/**\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
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.Extension;\r
import eu.etaxonomy.cdm.model.common.ExtensionType;\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.common.TermType;\r
+import eu.etaxonomy.cdm.model.common.TermVocabulary;\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.name.TaxonNameBase;\r
+import eu.etaxonomy.cdm.model.name.TaxonName;\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
- * \r
+ *\r
* @author a.mueller\r
- * @created 20.03.2008\r
+ * @since 20.03.2008\r
*/\r
@Component\r
public class BerlinModelCommonNamesImport extends BerlinModelImportBase {\r
- private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImport.class);\r
+ private static final long serialVersionUID = -8921948187177864321L;\r
+\r
+ private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImport.class);\r
\r
public static final UUID REFERENCE_LANGUAGE_ISO639_2_UUID = UUID.fromString("40c4f8dd-3d9c-44a4-b77a-76e137a89a5f");\r
public static final UUID REFERENCE_LANGUAGE_STRING_UUID = UUID.fromString("2a1b678f-c27d-48c1-b43e-98fd0d426305");\r
- public static final UUID STATUS_ANNOTATION_UUID = UUID.fromString("e3f7b80a-1286-458d-812c-5e818f731968");\r
- \r
+ public static final UUID COMMONNAME_STATUS_RECOMMENDED_UUID = UUID.fromString("e3f7b80a-1286-458d-812c-5e818f731968");\r
+ public static final UUID COMMONNAME_STATUS_SYNONYM_UUID = UUID.fromString("169b2d97-a706-49de-b28b-c67f0ee6764b");\r
+\r
public static final String NAMESPACE = "common name";\r
- \r
- \r
+\r
+\r
private static final String pluralString = "common names";\r
private static final String dbTableName = "emCommonName";\r
\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
+ private Map<String, NamedArea> regionMap = new HashMap<>();\r
\r
public BerlinModelCommonNamesImport(){\r
super(dbTableName, pluralString);\r
}\r
- \r
+\r
@Override\r
protected String getIdQuery(BerlinModelImportState state) {\r
String result = " SELECT CommonNameId FROM emCommonName WHERE (1=1) ";\r
- if (StringUtils.isNotBlank(state.getConfig().getCommonNameFilter())){\r
+ if (isNotBlank(state.getConfig().getCommonNameFilter())){\r
result += " AND " + state.getConfig().getCommonNameFilter();\r
}\r
- \r
+ result += " ORDER BY CommonNameId ";\r
+\r
return result;\r
}\r
\r
@Override\r
protected String getRecordQuery(BerlinModelImportConfigurator config) {\r
String recordQuery = "";\r
- recordQuery = \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
+ recordQuery =\r
+ " SELECT rel.RelPTaxonId, rel.RelQualifierFk, acc.RIdentifier accTaxonId, factTaxon.RIdentifier factTaxonId, accName.NameId, f.FactId, " +\r
+ " cn.CommonNameId, cn.CommonName, tax.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 AS tax ON cn.PTNameFk = tax.PTNameFk AND cn.PTRefFk = tax.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
+\r
+ " LEFT OUTER JOIN Fact f ON cn.CommonNameId = f.ExtensionFk " +\r
+ " LEFT OUTER JOIN PTaxon factTaxon ON factTaxon.PTNameFk = f.PTNameFk AND factTaxon.PTRefFk = f.PTRefFk " +\r
+ " LEFT OUTER JOIN RelPTaxon rel ON rel.PTNameFk1 = tax.PTNameFk AND rel.PTRefFk1 = tax.PTRefFk AND rel.RelQualifierFk IN (2,6,7) " +\r
+ " LEFT OUTER JOIN PTaxon acc ON rel.PTNameFk2 = acc.PTNameFk AND rel.PTRefFk2 = acc.PTRefFk " +\r
+ " LEFT OUTER JOIN Name accName ON accName.NameId = acc.PTNameFk " +\r
+ " WHERE cn.CommonNameId IN (" + ID_LIST_TOKEN + ") " +\r
+ " ORDER BY cn.CommonNameId ";\r
+\r
return recordQuery;\r
}\r
- \r
+\r
@Override\r
protected void doInvoke(BerlinModelImportState state) {\r
try {\r
super.doInvoke(state);\r
return;\r
}\r
- \r
+\r
/**\r
- * @param state \r
- * \r
+ * @param state\r
+ *\r
*/\r
private void makeRegions(BerlinModelImportState state) {\r
try {\r
- SortedSet<Integer> regionFks = new TreeSet<Integer>();\r
+ SortedSet<Integer> regionFks = new TreeSet<>();\r
Source source = state.getConfig().getSource();\r
- \r
+\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
+\r
//get E+M - TDWG Mapping\r
Map<String, String> emTdwgMap = getEmTdwgMap(source);\r
//fill regionMap\r
fillRegionMap(state, sqlWhere, emTdwgMap);\r
- \r
+\r
return;\r
} catch (NumberFormatException e) {\r
e.printStackTrace();\r
@Override\r
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {\r
boolean success = true ;\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> refMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);\r
- \r
- Map<String, Language> iso6392Map = new HashMap<String, Language>();\r
- \r
+\r
+ Set<TaxonBase> taxaToSave = new HashSet<>();\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, Taxon> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, TaxonName> taxonNameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);\r
+\r
+ Map<String, Language> iso6392Map = new HashMap<>();\r
+\r
// logger.warn("MisappliedNameRefFk not yet implemented for Common Names");\r
- \r
+\r
ResultSet rs = partitioner.getResultSet();\r
+ Integer lastCommonNameId = null;\r
try{\r
while (rs.next()){\r
\r
//create TaxonName element\r
- Object commonNameId = rs.getObject("CommonNameId");\r
+ Integer commonNameId = rs.getInt("CommonNameId");\r
int taxonId = rs.getInt("taxonId");\r
- Object refId = rs.getObject("refId");\r
- Object ptNameFk = rs.getObject("PTNameFk");\r
+ Integer factTaxonId = nullSafeInt(rs, "factTaxonId");\r
+ Integer accTaxonId = nullSafeInt(rs, "accTaxonId"); //if common name is related to synonym this is the accepted taxon id\r
+\r
+ Integer refId = nullSafeInt(rs, "refId");\r
+// Integer ptNameFk = nullSafeInt(rs,"PTNameFk");\r
String commonNameString = rs.getString("CommonName");\r
String iso639_2 = rs.getString("ISO639_2");\r
String iso639_1 = rs.getString("ISO639_1");\r
String languageString = rs.getString("Language");\r
String originalLanguageString = rs.getString("LanguageOriginal");\r
- Object misNameRefFk = rs.getObject("MisNameRefFk");\r
- Object languageRefRefFk = rs.getObject("languageRefRefFk");\r
+ Integer misNameRefFk = nullSafeInt(rs, "MisNameRefFk");\r
+ Integer languageRefRefFk = nullSafeInt(rs, "languageRefRefFk");\r
String refLanguage = rs.getString("refLanguage");\r
String refLanguageIso639_2 = rs.getString("refLanguageIso639_2");\r
String status = rs.getString("Status");\r
- Object nameInSourceFk = rs.getObject("NameInSourceFk");\r
- Object misappliedTaxonId = rs.getObject("misappliedTaxonId");\r
- \r
+ Integer nameInSourceFk = nullSafeInt( rs, "NameInSourceFk");\r
+ Integer misappliedTaxonId = nullSafeInt( rs, "misappliedTaxonId");\r
+\r
+ if (commonNameId == lastCommonNameId){\r
+ logger.warn("CommonNameId >1 times in query. This may happen due to LEFT JOINS to fact and/or accepted taxon and e.g. multiple taxon relationships. 2018-04-01 no such double relation existed in E+M. ");\r
+ }else{\r
+ lastCommonNameId = commonNameId;\r
+ }\r
+\r
//regions\r
String regionFks = rs.getString("RegionFks");\r
- String[] regionFkSplit = regionFks.split(",");\r
- \r
+ String[] regionFkSplit = (regionFks==null)? new String[0] : regionFks.split(",");\r
+\r
//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
- \r
+\r
//taxon\r
Taxon taxon = null;\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
- }else if (! taxonBase.isInstanceOf(Taxon.class)){\r
- logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " + commonNameId);\r
- continue;\r
+ }else if (taxonBase.isInstanceOf(Taxon.class)){\r
+ taxon = CdmBase.deproxy(taxonBase, Taxon.class);\r
+ if (factTaxonId != null && !factTaxonId.equals(taxonId)){\r
+ logger.warn("Fact taxon ("+factTaxonId+") for common name "+commonNameId+" differs from common name taxon " + taxonId);\r
+ }\r
}else{\r
- taxon = CdmBase.deproxy(taxonBase, Taxon.class);\r
+ Taxon factTaxon = null;\r
+ if (factTaxonId != null && factTaxonId.equals(accTaxonId)){\r
+ factTaxon = taxonMap.get(String.valueOf(factTaxonId));\r
+ }\r
+ if (factTaxon != null){\r
+ taxon = factTaxon;\r
+ }else{\r
+ logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " + commonNameId + ". FactTaxonId= " + factTaxonId + "; accTaxonId = " + accTaxonId);\r
+ continue;\r
+ }\r
}\r
- \r
+\r
//Language\r
Language language = getAndHandleLanguage(iso6392Map, iso639_2, iso639_1, languageString, originalLanguageString, state);\r
- \r
+\r
//CommonTaxonName\r
- List<CommonTaxonName> commonTaxonNames = new ArrayList<CommonTaxonName>();\r
+ List<CommonTaxonName> commonTaxonNames = new ArrayList<>();\r
for (String regionFk : regionFkSplit){ //\r
CommonTaxonName commonTaxonName;\r
if (commonTaxonNames.size() == 0){\r
regionFk = regionFk.trim();\r
NamedArea area = regionMap.get(regionFk);\r
if (area == null){\r
- if (regionFkSplit.length > 1 && StringUtils.isNotBlank(regionFk)){\r
+ if (regionFkSplit.length > 1 && isNotBlank(regionFk)){\r
logger.warn("Area for " + regionFk + " not defined in regionMap.");\r
}else{\r
//no region is defined\r
description.addElement(commonTaxonName);\r
}\r
}\r
- \r
+\r
//Reference/Source\r
- String strRefId = String.valueOf(refId);\r
- String languageRefFk = String.valueOf(languageRefRefFk);\r
- if (! CdmUtils.nullSafeEqual(strRefId, languageRefFk)){\r
+ if (! CdmUtils.nullSafeEqual(refId, languageRefRefFk)){\r
//use strRefId if languageRefFk is null\r
if (languageRefRefFk == null){\r
- languageRefFk = strRefId;\r
+ languageRefRefFk = refId;\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
+ logger.warn("CommonName.RefFk (" + CdmUtils.Nz(refId) + ") and LanguageReference.RefFk " + languageRefRefFk + " are not equal. I will import only languageReference.RefFk");\r
}\r
}\r
- \r
- Reference<?> reference = refMap.get(String.valueOf(languageRefRefFk));\r
+\r
+ Reference reference = refMap.get(String.valueOf(languageRefRefFk));\r
+ if (reference == null && languageRefRefFk != null){\r
+ logger.warn("CommonName reference was null but reference exists. languageRefRefFk = " + languageRefRefFk + "; commonNameId = " + commonNameId);\r
+ }\r
String microCitation = null;\r
String originalNameString = null;\r
- \r
- TaxonNameBase<?,?> nameUsedInSource = taxonNameMap.get(String.valueOf(nameInSourceFk));\r
+\r
+ TaxonName nameUsedInSource = taxonNameMap.get(String.valueOf(nameInSourceFk));\r
if (nameInSourceFk != null && nameUsedInSource == null){\r
- logger.warn("Name used in source (" + nameInSourceFk + ") was not found for common name " + commonNameId);\r
+ if (nameInSourceFk != -1 || !state.getConfig().isEuroMed()){\r
+ logger.warn("Name used in source (" + nameInSourceFk + ") was not found for common name " + commonNameId);\r
+ }\r
}\r
- DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation, nameUsedInSource, originalNameString);\r
for (CommonTaxonName commonTaxonName : commonTaxonNames){\r
- commonTaxonName.addSource(source);\r
+ DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation, nameUsedInSource, originalNameString);\r
+ commonTaxonName.addSource(source);\r
}\r
- \r
- \r
+\r
+\r
//MisNameRef\r
if (misNameRefFk != null){\r
//Taxon misappliedName = getMisappliedName(biblioRefMap, nomRefMap, misNameRefFk, taxon);\r
logger.warn("Misapplied name taxon is not of type Taxon but " + misTaxonBase.getClass().getSimpleName());\r
}\r
}else{\r
- \r
- Reference<?> sec = refMap.get(String.valueOf(misNameRefFk));\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
}\r
}\r
if (misappliedNameTaxon != null){\r
- \r
- if (! taxon.getMisappliedNames().contains(misappliedNameTaxon)){\r
+\r
+ if (! taxon.getMisappliedNames(false).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
+\r
TaxonDescription misappliedNameDescription = getDescription(misappliedNameTaxon);\r
for (CommonTaxonName commonTaxonName : commonTaxonNames){\r
CommonTaxonName commonNameClone = (CommonTaxonName)commonTaxonName.clone();\r
misappliedNameDescription.addElement(commonNameClone);\r
- } \r
+ }\r
}else{\r
- logger.warn("Misapplied name is null for common name " + commonNameId);\r
+ //wird schon oben gelogged\r
+ //logger.warn("Misapplied name is null for common name " + commonNameId);\r
}\r
- \r
+\r
}\r
- \r
- \r
+\r
+\r
//reference extensions\r
if (reference != null){\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
+\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
}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
+\r
//status\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
+ TermVocabulary<MarkerType> markerTypeVoc = getVocabulary(TermType.MarkerType, BerlinModelTransformer.uuidVocEMMarkerType,\r
+ "Euro+Med marker type vocabulary", "E+M marker types", null, null, false, MarkerType.COMPLETE());\r
+ MarkerType recommendedMarkerType = getMarkerType( state, COMMONNAME_STATUS_RECOMMENDED_UUID, "recommended","If the common name has the status recommended (see also status 'synonym', if none of them is true the default status is 'unassessed')",\r
+ "recommended", markerTypeVoc);\r
+ MarkerType synonymMarkerType = getMarkerType( state, COMMONNAME_STATUS_SYNONYM_UUID, "synonym","If the common name has the status synonym (see also status 'recommended', if none of them is true the default status is 'unassessed')",\r
+ "synonym", markerTypeVoc);\r
+ for (CommonTaxonName commonTaxonName : commonTaxonNames){\r
+ Marker marker = null;\r
+ if (status.equals("recommended")){\r
+ marker = Marker.NewInstance(recommendedMarkerType, true);\r
+ }else if (status.equals("synonym")){\r
+ marker = Marker.NewInstance(synonymMarkerType, true);\r
+ }else if (status.equals("unassessed")){\r
+ //do nothing\r
+ }else{\r
+ logger.warn("Unknown common name status: " + status);\r
+ }\r
+ if (marker != null){\r
+ commonTaxonName.addMarker(marker);\r
+ }\r
}\r
}\r
- \r
+\r
//Notes\r
for (CommonTaxonName commonTaxonName : commonTaxonNames){\r
doIdCreatedUpdatedNotes(state, commonTaxonName, rs, String.valueOf(commonNameId), NAMESPACE);\r
return false;\r
} catch (ClassCastException e) {\r
e.printStackTrace();\r
- } \r
- \r
+ } catch (Exception e) {\r
+ throw e;\r
+ }\r
+\r
// logger.info( i + " names handled");\r
getTaxonService().save(taxaToSave);\r
return success;\r
* @param iso639_2\r
* @param languageString\r
* @param originalLanguageString\r
- * @param state \r
+ * @param state\r
* @return\r
*/\r
private Language getAndHandleLanguage(Map<String, Language> iso639Map, String iso639_2, String iso639_1, String languageString, String originalLanguageString, BerlinModelImportState state) {\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
+\r
if (language == null){\r
language = getTermService().getLanguageByIso(iso639_2);\r
iso639Map.put(iso639_2, language);\r
getTermService().saveOrUpdate(language);\r
}\r
}\r
- \r
+\r
}\r
- \r
+\r
\r
\r
/**\r
* @param source\r
* @return\r
* @throws SQLException\r
- * \r
+ *\r
*/\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
+ sql += " WHERE " + state.getConfig().getCommonNameFilter();\r
}\r
- \r
+\r
ResultSet rs = source.getResultSet(sql);\r
while (rs.next()){\r
- String strRegionFks = rs.getString("RegionFks"); \r
+ String strRegionFks = rs.getString("RegionFks");\r
if (isBlank(strRegionFks)){\r
continue;\r
}\r
- \r
+\r
String[] regionFkArray = strRegionFks.split(",");\r
for (String regionFk: regionFkArray){\r
regionFk = regionFk.trim();\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
+ logger.info("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
+ if (isNotBlank(tdwgCode) ){\r
NamedArea tdwgArea = getNamedArea(state, tdwgCode);\r
regionMap.put(String.valueOf(regionId), tdwgArea);\r
}else {\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 state\r
* @param tdwgCode\r
*/\r
private NamedArea getNamedArea(BerlinModelImportState state, String tdwgCode) {\r
NamedArea area;\r
if (tdwgCode.equalsIgnoreCase("Ab")){\r
- area = getNamedArea(state, BerlinModelTransformer.uuidAzerbaijanNakhichevan, "Azerbaijan & Nakhichevan", "Azerbaijan (including Nakhichevan)", "Ab", null, null);\r
+ area = getNamedArea(state, BerlinModelTransformer.uuidAb, "Azerbaijan & Nakhichevan", "Azerbaijan (including Nakhichevan)", "Ab", null, null);\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
+ area = getNamedArea(state, BerlinModelTransformer.uuidUk , "Ukraine & Crimea", "Ukraine (including Crimea)", "Uk", null, null);\r
getTermService().saveOrUpdate(area);\r
}else if (tdwgCode.equalsIgnoreCase("Rf")){\r
+// area = getNamedArea(state, BerlinModelTransformer.uuidRf , "Ukraine & Crimea", "Ukraine (including Crimea)", "Uk", null, null);\r
+// getTermService().saveOrUpdate(area);\r
area = Country.RUSSIANFEDERATION();\r
}else if (tdwgCode.equalsIgnoreCase("Gg")){\r
area = Country.GEORGIA();\r
- }else{\r
+ }else if (tdwgCode.equalsIgnoreCase("SM")){\r
+ area = getNamedArea(state, BerlinModelTransformer.uuidSM , "Serbia & Montenegro", "Serbia & Montenegro", "SM", null, null);\r
+ getTermService().saveOrUpdate(area);\r
+ }else if (tdwgCode.equalsIgnoreCase("Tu")){\r
+ area = Country.TURKEYREPUBLICOF();\r
+ }else{\r
area = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode);\r
}\r
if (area == null){\r
private String getSqlWhere(SortedSet<Integer> regionFks) {\r
String sqlWhere = "";\r
for (Integer regionFk : regionFks){\r
- sqlWhere += regionFk + ","; \r
+ sqlWhere += regionFk + ",";\r
}\r
sqlWhere = sqlWhere.substring(0, sqlWhere.length()-1);\r
return sqlWhere;\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
+ * 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
private Map<String, String> getEmTdwgMap(Source source) throws SQLException {\r
String sql;\r
ResultSet rs;\r
- Map<String, String> emTdwgMap = new HashMap<String, String>();\r
+ Map<String, String> emTdwgMap = new HashMap<>();\r
sql = " SELECT EmCode, TDWGCode FROM emArea ";\r
rs = source.getResultSet(sql);\r
while (rs.next()){\r
String emCode = rs.getString("EMCode");\r
String TDWGCode = rs.getString("TDWGCode");\r
- if (StringUtils.isNotBlank(emCode) ){\r
+ if (isNotBlank(emCode) ){\r
emCode = emCode.trim();\r
- if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")|| \r
- emCode.equalsIgnoreCase("Uk") || emCode.equalsIgnoreCase("Gg")){\r
+ if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")||\r
+ emCode.equalsIgnoreCase("Uk") || emCode.equalsIgnoreCase("Gg")\r
+ || emCode.equalsIgnoreCase("SM") || emCode.equalsIgnoreCase("Tu")){\r
emTdwgMap.put(emCode, emCode);\r
- }else if (StringUtils.isNotBlank(TDWGCode)){\r
+ }else if (isNotBlank(TDWGCode)){\r
emTdwgMap.put(emCode, TDWGCode.trim());\r
}\r
}\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
+ emTdwgMap.put("Hb / Hb(E)", "IRE-IR");\r
+\r
return emTdwgMap;\r
}\r
\r
}\r
\r
@Override\r
- public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {\r
+ public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {\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
+ Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();\r
+\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
+ Set<String> taxonIdSet = new HashSet<>();\r
+ Set<String> nameIdSet = new HashSet<>();\r
+ Set<String> referenceIdSet = new HashSet<>();\r
while (rs.next()){\r
handleForeignKey(rs, taxonIdSet, "taxonId");\r
- handleForeignKey(rs, taxonIdSet, "misappliedTaxonId");\r
+ handleForeignKey(rs, taxonIdSet, "factTaxonId");\r
+ handleForeignKey(rs, taxonIdSet, "misappliedTaxonId");\r
handleForeignKey(rs, referenceIdSet, "refId");\r
handleForeignKey(rs, referenceIdSet, "languageRefRefFk");\r
handleForeignKey(rs, nameIdSet, "NameInSourceFk");\r
handleForeignKey(rs, nameIdSet, "PTNameFk");\r
handleForeignKey(rs, referenceIdSet, "MisNameRefFk");\r
}\r
- \r
+\r
//name map\r
nameSpace = BerlinModelTaxonNameImport.NAMESPACE;\r
- cdmClass = TaxonNameBase.class;\r
+ cdmClass = TaxonName.class;\r
idSet = nameIdSet;\r
- Map<String, TaxonNameBase<?,?>> nameMap = (Map<String, TaxonNameBase<?,?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, TaxonName> nameMap = (Map<String, TaxonName>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, nameMap);\r
- \r
+\r
//taxon map\r
nameSpace = BerlinModelTaxonImport.NAMESPACE;\r
cdmClass = TaxonBase.class;\r
idSet = taxonIdSet;\r
- Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ @SuppressWarnings("unchecked")\r
+ Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
result.put(nameSpace, taxonMap);\r
- \r
+\r
//reference map\r
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;\r
cdmClass = Reference.class;\r
idSet = referenceIdSet;\r
- Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);\r
+ @SuppressWarnings("unchecked")\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
}\r
return result;\r
}\r
- \r
\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)\r
- */\r
@Override\r
protected boolean doCheck(BerlinModelImportState state){\r
IOValidator<BerlinModelImportState> validator = new BerlinModelCommonNamesImportValidator();\r
return validator.validate(state);\r
}\r
\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
- */\r
+\r
+ @Override\r
protected boolean isIgnore(BerlinModelImportState state){\r
return ! state.getConfig().isDoCommonNames();\r
}\r
BGBM BDI Projects / cdmlib-apps.git / blobdiff