/**\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 org.apache.commons.lang.StringUtils;\r
import org.apache.log4j.Logger;\r
+import org.hibernate.NonUniqueObjectException;\r
import org.joda.time.DateTime;\r
\r
import eu.etaxonomy.cdm.io.common.CdmImportBase;\r
import eu.etaxonomy.cdm.io.common.Source;\r
import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;\r
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
+import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;\r
+import eu.etaxonomy.cdm.model.agent.Person;\r
+import eu.etaxonomy.cdm.model.agent.Team;\r
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;\r
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;\r
import eu.etaxonomy.cdm.model.common.Annotation;\r
import eu.etaxonomy.cdm.model.common.AnnotationType;\r
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
import eu.etaxonomy.cdm.model.common.Language;\r
import eu.etaxonomy.cdm.model.common.User;\r
-import eu.etaxonomy.cdm.model.location.NamedArea;\r
import eu.etaxonomy.cdm.model.location.Country;\r
+import eu.etaxonomy.cdm.model.location.NamedArea;\r
import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException;\r
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;\r
*/\r
public abstract class GlobisImportBase<CDM_BASE extends CdmBase> extends CdmImportBase<GlobisImportConfigurator, GlobisImportState> implements ICdmIO<GlobisImportState>, IPartitionedIO<GlobisImportState> {\r
private static final Logger logger = Logger.getLogger(GlobisImportBase.class);\r
- \r
+\r
public static final UUID ID_IN_SOURCE_EXT_UUID = UUID.fromString("23dac094-e793-40a4-bad9-649fc4fcfd44");\r
- \r
+\r
//NAMESPACES\r
- \r
+\r
protected static final String REFERENCE_NAMESPACE = "Literatur";\r
protected static final String TAXON_NAMESPACE = "current_species";\r
protected static final String COLLECTION_NAMESPACE = "Collection";\r
protected static final String IMAGE_NAMESPACE = "Einzelbilder";\r
protected static final String SPEC_TAX_NAMESPACE = "specTax";\r
protected static final String TYPE_NAMESPACE = "specTax.SpecTypeDepository";\r
- \r
- private String pluralString;\r
- private String dbTableName;\r
- //TODO needed?\r
- private Class cdmTargetClass;\r
\r
- private INonViralNameParser parser = NonViralNameParserImpl.NewInstance();\r
+ private final String pluralString;\r
+ private final String dbTableName;\r
+ private final Class cdmTargetClass;\r
+\r
+ private final INonViralNameParser<?> parser = NonViralNameParserImpl.NewInstance();\r
+\r
\r
- \r
/**\r
* @param dbTableName\r
- * @param dbTableName2 \r
+ * @param dbTableName2\r
*/\r
- public GlobisImportBase(String pluralString, String dbTableName, Class cdmTargetClass) {\r
+ public GlobisImportBase(String pluralString, String dbTableName, Class<?> cdmTargetClass) {\r
this.pluralString = pluralString;\r
this.dbTableName = dbTableName;\r
this.cdmTargetClass = cdmTargetClass;\r
}\r
\r
- protected void doInvoke(GlobisImportState state){\r
+ @Override\r
+ protected void doInvoke(GlobisImportState state){\r
logger.info("start make " + getPluralString() + " ...");\r
GlobisImportConfigurator config = state.getConfig();\r
Source source = config.getSource();\r
- \r
+\r
String strIdQuery = getIdQuery();\r
String strRecordQuery = getRecordQuery(config);\r
\r
logger.error("SQLException:" + e);\r
state.setUnsuccessfull();\r
}\r
- \r
+\r
logger.info("end make " + getPluralString() + " ... " + getSuccessString(true));\r
return;\r
}\r
* @param authorAndYear\r
* @param zooName\r
*/\r
- protected void handleAuthorAndYear(String authorAndYear, ZoologicalName zooName, Integer id) {\r
+ protected void handleAuthorAndYear(String authorAndYear, ZoologicalName zooName, Integer id, GlobisImportState state) {\r
if (isBlank(authorAndYear)){\r
return;\r
- }\r
- try {\r
- String doubtfulAuthorAndYear = null;\r
- if(authorAndYear.matches(".+\\,\\s\\[\\d{4}\\].*")){\r
- doubtfulAuthorAndYear = authorAndYear;\r
- authorAndYear = authorAndYear.replace("[", "").replace("]", "");\r
+ }else if ("[Denis & Schifferm\u00FCller], 1775".equals(authorAndYear)){\r
+ handleDenisSchiffermueller(zooName, state);\r
+ return;\r
+ }else{\r
+ try {\r
+ String doubtfulAuthorAndYear = null;\r
+ if(authorAndYear.matches(".+\\,\\s\\[\\d{4}\\].*")){\r
+ doubtfulAuthorAndYear = authorAndYear;\r
+ authorAndYear = authorAndYear.replace("[", "").replace("]", "");\r
+ }\r
+\r
+ parser.parseAuthors(zooName, authorAndYear);\r
+ deduplicateAuthors(zooName, state);\r
+\r
+ if (doubtfulAuthorAndYear != null){\r
+ zooName.setAuthorshipCache(doubtfulAuthorAndYear, true);\r
+ }\r
+\r
+ } catch (StringNotParsableException e) {\r
+ logger.warn("Author could not be parsed: " + authorAndYear + " for id " +id);\r
+ zooName.setAuthorshipCache(authorAndYear, true);\r
}\r
- if (authorAndYear.contains("?")){\r
- authorAndYear = authorAndYear.replace("H?bner", "H\u00fcbner");\r
- authorAndYear = authorAndYear.replace("Oberth?r", "Oberth\u00fcr");\r
- authorAndYear = authorAndYear.replace("M?n?tri?s","M\u00E9n\u00E9tri\u00E9s");\r
- authorAndYear = authorAndYear.replace("Schifferm?ller","Schifferm\u00fcller");\r
- \r
- //TODO remove\r
- authorAndYear = authorAndYear.replace("?", "");\r
- \r
+ }\r
+ }\r
+\r
+ /**\r
+ * @param zooName\r
+ * @param state\r
+ */\r
+ private void handleDenisSchiffermueller(ZoologicalName zooName,\r
+ GlobisImportState state) {\r
+ String teamStr = "Denis & Schifferm\u00FCller";\r
+ Team team = state.getTeam(teamStr);\r
+ if (team == null){\r
+ team = Team.NewInstance();\r
+ state.putTeam(teamStr, team);\r
+ getAgentService().save(team);\r
+ }\r
+ zooName.setCombinationAuthorship(team);\r
+ zooName.setPublicationYear(1775);\r
+ zooName.setAuthorshipCache("[Denis & Schifferm\u00FCller], 1775", true);\r
+ }\r
+\r
+\r
+ private void deduplicateAuthors(ZoologicalName zooName, GlobisImportState state) {\r
+ zooName.setCombinationAuthorship(getExistingAuthor(zooName.getCombinationAuthorship(), state));\r
+ zooName.setExCombinationAuthorship(getExistingAuthor(zooName.getExCombinationAuthorship(), state));\r
+ zooName.setBasionymAuthorship(getExistingAuthor(zooName.getBasionymAuthorship(), state));\r
+ zooName.setExBasionymAuthorship(getExistingAuthor(zooName.getExBasionymAuthorship(), state));\r
+ }\r
+\r
+ private TeamOrPersonBase<?> getExistingAuthor(INomenclaturalAuthor nomAuthor, GlobisImportState state) {\r
+ TeamOrPersonBase<?> author = (TeamOrPersonBase<?>)nomAuthor;\r
+ if (author == null){\r
+ return null;\r
+ }\r
+ if (author instanceof Person){\r
+ Person person = state.getPerson(author.getTitleCache());\r
+ return saveAndDecide(person, author, author.getTitleCache(), state);\r
+ }else if (author instanceof Team){\r
+ String key = GlobisAuthorImport.makeTeamKey((Team)author, state, getAgentService());\r
+ Team existingTeam = state.getTeam(key);\r
+ if (existingTeam == null){\r
+ Team newTeam = Team.NewInstance();\r
+ for (Person member :((Team) author).getTeamMembers()){\r
+ Person existingPerson = state.getPerson(member.getTitleCache());\r
+ if (existingPerson != null){\r
+ try {\r
+ getAgentService().update(existingPerson);\r
+ } catch (NonUniqueObjectException nuoe){\r
+ // person already exists in\r
+ existingPerson = CdmBase.deproxy(getAgentService().find(existingPerson.getUuid()), Person.class);\r
+ state.putPerson(existingPerson.getTitleCache(), existingPerson);\r
+ } catch (Exception e) {\r
+ throw new RuntimeException (e);\r
+ }\r
+ newTeam.addTeamMember(existingPerson);\r
+//\r
+// logger.warn("newTeam " + newTeam.getId());\r
+ }else{\r
+ newTeam.addTeamMember(member);\r
+ }\r
+ }\r
+ author = newTeam;\r
}\r
- \r
- parser.parseAuthors(zooName, authorAndYear);\r
- if (doubtfulAuthorAndYear != null){\r
- zooName.setAuthorshipCache(doubtfulAuthorAndYear, true);\r
+\r
+ return saveAndDecide(existingTeam, author, key, state);\r
+ }else{\r
+ logger.warn("Author type not supported: " + author.getClass().getName());\r
+ return author;\r
+ }\r
+ }\r
+\r
+ private TeamOrPersonBase<?> saveAndDecide(TeamOrPersonBase<?> existing, TeamOrPersonBase<?> author, String key, GlobisImportState state) {\r
+ if (existing != null){\r
+ try {\r
+ getAgentService().update(existing);\r
+ } catch (NonUniqueObjectException nuoe){\r
+ // person already exists in\r
+ existing = CdmBase.deproxy(getAgentService().find(existing.getUuid()), TeamOrPersonBase.class);\r
+ putAgent(existing, key, state);\r
+ } catch (Exception e) {\r
+ throw new RuntimeException (e);\r
}\r
- \r
- } catch (StringNotParsableException e) {\r
- logger.warn("Author could not be parsed: " + authorAndYear + " for id " +id);\r
- zooName.setAuthorshipCache(authorAndYear, true);\r
+ return existing;\r
+ }else{\r
+ getAgentService().save(author);\r
+ putAgent(author, key, state);\r
+ return author;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * @param author\r
+ * @param key\r
+ * @param state\r
+ */\r
+ private void putAgent(TeamOrPersonBase<?> agent, String key, GlobisImportState state) {\r
+ if (agent instanceof Team){\r
+ state.putTeam(key, (Team)agent);\r
+ }else{\r
+ state.putPerson(key, (Person)agent);\r
}\r
}\r
- \r
\r
/**\r
* @param state\r
NamedArea country = Country.getCountryByLabel(countryStr);\r
if (country == null){\r
try {\r
- country = (NamedArea)state.getTransformer().getNamedAreaByKey(countryStr);\r
+ country = state.getTransformer().getNamedAreaByKey(countryStr);\r
} catch (UndefinedTransformerMethodException e) {\r
e.printStackTrace();\r
}\r
return country;\r
}\r
\r
- \r
\r
- public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {\r
+\r
+ @Override\r
+ public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {\r
boolean success = true ;\r
Set objectsToSave = new HashSet();\r
- \r
+\r
DbImportMapping<?, ?> mapping = getMapping();\r
mapping.initialize(state, cdmTargetClass);\r
- \r
+\r
ResultSet rs = partitioner.getResultSet();\r
try{\r
while (rs.next()){\r
logger.error("SQLException:" + e);\r
return false;\r
}\r
- \r
+\r
partitioner.startDoSave();\r
getCommonService().save(objectsToSave);\r
return success;\r
}\r
\r
\r
- \r
+\r
/**\r
* @return\r
*/\r
protected /*abstract*/ DbImportMapping<?, ?> getMapping(){\r
return null;\r
}\r
- \r
+\r
/**\r
* @return\r
*/\r
String result = " SELECT id FROM " + getTableName();\r
return result;\r
}\r
- \r
+\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getPluralString()\r
*/\r
- public String getPluralString(){\r
+ @Override\r
+ public String getPluralString(){\r
return pluralString;\r
}\r
\r
protected String getTableName(){\r
return this.dbTableName;\r
}\r
- \r
+\r
protected boolean doIdCreatedUpdatedNotes(GlobisImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace)\r
throws SQLException{\r
boolean success = true;\r
success &= doCreatedUpdatedNotes(state, identifiableEntity, rs, namespace);\r
return success;\r
}\r
- \r
- \r
+\r
+\r
protected boolean doCreatedUpdatedNotes(GlobisImportState state, AnnotatableEntity annotatableEntity, ResultSet rs, String namespace)\r
throws SQLException{\r
\r
GlobisImportConfigurator config = state.getConfig();\r
Object createdWhen = rs.getObject("Created_When");\r
String createdWho = rs.getString("Created_Who");\r
- Object updatedWhen = null;\r
- String updatedWho = null;\r
- try {\r
- updatedWhen = rs.getObject("Updated_When");\r
- updatedWho = rs.getString("Updated_who");\r
- } catch (SQLException e) {\r
- //Table "Name" has no updated when/who\r
- }\r
+ Object updatedWhen = rs.getObject("Updated_When");\r
+ String updatedWho = rs.getString("Updated_who");\r
String notes = rs.getString("notes");\r
- \r
+\r
boolean success = true;\r
- \r
+\r
//Created When, Who, Updated When Who\r
if (config.getEditor() == null || config.getEditor().equals(EDITOR.NO_EDITORS)){\r
//do nothing\r
}else {\r
logger.warn("Editor type not yet implemented: " + config.getEditor());\r
}\r
- \r
- \r
+\r
+\r
//notes\r
if (StringUtils.isNotBlank(notes)){\r
String notesString = String.valueOf(notes);\r
}\r
return success;\r
}\r
- \r
+\r
private User getUser(String userString, GlobisImportState state){\r
- if (StringUtils.isBlank(userString)){\r
+ if (isBlank(userString)){\r
return null;\r
}\r
userString = userString.trim();\r
- \r
+\r
User user = state.getUser(userString);\r
if (user == null){\r
user = getTransformedUser(userString,state);\r
}\r
return user;\r
}\r
- \r
+\r
private User getTransformedUser(String userString, GlobisImportState state){\r
Method method = state.getConfig().getUserTransformationMethod();\r
if (method == null){\r
}\r
\r
private User makeNewUser(String userString, GlobisImportState state){\r
- String pwd = getPassword(); \r
+ String pwd = getPassword();\r
User user = User.NewInstance(userString, pwd);\r
state.putUser(userString, user);\r
getUserService().save(user);\r
logger.info("Added new user: " + userString);\r
return user;\r
}\r
- \r
+\r
private String getPassword(){\r
String result = UUID.randomUUID().toString();\r
return result;\r
}\r
- \r
+\r
private DateTime getDateTime(Object timeString){\r
if (timeString == null){\r
return null;\r
}\r
return dateTime;\r
}\r
- \r
- \r
- \r
+\r
+\r
+\r
/**\r
* Reads a foreign key field from the result set and adds its value to the idSet.\r
* @param rs\r
idSet.add(id);\r
}\r
}\r
- \r
- \r
- \r
- \r
+\r
+\r
+\r
+\r
/**\r
* Returns true if i is a multiple of recordsPerTransaction\r
* @param i\r
startTransaction();\r
return (i % recordsPerLoop) == 0;\r
}\r
- \r
+\r
protected void doLogPerLoop(int count, int recordsPerLog, String pluralString){\r
if ((count % recordsPerLog ) == 0 && count!= 0 ){ logger.info(pluralString + " handled: " + (count));}\r
}\r
- \r
\r
\r
- \r
+\r
+\r
}\r
BGBM BDI Projects / cdmlib-apps.git / blobdiff