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Revision b3273569

Added by Andreas Müller about 4 years ago

ref #1447 implement PESI commandline merger

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsMergeActivator.java
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package eu.etaxonomy.cdm.app.pesi.merging;
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import java.io.BufferedReader;


  		




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import java.io.File;


  		




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import java.io.FileReader;


  		




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import java.io.IOException;


  		




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import java.util.ArrayList;


  		




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import java.util.HashSet;


  		




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import java.util.Iterator;


  		




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import java.util.List;


  		




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import java.util.Set;


  		




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import java.util.StringTokenizer;


  		




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import java.util.UUID;


  		




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import org.apache.log4j.Logger;


  		




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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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public class FaunaEuErmsMergeActivator {


  		




  
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public class FaunaEuErmsMergeActivator extends PesiMergeBase{


  		




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//	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.cdm_test_patricia();


  		




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	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();


  		




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	static final int faunaEuUuid = 0;


  		




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	static final int ermsUuid = 9;


  		




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	static final int rankFaunaEu = 4;


  		




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	static final int rankErms = 13;


  		




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	Classification faunaEuClassification;


  		




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	Classification ermsClassification;


  		




  
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	private Classification faunaEuClassification;


  		




  
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	private Classification ermsClassification;


  		




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	CdmApplicationController appCtrInit;


  		




  
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	private CdmApplicationController appCtrInit;


  		




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	private static final Logger logger = Logger.getLogger(FaunaEuErmsMergeActivator.class);


  		




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		//set the ranks of Agnatha and Gnathostomata to 50 instead of 45


  		




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


  		




  
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		Pager<TaxonBase> agnatha = sc.appCtrInit.getTaxonService().findTaxaByName(TaxonBase.class, "Agnatha", null, null, null, "*", Rank.INFRAPHYLUM(), 10, 0, null);


  		




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		List<TaxonBase> agnathaList = agnatha.getRecords();


  		




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		taxaToChangeRank.addAll(agnathaList);


  		




  
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		Pager<TaxonBase> gnathostomata = sc.appCtrInit.getTaxonService().findTaxaByName(TaxonBase.class, "Gnathostomata", null, null, null, "*", Rank.INFRAPHYLUM(), 10, 0, null);


  		




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		List<TaxonBase> gnathostomataList = gnathostomata.getRecords();


  		




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		taxaToChangeRank.addAll(gnathostomataList);


  		




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		sc.setSpecificRank(taxaToChangeRank, Rank.SUPERCLASS());


  		




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		//ermsTaxon is accepted, fauna eu taxon is synonym


  		




  
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		//ermsTaxon is accepted, faunaEu taxon is synonym


  		




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		//ermsTaxon is synonym, faunaEu is accepted


  		




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		sc.mergeDiffStatus();


  		




  ......




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	}


  		




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	private static List<List<String>> readCsvFile(String fileName){


  		




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


  		




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		File file = new File(fileName);


  		




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		BufferedReader bufRdr;


  		




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		try {


  		




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			bufRdr = new BufferedReader(new FileReader(file));


  		




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			String line = null;


  		




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			//read each line of text file


  		




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			while((line = bufRdr.readLine()) != null){


  		




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				StringTokenizer st = new StringTokenizer(line,",");


  		




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


  		




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				while (st.hasMoreTokens()){


  		




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					//get next token and store it in the array


  		




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					rowList.add(st.nextToken());


  		




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				}


  		




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			result.add(rowList);


  		




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			}


  		




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			//close the file


  		




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			bufRdr.close();


  		




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		} catch (IOException e) {


  		




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			e.printStackTrace();


  		




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		}


  		




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		return result;


  		




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	}


  		




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	private void mergeAuthors(){


  		




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		List<List<String>> authors = readCsvFile(sFileName + "_authors.csv");


  		




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		//authors: get firstAuthor if isFauEu = 1 otherwise get secondAuthor


  		




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		Iterator<List<String>> authorIterator = authors.iterator();


  		




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		List<String> row;


  		




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		TaxonBase<?> taxonFaunaEu;


  		




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		TaxonBase<?> taxonErms;


  		




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		List<TaxonBase<?>> taxaToSave = new ArrayList<>();


  		




  
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		List<TaxonBase<?>> taxaToSave = new ArrayList<>();  //TODO: needed?


  		




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		while (authorIterator.hasNext()){


  		




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			row = authorIterator.next();


  		




  
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		    List<String> row = authorIterator.next();


  		




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			UUID uuidFaunaEu = UUID.fromString(row.get(faunaEuUuid));


  		




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			UUID uuidErms = UUID.fromString(row.get(ermsUuid));


  		




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			taxonFaunaEu = appCtrInit.getTaxonService().find(uuidFaunaEu);


  		




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			taxonErms = appCtrInit.getTaxonService().find(uuidErms);


  		




  
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			TaxonBase<?> taxonFaunaEu = appCtrInit.getTaxonService().find(uuidFaunaEu);


  		




  
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			TaxonBase<?> taxonErms = appCtrInit.getTaxonService().find(uuidErms);


  		




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// which information should be used can be found in last row -> needs to be done manually


  		




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			if (Integer.parseInt(row.get(18)) == 1){


  		




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				//isFaunaEu = 1 -> copy the author of Fauna Europaea to Erms


  		




  ......




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		List<List<String>> diffStatus = readCsvFile(sFileName + "_status.csv");


  		




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		//find all taxa accepted in erms, but synonyms in FauEu  and the same rank


  		




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


  		




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


  		




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		for (List<String> rowList: diffStatus){


  		




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			if ((rowList.get(5).equals("synonym")) && (rowList.get(rankFaunaEu).equals(rowList.get(rankErms)))){


  		




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				//both conditions are true


  		












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