 167 | 188 |
|
| 168 | 189 |
|
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//source |
|
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specimen.addSource(String.valueOf(bildID), IMAGE_NAMESPACE, state.getTransactionalSourceReference(), null); |
|
| 169 | 192 |
|
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//GART id (specimenID) |
|
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if (isNotBlank(specimenId)){
|
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specimen.addSource(specimenId, "", refGart, null); |
|
| 196 |
} |
|
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//bemerkungen |
|
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if (isNotBlank(bemerkungen)){
|
|
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Annotation annotation = Annotation.NewInstance(bemerkungen, null, null); |
|
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specimen.addAnnotation(annotation); |
|
| 201 |
} |
|
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//media |
|
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(specimen); |
|
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for (Media media: recordMedia){
|
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facade.addDerivedUnitMedia(media); |
|
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} |
|
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//art non spectax |
|
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if (isNotBlank(artNotSpecTax)){
|
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if (artNotSpecTax.equalsIgnoreCase("ja")){
|
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MarkerType artNotSpecTaxMarker = getMarkerType(state, uuidArtNonSpecTaxMarkerType , "Art non spectax", "This marker is true if in the orginal data the 'Art non spectax' was 'ja'", null) ; |
|
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specimen.addMarker(Marker.NewInstance(artNotSpecTaxMarker, true)); |
|
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}else{
|
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logger.warn(artNotSpecTax + " is not a valid value for 'Art non spectax' (BildID: " + bildID + ")" ); |
|
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} |
|
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} |
|
| 216 |
|
|
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if (spectaxID != null){
|
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|
|
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//add to image gallery (discuss if this is also needed if taxon is already added to type specimen |
|
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// Taxon taxon = taxonMap.get(String.valueOf(taxonID)); |
|
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ZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID)); |
|
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|
|
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// |
|
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// if (taxon == null){
|
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//// taxon = specTaxMap.get(String.valueOf(spectaxID)); |
|
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//// specTaxName = specTaxMap.g |
|
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// } |
|
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// if (taxon == null){
|
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// logger.warn("No taxon available for specTaxID: " + spectaxID);
|
|
| 230 |
// }else{
|
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// name = CdmBase.deproxy(taxon.getName(), ZoologicalName.class); |
|
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// } |
|
| 233 |
|
|
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//TODO FIXME |
|
| 235 |
|
|
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if (specTaxTaxonName == null){
|
|
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logger.warn("Name could not be found for spectaxID: " + spectaxID + " in BildID: " + bildID);
|
|
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}else{
|
|
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Taxon taxon = null; |
|
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for (Taxon specTaxTaxon: specTaxTaxonName.getTaxa()){
|
|
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taxon = specTaxTaxon; |
|
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} |
|
| 243 |
if (taxon == null){
|
|
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//FIXME |
|
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Reference undefinedSec = null; |
|
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taxon = Taxon.NewInstance(specTaxTaxonName, undefinedSec); |
|
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} |
|
| 248 |
|
|
| 249 |
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(); |
|
| 250 |
determinationEvent.setTaxon(taxon); |
|
| 251 |
determinationEvent.setIdentifiedUnit(specimen); |
|
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} |
|
| 253 |
|
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| 254 |
|
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| 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 |
|
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| 293 |
|
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| 294 |
|
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| 295 |
|
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| 296 |
private String getNameFromFileOs(ResultSet rs) throws SQLException {
|
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| 297 |
String fileOS = rs.getString("file OS");
|
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| 298 |
Pattern pattern = Pattern.compile("(.+)(_...._..\\.jpg)");
|
|
| 299 |
Matcher matcher = pattern.matcher(fileOS); |
|
| 300 |
if (matcher.matches()){
|
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| 301 |
String match = matcher.group(1); |
|
| 302 |
return match; |
|
| 303 |
}else{
|
|
| 304 |
logger.warn("FileOS does not match: " + fileOS);
|
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| 305 |
return fileOS; |
|
| 306 |
} |
|
| 307 |
} |
|
| 308 |
|
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| 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 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImportBase.java | ||
|---|---|---|
| 57 | 57 |
|
| 58 | 58 |
protected static final String REFERENCE_NAMESPACE = "Literatur"; |
| 59 | 59 |
protected static final String TAXON_NAMESPACE = "current_species"; |
| 60 |
|
|
| 61 |
|
|
| 60 |
protected static final String COLLECTION_NAMESPACE = "Collection"; |
|
| 61 |
|
|
| 62 | 62 |
private String pluralString; |
| 63 | 63 |
private String dbTableName; |
| 64 | 64 |
//TODO needed? |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.java | ||
|---|---|---|
| 13 | 13 |
import java.sql.SQLException; |
| 14 | 14 |
import java.util.HashMap; |
| 15 | 15 |
import java.util.HashSet; |
| 16 |
import java.util.List; |
|
| 16 | 17 |
import java.util.Map; |
| 17 | 18 |
import java.util.Set; |
| 18 | 19 |
import java.util.regex.Matcher; |
| 19 | 20 |
import java.util.regex.Pattern; |
| 20 | 21 |
|
| 21 |
import org.apache.commons.lang.StringUtils; |
|
| 22 | 22 |
import org.apache.log4j.Logger; |
| 23 | 23 |
import org.springframework.stereotype.Component; |
| 24 | 24 |
|
| 25 | 25 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 26 | 26 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType; |
| 27 | 27 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 28 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
|
| 29 | 28 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
| 30 | 29 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 31 | 30 |
import eu.etaxonomy.cdm.io.common.mapping.IMappingImport; |
| 32 |
import eu.etaxonomy.cdm.io.globis.validation.GlobisReferenceImportValidator; |
|
| 33 | 31 |
import eu.etaxonomy.cdm.io.globis.validation.GlobisSpecTaxaImportValidator; |
| 34 | 32 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 35 |
import eu.etaxonomy.cdm.model.common.Extension; |
|
| 36 | 33 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 37 | 34 |
import eu.etaxonomy.cdm.model.common.Marker; |
| 38 | 35 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| ... | ... | |
| 41 | 38 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 42 | 39 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 43 | 40 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 44 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationTest; |
|
| 45 | 41 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 46 | 42 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
| 47 | 43 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 48 | 44 |
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; |
| 49 |
import eu.etaxonomy.cdm.model.occurrence.DerivationEventType; |
|
| 50 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase; |
|
| 51 | 45 |
import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
| 52 | 46 |
import eu.etaxonomy.cdm.model.occurrence.Specimen; |
| 53 | 47 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 54 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
| 55 |
import eu.etaxonomy.cdm.model.reference.ReferenceType; |
|
| 56 | 48 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 57 | 49 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| 58 | 50 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| ... | ... | |
| 150 | 142 |
|
| 151 | 143 |
ZoologicalName name = null; |
| 152 | 144 |
if (isBlank(specSystaxRank) ){
|
| 153 |
name = makeName(state, rs); |
|
| 145 |
name = makeName(state, rs, specTaxId);
|
|
| 154 | 146 |
}else if (specSystaxRank.equals("synonym")){
|
| 155 |
Synonym synonym = getSynonym(state, rs); |
|
| 147 |
Synonym synonym = getSynonym(state, rs, specTaxId);
|
|
| 156 | 148 |
if (acceptedTaxon == null){
|
| 157 | 149 |
if (acceptedTaxonId == null){
|
| 158 | 150 |
logger.warn("Synonym has no accepted taxon defined. SpecTaxId: "+ specTaxId);
|
| ... | ... | |
| 168 | 160 |
thisTaxon = acceptedTaxon; |
| 169 | 161 |
}else{
|
| 170 | 162 |
logger.warn(String.format("Unhandled specSystaxRank %s in specTaxId %d", specSystaxRank, specTaxId));
|
| 171 |
name = makeName(state, rs); |
|
| 163 |
name = makeName(state, rs, specTaxId);
|
|
| 172 | 164 |
} |
| 173 | 165 |
|
| 174 | 166 |
if (thisTaxon != null){
|
| 175 | 167 |
name = CdmBase.deproxy(thisTaxon.getName(), ZoologicalName.class); |
| 176 |
} |
|
| 177 |
if (name == null){
|
|
| 178 |
name = makeName(state, rs); |
|
| 168 |
}else{
|
|
| 169 |
if (name == null){
|
|
| 170 |
name = makeName(state, rs, specTaxId); |
|
| 171 |
} |
|
| 172 |
thisTaxon = Taxon.NewInstance(name, sourceRef); |
|
| 173 |
objectsToSave.add(thisTaxon); |
|
| 179 | 174 |
} |
| 180 | 175 |
|
| 181 | 176 |
handleNomRef(state, referenceMap, rs, name); |
| ... | ... | |
| 214 | 209 |
|
| 215 | 210 |
|
| 216 | 211 |
private void handleTypeInformation(GlobisImportState state, ResultSet rs, ZoologicalName name, Integer specTaxId) throws SQLException {
|
| 217 |
|
|
| 218 |
|
|
| 219 | 212 |
if (! hasTypeInformation(rs)){
|
| 220 | 213 |
return; |
| 221 | 214 |
} |
| ... | ... | |
| 252 | 245 |
specTypeDepositoryStr = makeAdditionalSpecimenInformation( |
| 253 | 246 |
specTypeDepositoryStr, specimen, specTaxId); |
| 254 | 247 |
|
| 255 |
Collection collection = makeCollection(specTypeDepositoryStr, specimen, specTaxId); |
|
| 248 |
Collection collection = makeCollection(state, specTypeDepositoryStr, specimen, specTaxId);
|
|
| 256 | 249 |
String collectionCode = collection.getCode(); |
| 257 | 250 |
if (isBlank(collectionCode)){
|
| 258 | 251 |
collectionCode = collection.getName(); |
| ... | ... | |
| 302 | 295 |
|
| 303 | 296 |
|
| 304 | 297 |
/** |
| 298 |
* @param state |
|
| 305 | 299 |
* @param specTypeDepositoryStr |
| 306 | 300 |
* @param specimen |
| 307 | 301 |
* @param specTaxId |
| 308 | 302 |
*/ |
| 309 |
protected Collection makeCollection(String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
|
|
| 310 |
//TODO deduplicate |
|
| 311 |
Map<String, Collection> collectionMap = new HashMap<String, Collection>(); |
|
| 303 |
protected Collection makeCollection(GlobisImportState state, String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
|
|
| 312 | 304 |
|
| 313 | 305 |
//Collection |
| 314 | 306 |
specTypeDepositoryStr = specTypeDepositoryStr.replace("Washington, D.C.", "Washington@ D.C.");
|
| 315 | 307 |
|
| 316 | 308 |
Collection collection; |
| 317 | 309 |
if (specTypeDepositoryStr.equals("BMNH, London and/or MNHN, Paris")){
|
| 318 |
//TODO deduplicate |
|
| 319 |
collection = Collection.NewInstance(); |
|
| 320 |
collection.setName(specTypeDepositoryStr); |
|
| 310 |
collection = state.getRelatedObject(COLLECTION_NAMESPACE, specTypeDepositoryStr, Collection.class); |
|
| 311 |
if (collection == null){
|
|
| 312 |
collection = Collection.NewInstance(); |
|
| 313 |
collection.setName(specTypeDepositoryStr); |
|
| 314 |
collection.setTownOrLocation("London or Paris");
|
|
| 315 |
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection); |
|
| 316 |
} |
|
| 321 | 317 |
specimen.setCollection(collection); |
| 322 | 318 |
}else if (specTypeDepositoryStr.equals("coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov, Moscow")){
|
| 323 |
collection = Collection.NewInstance(); |
|
| 324 |
collection.setName("coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov");
|
|
| 325 |
collection.setTownOrLocation("Moscow");
|
|
| 319 |
String colName = "coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov"; |
|
| 320 |
collection = state.getRelatedObject(COLLECTION_NAMESPACE, colName, Collection.class); |
|
| 321 |
if (collection == null){
|
|
| 322 |
collection = Collection.NewInstance(); |
|
| 323 |
collection.setName(colName); |
|
| 324 |
collection.setTownOrLocation("Moscow");
|
|
| 325 |
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection); |
|
| 326 |
} |
|
| 326 | 327 |
specimen.setCollection(collection); |
| 327 | 328 |
}else if (specTypeDepositoryStr.matches("coll. R. E. Parrott?, Port Hope, Ontario")){
|
| 328 |
//TODO deduplicate |
|
| 329 |
collection = Collection.NewInstance(); |
|
| 330 |
collection.setName("coll. R. E. Parrott");
|
|
| 331 |
collection.setTownOrLocation("Port Hope, Ontario");
|
|
| 329 |
String colName = "coll. R. E. Parrott"; |
|
| 330 |
collection = state.getRelatedObject(COLLECTION_NAMESPACE, colName, Collection.class); |
|
| 331 |
if (collection == null){
|
|
| 332 |
collection = Collection.NewInstance(); |
|
| 333 |
collection.setName(colName); |
|
| 334 |
collection.setTownOrLocation("Port Hope, Ontario");
|
|
| 335 |
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection); |
|
| 336 |
} |
|
| 332 | 337 |
specimen.setCollection(collection); |
| 333 | 338 |
}else{
|
| 334 | 339 |
|
| 335 | 340 |
String[] split = specTypeDepositoryStr.split(",");
|
| 336 | 341 |
if (split.length != 2){
|
| 337 | 342 |
if (split.length == 1 && split[0].startsWith("coll.")){
|
| 338 |
collection = Collection.NewInstance(); |
|
| 339 |
collection.setName(split[0]); |
|
| 343 |
collection = state.getRelatedObject(COLLECTION_NAMESPACE, split[0], Collection.class); |
|
| 344 |
if (collection == null){
|
|
| 345 |
collection = Collection.NewInstance(); |
|
| 346 |
collection.setName(split[0]); |
|
| 347 |
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection); |
|
| 348 |
} |
|
| 340 | 349 |
specimen.setCollection(collection); |
| 341 | 350 |
}else{
|
| 342 | 351 |
logger.warn("Split size is not 2: " + specTypeDepositoryStr + " (specTaxID:" + specTaxId + ")");
|
| 343 | 352 |
collection = Collection.NewInstance(); |
| 344 | 353 |
collection.setCode("??");
|
| 354 |
//TODO deduplicate ?? |
|
| 345 | 355 |
} |
| 346 | 356 |
|
| 347 | 357 |
}else{
|
| 348 | 358 |
String collectionStr = split[0]; |
| 349 | 359 |
String location = split[1].replace("Washington@ D.C.", "Washington, D.C.");
|
| 350 | 360 |
|
| 351 |
collection = collectionMap.get(collectionStr);
|
|
| 361 |
collection = state.getRelatedObject(COLLECTION_NAMESPACE, collectionStr, Collection.class);
|
|
| 352 | 362 |
if (collection == null){
|
| 353 | 363 |
collection = Collection.NewInstance(); |
| 354 | 364 |
collection.setCode(collectionStr); |
| 355 | 365 |
collection.setTownOrLocation(split[1]); |
| 356 |
}else if (CdmUtils.nullSafeEqual(location, collection.getTownOrLocation())){
|
|
| 366 |
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getCode(), collection); |
|
| 367 |
|
|
| 368 |
}else if (! CdmUtils.nullSafeEqual(location, collection.getTownOrLocation())){
|
|
| 357 | 369 |
String message = "Location (%s) is not equal to location (%s) of existing collection"; |
| 358 | 370 |
logger.warn(String.format(message, location, collection.getTownOrLocation(), collection.getCode())); |
| 359 | 371 |
} |
| ... | ... | |
| 540 | 552 |
|
| 541 | 553 |
|
| 542 | 554 |
|
| 543 |
private Synonym getSynonym(GlobisImportState state, ResultSet rs) throws SQLException {
|
|
| 544 |
ZoologicalName name = makeName(state, rs); |
|
| 555 |
private Synonym getSynonym(GlobisImportState state, ResultSet rs, Integer specTaxId) throws SQLException {
|
|
| 556 |
ZoologicalName name = makeName(state, rs, specTaxId);
|
|
| 545 | 557 |
|
| 546 | 558 |
Synonym synonym = Synonym.NewInstance(name, state.getTransactionalSourceReference()); |
| 547 | 559 |
|
| ... | ... | |
| 554 | 566 |
/** |
| 555 | 567 |
* @param state |
| 556 | 568 |
* @param rs |
| 569 |
* @param specTaxId |
|
| 557 | 570 |
* @return |
| 558 | 571 |
* @throws SQLException |
| 559 | 572 |
*/ |
| 560 |
protected ZoologicalName makeName(GlobisImportState state, ResultSet rs) |
|
| 573 |
protected ZoologicalName makeName(GlobisImportState state, ResultSet rs, Integer specTaxId)
|
|
| 561 | 574 |
throws SQLException {
|
| 562 | 575 |
//rank |
| 563 | 576 |
String rankStr = rs.getString("SpecRank");
|
| ... | ... | |
| 580 | 593 |
String yearStr = rs.getString("SpecYear");
|
| 581 | 594 |
String authorAndYearStr = CdmUtils.concat(", ", authorStr, yearStr);
|
| 582 | 595 |
handleAuthorAndYear(authorAndYearStr, name); |
| 596 |
|
|
| 597 |
name.addSource(String.valueOf(specTaxId), SPEC_TAX_NAMESPACE, state.getTransactionalSourceReference(), null); |
|
| 583 | 598 |
return name; |
| 584 | 599 |
} |
| 585 | 600 |
|
| ... | ... | |
| 611 | 626 |
} |
| 612 | 627 |
|
| 613 | 628 |
|
| 614 |
|
|
| 615 |
|
|
| 616 |
private boolean isInfraSpecies(GlobisImportState state, ResultSet rs, Rank rank) {
|
|
| 617 |
// TODO Auto-generated method stub |
|
| 618 |
return false; |
|
| 619 |
} |
|
| 620 |
|
|
| 621 |
|
|
| 622 |
|
|
| 623 |
|
|
| 624 |
private Reference<?> getJournal(GlobisImportState state, ResultSet rs, String refJournal) throws SQLException {
|
|
| 625 |
|
|
| 626 |
|
|
| 627 |
Reference<?> journal = ReferenceFactory.newJournal(); |
|
| 628 |
String issn = rs.getString("RefISSN");
|
|
| 629 |
if (StringUtils.isNotBlank(issn)){
|
|
| 630 |
issn.replaceAll("ISSN", "").trim();
|
|
| 631 |
journal.setIssn(issn); |
|
| 632 |
} |
|
| 633 |
|
|
| 634 |
|
|
| 635 |
|
|
| 636 |
//TODO deduplicate |
|
| 637 |
journal.setTitle(refJournal); |
|
| 638 |
return journal; |
|
| 639 |
} |
|
| 640 |
|
|
| 641 |
|
|
| 642 |
|
|
| 643 |
|
|
| 644 |
/* (non-Javadoc) |
|
| 645 |
* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase) |
|
| 646 |
*/ |
|
| 647 |
public Reference<?> createObject(ResultSet rs, GlobisImportState state) |
|
| 648 |
throws SQLException {
|
|
| 649 |
Reference<?> ref; |
|
| 650 |
String refType = rs.getString("RefType");
|
|
| 651 |
if (refType == null){
|
|
| 652 |
ref = ReferenceFactory.newGeneric(); |
|
| 653 |
}else if (refType == "book"){
|
|
| 654 |
ref = ReferenceFactory.newBook(); |
|
| 655 |
}else if (refType == "paper in journal"){
|
|
| 656 |
ref = ReferenceFactory.newArticle(); |
|
| 657 |
}else if (refType.startsWith("unpublished") ){
|
|
| 658 |
ref = ReferenceFactory.newGeneric(); |
|
| 659 |
}else if (refType.endsWith("paper in journal")){
|
|
| 660 |
ref = ReferenceFactory.newArticle(); |
|
| 661 |
}else if (refType == "paper in book"){
|
|
| 662 |
ref = ReferenceFactory.newBookSection(); |
|
| 663 |
}else if (refType == "paper in journalwebsite"){
|
|
| 664 |
ref = ReferenceFactory.newArticle(); |
|
| 665 |
}else{
|
|
| 666 |
logger.warn("Unknown reference type: " + refType);
|
|
| 667 |
ref = ReferenceFactory.newGeneric(); |
|
| 668 |
} |
|
| 669 |
return ref; |
|
| 670 |
} |
|
| 671 |
|
|
| 672 | 629 |
/* (non-Javadoc) |
| 673 | 630 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
| 674 | 631 |
*/ |
| ... | ... | |
| 700 | 657 |
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
| 701 | 658 |
result.put(nameSpace, referenceMap); |
| 702 | 659 |
|
| 660 |
//collection map |
|
| 661 |
nameSpace = COLLECTION_NAMESPACE; |
|
| 662 |
List<Collection> listCollection = getCollectionService().list(Collection.class, null, null, null, null); |
|
| 663 |
Map<String, Collection> collectionMap = new HashMap<String, Collection>(); |
|
| 664 |
for (Collection collection : listCollection){
|
|
| 665 |
collectionMap.put(collection.getCode(), collection); |
|
| 666 |
if (isBlank(collection.getCode())){
|
|
| 667 |
logger.warn("Collection code is blank: " + collection);
|
|
| 668 |
} |
|
| 669 |
} |
|
| 670 |
result.put(nameSpace, collectionMap); |
|
| 703 | 671 |
|
| 704 | 672 |
} catch (SQLException e) {
|
| 705 | 673 |
throw new RuntimeException(e); |
| ... | ... | |
| 727 | 695 |
|
| 728 | 696 |
|
| 729 | 697 |
|
| 698 |
@Override |
|
| 699 |
public Reference createObject(ResultSet rs, GlobisImportState state) |
|
| 700 |
throws SQLException {
|
|
| 701 |
// not needed |
|
| 702 |
return null; |
|
| 703 |
} |
|
| 704 |
|
|
| 705 |
|
|
| 706 |
|
|
| 707 |
|
|
| 730 | 708 |
|
| 731 | 709 |
} |
Also available in: Unified diff
latest globis