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Revision e5920e99

Added by Katja Luther over 9 years ago

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportConfigurator.java
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				, IndexFungorumHigherClassificationImport.class
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				, IndexFungorumGeneraImport.class
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				, IndexFungorumSpeciesImport.class
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				, IndexFungorumSubSpeciesImport.class
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				, IndexFungorumDistributionImport.class
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		};
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	}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportState.java
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package eu.etaxonomy.cdm.io.pesi.indexFungorum;


  		




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import java.util.ArrayList;


  		




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import java.util.HashMap;


  		




  
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import java.util.HashSet;


  		




  
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import java.util.List;


  		




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import java.util.Map;


  		




  
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import java.util.Set;


  		




  
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import java.util.UUID;


  		




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import org.apache.log4j.Logger;


  		




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  ......




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	private Map<Integer, Map<Integer,Rank>> rankMap;


  		




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	private Map<String, TaxonBase> speciesMap;


  		




  
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	private List<UUID> infraspecificTaxaUUIDs = new ArrayList<UUID>();


  		




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    public IndexFungorumImportState(IndexFungorumImportConfigurator config) {


  		




  
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    public List<UUID> getInfraspecificTaxaUUIDs() {


  		




  
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		return infraspecificTaxaUUIDs;


  		




  
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	}


  		




  
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	public void setInfraspecificTaxaUUIDs(List<UUID> infraspecificTaxaUUIDs) {


  		




  
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		this.infraspecificTaxaUUIDs = infraspecificTaxaUUIDs;


  		




  
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	}


  		




  
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	public IndexFungorumImportState(IndexFungorumImportConfigurator config) {


  		




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		super(config);


  		




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	}


  		




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      cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSpeciesImport.java
    
  





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import eu.etaxonomy.cdm.model.taxon.Classification;


  		




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import eu.etaxonomy.cdm.model.taxon.Taxon;


  		




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import eu.etaxonomy.cdm.model.taxon.TaxonBase;


  		




  
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;


  		




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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;


  		




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	private static final String pluralString = "species";


  		




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	private static final String dbTableName = "[tblPESIfungi-IFdata]";


  		




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	private final Set<UUID> infraspecificTaxaUUIDs = new HashSet<UUID>();


  		




  
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	public IndexFungorumSpeciesImport(){


  		




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		super(pluralString, dbTableName, null);


  		




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	@Override


  		




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    protected void doInvoke(IndexFungorumImportState state){


  		




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        System.out.println("start make " + getPluralString() + " ...");


  		




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        IndexFungorumImportConfigurator config = state.getConfig();


  		




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        Source source = config.getSource();


  		




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        super.doInvoke(state);


  		




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        Classification classification = getClassification(state);


  		




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        List<TaxonBase> infraspecificTaxa = new ArrayList<TaxonBase>();


  		




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        for (UUID uuid: infraspecificTaxaUUIDs){


  		




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            infraspecificTaxa.add(getTaxonService().load(uuid));


  		




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        }


  		




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        System.out.println("create infraspecific - specific relationship: " + infraspecificTaxa.size() + " taxa");


  		




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        for (TaxonBase infraspecificTaxon: infraspecificTaxa){


  		




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            HibernateProxyHelper.deproxy(infraspecificTaxon);


  		




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            TaxonNameBase name = infraspecificTaxon.getName();


  		




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            UUID uuid = getNameService().saveOrUpdate(name);


  		




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            String parentNameString = getParentNameInfraSpecific(name);


  		




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            System.out.println("Parent name string: " + parentNameString);


  		




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            MatchingTaxonConfigurator matchingConfig = new MatchingTaxonConfigurator();


  		




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            matchingConfig.setTaxonNameTitle(parentNameString);


  		




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            List<String> propertyPaths = new ArrayList<String>();


  		




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            propertyPaths.add("taxonNodes.*");


  		




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            propertyPaths.add("taxonNodes.classification");


  		




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            propertyPaths.add("taxonNodes.childNodes.*");


  		




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            propertyPaths.add("taxonNodes.childNodes.taxon.*");


  		




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            propertyPaths.add("taxonNodes.parent.*");


  		




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            propertyPaths.add("taxonNodes.parent.taxon.*");


  		




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            matchingConfig.setPropertyPath(propertyPaths);


  		




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            List<TaxonBase> potentialParents = getTaxonService().findTaxaByName(matchingConfig);


  		




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                    //Taxon.class, parentNameString + "sec. ", MatchMode.BEGINNING, , pageSize, pageNumber, orderHints, propertyPaths)


  		




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                    //.searchNames(String uninomial,String infraGenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,


  		




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            if (potentialParents.size()>1){


  		




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                for (TaxonBase potentialParent:potentialParents){


  		




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                    if (potentialParent.getTitleCache().equals(parentNameString + " sec*")){


  		




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                        classification.addParentChild((Taxon)potentialParent, (Taxon)infraspecificTaxon, null, null);


  		




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                    }


  		




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                }


  		




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            }else if (!potentialParents.isEmpty()){


  		




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                Taxon parent = HibernateProxyHelper.deproxy(potentialParents.get(0), Taxon.class);


  		




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                Taxon child = (Taxon)getTaxonService().load(infraspecificTaxon.getUuid(), propertyPaths);


  		




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                classification.addParentChild(parent, child, null, null);


  		




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            } else{


  		




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                System.out.println("No parent for: " + name.getTitleCache());


  		




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            }


  		




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            getTaxonService().saveOrUpdate(infraspecificTaxon);


  		




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        }


  		




  
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	}


  		




  ......




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				//save


  		




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				UUID uuidTaxon = getTaxonService().saveOrUpdate(taxon);


  		




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				getNameService().saveOrUpdate(name);


  		




  
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				//getNameService().saveOrUpdate(name);


  		




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				if (name.isInfraSpecific()){


  		




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                    infraspecificTaxaUUIDs.add(uuidTaxon);


  		




  
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                    state.getInfraspecificTaxaUUIDs().add(uuidTaxon);


  		




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                }


  		




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			}


  		




  ......




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	}


  		




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	/**


  		




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     * @param taxon


  		




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     * @return


  		




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     */


  		




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    private String getParentNameInfraSpecific(TaxonNameBase taxonName){


  		




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       NonViralName<NonViralName> name =  HibernateProxyHelper.deproxy(taxonName, NonViralName.class);


  		




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       String parentName = name.getGenusOrUninomial() + " " + name.getSpecificEpithet();


  		




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       return parentName;


  		




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    }


  		




  
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