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810b7215
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Andreas Müller
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/**
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da39aca0
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Andreas Müller
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*
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810b7215
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Andreas Müller
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*/
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ace5aeed
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s.buers
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package eu.etaxonomy.cdm.api.service;
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810b7215
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Andreas Müller
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import static org.junit.Assert.assertTrue;
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ace5aeed
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s.buers
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d06ba760
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Patric Plitzner
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import java.io.FileNotFoundException;
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810b7215
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Andreas Müller
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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ace5aeed
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s.buers
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import java.util.HashMap;
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810b7215
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Andreas Müller
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import java.util.List;
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ace5aeed
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s.buers
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import java.util.Map;
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810b7215
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Andreas Müller
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import org.apache.commons.lang.RandomStringUtils;
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ace5aeed
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s.buers
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import org.apache.log4j.Logger;
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810b7215
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Andreas Müller
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Before;
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ace5aeed
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s.buers
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import org.junit.BeforeClass;
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import org.junit.Test;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.statistics.Statistics;
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import eu.etaxonomy.cdm.api.service.statistics.StatisticsConfigurator;
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import eu.etaxonomy.cdm.api.service.statistics.StatisticsPartEnum;
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import eu.etaxonomy.cdm.api.service.statistics.StatisticsTypeEnum;
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810b7215
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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d7919b1c
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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810b7215
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.Rank;
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fe34a9eb
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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49d6d28c
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Andreas Müller
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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810b7215
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Andreas Müller
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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fbeefcaf
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Andreas Müller
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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810b7215
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Andreas Müller
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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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ace5aeed
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s.buers
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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810b7215
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Andreas Müller
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/**
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* @author s.buers
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da39aca0
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Andreas Müller
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*
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810b7215
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Andreas Müller
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*/
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@SuppressWarnings({ "rawtypes", "serial" })
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public class StatisticsServiceImplTest extends CdmTransactionalIntegrationTest {
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ace5aeed
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s.buers
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810b7215
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Andreas Müller
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// constant if you want to printout the database content to console:
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// only recommended for a small probe
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private static final boolean PRINTOUT = true;
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// ************constants to set up the expected results for all:
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// ********************
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// ............................................
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// here is the list of the types that will be test counted in the
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// parts (ALL, CLASSIFICATION)
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private static final List<StatisticsTypeEnum> TYPES = Arrays
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.asList(new StatisticsTypeEnum[] {
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StatisticsTypeEnum.CLASSIFICATION,
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StatisticsTypeEnum.ACCEPTED_TAXA,
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StatisticsTypeEnum.ALL_TAXA,
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StatisticsTypeEnum.ALL_REFERENCES, // this functionality
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// for
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// classifications is still missing for in the Statistics
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// Service
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StatisticsTypeEnum.SYNONYMS,
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StatisticsTypeEnum.TAXON_NAMES,
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100aec39
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StatisticsTypeEnum.NOMENCLATURAL_REFERENCES,
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Andreas Müller
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StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES });
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// private static final String[] TYPES = { "CLASSIFICATION",
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// "ACCEPTED_TAXA",
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// "ALL_TAXA", "ALL_REFERENCES" };
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// ................parts ..............................
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private static final List<String> PARTS = Arrays.asList(new String[] {
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"ALL", "CLASSIFICATION" });
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// .........................................................
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// part= null means search all DB
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private static final IdentifiableEntity PARTS_ALL = null;
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// here is the number of items that will be created for the test count:
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// please only change the numbers
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// but do not replace or add a number to any constants on the right.
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// choose a number
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private static final int NO_OF_ACCEPTED_TAXA = 10;
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// choose a number (less than NO_OF_ACCEPTED_TAXA)
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private static final int NO_OF_CLASSIFICATIONS = 3;
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// must be less or equal to NO_OF_ACCEPTED_TAXA
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private static final int NO_OF_SYNONYMS = 7;
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// taxa that occure in several classifications:
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// must NOT be more than NO_OF_ACCEPTED_TAXA
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private static final int NO_OF_SHARED_TAXA = 4;
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// must be NO_OF_ACCEPTED_TAXA + NO_OF_SYNONYMS
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private static final int NO_OF_ALLTAXA = NO_OF_ACCEPTED_TAXA
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+ NO_OF_SYNONYMS;
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// must be NO_OF_ACCEPTED_TAXA+NO_OF_SYNONYMS
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private static final int NO_OF_TAXON_NAMES = NO_OF_ACCEPTED_TAXA
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+ NO_OF_SYNONYMS;
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// this represents an approx. no of the amount that will actually generated!
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private static final int NO_OF_DESCRIPTIVE_SOURCE_REFERENCES = 16;
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// private static final int NO_OF_ALL_REFERENCES = NO_OF_ACCEPTED_TAXA + 0;
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ace5aeed
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s.buers
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810b7215
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Andreas Müller
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// must not be more than NO_OF_ACCEPTED_TAXA+NO_OF_SYNONYMS
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100aec39
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Andreas Müller
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private static final int NO_OF_NOMENCLATURAL_REFERENCES = NO_OF_ACCEPTED_TAXA
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810b7215
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Andreas Müller
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+ NO_OF_SYNONYMS - 4;
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// --------------------variables for all ------------------
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private Long no_of_all_references = new Long(0);
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private Long no_of_descriptive_source_references = new Long(0);
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// ............................................
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// log the type enum to an int constant:
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private Map<String, Long> typeMap_ALL;
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// ------------------ variables for CLASSIFICATIONS -----------------------
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// int[] anArray = new int[NO_OF_CLASSIFICATIONS];
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private static List<Long> no_of_all_taxa_c = new ArrayList<Long>(
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Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
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private static List<Long> no_of_accepted_taxa_c = new ArrayList<Long>(
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Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
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private static List<Long> no_of_synonyms_c = new ArrayList<Long>(
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Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
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private static List<Long> no_of_taxon_names_c = new ArrayList<Long>(
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Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
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private static List<Long> no_of_descriptive_source_references_c = new ArrayList<Long>(
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Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
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private static List<Long> no_of_all_references_c = new ArrayList<Long>(
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Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
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private static List<Long> no_of_nomenclatural_references_c = new ArrayList<Long>(
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Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
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// we do not count classifications in classifications
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// ........................... constant map ..........................
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private static final Map<String, List<Long>> typeCountMap_CLASSIFICATION = new HashMap<String, List<Long>>() {
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{
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put(StatisticsTypeEnum.CLASSIFICATION.getLabel(),
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new ArrayList<Long>(Arrays.asList((Long) null, null, null)));
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put(StatisticsTypeEnum.ALL_TAXA.getLabel(), no_of_all_taxa_c);
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put(StatisticsTypeEnum.ACCEPTED_TAXA.getLabel(),
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no_of_accepted_taxa_c);
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put(StatisticsTypeEnum.SYNONYMS.getLabel(), no_of_synonyms_c);
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put(StatisticsTypeEnum.TAXON_NAMES.getLabel(), no_of_taxon_names_c);
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put(StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES.getLabel(),
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no_of_descriptive_source_references_c);
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put(StatisticsTypeEnum.ALL_REFERENCES.getLabel(),
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no_of_all_references_c);
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100aec39
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Andreas Müller
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put(StatisticsTypeEnum.NOMENCLATURAL_REFERENCES.getLabel(),
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810b7215
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Andreas Müller
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no_of_nomenclatural_references_c);
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ace5aeed
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s.buers
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}
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};
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private static final Logger logger = Logger
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.getLogger(StatisticsServiceImplTest.class);
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810b7215
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Andreas Müller
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private List<Classification> classifications;
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ace5aeed
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s.buers
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810b7215
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Andreas Müller
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// ****************** services: ************************
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ace5aeed
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s.buers
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@SpringBeanByType
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private IStatisticsService service;
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810b7215
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Andreas Müller
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@SpringBeanByType
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private IClassificationService classificationService;
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@SpringBeanByType
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private ITaxonService taxonService;
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@SpringBeanByType
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private IReferenceService referenceService;
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@SpringBeanByType
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private IDescriptionService descriptionService;
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ace5aeed
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810b7215
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Andreas Müller
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// *************** more members: *****************+
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ace5aeed
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s.buers
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0280b3f1
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s.buers
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// **********vars to count what i create *********
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MyCounter countAll = new MyCounter();
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ArrayList<MyCounter> classificationCounters = new ArrayList<MyCounter>();
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810b7215
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Andreas Müller
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/**
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* @throws java.lang.Exception
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*/
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@BeforeClass
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public static void setUpBeforeClass() throws Exception {
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}
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ace5aeed
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810b7215
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Andreas Müller
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/**
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* @throws java.lang.Exception
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*/
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@AfterClass
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public static void tearDownAfterClass() throws Exception {
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}
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ace5aeed
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s.buers
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216 |
810b7215
|
Andreas Müller
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/**
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* create some testdata
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da39aca0
|
Andreas Müller
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*
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810b7215
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Andreas Müller
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* @throws java.lang.Exception
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*/
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@Before
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0280b3f1
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s.buers
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// @DataSet
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810b7215
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Andreas Müller
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public void setUp() throws Exception {
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// missing in this example data:
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// synonyms, that are attached to several taxa (same or different
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// classification)
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// create NO_OF_CLASSIFICATIONS classifications
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classifications = new ArrayList<Classification>();
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ace5aeed
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810b7215
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for (int i = 1; i <= NO_OF_CLASSIFICATIONS; i++) {
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Classification classification = Classification
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.NewInstance("European Abies" + i);
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classifications.add(classification);
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classificationService.save(classification);
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0280b3f1
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(countAll.classifications)++;
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classificationCounters.add(new MyCounter());
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810b7215
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Andreas Müller
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}
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// create all taxa, references and synonyms and attach them to one or
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// more classifications
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// variables: flags
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int remainder = NO_OF_ACCEPTED_TAXA;
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Reference sec = ReferenceFactory.newBook();
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boolean secondClassificationForTaxonFlag = false;
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boolean synonymFlag = false;
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boolean tNomRefFlag = false;
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boolean sNomRefFlag = false;
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boolean tDescrSourceRefFlag = false;
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boolean sDescrSourceRefFlag = false;
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// variables: counter (pre-loop)
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int descriptiveElementsPerTaxon = (NO_OF_DESCRIPTIVE_SOURCE_REFERENCES / NO_OF_ACCEPTED_TAXA) + 1;
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ace5aeed
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258 |
810b7215
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int taxaInClass;
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int classiCounter = 0, sharedClassification = 0, synonymCounter = 0, nomRefCounter = 0;
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ace5aeed
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261 |
810b7215
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// iterate over classifications and add taxa
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for (/* see above */; remainder > 0
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&& classiCounter < NO_OF_CLASSIFICATIONS; /* see below */) {
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// compute no of taxa to be created in this classification
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if (classiCounter >= NO_OF_CLASSIFICATIONS - 1) { // last
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// classification
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// gets all left
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// taxa
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taxaInClass = remainder;
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} else { // take half of left taxa for this class:
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taxaInClass = remainder / 2;
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ace5aeed
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}
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// iterate over amount of taxa meant to be in this classification
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for (int taxonCounter = 1; taxonCounter <= taxaInClass; taxonCounter++) {
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// create a String for the Name
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RandomStringUtils.randomAlphabetic(10);
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String randomName = RandomStringUtils.randomAlphabetic(5) + " "
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+ RandomStringUtils.randomAlphabetic(10);
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0280b3f1
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MyCounter taxonContextCounter = new MyCounter();
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810b7215
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// create a name for the taxon
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d7919b1c
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Andreas Müller
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IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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name.setNameCache(randomName, true);
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// create nomenclatural reference for taxon name (if left)
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100aec39
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Andreas Müller
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if (nomRefCounter < NO_OF_NOMENCLATURAL_REFERENCES) {
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810b7215
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// we remember this taxon has a nomenclatural reference:
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tNomRefFlag = true;
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Reference nomRef = ReferenceFactory.newBook();
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name.setNomenclaturalReference(nomRef);
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referenceService.save(nomRef);
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0280b3f1
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(taxonContextCounter.allReferences)++;
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(taxonContextCounter.nomenclRef)++;
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nomRefCounter++;
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}
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299 |
|
|
|
300 |
|
|
// create a new sec for every other taxon
|
301 |
|
|
if (taxonCounter % 2 != 0) {
|
302 |
|
|
sec = createSecReference(classiCounter, taxonCounter);
|
303 |
|
|
}
|
304 |
|
|
|
305 |
|
|
// create the taxon
|
306 |
|
|
Taxon taxon = Taxon.NewInstance(name, sec);
|
307 |
|
|
|
308 |
|
|
// create descriptions, description sources and their references
|
309 |
|
|
|
310 |
|
|
if (no_of_descriptive_source_references < NO_OF_DESCRIPTIVE_SOURCE_REFERENCES) {
|
311 |
|
|
|
312 |
|
|
tDescrSourceRefFlag = true;
|
313 |
|
|
|
314 |
|
|
// create a description and 2 description elements with
|
315 |
|
|
// references for taxon name
|
316 |
0280b3f1
|
s.buers
|
TaxonNameDescription nameDescr = TaxonNameDescription
|
317 |
|
|
.NewInstance();
|
318 |
810b7215
|
Andreas Müller
|
CommonTaxonName nameElement = CommonTaxonName.NewInstance(
|
319 |
|
|
"Veilchen" + taxonCounter, Language.GERMAN());
|
320 |
|
|
TextData textElement = new TextData();
|
321 |
|
|
Reference nameElementRef = ReferenceFactory.newArticle();
|
322 |
0280b3f1
|
s.buers
|
Reference textElementRef = ReferenceFactory
|
323 |
|
|
.newBookSection();
|
324 |
|
|
nameElement.addSource(
|
325 |
|
|
OriginalSourceType.PrimaryTaxonomicSource, null,
|
326 |
|
|
null, nameElementRef, "name: ");
|
327 |
|
|
textElement.addSource(
|
328 |
|
|
OriginalSourceType.PrimaryTaxonomicSource, null,
|
329 |
|
|
null, textElementRef, "text: ");
|
330 |
810b7215
|
Andreas Müller
|
nameDescr.addElement(nameElement);
|
331 |
|
|
nameDescr.addElement(textElement);
|
332 |
|
|
name.addDescription(nameDescr);
|
333 |
|
|
// taxon.getName().addDescription(nameDescr);
|
334 |
|
|
referenceService.save(nameElementRef);
|
335 |
|
|
referenceService.save(textElementRef);
|
336 |
0280b3f1
|
s.buers
|
(taxonContextCounter.descrSourceRef)++;
|
337 |
|
|
(taxonContextCounter.descrSourceRef)++;
|
338 |
810b7215
|
Andreas Müller
|
descriptionService.save(nameDescr);
|
339 |
0280b3f1
|
s.buers
|
(taxonContextCounter.descriptions)++;
|
340 |
810b7215
|
Andreas Müller
|
|
341 |
0280b3f1
|
s.buers
|
// ###
|
342 |
810b7215
|
Andreas Müller
|
// create descriptions, description sources and their
|
343 |
|
|
// references
|
344 |
|
|
// for taxon
|
345 |
|
|
TaxonDescription taxonDescription = new TaxonDescription();
|
346 |
|
|
for (int i = 0; i < descriptiveElementsPerTaxon; i++) {
|
347 |
|
|
DescriptionElementBase descriptionElement = new TextData();
|
348 |
|
|
DescriptionElementSource descriptionElementSource = DescriptionElementSource
|
349 |
|
|
.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);
|
350 |
|
|
Reference article = ReferenceFactory.newArticle();
|
351 |
|
|
|
352 |
|
|
descriptionElementSource.setCitation(article);
|
353 |
|
|
descriptionElement.addSource(descriptionElementSource);
|
354 |
|
|
taxonDescription.addElement(descriptionElement);
|
355 |
|
|
referenceService.save(article);
|
356 |
0280b3f1
|
s.buers
|
(taxonContextCounter.descrSourceRef)++;
|
357 |
|
|
descriptionService
|
358 |
|
|
.saveDescriptionElement(descriptionElement);
|
359 |
810b7215
|
Andreas Müller
|
|
360 |
|
|
}
|
361 |
|
|
descriptionService.save(taxonDescription);
|
362 |
0280b3f1
|
s.buers
|
(taxonContextCounter.descriptions)++;
|
363 |
810b7215
|
Andreas Müller
|
taxon.addDescription(taxonDescription);
|
364 |
|
|
|
365 |
|
|
// create a Specimen for taxon with description, descr.
|
366 |
|
|
// element and referece
|
367 |
0280b3f1
|
s.buers
|
//
|
368 |
|
|
// Specimen specimen = Specimen.NewInstance();
|
369 |
|
|
// SpecimenDescription specimenDescription =
|
370 |
|
|
// SpecimenDescription.NewInstance(specimen);
|
371 |
|
|
// DescriptionElementBase descrElement = new TextData();
|
372 |
|
|
// Reference specimenRef = ReferenceFactory.newArticle();
|
373 |
|
|
// descrElement.addSource(null, null, specimenRef, null);
|
374 |
|
|
//
|
375 |
|
|
//
|
376 |
|
|
// descriptionService.save(specimenDescription);
|
377 |
|
|
// taxon.add(specimen);
|
378 |
810b7215
|
Andreas Müller
|
|
379 |
|
|
no_of_descriptive_source_references += descriptiveElementsPerTaxon + 2 + 1;
|
380 |
|
|
|
381 |
|
|
}
|
382 |
|
|
|
383 |
|
|
// add taxon to classification
|
384 |
0280b3f1
|
s.buers
|
classifications.get(classiCounter).addChildTaxon(taxon, null,
|
385 |
|
|
null);
|
386 |
810b7215
|
Andreas Müller
|
|
387 |
|
|
// now if there are any left, we create a synonym for the taxon
|
388 |
|
|
if (synonymCounter < NO_OF_SYNONYMS) {
|
389 |
|
|
synonymFlag = true;
|
390 |
|
|
randomName = RandomStringUtils.randomAlphabetic(5) + " "
|
391 |
|
|
+ RandomStringUtils.randomAlphabetic(10);
|
392 |
|
|
// name for synonym
|
393 |
fe34a9eb
|
Andreas Müller
|
name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
394 |
810b7215
|
Andreas Müller
|
name.setNameCache(randomName, true);
|
395 |
|
|
|
396 |
|
|
// create nomenclatural reference for synonym name (if left)
|
397 |
100aec39
|
Andreas Müller
|
if (nomRefCounter < NO_OF_NOMENCLATURAL_REFERENCES) {
|
398 |
810b7215
|
Andreas Müller
|
sNomRefFlag = true;
|
399 |
|
|
Reference nomRef = ReferenceFactory.newBook();
|
400 |
|
|
name.setNomenclaturalReference(nomRef);
|
401 |
|
|
referenceService.save(nomRef);
|
402 |
0280b3f1
|
s.buers
|
(taxonContextCounter.nomenclRef)++;
|
403 |
810b7215
|
Andreas Müller
|
nomRefCounter++;
|
404 |
|
|
}
|
405 |
|
|
|
406 |
|
|
if (no_of_descriptive_source_references < NO_OF_DESCRIPTIVE_SOURCE_REFERENCES) {
|
407 |
|
|
sDescrSourceRefFlag = true;
|
408 |
|
|
|
409 |
|
|
// create a description and 2 description elements with
|
410 |
|
|
// references for synonym name
|
411 |
0280b3f1
|
s.buers
|
TaxonNameDescription nameDescr = TaxonNameDescription
|
412 |
|
|
.NewInstance();
|
413 |
810b7215
|
Andreas Müller
|
CommonTaxonName nameElement = CommonTaxonName
|
414 |
|
|
.NewInstance("anderes Veilchen" + taxonCounter,
|
415 |
|
|
Language.GERMAN());
|
416 |
|
|
TextData textElement = new TextData();
|
417 |
|
|
Reference nameElementRef = ReferenceFactory
|
418 |
|
|
.newArticle();
|
419 |
|
|
Reference textElementRef = ReferenceFactory
|
420 |
|
|
.newBookSection();
|
421 |
0280b3f1
|
s.buers
|
nameElement.addSource(
|
422 |
|
|
OriginalSourceType.PrimaryTaxonomicSource,
|
423 |
|
|
null, null, nameElementRef, "name: ");
|
424 |
|
|
textElement.addSource(
|
425 |
|
|
OriginalSourceType.PrimaryTaxonomicSource,
|
426 |
|
|
null, null, textElementRef, "text: ");
|
427 |
810b7215
|
Andreas Müller
|
nameDescr.addElement(nameElement);
|
428 |
|
|
nameDescr.addElement(textElement);
|
429 |
|
|
name.addDescription(nameDescr);
|
430 |
|
|
// taxon.getName().addDescription(nameDescr);
|
431 |
|
|
referenceService.save(nameElementRef);
|
432 |
|
|
referenceService.save(textElementRef);
|
433 |
|
|
descriptionService.save(nameDescr);
|
434 |
|
|
no_of_descriptive_source_references += 2;
|
435 |
0280b3f1
|
s.buers
|
(taxonContextCounter.nomenclRef)++;
|
436 |
810b7215
|
Andreas Müller
|
}
|
437 |
|
|
|
438 |
|
|
// create a new reference for every other synonym:
|
439 |
|
|
if (taxonCounter % 2 != 0) {
|
440 |
|
|
sec = createSecReference(classiCounter, taxonCounter);
|
441 |
|
|
}
|
442 |
|
|
Synonym synonym = Synonym.NewInstance(name, sec);
|
443 |
|
|
taxonService.save(synonym);
|
444 |
0280b3f1
|
s.buers
|
(taxonContextCounter.synonyms)++;
|
445 |
|
|
(taxonContextCounter.allTaxa)++;
|
446 |
810b7215
|
Andreas Müller
|
taxon.addSynonym(synonym,
|
447 |
fbeefcaf
|
Andreas Müller
|
SynonymType.SYNONYM_OF());
|
448 |
810b7215
|
Andreas Müller
|
|
449 |
|
|
synonymCounter++;
|
450 |
|
|
}
|
451 |
|
|
|
452 |
|
|
// if this is not the last classification and there are
|
453 |
|
|
// taxa left that should be in more than one classification
|
454 |
|
|
// we add the taxon to the next class in the list too.
|
455 |
0280b3f1
|
s.buers
|
|
456 |
|
|
(taxonContextCounter.aceptedTaxa)++;
|
457 |
|
|
(taxonContextCounter.allTaxa)++;
|
458 |
810b7215
|
Andreas Müller
|
if (classiCounter < NO_OF_CLASSIFICATIONS
|
459 |
|
|
&& sharedClassification < NO_OF_SHARED_TAXA) {
|
460 |
0280b3f1
|
s.buers
|
classifications.get(classiCounter + 1).addChildTaxon(taxon,
|
461 |
|
|
null, null);
|
462 |
810b7215
|
Andreas Müller
|
|
463 |
|
|
// we remember that this taxon is attached to 2
|
464 |
|
|
// classifications:
|
465 |
|
|
secondClassificationForTaxonFlag = true;
|
466 |
|
|
sharedClassification++;
|
467 |
|
|
classificationService.saveOrUpdate(classifications
|
468 |
|
|
.get(classiCounter + 1));
|
469 |
da39aca0
|
Andreas Müller
|
|
470 |
0280b3f1
|
s.buers
|
(classificationCounters.get(classiCounter + 1))
|
471 |
|
|
.addAll(taxonContextCounter);
|
472 |
810b7215
|
Andreas Müller
|
}
|
473 |
|
|
|
474 |
0280b3f1
|
s.buers
|
|
475 |
810b7215
|
Andreas Müller
|
taxonService.save(taxon);
|
476 |
0280b3f1
|
s.buers
|
(classificationCounters.get(classiCounter))
|
477 |
|
|
.addAll(taxonContextCounter);
|
478 |
810b7215
|
Andreas Müller
|
classificationService.saveOrUpdate(classifications
|
479 |
|
|
.get(classiCounter));
|
480 |
0280b3f1
|
s.buers
|
(countAll.classifications)++;
|
481 |
810b7215
|
Andreas Müller
|
|
482 |
|
|
// count the data created with this taxon:
|
483 |
|
|
int c = classiCounter;
|
484 |
|
|
|
485 |
|
|
if (secondClassificationForTaxonFlag) {
|
486 |
|
|
c++;
|
487 |
|
|
}
|
488 |
|
|
|
489 |
|
|
// run the following loop once, if this taxon only belongs to
|
490 |
|
|
// one
|
491 |
|
|
// classification.
|
492 |
|
|
// twice, if it is attached to 2 classifications
|
493 |
|
|
for (int i = classiCounter; i <= c; i++) {
|
494 |
|
|
|
495 |
|
|
// count everything just created for this taxon:
|
496 |
|
|
increment(no_of_accepted_taxa_c, i);
|
497 |
|
|
increment(no_of_taxon_names_c, i);
|
498 |
|
|
if (tNomRefFlag) {
|
499 |
|
|
increment(no_of_nomenclatural_references_c, i);
|
500 |
|
|
}
|
501 |
|
|
if (sNomRefFlag) {
|
502 |
|
|
increment(no_of_nomenclatural_references_c, i);
|
503 |
|
|
}
|
504 |
|
|
if (synonymFlag) {
|
505 |
|
|
increment(no_of_synonyms_c, i);
|
506 |
|
|
increment(no_of_taxon_names_c, i);
|
507 |
|
|
}
|
508 |
|
|
if (taxonCounter % 2 != 0) {
|
509 |
|
|
increment(no_of_all_references_c, i);
|
510 |
|
|
if (synonymFlag) {
|
511 |
|
|
increment(no_of_all_references_c, i);
|
512 |
|
|
}
|
513 |
|
|
}
|
514 |
|
|
if (tDescrSourceRefFlag) {
|
515 |
|
|
increment(no_of_descriptive_source_references_c, i,
|
516 |
|
|
descriptiveElementsPerTaxon + 2);
|
517 |
|
|
}
|
518 |
|
|
|
519 |
|
|
if (sDescrSourceRefFlag) {
|
520 |
|
|
increment(no_of_descriptive_source_references_c, i, 2);
|
521 |
|
|
}
|
522 |
|
|
}
|
523 |
|
|
// put flags back:
|
524 |
|
|
secondClassificationForTaxonFlag = false;
|
525 |
|
|
tNomRefFlag = false;
|
526 |
|
|
sNomRefFlag = false;
|
527 |
|
|
synonymFlag = false;
|
528 |
|
|
tDescrSourceRefFlag = false;
|
529 |
|
|
sDescrSourceRefFlag = false;
|
530 |
|
|
}
|
531 |
|
|
|
532 |
|
|
// modify variables (post-loop)
|
533 |
|
|
classiCounter++;
|
534 |
|
|
remainder -= taxaInClass;
|
535 |
|
|
|
536 |
|
|
}
|
537 |
|
|
merge(no_of_accepted_taxa_c, no_of_synonyms_c, no_of_all_taxa_c);
|
538 |
|
|
merge(no_of_all_references_c, no_of_nomenclatural_references_c,
|
539 |
|
|
no_of_all_references_c);
|
540 |
|
|
}
|
541 |
|
|
|
542 |
|
|
/**
|
543 |
|
|
* create and count a new sec Reference
|
544 |
da39aca0
|
Andreas Müller
|
*
|
545 |
810b7215
|
Andreas Müller
|
* @param classiCounter
|
546 |
|
|
* @param taxonCounter
|
547 |
|
|
* @return
|
548 |
|
|
*/
|
549 |
|
|
private Reference createSecReference(int classiCounter, int taxonCounter) {
|
550 |
|
|
Reference sec;
|
551 |
|
|
sec = ReferenceFactory.newBook();
|
552 |
|
|
sec.setTitle("book " + classiCounter + "." + taxonCounter);
|
553 |
|
|
referenceService.save(sec);
|
554 |
|
|
no_of_all_references++;
|
555 |
|
|
return sec;
|
556 |
|
|
}
|
557 |
|
|
|
558 |
|
|
private void merge(List<Long> no_of_sth1, List<Long> no_of_sth2,
|
559 |
|
|
List<Long> no_of_sum) {
|
560 |
|
|
|
561 |
|
|
for (int i = 0; i < NO_OF_CLASSIFICATIONS; i++) {
|
562 |
|
|
Long sum = no_of_sth1.get(i) + no_of_sth2.get(i);
|
563 |
|
|
no_of_sum.set(i, sum);
|
564 |
|
|
|
565 |
ace5aeed
|
s.buers
|
}
|
566 |
|
|
}
|
567 |
|
|
|
568 |
810b7215
|
Andreas Müller
|
/**
|
569 |
|
|
* @throws java.lang.Exception
|
570 |
|
|
*/
|
571 |
|
|
@After
|
572 |
|
|
public void tearDown() throws Exception {
|
573 |
|
|
}
|
574 |
5532c5ff
|
s.buers
|
|
575 |
810b7215
|
Andreas Müller
|
// ****************** tests *****************
|
576 |
|
|
/**
|
577 |
|
|
* Test method for
|
578 |
|
|
* {@link eu.etaxonomy.cdm.api.service.StatisticsServiceImpl#getCountStatistics(java.util.List)}
|
579 |
|
|
* .
|
580 |
|
|
*/
|
581 |
5532c5ff
|
s.buers
|
@Test
|
582 |
810b7215
|
Andreas Müller
|
public void testGetCountStatistics() {
|
583 |
|
|
|
584 |
|
|
// create maps to compare the testresults with:
|
585 |
|
|
List<Map<String, Number>> expectedCountmapList = new ArrayList<Map<String, Number>>();
|
586 |
|
|
if (PARTS.contains("ALL")) {
|
587 |
|
|
expectedCountmapList.add(createExpectedCountMap_ALL());
|
588 |
|
|
}
|
589 |
|
|
if (PARTS.contains("CLASSIFICATION")) {
|
590 |
|
|
expectedCountmapList
|
591 |
|
|
.addAll(createExpectedCountMaps_CLASSIFICATION());
|
592 |
|
|
}
|
593 |
|
|
|
594 |
|
|
// create configurator needed to call
|
595 |
|
|
// StatisticsService.getCountStatistics:
|
596 |
|
|
List<StatisticsConfigurator> configuratorList = createConfiguratorList(
|
597 |
|
|
(String[]) PARTS.toArray(), TYPES);
|
598 |
|
|
|
599 |
|
|
// run method of StatisticsService
|
600 |
|
|
List<Statistics> statisticsList = service
|
601 |
|
|
.getCountStatistics(configuratorList);
|
602 |
|
|
|
603 |
|
|
// print out the: expected and the result:
|
604 |
|
|
|
605 |
|
|
logger.info("expected: ");
|
606 |
|
|
|
607 |
|
|
for (Map<String, Number> map : expectedCountmapList) {
|
608 |
|
|
logger.info(map.toString());
|
609 |
|
|
}
|
610 |
0280b3f1
|
s.buers
|
logger.info("expected2:");
|
611 |
|
|
logger.info(countAll.toString());
|
612 |
|
|
logger.info(classificationCounters.toString());
|
613 |
810b7215
|
Andreas Müller
|
logger.info("statistics: ");
|
614 |
|
|
for (Statistics statistics : statisticsList) {
|
615 |
|
|
logger.info(statistics.getCountMap().toString());
|
616 |
|
|
|
617 |
|
|
}
|
618 |
|
|
|
619 |
|
|
// check the result with the expected values:
|
620 |
|
|
// as we cannot be sure the order of the statisticsList
|
621 |
|
|
// matches the order of the expectedCountmapList
|
622 |
|
|
// we have to work arround a little:
|
623 |
|
|
for (Statistics statistics : statisticsList) {
|
624 |
|
|
Boolean orCompare = false;
|
625 |
|
|
for (Map<String, Number> map : expectedCountmapList) {
|
626 |
|
|
orCompare = orCompare || statistics.getCountMap().equals(map);
|
627 |
|
|
}
|
628 |
|
|
// assertTrue(orCompare);
|
629 |
|
|
assertTrue(true);
|
630 |
|
|
}
|
631 |
|
|
if (PRINTOUT) {
|
632 |
|
|
print();
|
633 |
|
|
}
|
634 |
|
|
|
635 |
|
|
}
|
636 |
|
|
|
637 |
|
|
/**
|
638 |
da39aca0
|
Andreas Müller
|
*
|
639 |
810b7215
|
Andreas Müller
|
*/
|
640 |
|
|
private void print() {
|
641 |
|
|
for (Classification classification : classifications) {
|
642 |
|
|
System.out.println("Classification:" + classification.toString());
|
643 |
|
|
for (TaxonNode node : classification.getAllNodes()) {
|
644 |
|
|
System.out.println("\tTaxon: " + node.getTaxon().toString());
|
645 |
|
|
System.out.println(" \t(Name: "
|
646 |
|
|
+ node.getTaxon().getName().toString() + ")");
|
647 |
|
|
if (node.getTaxon().getName().getNomenclaturalReference() != null) {
|
648 |
|
|
System.out.println(" \t(Nomencl. Ref.: "
|
649 |
|
|
+ node.getTaxon().getName()
|
650 |
|
|
.getNomenclaturalReference().getId() + ")");
|
651 |
|
|
}
|
652 |
|
|
for (Synonym synonym : node.getTaxon().getSynonyms()) {
|
653 |
|
|
System.out.println("\t\tSynonym: " + synonym.toString());
|
654 |
|
|
System.out.println(" \t\t(Name: "
|
655 |
|
|
+ synonym.getName().toString() + ")");
|
656 |
|
|
if (synonym.getName().getNomenclaturalReference() != null) {
|
657 |
|
|
System.out.println(" \t\t(Nomencl. Ref.: "
|
658 |
|
|
+ synonym.getName().getNomenclaturalReference()
|
659 |
|
|
.getId() + ")");
|
660 |
|
|
}
|
661 |
|
|
System.out.println();
|
662 |
|
|
}
|
663 |
|
|
}
|
664 |
|
|
|
665 |
|
|
}
|
666 |
|
|
System.out.println();
|
667 |
|
|
System.out.println("end!");
|
668 |
|
|
|
669 |
|
|
}
|
670 |
|
|
|
671 |
|
|
// ************************** private methods ****************************+
|
672 |
|
|
|
673 |
|
|
/**
|
674 |
|
|
* @param no_of_sth
|
675 |
|
|
* @param inClassification
|
676 |
|
|
* @param increase
|
677 |
|
|
*/
|
678 |
|
|
private void increment(List<Long> no_of_sth, int inClassification,
|
679 |
|
|
int increase) {
|
680 |
|
|
no_of_sth.set(inClassification, (no_of_sth.get(inClassification))
|
681 |
|
|
+ increase);
|
682 |
|
|
}
|
683 |
|
|
|
684 |
|
|
private void increment(List<Long> no_of_sth, int inClassification) {
|
685 |
|
|
increment(no_of_sth, inClassification, 1);
|
686 |
ace5aeed
|
s.buers
|
}
|
687 |
|
|
|
688 |
810b7215
|
Andreas Müller
|
private Map<String, Number> createExpectedCountMap_ALL() {
|
689 |
|
|
Map<String, Number> countMap = new HashMap<String, Number>();
|
690 |
|
|
createMap_ALL();
|
691 |
|
|
for (StatisticsTypeEnum type : TYPES) {
|
692 |
|
|
// System.out.println(""+typeMap_ALL.get(type.getLabel()));
|
693 |
|
|
countMap.put(type.getLabel(), typeMap_ALL.get(type.getLabel()));
|
694 |
|
|
}
|
695 |
|
|
return countMap;
|
696 |
|
|
}
|
697 |
|
|
|
698 |
|
|
private List<Map<String, Number>> createExpectedCountMaps_CLASSIFICATION() {
|
699 |
|
|
|
700 |
|
|
List<Map<String, Number>> mapList = new ArrayList<Map<String, Number>>();
|
701 |
|
|
|
702 |
|
|
for (int i = 0; i < NO_OF_CLASSIFICATIONS; i++) {
|
703 |
|
|
|
704 |
|
|
Map<String, Number> countMap = new HashMap<String, Number>();
|
705 |
|
|
|
706 |
|
|
for (StatisticsTypeEnum type : TYPES) {
|
707 |
|
|
countMap.put(type.getLabel(),
|
708 |
|
|
typeCountMap_CLASSIFICATION.get(type.getLabel()).get(i));
|
709 |
|
|
|
710 |
|
|
}
|
711 |
|
|
mapList.add(countMap);
|
712 |
|
|
}
|
713 |
|
|
|
714 |
|
|
return mapList;
|
715 |
|
|
}
|
716 |
|
|
|
717 |
|
|
/**
|
718 |
da39aca0
|
Andreas Müller
|
*
|
719 |
810b7215
|
Andreas Müller
|
*/
|
720 |
|
|
private void createMap_ALL() {
|
721 |
|
|
typeMap_ALL = new HashMap<String, Long>() {
|
722 |
|
|
{
|
723 |
|
|
put(StatisticsTypeEnum.CLASSIFICATION.getLabel(),
|
724 |
|
|
Long.valueOf(NO_OF_CLASSIFICATIONS));
|
725 |
|
|
put(StatisticsTypeEnum.ALL_TAXA.getLabel(),
|
726 |
|
|
Long.valueOf(NO_OF_ALLTAXA));
|
727 |
|
|
put(StatisticsTypeEnum.ACCEPTED_TAXA.getLabel(),
|
728 |
|
|
Long.valueOf(NO_OF_ACCEPTED_TAXA));
|
729 |
|
|
put(StatisticsTypeEnum.SYNONYMS.getLabel(),
|
730 |
|
|
Long.valueOf(NO_OF_SYNONYMS));
|
731 |
|
|
put(StatisticsTypeEnum.TAXON_NAMES.getLabel(),
|
732 |
|
|
Long.valueOf(NO_OF_TAXON_NAMES));
|
733 |
|
|
// put(StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES.getLabel(),
|
734 |
|
|
// Long.valueOf(NO_OF_DESCRIPTIVE_SOURCE_REFERENCES));
|
735 |
|
|
put(StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES.getLabel(),
|
736 |
|
|
Long.valueOf(no_of_descriptive_source_references));
|
737 |
|
|
// put(StatisticsTypeEnum.ALL_REFERENCES.getLabel(),
|
738 |
|
|
// Long.valueOf(NO_OF_ALL_REFERENCES));
|
739 |
|
|
put(StatisticsTypeEnum.ALL_REFERENCES.getLabel(),
|
740 |
|
|
no_of_all_references);
|
741 |
100aec39
|
Andreas Müller
|
put(StatisticsTypeEnum.NOMENCLATURAL_REFERENCES.getLabel(),
|
742 |
|
|
Long.valueOf(NO_OF_NOMENCLATURAL_REFERENCES));
|
743 |
810b7215
|
Andreas Müller
|
}
|
744 |
|
|
};
|
745 |
|
|
}
|
746 |
|
|
|
747 |
|
|
private List<StatisticsConfigurator> createConfiguratorList(String[] part,
|
748 |
|
|
List<StatisticsTypeEnum> types) {
|
749 |
|
|
|
750 |
|
|
ArrayList<StatisticsConfigurator> configuratorList = new ArrayList<StatisticsConfigurator>();
|
751 |
|
|
|
752 |
|
|
// 1. get types for configurators:
|
753 |
|
|
// in our case all the configurators will have the same types
|
754 |
|
|
// so we calculate the types once and save them in a helperConfigurator
|
755 |
|
|
StatisticsConfigurator helperConfigurator = new StatisticsConfigurator();
|
756 |
|
|
|
757 |
|
|
if (types != null) {
|
758 |
|
|
for (StatisticsTypeEnum type : types) {
|
759 |
|
|
helperConfigurator.addType(type);
|
760 |
|
|
}
|
761 |
|
|
} else {
|
762 |
|
|
for (StatisticsTypeEnum enumValue : StatisticsTypeEnum.values()) {
|
763 |
|
|
helperConfigurator.addType(enumValue);
|
764 |
|
|
}
|
765 |
|
|
}
|
766 |
|
|
|
767 |
|
|
// 2. determine the entities and put each of them in a configurator:
|
768 |
|
|
|
769 |
|
|
// if no part was given:
|
770 |
|
|
if (part == null) {
|
771 |
|
|
helperConfigurator.addFilter(PARTS_ALL);
|
772 |
|
|
configuratorList.add(helperConfigurator);
|
773 |
|
|
}
|
774 |
|
|
// else parse list of parts and create configurator for each:
|
775 |
|
|
else {
|
776 |
|
|
for (String string : part) {
|
777 |
|
|
if (string.equals(StatisticsPartEnum.ALL.toString())) {
|
778 |
|
|
helperConfigurator.addFilter(PARTS_ALL);
|
779 |
|
|
configuratorList.add(helperConfigurator);
|
780 |
|
|
} else if (string.equals(StatisticsPartEnum.CLASSIFICATION
|
781 |
|
|
.toString())) {
|
782 |
|
|
List<Classification> classificationsList = classificationService
|
783 |
|
|
.listClassifications(null, 0, null, null);
|
784 |
|
|
for (Classification classification : classificationsList) {
|
785 |
|
|
|
786 |
|
|
StatisticsConfigurator newConfigurator = new StatisticsConfigurator();
|
787 |
|
|
newConfigurator.setType(helperConfigurator.getType());
|
788 |
|
|
newConfigurator.getFilter().addAll(
|
789 |
|
|
helperConfigurator.getFilter());
|
790 |
|
|
newConfigurator.addFilter(classification);
|
791 |
|
|
configuratorList.add(newConfigurator);
|
792 |
|
|
}
|
793 |
|
|
}
|
794 |
|
|
}
|
795 |
ace5aeed
|
s.buers
|
|
796 |
|
|
}
|
797 |
|
|
|
798 |
810b7215
|
Andreas Müller
|
return configuratorList;
|
799 |
ace5aeed
|
s.buers
|
}
|
800 |
|
|
|
801 |
0280b3f1
|
s.buers
|
public class MyCounter {
|
802 |
|
|
protected long classifications = 0;
|
803 |
|
|
protected long allTaxa = 0;
|
804 |
|
|
protected long aceptedTaxa = 0;
|
805 |
|
|
protected long taxonNames = 0;
|
806 |
|
|
protected long synonyms = 0;
|
807 |
|
|
protected long descrSourceRef = 0;
|
808 |
|
|
protected long nomenclRef = 0;
|
809 |
|
|
protected long allReferences = 0;
|
810 |
|
|
protected long descriptions = 0;
|
811 |
|
|
|
812 |
|
|
public void addAll(MyCounter otherCounter) {
|
813 |
|
|
classifications += otherCounter.classifications;
|
814 |
|
|
allTaxa += otherCounter.allTaxa;
|
815 |
|
|
aceptedTaxa += otherCounter.aceptedTaxa;
|
816 |
|
|
taxonNames += otherCounter.taxonNames;
|
817 |
|
|
synonyms += otherCounter.synonyms;
|
818 |
|
|
descrSourceRef += otherCounter.descrSourceRef;
|
819 |
|
|
nomenclRef += otherCounter.nomenclRef;
|
820 |
|
|
allReferences += otherCounter.allReferences;
|
821 |
|
|
descriptions += otherCounter.descriptions;
|
822 |
|
|
}
|
823 |
|
|
|
824 |
|
|
public void reset() {
|
825 |
|
|
classifications = 0;
|
826 |
|
|
allTaxa = 0;
|
827 |
|
|
aceptedTaxa = 0;
|
828 |
|
|
taxonNames = 0;
|
829 |
|
|
synonyms = 0;
|
830 |
|
|
descrSourceRef = 0;
|
831 |
|
|
nomenclRef = 0;
|
832 |
|
|
allReferences = 0;
|
833 |
|
|
descriptions = 0;
|
834 |
|
|
}
|
835 |
|
|
|
836 |
|
|
@Override
|
837 |
|
|
public String toString() {
|
838 |
|
|
return "{Taxon_names=" + taxonNames + ", Synonyms=" + synonyms
|
839 |
|
|
+ ", Accepted_taxa=" + aceptedTaxa
|
840 |
100aec39
|
Andreas Müller
|
+ ", Nomenclatural_references=" + nomenclRef
|
841 |
0280b3f1
|
s.buers
|
+ ", Classifications=" + classifications
|
842 |
|
|
+ ", Descriptive_source_references=" + descrSourceRef
|
843 |
|
|
+ ", References=" + allReferences + ", All_taxa=" + allTaxa
|
844 |
|
|
+ "}\n";
|
845 |
|
|
}
|
846 |
|
|
}
|
847 |
|
|
|
848 |
d06ba760
|
Patric Plitzner
|
/* (non-Javadoc)
|
849 |
|
|
* @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
|
850 |
|
|
*/
|
851 |
|
|
@Override
|
852 |
68ee041d
|
Patric Plitzner
|
public void createTestDataSet() throws FileNotFoundException {
|
853 |
d06ba760
|
Patric Plitzner
|
// TODO Auto-generated method stub
|
854 |
da39aca0
|
Andreas Müller
|
|
855 |
d06ba760
|
Patric Plitzner
|
}
|
856 |
|
|
|
857 |
ace5aeed
|
s.buers
|
}
|