NameUsageServiceMyBatisIT.java

package org.gbif.checklistbank.service.mybatis;

import org.gbif.api.model.checklistbank.NameUsage;
import org.gbif.api.model.checklistbank.NameUsageMetrics;
import org.gbif.api.model.checklistbank.ParsedName;
import org.gbif.api.model.common.paging.Pageable;
import org.gbif.api.model.common.paging.PagingConstants;
import org.gbif.api.model.common.paging.PagingRequest;
import org.gbif.api.service.checklistbank.NameUsageService;
import org.gbif.api.vocabulary.NameUsageIssue;
import org.gbif.api.vocabulary.Origin;
import org.gbif.api.vocabulary.Rank;
import org.gbif.checklistbank.model.RawUsage;
import org.gbif.checklistbank.service.mybatis.guice.InternalChecklistBankServiceMyBatisModule;

import java.net.URI;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.util.EnumSet;
import java.util.List;
import java.util.Locale;
import java.util.UUID;

import com.google.common.base.Joiner;
import com.zaxxer.hikari.HikariDataSource;
import org.gbif.checklistbank.service.mybatis.postgres.ClbDbTestRule;
import org.junit.Assert;
import org.junit.Test;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;

public class NameUsageServiceMyBatisIT extends MyBatisServiceITBase<NameUsageService> {

  public NameUsageServiceMyBatisIT() {
    super(NameUsageService.class);
  }

  private final int NOT_FOUND_KEY = -10;

  @Test
  public void testGet() {
    final NameUsage rodentia = service.get(100000004, Locale.UK);
    final NameUsageMetrics rodentiaM = service.getMetrics(100000004);
    assertNotNull(rodentia);
    assertEquals((Integer) 10, rodentia.getNubKey());
    assertFalse(rodentia.isSynonym());
    assertEquals("1000", rodentia.getTaxonID());
    assertEquals("Rodentia", rodentia.getCanonicalName());
    assertEquals("Rodentia Bowdich, 1821", rodentia.getScientificName());
    assertEquals("Bowdich, 1821", rodentia.getAuthorship());
    assertEquals(Rank.ORDER, rodentia.getRank());
    assertEquals((Integer) 100000003, rodentia.getParentKey());

    assertEquals("Animalia", rodentia.getKingdom());
    assertEquals((Integer) 100000001, rodentia.getKingdomKey());

    assertEquals("Chordata", rodentia.getPhylum());
    assertEquals((Integer) 100000002, rodentia.getPhylumKey());
    assertEquals(0, rodentiaM.getNumPhylum());

    assertEquals("Mammalia", rodentia.getClazz());
    assertEquals((Integer) 100000003, rodentia.getClassKey());
    assertEquals(0, rodentiaM.getNumClass());

    assertEquals(1, rodentiaM.getNumOrder());
    assertEquals(1, rodentiaM.getNumFamily());
    assertEquals(2, rodentiaM.getNumGenus());
    assertEquals(3, rodentiaM.getNumSpecies());
    assertEquals(8, rodentiaM.getNumSynonyms());
    assertEquals(1, rodentiaM.getNumChildren());
    assertEquals(24, rodentia.getNumDescendants());

    assertEquals(Origin.SOURCE, rodentia.getOrigin());

    assertEquals(ClbDbTestRule.SQUIRRELS_DATASET_KEY, rodentia.getDatasetKey());
    assertNull(rodentia.getPublishedIn());

    assertEquals("1000", rodentia.getTaxonID());


    NameUsage squirrel = service.get(100000025, Locale.UK);
    final NameUsageMetrics squirrelM = service.getMetrics(100000025);
    assertNotNull(squirrel);
    assertNull(squirrel.getNubKey());
    assertFalse(squirrel.isSynonym());
    assertEquals("Sciurus vulgaris", squirrel.getCanonicalName());
    assertEquals("Sciurus vulgaris Linnaeus, 1758", squirrel.getScientificName());
    assertEquals("Linnaeus, 1758", squirrel.getAuthorship());
    assertEquals("Eurasian Red Squirrel", squirrel.getVernacularName());
    assertEquals(Rank.SPECIES, squirrel.getRank());
    assertEquals((Integer) 100000024, squirrel.getParentKey());

    assertEquals("Animalia", squirrel.getKingdom());
    assertEquals((Integer) 100000001, squirrel.getKingdomKey());

    assertEquals("Chordata", squirrel.getPhylum());
    assertEquals((Integer) 100000002, squirrel.getPhylumKey());
    assertEquals(0, squirrelM.getNumPhylum());

    assertEquals("Mammalia", squirrel.getClazz());
    assertEquals((Integer) 100000003, squirrel.getClassKey());
    assertEquals(0, squirrelM.getNumClass());

    assertEquals("Rodentia", squirrel.getOrder());
    assertEquals((Integer) 100000004, squirrel.getOrderKey());
    assertEquals(0, squirrelM.getNumOrder());

    assertEquals("Sciuridae", squirrel.getFamily());
    assertEquals((Integer) 100000005, squirrel.getFamilyKey());
    assertEquals(0, squirrelM.getNumFamily());

    assertEquals("Sciurus", squirrel.getGenus());
    assertEquals((Integer) 100000011, squirrel.getGenusKey());
    assertEquals(0, squirrelM.getNumGenus());

    assertEquals(1, squirrelM.getNumSpecies());
    assertEquals(9, squirrelM.getNumChildren());
    assertEquals(4, squirrelM.getNumSynonyms());

    assertEquals(ClbDbTestRule.SQUIRRELS_DATASET_KEY, squirrel.getDatasetKey());
    assertEquals("Syst. Nat. , 10th ed. vol. 1 p. 63", squirrel.getPublishedIn());

    assertEquals("2010030", squirrel.getTaxonID());


    // TEST VERNACULAR
    squirrel = service.get(100000040, null);
    assertNull(squirrel.getVernacularName());

    squirrel = service.get(100000040, Locale.ENGLISH);
    assertEquals("Caucasian Squirrel", squirrel.getVernacularName());

    squirrel = service.get(100000040, Locale.GERMANY);
    assertEquals("Kaukasischen Eichhörnchen", squirrel.getVernacularName());

    // TEST non existing language VERNACULAR
    squirrel = service.get(100000040, Locale.CHINESE);
    assertNull(squirrel.getVernacularName());

    // TEST MULTIPLE IDENTIFIERS
    squirrel = service.get(100000007, Locale.GERMANY);
    assertEquals("6905528", squirrel.getTaxonID());
    assertEquals(URI.create("http://www.catalogueoflife.org/details/species/id/6905528"), squirrel.getReferences());

    // TEST SYNONYM
    NameUsage syn = service.get(100000027, Locale.FRENCH);
    assertNotNull(syn);
    assertTrue(syn.isSynonym());
    assertEquals("Sciurus nadymensis", syn.getCanonicalName());
    assertEquals("Sciurus nadymensis Serebrennikov, 1928", syn.getScientificName());
    assertNull(syn.getVernacularName());
    assertEquals(Rank.SPECIES, syn.getRank());
    assertEquals((Integer) 100000024, syn.getParentKey());
    assertEquals((Integer) 100000025, syn.getAcceptedKey());
    assertEquals("Sciurus vulgaris Linnaeus, 1758", syn.getAccepted());
    assertFalse(syn.isProParte());

  }

  @Test
  public void testArraySet() {
    // test nomenclatoral status set
    NameUsage syn = service.get(100000026, Locale.FRENCH);
    assertEquals(2, syn.getNomenclaturalStatus().size());
  }

  @Test
  public void testGetNotFound() {
    assertNull(service.get(NOT_FOUND_KEY, Locale.UK));
  }

  @Test
  public void testGetParsedName() {
    final ParsedName rodentia = service.getParsedName(100000004);
    assertNotNull(rodentia);
    assertEquals("Rodentia", rodentia.getGenusOrAbove());
    assertEquals("Bowdich", rodentia.getAuthorship());
    assertEquals("1821", rodentia.getYear());
    assertEquals(Rank.ORDER, rodentia.getRank());
  }

  @Test
  public void testGetParsedNameNotFound() {
    assertNull(service.getParsedName(NOT_FOUND_KEY));
  }

  @Test
  public void testList() {
    List<NameUsage> usages = service.list(Locale.UK, null, null, null).getResults();
    assertEquals(PagingConstants.DEFAULT_PARAM_LIMIT, usages.size());

    // test paging
    Pageable page = new PagingRequest(1l, 1);
    usages = service.list(Locale.UK, null, null, page).getResults();
    assertEquals(1, usages.size());
    NameUsage u1 = usages.get(0);

    page = new PagingRequest(0l, 2);
    usages = service.list(Locale.UK, null, null, page).getResults();
    assertEquals(2, usages.size());
    assertEquals(u1, usages.get(1));

    // test by source id
    usages = service.list(Locale.UK, null, "1", null).getResults();
    assertEquals(1, usages.size());
    assertEquals((Integer) 100000001, usages.get(0).getKey());

    // test by checklist key
    usages = service.list(Locale.UK, UUID.fromString("d7dddbf4-2cf0-4f39-9b2a-bb099caae36c"), null, null)
        .getResults();
    assertEquals(2, usages.size());

    // test combined
    usages =
        service.list(Locale.UK, ClbDbTestRule.SQUIRRELS_DATASET_KEY, "1", null).getResults();
    assertEquals(1, usages.size());
    assertEquals((Integer) 100000001, usages.get(0).getKey());
  }

  @Test
  public void testByTaxonId() {
    List<NameUsage> usages = service.list(Locale.UK, ClbDbTestRule.SQUIRRELS_DATASET_KEY, "100000", null).getResults();
    assertEquals(1, usages.size());

    assertEquals(service.get(100000006, Locale.UK), usages.get(0));
  }

  @Test
  public void testListRelated() {
    List<NameUsage> usages = service.listRelated(1, Locale.UK, null).getResults();
    ;
    assertEquals(1, usages.size());

    usages = service.listRelated(1, Locale.UK, null, ClbDbTestRule.SQUIRRELS_DATASET_KEY).getResults();
    assertEquals(1, usages.size());

    usages = service.listRelated(1, Locale.UK, null, ClbDbTestRule.SQUIRRELS_DATASET_KEY,
        UUID.fromString("109aea14-c252-4a85-96e2-f5f4d5d088f5")).getResults();
    assertEquals(1, usages.size());

    usages = service.listRelated(1, Locale.UK, null, UUID.fromString("109aea14-c252-4a85-96e2-f5f4d5d088ff")).getResults();
    assertEquals(0, usages.size());
  }

  @Test
  public void testListCombinations() {
    List<NameUsage> usages = service.listCombinations(1, Locale.UK);
    assertEquals(0, usages.size());

    usages = service.listCombinations(100000025, Locale.UK);
    assertEquals(2, usages.size());
  }

  @Test
  public void testListRelatedNotFound() {
    assertTrue(service.listRelated(NOT_FOUND_KEY, Locale.UK, null).getResults().isEmpty());
  }

  @Test
  public void testListChildren() {
    List<NameUsage> usages = service.listChildren(100000025, Locale.UK, null).getResults();
    assertEquals(9, usages.size());

    // assert we start with highest ranks, then lower ones
    assertEquals(Rank.SUBSPECIES, usages.get(0).getRank());
    assertEquals(Rank.SUBSPECIES, usages.get(1).getRank());
    assertEquals(Rank.VARIETY, usages.get(7).getRank());
    assertEquals(Rank.VARIETY, usages.get(8).getRank());

    // test paging
    Pageable page = new PagingRequest(3, 2);
    usages = service.listChildren(100000025, Locale.UK, page).getResults();
    assertEquals(2, usages.size());

    page = new PagingRequest(2, 5);
    List<NameUsage> usages2 = service.listChildren(100000025, Locale.UK, page).getResults();
    assertEquals(5, usages2.size());
    assertEquals(usages.get(0), usages2.get(1));
    assertEquals(usages.get(1), usages2.get(2));
  }

  @Test
  public void testListChildrenNotFound() {
    assertTrue(service.listChildren(NOT_FOUND_KEY, Locale.UK, null).getResults().isEmpty());
  }

  @Test
  public void testListRoot() {
    List<NameUsage> usages = service.listRoot(ClbDbTestRule.SQUIRRELS_DATASET_KEY, Locale.UK, null).getResults();
    assertEquals(1, usages.size());

    // test paging
    Pageable page = new PagingRequest(1l, 1);
    usages = service.listRoot(ClbDbTestRule.SQUIRRELS_DATASET_KEY, Locale.UK, page).getResults();
    assertEquals(0, usages.size());

    page = new PagingRequest(0l, 2);
    usages = service.listRoot(ClbDbTestRule.SQUIRRELS_DATASET_KEY, Locale.UK, page).getResults();
    assertEquals(1, usages.size());
  }

  @Test
  public void testListSynonyms() {
    List<NameUsage> usages = service.listSynonyms(100000025, Locale.UK, null).getResults();
    assertEquals(4, usages.size());

    // test paging
    Pageable page = new PagingRequest(0, 2);
    usages = service.listSynonyms(100000025, Locale.UK, page).getResults();
    assertEquals(2, usages.size());

    page = new PagingRequest(1, 2);
    List<NameUsage> usages2 = service.listSynonyms(100000025, Locale.UK, page).getResults();
    assertEquals(2, usages2.size());
    assertEquals(usages.get(1), usages2.get(0));
  }

  @Test
  public void testListSynonymsNotFound() {
    assertTrue(service.listSynonyms(NOT_FOUND_KEY, Locale.UK, null).getResults().isEmpty());
  }

  @Test
  public void testVerbatim() {
    // even though the record exists the verbatim smile data is empty, so null here
    assertNull(service.getVerbatim(100000011));
    assertNull(service.getVerbatim(NOT_FOUND_KEY));
  }

  @Test
  public void testUsageMetrics() {
    NameUsageMetrics m = service.getMetrics(100000011);
    assertNotNull(m);
    assertEquals((Integer) 100000011, m.getKey());
    assertEquals(2, m.getNumChildren());
    assertEquals(12, m.getNumSynonyms());
    assertEquals(1, m.getNumGenus());
    assertEquals(2, m.getNumSubgenus());
    assertEquals(2, m.getNumSpecies());
    // not set in dbSetup file
    assertEquals(3, m.getNumDescendants());
    assertEquals(0, m.getNumFamily());

    assertNull(service.getMetrics(NOT_FOUND_KEY));
  }

  /**
   * http://dev.gbif.org/issues/browse/POR-3032
   */
  @Test
  public void testUsageIssues() {
    NameUsage u = service.get(100000040, null);
    assertNotNull(u);
    assertEquals(1, u.getIssues().size());

    EnumSet expected = EnumSet.of(NameUsageIssue.RANK_INVALID);
    assertEquals(expected, u.getIssues());

    Joiner j = Joiner.on(",").skipNulls();
    for (int x = 0; x < 10; x++) {
      u = service.get(100000040, null);
      assertEquals("Call "+x+" should be correct", expected, u.getIssues());
    }
  }

  /**
   * Prepared statements in postgres jdbc have a bug when caching text[] array types.
   * This test shows it and we circumvent this behavior by telling mybatis not to cache results.
   *
   * http://dev.gbif.org/issues/browse/POR-3032
   *
   * https://github.com/pgjdbc/pgjdbc/issues/517
   */
  @Test
  public void testUsageIssuesJdbc() throws Exception {
    HikariDataSource ds = (HikariDataSource) getInstance(InternalChecklistBankServiceMyBatisModule.DATASOURCE_KEY);
    try (Connection cn = ds.getConnection()) {
      PreparedStatement st = cn.prepareStatement("select issues from name_usage where id=?");
      for (int x = 0; x < 10; x++) {
        st.setInt(1, 100000040);
        st.execute();
        ResultSet rs = st.getResultSet();
        rs.next();
        System.out.println(rs.getString(1));
      }
    } finally {
      ds.close();
    }
  }

  @Test
  public void insertRaw() {
    final int key = 100000001;
    final String data = "xeghwax542tgld@";
    RawUsage raw = new RawUsage();
    raw.setUsageKey(key);
    raw.setDatasetKey(ClbDbTestRule.SQUIRRELS_DATASET_KEY);
    // date is null in dataset_metrics table
    //raw.setLastCrawled(new Date());
    raw.setJson(data);

    ((NameUsageServiceMyBatis) service).insertRaw(raw);

    RawUsage raw2 = ((NameUsageServiceMyBatis) service).getRaw(key);
    Assert.assertEquals(raw, raw2);
  }

}