Revision 5c01c676
getUuidAndTitleCache of classificationservice does not need the excluded taxa
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206ImportReport.java | ||
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// $Id$ |
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/** |
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* Copyright (C) 2015 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.io.specimen.abcd206.in; |
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import java.io.File; |
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import java.io.FileNotFoundException; |
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import java.io.PrintStream; |
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import java.io.PrintWriter; |
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import java.io.StringWriter; |
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import java.net.URI; |
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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.Map.Entry; |
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import java.util.Set; |
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import org.apache.log4j.Logger; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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/** |
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* Gathers information about the ABCD import and presents them in a suitable way. |
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* @author pplitzner |
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* @date Jan 23, 2015 |
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* |
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*/ |
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public class Abcd206ImportReport { |
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static private final Logger logger = Logger.getLogger(Abcd206ImportReport.class); |
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private final List<Taxon> createdTaxa = new ArrayList<Taxon>(); |
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private final Map<Taxon, List<UnitIdSpecimen>> taxonToAssociatedSpecimens = new HashMap<Taxon, List<UnitIdSpecimen>>(); |
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private final Map<UnitIdSpecimen, List<UnitIdSpecimen>> derivateMap = new HashMap<UnitIdSpecimen, List<UnitIdSpecimen>>(); |
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private final List<UnitIdSpecimen> alreadyExistingSpecimens = new ArrayList<UnitIdSpecimen>(); |
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private final List<TaxonNameBase<?, ?>> createdNames = new ArrayList<TaxonNameBase<?,?>>(); |
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private final List<TaxonNode> createdTaxonNodes = new ArrayList<TaxonNode>(); |
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private final List<String> infoMessages = new ArrayList<String>(); |
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public void addTaxon(Taxon taxon){ |
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createdTaxa.add(taxon); |
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} |
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public void addName(TaxonNameBase<?, ?> taxonName){ |
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createdNames.add(taxonName); |
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} |
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public void addTaxonNode(TaxonNode taxonNode){ |
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createdTaxonNodes.add(taxonNode); |
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} |
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public void addDerivate(DerivedUnit parent, Abcd206ImportConfigurator config){ |
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addDerivate(parent, null, config); |
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} |
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public void addDerivate(DerivedUnit parent, DerivedUnit child, Abcd206ImportConfigurator config){ |
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UnitIdSpecimen parentUnitIdSpecimen = new UnitIdSpecimen(AbcdImportUtility.getUnitID(parent, config), parent); |
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List<UnitIdSpecimen> children = derivateMap.get(parentUnitIdSpecimen); |
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if(children==null){ |
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children = new ArrayList<UnitIdSpecimen>(); |
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} |
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if(child!=null){ |
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children.add(new UnitIdSpecimen(AbcdImportUtility.getUnitID(child, config), child)); |
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} |
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derivateMap.put(parentUnitIdSpecimen, children); |
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} |
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public void addIndividualAssociation(Taxon taxon, String derivedUnitId, DerivedUnit derivedUnitBase) { |
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UnitIdSpecimen derivedUnitIdSpecimen = new UnitIdSpecimen(derivedUnitId, derivedUnitBase); |
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List<UnitIdSpecimen> associatedSpecimens = taxonToAssociatedSpecimens.get(taxon); |
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if(associatedSpecimens==null){ |
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associatedSpecimens = new ArrayList<UnitIdSpecimen>(); |
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} |
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associatedSpecimens.add(derivedUnitIdSpecimen); |
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taxonToAssociatedSpecimens.put(taxon, associatedSpecimens); |
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} |
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public void addAlreadyExistingSpecimen(String unitId, DerivedUnit derivedUnit){ |
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alreadyExistingSpecimens.add(new UnitIdSpecimen(unitId, derivedUnit)); |
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} |
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public void addException(String message, Exception e) { |
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StringWriter errors = new StringWriter(); |
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e.printStackTrace(new PrintWriter(errors)); |
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infoMessages.add(message+"\n"+e.getMessage()+"\n"+errors.toString()); |
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} |
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public void addInfoMessage(String message) { |
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infoMessages.add(message); |
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} |
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public void printReport(URI reportUri) { |
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PrintStream out; |
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if(reportUri != null){ |
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try { |
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out = new PrintStream(new File(reportUri)); |
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} catch (FileNotFoundException e) { |
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logger.warn("Report file could not be found."); |
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out = System.out; |
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} |
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} |
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else{ |
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out = System.out; |
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} |
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printReport(out); |
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} |
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public void printReport(PrintStream out) { |
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out.println("++++++++Import Report+++++++++"); |
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//all specimens |
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Set<UnitIdSpecimen> allSpecimens = new HashSet<UnitIdSpecimen>(); |
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for (Entry<UnitIdSpecimen, List<UnitIdSpecimen>> entry : derivateMap.entrySet()) { |
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UnitIdSpecimen parentSpecimen = entry.getKey(); |
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allSpecimens.add(parentSpecimen); |
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for (UnitIdSpecimen childSpecimen : entry.getValue()) { |
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allSpecimens.add(childSpecimen); |
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} |
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} |
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out.println("Specimens created: "+allSpecimens.size()); |
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Map<SpecimenOrObservationType, Integer> specimenTypeToCount = new HashMap<SpecimenOrObservationType, Integer>(); |
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for (UnitIdSpecimen unitIdSpecimen : allSpecimens) { |
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incrementSpecimenTypeCount(specimenTypeToCount, unitIdSpecimen); |
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} |
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for(Entry<SpecimenOrObservationType, Integer> entry:specimenTypeToCount.entrySet()){ |
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SpecimenOrObservationType type = entry.getKey(); |
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out.println(type+": "+entry.getValue()); |
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} |
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out.println("\n"); |
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//taxon name |
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out.println("---Created Taxon Names ("+createdNames.size()+")---"); |
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for (TaxonNameBase<?, ?> taxonName : createdNames) { |
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out.println(taxonName.getTitleCache()); |
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} |
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out.println("\n"); |
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//taxa |
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out.println("---Created Taxa ("+createdTaxa.size()+")---"); |
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for (Taxon taxon : createdTaxa) { |
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out.println(taxon.getTitleCache()); |
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} |
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out.println("\n"); |
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//taxon nodes |
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out.println("---Created Taxon Nodes ("+createdTaxonNodes.size()+")---"); |
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for (TaxonNode taxonNode : createdTaxonNodes) { |
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String nodeString = taxonNode.toString(); |
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if(taxonNode.getTaxon()!=null){ |
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nodeString += " ("+taxonNode.getTaxon().getTitleCache()+")"; |
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} |
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if(taxonNode.getParent()!=null){ |
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nodeString += " with parent "+taxonNode.getParent(); |
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if(taxonNode.getParent().getTaxon()!=null){ |
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nodeString += " ("+taxonNode.getParent().getTaxon().getTitleCache()+")"; |
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} |
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} |
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out.println(nodeString); |
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} |
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out.println("\n"); |
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//not imported |
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out.println("---Already existing specimen (not imported)---"); |
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for(UnitIdSpecimen specimen:alreadyExistingSpecimens){ |
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out.println(formatSpecimen(specimen)); |
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} |
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out.println("\n"); |
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//taxa with associated specimens |
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out.println("---Taxa with associated specimens---"); |
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for(Entry<Taxon, List<UnitIdSpecimen>> entry:taxonToAssociatedSpecimens.entrySet()){ |
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Taxon taxon = entry.getKey(); |
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List<UnitIdSpecimen> specimens = entry.getValue(); |
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out.println(taxon.getTitleCache() + " ("+specimens.size()+")"); |
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for (UnitIdSpecimen derivedUnit : specimens) { |
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out.println("\t- "+formatSpecimen(derivedUnit)); |
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//check for derivatives |
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List<UnitIdSpecimen> list = derivateMap.get(derivedUnit); |
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for (UnitIdSpecimen derivate : list) { |
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out.println("\t\t- "+formatSpecimen(derivate)); |
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} |
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} |
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} |
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out.println("\n"); |
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out.println("\n"); |
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//info messages |
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out.println("---Info messages---"); |
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for(String message:infoMessages){ |
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out.println(message); |
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out.println("---"); |
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} |
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if(out!=System.out){ |
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out.close(); |
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} |
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} |
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private void incrementSpecimenTypeCount(Map<SpecimenOrObservationType, Integer> specimenTypeToCount, |
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UnitIdSpecimen specimen) { |
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SpecimenOrObservationType specimenType = specimen.getSpecimen().getRecordBasis(); |
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Integer count = specimenTypeToCount.get(specimenType); |
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if(count==null){ |
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count = 1; |
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} |
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else{ |
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count++; |
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} |
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specimenTypeToCount.put(specimenType, count); |
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} |
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private String formatSpecimen(UnitIdSpecimen specimen){ |
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return "("+specimen.getUnitId()+") ["+specimen.getSpecimen().getRecordBasis()+"] "+specimen.getSpecimen().getTitleCache(); |
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} |
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private class UnitIdSpecimen{ |
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private final String unitId; |
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private final SpecimenOrObservationBase<?> specimen; |
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public UnitIdSpecimen(String unitId, SpecimenOrObservationBase<?> specimen) { |
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super(); |
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this.unitId = unitId; |
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this.specimen = specimen; |
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} |
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public String getUnitId() { |
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return unitId; |
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} |
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public SpecimenOrObservationBase<?> getSpecimen() { |
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return specimen; |
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} |
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@Override |
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public int hashCode() { |
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final int prime = 31; |
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int result = 1; |
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result = prime * result + ((specimen == null) ? 0 : specimen.hashCode()); |
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result = prime * result + ((unitId == null) ? 0 : unitId.hashCode()); |
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return result; |
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} |
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@Override |
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public boolean equals(Object obj) { |
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if (this == obj) { |
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return true; |
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} |
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if (obj == null) { |
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return false; |
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} |
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if (getClass() != obj.getClass()) { |
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return false; |
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} |
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UnitIdSpecimen other = (UnitIdSpecimen) obj; |
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if (specimen == null) { |
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if (other.specimen != null) { |
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return false; |
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} |
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} else if (!specimen.equals(other.specimen)) { |
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return false; |
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} |
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if (unitId == null) { |
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if (other.unitId != null) { |
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return false; |
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} |
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} else if (!unitId.equals(other.unitId)) { |
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return false; |
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} |
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return true; |
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} |
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} |
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} |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/AbcdImportUtility.java | ||
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// $Id$ |
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/** |
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* Copyright (C) 2015 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.io.specimen.abcd206.in; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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/** |
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* @author pplitzner |
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* @date 16.06.2015 |
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* |
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*/ |
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public class AbcdImportUtility { |
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public static String getUnitID(DerivedUnit derivedUnit, Abcd206ImportConfigurator config){ |
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if(config.isMapUnitIdToAccessionNumber()){ |
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return derivedUnit.getAccessionNumber(); |
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} |
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if(config.isMapUnitIdToBarcode()){ |
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return derivedUnit.getBarcode(); |
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} |
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return derivedUnit.getCatalogNumber(); |
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} |
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public static void setUnitID(DerivedUnit derivedUnit, String unitId, Abcd206ImportConfigurator config){ |
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if(config.isMapUnitIdToCatalogNumber() |
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|| !(config.isMapUnitIdToAccessionNumber() || config.isMapUnitIdToBarcode() || config.isMapUnitIdToCatalogNumber())){ |
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// set catalog number (default if nothing is set) |
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derivedUnit.setCatalogNumber(unitId); |
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} |
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if(config.isMapUnitIdToAccessionNumber()){ |
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derivedUnit.setAccessionNumber(unitId); |
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} |
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if(config.isMapUnitIdToBarcode()){ |
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derivedUnit.setBarcode(unitId); |
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} |
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} |
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} |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportReport.java | ||
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// $Id$ |
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/** |
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* Copyright (C) 2015 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.io.specimen.abcd206.in; |
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import java.io.File; |
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import java.io.FileNotFoundException; |
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import java.io.PrintStream; |
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import java.io.PrintWriter; |
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import java.io.StringWriter; |
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import java.net.URI; |
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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.Map.Entry; |
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import java.util.Set; |
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|
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import org.apache.log4j.Logger; |
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|
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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|
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/** |
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* Gathers information about the ABCD import and presents them in a suitable way. |
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* @author pplitzner |
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* @date Jan 23, 2015 |
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* |
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*/ |
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public class Abcd206ImportReport { |
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static private final Logger logger = Logger.getLogger(Abcd206ImportReport.class); |
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private final List<Taxon> createdTaxa = new ArrayList<Taxon>(); |
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private final Map<Taxon, List<UnitIdSpecimen>> taxonToAssociatedSpecimens = new HashMap<Taxon, List<UnitIdSpecimen>>(); |
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private final Map<UnitIdSpecimen, List<UnitIdSpecimen>> derivateMap = new HashMap<UnitIdSpecimen, List<UnitIdSpecimen>>(); |
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private final List<UnitIdSpecimen> alreadyExistingSpecimens = new ArrayList<UnitIdSpecimen>(); |
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private final List<TaxonNameBase<?, ?>> createdNames = new ArrayList<TaxonNameBase<?,?>>(); |
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private final List<TaxonNode> createdTaxonNodes = new ArrayList<TaxonNode>(); |
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private final List<String> infoMessages = new ArrayList<String>(); |
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public void addTaxon(Taxon taxon){ |
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createdTaxa.add(taxon); |
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} |
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public void addName(TaxonNameBase<?, ?> taxonName){ |
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createdNames.add(taxonName); |
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} |
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public void addTaxonNode(TaxonNode taxonNode){ |
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createdTaxonNodes.add(taxonNode); |
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} |
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|
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public void addDerivate(DerivedUnit parent, Abcd206ImportConfigurator config){ |
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addDerivate(parent, null, config); |
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} |
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public void addDerivate(DerivedUnit parent, DerivedUnit child, Abcd206ImportConfigurator config){ |
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UnitIdSpecimen parentUnitIdSpecimen = new UnitIdSpecimen(AbcdImportUtility.getUnitID(parent, config), parent); |
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List<UnitIdSpecimen> children = derivateMap.get(parentUnitIdSpecimen); |
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if(children==null){ |
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children = new ArrayList<UnitIdSpecimen>(); |
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} |
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if(child!=null){ |
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children.add(new UnitIdSpecimen(AbcdImportUtility.getUnitID(child, config), child)); |
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} |
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derivateMap.put(parentUnitIdSpecimen, children); |
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} |
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|
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public void addIndividualAssociation(Taxon taxon, String derivedUnitId, DerivedUnit derivedUnitBase) { |
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UnitIdSpecimen derivedUnitIdSpecimen = new UnitIdSpecimen(derivedUnitId, derivedUnitBase); |
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List<UnitIdSpecimen> associatedSpecimens = taxonToAssociatedSpecimens.get(taxon); |
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if(associatedSpecimens==null){ |
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associatedSpecimens = new ArrayList<UnitIdSpecimen>(); |
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} |
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associatedSpecimens.add(derivedUnitIdSpecimen); |
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taxonToAssociatedSpecimens.put(taxon, associatedSpecimens); |
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} |
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|
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public void addAlreadyExistingSpecimen(String unitId, DerivedUnit derivedUnit){ |
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alreadyExistingSpecimens.add(new UnitIdSpecimen(unitId, derivedUnit)); |
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} |
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public void addException(String message, Exception e) { |
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StringWriter errors = new StringWriter(); |
|
98 |
e.printStackTrace(new PrintWriter(errors)); |
|
99 |
infoMessages.add(message+"\n"+e.getMessage()+"\n"+errors.toString()); |
|
100 |
} |
|
101 |
|
|
102 |
public void addInfoMessage(String message) { |
|
103 |
infoMessages.add(message); |
|
104 |
} |
|
105 |
|
|
106 |
public void printReport(URI reportUri) { |
|
107 |
PrintStream out; |
|
108 |
if(reportUri != null){ |
|
109 |
try { |
|
110 |
out = new PrintStream(new File(reportUri)); |
|
111 |
} catch (FileNotFoundException e) { |
|
112 |
logger.warn("Report file could not be found."); |
|
113 |
out = System.out; |
|
114 |
} |
|
115 |
} |
|
116 |
else{ |
|
117 |
out = System.out; |
|
118 |
} |
|
119 |
printReport(out); |
|
120 |
} |
|
121 |
|
|
122 |
|
|
123 |
public void printReport(PrintStream out) { |
|
124 |
|
|
125 |
out.println("++++++++Import Report+++++++++"); |
|
126 |
//all specimens |
|
127 |
Set<UnitIdSpecimen> allSpecimens = new HashSet<UnitIdSpecimen>(); |
|
128 |
for (Entry<UnitIdSpecimen, List<UnitIdSpecimen>> entry : derivateMap.entrySet()) { |
|
129 |
UnitIdSpecimen parentSpecimen = entry.getKey(); |
|
130 |
allSpecimens.add(parentSpecimen); |
|
131 |
for (UnitIdSpecimen childSpecimen : entry.getValue()) { |
|
132 |
allSpecimens.add(childSpecimen); |
|
133 |
} |
|
134 |
} |
|
135 |
out.println("Specimens created: "+allSpecimens.size()); |
|
136 |
Map<SpecimenOrObservationType, Integer> specimenTypeToCount = new HashMap<SpecimenOrObservationType, Integer>(); |
|
137 |
for (UnitIdSpecimen unitIdSpecimen : allSpecimens) { |
|
138 |
incrementSpecimenTypeCount(specimenTypeToCount, unitIdSpecimen); |
|
139 |
} |
|
140 |
for(Entry<SpecimenOrObservationType, Integer> entry:specimenTypeToCount.entrySet()){ |
|
141 |
SpecimenOrObservationType type = entry.getKey(); |
|
142 |
out.println(type+": "+entry.getValue()); |
|
143 |
} |
|
144 |
out.println("\n"); |
|
145 |
|
|
146 |
//taxon name |
|
147 |
out.println("---Created Taxon Names ("+createdNames.size()+")---"); |
|
148 |
for (TaxonNameBase<?, ?> taxonName : createdNames) { |
|
149 |
out.println(taxonName.getTitleCache()); |
|
150 |
} |
|
151 |
out.println("\n"); |
|
152 |
|
|
153 |
//taxa |
|
154 |
out.println("---Created Taxa ("+createdTaxa.size()+")---"); |
|
155 |
for (Taxon taxon : createdTaxa) { |
|
156 |
out.println(taxon.getTitleCache()); |
|
157 |
} |
|
158 |
out.println("\n"); |
|
159 |
|
|
160 |
//taxon nodes |
|
161 |
out.println("---Created Taxon Nodes ("+createdTaxonNodes.size()+")---"); |
|
162 |
for (TaxonNode taxonNode : createdTaxonNodes) { |
|
163 |
String nodeString = taxonNode.toString(); |
|
164 |
if(taxonNode.getTaxon()!=null){ |
|
165 |
nodeString += " ("+taxonNode.getTaxon().getTitleCache()+")"; |
|
166 |
} |
|
167 |
if(taxonNode.getParent()!=null){ |
|
168 |
nodeString += " with parent "+taxonNode.getParent(); |
|
169 |
if(taxonNode.getParent().getTaxon()!=null){ |
|
170 |
nodeString += " ("+taxonNode.getParent().getTaxon().getTitleCache()+")"; |
|
171 |
} |
|
172 |
} |
|
173 |
out.println(nodeString); |
|
174 |
} |
|
175 |
out.println("\n"); |
|
176 |
|
|
177 |
//not imported |
|
178 |
out.println("---Already existing specimen (not imported)---"); |
|
179 |
for(UnitIdSpecimen specimen:alreadyExistingSpecimens){ |
|
180 |
out.println(formatSpecimen(specimen)); |
|
181 |
} |
|
182 |
out.println("\n"); |
|
183 |
|
|
184 |
//taxa with associated specimens |
|
185 |
out.println("---Taxa with associated specimens---"); |
|
186 |
for(Entry<Taxon, List<UnitIdSpecimen>> entry:taxonToAssociatedSpecimens.entrySet()){ |
|
187 |
Taxon taxon = entry.getKey(); |
|
188 |
List<UnitIdSpecimen> specimens = entry.getValue(); |
|
189 |
out.println(taxon.getTitleCache() + " ("+specimens.size()+")"); |
|
190 |
for (UnitIdSpecimen derivedUnit : specimens) { |
|
191 |
out.println("\t- "+formatSpecimen(derivedUnit)); |
|
192 |
//check for derivatives |
|
193 |
List<UnitIdSpecimen> list = derivateMap.get(derivedUnit); |
|
194 |
for (UnitIdSpecimen derivate : list) { |
|
195 |
out.println("\t\t- "+formatSpecimen(derivate)); |
|
196 |
} |
|
197 |
} |
|
198 |
} |
|
199 |
out.println("\n"); |
|
200 |
out.println("\n"); |
|
201 |
//info messages |
|
202 |
out.println("---Info messages---"); |
|
203 |
for(String message:infoMessages){ |
|
204 |
out.println(message); |
|
205 |
out.println("---"); |
|
206 |
} |
|
207 |
if(out!=System.out){ |
|
208 |
out.close(); |
|
209 |
} |
|
210 |
} |
|
211 |
|
|
212 |
private void incrementSpecimenTypeCount(Map<SpecimenOrObservationType, Integer> specimenTypeToCount, |
|
213 |
UnitIdSpecimen specimen) { |
|
214 |
SpecimenOrObservationType specimenType = specimen.getSpecimen().getRecordBasis(); |
|
215 |
Integer count = specimenTypeToCount.get(specimenType); |
|
216 |
if(count==null){ |
|
217 |
count = 1; |
|
218 |
} |
|
219 |
else{ |
|
220 |
count++; |
|
221 |
} |
|
222 |
specimenTypeToCount.put(specimenType, count); |
|
223 |
} |
|
224 |
|
|
225 |
private String formatSpecimen(UnitIdSpecimen specimen){ |
|
226 |
return "("+specimen.getUnitId()+") ["+specimen.getSpecimen().getRecordBasis()+"] "+specimen.getSpecimen().getTitleCache(); |
|
227 |
} |
|
228 |
|
|
229 |
private class UnitIdSpecimen{ |
|
230 |
private final String unitId; |
|
231 |
private final SpecimenOrObservationBase<?> specimen; |
|
232 |
|
|
233 |
|
|
234 |
public UnitIdSpecimen(String unitId, SpecimenOrObservationBase<?> specimen) { |
|
235 |
super(); |
|
236 |
this.unitId = unitId; |
|
237 |
this.specimen = specimen; |
|
238 |
} |
|
239 |
public String getUnitId() { |
|
240 |
return unitId; |
|
241 |
} |
|
242 |
public SpecimenOrObservationBase<?> getSpecimen() { |
|
243 |
return specimen; |
|
244 |
} |
|
245 |
@Override |
|
246 |
public int hashCode() { |
|
247 |
final int prime = 31; |
|
248 |
int result = 1; |
|
249 |
result = prime * result + ((specimen == null) ? 0 : specimen.hashCode()); |
|
250 |
result = prime * result + ((unitId == null) ? 0 : unitId.hashCode()); |
|
251 |
return result; |
|
252 |
} |
|
253 |
@Override |
|
254 |
public boolean equals(Object obj) { |
|
255 |
if (this == obj) { |
|
256 |
return true; |
|
257 |
} |
|
258 |
if (obj == null) { |
|
259 |
return false; |
|
260 |
} |
|
261 |
if (getClass() != obj.getClass()) { |
|
262 |
return false; |
|
263 |
} |
|
264 |
UnitIdSpecimen other = (UnitIdSpecimen) obj; |
|
265 |
if (specimen == null) { |
|
266 |
if (other.specimen != null) { |
|
267 |
return false; |
|
268 |
} |
|
269 |
} else if (!specimen.equals(other.specimen)) { |
|
270 |
return false; |
|
271 |
} |
|
272 |
if (unitId == null) { |
|
273 |
if (other.unitId != null) { |
|
274 |
return false; |
|
275 |
} |
|
276 |
} else if (!unitId.equals(other.unitId)) { |
|
277 |
return false; |
|
278 |
} |
|
279 |
return true; |
|
280 |
} |
|
281 |
|
|
282 |
} |
|
283 |
|
|
284 |
} |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportUtility.java | ||
---|---|---|
1 |
// $Id$ |
|
2 |
/** |
|
3 |
* Copyright (C) 2015 EDIT |
|
4 |
* European Distributed Institute of Taxonomy |
|
5 |
* http://www.e-taxonomy.eu |
|
6 |
* |
|
7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
9 |
*/ |
|
10 |
package eu.etaxonomy.cdm.io.specimen.abcd206.in; |
|
11 |
|
|
12 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
13 |
|
|
14 |
/** |
|
15 |
* @author pplitzner |
|
16 |
* @date 16.06.2015 |
|
17 |
* |
|
18 |
*/ |
|
19 |
public class AbcdImportUtility { |
|
20 |
|
|
21 |
public static String getUnitID(DerivedUnit derivedUnit, Abcd206ImportConfigurator config){ |
|
22 |
if(config.isMapUnitIdToAccessionNumber()){ |
|
23 |
return derivedUnit.getAccessionNumber(); |
|
24 |
} |
|
25 |
if(config.isMapUnitIdToBarcode()){ |
|
26 |
return derivedUnit.getBarcode(); |
|
27 |
} |
|
28 |
return derivedUnit.getCatalogNumber(); |
|
29 |
} |
|
30 |
|
|
31 |
public static void setUnitID(DerivedUnit derivedUnit, String unitId, Abcd206ImportConfigurator config){ |
|
32 |
if(config.isMapUnitIdToCatalogNumber() |
|
33 |
|| !(config.isMapUnitIdToAccessionNumber() || config.isMapUnitIdToBarcode() || config.isMapUnitIdToCatalogNumber())){ |
|
34 |
// set catalog number (default if nothing is set) |
|
35 |
derivedUnit.setCatalogNumber(unitId); |
|
36 |
} |
|
37 |
if(config.isMapUnitIdToAccessionNumber()){ |
|
38 |
derivedUnit.setAccessionNumber(unitId); |
|
39 |
} |
|
40 |
if(config.isMapUnitIdToBarcode()){ |
|
41 |
derivedUnit.setBarcode(unitId); |
|
42 |
} |
|
43 |
} |
|
44 |
|
|
45 |
} |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImpl.java | ||
---|---|---|
332 | 332 |
} |
333 | 333 |
|
334 | 334 |
@Override |
335 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, List<UUID> excludeTaxa, Integer limit, String pattern) {
|
|
336 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), excludeTaxa, limit, pattern);
|
|
335 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern) { |
|
336 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), limit, pattern); |
|
337 | 337 |
} |
338 | 338 |
|
339 | 339 |
@Override |
340 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, List<UUID> excludeTaxa, Integer limit, String pattern) {
|
|
341 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, excludeTaxa, limit, pattern);
|
|
340 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, Integer limit, String pattern) { |
|
341 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern); |
|
342 | 342 |
} |
343 | 343 |
|
344 | 344 |
@Override |
345 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, List<UUID> excludeTaxa) {
|
|
346 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), excludeTaxa, null, null);
|
|
345 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid ) {
|
|
346 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null); |
|
347 | 347 |
} |
348 | 348 |
|
349 | 349 |
@Override |
350 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, List<UUID> excludeTaxa) {
|
|
351 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, excludeTaxa, null, null);
|
|
350 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification){
|
|
351 |
return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null); |
|
352 | 352 |
} |
353 | 353 |
|
354 | 354 |
@Override |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IClassificationService.java | ||
---|---|---|
49 | 49 |
* @return |
50 | 50 |
*/ |
51 | 51 |
public ITaxonTreeNode getTreeNodeByUuid(UUID uuid); |
52 |
|
|
52 |
|
|
53 | 53 |
/** |
54 |
*
|
|
54 |
* |
|
55 | 55 |
* Returns the root node of the the given classification (specified by its UUID) |
56 | 56 |
* @param classificationUuid the uuid of the classification |
57 | 57 |
* @return the root node of the classification |
... | ... | |
187 | 187 |
* @param classification |
188 | 188 |
* @return |
189 | 189 |
*/ |
190 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, List<UUID> excludeTaxa);
|
|
190 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification); |
|
191 | 191 |
|
192 | 192 |
/** |
193 | 193 |
* @param taxon |
... | ... | |
269 | 269 |
* @param excludeTaxa |
270 | 270 |
* @return |
271 | 271 |
*/ |
272 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, List<UUID> excludeTaxa);
|
|
272 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid); |
|
273 | 273 |
|
274 | 274 |
/** |
275 | 275 |
* @param classificationUuid |
... | ... | |
279 | 279 |
* @return |
280 | 280 |
*/ |
281 | 281 |
List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification( |
282 |
UUID classificationUuid, List<UUID> excludeTaxa, Integer limit, String pattern);
|
|
282 |
UUID classificationUuid, Integer limit, String pattern); |
|
283 | 283 |
|
284 | 284 |
/** |
285 | 285 |
* @param classification |
... | ... | |
289 | 289 |
* @return |
290 | 290 |
*/ |
291 | 291 |
List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification( |
292 |
Classification classification, List<UUID> excludeTaxa, Integer limit, String pattern);
|
|
292 |
Classification classification, Integer limit, String pattern); |
|
293 | 293 |
|
294 | 294 |
/** |
295 | 295 |
* @param taxonUuid |
Also available in: Unified diff