Java tutorial
/* * To change this license header, choose License Headers in Project Properties. * To change this template file, choose Tools | Templates * and open the template in the editor. */ package uk.ac.ebi.ep.data.repositories; import java.sql.SQLException; import java.util.ArrayList; import java.util.LinkedList; import java.util.List; import java.util.stream.Collectors; import javax.persistence.EntityManager; import javax.persistence.PersistenceContext; import org.junit.After; import org.junit.Test; import org.springframework.data.domain.Page; import org.springframework.data.domain.PageRequest; import org.springframework.data.domain.Pageable; import org.springframework.data.domain.Sort; import uk.ac.ebi.ep.data.domain.UniprotEntry; import uk.ac.ebi.ep.data.search.model.EnzymeSummary; import uk.ac.ebi.ep.data.search.model.Species; import uk.ac.ebi.ep.data.search.model.Taxonomy; import uk.ac.ebi.ep.data.service.AbstractDataTest; /** * * @author joseph */ public class UniprotEntryRepositoryImplTest extends AbstractDataTest { @PersistenceContext private EntityManager entityManager; private final UniprotEntryRepositoryImpl instance = new UniprotEntryRepositoryImpl(); @After @Override public void tearDown() throws SQLException { dataSource.getConnection().close(); entityManager.close(); } /** * Test of setEntityManager method, of class UniprotEntryRepositoryImpl. */ @Test public void testSetEntityManager() { LOGGER.info("setEntityManager"); instance.setEntityManager(entityManager); EntityManager manager = instance.getEntityManager(); assertNotNull(manager); } /** * Test of findEnzymesByNamePrefixes method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymesByNamePrefixes() { LOGGER.info("findEnzymesByNamePrefixes"); List<String> namePrefixes = new ArrayList<>(); namePrefixes.add("CP24A"); namePrefixes.add("FAKEGENE"); namePrefixes.add("CP7B1"); int expResult = 6; List<UniprotEntry> result = uniprotEntryRepository.findEnzymesByNamePrefixes(namePrefixes); assertEquals(expResult, result.size()); } /** * Test of findEnzymesByAccessions method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymesByAccessions_List() { LOGGER.info("findEnzymesByAccessions"); List<String> accessions = new ArrayList<>(); accessions.add("Q60991"); accessions.add("M636T8"); accessions.add("Q0III2"); accessions.add("Q64441"); accessions.add("PK5671"); accessions.add("fakeAccession"); int expResult = 3; List<UniprotEntry> result = uniprotEntryRepository.findEnzymesByAccessions(accessions); assertEquals(expResult, result.size()); } /** * Test of findEnzymeByNamePrefix method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymeByNamePrefix() { LOGGER.info("findEnzymeByNamePrefix"); String namePrefix = "CP24A"; int expResult = 3; List<UniprotEntry> result = uniprotEntryRepository.findEnzymeByNamePrefix(namePrefix); assertEquals(expResult, result.size()); } /** * Test of filterEnzymesInAccessions method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFilterEnzymesInAccessions() { LOGGER.info("filterEnzymesInAccessions"); List<String> accessions = new ArrayList<>(); accessions.add("Q60991"); accessions.add("Q63688"); accessions.add("Q0III2"); accessions.add("Q64441"); accessions.add("NotAnEnzyme"); // List<String> expResult = new LinkedList<>(); // // expResult.add("Q0III2"); // expResult.add("Q63688"); // expResult.add("Q60991"); List<String> result = uniprotEntryRepository.filterEnzymesInAccessions(accessions).stream().distinct() .collect(Collectors.toList()); assertTrue(result.size() > 1); } /** * Test of findEnzymesByAccession method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymesByAccession() { LOGGER.info("findEnzymesByAccession"); String accession = "Q64441"; int expResult = 1; List<UniprotEntry> result = uniprotEntryRepository.findEnzymesByAccession(accession).stream().distinct() .collect(Collectors.toList()); assertEquals(expResult, result.size()); } /** * Test of getCountForOrganisms method, of class UniprotEntryRepositoryImpl. */ @Test public void testGetCountForOrganisms() { LOGGER.info("getCountForOrganisms"); List<Long> taxids = new ArrayList<>(); taxids.add(9606L); taxids.add(10116L); taxids.add(7955L); taxids.add(9913L); taxids.add(10090L); int expResult = 4; List<Taxonomy> result = uniprotEntryRepository.getCountForOrganisms(taxids); assertEquals(expResult, result.size()); } /** * Test of findAccessionsByTaxId method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindAccessionsByTaxId() { LOGGER.info("findAccessionsByTaxId"); Long taxId = 9606L; List<String> expResult = new LinkedList<>(); expResult.add("O43462"); expResult.add("O75881"); expResult.add("Q07973"); expResult.add("P08183"); expResult.add("O76074"); List<String> result = uniprotEntryRepository.findAccessionsByTaxId(taxId); assertEquals(expResult, result); assertEquals(expResult.size(), result.size()); } /** * Test of findEnzymesByTaxId method, of class UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymesByTaxId() { LOGGER.info("findEnzymesByTaxId"); Long taxId = 9606L; int expResult = 5; List<UniprotEntry> result = uniprotEntryRepository.findEnzymesByTaxId(taxId); assertEquals(expResult, result.size()); } /** * Test of findEnzymesByAccessions method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymesByAccessions_List_Pageable() { LOGGER.info("findEnzymesByAccessions"); List<String> accessions = new ArrayList<>(); accessions.add("Q60991"); accessions.add("Q63688"); accessions.add("Q0III2"); accessions.add("Q64441"); accessions.add("fakeAccession"); Pageable pageable = new PageRequest(0, 500, Sort.Direction.ASC, "function", "entryType"); int expResult = 4; Page<EnzymeSummary> result = uniprotEntryRepository.findEnzymesByAccessions(accessions, pageable); assertEquals(expResult, result.getContent().size()); assertEquals(4, result.getTotalElements()); assertEquals(1, result.getTotalPages()); } /** * Test of findSpeciesByTaxId method, of class UniprotEntryRepositoryImpl. */ @Test public void testFindSpeciesByTaxId() { LOGGER.info("findSpeciesByTaxId"); Long taxId = 9606L; Species species = new Species("Homo sapiens", "Human", taxId); List<Species> expResult = new ArrayList<>(); expResult.add(species); List<Species> result = uniprotEntryRepository.findSpeciesByTaxId(taxId); assertEquals(expResult, result); assertEquals(expResult.size(), result.size()); } /** * Test of findSpeciesByScientificName method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindSpeciesByScientificName() { LOGGER.info("findSpeciesByScientificName"); String sName = "Homo sapiens"; Species species = new Species("Homo sapiens", "Human", 9606L); List<Species> expResult = new ArrayList<>(); expResult.add(species); List<Species> result = uniprotEntryRepository.findSpeciesByScientificName(sName); assertEquals(expResult, result); } /** * Test of findEnzymesByMeshId method, of class UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymesByMeshId() { LOGGER.info("findEnzymesByMeshId"); String meshId = "D006934"; int expResult = 1; List<UniprotEntry> result = uniprotEntryRepository.findEnzymesByMeshId(meshId); assertEquals(expResult, result.size()); } /** * Test of findEnzymesByPathwayId method, of class * UniprotEntryRepositoryImpl. */ @Test public void testFindEnzymesByPathwayId() { LOGGER.info("findEnzymesByPathwayId"); String pathwayId = "REACT_147797"; int expResult = 1; List<UniprotEntry> result = uniprotEntryRepository.findEnzymesByPathwayId(pathwayId); assertEquals(expResult, result.size()); } }