protected Map<String, DefinedTerm> kindOfUnitsMap;
-
@Override
protected abstract void doInvoke(STATE state);
/**
* Handle a single unit
- * @param state
- * @param item
*/
protected abstract void handleSingleUnit(STATE state, Object item) ;
-
-
protected TaxonName getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
TaxonName taxonName = null;
SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
}
}
-
}
-
}
- if(taxonName==null && atomisedTaxonName!=null){
+ if(taxonName==null && atomisedTaxonName != null){
taxonName = atomisedTaxonName;
state.getReport().addName(taxonName);
logger.info("Created new taxon name "+taxonName);
state.getReport().addInfoMessage(String.format("Taxon %s was parsed as %s", scientificName, atomisedTaxonName.getTitleCache()));
}
}
- else if(taxonName==null){
+ else if(taxonName == null){
//create new taxon name
if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP)){
state.getReport().addName(taxonName);
logger.info("Created new taxon name "+taxonName);
}
- if (taxonName != null){
- state.names.put(taxonName.getNameCache(), taxonName);
- }
- if(!taxonName.isPersited()) {
+ state.names.put(taxonName.getNameCache(), taxonName);
+
+ if(!taxonName.isPersisted()) {
save(taxonName, state);
}
return taxonName;
}
- protected TaxonName getBestMatchingName(String scientificName, java.util.Collection<TaxonName> names, STATE state){
- Set<TaxonName> namesWithAcceptedTaxa = new HashSet<>();
- List<TaxonName> namesWithAcceptedTaxaInClassification = new ArrayList<>();
- for (TaxonName name : names) {
- if(!name.getTaxa().isEmpty()){
- Set<Taxon> taxa = name.getTaxa();
- for (Taxon taxon:taxa){
- if (!taxon.getTaxonNodes().isEmpty()){
- //use only taxa included in a classification
- for (TaxonNode node:taxon.getTaxonNodes()){
- if (state.getClassification() != null && node.getClassification().equals(state.getClassification())){
- namesWithAcceptedTaxaInClassification.add(name);
- }else {
- namesWithAcceptedTaxa.add(name);
- }
- }
+ protected TaxonName getBestMatchingName(String scientificName, java.util.Collection<TaxonName> names, STATE state){
+ Set<TaxonName> namesWithAcceptedTaxa = new HashSet<>();
+ List<TaxonName> namesWithAcceptedTaxaInClassification = new ArrayList<>();
+ for (TaxonName name : names) {
+ if(!name.getTaxonBases().isEmpty()){
+ Set<TaxonBase> taxa = name.getTaxonBases();
+ for (TaxonBase taxonBase:taxa){
+ Taxon acceptedTaxon= null;
+ if (taxonBase instanceof Synonym) {
+ Synonym syn = (Synonym) taxonBase;
+ acceptedTaxon = syn.getAcceptedTaxon();
+ }else {
+ acceptedTaxon = (Taxon)taxonBase;
+ }
+ if (!(acceptedTaxon).getTaxonNodes().isEmpty()){
+ //use only taxa included in a classification
+ for (TaxonNode node:(acceptedTaxon).getTaxonNodes()){
+ if (state.getClassification() != null && node.getClassification().equals(state.getClassification())){
+ namesWithAcceptedTaxaInClassification.add(name);
+ }else {
+ namesWithAcceptedTaxa.add(name);
+ }
+ }
+ }
+ }
+ }
+ }
+ String message = String.format("More than one taxon name was found for %s, maybe in other classifications!", scientificName);
+ //check for names with accepted taxa in classification
+ if(namesWithAcceptedTaxaInClassification.size()>0){
+ if(namesWithAcceptedTaxaInClassification.size()>1){
+
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+ return namesWithAcceptedTaxaInClassification.iterator().next();
+ }
+ //check for any names with accepted taxa
+ if(namesWithAcceptedTaxa.size()>0){
+ if(namesWithAcceptedTaxa.size()>1){
- }
- }
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+ return namesWithAcceptedTaxa.iterator().next();
+ }
+// //no names with accepted taxa found -> check accepted taxa of synonyms -> this is handled in the first block now!
+// List<Taxon> taxaFromSynonyms = new ArrayList<>();
+// for (TaxonName name : names) {
+// Set<TaxonBase> taxonBases = name.getTaxonBases();
+// for (TaxonBase taxonBase : taxonBases) {
+// if(taxonBase.isInstanceOf(Synonym.class)){
+// Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
+// taxaFromSynonyms.add(synonym.getAcceptedTaxon());
+// }
+// }
+// }
+// if(taxaFromSynonyms.size()>0){
+// if(taxaFromSynonyms.size()>1){
+// state.getReport().addInfoMessage(message);
+// logger.warn(message);
+// return null;
+// }
+// return taxaFromSynonyms.iterator().next().getName();
+// }
+ //no accepted and no synonyms -> return one of the names and create a new taxon
+ if (names.isEmpty()){
+ return null;
+ }else{
+ return names.iterator().next();
+ }
+ }
- }
- }
- String message = String.format("More than one taxon name was found for %s, maybe in other classifications!", scientificName);
- //check for names with accepted taxa in classification
- if(namesWithAcceptedTaxaInClassification.size()>0){
- if(namesWithAcceptedTaxaInClassification.size()>1){
-
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- return null;
+ /**
+ * Parse automatically the scientific name
+ * @param scientificName the scientific name to parse
+ * @param state the current import state
+ * @param report the import report
+ * @return a parsed name
+ */
+ protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
+
+ NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
+ TaxonName taxonName = null;
+ boolean problem = false;
+
+ if (logger.isDebugEnabled()){
+ logger.debug("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
+ }
+
+ if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN"))) {
+ taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNAFP"))) {
+ taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN"))) {
+ taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNP, rank);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP"))) {
+ taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ if (problem) {
+ String message = String.format("Parsing problems for %s", scientificName);
+ if(taxonName!=null){
+ for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
+ message += "\n\t- "+parserProblem;
}
- return namesWithAcceptedTaxaInClassification.iterator().next();
}
- //check for any names with accepted taxa
- if(namesWithAcceptedTaxa.size()>0){
- if(namesWithAcceptedTaxa.size()>1){
+ report.addInfoMessage(message);
+ logger.info(message);
+ }
+ return taxonName;
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- return null;
- }
- return namesWithAcceptedTaxa.iterator().next();
- }
- //no names with accepted taxa found -> check accepted taxa of synonyms
- List<Taxon> taxaFromSynonyms = new ArrayList<>();
- for (TaxonName name : names) {
- Set<TaxonBase> taxonBases = name.getTaxonBases();
- for (TaxonBase taxonBase : taxonBases) {
- if(taxonBase.isInstanceOf(Synonym.class)){
- Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
- taxaFromSynonyms.add(synonym.getAcceptedTaxon());
- }
- }
- }
- if(taxaFromSynonyms.size()>0){
- if(taxaFromSynonyms.size()>1){
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- return null;
- }
- return taxaFromSynonyms.iterator().next().getName();
- }
- //no accepted and no synonyms -> return one of the names and create a new taxon
- if (names.isEmpty()){
- return null;
- }else{
- return names.iterator().next();
- }
- }
- /**
- * Parse automatically the scientific name
- * @param scientificName the scientific name to parse
- * @param state the current import state
- * @param report the import report
- * @return a parsed name
- */
-
- protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
-
- NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
- TaxonName taxonName = null;
- boolean problem = false;
-
- if (logger.isDebugEnabled()){
- logger.debug("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
- }
+ }
- if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN"))) {
- taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNAFP"))) {
- taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN"))) {
- taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNP, rank);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- else if (state.getDataHolder().getNomenclatureCode() != null && (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP"))) {
- taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- if (problem) {
- String message = String.format("Parsing problems for %s", scientificName);
- if(taxonName!=null){
- for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
- message += "\n\t- "+parserProblem;
- }
- }
- report.addInfoMessage(message);
- logger.info(message);
- }
- return taxonName;
-
- }
-
- /**
- * Create the name without automatic parsing, either because it failed, or because the user deactivated it.
- * The name is built upon the ABCD fields
- * @param atomisedMap : the ABCD atomised fields
- * @param fullName : the full scientific name
- * @param state
- * @return the corresponding Botanical or Zoological or... name
- */
- protected TaxonName setTaxonNameByType(
- HashMap<String, String> atomisedMap, String fullName, STATE state) {
- boolean problem = false;
- if (logger.isDebugEnabled()){
- logger.debug("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
- }
+ /**
+ * Create the name without automatic parsing, either because it failed, or because the user deactivated it.
+ * The name is built upon the ABCD fields
+ * @param atomisedMap : the ABCD atomised fields
+ * @param fullName : the full scientific name
+ * @param state
+ * @return the corresponding Botanical or Zoological or... name
+ */
+ protected TaxonName setTaxonNameByType(
+ HashMap<String, String> atomisedMap, String fullName, STATE state) {
+ boolean problem = false;
+ if (logger.isDebugEnabled()){
+ logger.debug("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
+ }
- if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
- TaxonName taxonName = TaxonNameFactory.NewZoologicalInstance(null);
- taxonName.setFullTitleCache(fullName, true);
- taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
- taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
- taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
- taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
+ if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
+ TaxonName taxonName = TaxonNameFactory.NewZoologicalInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
+ taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
- if (taxonName.getGenusOrUninomial() != null){
- taxonName.setRank(Rank.GENUS());
- }
+ if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
- if (taxonName.getInfraGenericEpithet() != null){
- taxonName.setRank(Rank.SUBGENUS());
- }
+ if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
- if (taxonName.getSpecificEpithet() != null){
- taxonName.setRank(Rank.SPECIES());
- }
+ if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
- if (taxonName.getInfraSpecificEpithet() != null){
- taxonName.setRank(Rank.SUBSPECIES());
- }
+ if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
- Team team = null;
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
- }
- else {
- if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
- }
- }
- if (team != null) {
- taxonName.setBasionymAuthorship(team);
- }
- else {
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
- }
- else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
- }
- }
- if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (taxonName.hasProblem()) {
- logger.info("pb ICZN");
- problem = true;
- }
- else {
- return taxonName;
- }
- }
- else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
- TaxonName taxonName = parseScientificName(fullName, state, state.getReport(), null);
- if (taxonName != null){
- return taxonName;
- }
- else{
- taxonName = TaxonNameFactory.NewBotanicalInstance(null);
- }
- taxonName.setFullTitleCache(fullName, true);
- taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
- taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
- taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
- try {
- taxonName.setRank(Rank.getRankByLatinName(getFromMap(atomisedMap, "Rank")));
- } catch (Exception e) {
- if (taxonName.getInfraSpecificEpithet() != null){
- taxonName.setRank(Rank.SUBSPECIES());
- }
- else if (taxonName.getSpecificEpithet() != null){
- taxonName.setRank(Rank.SPECIES());
- }
- else if (taxonName.getInfraGenericEpithet() != null){
- taxonName.setRank(Rank.SUBGENUS());
- }
- else if (taxonName.getGenusOrUninomial() != null){
- taxonName.setRank(Rank.GENUS());
- }
- }
- Team team = null;
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
- taxonName.setBasionymAuthorship(team);
- }
- if (getFromMap(atomisedMap, "AuthorTeam") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (team == null) {
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
- }
- else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
- }
- }
- if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (taxonName.hasProblem()) {
- logger.info("pb ICBN");
- problem = true;
- }
- else {
- return taxonName;
- }
- }
- else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNP.getUuid())) {
- TaxonName taxonName = TaxonNameFactory.NewBacterialInstance(null);
- taxonName.setFullTitleCache(fullName, true);
- taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
- taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
- taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
- taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
-
- if (taxonName.getGenusOrUninomial() != null){
- taxonName.setRank(Rank.GENUS());
- }
- else if (taxonName.getInfraGenericEpithet() != null){
- taxonName.setRank(Rank.SUBGENUS());
- }
- else if (taxonName.getSpecificEpithet() != null){
- taxonName.setRank(Rank.SPECIES());
- }
- else if (taxonName.getInfraSpecificEpithet() != null){
- taxonName.setRank(Rank.SUBSPECIES());
- }
+ Team team = null;
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
+ }
+ else {
+ if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
+ }
+ }
+ if (team != null) {
+ taxonName.setBasionymAuthorship(team);
+ }
+ else {
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
+ }
+ else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
+ }
+ }
+ if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICZN");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
+ TaxonName taxonName = parseScientificName(fullName, state, state.getReport(), null);
+ if (taxonName != null){
+ return taxonName;
+ }
+ else{
+ taxonName = TaxonNameFactory.NewBotanicalInstance(null);
+ }
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
+ try {
+ taxonName.setRank(Rank.getRankByLatinName(getFromMap(atomisedMap, "Rank")));
+ } catch (Exception e) {
+ if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
+ else if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+ else if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+ else if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+ }
+ Team team = null;
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
+ taxonName.setBasionymAuthorship(team);
+ }
+ if (getFromMap(atomisedMap, "AuthorTeam") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (team == null) {
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
+ }
+ else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
+ }
+ }
+ if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICBN");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNP.getUuid())) {
+ TaxonName taxonName = TaxonNameFactory.NewBacterialInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
+ taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
+
+ if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+ else if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+ else if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+ else if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
- if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
- Team team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
- Team team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
- taxonName.setBasionymAuthorship(team);
- }
- if (taxonName.hasProblem()) {
- logger.info("pb ICNP");
- problem = true;
- }
- else {
- return taxonName;
- }
- }
- else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
- TaxonName taxonName = TaxonNameFactory.NewCultivarInstance(null);
+ if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ Team team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
+ Team team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
+ taxonName.setBasionymAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICNP");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
+ TaxonName taxonName = TaxonNameFactory.NewCultivarInstance(null);
- if (taxonName.hasProblem()) {
- logger.info("pb ICNCP");
- problem = true;
- }
- else {
- return taxonName;
- }
- return taxonName;
- }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICNCP");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ return taxonName;
+ }
- if (problem) {
- logger.info("Problem im setTaxonNameByType ");
- TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);
- taxonName.setFullTitleCache(fullName, true);
- return taxonName;
- }
- TaxonName tn = TaxonNameFactory.NewNonViralInstance(null);
- return tn;
- }
-
- /**
- * Get a formated string from a hashmap
- * @param atomisedMap
- * @param key
- * @return
- */
- private String getFromMap(HashMap<String, String> atomisedMap, String key) {
- String value = null;
- if (atomisedMap.containsKey(key)) {
- value = atomisedMap.get(key);
- }
+ if (problem) {
+ logger.info("Problem im setTaxonNameByType ");
+ TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ return taxonName;
+ }
+ TaxonName tn = TaxonNameFactory.NewNonViralInstance(null);
+ return tn;
+ }
- try {
- if (value != null && key.matches(".*Year.*")) {
- value = value.trim();
- if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
- String tmp = value.split("[0-9]{4}$")[0];
- int year = Integer.parseInt(value.split(tmp)[1]);
- if (year >= 1752) {
- value = tmp;
- }
- else {
- value = null;
- }
- }
- else {
- value = null;
- }
- }
- }
- catch (Exception e) {
- value = null;
- }
- return value;
- }
-
- /**
- * Very fast and dirty implementation to allow handling of transient objects as described in
- * https://dev.e-taxonomy.eu/redmine/issues/3726
- *
- * Not yet complete.
- *
- * @param cdmBase
- * @param state
- */
- protected UUID save(CdmBase cdmBase, SpecimenImportStateBase state) {
- ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
- if (cdmRepository == null){
- cdmRepository = this;
- }
+ /**
+ * Get a formated string from a hashmap
+ * @param atomisedMap
+ * @param key
+ * @return
+ */
+ private String getFromMap(HashMap<String, String> atomisedMap, String key) {
+ String value = null;
+ if (atomisedMap.containsKey(key)) {
+ value = atomisedMap.get(key);
+ }
- if (cdmBase.isInstanceOf(LanguageString.class)){
- return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
- }else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
- SpecimenOrObservationBase specimen = CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class);
-
- return cdmRepository.getOccurrenceService().saveOrUpdate(specimen);
- }else if (cdmBase.isInstanceOf(Reference.class)){
- return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
- }else if (cdmBase.isInstanceOf(Classification.class)){
- return cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
- }else if (cdmBase.isInstanceOf(AgentBase.class)){
- return cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
- }else if (cdmBase.isInstanceOf(Collection.class)){
- return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
- }else if (cdmBase.isInstanceOf(DescriptionBase.class)){
- DescriptionBase description = CdmBase.deproxy(cdmBase, DescriptionBase.class);
-
- return cdmRepository.getDescriptionService().saveOrUpdate(description);
- }else if (cdmBase.isInstanceOf(TaxonBase.class)){
- return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
- }else if (cdmBase.isInstanceOf(TaxonName.class)){
- return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonName.class));
- }else if (cdmBase.isInstanceOf(TaxonNode.class)){
- return cdmRepository.getTaxonNodeService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNode.class));
- }else{
- throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
- }
+ try {
+ if (value != null && key.matches(".*Year.*")) {
+ value = value.trim();
+ if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
+ String tmp = value.split("[0-9]{4}$")[0];
+ int year = Integer.parseInt(value.split(tmp)[1]);
+ if (year >= 1752) {
+ value = tmp;
+ }
+ else {
+ value = null;
+ }
+ }
+ else {
+ value = null;
+ }
+ }
+ }
+ catch (Exception e) {
+ value = null;
+ }
+ return value;
+ }
- }
+ /**
+ * Very fast and dirty implementation to allow handling of transient objects as described in
+ * https://dev.e-taxonomy.eu/redmine/issues/3726
+ *
+ * Not yet complete.
+ */
+ protected UUID save(CdmBase cdmBase, SpecimenImportStateBase<?,?> state) {
+ ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
+ if (cdmRepository == null){
+ cdmRepository = this;
+ }
+ if (cdmBase.isInstanceOf(LanguageString.class)){
+ return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
+ }else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
+ SpecimenOrObservationBase<?> specimen = CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class);
+ return cdmRepository.getOccurrenceService().saveOrUpdate(specimen);
+ }else if (cdmBase.isInstanceOf(Reference.class)){
+ return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
+ }else if (cdmBase.isInstanceOf(Classification.class)){
+ return cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
+ }else if (cdmBase.isInstanceOf(AgentBase.class)){
+ return cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
+ }else if (cdmBase.isInstanceOf(Collection.class)){
+ return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
+ }else if (cdmBase.isInstanceOf(DescriptionBase.class)){
+ DescriptionBase<?> description = CdmBase.deproxy(cdmBase, DescriptionBase.class);
+ return cdmRepository.getDescriptionService().saveOrUpdate(description);
+ }else if (cdmBase.isInstanceOf(TaxonBase.class)){
+ return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
+ }else if (cdmBase.isInstanceOf(TaxonName.class)){
+ return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonName.class));
+ }else if (cdmBase.isInstanceOf(TaxonNode.class)){
+ return cdmRepository.getTaxonNodeService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNode.class));
+ }else{
+ throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
+ }
+ }
- protected SpecimenOrObservationBase findExistingSpecimen(String unitId, SpecimenImportStateBase state){
- ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
- if(cdmAppController==null){
- cdmAppController = this;
- }
- FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
- config.setSignificantIdentifier(unitId);
- List<String> propertyPaths = new ArrayList<>();
- propertyPaths.add("derivedFrom.*");
- config.setPropertyPaths(propertyPaths);
- commitTransaction(state.getTx());
- state.setTx(startTransaction());
- try{
- Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
- if(!existingSpecimens.getRecords().isEmpty()){
- if(existingSpecimens.getRecords().size()==1){
- return existingSpecimens.getRecords().iterator().next();
- }
- }
-
- }catch(NullPointerException e){
- logger.error("searching for existing specimen creates NPE: " + config.getSignificantIdentifier());
- e.printStackTrace();
+ protected SpecimenOrObservationBase<?> findExistingSpecimen(String unitId, SpecimenImportStateBase<?,?> state){
+ ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
+ if(cdmAppController==null){
+ cdmAppController = this;
+ }
+ FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
+ config.setSignificantIdentifier(unitId);
+ List<String> propertyPaths = new ArrayList<>();
+ propertyPaths.add("derivedFrom.*");
+ config.setPropertyPaths(propertyPaths);
+ commitTransaction(state.getTx());
+ state.setTx(startTransaction());
+ try{
+ @SuppressWarnings("rawtypes")
+ Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
+ if(!existingSpecimens.getRecords().isEmpty()){
+ if(existingSpecimens.getRecords().size()==1){
+ return existingSpecimens.getRecords().iterator().next();
+ }
}
+ }catch(NullPointerException e){
+ logger.error("searching for existing specimen creates NPE: " + config.getSignificantIdentifier());
+ e.printStackTrace();
+ }
- return null;
- }
- protected abstract void importAssociatedUnits(STATE state, Object item, DerivedUnitFacade derivedUnitFacade);
+ return null;
+ }
- /**
- * getFacade : get the DerivedUnitFacade based on the recordBasis
- * @param state
- *
- * @return DerivedUnitFacade
- */
- protected DerivedUnitFacade getFacade(STATE state) {
- if (logger.isDebugEnabled()){
- logger.info("getFacade()");
- }
- SpecimenOrObservationType type = null;
+ protected abstract void importAssociatedUnits(STATE state, Object item, DerivedUnitFacade derivedUnitFacade);
+
+ /**
+ * getFacade : get the DerivedUnitFacade based on the recordBasis
+ * @param state
+ *
+ * @return DerivedUnitFacade
+ */
+ protected DerivedUnitFacade getFacade(STATE state) {
+ if (logger.isDebugEnabled()){
+ logger.info("getFacade()");
+ }
+ SpecimenOrObservationType type = null;
- // create specimen
- if (NB((state.getDataHolder().getRecordBasis())) != null) {
- if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
- type = SpecimenOrObservationType.PreservedSpecimen;
- }
- if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
- type = SpecimenOrObservationType.Observation;
- }
- if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
- type = SpecimenOrObservationType.Fossil;
- }
- if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
- type = SpecimenOrObservationType.LivingSpecimen;
- }
- if (type == null) {
- logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
- type = SpecimenOrObservationType.DerivedUnit;
- }
- // TODO fossils?
- } else {
- logger.info("The basis of record is null");
- type = SpecimenOrObservationType.DerivedUnit;
- }
- DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
- return derivedUnitFacade;
- }
-
- /**
- * Look if the Institution does already exist
- * @param institutionCode: a string with the institutioncode
- * @param config : the configurator
- * @return the Institution (existing or new)
- */
- protected Institution getInstitution(String institutionCode, STATE state) {
- SpecimenImportConfiguratorBase config = state.getConfig();
- Institution institution=null;
- institution = (Institution)state.institutions.get(institutionCode);
- if (institution != null){
- return institution;
- }
- List<Institution> institutions;
- try {
- institutions = getAgentService().searchInstitutionByCode(institutionCode);
+ // create specimen
+ if (NB((state.getDataHolder().getRecordBasis())) != null) {
+ if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
+ type = SpecimenOrObservationType.PreservedSpecimen;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
+ type = SpecimenOrObservationType.Observation;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
+ type = SpecimenOrObservationType.Fossil;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
+ type = SpecimenOrObservationType.LivingSpecimen;
+ }
+ if (type == null) {
+ logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
+ type = SpecimenOrObservationType.DerivedUnit;
+ }
+ // TODO fossils?
+ } else {
+ logger.info("The basis of record is null");
+ type = SpecimenOrObservationType.DerivedUnit;
+ }
+ DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
+ return derivedUnitFacade;
+ }
- } catch (Exception e) {
- institutions = new ArrayList<Institution>();
- logger.warn(e);
- }
- if (institutions.size() > 0 && config.isReuseExistingMetaData()) {
- for (Institution institut:institutions){
- try{
- if (institut.getCode().equalsIgnoreCase(institutionCode)) {
- institution=institut;
- break;
- }
- }catch(Exception e){logger.warn("no institution code in the db");}
- }
- }
- if (logger.isDebugEnabled()){
- if(institution !=null) {
- logger.info("getinstitution " + institution.toString());
- }
- }
- if (institution == null){
- // create institution
- institution = Institution.NewInstance();
- institution.setCode(institutionCode);
- institution.setTitleCache(institutionCode, true);
- UUID uuid = save(institution, state);
- }
+ /**
+ * Look if the Institution does already exist
+ * @param institutionCode: a string with the institutioncode
+ * @param config : the configurator
+ * @return the Institution (existing or new)
+ */
+ protected Institution getInstitution(String institutionCode, STATE state) {
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
+ Institution institution=null;
+ institution = (Institution)state.institutions.get(institutionCode);
+ if (institution != null){
+ return institution;
+ }
+ List<Institution> institutions;
+ try {
+ institutions = getAgentService().searchInstitutionByCode(institutionCode);
+
+ } catch (Exception e) {
+ institutions = new ArrayList<Institution>();
+ logger.warn(e);
+ }
+ if (institutions.size() > 0 && config.isReuseExistingMetaData()) {
+ for (Institution institut:institutions){
+ try{
+ if (institut.getCode().equalsIgnoreCase(institutionCode)) {
+ institution=institut;
+ break;
+ }
+ }catch(Exception e){logger.warn("no institution code in the db");}
+ }
+ }
+ if (logger.isDebugEnabled()){
+ if(institution !=null) {
+ logger.info("getinstitution " + institution.toString());
+ }
+ }
+ if (institution == null){
+ // create institution
+ institution = Institution.NewInstance();
+ institution.setCode(institutionCode);
+ institution.setTitleCache(institutionCode, true);
+ save(institution, state);
+ }
+ state.institutions.put(institutionCode, institution);
+ return institution;
+ }
- state.institutions.put(institutionCode, institution);
- return institution;
- }
-
- /**
- * Look if the Collection does already exist
- * @param collectionCode
- * @param collectionCode: a string
- * @param config : the configurator
- * @return the Collection (existing or new)
- */
- protected Collection getCollection(Institution institution, String collectionCode, STATE state) {
- SpecimenImportConfiguratorBase config = state.getConfig();
- Collection collection = null;
- List<Collection> collections;
- collection = (Collection) state.collections.get(collectionCode);
- if (collection != null){
- return collection;
- }
- try {
- collections = getCollectionService().searchByCode(collectionCode);
- } catch (Exception e) {
- collections = new ArrayList<Collection>();
- }
- if (collections.size() > 0 && config.isReuseExistingMetaData()) {
- for (Collection coll:collections){
- if (coll.getCode() != null && coll.getInstitute() != null
- && coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
- collection = coll;
- break;
- }
- }
- }
+ /**
+ * Look if the Collection does already exist
+ * @param collectionCode
+ * @param collectionCode: a string
+ * @param config : the configurator
+ * @return the Collection (existing or new)
+ */
+ protected Collection getCollection(Institution institution, String collectionCode, STATE state) {
- if(collection == null){
- collection =Collection.NewInstance();
- collection.setCode(collectionCode);
- collection.setInstitute(institution);
- collection.setTitleCache(collectionCode);
- UUID uuid = save(collection, state);
- }
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
+ Collection collection = null;
+ List<Collection> collections;
+ collection = (Collection) state.collections.get(collectionCode);
+ if (collection != null){
+ return collection;
+ }
+ try {
+ collections = getCollectionService().searchByCode(collectionCode);
+ } catch (Exception e) {
+ collections = new ArrayList<>();
+ }
+ if (collections.size() > 0 && config.isReuseExistingMetaData()) {
+ for (Collection coll:collections){
+ if (coll.getCode() != null && coll.getInstitute() != null
+ && coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
+ collection = coll;
+ break;
+ }
+ }
+ }
+ if(collection == null){
+ collection =Collection.NewInstance();
+ collection.setCode(collectionCode);
+ collection.setInstitute(institution);
+ save(collection, state);
+ }
+ state.collections.put(collectionCode, collection);
- state.collections.put(collectionCode, collection);
-
- return collection;
- }
-
- /**
- * @param reference
- * @param citationDetail
- * @return
- */
- //FIXME this method is highly critical, because
- // * it will have serious performance and memory problems with large databases
- // (databases may easily have >1 Mio source records)
- // * it does not make sense to search for existing sources and then clone them
- // we need to search for existing references instead and use them (if exist)
- // for our new source.
- protected IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
-
- IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
- return sour;
- }
-
- /**
- * Add the hierarchy for a Taxon(add higher taxa)
- * @param classification
- * @param taxon: a taxon to add as a node
- * @param state: the ABCD import state
- */
- protected void addParentTaxon(Taxon taxon, STATE state, boolean preferredFlag, Classification classification){
- INonViralName nvname = taxon.getName();
- Rank rank = nvname.getRank();
- Taxon genus =null;
- Taxon subgenus =null;
- Taxon species = null;
- Taxon subspecies = null;
- Taxon parent = null;
- if(rank!=null){
- if (rank.isLowerThan(RankClass.Genus)){
- String genusOrUninomial = nvname.getGenusOrUninomial();
- TaxonName taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
- genus = getOrCreateTaxonForName(taxonName, state);
- if (genus == null){
- logger.debug("The genus should not be null " + taxonName);
- }
- if (preferredFlag) {
- parent = linkParentChildNode(null, genus, classification, state);
- }
+ return collection;
+ }
- }
- if (rank.isLower(Rank.SUBGENUS())){
- String prefix = nvname.getGenusOrUninomial();
- String name = nvname.getInfraGenericEpithet();
- if (name != null){
- TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
- subgenus = getOrCreateTaxonForName(taxonName, state);
- if (preferredFlag) {
- parent = linkParentChildNode(genus, subgenus, classification, state);
- } }
- }
- if (rank.isLowerThan(RankClass.Species)){
- if (subgenus!=null){
- String prefix = nvname.getGenusOrUninomial();
- String name = nvname.getInfraGenericEpithet();
- String spe = nvname.getSpecificEpithet();
- if (spe != null){
- TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
- species = getOrCreateTaxonForName(taxonName, state);
- if (preferredFlag) {
- parent = linkParentChildNode(subgenus, species, classification, state);
- }
- }
- }
- else{
- String prefix = nvname.getGenusOrUninomial();
- String name = nvname.getSpecificEpithet();
- if (name != null){
- TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
- species = getOrCreateTaxonForName(taxonName, state);
- if (preferredFlag) {
- parent = linkParentChildNode(genus, species, classification, state);
- }
- }
- }
- }
- if (rank.isLower(Rank.INFRASPECIES())){
- TaxonName taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
- subspecies = getOrCreateTaxonForName(taxonName, state);
- if (preferredFlag) {
- parent = linkParentChildNode(species, subspecies, classification, state);
- }
- }
- }else{
- //handle cf. and aff. taxa
- String genusEpithet = null;
- if (nvname.getTitleCache().contains("cf.")){
- genusEpithet = nvname.getTitleCache().substring(0, nvname.getTitleCache().indexOf("cf."));
- } else if (nvname.getTitleCache().contains("aff.")){
- genusEpithet = nvname.getTitleCache().substring(0, nvname.getTitleCache().indexOf("aff."));
- }
- if (genusEpithet != null){
- genusEpithet = genusEpithet.trim();
- TaxonName taxonName = null;
- if (genusEpithet.contains(" ")){
- taxonName = getOrCreateTaxonName(genusEpithet, Rank.SPECIES(), preferredFlag, state, -1);
- }else{
- taxonName = getOrCreateTaxonName(genusEpithet, Rank.GENUS(), preferredFlag, state, -1);
- }
- genus = getOrCreateTaxonForName(taxonName, state);
- if (genus == null){
- logger.debug("The genus should not be null " + taxonName);
- }
+ /**
+ * @param reference
+ * @param citationDetail
+ * @return
+ */
+ //FIXME this method is highly critical, because
+ // * it will have serious performance and memory problems with large databases
+ // (databases may easily have >1 Mio source records)
+ // * it does not make sense to search for existing sources and then clone them
+ // we need to search for existing references instead and use them (if exist)
+ // for our new source.
+ protected IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
+
+ IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
+ return sour;
+ }
+
+ /**
+ * Add the hierarchy for a Taxon(add higher taxa)
+ * @param classification
+ * @param taxon: a taxon to add as a node
+ * @param state: the ABCD import state
+ */
+ protected void addParentTaxon(Taxon taxon, STATE state, boolean preferredFlag, Classification classification){
+ INonViralName nvname = taxon.getName();
+ Rank rank = nvname.getRank();
+ Taxon genus =null;
+ Taxon subgenus =null;
+ Taxon species = null;
+ Taxon subspecies = null;
+ Taxon parent = null;
+ if(rank!=null){
+ if (rank.isLowerThan(RankClass.Genus)){
+ String genusOrUninomial = nvname.getGenusOrUninomial();
+ TaxonName taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
+ genus = getOrCreateTaxonForName(taxonName, state);
+ if (genus == null){
+ logger.debug("The genus should not be null " + taxonName);
+ }
+ if (preferredFlag) {
+ parent = linkParentChildNode(null, genus, classification, state);
+ }
+
+ }
+ if (rank.isLower(Rank.SUBGENUS())){
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getInfraGenericEpithet();
+ if (name != null){
+ TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
+ subgenus = getOrCreateTaxonForName(taxonName, state);
if (preferredFlag) {
- parent = linkParentChildNode(null, genus, classification, state);
+ parent = linkParentChildNode(genus, subgenus, classification, state);
}
+ }
+ }
+ if (rank.isLowerThan(RankClass.Species)){
+ if (subgenus!=null){
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getInfraGenericEpithet();
+ String spe = nvname.getSpecificEpithet();
+ if (spe != null){
+ TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
+ species = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(subgenus, species, classification, state);
+ }
+ }
+ }
+ else{
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getSpecificEpithet();
+ if (name != null){
+ TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
+ species = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(genus, species, classification, state);
+ }
+ }
+ }
+ }
+ if (rank.isLower(Rank.INFRASPECIES())){
+ TaxonName taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
+ subspecies = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(species, subspecies, classification, state);
+ }
+ }
+ }else{
+ //handle cf. and aff. taxa
+ String genusEpithet = null;
+ if (nvname.getTitleCache().contains("cf.")){
+ genusEpithet = nvname.getTitleCache().substring(0, nvname.getTitleCache().indexOf("cf."));
+ } else if (nvname.getTitleCache().contains("aff.")){
+ genusEpithet = nvname.getTitleCache().substring(0, nvname.getTitleCache().indexOf("aff."));
+ }
+ if (genusEpithet != null){
+ genusEpithet = genusEpithet.trim();
+ TaxonName taxonName = null;
+ if (genusEpithet.contains(" ")){
+ taxonName = getOrCreateTaxonName(genusEpithet, Rank.SPECIES(), preferredFlag, state, -1);
+ }else{
+ taxonName = getOrCreateTaxonName(genusEpithet, Rank.GENUS(), preferredFlag, state, -1);
}
- }
- if (preferredFlag && parent!=taxon ) {
- linkParentChildNode(parent, taxon, classification, state);
- }
- }
-
- /**
- * Link a parent to a child and save it in the current classification
- * @param parent: the higher Taxon
- * @param child : the lower (or current) Taxon
- * return the Taxon from the new created Node
- * @param classification
- * @param state
- */
- protected Taxon linkParentChildNode(Taxon parent, Taxon child, Classification classification, STATE state) {
- TaxonNode node =null;
- List<String> propertyPaths = new ArrayList<>();
- propertyPaths.add("childNodes");
- if (parent != null) {
-
- parent = (Taxon) getTaxonService().load(parent.getUuid(), propertyPaths);
- child = (Taxon) getTaxonService().load(child.getUuid(), propertyPaths);
- //here we do not have to check if the taxon nodes already exists
- //this is done by classification.addParentChild()
- //do not add child node if it already exists
- if(hasTaxonNodeInClassification(child, classification)){
- return child;
- }
- else{
- node = classification.addParentChild(parent, child, state.getRef(), "");
- save(node, state);
- }
- }
- else {
- if (child == null){
- logger.debug("The child should not be null!");
- }
- child = (Taxon) getTaxonService().find(child.getUuid());
- //do not add child node if it already exists
- if(hasTaxonNodeInClassification(child, classification)){
- return child;
+ genus = getOrCreateTaxonForName(taxonName, state);
+ if (genus == null){
+ logger.debug("The genus should not be null " + taxonName);
+ }
+ if (preferredFlag) {
+ parent = linkParentChildNode(null, genus, classification, state);
+ }
+ }
+ }
+ if (preferredFlag && parent!=taxon ) {
+ linkParentChildNode(parent, taxon, classification, state);
+ }
+ }
+
+ /**
+ * Link a parent to a child and save it in the current classification
+ * @param parent: the higher Taxon
+ * @param child : the lower (or current) Taxon
+ * return the Taxon from the new created Node
+ * @param classification
+ * @param state
+ */
+ protected Taxon linkParentChildNode(Taxon parent, Taxon child, Classification classification, STATE state) {
+ TaxonNode node =null;
+ List<String> propertyPaths = new ArrayList<>();
+ propertyPaths.add("childNodes");
+ if (parent != null) {
+
+ parent = (Taxon) getTaxonService().load(parent.getUuid(), propertyPaths);
+ child = (Taxon) getTaxonService().load(child.getUuid(), propertyPaths);
+ //here we do not have to check if the taxon nodes already exists
+ //this is done by classification.addParentChild()
+ //do not add child node if it already exists
+ if(hasTaxonNodeInClassification(child, classification)){
+ return child;
+ }
+ else{
+ node = classification.addParentChild(parent, child, state.getRef(), "");
+ save(node, state);
+ }
+ }
+ else {
+ if (child == null){
+ logger.debug("The child should not be null!");
+ }
+ child = (Taxon) getTaxonService().find(child.getUuid());
+ //do not add child node if it already exists
+ if(hasTaxonNodeInClassification(child, classification)){
+ return child;
+ }
+ else{
+ node = classification.addChildTaxon(child, state.getRef(), null);
+ save(node, state);
+ }
+ }
+ if(node!=null){
+ state.getReport().addTaxonNode(node);
+ return node.getTaxon();
+ }
+ String message = "Could not create taxon node for " +child;
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+
+ protected Taxon getOrCreateTaxonForName(TaxonName taxonName, STATE state){
+ if (taxonName != null){
+ Set<Taxon> acceptedTaxa = taxonName.getTaxa();
+ if(acceptedTaxa.size()>0){
+ Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next();
+ if(acceptedTaxa.size()>1){
+ String message = "More than one accepted taxon was found for taxon name: "
+ + taxonName.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
}
else{
- node = classification.addChildTaxon(child, state.getRef(), null);
- save(node, state);
+ return firstAcceptedTaxon;
}
}
- if(node!=null){
- state.getReport().addTaxonNode(node);
- return node.getTaxon();
- }
- String message = "Could not create taxon node for " +child;
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- return null;
- }
-
- protected Taxon getOrCreateTaxonForName(TaxonName taxonName, STATE state){
- if (taxonName != null){
- Set<Taxon> acceptedTaxa = taxonName.getTaxa();
- if(acceptedTaxa.size()>0){
- Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next();
- if(acceptedTaxa.size()>1){
- String message = "More than one accepted taxon was found for taxon name: "
- + taxonName.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- }
- else{
- return firstAcceptedTaxon;
- }
- }
- else{
- Set<TaxonBase> taxonAndSynonyms = taxonName.getTaxonBases();
- for (TaxonBase taxonBase : taxonAndSynonyms) {
- if(taxonBase.isInstanceOf(Synonym.class)){
- Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
- Taxon acceptedTaxonOfSynonym = synonym.getAcceptedTaxon();
- if(acceptedTaxonOfSynonym == null){
- String message = "No accepted taxon could be found for taxon name: "
- + taxonName.getTitleCache()
- + "!";
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- }
- else{
- return acceptedTaxonOfSynonym;
- }
- }
- }
- }
- Taxon taxon = Taxon.NewInstance(taxonName, state.getRef());
- save(taxon, state);
- state.getReport().addTaxon(taxon);
- logger.info("Created new taxon "+ taxon);
- return taxon;
- }
- return null;
-
- }
-
- private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
- if(taxon.getTaxonNodes()!=null){
- for (TaxonNode node : taxon.getTaxonNodes()){
- if(node.getClassification().equals(classification)){
- return true;
+ else{
+ @SuppressWarnings("rawtypes")
+ Set<TaxonBase> taxonAndSynonyms = taxonName.getTaxonBases();
+ for (TaxonBase<?> taxonBase : taxonAndSynonyms) {
+ if(taxonBase.isInstanceOf(Synonym.class)){
+ Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
+ Taxon acceptedTaxonOfSynonym = synonym.getAcceptedTaxon();
+ if(acceptedTaxonOfSynonym == null){
+ String message = "No accepted taxon could be found for taxon name: "
+ + taxonName.getTitleCache()
+ + "!";
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ }
+ else{
+ return acceptedTaxonOfSynonym;
+ }
}
}
}
- return false;
- }
-
- /**
- * HandleIdentifications : get the scientific names present in the ABCD
- * document and store link them with the observation/specimen data
- * @param state: the current ABCD import state
- * @param derivedUnitFacade : the current derivedunitfacade
- */
- protected void handleIdentifications(STATE state, DerivedUnitFacade derivedUnitFacade) {
+ Taxon taxon = Taxon.NewInstance(taxonName, state.getRef());
+ save(taxon, state);
+ state.getReport().addTaxon(taxon);
+ logger.info("Created new taxon "+ taxon);
+ return taxon;
+ }
+ return null;
+ }
- SpecimenImportConfiguratorBase config = state.getConfig();
+ private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
+ if(taxon.getTaxonNodes()!=null){
+ for (TaxonNode node : taxon.getTaxonNodes()){
+ if(node.getClassification().equals(classification)){
+ return true;
+ }
+ }
+ }
+ return false;
+ }
- String scientificName = "";
- boolean preferredFlag = false;
+ /**
+ * HandleIdentifications : get the scientific names present in the ABCD
+ * document and store link them with the observation/specimen data
+ * @param state: the current ABCD import state
+ * @param derivedUnitFacade : the current derivedunitfacade
+ */
+ protected void handleIdentifications(STATE state, DerivedUnitFacade derivedUnitFacade) {
- if (state.getDataHolder().getNomenclatureCode() == ""){
- if (config.getNomenclaturalCode() != null){
- if (config.getNomenclaturalCode() != null){
- state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().toString());
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
- }
- }
- }
+ String scientificName = "";
+ boolean preferredFlag = false;
- for (int i = 0; i < state.getDataHolder().getIdentificationList().size(); i++) {
- Identification identification = state.getDataHolder().getIdentificationList().get(i);
- scientificName = identification.getScientificName().replaceAll(" et ", " & ");
+ if (state.getDataHolder().getNomenclatureCode() == ""){
+ if (config.getNomenclaturalCode() != null){
+ if (config.getNomenclaturalCode() != null){
+ state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().toString());
+ }
+ }
+ }
- String preferred = identification.getPreferred();
- preferredFlag = false;
- if (preferred != null || state.getDataHolder().getIdentificationList().size()==1){
- if (state.getDataHolder().getIdentificationList().size()==1){
- preferredFlag = true;
- }else if (preferred != null && (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1) ) {
- preferredFlag = true;
- }
+ for (int i = 0; i < state.getDataHolder().getIdentificationList().size(); i++) {
+ Identification identification = state.getDataHolder().getIdentificationList().get(i);
+ scientificName = identification.getScientificName().replaceAll(" et ", " & ");
+ String preferred = identification.getPreferred();
+ preferredFlag = false;
+ if (preferred != null || state.getDataHolder().getIdentificationList().size()==1){
+ if (state.getDataHolder().getIdentificationList().size()==1){
+ preferredFlag = true;
+ }else if (preferred != null && (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1) ) {
+ preferredFlag = true;
}
- if (identification.getCode() != null){
- if (identification.getCode().indexOf(':') != -1) {
- state.getDataHolder().setNomenclatureCode(identification.getCode().split(COLON)[1]);
- }
- else{
- state.getDataHolder().setNomenclatureCode(identification.getCode());
- }
+
+ }
+ if (identification.getCode() != null){
+ if (identification.getCode().indexOf(':') != -1) {
+ state.getDataHolder().setNomenclatureCode(identification.getCode().split(COLON)[1]);
}
- TaxonName taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
- Taxon taxon = getOrCreateTaxonForName(taxonName, state);
- addTaxonNode(taxon, state,preferredFlag);
- linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade, identification.getIdentifier(), identification.getDate(), identification.getModifier());
- }
- }
-
- /**
- * @param taxon : a taxon to add as a node
- * @param state : the ABCD import state
- */
- protected void addTaxonNode(Taxon taxon, STATE state, boolean preferredFlag) {
- SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
- logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
- //only add nodes if not already existing in current classification or default classification
-
- //check if node exists in current classification
- //NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
- if (!existsInClassification(taxon,state.getClassification(), state)){
- if(config.isMoveNewTaxaToDefaultClassification()){
- //check if node exists in default classification
- if (!existsInClassification(taxon, state.getDefaultClassification(true), state)){
- addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification(true));
- }
- }else{
- //add non-existing taxon to current classification
- addParentTaxon(taxon, state, preferredFlag, state.getClassification());
+ else{
+ state.getDataHolder().setNomenclatureCode(identification.getCode());
}
+ }
+ TaxonName taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
+ Taxon taxon = getOrCreateTaxonForName(taxonName, state);
+ addTaxonNode(taxon, state, preferredFlag);
+ linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade, identification.getIdentifier(), identification.getDate(), identification.getModifier());
+ }
+ }
- }
- }
+ /**
+ * @param taxon : a taxon to add as a node
+ * @param state : the ABCD import state
+ */
+ protected void addTaxonNode(Taxon taxon, STATE state, boolean preferredFlag) {
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
+ logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
+ //only add nodes if not already existing in current classification or default classification
+
+ //check if node exists in current classification
+ //NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
+ if (!existsInClassification(taxon,state.getClassification(), state)){
+ if(config.isMoveNewTaxaToDefaultClassification()){
+ //check if node exists in default classification
+ if (!existsInClassification(taxon, state.getDefaultClassification(true), state)){
+ addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification(true));
+ }
+ }else{
+ //add non-existing taxon to current classification
+ addParentTaxon(taxon, state, preferredFlag, state.getClassification());
+ }
+
+ }
+ }
- private boolean existsInClassification(Taxon taxon, Classification classification, STATE state){
- boolean exist = false;
- ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
- if(cdmAppController==null){
- cdmAppController = this;
- }
- if (classification != null){
- if (!taxon.getTaxonNodes().isEmpty()){
- for (TaxonNode node:taxon.getTaxonNodes()){
- if (node.getClassification().equals(classification)){
- return true;
- }
+ private boolean existsInClassification(Taxon taxon, Classification classification, STATE state){
+ boolean exist = false;
+ ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
+ if(cdmAppController==null){
+ cdmAppController = this;
+ }
+ if (classification != null){
+ if (!taxon.getTaxonNodes().isEmpty()){
+ for (TaxonNode node:taxon.getTaxonNodes()){
+ if (node.getClassification().equals(classification)){
+ return true;
}
}
+ }
// we do not need this because we already searched for taxa in db in the previous steps
// List<UuidAndTitleCache<TaxonNode>> uuidAndTitleCacheOfAllTaxa = cdmAppController.getClassificationService().getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification.getUuid());
// if (uuidAndTitleCacheOfAllTaxa != null){
// }
// }
// }
+ }
+ return exist;
+ }
+
+ /**
+ * join DeterminationEvent to the Taxon Object
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param preferredFlag :if the current name is preferred
+ * @param derivedFacade : the derived Unit Facade
+ */
+ @SuppressWarnings("rawtypes")
+ protected void linkDeterminationEvent(STATE state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade, String identifierStr, String dateStr, String modifier) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ if (logger.isDebugEnabled()){
+ logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
+ }
+
+ DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
+ //determinationEvent.setTaxon(taxon);
+ determinationEvent.setTaxonName(taxon.getName());
+ determinationEvent.setPreferredFlag(preferredFlag);
+
+
+ determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
+ if (state.getPersonStore().get(identifierStr) != null){
+ determinationEvent.setActor((AgentBase)state.getPersonStore().get(identifierStr));
+ } else if (identifierStr != null){
+ Person identifier = Person.NewTitledInstance(identifierStr);
+ determinationEvent.setActor(identifier);
+ }
+ if (dateStr != null){
+ determinationEvent.setTimeperiod(TimePeriodParser.parseString(dateStr));
+ }
+ if (modifier != null){
+ if (modifier.equals("cf.")){
+ determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_CONFER());
+ }else if (modifier.equals("aff.")){
+ determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
}
- return exist;
- }
-
- /**
- * join DeterminationEvent to the Taxon Object
- * @param state : the ABCD import state
- * @param taxon: the current Taxon
- * @param preferredFlag :if the current name is preferred
- * @param derivedFacade : the derived Unit Facade
- */
- @SuppressWarnings("rawtypes")
- protected void linkDeterminationEvent(STATE state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade, String identifierStr, String dateStr, String modifier) {
- SpecimenImportConfiguratorBase config = state.getConfig();
- if (logger.isDebugEnabled()){
- logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
- }
+ }
+ if (config.isAddDeterminations()) {
+ state.getDerivedUnitBase().addDetermination(determinationEvent);
+ }
- DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
- //determinationEvent.setTaxon(taxon);
- determinationEvent.setTaxonName(taxon.getName());
- determinationEvent.setPreferredFlag(preferredFlag);
+ if (logger.isDebugEnabled()){
+ logger.debug("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
+ }
+ for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().getStatusList()) {
+ if (specimenTypeDesignationstatus != null) {
+ if (logger.isDebugEnabled()){
+ logger.debug("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
+ }
- determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
- if (state.getPersonStore().get(identifierStr) != null){
- determinationEvent.setActor((AgentBase)state.getPersonStore().get(identifierStr));
- } else if (identifierStr != null){
- Person identifier = Person.NewTitledInstance(identifierStr);
- determinationEvent.setActor(identifier);
- }
- if (dateStr != null){
- determinationEvent.setTimeperiod(TimePeriodParser.parseString(dateStr));
- }
- if (modifier != null){
- if (modifier.equals("cf.")){
- determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_CONFER());
- }else if (modifier.equals("aff.")){
- determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
- }
- }
- state.getDerivedUnitBase().addDetermination(determinationEvent);
+ ICdmRepository cdmAppController = config.getCdmAppController();
+ if(cdmAppController == null){
+ cdmAppController = this;
+ }
+ specimenTypeDesignationstatus = HibernateProxyHelper.deproxy(cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid()), SpecimenTypeDesignationStatus.class);
+ //Designation
+ TaxonName name = taxon.getName();
+ SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
+
+ designation.setTypeStatus(specimenTypeDesignationstatus);
+ designation.setTypeSpecimen(state.getDerivedUnitBase());
+ name.addTypeDesignation(designation, false);
+ }
+ }
+ save(state.getDerivedUnitBase(), state);
- if (logger.isDebugEnabled()){
- logger.debug("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
- }
- for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().getStatusList()) {
- if (specimenTypeDesignationstatus != null) {
- if (logger.isDebugEnabled()){
- logger.debug("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
- }
+ for (String[] fullReference : state.getDataHolder().getReferenceList()) {
- ICdmRepository cdmAppController = config.getCdmAppController();
- if(cdmAppController == null){
- cdmAppController = this;
- }
- specimenTypeDesignationstatus = HibernateProxyHelper.deproxy(cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid()), SpecimenTypeDesignationStatus.class);
- //Designation
- TaxonName name = taxon.getName();
- SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
-
- designation.setTypeStatus(specimenTypeDesignationstatus);
- designation.setTypeSpecimen(state.getDerivedUnitBase());
- name.addTypeDesignation(designation, false);
- }
- }
- save(state.getDerivedUnitBase(), state);
- for (String[] fullReference : state.getDataHolder().getReferenceList()) {
+ String strReference=fullReference[0];
+ String citationDetail = fullReference[1];
+ String citationURL = fullReference[2];
+ List<Reference> references = getReferenceService().listByTitleWithRestrictions(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
+ if (!references.isEmpty()){
+ Reference reference = null;
+ for (Reference refe: references) {
+ if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
+ reference =refe;
+ break;
+ }
+ }
+ if (reference ==null){
+ reference = ReferenceFactory.newGeneric();
+ reference.setTitleCache(strReference, true);
+ save(reference, state);
+ }
+ determinationEvent.addReference(reference);
+ }
+ }
+ save(state.getDerivedUnitBase(), state);
- String strReference=fullReference[0];
- String citationDetail = fullReference[1];
- String citationURL = fullReference[2];
- List<Reference> references = getReferenceService().listByTitleWithRestrictions(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
+ if (config.isAddIndividualsAssociations() && preferredFlag) {
+ //do not add IndividualsAssociation to non-preferred taxa
+ if (logger.isDebugEnabled()){
+ logger.debug("isDoCreateIndividualsAssociations");
+ }
- if (!references.isEmpty()){
- Reference reference = null;
- for (Reference refe: references) {
- if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
- reference =refe;
- break;
- }
- }
- if (reference ==null){
- reference = ReferenceFactory.newGeneric();
- reference.setTitleCache(strReference, true);
- save(reference, state);
- }
- determinationEvent.addReference(reference);
- }
- }
- save(state.getDerivedUnitBase(), state);
+ makeIndividualsAssociation(state, taxon, determinationEvent);
- if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
- //do not add IndividualsAssociation to non-preferred taxa
- if (logger.isDebugEnabled()){
- logger.debug("isDoCreateIndividualsAssociations");
- }
+ save(state.getDerivedUnitBase(), state);
+ }
+ }
- makeIndividualsAssociation(state, taxon, determinationEvent);
+ /**
+ * create and link each association (specimen, observation..) to the accepted taxon
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param determinationEvent:the determinationevent
+ */
+ protected void makeIndividualsAssociation(STATE state, Taxon taxon, DeterminationEvent determinationEvent) {
+ SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
+ SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
- save(state.getDerivedUnitBase(), state);
- }
- }
-
- /**
- * create and link each association (specimen, observation..) to the accepted taxon
- * @param state : the ABCD import state
- * @param taxon: the current Taxon
- * @param determinationEvent:the determinationevent
- */
- protected void makeIndividualsAssociation(STATE state, Taxon taxon, DeterminationEvent determinationEvent) {
- SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
- SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
-
- if (logger.isDebugEnabled()){
- logger.info("MAKE INDIVIDUALS ASSOCIATION");
- }
+ if (logger.isDebugEnabled()){
+ logger.info("MAKE INDIVIDUALS ASSOCIATION");
+ }
- TaxonDescription taxonDescription = null;
- Set<TaxonDescription> descriptions= taxon.getDescriptions();
- if (state.getIndividualsAssociationDescriptionPerTaxon(taxon.getUuid()) != null){
- taxonDescription = state.getIndividualsAssociationDescriptionPerTaxon(taxon.getUuid());
- }
- if (taxonDescription == null && !descriptions.isEmpty() && state.getConfig().isReuseExistingDescriptiveGroups()){
- for (TaxonDescription desc: descriptions){
- if (desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION)){
- taxonDescription = desc;
- break;
- }
- }
- }
-
- if (taxonDescription == null){
- taxonDescription = TaxonDescription.NewInstance(taxon, false);
- taxonDescription.setTypes(EnumSet.of(DescriptionType.INDIVIDUALS_ASSOCIATION));
- if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
- taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
- }
- state.setIndividualsAssociationDescriptionPerTaxon(taxonDescription);
- taxon.addDescription(taxonDescription);
- }
+ TaxonDescription taxonDescription = null;
+ Set<TaxonDescription> descriptions= taxon.getDescriptions();
+ if (state.getIndividualsAssociationDescriptionPerTaxon(taxon.getUuid()) != null){
+ taxonDescription = state.getIndividualsAssociationDescriptionPerTaxon(taxon.getUuid());
+ }
+ if (taxonDescription == null && !descriptions.isEmpty() && state.getConfig().isReuseExistingDescriptiveGroups()){
+ for (TaxonDescription desc: descriptions){
+ if (desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION)){
+ taxonDescription = desc;
+ break;
+ }
+ }
+ }
+
+ if (taxonDescription == null){
+ taxonDescription = TaxonDescription.NewInstance(taxon, false);
+ taxonDescription.setTypes(EnumSet.of(DescriptionType.INDIVIDUALS_ASSOCIATION));
+ if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
+ taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
+ }
+ state.setIndividualsAssociationDescriptionPerTaxon(taxonDescription);
+ taxon.addDescription(taxonDescription);
+ }
- //PREPARE REFERENCE QUESTIONS
+ //PREPARE REFERENCE QUESTIONS
- Map<String,OriginalSourceBase> sourceMap = new HashMap<>();
+ Map<String,OriginalSourceBase> sourceMap = new HashMap<>();
- List<IdentifiableSource> issTmp = new ArrayList<>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
- List<DescriptionElementSource> issTmp2 = new ArrayList<>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
+ List<IdentifiableSource> issTmp = new ArrayList<>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
+ List<DescriptionElementSource> issTmp2 = new ArrayList<>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
- Set<OriginalSourceBase> osbSet = new HashSet<>();
- if(issTmp2!=null) {
- osbSet.addAll(issTmp2);
- }
- if(issTmp!=null) {
- osbSet.addAll(issTmp);
- }
+ Set<OriginalSourceBase> osbSet = new HashSet<>();
+ if(issTmp2!=null) {
+ osbSet.addAll(issTmp2);
+ }
+ if(issTmp!=null) {
+ osbSet.addAll(issTmp);
+ }
- addToSourceMap(sourceMap, osbSet);
+ addToSourceMap(sourceMap, osbSet);
- if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
- taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
- }
+ if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
+ taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
- state.setIndividualsAssociationDescriptionPerTaxon(taxonDescription);
+ state.setIndividualsAssociationDescriptionPerTaxon(taxonDescription);
- IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
- Feature feature = makeFeature(state.getDerivedUnitBase());
- indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
- indAssociation.setFeature(feature);
+ IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
+ Feature feature = makeFeature(state.getDerivedUnitBase());
+ indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
+ indAssociation.setFeature(feature);
- if(sourceNotLinkedToElement(indAssociation,state.getImportReference(state.getActualAccessPoint()),null)) {
- indAssociation.addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
+ if(sourceNotLinkedToElement(indAssociation,state.getImportReference(state.getActualAccessPoint()),null)) {
+ indAssociation.addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
+ }
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getImportReference(state.getActualAccessPoint()),null)) {
+ state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
+ }
+ for (Reference citation : determinationEvent.getReferences()) {
+ if(sourceNotLinkedToElement(indAssociation,citation,null))
+ {
+ indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
}
if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getImportReference(state.getActualAccessPoint()),null)) {
state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
}
- for (Reference citation : determinationEvent.getReferences()) {
- if(sourceNotLinkedToElement(indAssociation,citation,null))
- {
- indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
- }
- if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getImportReference(state.getActualAccessPoint()),null)) {
- state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getImportReference(state.getActualAccessPoint()), null);
- }
- }
-
-
- taxonDescription.addElement(indAssociation);
-
- save(taxonDescription, state);
- save(taxon, state);
- state.getReport().addDerivate(state.getDerivedUnitBase(), config);
- state.getReport().addIndividualAssociation(taxon, state.getDataHolder().getUnitID(), state.getDerivedUnitBase());
- }
-
- /**
- * @param derivedUnitBase2
- * @param ref2
- * @param object
- * @return
- */
- private boolean sourceNotLinkedToElement(DerivedUnit derivedUnitBase2, Reference b, String d) {
- Set<IdentifiableSource> linkedSources = derivedUnitBase2.getSources();
- for (IdentifiableSource is:linkedSources){
- Reference a = is.getCitation();
- String c = is.getCitationMicroReference();
-
- boolean refMatch=false;
- boolean microMatch=false;
-
- try{
- if (a==null && b==null) {
- refMatch=true;
- }
- if (a!=null && b!=null) {
- if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
- refMatch=true;
- }
- }
- }catch(Exception e){}
+ }
+ taxonDescription.addElement(indAssociation);
- try{
- if (c==null && d==null) {
- microMatch=true;
- }
- if(c!=null && d!=null) {
- if(c.equalsIgnoreCase(d)) {
- microMatch=true;
- }
- }
- }
- catch(Exception e){}
+ save(taxonDescription, state);
+ save(taxon, state);
+ state.getReport().addDerivate(state.getDerivedUnitBase(), config);
+ state.getReport().addIndividualAssociation(taxon, state.getDataHolder().getUnitID(), state.getDerivedUnitBase());
+ }
- if (microMatch && refMatch) {
- return false;
- }
+ private boolean sourceNotLinkedToElement(DerivedUnit derivedUnitBase2, Reference b, String d) {
+ Set<IdentifiableSource> linkedSources = derivedUnitBase2.getSources();
+ for (IdentifiableSource is:linkedSources){
+ Reference a = is.getCitation();
+ String c = is.getCitationMicroReference();
+ boolean refMatch=false;
+ boolean microMatch=false;
- }
- return true;
- }
+ try{
+ if (a==null && b==null) {
+ refMatch=true;
+ }
+ if (a!=null && b!=null) {
+ if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
+ refMatch=true;
+ }
+ }
+ }catch(Exception e){}
- private <T extends OriginalSourceBase> boolean sourceNotLinkedToElement(ISourceable<T> sourcable, Reference reference, String microReference) {
- Set<T> linkedSources = sourcable.getSources();
- for (T is:linkedSources){
- Reference unitReference = is.getCitation();
- String unitMicroReference = is.getCitationMicroReference();
+ try{
+ if (c==null && d==null) {
+ microMatch=true;
+ }
+ if(c!=null && d!=null) {
+ if(c.equalsIgnoreCase(d)) {
+ microMatch=true;
+ }
+ }
+ }
+ catch(Exception e){}
- boolean refMatch=false;
- boolean microMatch=false;
+ if (microMatch && refMatch) {
+ return false;
+ }
+ }
+ return true;
+ }
- try{
- if (unitReference==null && reference==null) {
- refMatch=true;
- }
- if (unitReference!=null && reference!=null) {
- if (unitReference.getTitleCache().equalsIgnoreCase(reference.getTitleCache())) {
- refMatch=true;
- }
- }
- }catch(Exception e){}
+ private <T extends OriginalSourceBase> boolean sourceNotLinkedToElement(
+ ISourceable<T> sourcable, Reference reference, String microReference) {
- try{
- if (unitMicroReference==null && microReference==null) {
- microMatch=true;
- }
- if(unitMicroReference!=null && microReference!=null) {
- if(unitMicroReference.equalsIgnoreCase(microReference)) {
- microMatch=true;
- }
- }
- }
- catch(Exception e){}
+ Set<T> linkedSources = sourcable.getSources();
+ for (T is:linkedSources){
+ Reference unitReference = is.getCitation();
+ String unitMicroReference = is.getCitationMicroReference();
- if (microMatch && refMatch) {
- return false;
- }
- }
- return true;
- }
-
- /**
- * look for the Feature object (FieldObs, Specimen,...)
- * @param unit : a specimen or obersvation base
- * @return the corresponding Feature
- */
- private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
- SpecimenOrObservationType type = unit.getRecordBasis();
-
-
-
- if (type.isFeatureObservation()){
- return Feature.OBSERVATION();
- }else if (type.isFeatureSpecimen()){
- return Feature.SPECIMEN();
- }else if (type == SpecimenOrObservationType.DerivedUnit){
- return Feature.OBSERVATION();
- // return getFeature("Specimen or observation");
- }else{
- String message = "Unhandled record basis '%s' for defining individuals association feature type. Use default.";
- logger.warn(String.format(message, type.getLabel()));
- return Feature.OBSERVATION();
- // return getFeature("Specimen or observation");
+ boolean refMatch=false;
+ boolean microMatch=false;
- }
- }
-
-
- /**
- * @param sourceMap
- * @param osbSet
- */
- protected void addToSourceMap(Map<String, OriginalSourceBase> sourceMap, Set<OriginalSourceBase> osbSet) {
- for( OriginalSourceBase osb:osbSet) {
- if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null && !osb.getCitationMicroReference().isEmpty()) {
- try{
- sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
- }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
- } else if(osb.getCitation()!=null){
- try{
- sourceMap.put(osb.getCitation().getTitleCache(),osb);
- }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
- }
- }
- }
+ try{
+ if (unitReference==null && reference==null) {
+ refMatch=true;
+ }
+ if (unitReference!=null && reference!=null) {
+ if (unitReference.getTitleCache().equalsIgnoreCase(reference.getTitleCache())) {
+ refMatch=true;
+ }
+ }
+ }catch(Exception e){}
+ try{
+ if (unitMicroReference==null && microReference==null) {
+ microMatch=true;
+ }
+ if(unitMicroReference!=null && microReference!=null) {
+ if(unitMicroReference.equalsIgnoreCase(microReference)) {
+ microMatch=true;
+ }
+ }
+ }
+ catch(Exception e){}
+ if (microMatch && refMatch) {
+ return false;
+ }
+ }
+ return true;
+ }
+ /**
+ * look for the Feature object (FieldObs, Specimen,...)
+ * @param unit : a specimen or obersvation base
+ * @return the corresponding Feature
+ */
+ private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
+ SpecimenOrObservationType type = unit.getRecordBasis();
+
+ if (type.isFeatureObservation()){
+ return Feature.OBSERVATION();
+ }else if (type.isFeatureSpecimen()){
+ return Feature.SPECIMEN();
+ }else if (type == SpecimenOrObservationType.DerivedUnit){
+ return Feature.OBSERVATION();
+ // return getFeature("Specimen or observation");
+ }else{
+ String message = "Unhandled record basis '%s' for defining individuals association feature type. Use default.";
+ logger.warn(String.format(message, type.getLabel()));
+ return Feature.OBSERVATION();
+ // return getFeature("Specimen or observation");
+ }
+ }
-}
+ protected void addToSourceMap(Map<String, OriginalSourceBase> sourceMap, Set<OriginalSourceBase> osbSet) {
+ for( OriginalSourceBase osb:osbSet) {
+ if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null && !osb.getCitationMicroReference().isEmpty()) {
+ try{
+ sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
+ }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
+ } else if(osb.getCitation()!=null){
+ try{
+ sourceMap.put(osb.getCitation().getTitleCache(),osb);
+ }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
+ }
+ }
+ }
+}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff