import eu.etaxonomy.cdm.io.common.IOValidator;\r
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;\r
import eu.etaxonomy.cdm.io.common.Source;\r
+import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;\r
import eu.etaxonomy.cdm.model.common.Annotation;\r
import eu.etaxonomy.cdm.model.common.AnnotationType;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
-import eu.etaxonomy.cdm.model.common.DescriptionElementSource;\r
import eu.etaxonomy.cdm.model.common.Extension;\r
import eu.etaxonomy.cdm.model.common.ExtensionType;\r
import eu.etaxonomy.cdm.model.common.Language;\r
import eu.etaxonomy.cdm.model.common.MarkerType;\r
import eu.etaxonomy.cdm.model.common.Representation;\r
import eu.etaxonomy.cdm.model.description.CommonTaxonName;\r
+import eu.etaxonomy.cdm.model.description.DescriptionElementSource;\r
import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.location.Country;\r
import eu.etaxonomy.cdm.model.location.NamedArea;\r
-import eu.etaxonomy.cdm.model.location.TdwgArea;\r
-import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
* \r
* @author a.mueller\r
* @created 20.03.2008\r
- * @version 1.0\r
*/\r
@Component\r
public class BerlinModelCommonNamesImport extends BerlinModelImportBase {\r
//map that stores the regions (named areas) and makes them accessible via the regionFk\r
private Map<String, NamedArea> regionMap = new HashMap<String, NamedArea>();\r
\r
- \r
-\r
public BerlinModelCommonNamesImport(){\r
super(dbTableName, pluralString);\r
}\r
\r
- \r
-\r
@Override\r
protected String getIdQuery(BerlinModelImportState state) {\r
String result = " SELECT CommonNameId FROM emCommonName WHERE (1=1) ";\r
return result;\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(BerlinModelImportConfigurator config) {\r
String recordQuery = "";\r
return recordQuery;\r
}\r
\r
- \r
-\r
@Override\r
protected void doInvoke(BerlinModelImportState state) {\r
try {\r
}\r
\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)\r
- */\r
+ @Override\r
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {\r
boolean success = true ;\r
- BerlinModelImportConfigurator config = state.getConfig();\r
+ \r
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();\r
Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);\r
Map<String, TaxonNameBase> taxonNameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);\r
\r
- Map<String, Reference> biblioRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);\r
- Map<String, Reference> nomRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE);\r
+ Map<String, Reference> refMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);\r
\r
Map<String, Language> iso6392Map = new HashMap<String, Language>();\r
\r
String[] regionFkSplit = regionFks.split(",");\r
\r
//commonNameString\r
- if (CdmUtils.isBlank(commonNameString)){\r
+ if (isBlank(commonNameString)){\r
String message = "CommonName is empty or null. Do not import record for taxon " + taxonId;\r
logger.warn(message);\r
continue;\r
\r
//taxon\r
Taxon taxon = null;\r
- TaxonBase taxonBase = taxonMap.get(String.valueOf(taxonId));\r
+ TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));\r
if (taxonBase == null){\r
logger.warn("Taxon (" + taxonId + ") could not be found. Common name " + commonNameString + "(" + commonNameId + ") not imported");\r
continue;\r
NamedArea area = regionMap.get(regionFk);\r
if (area == null){\r
if (regionFkSplit.length > 1 && StringUtils.isNotBlank(regionFk)){\r
- logger.warn("Area for " + regionFk + " not defined.");\r
+ logger.warn("Area for " + regionFk + " not defined in regionMap.");\r
}else{\r
//no region is defined\r
}\r
}\r
}\r
\r
- Reference<?> reference = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(languageRefRefFk));\r
+ Reference<?> reference = refMap.get(String.valueOf(languageRefRefFk));\r
String microCitation = null;\r
String originalNameString = null;\r
\r
if (nameInSourceFk != null && nameUsedInSource == null){\r
logger.warn("Name used in source (" + nameInSourceFk + ") was not found for common name " + commonNameId);\r
}\r
- DescriptionElementSource source = DescriptionElementSource.NewInstance(reference, microCitation, nameUsedInSource, originalNameString);\r
+ DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation, nameUsedInSource, originalNameString);\r
for (CommonTaxonName commonTaxonName : commonTaxonNames){\r
commonTaxonName.addSource(source);\r
}\r
//Taxon misappliedName = getMisappliedName(biblioRefMap, nomRefMap, misNameRefFk, taxon);\r
Taxon misappliedNameTaxon = null;\r
if (misappliedTaxonId != null){\r
- TaxonBase misTaxonBase = taxonMap.get(String.valueOf(misappliedTaxonId));\r
+ TaxonBase<?> misTaxonBase = taxonMap.get(String.valueOf(misappliedTaxonId));\r
if (misTaxonBase == null){\r
logger.warn("MisappliedName not found for misappliedTaxonId " + misappliedTaxonId + "; commonNameId: " + commonNameId);\r
}else if (misTaxonBase.isInstanceOf(Taxon.class)){\r
}\r
}else{\r
\r
- Reference<?> sec = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));\r
+ Reference<?> sec = refMap.get(String.valueOf(misNameRefFk));\r
if (nameUsedInSource == null || sec == null){\r
logger.warn("Taxon name or misapplied name reference is null for common name " + commonNameId);\r
}else{\r
\r
//reference extensions\r
if (reference != null){\r
- if (CdmUtils.isNotEmpty(refLanguage)){\r
+ if (StringUtils.isNotBlank(refLanguage)){\r
ExtensionType refLanguageExtensionType = getExtensionType( state, REFERENCE_LANGUAGE_STRING_UUID, "reference language","The language of the reference","ref. lang.");\r
Extension.NewInstance(reference, refLanguage, refLanguageExtensionType);\r
}\r
\r
- if (CdmUtils.isNotEmpty(refLanguageIso639_2)){\r
+ if (StringUtils.isNotBlank(refLanguageIso639_2)){\r
ExtensionType refLanguageIsoExtensionType = getExtensionType( state, REFERENCE_LANGUAGE_ISO639_2_UUID, "reference language iso 639-2","The iso 639-2 code of the references language","ref. lang. 639-2");\r
Extension.NewInstance(reference, refLanguageIso639_2, refLanguageIsoExtensionType);\r
}\r
- }else if (CdmUtils.isNotEmpty(refLanguage) || CdmUtils.isNotEmpty(refLanguageIso639_2)){\r
+ }else if (isNotBlank(refLanguage) || isNotBlank(refLanguageIso639_2)){\r
logger.warn("Reference is null (" + languageRefRefFk + ") but refLanguage (" + CdmUtils.Nz(refLanguage) + ") or iso639_2 (" + CdmUtils.Nz(refLanguageIso639_2) + ") was not null for common name ("+ commonNameId +")");\r
}\r
\r
//status\r
- if (CdmUtils.isNotEmpty(status)){\r
+ if (isNotBlank(status)){\r
AnnotationType statusAnnotationType = getAnnotationType( state, STATUS_ANNOTATION_UUID, "status","The status of this object","status", null);\r
- Annotation annotation = Annotation.NewInstance(status, statusAnnotationType, Language.DEFAULT());\r
for (CommonTaxonName commonTaxonName : commonTaxonNames){\r
+ Annotation annotation = Annotation.NewInstance(status, statusAnnotationType, Language.DEFAULT());\r
commonTaxonName.addAnnotation(annotation);\r
}\r
- \r
}\r
\r
//Notes\r
\r
}\r
\r
-\r
-\r
- /**\r
- * Not used anymore. Use MisappliedName RIdentifier instead\r
- * @param biblioRefMap\r
- * @param nomRefMap\r
- * @param misNameRefFk\r
- * @param taxon\r
- */\r
- private boolean isFirstMisappliedName = true;\r
- private Taxon getMisappliedName(Map<String, Reference> biblioRefMap, Map<String, Reference> nomRefMap, Object misNameRefFk, Taxon taxon) {\r
- Taxon misappliedTaxon = null;\r
- Reference<?> misNameRef = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));\r
- misappliedTaxon = Taxon.NewInstance(taxon.getName(), misNameRef);\r
- Set<String> includeProperty = new HashSet<String>();\r
- try {\r
-// //IMatchStrategy matchStrategy = DefaultMatchStrategy.NewInstance(TaxonBase.class);\r
-// //List<TaxonBase> misappliedList1 = getCommonService().findMatching(misappliedTaxon, matchStrategy);\r
- List<TaxonBase> misappliedList = getTaxonService().list(misappliedTaxon, includeProperty, null, null, null, null);\r
- if (misappliedList.size() > 0){\r
- misappliedTaxon = CdmBase.deproxy(misappliedList.get(0), Taxon.class);\r
- }\r
- } catch (ClassCastException e) {\r
- logger.error(e.getMessage());\r
- if (isFirstMisappliedName){\r
- e.printStackTrace();\r
- isFirstMisappliedName = false;\r
- }\r
- }\r
- return misappliedTaxon;\r
- }\r
-\r
-\r
-\r
/**\r
* @param iso6392Map\r
* @param iso639_2\r
*/\r
private Language getAndHandleLanguage(Map<String, Language> iso639Map, String iso639_2, String iso639_1, String languageString, String originalLanguageString, BerlinModelImportState state) {\r
Language language;\r
- if (CdmUtils.isNotEmpty(iso639_2)|| CdmUtils.isNotEmpty(iso639_1) ){\r
+ if (isNotBlank(iso639_2)|| isNotBlank(iso639_1) ){\r
//TODO test performance, implement in state\r
language = getLanguageFromIsoMap(iso639Map, iso639_2, iso639_1);\r
\r
language = getTermService().getLanguageByIso(iso639_2);\r
iso639Map.put(iso639_2, language);\r
if (language == null){\r
- language = getTermService().getLanguageByIso(iso639_1);\r
+ try {\r
+ language = getTermService().getLanguageByIso(iso639_1);\r
+ } catch (Exception e) {\r
+ // TODO Auto-generated catch block\r
+ // TODO remove if problem with duplicate DescElement_Annot id is solved\r
+ e.printStackTrace();\r
+ }\r
iso639Map.put(iso639_1, language);\r
}\r
if (language == null){\r
* @param originalLanguageString\r
*/\r
private void addOriginalLanguage(Language language, String originalLanguageString) {\r
- if (CdmUtils.isBlank(originalLanguageString)){\r
+ if (isBlank(originalLanguageString)){\r
return;\r
}else if (language == null){\r
logger.warn("Language could not be defined, but originalLanguageString exists: " + originalLanguageString);\r
ResultSet rs = source.getResultSet(sql);\r
while (rs.next()){\r
String strRegionFks = rs.getString("RegionFks"); \r
- if (StringUtils.isBlank(strRegionFks)){\r
+ if (isBlank(strRegionFks)){\r
continue;\r
}\r
\r
NamedArea area;\r
if (tdwgCode.equalsIgnoreCase("Ab")){\r
area = getNamedArea(state, BerlinModelTransformer.uuidAzerbaijanNakhichevan, "Azerbaijan & Nakhichevan", "Azerbaijan (including Nakhichevan)", "Ab", null, null);\r
- getTermService().save(area);\r
+ getTermService().saveOrUpdate(area);\r
}else if (tdwgCode.equalsIgnoreCase("Uk")){\r
area = getNamedArea(state, BerlinModelTransformer.uuidUkraineAndCrimea , "Ukraine & Crimea", "Ukraine (including Crimea)", "Uk", null, null);\r
- getTermService().save(area);\r
+ getTermService().saveOrUpdate(area);\r
}else if (tdwgCode.equalsIgnoreCase("Rf")){\r
- area = WaterbodyOrCountry.RUSSIANFEDERATION();\r
+ area = Country.RUSSIANFEDERATION();\r
}else if (tdwgCode.equalsIgnoreCase("Gg")){\r
- area = WaterbodyOrCountry.GEORGIA();\r
+ area = Country.GEORGIA();\r
}else{\r
- area = TdwgArea.getAreaByTdwgAbbreviation(tdwgCode);\r
+ area = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode);\r
}\r
if (area == null){\r
logger.warn("Area is null for " + tdwgCode);\r
return sqlWhere;\r
}\r
\r
-\r
-\r
/**\r
* Returns a map which is filled by the emCode->TdwgCode mapping defined in emArea.\r
* Some exceptions are defined for emCode 'Ab','Rf','Uk' and some additional mapping is added \r
}\r
\r
\r
-\r
-\r
/**\r
* Returns the first non-image gallery description. Creates a new one if no description exists.\r
* @param taxon\r
return result;\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)\r
- */\r
+ @Override\r
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {\r
String nameSpace;\r
Class<?> cdmClass;\r
Set<String> idSet;\r
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();\r
\r
- int pos = -1;\r
+ String pos = "0";\r
try{\r
Set<String> taxonIdSet = new HashSet<String>();\r
Set<String> nameIdSet = new HashSet<String>();\r
Set<String> referenceIdSet = new HashSet<String>();\r
while (rs.next()){\r
- pos = 0;\r
handleForeignKey(rs, taxonIdSet, "taxonId");\r
- pos = 1;\r
handleForeignKey(rs, taxonIdSet, "misappliedTaxonId");\r
- pos = 2;\r
handleForeignKey(rs, referenceIdSet, "refId");\r
- pos = 3;\r
handleForeignKey(rs, referenceIdSet, "languageRefRefFk");\r
- pos = 4;\r
handleForeignKey(rs, nameIdSet, "NameInSourceFk");\r
- pos = 5;\r
handleForeignKey(rs, nameIdSet, "PTNameFk");\r
- pos = 6;\r
handleForeignKey(rs, referenceIdSet, "MisNameRefFk");\r
- pos = -2;\r
- \r
}\r
\r
- pos = 7;\r
- \r
//name map\r
nameSpace = BerlinModelTaxonNameImport.NAMESPACE;\r
cdmClass = TaxonNameBase.class;\r
idSet = nameIdSet;\r
Map<String, TaxonNameBase<?,?>> nameMap = (Map<String, TaxonNameBase<?,?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, nameMap);\r
-\r
- pos = 8;\r
\r
//taxon map\r
nameSpace = BerlinModelTaxonImport.NAMESPACE;\r
idSet = taxonIdSet;\r
Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, taxonMap);\r
-\r
- pos = 9;\r
\r
- //nom reference map\r
- nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;\r
+ //reference map\r
+ nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;\r
cdmClass = Reference.class;\r
idSet = referenceIdSet;\r
- Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
- result.put(nameSpace, nomReferenceMap);\r
-\r
- pos = 10;\r
- \r
- //biblio reference map\r
- nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;\r
- cdmClass = Reference.class;\r
- idSet = referenceIdSet;\r
- Map<String, Reference<?>> biblioReferenceMap = (Map<String, Reference<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
- result.put(nameSpace, biblioReferenceMap);\r
-\r
- pos = 11;\r
- \r
+ Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ result.put(nameSpace, referenceMap);\r
+ // TODO remove if problem with duplicate DescElement_Annot id is solved\r
} catch (SQLException e) {\r
throw new RuntimeException("pos: " +pos, e);\r
} catch (NullPointerException nep){\r
BGBM BDI Projects / cdmlib.git / blobdiff