NeoInserterTest.java

package org.gbif.checklistbank.neo;

import org.gbif.api.model.checklistbank.NameUsage;
import org.gbif.api.model.checklistbank.NameUsageContainer;
import org.gbif.api.model.checklistbank.VerbatimNameUsage;
import org.gbif.api.vocabulary.NameType;
import org.gbif.api.vocabulary.Rank;
import org.gbif.checklistbank.cli.normalizer.IgnoreNameUsageException;
import org.gbif.dwc.terms.DcTerm;
import org.gbif.dwc.terms.DwcTerm;
import org.gbif.dwc.terms.Term;
import org.gbif.dwca.io.ArchiveField;
import org.gbif.dwca.record.RecordImpl;
import org.gbif.dwca.record.StarRecordImpl;

import java.net.URI;
import java.util.List;

import com.google.common.collect.Lists;
import org.junit.Before;
import org.junit.Test;
import org.neo4j.graphdb.Node;
import org.neo4j.graphdb.Transaction;
import org.neo4j.helpers.collection.Iterators;


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

public class NeoInserterTest {
    NeoInserter ins;
    List<String> values;
    List<ArchiveField> fields;
    UsageDao dao;

    @Before
    public void init() throws Exception {
        values = Lists.newArrayList();
        fields = Lists.newArrayList();
        dao = UsageDao.temporaryDao(10);
        ins = dao.createBatchInserter(100);
    }

    private void addColumn(Term term, String value) {
        ArchiveField f = new ArchiveField(fields.size(), term, null, ArchiveField.DataType.string);
        fields.add(f);
        values.add(value);
    }

    @Test
    public void testNonDwcProperties() throws Exception {

        addColumn(DwcTerm.taxonID, "1");
        addColumn(DwcTerm.scientificName, "Abies alba Mill., 1982");
        addColumn(DwcTerm.scientificNameAuthorship, "Mill.");
        addColumn(DwcTerm.namePublishedIn, "Führ. Pilzk. (Zwickau) 136 (1871)");
        addColumn(DwcTerm.namePublishedInID, "12345678");
        addColumn(DwcTerm.namePublishedInYear, "1871");
        addColumn(DwcTerm.nameAccordingTo, "Miller");
        addColumn(DwcTerm.nameAccordingToID, "123456");
        addColumn(DwcTerm.taxonRemarks, "bugger off");
        addColumn(DcTerm.references, "http://gbif.org");

        StarRecordImpl star = new StarRecordImpl(Lists.<Term>newArrayList());
        RecordImpl rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
        rec.setRow(values.toArray(new String[]{}));
        star.newCoreRecord(rec);
        ins.insertStarRecord(star);
        ins.close();

        try (Transaction tx = dao.beginTx()) {
            Node n = dao.getNeo().getNodeById(0);
            assertEquals("1", n.getProperty(NeoProperties.TAXON_ID));

            VerbatimNameUsage v = dao.readVerbatim(n.getId());
            assertEquals("1", v.getCoreField(DwcTerm.taxonID));
            assertEquals("Abies alba Mill., 1982", v.getCoreField(DwcTerm.scientificName));
            assertEquals("Mill.", v.getCoreField(DwcTerm.scientificNameAuthorship));
            assertEquals("Führ. Pilzk. (Zwickau) 136 (1871)", v.getCoreField(DwcTerm.namePublishedIn));
            assertEquals("12345678", v.getCoreField(DwcTerm.namePublishedInID));
            assertEquals("1871", v.getCoreField(DwcTerm.namePublishedInYear));
            assertEquals("Miller", v.getCoreField(DwcTerm.nameAccordingTo));
            assertEquals("123456", v.getCoreField(DwcTerm.nameAccordingToID));
            assertEquals("bugger off", v.getCoreField(DwcTerm.taxonRemarks));
            assertEquals("http://gbif.org", v.getCoreField(DcTerm.references));

            NameUsage u = dao.readUsage(n, true);
            assertEquals("1", u.getTaxonID());
            assertEquals("Abies alba Mill., 1982", u.getScientificName());
            assertEquals("Mill.", u.getAuthorship());
            assertEquals("Führ. Pilzk. (Zwickau) 136 (1871)", u.getPublishedIn());
            assertEquals("Miller", u.getAccordingTo());
            assertEquals("bugger off", u.getRemarks());
            assertEquals(URI.create("http://gbif.org"), u.getReferences());
        }
    }

    @Test
    public void testTaxonIDUnique() throws Exception {

        addColumn(DwcTerm.taxonID, "1");
        addColumn(DwcTerm.scientificName, "Abies alba Mill., 1982");
        StarRecordImpl star = new StarRecordImpl(Lists.<Term>newArrayList());
        RecordImpl rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
        rec.setRow(values.toArray(new String[]{}));
        star.newCoreRecord(rec);
        ins.insertStarRecord(star);

        values = Lists.newArrayList();
        fields = Lists.newArrayList();
        addColumn(DwcTerm.taxonID, "2");
        addColumn(DwcTerm.scientificName, "Picea alba");
        rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
        rec.setRow(values.toArray(new String[]{}));
        star.newCoreRecord(rec);
        ins.insertStarRecord(star);

        ins.close();

        try (Transaction tx = dao.beginTx()) {
            assertNotNull(Iterators.singleOrNull(dao.getNeo().findNodes(Labels.TAXON, NeoProperties.TAXON_ID, "1")));
        }
    }

    @Test(expected = NotUniqueRuntimeException.class)
    public void testTaxonIDNotUnique() throws Exception {

        addColumn(DwcTerm.taxonID, "1");
        addColumn(DwcTerm.scientificName, "Abies alba Mill., 1982");
        StarRecordImpl star = new StarRecordImpl(Lists.<Term>newArrayList());
        RecordImpl rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
        rec.setRow(values.toArray(new String[]{}));
        star.newCoreRecord(rec);
        ins.insertStarRecord(star);

        values = Lists.newArrayList();
        fields = Lists.newArrayList();
        addColumn(DwcTerm.taxonID, "1");
        addColumn(DwcTerm.scientificName, "Picea alba");
        rec = new RecordImpl(fields.get(0), fields, DwcTerm.Taxon, true, true);
        rec.setRow(values.toArray(new String[]{}));
        star.newCoreRecord(rec);
        ins.insertStarRecord(star);

        ins.close();
    }

    @Test
    public void testSetScientificName() throws Exception {

        VerbatimNameUsage v = new VerbatimNameUsage();
        v.setCoreField(DwcTerm.scientificName, "Abies alba Mill., 1982");
        assertName(v, Rank.SPECIES, "Abies alba Mill., 1982", "Abies alba", NameType.SCIENTIFIC);

        v = new VerbatimNameUsage();
        v.setCoreField(DwcTerm.scientificName, "Abies alba");
        assertName(v, Rank.SPECIES, "Abies alba", "Abies alba", NameType.SCIENTIFIC);

        v = new VerbatimNameUsage();
        v.setCoreField(DwcTerm.scientificName, "? alba");
        assertName(v, Rank.SPECIES, "? alba", "? alba", NameType.PLACEHOLDER);

        v = new VerbatimNameUsage();
        v.setCoreField(DwcTerm.genus, "Abies");
        v.setCoreField(DwcTerm.specificEpithet, "alba");
        assertName(v, Rank.SPECIES, "Abies alba", "Abies alba", NameType.SCIENTIFIC);

        v = new VerbatimNameUsage();
        v.setCoreField(DwcTerm.genus, "Abies");
        v.setCoreField(DwcTerm.infraspecificEpithet, "alpina");
        assertName(v, Rank.SUBSPECIES, "Abies subsp.", "Abies subsp.", NameType.SCIENTIFIC);

        v = new VerbatimNameUsage();
        v.setCoreField(DwcTerm.genus, "Abies");
        v.setCoreField(DwcTerm.specificEpithet, "alba");
        v.setCoreField(DwcTerm.infraspecificEpithet, "alpina");
        assertName(v, Rank.SUBSPECIES, "Abies alba subsp. alpina", "Abies alba alpina", NameType.SCIENTIFIC);

        v.setCoreField(DwcTerm.scientificNameAuthorship, "Duméril & Bibron");
        assertName(v, Rank.SUBSPECIES, "Abies alba subsp. alpina Duméril & Bibron", "Abies alba alpina", NameType.SCIENTIFIC);

        v.setCoreField(DwcTerm.namePublishedInYear, "1937");
        assertName(v, Rank.SUBSPECIES, "Abies alba subsp. alpina Duméril & Bibron, 1937", "Abies alba alpina", NameType.SCIENTIFIC);

        v.setCoreField(DwcTerm.scientificNameAuthorship, "Duméril & Bibron 1937");
        assertName(v, Rank.SUBSPECIES, "Abies alba subsp. alpina Duméril & Bibron 1937", "Abies alba alpina", NameType.SCIENTIFIC);
    }

    @Test(expected = IgnoreNameUsageException.class)
    public void testSetScientificNameExc() throws Exception {
        VerbatimNameUsage v = new VerbatimNameUsage();
        assertName(v, Rank.SPECIES, null, null, NameType.NO_NAME);
    }

    private NameUsageContainer assertName(VerbatimNameUsage v, Rank rank, String sciname, String canonical, NameType ntype)
            throws IgnoreNameUsageException {
        NameUsageContainer u = new NameUsageContainer();
        ins.setScientificName(u, v, rank);
        if (sciname != null) {
            assertEquals(sciname, u.getScientificName());
        } else {
            assertNull(u.getScientificName());
        }
        if (canonical != null) {
            assertEquals(canonical, u.getCanonicalName());
        } else {
            assertNull(u.getCanonicalName());
        }
        if (ntype != null) {
            assertEquals(ntype, u.getNameType());
        } else {
            assertNull(u.getNameType());
        }
        return u;
    }

    @Test
    public void testClean() throws Exception {
        assertNull(NeoInserter.clean(null));
        assertNull(NeoInserter.clean(" "));
        assertNull(NeoInserter.clean("   "));
        assertNull(NeoInserter.clean("\\N"));
        assertNull(NeoInserter.clean("NULL"));
        assertNull(NeoInserter.clean("\t "));

        assertEquals("Abies", NeoInserter.clean("Abies"));
        assertEquals("öAbies", NeoInserter.clean("öAbies"));
        assertEquals("Abies  mille", NeoInserter.clean(" Abies  mille"));
    }

}