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/**
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*
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*/
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package eu.etaxonomy.taxeditor.parser;
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import java.util.ArrayList;
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import java.util.List;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.strategy.match.MatchException;
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import eu.etaxonomy.cdm.strategy.match.MatchStrategyConfigurator.MatchStrategy;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.taxeditor.model.MessagingUtils;
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import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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/**
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* <p>ParseHandler class.</p>
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*
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* @author n.hoffmann
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*/
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public class ParseHandler{
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private TaxonName taxonName;
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private class MatchMatrix {
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List<TaxonName> duplicateNames = new ArrayList<>();
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List<INomenclaturalReference> duplicateReferences = new ArrayList<>();
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List<INomenclaturalReference> duplicateInReferences = new ArrayList<>();
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List<TeamOrPersonBase> duplicateCombinationAuthorships = new ArrayList<>();
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List<TeamOrPersonBase> duplicateExCombinationAuthorships = new ArrayList<>();
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List<TeamOrPersonBase> duplicateBasionymAuthorships = new ArrayList<>();
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List<TeamOrPersonBase> duplicateExBasionymAuthorships = new ArrayList<>();
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}
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private static NonViralNameParserImpl nonViralNameParser = NonViralNameParserImpl.NewInstance();
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/**
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* The name that should get parsed
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*/
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private INonViralName name;
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private boolean doResolveInReferences;
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/**
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* Creates a new instance
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*
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* @param textWidget
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* @param name
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*/
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private ParseHandler(TaxonName name){
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if(name == null){
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this.name = nonViralNameParser.getNonViralNameInstance("", PreferencesUtil.getPreferredNomenclaturalCode());
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}else{
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this.name = (INonViralName) HibernateProxyHelper.deproxy(name);
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}
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}
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/**
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* Factory method to create a new instance of the this class
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*
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* @param textWidget The text widget where the NonViralName may be entered into
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* @param name An initial NonViralName or null when creating a new name
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* @return An instance of this class
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*/
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public static ParseHandler NewInstance(TaxonName name){
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return new ParseHandler(name);
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}
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/**
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* Parses a given string and returns a <code>TaxonNameBase</code> instance with the
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* results of the parsing.
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*
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* This method should be used to quickly create a new name from a string.
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* Wherever the string will be parsed again in subsequent editing, an instance
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* of <code>ParseHandler</code> should be attached to the text widget.
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*
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* @param unparsedNameString a {@link java.lang.String} object.
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* @return a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase} object.
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*/
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public static INonViralName parseReferencedName(String unparsedNameString, Rank rank){
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INonViralName name = nonViralNameParser.parseReferencedName(unparsedNameString,
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PreferencesUtil.getPreferredNomenclaturalCode(), rank);
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// if (name.hasProblem()) {
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// name.setFullTitleCache(unparsedNameString);
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// }
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return name;
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}
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public static TaxonName parseName(String unparsedNameString, Rank rank){
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INonViralName name = nonViralNameParser.parseFullName(unparsedNameString,
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PreferencesUtil.getPreferredNomenclaturalCode(), rank);
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return (TaxonName)name;
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}
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/**
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* Creates an empty <code>TaxonNameBase</code> instance with the nomenclatural code
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* currently set in preferences.
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*
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* @return a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase} object.
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*/
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public static TaxonName createEmptyName(){
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return (TaxonName)nonViralNameParser.getNonViralNameInstance("", PreferencesUtil.getPreferredNomenclaturalCode());
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}
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/**
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* Parses the string that was entered into the text widget and returns a
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* NonViralName object that resulted from the parsing process.
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*
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* @return The parsed NonViralName object
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*/
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public INonViralName parse(String unparsedNameString){
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// String unparsedNameString = "";
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// try {
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// Method getText;
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// getText = textWidget.getClass().getDeclaredMethod("getText", null);
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// unparsedNameString = (String) getText.invoke(textWidget, null);
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// } catch (Exception e) {
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// // we should never get here
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// StoreUtil.error(this.getClass(), "Error trying to invoke getText method", e);
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// }
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nonViralNameParser.parseReferencedName(name, unparsedNameString,
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name.getRank(), true);
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// if (name.hasProblem()) {
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// name.setFullTitleCache(unparsedNameString);
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// }
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return name;
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}
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/**
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* Parses the string that was entered into the text widget and returns a
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* NonViralName object that resulted from the parsing process.
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*
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* The atomized fields (scientific name, author and reference) will be matched
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* against the database to find possible duplicates. If duplicates were found
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* the respective parts of the NonViralName will be replaced with the found
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* objects.
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*
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* @return The parsed NonViralName object
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*/
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public INonViralName parseAndResolveDuplicates(String unparsedNameString){
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INonViralName parsedName = parse(unparsedNameString);
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MatchMatrix matchMatrix = findMatches(parsedName);
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resolveDuplicates(parsedName, matchMatrix);
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return parsedName;
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}
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/**
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* @param name The name to resolve duplicates for.
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*/
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private void resolveDuplicates(INonViralName name, MatchMatrix matchMatrix) {
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resolveDuplicateNames(name, matchMatrix);
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resolveAllDuplicateAuthors(name, matchMatrix);
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resolveDuplicateReferences(name, matchMatrix);
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if(matchMatrix.duplicateInReferences != null) {
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resolveDuplicateInReferences(name, matchMatrix);
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}
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}
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/**
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* @param name The name to resolve duplicates for.
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*/
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private void resolveDuplicateNames(INonViralName name, MatchMatrix matchMatrix) {
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if (matchMatrix.duplicateNames.size() == 1){
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name = matchMatrix.duplicateNames.iterator().next();
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}else if(matchMatrix.duplicateNames.size() > 1){
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// FIXME TODO resolve multiple duplications. Use first match for a start
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name = matchMatrix.duplicateNames.iterator().next();
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}
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}
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/**
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* @param name The name to resolve duplicates for.
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*/
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private void resolveDuplicateReferences(INonViralName name, MatchMatrix matchMatrix) {
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if(matchMatrix.duplicateReferences.size() == 1){
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// exactly one match. We assume that the user wants this reference
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INomenclaturalReference duplicate = matchMatrix.duplicateReferences.iterator().next();
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name.setNomenclaturalReference(duplicate);
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}else if(matchMatrix.duplicateReferences.size() > 1){
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// FIXME TODO resolve multiple duplications. Use first match for a start
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INomenclaturalReference duplicate = matchMatrix.duplicateReferences.iterator().next();
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name.setNomenclaturalReference(duplicate);
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}
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}
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/**
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* @param name The name to resolve duplicates for.
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*/
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private void resolveDuplicateInReferences(INonViralName name, MatchMatrix matchMatrix) {
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Reference reference = (Reference) HibernateProxyHelper.deproxy(name.getNomenclaturalReference());
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if(matchMatrix.duplicateInReferences.size() > 0){
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Reference inReference = (Reference) matchMatrix.duplicateInReferences.iterator().next();
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reference.setInReference(inReference);
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MessagingUtils.warn(this.getClass(), reference.generateTitle());
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// FIXME TODO resolve multiple duplications. We use first match for a start
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MessagingUtils.warn(this.getClass(), reference.getTitleCache());
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}
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}
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/**
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* @param name The name to resolve duplicates for.
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*/
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private void resolveAllDuplicateAuthors(INonViralName name, MatchMatrix matchMatrix) {
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if(matchMatrix.duplicateCombinationAuthorships.size() > 0){
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name.setCombinationAuthorship(matchMatrix.duplicateCombinationAuthorships.iterator().next());
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Reference reference = (Reference) name.getNomenclaturalReference();
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if(reference != null){
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reference.setAuthorship(matchMatrix.duplicateCombinationAuthorships.iterator().next());
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}
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// FIXME TODO resolve multiple duplications. We use first match for a start.
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}
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if(matchMatrix.duplicateExCombinationAuthorships.size() > 0){
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name.setExCombinationAuthorship(matchMatrix.duplicateExCombinationAuthorships.iterator().next());
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// FIXME TODO resolve multiple duplications. We use first match for a start.
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}
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if(matchMatrix.duplicateBasionymAuthorships.size() > 0){
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name.setBasionymAuthorship(matchMatrix.duplicateBasionymAuthorships.iterator().next());
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// FIXME TODO resolve multiple duplications. We use first match for a start.
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}
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if(matchMatrix.duplicateExBasionymAuthorships.size() > 0){
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name.setExBasionymAuthorship(matchMatrix.duplicateExBasionymAuthorships.iterator().next());
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// FIXME TODO resolve multiple duplications. We use first match for a start.
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}
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}
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/**
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* Splits a NonViralName into its parts and calls methods to find matches for these
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* parts in the database.
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*
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* @param name The NonViralName to find matches for.
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*/
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private MatchMatrix findMatches(INonViralName name){
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MatchMatrix matchMatrix = new MatchMatrix();
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matchMatrix.duplicateNames = findMatchingLatinNames(name);
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matchMatrix.duplicateCombinationAuthorships = findMatchingAuthors(name.getCombinationAuthorship());
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matchMatrix.duplicateExCombinationAuthorships = findMatchingAuthors(name.getExCombinationAuthorship());
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matchMatrix.duplicateBasionymAuthorships = findMatchingAuthors(name.getBasionymAuthorship());
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matchMatrix.duplicateExBasionymAuthorships = findMatchingAuthors(name.getExBasionymAuthorship());
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INomenclaturalReference nomenclaturalReference = name.getNomenclaturalReference();
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// check if the reference has an inreference and also check if the inReference already exists
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if(nomenclaturalReference != null){
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Reference inReference = ((Reference)nomenclaturalReference).getInReference();
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if(inReference != null){
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doResolveInReferences = true;
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matchMatrix.duplicateInReferences = findMatchingNomenclaturalReference(inReference);
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}
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}
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matchMatrix.duplicateReferences = findMatchingNomenclaturalReference(nomenclaturalReference);
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return matchMatrix;
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}
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/**
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* @param nomenclaturalReference The NomenclaturalReference to find matches for.
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* @return A <code>List</code> of possibly matching NomenclaturalReference's.
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*/
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private List<INomenclaturalReference> findMatchingNomenclaturalReference(INomenclaturalReference nomenclaturalReference) {
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if(nomenclaturalReference == null) {
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return new ArrayList<INomenclaturalReference>();
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}
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try{
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return CdmStore.getCommonService().findMatching(nomenclaturalReference, MatchStrategy.Reference);
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}catch (MatchException e) {
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MessagingUtils.error(this.getClass(), "Error finding matching references", e);
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}
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return null;
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}
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/**
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* @param authorTeam The TeamOrPersonBase to find matches for.
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* @return A <code>List</code> of possibly matching TeamOrPersonBase's.
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*/
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private List<TeamOrPersonBase> findMatchingAuthors(TeamOrPersonBase authorTeam) {
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if(authorTeam == null){
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return new ArrayList<TeamOrPersonBase>();
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}
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try{
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return CdmStore.getCommonService().findMatching(authorTeam, MatchStrategy.TeamOrPerson);
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}catch (MatchException e) {
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MessagingUtils.error(this.getClass(), "Error finding matching authors", e);
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}
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return null;
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}
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/**
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* @param taxonName The TaxonNameBase to find matches for.
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* @return A <code>List</code> of possibly matching TaxonNameBase's.
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*/
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private List<TaxonName> findMatchingLatinNames(ITaxonNameBase taxonName) {
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try {
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return CdmStore.getCommonService().findMatching(TaxonName.castAndDeproxy(taxonName), MatchStrategy.NonViralName);
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} catch (MatchException e) {
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MessagingUtils.error(this.getClass(), "Error finding matching names", e);
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}
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return null;
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}
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}
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