import org.springframework.stereotype.Component;\r
\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
+import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;\r
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelCommonNamesImportValidator;\r
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.Marker;\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.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
\r
/**\r
- * FIXME TO BE IMPLEMENTED (Common names)\r
* \r
* @author a.mueller\r
* @created 20.03.2008\r
- * @version 1.0\r
*/\r
@Component\r
public class BerlinModelCommonNamesImport extends BerlinModelImportBase {\r
public static final String NAMESPACE = "common name";\r
\r
\r
- private static int modCount = 10000;\r
private static final String pluralString = "common names";\r
private static final String dbTableName = "emCommonName";\r
\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();\r
+ super(dbTableName, pluralString);\r
}\r
\r
- \r
-\r
@Override\r
- protected String getIdQuery() {\r
- String result = " SELECT CommonNameId FROM emCommonName ";\r
+ protected String getIdQuery(BerlinModelImportState state) {\r
+ String result = " SELECT CommonNameId FROM emCommonName WHERE (1=1) ";\r
+ if (StringUtils.isNotBlank(state.getConfig().getCommonNameFilter())){\r
+ result += " AND " + state.getConfig().getCommonNameFilter();\r
+ }\r
+ \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
recordQuery = \r
- " SELECT emCommonName.CommonNameId, emCommonName.CommonName, PTaxon.RIdentifier AS taxonId, emCommonName.PTNameFk, emCommonName.RefFk AS refId, emCommonName.Status, " + \r
- " emCommonName.RegionFks, emCommonName.MisNameRefFk, emCommonName.NameInSourceFk , emCommonName.Created_When, emCommonName.Updated_When, emCommonName.Created_Who, emCommonName.Updated_Who, emCommonName.Note as Notes," + \r
- " regionLanguage.Language AS regionLanguage, languageCommonName.Language, languageCommonName.LanguageOriginal, languageCommonName.ISO639_1, languageCommonName.ISO639_2, " + \r
- " emLanguageRegion.Region, emLanguageReference.RefFk as languageRefRefFk, emLanguageReference.ReferenceShort, " + \r
- " emLanguageReference.ReferenceLong, emLanguageReference.LanguageFk, languageReferenceLanguage.Language AS refLanguage, " +\r
- " languageReferenceLanguage.ISO639_2 AS refLanguageIso639_2, regionLanguage.ISO639_2 AS regionLanguageIso, " +\r
- " misappliedTaxon.RIdentifier AS misappliedTaxonId " + \r
- " FROM emLanguage as regionLanguage RIGHT OUTER JOIN " + \r
- " emLanguageRegion ON regionLanguage.LanguageId = emLanguageRegion.LanguageFk RIGHT OUTER JOIN " +\r
- " emLanguage AS languageReferenceLanguage RIGHT OUTER JOIN " +\r
- " emLanguageReference ON languageReferenceLanguage.LanguageId = emLanguageReference.LanguageFk RIGHT OUTER JOIN " +\r
- " emCommonName INNER JOIN " +\r
- " PTaxon ON emCommonName.PTNameFk = PTaxon.PTNameFk AND emCommonName.PTRefFk = PTaxon.PTRefFk ON " + \r
- " emLanguageReference.ReferenceId = emCommonName.LanguageRefFk LEFT OUTER JOIN " +\r
- " emLanguage AS languageCommonName ON emCommonName.LanguageFk = languageCommonName.LanguageId ON " + \r
- " emLanguageRegion.RegionId = emCommonName.RegionFks LEFT OUTER JOIN " +\r
- " PTaxon as misappliedTaxon ON emCommonName.PTNameFk = misappliedTaxon.PTNameFk AND emCommonName.MisNameRefFk = misappliedTaxon.PTRefFk " + \r
- " WHERE emCommonName.CommonNameId IN (" + ID_LIST_TOKEN + ")";\r
+ " SELECT cn.CommonNameId, cn.CommonName, PTaxon.RIdentifier AS taxonId, cn.PTNameFk, cn.RefFk AS refId, cn.Status, cn.RegionFks, cn.MisNameRefFk, " +\r
+ " cn.NameInSourceFk, cn.Created_When, cn.Updated_When, cn.Created_Who, cn.Updated_Who, cn.Note AS Notes, languageCommonName.Language, " +\r
+ " languageCommonName.LanguageOriginal, languageCommonName.ISO639_1, languageCommonName.ISO639_2, " +\r
+ " emLanguageReference.RefFk AS languageRefRefFk, emLanguageReference.ReferenceShort, emLanguageReference.ReferenceLong, " +\r
+ " emLanguageReference.LanguageFk, languageReferenceLanguage.Language AS refLanguage, languageReferenceLanguage.ISO639_2 AS refLanguageIso639_2, "+ \r
+ " misappliedTaxon.RIdentifier AS misappliedTaxonId " +\r
+ " FROM PTaxon AS misappliedTaxon RIGHT OUTER JOIN " +\r
+ " emLanguage AS languageReferenceLanguage RIGHT OUTER JOIN " + \r
+ " emLanguageReference ON languageReferenceLanguage.LanguageId = emLanguageReference.LanguageFk RIGHT OUTER JOIN " +\r
+ " emCommonName AS cn INNER JOIN " +\r
+ " PTaxon ON cn.PTNameFk = PTaxon.PTNameFk AND cn.PTRefFk = PTaxon.PTRefFk ON " +\r
+ " emLanguageReference.ReferenceId = cn.LanguageRefFk LEFT OUTER JOIN " +\r
+ " emLanguage AS languageCommonName ON cn.LanguageFk = languageCommonName.LanguageId ON misappliedTaxon.PTNameFk = cn.NameInSourceFk AND " +\r
+ " misappliedTaxon.PTRefFk = cn.MisNameRefFk " +\r
+ " WHERE cn.CommonNameId IN (" + ID_LIST_TOKEN + ")";\r
return recordQuery;\r
}\r
\r
- \r
-\r
@Override\r
- protected boolean doInvoke(BerlinModelImportState state) {\r
- boolean result = true;\r
+ protected void doInvoke(BerlinModelImportState state) {\r
try {\r
- result &= makeRegions(state);\r
+ makeRegions(state);\r
} catch (Exception e) {\r
logger.error("Error when creating common name regions:" + e.getMessage());\r
- result = false;\r
+ e.printStackTrace();\r
+ state.setUnsuccessfull();\r
}\r
- result &= super.doInvoke(state);\r
- return result;\r
+ super.doInvoke(state);\r
+ return;\r
}\r
\r
/**\r
* @param state \r
* \r
*/\r
- private boolean makeRegions(BerlinModelImportState state) {\r
- boolean result = true;\r
+ private void makeRegions(BerlinModelImportState state) {\r
try {\r
SortedSet<Integer> regionFks = new TreeSet<Integer>();\r
Source source = state.getConfig().getSource();\r
\r
- result = getRegionFks(result, regionFks, source);\r
+ //fill set with all regionFk from emCommonName.regionFks\r
+ getRegionFks(state, regionFks, source);\r
//concat filter string\r
String sqlWhere = getSqlWhere(regionFks);\r
\r
//get E+M - TDWG Mapping\r
Map<String, String> emTdwgMap = getEmTdwgMap(source);\r
//fill regionMap\r
- fillRegionMap(source, sqlWhere, emTdwgMap);\r
+ fillRegionMap(state, sqlWhere, emTdwgMap);\r
\r
- return result;\r
+ return;\r
} catch (NumberFormatException e) {\r
e.printStackTrace();\r
- return false;\r
+ state.setUnsuccessfull();\r
+ return;\r
} catch (SQLException e) {\r
e.printStackTrace();\r
- return false;\r
+ state.setUnsuccessfull();\r
+ return;\r
}\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
Object misappliedTaxonId = rs.getObject("misappliedTaxonId");\r
\r
//regions\r
- String region = rs.getString("Region");\r
String regionFks = rs.getString("RegionFks");\r
String[] regionFkSplit = regionFks.split(",");\r
\r
//commonNameString\r
- if (CdmUtils.isEmpty(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 = null;\r
- 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 + " not imported");\r
+ logger.warn("Taxon (" + taxonId + ") could not be found. Common name " + commonNameString + "(" + commonNameId + ") not imported");\r
continue;\r
}else if (! taxonBase.isInstanceOf(Taxon.class)){\r
logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " + commonNameId);\r
}\r
\r
//Language\r
- Language language = getAndHandleLanguage(iso6392Map, iso639_2, iso639_1, languageString, originalLanguageString);\r
+ Language language = getAndHandleLanguage(iso6392Map, iso639_2, iso639_1, languageString, originalLanguageString, state);\r
\r
//CommonTaxonName\r
List<CommonTaxonName> commonTaxonNames = new ArrayList<CommonTaxonName>();\r
- for (String regionFk : regionFkSplit){ \r
+ for (String regionFk : regionFkSplit){ //\r
CommonTaxonName commonTaxonName;\r
if (commonTaxonNames.size() == 0){\r
commonTaxonName = CommonTaxonName.NewInstance(commonNameString, language);\r
regionFk = regionFk.trim();\r
NamedArea area = regionMap.get(regionFk);\r
if (area == null){\r
- logger.warn("Area for " + regionFk + " not defined.");\r
+ if (regionFkSplit.length > 1 && StringUtils.isNotBlank(regionFk)){\r
+ logger.warn("Area for " + regionFk + " not defined in regionMap.");\r
+ }else{\r
+ //no region is defined\r
+ }\r
}else{\r
commonTaxonName.setArea(area);\r
TaxonDescription description = getDescription(taxon);\r
String strRefId = String.valueOf(refId);\r
String languageRefFk = String.valueOf(languageRefRefFk);\r
if (! CdmUtils.nullSafeEqual(strRefId, languageRefFk)){\r
- logger.warn("CommonName.RefFk (" + CdmUtils.Nz(strRefId) + ") and LanguageReference.RefFk " + CdmUtils.Nz(languageRefFk) + " are not equal. I will import only languageRefFk");\r
+ //use strRefId if languageRefFk is null\r
+ if (languageRefRefFk == null){\r
+ languageRefFk = strRefId;\r
+ }else{\r
+ logger.warn("CommonName.RefFk (" + CdmUtils.Nz(strRefId) + ") and LanguageReference.RefFk " + CdmUtils.Nz(languageRefFk) + " are not equal. I will import only languageReference.RefFk");\r
+ }\r
}\r
- \r
- Reference reference = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(languageRefRefFk));\r
+ \r
+ Reference<?> reference = refMap.get(String.valueOf(languageRefRefFk));\r
String microCitation = null;\r
String originalNameString = null;\r
\r
- TaxonNameBase nameUsedInSource = taxonNameMap.get(String.valueOf(nameInSourceFk));\r
+ TaxonNameBase<?,?> nameUsedInSource = taxonNameMap.get(String.valueOf(nameInSourceFk));\r
if (nameInSourceFk != null && nameUsedInSource == null){\r
- logger.warn("Name used in source (" + nameInSourceFk + ") was not found");\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
\r
+ \r
//MisNameRef\r
if (misNameRefFk != null){\r
//Taxon misappliedName = getMisappliedName(biblioRefMap, nomRefMap, misNameRefFk, taxon);\r
- Taxon misappliedName = null;\r
+ Taxon misappliedNameTaxon = null;\r
if (misappliedTaxonId != null){\r
- misappliedName = 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
+ misappliedNameTaxon = CdmBase.deproxy(misTaxonBase, Taxon.class);\r
+ }else{\r
+ logger.warn("Misapplied name taxon is not of type Taxon but " + misTaxonBase.getClass().getSimpleName());\r
+ }\r
}else{\r
- TaxonNameBase taxonName = taxonNameMap.get(String.valueOf(ptNameFk));\r
- Reference sec = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));\r
- if (taxonName == null || sec == null){\r
- logger.info("Taxon name or misapplied name reference is null for common name " + commonNameId);\r
+ \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
- misappliedName = Taxon.NewInstance(taxonName, sec);\r
- taxaToSave.add(misappliedName);\r
+ misappliedNameTaxon = Taxon.NewInstance(nameUsedInSource, sec);\r
+ MarkerType misCommonNameMarker = getMarkerType(state, BerlinModelTransformer.uuidMisappliedCommonName,"Misapplied Common Name in Berlin Model", "Misapplied taxon was automatically created by Berlin Model import for a common name with a misapplied name reference", "MCN");\r
+ Marker marker = Marker.NewInstance(misCommonNameMarker, true);\r
+ misappliedNameTaxon.addMarker(marker);\r
+ taxaToSave.add(misappliedNameTaxon);\r
+ logger.warn("Misapplied name taxon could not be found in database but misapplied name reference exists for common name. " +\r
+ "New misapplied name for misapplied reference common name was added. CommonNameId: " + commonNameId);\r
}\r
}\r
- if (misappliedName != null){\r
- taxon.addMisappliedName(misappliedName, config.getSourceReference(), null);\r
- TaxonDescription misappliedNameDescription = getDescription(misappliedName);\r
+ if (misappliedNameTaxon != null){\r
+ \r
+ if (! taxon.getMisappliedNames().contains(misappliedNameTaxon)){\r
+ taxon.addMisappliedName(misappliedNameTaxon,state.getTransactionalSourceReference(), null);\r
+ logger.warn("Misapplied name for common name was not found related to the accepted taxon. Created new relationship. CommonNameId: " + commonNameId);\r
+ }\r
+ \r
+ TaxonDescription misappliedNameDescription = getDescription(misappliedNameTaxon);\r
for (CommonTaxonName commonTaxonName : commonTaxonNames){\r
CommonTaxonName commonNameClone = (CommonTaxonName)commonTaxonName.clone();\r
misappliedNameDescription.addElement(commonNameClone);\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
- logger.warn("Reference is null (" + languageRefRefFk + ") but refLanguage (" + CdmUtils.Nz(refLanguage) + ") or iso639_2 (" + CdmUtils.Nz(refLanguageIso639_2) + ") was not null");\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
- AnnotationType statusAnnotationType = getAnnotationType( state, STATUS_ANNOTATION_UUID, "status","The status of this object","status");\r
- Annotation annotation = Annotation.NewInstance(status, statusAnnotationType, Language.DEFAULT());\r
+ if (isNotBlank(status)){\r
+ AnnotationType statusAnnotationType = getAnnotationType( state, STATUS_ANNOTATION_UUID, "status","The status of this object","status", null);\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, \r
- 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
* @param languageString\r
* @param originalLanguageString\r
+ * @param state \r
* @return\r
*/\r
- private Language getAndHandleLanguage(Map<String, Language> iso639Map, String iso639_2, String iso639_1, String languageString, String originalLanguageString) {\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
logger.warn("Language for code ISO693-2 '" + iso639_2 + "' and ISO693-1 '" + iso639_1 + "' was not found");\r
}\r
}\r
+ } else if ("unknown".equals(languageString)){\r
+ language = Language.UNKNOWN_LANGUAGE();\r
+ } else if ("Majorcan".equalsIgnoreCase(languageString)){\r
+ language = getLanguage(state, BerlinModelTransformer.uuidLangMajorcan, "Majorcan", "Majorcan (original 'mallorqu\u00EDn')", null);\r
}else{\r
logger.warn("language ISO 639_1 and ISO 639_2 were empty for " + languageString);\r
language = null;\r
* @param iso639_1\r
* @return\r
*/\r
- private Language getLanguageFromIsoMap(Map<String, Language> iso639Map,\r
- String iso639_2, String iso639_1) {\r
+ private Language getLanguageFromIsoMap(Map<String, Language> iso639Map, String iso639_2, String iso639_1) {\r
Language language;\r
language = iso639Map.get(iso639_2);\r
if (language == null){\r
* @param originalLanguageString\r
*/\r
private void addOriginalLanguage(Language language, String originalLanguageString) {\r
- if (CdmUtils.isEmpty(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
\r
\r
/**\r
- * @param result\r
+ * Fills the regionFks with all regionFks from emCommonName. Comma separated regionFks will be split.\r
+ * @param state\r
* @param regionFks\r
* @param source\r
* @return\r
* @throws SQLException\r
+ * \r
*/\r
- private boolean getRegionFks(boolean result, SortedSet<Integer> regionFks,\r
- Source source) throws SQLException {\r
+ private void getRegionFks(BerlinModelImportState state, SortedSet<Integer> regionFks, Source source) throws SQLException {\r
String sql = " SELECT DISTINCT RegionFks FROM emCommonName";\r
+ if (state.getConfig().getCommonNameFilter() != null){\r
+ sql += " WHERE " + state.getConfig().getCommonNameFilter(); \r
+ }\r
+ \r
ResultSet rs = source.getResultSet(sql);\r
while (rs.next()){\r
String strRegionFks = rs.getString("RegionFks"); \r
+ if (isBlank(strRegionFks)){\r
+ continue;\r
+ }\r
+ \r
String[] regionFkArray = strRegionFks.split(",");\r
for (String regionFk: regionFkArray){\r
regionFk = regionFk.trim();\r
- if (! StringUtils.isNumeric(regionFk)){\r
- result = false;\r
- logger.warn("RegionFk is not numeric: " + regionFk);\r
+ if (! StringUtils.isNumeric(regionFk) || "".equals(regionFk) ){\r
+ state.setUnsuccessfull();\r
+ logger.warn("RegionFk is not numeric: " + regionFk + " ( part of " + strRegionFks + ")");\r
}else{\r
regionFks.add(Integer.valueOf(regionFk));\r
}\r
}\r
}\r
- return result;\r
+ return;\r
}\r
\r
\r
\r
/**\r
- * @param source\r
+ * Fills the {@link #regionMap} by all emLanguageRegion regions defined in the sql filter.\r
+ * {@link #regionMap} maps emLanguageRegion.RegionId to named areas.\r
+ * @param state\r
* @param sqlWhere\r
* @param emTdwgMap\r
* @throws SQLException\r
*/\r
- private void fillRegionMap(Source source, String sqlWhere,\r
+ private void fillRegionMap(BerlinModelImportState state, String sqlWhere,\r
Map<String, String> emTdwgMap) throws SQLException {\r
+ Source source = state.getConfig().getSource();\r
String sql;\r
ResultSet rs;\r
sql = " SELECT RegionId, Region FROM emLanguageRegion WHERE RegionId IN ("+ sqlWhere+ ") ";\r
String region = rs.getString("Region");\r
String[] splitRegion = region.split("-");\r
if (splitRegion.length <= 1){\r
- NamedArea newArea = NamedArea.NewInstance(region, region, null);\r
- getTermService().save(newArea);\r
+ NamedArea newArea = getNamedArea(state, null, region, "Language region '" + region + "'", null, null, null);\r
+// getTermService().save(newArea);\r
regionMap.put(String.valueOf(regionId), newArea);\r
logger.warn("Found new area: " + region);\r
}else if (splitRegion.length == 2){\r
String emCode = splitRegion[1].trim();\r
String tdwgCode = emTdwgMap.get(emCode);\r
if (StringUtils.isNotBlank(tdwgCode) ){\r
- NamedArea tdwgArea = getNamedArea(tdwgCode);\r
+ NamedArea tdwgArea = getNamedArea(state, tdwgCode);\r
regionMap.put(String.valueOf(regionId), tdwgArea);\r
- }else{\r
- logger.warn("emCode did not map to valid tdwgCode: " + CdmUtils.Nz(emCode) + "->" + CdmUtils.Nz(tdwgCode));\r
+ }else {\r
+ NamedArea area = getOtherAreas(state, emCode, tdwgCode);\r
+ if (area != null){\r
+ regionMap.put(String.valueOf(regionId), area);\r
+ }else{\r
+ logger.warn("emCode did not map to valid tdwgCode: " + CdmUtils.Nz(emCode) + "->" + CdmUtils.Nz(tdwgCode));\r
+ }\r
}\r
}\r
}\r
\r
\r
/**\r
+ * Returns the are for a given TDWG code. See {@link #getEmTdwgMap(Source)} for exceptions from\r
+ * the TDWG code\r
+ * @param state \r
* @param tdwgCode\r
*/\r
- private NamedArea getNamedArea(String tdwgCode) {\r
+ private NamedArea getNamedArea(BerlinModelImportState state, String tdwgCode) {\r
NamedArea area;\r
if (tdwgCode.equalsIgnoreCase("Ab")){\r
- area = NamedArea.NewInstance("Azerbaijan (including Nakhichevan)", "Azerbaijan & Nakhichevan", "Ab");\r
- getTermService().save(area);\r
- }else if (tdwgCode.equalsIgnoreCase("Rf")){\r
- area = NamedArea.NewInstance("The Russian Federation", "The Russian Federation", "Rf");\r
- getTermService().save(area);\r
+ area = getNamedArea(state, BerlinModelTransformer.uuidAzerbaijanNakhichevan, "Azerbaijan & Nakhichevan", "Azerbaijan (including Nakhichevan)", "Ab", null, null);\r
+ getTermService().saveOrUpdate(area);\r
}else if (tdwgCode.equalsIgnoreCase("Uk")){\r
- area = NamedArea.NewInstance("Ukraine (including Crimea)", "Ukraine & Crimea", "Uk");\r
- getTermService().save(area);\r
+ area = getNamedArea(state, BerlinModelTransformer.uuidUkraineAndCrimea , "Ukraine & Crimea", "Ukraine (including Crimea)", "Uk", null, null);\r
+ getTermService().saveOrUpdate(area);\r
+ }else if (tdwgCode.equalsIgnoreCase("Rf")){\r
+ area = Country.RUSSIANFEDERATION();\r
+ }else if (tdwgCode.equalsIgnoreCase("Gg")){\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
}\r
return area;\r
}\r
\r
-\r
-\r
/**\r
* @param regionFks\r
* @return\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
+ * for 'Ab / Ab(A)', 'Ga / Ga(F)', 'It / It(I)', 'Ar / Ar(A)','Hs / Hs(S)'\r
* @param source\r
* @throws SQLException\r
*/\r
String TDWGCode = rs.getString("TDWGCode");\r
if (StringUtils.isNotBlank(emCode) ){\r
emCode = emCode.trim();\r
- if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")|| emCode.equalsIgnoreCase("Uk") ){\r
+ if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")|| \r
+ emCode.equalsIgnoreCase("Uk") || emCode.equalsIgnoreCase("Gg")){\r
emTdwgMap.put(emCode, emCode);\r
}else if (StringUtils.isNotBlank(TDWGCode)){\r
emTdwgMap.put(emCode, TDWGCode.trim());\r
}\r
}\r
}\r
+ emTdwgMap.put("Ab / Ab(A)", "Ab");\r
+ emTdwgMap.put("Ga / Ga(F)", "FRA-FR");\r
+ emTdwgMap.put("It / It(I)", "ITA");\r
+ emTdwgMap.put("Uk / Uk(U)", "Uk");\r
+ emTdwgMap.put("Ar / Ar(A)", "TCS-AR");\r
+ emTdwgMap.put("Hs / Hs(S)", "SPA-SP");\r
+ \r
return emTdwgMap;\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
+ Class<?> cdmClass;\r
Set<String> idSet;\r
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();\r
\r
+ String pos = "0";\r
try{\r
Set<String> taxonIdSet = new HashSet<String>();\r
Set<String> nameIdSet = new HashSet<String>();\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
+ Map<String, TaxonNameBase<?,?>> nameMap = (Map<String, TaxonNameBase<?,?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, nameMap);\r
-\r
- //name map\r
+ \r
+ //taxon map\r
nameSpace = BerlinModelTaxonImport.NAMESPACE;\r
- cdmClass = Taxon.class;\r
+ cdmClass = TaxonBase.class;\r
idSet = taxonIdSet;\r
- Map<String, TaxonNameBase> taxonMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, taxonMap);\r
-\r
- //nom reference map\r
- nameSpace = BerlinModelReferenceImport.NOM_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
- //biblio reference map\r
- nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;\r
+ \r
+ //reference map\r
+ nameSpace = BerlinModelReferenceImport.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
+ 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(e);\r
+ throw new RuntimeException("pos: " +pos, e);\r
} catch (NullPointerException nep){\r
logger.error("NullPointerException in getRelatedObjectsForPartition()");\r
}\r
IOValidator<BerlinModelImportState> validator = new BerlinModelCommonNamesImportValidator();\r
return validator.validate(state);\r
}\r
- \r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()\r
- */\r
- @Override\r
- protected String getTableName() {\r
- return dbTableName;\r
- }\r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()\r
- */\r
- @Override\r
- public String getPluralString() {\r
- return pluralString;\r
- }\r
\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r