/**\r
* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy \r
+* European Distributed Institute of Taxonomy\r
* http://www.e-taxonomy.eu\r
-* \r
+*\r
* The contents of this file are subject to the Mozilla Public License Version 1.1\r
* See LICENSE.TXT at the top of this package for the full license terms.\r
*/\r
\r
import java.io.IOException;\r
import java.net.MalformedURLException;\r
-import java.net.URI;\r
import java.sql.ResultSet;\r
import java.sql.SQLException;\r
import java.util.HashMap;\r
import java.util.regex.Pattern;\r
\r
import org.apache.http.client.ClientProtocolException;\r
-import org.apache.log4j.Logger;\r
+import org.apache.logging.log4j.LogManager;\r
+import org.apache.logging.log4j.Logger;\r
import org.springframework.stereotype.Component;\r
\r
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
+import eu.etaxonomy.cdm.common.URI;\r
import eu.etaxonomy.cdm.common.UriUtils;\r
+import eu.etaxonomy.cdm.facade.DerivedUnitFacade;\r
import eu.etaxonomy.cdm.io.common.IOValidator;\r
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;\r
import eu.etaxonomy.cdm.io.globis.validation.GlobisImageImportValidator;\r
import eu.etaxonomy.cdm.model.common.Marker;\r
import eu.etaxonomy.cdm.model.common.MarkerType;\r
import eu.etaxonomy.cdm.model.media.Media;\r
-import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
+import eu.etaxonomy.cdm.model.name.IZoologicalName;\r
+import eu.etaxonomy.cdm.model.name.TaxonName;\r
import eu.etaxonomy.cdm.model.occurrence.Collection;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;\r
-import eu.etaxonomy.cdm.model.occurrence.Specimen;\r
+import eu.etaxonomy.cdm.model.reference.OriginalSourceType;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
\r
/**\r
* @author a.mueller\r
- * @created 20.02.2010\r
- * @version 1.0\r
+ * @since 20.02.2010\r
*/\r
@Component\r
public class GlobisImageImport extends GlobisImportBase<Taxon> {\r
- private static final Logger logger = Logger.getLogger(GlobisImageImport.class);\r
- \r
+\r
+ private static final long serialVersionUID = 5697033145326415146L;\r
+ private static final Logger logger = LogManager.getLogger();\r
+\r
private int modCount = 1000;\r
\r
private UUID uuidArtNonSpecTaxMarkerType = UUID.fromString("be362085-0f5b-4314-96d1-78b9b129ef6d") ;\r
private static final String pluralString = "images";\r
private static final String dbTableName = "Einzelbilder";\r
- private static final Class cdmTargetClass = Media.class; //not needed\r
- \r
- private static UUID uuidGartRef = UUID.fromString("af85470f-6e54-4304-9d29-fd117cd56161"); \r
- \r
+ private static final Class<?> cdmTargetClass = Media.class; //not needed\r
+\r
+ private static UUID uuidGartRef = UUID.fromString("af85470f-6e54-4304-9d29-fd117cd56161");\r
+\r
public GlobisImageImport(){\r
super(pluralString, dbTableName, cdmTargetClass);\r
}\r
\r
-\r
- \r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#getIdQuery()\r
- */\r
@Override\r
protected String getIdQuery() {\r
- String strRecordQuery = \r
- " SELECT BildId " + \r
- " FROM " + dbTableName; \r
- return strRecordQuery; \r
+ String strRecordQuery =\r
+ " SELECT BildId " +\r
+ " FROM " + dbTableName;\r
+ return strRecordQuery;\r
}\r
\r
-\r
-\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)\r
- */\r
@Override\r
protected String getRecordQuery(GlobisImportConfigurator config) {\r
- String strRecordQuery = \r
+ String strRecordQuery =\r
" SELECT i.*, NULL as Created_When, NULL as Created_Who," +\r
- " NULL as Updated_who, NULL as Updated_When, NULL as Notes, st.SpecCurrspecID " + \r
+ " NULL as Updated_who, NULL as Updated_When, NULL as Notes, st.SpecCurrspecID " +\r
" FROM " + getTableName() + " i " +\r
" LEFT JOIN specTax st ON i.spectaxID = st.SpecTaxID " +\r
" WHERE ( i.BildId IN (" + ID_LIST_TOKEN + ") )";\r
return strRecordQuery;\r
}\r
- \r
\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState)\r
- */\r
@Override\r
- public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {\r
+ public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, GlobisImportState state) {\r
boolean success = true;\r
- \r
- Set<Media> objectsToSave = new HashSet<Media>();\r
- \r
- Map<String, Specimen> typeMap = (Map<String, Specimen>) partitioner.getObjectMap(TYPE_NAMESPACE);\r
- \r
- Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);\r
- Map<String, ZoologicalName> specTaxNameMap = (Map<String, ZoologicalName>) partitioner.getObjectMap(SPEC_TAX_NAMESPACE);\r
- \r
+\r
+ Set<Media> objectsToSave = new HashSet<>();\r
+\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, DerivedUnit> typeMap = partitioner.getObjectMap(TYPE_NAMESPACE);\r
+\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE);\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, TaxonName> specTaxNameMap = partitioner.getObjectMap(SPEC_TAX_NAMESPACE);\r
+\r
ResultSet rs = partitioner.getResultSet();\r
- \r
- Reference<?> refGart = getReferenceService().find(uuidGartRef);\r
- \r
- \r
+\r
+ Reference refGart = getReferenceService().find(uuidGartRef);\r
+\r
+\r
try {\r
- \r
+\r
int i = 0;\r
\r
//for each record\r
while (rs.next()){\r
- \r
+\r
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}\r
- \r
+\r
Integer bildID = rs.getInt("BildID");\r
Integer spectaxID = nullSafeInt(rs, "spectaxID");\r
Integer taxonID = nullSafeInt(rs, "SpecCurrspecID");\r
String bemerkungen = rs.getString("Bemerkungen");\r
String artNotSpecTax = rs.getString("Art non spectax");\r
String motiv = rs.getString("Motiv");\r
- \r
- //ignore: \r
+\r
+ //ignore:\r
// [file lab2], same as Dateiname04 but less data\r
// Dateipfad\r
\r
- Set<Media> recordMedia = new HashSet<Media>();\r
- \r
+ Set<Media> recordMedia = new HashSet<>();\r
+\r
try {\r
- \r
+\r
makeAllMedia(state, rs, recordMedia, objectsToSave);\r
- \r
+\r
String title = null;\r
- \r
- Specimen specimen = null;\r
+\r
+ DerivedUnit specimen = null;\r
if (spectaxID != null){\r
//try to find type specimen\r
if (isNotBlank(motiv) && (motiv.startsWith("type specimen"))){\r
String id = GlobisSpecTaxImport.getTypeId(spectaxID, collectionCode);\r
specimen = typeMap.get(id);\r
}\r
- \r
+\r
//try to find specTaxName\r
- ZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID));\r
+ IZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID));\r
if (specTaxTaxonName != null){\r
title = " taxon name " + specTaxTaxonName.getTitleCache();\r
}else{\r
}else{\r
title = " name " + getNameFromFileOs(rs) + (isBlank(specimenId)? "" : " (specimenId: " + specimenId + ")");\r
}\r
- \r
+\r
//not type specimen\r
if (specimen == null){\r
- specimen = Specimen.NewInstance();\r
- specimen.setTitleCache("Specimen for " + title );\r
+ specimen = DerivedUnit.NewPreservedSpecimenInstance();\r
+ specimen.setTitleCache("Specimen for " + title, true);\r
String collectionCode = transformCopyright2CollectionCode(copyright);\r
//TODO\r
Collection collection = getCollection(collectionCode);\r
specimen.setCollection(collection);\r
}\r
- \r
- \r
+\r
//source\r
- specimen.addSource(String.valueOf(bildID), IMAGE_NAMESPACE, state.getTransactionalSourceReference(), null);\r
- \r
+ specimen.addSource(OriginalSourceType.Import, String.valueOf(bildID), IMAGE_NAMESPACE, state.getTransactionalSourceReference(), null);\r
+\r
//GART id (specimenID)\r
if (isNotBlank(specimenId)){\r
- specimen.addSource(specimenId, "specimenId", refGart, null);\r
+ specimen.addSource(OriginalSourceType.Lineage, specimenId, "specimenId", refGart, null);\r
}\r
//bemerkungen\r
if (isNotBlank(bemerkungen)){\r
logger.warn(artNotSpecTax + " is not a valid value for 'Art non spectax' (BildID: " + bildID + ")" );\r
}\r
}\r
- \r
+\r
if (spectaxID != null){\r
- \r
+\r
//add to image gallery (discuss if this is also needed if taxon is already added to type specimen\r
// Taxon taxon = taxonMap.get(String.valueOf(taxonID));\r
- ZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID));\r
- \r
-// \r
+ IZoologicalName specTaxTaxonName = specTaxNameMap.get(String.valueOf(spectaxID));\r
+\r
+//\r
// if (taxon == null){\r
//// taxon = specTaxMap.get(String.valueOf(spectaxID));\r
//// specTaxName = specTaxMap.g\r
// }else{\r
// name = CdmBase.deproxy(taxon.getName(), ZoologicalName.class);\r
// }\r
- \r
+\r
//TODO FIXME\r
- \r
+\r
if (specTaxTaxonName == null){\r
logger.warn("Name could not be found for spectaxID: " + spectaxID + " in BildID: " + bildID);\r
}else{\r
}\r
if (taxon == null){\r
//FIXME\r
- Reference<?> undefinedSec = null;\r
+ Reference undefinedSec = null;\r
taxon = Taxon.NewInstance(specTaxTaxonName, undefinedSec);\r
}\r
- \r
+\r
DeterminationEvent.NewInstance(taxon, specimen);\r
\r
}\r
- \r
- \r
\r
- \r
+\r
+\r
+\r
// if (taxon != null){\r
// TaxonDescription taxonDescription = getTaxonDescription(taxon, true, true);\r
// if (taxonDescription.getElements().size() == 0){\r
// }\r
// }\r
}\r
- \r
+\r
} catch (Exception e) {\r
logger.warn("Exception in Einzelbilder: bildID " + bildID + ". " + e.getMessage());\r
e.printStackTrace();\r
- } \r
- \r
+ }\r
+\r
}\r
- \r
+\r
logger.info(pluralString + " to save: " + objectsToSave.size());\r
- getMediaService().save(objectsToSave); \r
- \r
+ getMediaService().save(objectsToSave);\r
+\r
return success;\r
} catch (SQLException e) {\r
logger.error("SQLException:" + e);\r
return false;\r
}\r
}\r
- \r
+\r
private Collection getCollection(String collectionCode) {\r
//TODO\r
return null;\r
}\r
\r
-\r
-\r
-\r
private String getNameFromFileOs(ResultSet rs) throws SQLException {\r
String fileOS = rs.getString("file OS");\r
Pattern pattern = Pattern.compile("(.+)(_.{4}(-.{1,3})?(_Nr\\d{3,4})?_.{2,3}\\.jpg)");\r
}\r
}\r
\r
-\r
-\r
-\r
private void makeAllMedia(GlobisImportState state, ResultSet rs, Set<Media> recordMedia, Set<Media> objectsToSave) throws SQLException{\r
//make image path\r
String pathShort = rs.getString("Dateipfad_kurz");\r
pathShort= pathShort.replace(fileOS, "");\r
String newPath = state.getConfig().getImageBaseUrl();\r
String path = pathShort.replace("image:Webversionen/", newPath);\r
- \r
+\r
Media singleMedia = makeMedia(state, rs, "file OS", "Legende 1", path, objectsToSave );\r
recordMedia.add(singleMedia);\r
singleMedia = makeMedia(state, rs, "Dateinamen02", "Legende 2", path, objectsToSave );\r
String fileName = rs.getString(fileNameAttr);\r
String legend = rs.getString(legendAttr);\r
Integer bildID = rs.getInt("BildID");\r
- \r
+\r
String uriStr = path+fileName;\r
uriStr = uriStr.replace(" ", "%20");\r
- \r
- URI uri = URI.create(uriStr); \r
- \r
+\r
+ URI uri = URI.create(uriStr);\r
+\r
// Media media = ImageInfo.NewInstanceWithMetaData(uri, null);\r
- \r
+\r
try {\r
boolean readMediaData = state.getConfig().isDoReadMediaData();\r
if (isBlank(legend) && readMediaData){\r
return null;\r
}\r
}\r
- \r
- media = this.getImageMedia(uri.toString(), readMediaData, false);\r
+\r
+ media = this.getImageMedia(uri.toString(), readMediaData);\r
media.putTitle(Language.ENGLISH(), legend);\r
this.doIdCreatedUpdatedNotes(state, media, rs, bildID, IMAGE_NAMESPACE);\r
- \r
+\r
objectsToSave.add(media);\r
- \r
- \r
+\r
+\r
} catch (MalformedURLException e) {\r
e.printStackTrace();\r
} catch (ClientProtocolException e) {\r
} catch (IOException e) {\r
e.printStackTrace();\r
}\r
- \r
+\r
return media;\r
}\r
- \r
+\r
private String transformCopyright2CollectionCode(String copyright){\r
- \r
+\r
if (isBlank(copyright)){\r
return "";\r
}else if(copyright.matches("Museum f.?r Naturkunde der Humboldt-Universit.?t, Berlin")){\r
logger.warn("Unknown copyright entry: " + copyright);\r
return "";\r
}\r
-\r
- \r
}\r
\r
\r
+ @Override\r
+ public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, GlobisImportState state) {\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)\r
- */\r
- public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {\r
- String nameSpace;\r
- Class cdmClass;\r
+ String nameSpace;\r
Set<String> idSet;\r
- Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();\r
+ Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();\r
try{\r
- Set<String> currSpecIdSet = new HashSet<String>();\r
- Set<String> specTaxIdSet = new HashSet<String>();\r
- Set<String> typeIdSet = new HashSet<String>();\r
- \r
+ Set<String> currSpecIdSet = new HashSet<>();\r
+ Set<String> specTaxIdSet = new HashSet<>();\r
+ Set<String> typeIdSet = new HashSet<>();\r
+\r
while (rs.next()){\r
handleForeignKey(rs, currSpecIdSet, "SpecCurrspecID");\r
handleForeignKey(rs, specTaxIdSet, "spectaxID");\r
handleTypeKey(rs, typeIdSet, "spectaxID", "copyright");\r
}\r
- \r
+\r
//specTax map\r
nameSpace = SPEC_TAX_NAMESPACE;\r
- cdmClass = ZoologicalName.class;\r
idSet = specTaxIdSet;\r
- Map<String, ZoologicalName> specTaxNameMap = (Map<String, ZoologicalName>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ Map<String, TaxonName> specTaxNameMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);\r
result.put(nameSpace, specTaxNameMap);\r
\r
// //taxon map\r
// nameSpace = TAXON_NAMESPACE;\r
-// cdmClass = Taxon.class;\r
// idSet = currSpecIdSet;\r
-// Map<String, Taxon> taxonMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+// Map<String, Taxon> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class, idSet, nameSpace);\r
// result.put(nameSpace, taxonMap);\r
\r
- \r
+\r
//type map\r
- nameSpace = GlobisSpecTaxImport.TYPE_NAMESPACE;\r
- cdmClass = Specimen.class;\r
+ nameSpace = GlobisImportBase.TYPE_NAMESPACE;\r
idSet = typeIdSet;\r
- Map<String, Specimen> typeMap = (Map<String, Specimen>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ Map<String, DerivedUnit> typeMap = getCommonService().getSourcedObjectsByIdInSourceC(DerivedUnit.class, idSet, nameSpace);\r
result.put(nameSpace, typeMap);\r
- \r
- \r
+\r
+\r
} catch (SQLException e) {\r
throw new RuntimeException(e);\r
}\r
return result;\r
}\r
- \r
+\r
private void handleTypeKey(ResultSet rs, Set<String> idSet, String specTaxIdAttr, String copyrightAttr) throws SQLException {\r
Integer specTaxId = nullSafeInt(rs, specTaxIdAttr);\r
if (specTaxId != null){\r
}\r
}\r
}\r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
- */\r
+\r
@Override\r
protected boolean doCheck(GlobisImportState state){\r
IOValidator<GlobisImportState> validator = new GlobisImageImportValidator();\r
return validator.validate(state);\r
}\r
- \r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
- */\r
- protected boolean isIgnore(GlobisImportState state){\r
+\r
+ @Override\r
+ protected boolean isIgnore(GlobisImportState state){\r
return ! state.getConfig().isDoImages();\r
}\r
\r
-\r
-\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doInvoke(eu.etaxonomy.cdm.io.globis.GlobisImportState)\r
- */\r
@Override\r
protected void doInvoke(GlobisImportState state) {\r
Reference refGart = ReferenceFactory.newGeneric();\r
- refGart.setTitleCache("GART");\r
+ refGart.setTitleCache("GART", true);\r
refGart.setUuid(uuidGartRef);\r
getReferenceService().saveOrUpdate(refGart);\r
super.doInvoke(state);\r
}\r
-\r
-\r
-\r
-\r
-\r
}\r
BGBM BDI Projects / cdmlib-apps.git / blobdiff