Revision 1669c273
Added by Andreas Müller over 11 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImageImport.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.globis; |
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|
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import java.io.IOException; |
|
| 12 | 13 |
import java.net.MalformedURLException; |
| 13 | 14 |
import java.net.URI; |
| 14 | 15 |
import java.sql.ResultSet; |
| ... | ... | |
| 18 | 19 |
import java.util.Map; |
| 19 | 20 |
import java.util.Set; |
| 20 | 21 |
|
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import org.apache.http.client.ClientProtocolException; |
|
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import org.apache.log4j.Logger; |
| 22 | 24 |
import org.springframework.stereotype.Component; |
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|
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
|
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import eu.etaxonomy.cdm.common.UriUtils; |
|
| 24 | 28 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
| 25 | 29 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
| 26 | 30 |
import eu.etaxonomy.cdm.io.globis.validation.GlobisImageImportValidator; |
| 27 | 31 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 28 | 32 |
import eu.etaxonomy.cdm.model.common.Language; |
| 33 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
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import eu.etaxonomy.cdm.model.description.SpecimenDescription; |
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import eu.etaxonomy.cdm.model.description.TextData; |
|
| 29 | 36 |
import eu.etaxonomy.cdm.model.media.Media; |
| 37 |
import eu.etaxonomy.cdm.model.occurrence.Specimen; |
|
| 30 | 38 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 31 | 39 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 32 | 40 |
|
| ... | ... | |
| 76 | 84 |
protected String getRecordQuery(GlobisImportConfigurator config) {
|
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String strRecordQuery = |
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" SELECT i.*, NULL as Created_When, NULL as Created_Who," + |
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" NULL as Updated_who, NULL as Updated_When, NULL as Notes " + |
|
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" NULL as Updated_who, NULL as Updated_When, NULL as Notes, st.SpecCurrspecID " +
|
|
| 80 | 88 |
" FROM " + getTableName() + " i " + |
| 89 |
" LEFT JOIN specTax st ON i.spectaxID = st.SpecTaxID " + |
|
| 81 | 90 |
" WHERE ( i.BildId IN (" + ID_LIST_TOKEN + ") )";
|
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return strRecordQuery; |
| 83 | 92 |
} |
| ... | ... | |
| 93 | 102 |
|
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Set<Media> objectsToSave = new HashSet<Media>(); |
| 95 | 104 |
|
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// Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE); |
|
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Map<String, Specimen> typeMap = (Map<String, Specimen>) partitioner.getObjectMap(GlobisSpecTaxImport.TYPE_NAMESPACE); |
|
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|
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Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 97 | 108 |
// Map<String, DerivedUnit> ecoFactDerivedUnitMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE); |
| 98 | 109 |
|
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ResultSet rs = partitioner.getResultSet(); |
| ... | ... | |
| 111 | 122 |
|
| 112 | 123 |
Integer spectaxID = nullSafeInt(rs, "spectaxID"); |
| 113 | 124 |
|
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//ignore: [file lab2], same as Dateiname04 but less data
|
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Integer taxonID = nullSafeInt(rs, "SpecCurrspecID");
|
|
| 115 | 126 |
|
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String copyright = rs.getString("copyright");
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|
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//ignore: |
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// [file lab2], same as Dateiname04 but less data |
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// Dateipfad |
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Set<Media> recordMedia = new HashSet<Media>(); |
|
| 117 | 133 |
|
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try {
|
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|
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//source ref |
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Reference<?> sourceRef = state.getTransactionalSourceReference(); |
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|
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//make image path |
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//make image path |
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String pathShort = rs.getString("Dateipfad_kurz");
|
| 125 | 138 |
String fileOS = rs.getString("file OS");
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pathShort.replace(fileOS, ""); |
|
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//TODO move to config |
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String newPath = "http://globis-images.insects-online.de/images/"; |
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String path = pathShort.replace("image:Webversionen", newPath);
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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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| 130 | 142 |
|
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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); |
|
| 131 | 151 |
|
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if (spectaxID != null){
|
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String collectionCode = transformCopyright2CollectionCode(copyright); |
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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); |
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} |
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}else{
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//TODO |
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} |
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}else{
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//TODO |
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} |
|
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Media media1 = makeMedia(state, rs, "file OS", "Legende 1", path ); |
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Media media2 = makeMedia(state, rs, "Dateiname02", "Legende 2", path ); |
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Media media3 = makeMedia(state, rs, "Dateiname03", "Legende 3", path ); |
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Media media4 = makeMedia(state, rs, "Dateiname04", "Legende 4", path ); |
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//TODO |
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this.doIdCreatedUpdatedNotes(state, media1, rs, bildID, IMAGE_NAMESPACE); |
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save(objectsToSave, media1); |
|
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} catch (Exception e) {
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logger.warn("Exception in Einzelbilder: bildID " + bildID + ". " + e.getMessage());
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// e.printStackTrace();
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e.printStackTrace(); |
|
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} |
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|
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} |
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// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
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|
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logger.warn(pluralString + " to save: " + objectsToSave.size()); |
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logger.info(pluralString + " to save: " + objectsToSave.size()); |
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getMediaService().save(objectsToSave); |
| 157 | 180 |
|
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return success; |
| ... | ... | |
| 162 | 185 |
} |
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} |
| 164 | 187 |
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private void save(Set<Media> objectsToSave, Media media) {
|
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if (media != null){
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objectsToSave.add(media); |
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} |
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} |
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private Media makeMedia(GlobisImportState state, ResultSet rs, String fileNameAttr, String legendAttr, String path) throws SQLException {
|
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private Media makeMedia(GlobisImportState state, ResultSet rs, String fileNameAttr, String legendAttr, String path, Set<Media> objectsToSave) throws SQLException {
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Media media = null; |
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String fileName = rs.getString(fileNameAttr); |
| 177 | 191 |
String legend = rs.getString(legendAttr); |
| 192 |
Integer bildID = rs.getInt("BildID");
|
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|
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URI uri = URI.create(path+fileName); |
| 180 | 195 |
|
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// Media media = ImageInfo.NewInstanceWithMetaData(uri, null); |
| 182 | 197 |
|
| 183 | 198 |
try {
|
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media = this.getImageMedia(uri.toString(), true, false); |
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boolean readMediaData = state.getConfig().isDoReadMediaData(); |
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if (isBlank(legend) && readMediaData){
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if (UriUtils.isOk(UriUtils.getResponse(uri, null))){
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logger.warn("Image exists but legend is null " + uri + ", bildID" + bildID );
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}else{
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return null; |
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} |
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} |
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|
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media = this.getImageMedia(uri.toString(), readMediaData, false); |
|
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media.putTitle(Language.ENGLISH(), legend); |
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this.doIdCreatedUpdatedNotes(state, media, rs, bildID, IMAGE_NAMESPACE); |
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objectsToSave.add(media); |
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} catch (MalformedURLException e) {
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e.printStackTrace(); |
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} catch (ClientProtocolException e) {
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e.printStackTrace(); |
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} catch (IOException e) {
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e.printStackTrace(); |
|
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} |
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return media; |
| 191 | 224 |
} |
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private String transformCopyright2CollectionCode(String copyright){
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|
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if (isBlank(copyright)){
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return ""; |
|
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}else if(copyright.matches("Museum f.?r Naturkunde der Humboldt-Universit.?t, Berlin")){
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return "MFNB"; |
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}else if(copyright.matches("Staatliches Museum f.?r Tierkunde Dresden")){
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return "SMTD"; |
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}else if(copyright.equals("Natural History Museum, London")){
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return "BMNH"; |
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}else if(copyright.matches("Zoologische Staatssammlung M.?nchen")){
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return "ZSSM"; |
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}else if(copyright.matches("Staatliches Museum f.?r Naturkunde Karlsruhe")){
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return "SMNK"; |
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}else if(copyright.matches("Deutsches Entomologisches Institut M.?ncheberg")){
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return "DEIE"; |
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}else if(copyright.equals("Forschungsinstitut und Naturmuseum Senckenberg")){
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return "SMFM"; |
|
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}else if(copyright.matches("Mus.?um National d.?Histoire Naturelle, Paris")){
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return "MNHN"; |
|
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}else if(copyright.equals("Naturhistorisches Museum Wien")){
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return "NHMW"; |
|
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}else if(copyright.equals("Naturhistoriska Riksmuseet Stockholm")){
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return "NRMS"; |
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}else if(copyright.matches("Staatliches Museum f.?r Naturkunde Stuttgart")){
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return "SMNS"; |
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}else if(copyright.equals("United States National Museum of Natural History, Washington")){
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return "USNM"; |
|
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}else if(copyright.matches("Zentrum f.?r Biodokumentation des Saarlandes")){
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return "ZFBS"; |
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}else if(copyright.equals("Zoological Museum, University of Copenhagen")){
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return "ZMUC"; |
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}else if(copyright.equals("Zoologisches Forschungsinstitut und Museum \"Alexander Koenig\", Bonn")){
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return "ZFMK"; |
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}else if(copyright.equals("Zoologisches Forschungsmuseum \"Alexander Koenig\", Bonn")){
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return "ZFMK"; |
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}else if(copyright.matches("Zoologisches Institut der Martin-Luther-Universit.?t Halle-Wittenberg")){
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return "ZIUH"; |
|
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}else if(copyright.matches("Zoologisches Institut Universit.?t T.?bingen")){
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return "ZIUT"; |
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}else{
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logger.warn("Unknown copyright entry: " + copyright);
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return ""; |
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} |
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|
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|
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} |
|
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|
| 193 | 274 |
|
| 194 | 275 |
|
| ... | ... | |
| 196 | 277 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
| 197 | 278 |
*/ |
| 198 | 279 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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String nameSpace; |
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Class cdmClass; |
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Set<String> idSet; |
|
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 200 |
return result; //not needed |
|
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try{
|
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Set<String> currSpecIdSet = new HashSet<String>(); |
|
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Set<String> typeIdSet = new HashSet<String>(); |
|
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|
|
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while (rs.next()){
|
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handleForeignKey(rs, currSpecIdSet, "SpecCurrspecID"); |
|
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handleTypeKey(rs, typeIdSet, "spectaxID", "copyright"); |
|
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} |
|
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|
|
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//taxon map |
|
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nameSpace = TAXON_NAMESPACE; |
|
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cdmClass = Taxon.class; |
|
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idSet = currSpecIdSet; |
|
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Map<String, Taxon> taxonMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
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result.put(nameSpace, taxonMap); |
|
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|
|
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//type map |
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nameSpace = GlobisSpecTaxImport.TYPE_NAMESPACE; |
|
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cdmClass = Specimen.class; |
|
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idSet = typeIdSet; |
|
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Map<String, Specimen> typeMap = (Map<String, Specimen>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
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result.put(nameSpace, typeMap); |
|
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|
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|
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} catch (SQLException e) {
|
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throw new RuntimeException(e); |
|
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} |
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return result; |
|
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} |
|
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|
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| 314 |
private void handleTypeKey(ResultSet rs, Set<String> idSet, String specTaxIdAttr, String copyrightAttr) |
|
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throws SQLException {
|
|
| 316 |
Integer specTaxId = nullSafeInt(rs, specTaxIdAttr); |
|
| 317 |
if (specTaxId != null){
|
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| 318 |
String copyright = rs.getString(copyrightAttr); |
|
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if (isNotBlank(copyright)){
|
|
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String id = GlobisSpecTaxImport.getTypeId(specTaxId, transformCopyright2CollectionCode(copyright)); |
|
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idSet.add(id); |
|
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} |
|
| 323 |
} |
|
| 201 | 324 |
} |
| 202 | 325 |
|
| 203 | 326 |
/* (non-Javadoc) |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImportBase.java | ||
|---|---|---|
| 215 | 215 |
throws SQLException{
|
| 216 | 216 |
boolean success = true; |
| 217 | 217 |
//id |
| 218 |
success &= ImportHelper.setOriginalSource(identifiableEntity, state.getConfig().getSourceReference(), id, namespace);
|
|
| 218 |
success &= ImportHelper.setOriginalSource(identifiableEntity, state.getTransactionalSourceReference(), id, namespace);
|
|
| 219 | 219 |
//createdUpdateNotes |
| 220 | 220 |
success &= doCreatedUpdatedNotes(state, identifiableEntity, rs, namespace); |
| 221 | 221 |
return success; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImportConfigurator.java | ||
|---|---|---|
| 46 | 46 |
private boolean doImages = true; |
| 47 | 47 |
private boolean doCurrentTaxa = true; |
| 48 | 48 |
private boolean doSpecTaxa = true; |
| 49 |
private boolean doCommonNames = true; |
|
| 50 |
|
|
| 51 |
private boolean doReadMediaData = true; |
|
| 52 |
|
|
| 49 | 53 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
| 50 | 54 |
|
| 55 |
private String imageBaseUrl = "http://globis-images.insects-online.de/images/"; |
|
| 51 | 56 |
|
| 52 | 57 |
private static IInputTransformer defaultTransformer = new GlobisTransformer(); |
| 53 | 58 |
|
| ... | ... | |
| 183 | 188 |
} |
| 184 | 189 |
|
| 185 | 190 |
|
| 191 |
public void setDoCommonNames(boolean doCommonNames) {
|
|
| 192 |
this.doCommonNames = doCommonNames; |
|
| 193 |
} |
|
| 194 |
|
|
| 195 |
|
|
| 196 |
public boolean isDoCommonNames() {
|
|
| 197 |
return doCommonNames; |
|
| 198 |
} |
|
| 199 |
|
|
| 200 |
|
|
| 201 |
public void setImageBaseUrl(String imageBaseUrl) {
|
|
| 202 |
this.imageBaseUrl = imageBaseUrl; |
|
| 203 |
} |
|
| 204 |
|
|
| 205 |
|
|
| 206 |
public String getImageBaseUrl() {
|
|
| 207 |
return imageBaseUrl; |
|
| 208 |
} |
|
| 209 |
|
|
| 210 |
|
|
| 211 |
public void setDoReadMediaData(boolean doReadMediaData) {
|
|
| 212 |
this.doReadMediaData = doReadMediaData; |
|
| 213 |
} |
|
| 214 |
|
|
| 215 |
|
|
| 216 |
public boolean isDoReadMediaData() {
|
|
| 217 |
return doReadMediaData; |
|
| 218 |
} |
|
| 219 |
|
|
| 220 |
|
|
| 186 | 221 |
|
| 187 | 222 |
|
| 188 | 223 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.io.globis.validation.GlobisSpecTaxaImportValidator; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.common.Extension; |
| 36 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
|
| 36 | 37 |
import eu.etaxonomy.cdm.model.common.Marker; |
| 37 | 38 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 38 | 39 |
import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry; |
| ... | ... | |
| 41 | 42 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 42 | 43 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 43 | 44 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationTest; |
| 45 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 44 | 46 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
| 45 | 47 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
| 46 | 48 |
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent; |
| ... | ... | |
| 71 | 73 |
private static final String pluralString = "taxa"; |
| 72 | 74 |
private static final String dbTableName = "specTax"; |
| 73 | 75 |
private static final Class cdmTargetClass = Reference.class; |
| 76 |
public static final String SPEC_TAX_NAMESPACE = dbTableName; |
|
| 77 |
public static final String TYPE_NAMESPACE = dbTableName + ".SpecTypeDepository"; |
|
| 74 | 78 |
|
| 75 | 79 |
public GlobisSpecTaxImport(){
|
| 76 | 80 |
super(pluralString, dbTableName, cdmTargetClass); |
| ... | ... | |
| 116 | 120 |
boolean success = true; |
| 117 | 121 |
|
| 118 | 122 |
Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>(); |
| 123 |
Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>(); |
|
| 119 | 124 |
|
| 120 | 125 |
Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE); |
| 121 | 126 |
Map<String, Reference> referenceMap = (Map<String, Reference>) partitioner.getObjectMap(REFERENCE_NAMESPACE); |
| ... | ... | |
| 143 | 148 |
Taxon acceptedTaxon = taxonMap.get(String.valueOf(acceptedTaxonId)); |
| 144 | 149 |
TaxonBase<?> thisTaxon = null; |
| 145 | 150 |
|
| 151 |
ZoologicalName name = null; |
|
| 146 | 152 |
if (isBlank(specSystaxRank) ){
|
| 147 |
//TODO
|
|
| 153 |
name = makeName(state, rs);
|
|
| 148 | 154 |
}else if (specSystaxRank.equals("synonym")){
|
| 149 | 155 |
Synonym synonym = getSynonym(state, rs); |
| 150 | 156 |
if (acceptedTaxon == null){
|
| ... | ... | |
| 162 | 168 |
thisTaxon = acceptedTaxon; |
| 163 | 169 |
}else{
|
| 164 | 170 |
logger.warn(String.format("Unhandled specSystaxRank %s in specTaxId %d", specSystaxRank, specTaxId));
|
| 171 |
name = makeName(state, rs); |
|
| 165 | 172 |
} |
| 166 | 173 |
|
| 167 | 174 |
if (thisTaxon != null){
|
| 168 |
ZoologicalName name = CdmBase.deproxy(thisTaxon.getName(), ZoologicalName.class); |
|
| 169 |
|
|
| 170 |
handleNomRef(state, referenceMap, rs, name); |
|
| 171 |
|
|
| 172 |
handleTypeInformation(state,rs, name, specTaxId); |
|
| 173 |
|
|
| 175 |
name = CdmBase.deproxy(thisTaxon.getName(), ZoologicalName.class); |
|
| 176 |
} |
|
| 177 |
if (name == null){
|
|
| 178 |
name = makeName(state, rs); |
|
| 179 |
} |
|
| 174 | 180 |
|
| 181 |
handleNomRef(state, referenceMap, rs, name); |
|
| 182 |
|
|
| 183 |
handleTypeInformation(state,rs, name, specTaxId); |
|
| 184 |
|
|
| 185 |
|
|
| 175 | 186 |
// this.doIdCreatedUpdatedNotes(state, ref, rs, refId, REFERENCE_NAMESPACE); |
| 176 |
|
|
| 187 |
|
|
| 188 |
if (acceptedTaxon != null){
|
|
| 177 | 189 |
objectsToSave.add(acceptedTaxon); |
| 178 | 190 |
} |
| 191 |
namesToSave.add(name); |
|
| 179 | 192 |
|
| 180 | 193 |
|
| 181 | 194 |
} catch (Exception e) {
|
| ... | ... | |
| 185 | 198 |
|
| 186 | 199 |
} |
| 187 | 200 |
|
| 188 |
// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
|
|
| 189 |
|
|
| 190 | 201 |
logger.warn(pluralString + " to save: " + objectsToSave.size()); |
| 191 | 202 |
getTaxonService().save(objectsToSave); |
| 203 |
getNameService().save(namesToSave); |
|
| 192 | 204 |
|
| 193 | 205 |
return success; |
| 194 | 206 |
} catch (Exception e) {
|
| ... | ... | |
| 223 | 235 |
if (specTypeDepositories.length == 0){
|
| 224 | 236 |
Specimen specimen = makeSingleTypeSpecimen(fieldObservation); |
| 225 | 237 |
makeTypeDesignation(name, rs, specimen); |
| 238 |
makeTypeIdInSource(state, specimen, "null", specTaxId); |
|
| 226 | 239 |
} |
| 227 | 240 |
for (String specTypeDepositoryStr : specTypeDepositories){
|
| 228 | 241 |
specTypeDepositoryStr = specTypeDepositoryStr.trim(); |
| ... | ... | |
| 233 | 246 |
if (specTypeDepositoryStr.equals("??")){
|
| 234 | 247 |
//unknown |
| 235 | 248 |
specimen.setTitleCache("??", true);
|
| 249 |
makeTypeIdInSource(state, specimen, "??", specTaxId); |
|
| 250 |
|
|
| 236 | 251 |
}else{
|
| 237 |
specTypeDepositoryStr = makeAdditionalSpecimenInformation(
|
|
| 252 |
specTypeDepositoryStr = makeAdditionalSpecimenInformation( |
|
| 238 | 253 |
specTypeDepositoryStr, specimen, specTaxId); |
| 239 | 254 |
|
| 240 |
makeCollection(specTypeDepositoryStr, specimen, specTaxId); |
|
| 255 |
Collection collection = makeCollection(specTypeDepositoryStr, specimen, specTaxId); |
|
| 256 |
String collectionCode = collection.getCode(); |
|
| 257 |
if (isBlank(collectionCode)){
|
|
| 258 |
collectionCode = collection.getName(); |
|
| 259 |
} |
|
| 260 |
if (isBlank(collectionCode)){
|
|
| 261 |
logger.warn("Collection has empty representation: " + specTypeDepositoryStr + ", specTaxId" + specTaxId);
|
|
| 262 |
} |
|
| 263 |
makeTypeIdInSource(state, specimen, collectionCode , specTaxId); |
|
| 241 | 264 |
} |
| 242 | 265 |
|
| 243 | 266 |
//type Designation |
| ... | ... | |
| 248 | 271 |
} |
| 249 | 272 |
|
| 250 | 273 |
|
| 274 |
private void makeTypeIdInSource(GlobisImportState state, Specimen specimen, String collectionCode, Integer specTaxId) {
|
|
| 275 |
String namespace = TYPE_NAMESPACE; |
|
| 276 |
String id = getTypeId(specTaxId, collectionCode); |
|
| 277 |
IdentifiableSource source = IdentifiableSource.NewInstance(id, namespace, state.getTransactionalSourceReference(), null); |
|
| 278 |
specimen.addSource(source); |
|
| 279 |
} |
|
| 280 |
|
|
| 281 |
|
|
| 282 |
|
|
| 283 |
|
|
| 284 |
public static String getTypeId(Integer specTaxId, String collectionCode) {
|
|
| 285 |
String result = String.valueOf(specTaxId) + "@" + collectionCode; |
|
| 286 |
return result; |
|
| 287 |
} |
|
| 288 |
|
|
| 289 |
|
|
| 251 | 290 |
|
| 252 | 291 |
|
| 253 | 292 |
private boolean hasTypeInformation(ResultSet rs) throws SQLException {
|
| ... | ... | |
| 267 | 306 |
* @param specimen |
| 268 | 307 |
* @param specTaxId |
| 269 | 308 |
*/ |
| 270 |
protected void makeCollection(String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
|
|
| 309 |
protected Collection makeCollection(String specTypeDepositoryStr, Specimen specimen, Integer specTaxId) {
|
|
| 271 | 310 |
//TODO deduplicate |
| 272 | 311 |
Map<String, Collection> collectionMap = new HashMap<String, Collection>(); |
| 273 | 312 |
|
| 274 |
|
|
| 275 | 313 |
//Collection |
| 276 | 314 |
specTypeDepositoryStr = specTypeDepositoryStr.replace("Washington, D.C.", "Washington@ D.C.");
|
| 277 | 315 |
|
| 316 |
Collection collection; |
|
| 278 | 317 |
if (specTypeDepositoryStr.equals("BMNH, London and/or MNHN, Paris")){
|
| 279 | 318 |
//TODO deduplicate |
| 280 |
Collection collection = Collection.NewInstance();
|
|
| 319 |
collection = Collection.NewInstance(); |
|
| 281 | 320 |
collection.setName(specTypeDepositoryStr); |
| 282 | 321 |
specimen.setCollection(collection); |
| 283 | 322 |
}else if (specTypeDepositoryStr.equals("coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov, Moscow")){
|
| 284 |
Collection collection = Collection.NewInstance();
|
|
| 323 |
collection = Collection.NewInstance(); |
|
| 285 | 324 |
collection.setName("coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov");
|
| 286 | 325 |
collection.setTownOrLocation("Moscow");
|
| 287 | 326 |
specimen.setCollection(collection); |
| 288 | 327 |
}else if (specTypeDepositoryStr.matches("coll. R. E. Parrott?, Port Hope, Ontario")){
|
| 289 | 328 |
//TODO deduplicate |
| 290 |
Collection collection = Collection.NewInstance();
|
|
| 329 |
collection = Collection.NewInstance(); |
|
| 291 | 330 |
collection.setName("coll. R. E. Parrott");
|
| 292 | 331 |
collection.setTownOrLocation("Port Hope, Ontario");
|
| 293 | 332 |
specimen.setCollection(collection); |
| ... | ... | |
| 296 | 335 |
String[] split = specTypeDepositoryStr.split(",");
|
| 297 | 336 |
if (split.length != 2){
|
| 298 | 337 |
if (split.length == 1 && split[0].startsWith("coll.")){
|
| 299 |
Collection collection = Collection.NewInstance();
|
|
| 338 |
collection = Collection.NewInstance(); |
|
| 300 | 339 |
collection.setName(split[0]); |
| 301 | 340 |
specimen.setCollection(collection); |
| 302 | 341 |
}else{
|
| 303 | 342 |
logger.warn("Split size is not 2: " + specTypeDepositoryStr + " (specTaxID:" + specTaxId + ")");
|
| 343 |
collection = Collection.NewInstance(); |
|
| 344 |
collection.setCode("??");
|
|
| 304 | 345 |
} |
| 305 | 346 |
|
| 306 | 347 |
}else{
|
| 307 | 348 |
String collectionStr = split[0]; |
| 308 | 349 |
String location = split[1].replace("Washington@ D.C.", "Washington, D.C.");
|
| 309 | 350 |
|
| 310 |
Collection collection = collectionMap.get(collectionStr);
|
|
| 351 |
collection = collectionMap.get(collectionStr); |
|
| 311 | 352 |
if (collection == null){
|
| 312 | 353 |
collection = Collection.NewInstance(); |
| 313 | 354 |
collection.setCode(collectionStr); |
| ... | ... | |
| 318 | 359 |
} |
| 319 | 360 |
|
| 320 | 361 |
specimen.setCollection(collection); |
| 321 |
|
|
| 322 | 362 |
} |
| 323 | 363 |
} |
| 364 |
return collection; |
|
| 324 | 365 |
} |
| 325 | 366 |
|
| 326 | 367 |
|
| ... | ... | |
| 500 | 541 |
|
| 501 | 542 |
|
| 502 | 543 |
private Synonym getSynonym(GlobisImportState state, ResultSet rs) throws SQLException {
|
| 544 |
ZoologicalName name = makeName(state, rs); |
|
| 545 |
|
|
| 546 |
Synonym synonym = Synonym.NewInstance(name, state.getTransactionalSourceReference()); |
|
| 547 |
|
|
| 548 |
return synonym; |
|
| 549 |
} |
|
| 550 |
|
|
| 551 |
|
|
| 552 |
|
|
| 553 |
|
|
| 554 |
/** |
|
| 555 |
* @param state |
|
| 556 |
* @param rs |
|
| 557 |
* @return |
|
| 558 |
* @throws SQLException |
|
| 559 |
*/ |
|
| 560 |
protected ZoologicalName makeName(GlobisImportState state, ResultSet rs) |
|
| 561 |
throws SQLException {
|
|
| 503 | 562 |
//rank |
| 504 | 563 |
String rankStr = rs.getString("SpecRank");
|
| 505 | 564 |
Rank rank = null; |
| ... | ... | |
| 521 | 580 |
String yearStr = rs.getString("SpecYear");
|
| 522 | 581 |
String authorAndYearStr = CdmUtils.concat(", ", authorStr, yearStr);
|
| 523 | 582 |
handleAuthorAndYear(authorAndYearStr, name); |
| 524 |
|
|
| 525 |
Synonym synonym = Synonym.NewInstance(name, state.getTransactionalSourceReference()); |
|
| 526 |
|
|
| 527 |
return synonym; |
|
| 583 |
return name; |
|
| 528 | 584 |
} |
| 529 | 585 |
|
| 530 | 586 |
|
Also available in: Unified diff
latest updates to the Globis import