import java.util.Map;\r
import java.util.Set;\r
\r
+import org.apache.commons.lang.StringUtils;\r
import org.apache.log4j.Logger;\r
import org.springframework.stereotype.Component;\r
\r
import eu.etaxonomy.cdm.io.common.DbImportBase;\r
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;\r
import eu.etaxonomy.cdm.io.common.Source;\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.CdmBase;\r
import eu.etaxonomy.cdm.model.common.Language;\r
+import eu.etaxonomy.cdm.model.common.TimePeriod;\r
import eu.etaxonomy.cdm.model.name.BotanicalName;\r
+import eu.etaxonomy.cdm.model.name.NameTypeDesignation;\r
+import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;\r
+import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.reference.IArticle;\r
+import eu.etaxonomy.cdm.model.reference.IBook;\r
+import eu.etaxonomy.cdm.model.reference.IBookSection;\r
+import eu.etaxonomy.cdm.model.reference.IJournal;\r
+import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
import eu.etaxonomy.cdm.model.taxon.Classification;\r
+import eu.etaxonomy.cdm.model.taxon.Synonym;\r
+import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
+import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;\r
+import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
+import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;\r
+import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;\r
\r
\r
/**\r
private int modCount = 10000;\r
private static final String pluralString = "taxa";\r
private static final String dbTableName = "CARYOPHYLLALES";\r
- private static final String FAMILY = "Family";\r
- private static final String PERSON = "Person";\r
- private static final String TEAM = "Team";\r
- private static final String JOURNAL = "Journal";\r
- private static final String BOOK = "Book";\r
+\r
\r
\r
private Map<String, Taxon> familyMap = new HashMap<String, Taxon>();\r
- private Map<String, TeamOrPersonBase> personMap = new HashMap<String, TeamOrPersonBase>();\r
- private Map<String, TeamOrPersonBase> teamMap = new HashMap<String, TeamOrPersonBase>();\r
- private Map<String, Reference> journalMap = new HashMap<String, Reference>();\r
- private Map<String, Reference> bookMap = new HashMap<String, Reference>();\r
+ private Map<String, Person> personMap = new HashMap<String, Person>();\r
+ private Map<String, Team> teamMap = new HashMap<String, Team>();\r
+ private Map<String, TeamOrPersonBase> inAuthorMap = new HashMap<String, TeamOrPersonBase>();\r
+ private Map<String, IJournal> journalMap = new HashMap<String, IJournal>();\r
+ private Map<String, IBook> bookMap = new HashMap<String, IBook>();\r
\r
\r
private Classification classification;\r
\r
\r
+ \r
public CaryoTaxonImport(){\r
- super(pluralString, dbTableName);\r
+ super(dbTableName, pluralString);\r
}\r
\r
\r
protected String getIdQuery(CaryoImportState state) {\r
String strRecordQuery = \r
" SELECT ID " + \r
- " FROM " + dbTableName; \r
+ " FROM " + dbTableName +\r
+ " ORDER BY id "; \r
return strRecordQuery; \r
}\r
\r
@Override\r
protected String getRecordQuery(CaryoImportConfigurator config) {\r
String strRecordQuery = \r
- " SELECT cs.* " + \r
+ " SELECT t.* " + \r
" FROM " + getTableName() + " t " +\r
" WHERE ( t.ID IN (" + ID_LIST_TOKEN + ") )";\r
return strRecordQuery;\r
try {\r
doFamilies(state);\r
doAuthors(state);\r
+ doInAuthors(state);\r
doJournals(state);\r
doBooks(state);\r
\r
ResultSet rs = partitioner.getResultSet();\r
\r
int i = 0;\r
+ Reference<?> sec = state.getTransactionalSourceReference();\r
\r
//for each reference\r
while (rs.next()){\r
\r
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}\r
\r
- Integer taxonId = rs.getInt("IDcurrentspec");\r
- \r
- \r
- //String dtSpcJahr -> ignore !\r
- //empty: fiSpcLiteratur\r
- \r
- //TODO\r
- //fiSpcspcgrptax\r
- \r
- \r
+ Integer id = rs.getInt("Id");\r
+ Integer taxonId = rs.getInt("NCUGenID");\r
+ String genus = rs.getString("Genus");\r
+ String family = rs.getString("Family");\r
+ String pages = rs.getString("Pages");\r
+ String autoren = rs.getString("Autoren");\r
+ String typeStr = rs.getString("Type");\r
+ String nomStatusStr = rs.getString("NomenclaturalStatus");\r
+ String basioStr = rs.getString("Basionym");\r
+ \r
+// ,[EtInCitation]\r
+// ,[Gender]\r
+ \r
+// ,[Basionym]\r
+// ,[OriginalCitation]\r
+ \r
\r
- try {\r
- \r
- \r
-// classification.addParentChild(nextHigherTaxon, species, sourceRef, null);\r
-// \r
-// \r
-// this.doIdCreatedUpdatedNotes(state, species, rs, taxonId, TAXON_NAMESPACE);\r
-// \r
-// objectsToSave.add(species); \r
- \r
+ BotanicalName name = BotanicalName.NewInstance(Rank.GENUS());\r
+ name.setGenusOrUninomial(genus);\r
+ makeAuthors(name, autoren, id);\r
+ INomenclaturalReference nomRef = makeNomRef(state, rs, id);\r
+ name.setNomenclaturalReference(nomRef);\r
+ name.setNomenclaturalMicroReference(pages);\r
+ makeStatus(name, nomStatusStr, id);\r
+ \r
+ \r
+ Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());\r
+ handleTypes(state, rs, taxon, typeStr, id);\r
+ handleBasionym(state, rs, taxon, basioStr, id);\r
+ \r
+ Taxon parent = familyMap.get(family);\r
+ \r
+ classification.addParentChild(parent, taxon, sec, null);\r
+ \r
+ taxon.addSource(String.valueOf(taxonId), "NCUGenID", sec, null);\r
+ \r
+ \r
+ \r
+ objectsToSave.add(taxon);\r
\r
- } catch (Exception e) {\r
- logger.warn("Exception in current_species: IDcurrentspec " + taxonId + ". " + e.getMessage());\r
-// e.printStackTrace();\r
- } \r
- \r
}\r
\r
-// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );\r
-\r
logger.warn(pluralString + " to save: " + objectsToSave.size());\r
getTaxonService().save(objectsToSave); \r
\r
}\r
}\r
\r
+ \r
+ private INonViralNameParser parser = NonViralNameParserImpl.NewInstance();\r
+ private void handleBasionym(CaryoImportState state, ResultSet rs, Taxon taxon, String basioStr, Integer id) {\r
+ if (StringUtils.isNotBlank(basioStr)){\r
+ BotanicalName name = (BotanicalName) taxon.getName();\r
+ BotanicalName basionym = BotanicalName.PARSED_NAME(basioStr);\r
+ name.addBasionym(basionym);\r
+ Synonym syn = Synonym.NewInstance(basionym, state.getTransactionalSourceReference());\r
+ taxon.addSynonym(syn, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());\r
+ getTaxonService().save(syn);\r
+ }\r
+ \r
+ }\r
+\r
+\r
+\r
+\r
+ private void handleTypes(CaryoImportState state, ResultSet rs, Taxon taxon, String origType, Integer id) {\r
+ NameTypeDesignation desig = NameTypeDesignation.NewInstance();\r
+ String type = origType;\r
+ if (StringUtils.isBlank(type) ){\r
+ return;\r
+ }else{\r
+ BotanicalName name = (BotanicalName)taxon.getName();\r
+ BotanicalName typeName = BotanicalName.NewInstance(Rank.SPECIES());\r
+ if ("not designated".equalsIgnoreCase(type)){\r
+ desig.setNotDesignated(true);\r
+ }else{\r
+ String genus = name.getGenusOrUninomial();\r
+ typeName.setGenusOrUninomial(genus);\r
+ if (! type.startsWith(genus.substring(0,1) + ". " )){\r
+ int i = type.indexOf(" ");\r
+ String genusOrig = type.substring(0, i);\r
+ logger.warn("First genus letter not recognized: " + genusOrig + "-" + genus + ":"+ id);\r
+ typeName.setGenusOrUninomial(genusOrig);\r
+ type = type.substring(i + 1).trim();\r
+ }else{\r
+ type = type.substring(3);\r
+ }\r
+ int i = type.indexOf(" ");\r
+ if (i <= 0){\r
+ logger.warn("No space: " + type +"; " + id);\r
+ }else{\r
+ String species = type.substring(0, i);\r
+ typeName.setSpecificEpithet(species);\r
+ type = type.substring(i + 1).trim();\r
+ \r
+ int posBracket = type.indexOf("(", 2);\r
+ if (posBracket > 0){\r
+ String bracket = type.substring(posBracket);\r
+ //TODO\r
+// logger.warn("Type has bracket("+id+"): " + bracket);\r
+ //TODO Annotation\r
+ type = type.substring(0, posBracket).trim();\r
+ }\r
+ type = makeTypeNomStatus(typeName, type);\r
+\r
+ \r
+ makeAuthors(typeName, type, id);\r
+ }\r
+ \r
+ desig.setTypeName(typeName);\r
+ }\r
+ name.addTypeDesignation(desig, true);\r
+ }\r
+ \r
+ \r
+ }\r
+\r
+\r
+\r
+\r
+ private String makeTypeNomStatus(BotanicalName typeName, String type) {\r
+ if (type.endsWith(", nom. illeg.")){\r
+ type = type.replaceAll(", nom. illeg.", "");\r
+ typeName.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE()));\r
+ }\r
+ return type;\r
+ }\r
+\r
+\r
+\r
+\r
+ private void makeStatus(BotanicalName name, String nomStatusStr, Integer id) throws SQLException {\r
+// ,[NomenclaturalStatus]\r
+ \r
+ if (StringUtils.isNotBlank(nomStatusStr)){\r
+ NomenclaturalStatusType nomStatusType;\r
+ try {\r
+ nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(nomStatusStr);\r
+ } catch (UnknownCdmTypeException e) {\r
+ if (nomStatusStr.startsWith("nom. rej. prop.")){\r
+ nomStatusType = NomenclaturalStatusType.REJECTED_PROP();\r
+ logger.warn("in favour not supported ("+id+"): " + nomStatusStr);\r
+ }else if (nomStatusStr.startsWith("nom. rej. in favour")){\r
+ nomStatusType = NomenclaturalStatusType.REJECTED();\r
+ logger.warn("in favour not supported ("+id+"): " + nomStatusStr);\r
+ }else if (nomStatusStr.startsWith("nom. cons. against")){\r
+ nomStatusType = NomenclaturalStatusType.CONSERVED();\r
+ logger.warn("against not supported ("+id+"): " + nomStatusStr);\r
+ }else if (nomStatusStr.startsWith("nom. cons. prop. against")){\r
+ nomStatusType = NomenclaturalStatusType.CONSERVED_PROP();\r
+ logger.warn("against not supported ("+id+"): " + nomStatusStr);\r
+ }else{\r
+ logger.warn("Unknown status type ("+id+"): " + nomStatusStr);\r
+ nomStatusType = NomenclaturalStatusType.DOUBTFUL();\r
+ }\r
+ }\r
+ \r
+ NomenclaturalStatus status = NomenclaturalStatus.NewInstance(nomStatusType);\r
+ name.addStatus(status);\r
+ }\r
+ \r
+ }\r
+\r
+\r
+\r
+\r
+ private INomenclaturalReference makeNomRef(CaryoImportState state, ResultSet rs, Integer id) throws SQLException {\r
+ INomenclaturalReference result;\r
+ String periodicalTitle = rs.getString("PeriodicalTitle");\r
+ String volume = rs.getString("PeriodicalVolume");\r
+ String bookTitle = rs.getString("BookTitle");\r
+ String inAutorStr = rs.getString("InAutor");\r
+ String autorenStr = rs.getString("Autoren");\r
+ \r
+ TeamOrPersonBase<?> author = getNomRefAuthor(autorenStr, id);\r
+ if (StringUtils.isNotBlank(periodicalTitle)){\r
+ IJournal journal = journalMap.get(periodicalTitle);\r
+ if (journal == null){\r
+ logger.warn("Journal not found: " + periodicalTitle + ";" + id);\r
+ }\r
+ IArticle article = ReferenceFactory.newArticle();\r
+ article.setInJournal(journal);\r
+ article.setVolume(volume);\r
+ result = article;\r
+ }else if (StringUtils.isNotBlank(bookTitle)){\r
+ IBook book = bookMap.get(bookTitle);\r
+ if (inAutorStr != null){\r
+ IBookSection section = ReferenceFactory.newBookSection();\r
+ section.setInBook(book);\r
+ TeamOrPersonBase<?> inAuthor = getInAuthor(inAutorStr);\r
+ book.setAuthorTeam(inAuthor);\r
+ result = section;\r
+ }else{\r
+ result = book;\r
+ }\r
+ }else{\r
+ logger.warn("No nomRef found: " + id);\r
+ result = null;\r
+ }\r
+ if (result != null){\r
+ result.setAuthorTeam(author);\r
+ makeDate(state, rs, result, id);\r
+ }\r
+ return result;\r
+ }\r
+\r
+ private void makeDate(CaryoImportState state, ResultSet rs, INomenclaturalReference ref, Integer id) throws SQLException {\r
+ TimePeriod tp = TimePeriod.NewInstance();\r
+ String pre1 = rs.getString("DatePre1");\r
+ String pre2 = rs.getString("DatePre2");\r
+ Float year1 = nullSafeFloat(rs, "DateYear1");\r
+ Float year2 = nullSafeFloat(rs, "DateYear2");\r
+ if (year2 == 0.0 ){\r
+ year2 = null;\r
+ }\r
+ String modi1 = rs.getString("DateModi1");\r
+ String modi2 = rs.getString("DateModi2");\r
+ String date = rs.getString("Date");\r
+\r
+ tp.setStartYear(year1.intValue());\r
+ Integer[] preDate1 = getDay(pre1,id);\r
+ tp.setStartMonth(preDate1[1]);\r
+ tp.setStartDay(preDate1[0]);\r
+ if (year2 != null){\r
+ tp.setEndYear(year2.intValue());\r
+ }\r
+ Integer[] preDate2 = getDay(pre2, id);\r
+ tp.setEndMonth(preDate2[1]);\r
+ tp.setEndDay(preDate2[0]);\r
+ \r
+ if (StringUtils.isNotBlank(modi1) || StringUtils.isNotBlank(modi2)){\r
+ tp.setFreeText(date);\r
+ }\r
+ ref.setDatePublished(tp);\r
+ }\r
+\r
+\r
+\r
+\r
+ private Integer[] getDay(String pre, Integer id) {\r
+ Integer[] result = new Integer[2];\r
+ if (! StringUtils.isBlank(pre)){\r
+ try {\r
+ String[] split = pre.split("\\s");\r
+ String monthStr;\r
+ if (split.length > 2){\r
+ logger.warn("L > 2: " + pre);\r
+ monthStr = "";\r
+ }else if(split.length == 2){\r
+ result[0] = Integer.valueOf(split[0]);\r
+ monthStr = split[1];\r
+ }else{\r
+ monthStr = split[0];\r
+ }\r
+ Integer month;\r
+ if ("Jan".equalsIgnoreCase(monthStr)){\r
+ month = 1;\r
+ }else if ("Feb".equalsIgnoreCase(monthStr)){\r
+ month = 2;\r
+ }else if ("Mar".equalsIgnoreCase(monthStr)){\r
+ month = 3;\r
+ }else if ("Apr".equalsIgnoreCase(monthStr)){\r
+ month = 4;\r
+ }else if ("Mai".equalsIgnoreCase(monthStr)){\r
+ month = 5;\r
+ }else if ("Jun".equalsIgnoreCase(monthStr)){\r
+ month = 6;\r
+ }else if ("Jul".equalsIgnoreCase(monthStr)){\r
+ month = 7;\r
+ }else if ("Aug".equalsIgnoreCase(monthStr)){\r
+ month = 8;\r
+ }else if ("Sep".equalsIgnoreCase(monthStr)){\r
+ month = 9;\r
+ }else if ("Oct".equalsIgnoreCase(monthStr)){\r
+ month = 10;\r
+ }else if ("Nov".equalsIgnoreCase(monthStr)){\r
+ month = 11;\r
+ }else if ("Dec".equalsIgnoreCase(monthStr)){\r
+ month = 12;\r
+ }else{\r
+ logger.warn("Unknown month ("+id+"): " + monthStr );\r
+ month = null;\r
+ }\r
+ result[1]= month;\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ return result;\r
+ }\r
+\r
+ \r
+ private TeamOrPersonBase<?> getInAuthor(String inAutorStr) {\r
+ if (StringUtils.isBlank(inAutorStr)){\r
+ return null;\r
+ }\r
+ TeamOrPersonBase<?> inAuthor = inAuthorMap.get(inAutorStr);\r
+ if (inAuthor == null){\r
+ logger.warn("Inauthor not found: " + inAutorStr);\r
+ }\r
+ return inAuthor;\r
+ }\r
+\r
\r
\r
+ private void makeAuthors(BotanicalName name, String autoren, Integer id) {\r
+ String[] parsedAuthorTeams = getParsedAuthors(autoren);\r
+ name.setBasionymAuthorTeam(getTeam(parsedAuthorTeams[0], id));\r
+ name.setExBasionymAuthorTeam(getTeam(parsedAuthorTeams[1], id));\r
+ name.setCombinationAuthorTeam(getTeam(parsedAuthorTeams[2], id));\r
+ name.setExCombinationAuthorTeam(getTeam(parsedAuthorTeams[3], id));\r
+ \r
+ }\r
+ \r
+ private TeamOrPersonBase<?> getNomRefAuthor(String authorStr, Integer id) {\r
+ String[] parsedAuthorTeams = getParsedAuthors(authorStr);\r
+ TeamOrPersonBase<?> team = getTeam(parsedAuthorTeams[2], id);\r
+ return team;\r
+ }\r
\r
\r
+ private TeamOrPersonBase<?> getTeam(String author, Integer id) {\r
+ if (StringUtils.isBlank(author)){\r
+ return null;\r
+ }\r
+ TeamOrPersonBase<?> result;\r
+ if (personMap.get(author) != null){\r
+ result = personMap.get(author);\r
+ }else{\r
+ result = teamMap.get(author);\r
+ }\r
+ if (result == null){\r
+ logger.warn("Team not found ("+id+"): " + author);\r
+ }\r
+ return result;\r
+ }\r
+ \r
\r
+ private void doInAuthors(CaryoImportState state) throws SQLException {\r
+ Source source = state.getConfig().getSource();\r
+ String sql = "SELECT DISTINCT inAutor FROM " + getTableName() + " WHERE inAutor IS NOT NULL AND inAutor <> '' ";\r
+ ResultSet rs = source.getResultSet(sql);\r
+ while (rs.next()){\r
+ String inAutorStr = rs.getString("inAutor");\r
+ if (inAuthorMap.get(inAutorStr) == null){\r
+ Team team = Team.NewTitledInstance(inAutorStr, inAutorStr);\r
\r
- private void doAuthors(CaryoImportState state) {\r
- // TODO Auto-generated method stub\r
+ inAuthorMap.put(inAutorStr, team);\r
+ getAgentService().save(team);\r
+ }\r
+ }\r
\r
}\r
\r
\r
+ private void doAuthors(CaryoImportState state) throws SQLException {\r
+ Source source = state.getConfig().getSource();\r
+ String sql = "SELECT DISTINCT Autoren FROM " + getTableName() + " WHERE Autoren IS NOT NULL AND Autoren <> '' ";\r
+ ResultSet rs = source.getResultSet(sql);\r
+ doTypeAuthors(state);\r
+ while (rs.next()){\r
+ String autorenStr = rs.getString("Autoren");\r
+ String[] parsedAuthorTeams = getParsedAuthors(autorenStr);\r
+ for (String teamStr : parsedAuthorTeams){\r
+ doTeam(teamStr);\r
+ }\r
+ }\r
+ }\r
+\r
\r
\r
- private void doBooks(CaryoImportState state) {\r
- // TODO Auto-generated method stub\r
+\r
+ private void doTypeAuthors(CaryoImportState state) {\r
+ doTeam("Dinter & Derenb.");\r
+ doTeam("Marloth");\r
+ doTeam("Engl.");\r
+ doTeam("Kensit");\r
+ doTeam("Sond.");\r
+ doTeam("L. f.");\r
+ doTeam("Dinter & A. Berger");\r
+ doTeam("Schltr.");\r
+ doTeam("Dinter & Berger");\r
+ doTeam("Poir.");\r
+ doTeam("J. C. Wendl.");\r
+ doTeam("Baker & Clarke");\r
+ doTeam("Vahl");\r
+ doTeam("Nicolai");\r
+ doTeam("Gürke");\r
+ doTeam("Cels");\r
+ doTeam("Dams");\r
+ doTeam("Coult.");\r
+ doTeam("A. Weber");\r
+ doTeam("Vaupel");\r
+ doTeam("Gay");\r
+ doTeam("Pall.");\r
+ doTeam("Moq. & Coss.");\r
+ doTeam("Durieu & Moq.");\r
+ doTeam("Lag. & Rodrigues");\r
+ doTeam("M. Martens & Galeotti");\r
+ doTeam("Steud.");\r
+ doTeam("Aitch. & Hemsl.");\r
+ doTeam("Ikonn.-Gal.");\r
+ doTeam("Freitag");\r
+ doTeam("Regel");\r
+ doTeam("Ledeb.");\r
+ doTeam("Schur");\r
+ doTeam("Asch.");\r
+ doTeam("G. Forst.");\r
+ doTeam("Gray");\r
+ doTeam("Curran");\r
+ doTeam("Donn. Sm.");\r
+ doTeam("Diels");\r
+ doTeam("Colla");\r
+ doTeam("Miers");\r
+ doTeam("Gillis");\r
+ doTeam("Royle");\r
+ doTeam("Monv.");\r
+ doTeam("Werderm. & Backeb.");\r
+ doTeam("Wright");\r
+ doTeam("Meyen");\r
+ doTeam("Runge");\r
+ doTeam("Böd.");\r
+ doTeam("Rol.-Goss.");\r
+ doTeam("Poselg.");\r
+ doTeam("Andreae & Backeberg");\r
+ doTeam("Miq.");\r
+ doTeam("Rol.");\r
+ doTeam("Backeb. & Voll");\r
+ doTeam("Engelm. & Bigelow");\r
+ doTeam("Pfeiffer & Otto");\r
+ doTeam("Humb. & Bonpl.");\r
+ doTeam("Schmalh.");\r
+ doTeam("Preobr.");\r
+ doTeam("Labill.");\r
+ doTeam("Barkoudah");\r
+ doTeam("Regel & Schmalh.");\r
+ doTeam("Cambess.");\r
+ doTeam("Pax & K. Hoff.");\r
+ doTeam("Bergeret");\r
+ doTeam("Walp.");\r
+ doTeam("Huds.");\r
+ doTeam("Kit.");\r
+ doTeam("Schott, Nymann & Kotschy");\r
+ doTeam("Boiss. & Buhse");\r
+ doTeam("Medik.");\r
+ doTeam("Coss. & Germ.");\r
+ doTeam("Moss");\r
+ doTeam("Pax & Hoffm.");\r
+ doTeam("Schischk.");\r
+ doTeam("Lipsch.");\r
+ doTeam("Maerkl.");\r
+ doTeam("Vierh.");\r
+ doTeam("Exell");\r
\r
}\r
\r
\r
\r
\r
- private void doJournals(CaryoImportState state) {\r
- // TODO Auto-generated method stub\r
+ /**\r
+ * @param teamStr\r
+ * @return\r
+ */\r
+ protected void doTeam(String teamStr) {\r
+ if (StringUtils.isBlank(teamStr)){\r
+ return;\r
+ }\r
+ String[] parsedTeam = parseTeam(teamStr);\r
+ if (parsedTeam.length == 1){\r
+ savePerson(parsedTeam[0]);\r
+ }else{\r
+ Team team = teamMap.get(teamStr);\r
+ if (team == null){\r
+ team = Team.NewInstance();\r
+ for (String member : parsedTeam){\r
+ Person person = savePerson(member);\r
+ team.addTeamMember(person);\r
+ }\r
+ teamMap.put(teamStr, team);\r
+ getAgentService().saveOrUpdate(team);\r
+ }\r
+ }\r
+ return;\r
+ }\r
+\r
+ private String[] parseTeam(String teamStr) {\r
+ String[] split = teamStr.split("[&,]");\r
+ for (int i = 0; i < split.length; i++){\r
+ split[i] = split[i].trim();\r
+ }\r
+ return split;\r
+ }\r
+\r
+ private Person savePerson(String personStr) {\r
+ Person result = personMap.get(personStr);\r
+ if (result == null ){\r
+ Person person = Person.NewTitledInstance(personStr);\r
+ personMap.put(personStr, person);\r
+ getAgentService().save(person);\r
+ result = person;\r
+ }\r
+ return result;\r
+ }\r
+\r
+\r
+\r
+\r
+ private String[] getParsedAuthors(String autorenStr) {\r
+ String[] result = new String[4]; \r
+ String basioFull = null;\r
+ String origFull;\r
+\r
+ String[] split = autorenStr.split("\\)");\r
+ if (split.length > 1){\r
+ basioFull = split[0].replace("(", "").trim();\r
+ origFull = split[1].trim();\r
+ }else{\r
+ origFull = split[0].trim();\r
+ }\r
+ String[] splitBasio = splitExAuthors(basioFull);\r
+ String[] splitOrig = splitExAuthors(origFull);\r
+ result[0] = splitBasio[0];\r
+ result[1] = splitBasio[1];\r
+ result[2] = splitOrig[0];\r
+ result[3] = splitOrig[1];\r
\r
+ return result;\r
+ }\r
+\r
+\r
+\r
+\r
+ private String[] splitExAuthors(String author) {\r
+ String[] result = new String[2]; \r
+ if (author != null){\r
+ String[] split = author.split("\\sex\\s");\r
+ if (split.length > 1){\r
+ //TODO richtige Reihenfolge ?\r
+ result[0] = split[1].trim();\r
+ result[1] = split[0].trim();\r
+ }else{\r
+ result[0] = split[0].trim();\r
+ }\r
+ }\r
+ return result;\r
+ }\r
+\r
+\r
+\r
+\r
+ private void doBooks(CaryoImportState state) throws SQLException {\r
+ Source source = state.getConfig().getSource();\r
+ String sql = "SELECT DISTINCT BookTitle FROM " + getTableName() + " WHERE BookTitle IS NOT NULL AND BookTitle <> '' ";\r
+ ResultSet rs = source.getResultSet(sql);\r
+ while (rs.next()){\r
+ String bookStr = rs.getString("BookTitle");\r
+ if (bookMap.get(bookStr) == null ){\r
+ \r
+ IBook book = ReferenceFactory.newBook(); \r
+\r
+ book.setTitle(bookStr);\r
+ \r
+ bookMap.put(bookStr, book);\r
+ getReferenceService().save((Reference<?>)book);\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+\r
+\r
+ private void doJournals(CaryoImportState state) throws SQLException {\r
+ Source source = state.getConfig().getSource();\r
+ String sqlPeriodical = "SELECT DISTINCT PeriodicalTitle FROM " + getTableName() + " WHERE PeriodicalTitle IS NOT NULL AND PeriodicalTitle <> '' ";\r
+ ResultSet rs = source.getResultSet(sqlPeriodical);\r
+ while (rs.next()){\r
+ String periodical = rs.getString("PeriodicalTitle");\r
+ if (journalMap.get(periodical) == null ){\r
+ \r
+ Reference<?> journal = ReferenceFactory.newJournal(); \r
+\r
+ journal.setTitle(periodical);\r
+ \r
+ journalMap.put(periodical, journal);\r
+ getReferenceService().save(journal);\r
+ }\r
+ }\r
}\r
\r
\r
\r
private void doFamilies(CaryoImportState state) throws SQLException {\r
Source source = state.getConfig().getSource();\r
- String sqlFamily = "SELECT DISTINCT family FROM table WHERE family IS NOT NULL";\r
+ String sqlFamily = "SELECT DISTINCT Family FROM " + getTableName() + " WHERE Family IS NOT NULL";\r
ResultSet rs = source.getResultSet(sqlFamily);\r
while (rs.next()){\r
String family = rs.getString("family");\r
- BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());\r
- name.setGenusOrUninomial(family);\r
- Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());\r
- classification.addChildTaxon(taxon, null, null, null);\r
-// taxon.addSource(id, idNamespace, citation, null);\r
- \r
- \r
- familyMap.put(family, taxon);\r
+ if (familyMap.get(family) == null ){\r
+ \r
+ BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());\r
+ name.setGenusOrUninomial(family);\r
+ Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());\r
+ classification.addChildTaxon(taxon, null, null, null);\r
+ // taxon.addSource(id, idNamespace, citation, null);\r
+ \r
+ familyMap.put(family, taxon);\r
+ getTaxonService().save(taxon);\r
+ }\r
}\r
\r
}\r
getClassificationService().save(classification);\r
}\r
return this.classification;\r
- \r
}\r
\r
\r
BGBM BDI Projects / cdmlib-apps.git / commitdiff