Examples with FindOccurrencesConfigurator eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator used on opensource projects

Example 1 with FindOccurrencesConfigurator

use of eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator in project cdmlib by cybertaxonomy.

the class AbcdGgbnImportTest method testImportGgbn.

/**
 * Tests import import of DNA unit and all its parameters
 * and sub derivatives (sequence, amplification, etc.)
 * @throws ParseException
 */
@Test
@DataSet(value = "/eu/etaxonomy/cdm/database/ClearDBDataSet.xml", loadStrategy = CleanSweepInsertLoadStrategy.class)
public void testImportGgbn() throws ParseException {
    String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6_without_association.xml";
    URL url = this.getClass().getResource(inputFile);
    assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
    Abcd206ImportConfigurator importConfigurator = null;
    try {
        importConfigurator = Abcd206ImportConfigurator.NewInstance(new URI(url), null, false);
    } catch (URISyntaxException e) {
        e.printStackTrace();
        Assert.fail();
    }
    assertNotNull("Configurator could not be created", importConfigurator);
    boolean result = defaultImport.invoke(importConfigurator).isSuccess();
    assertTrue("Return value for import.invoke should be true", result);
    assertEquals("Number of derived units is incorrect", 1, occurrenceService.count(DerivedUnit.class));
    assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
    assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));
    // dna sample
    FindOccurrencesConfigurator dnaConfig = new FindOccurrencesConfigurator();
    dnaConfig.setSignificantIdentifier("DB 6");
    List<SpecimenOrObservationBase> dnaRecords = occurrenceService.findByTitle(dnaConfig).getRecords();
    assertEquals(1, dnaRecords.size());
    SpecimenOrObservationBase dnaSpecimen = dnaRecords.iterator().next();
    assertEquals(DnaSample.class, dnaSpecimen.getClass());
    DnaSample dnaSample = (DnaSample) dnaSpecimen;
    DerivationEvent derivedFrom = dnaSample.getDerivedFrom();
    assertNotNull(derivedFrom);
    assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), derivedFrom.getType());
    assertEquals("Wrong number of originals", 1, derivedFrom.getOriginals().size());
    assertTrue(derivedFrom.getOriginals().iterator().next() instanceof FieldUnit);
    assertEquals("DNA Bank", dnaSample.getCollection().getCode());
    assertEquals(SpecimenOrObservationType.DnaSample, dnaSample.getRecordBasis());
    // preservation/preparation
    assertNotNull(derivedFrom.getActor());
    assertEquals("Bansemer, Jana", derivedFrom.getActor().getTitleCache());
    assertNotNull(derivedFrom.getTimeperiod());
    assertEquals((Integer) 2002, derivedFrom.getTimeperiod().getStartYear());
    assertEquals((Integer) 8, derivedFrom.getTimeperiod().getStartMonth());
    assertEquals((Integer) 13, derivedFrom.getTimeperiod().getStartDay());
    assertNotNull(dnaSample.getPreservation());
    assertEquals("DNeasy Plant Mini Spin Kit Qiagen", derivedFrom.getDescription());
    // sample designation
    Set<String> identifiers = dnaSample.getIdentifierStrings((DefinedTerm) termService.find(DefinedTerm.uuidSampleDesignation));
    assertNotNull(identifiers);
    assertEquals(1, identifiers.size());
    assertEquals("CAM010", identifiers.iterator().next());
    // dna quality
    DnaQuality dnaQuality = dnaSample.getDnaQuality();
    assertNotNull("Dna quality is null", dnaQuality != null);
    assertEquals(new Double("0.77"), dnaQuality.getRatioOfAbsorbance260_230());
    assertEquals(new Double("1.38"), dnaQuality.getRatioOfAbsorbance260_280());
    assertEquals(new DateTime(2008, 4, 15, 0, 0), dnaQuality.getQualityCheckDate());
    // assertEquals(MeasurementUnit.NewInstance(, label, labelAbbrev)DateTime(2008, 4, 15, 0, 0),dnaQuality.getQualityCheckDate());
    // amplifications
    Set<AmplificationResult> amplificationResults = dnaSample.getAmplificationResults();
    assertNotNull(amplificationResults);
    assertEquals(1, amplificationResults.size());
    AmplificationResult amplificationResult = amplificationResults.iterator().next();
    Amplification amplification = amplificationResult.getAmplification();
    assertNotNull("Amplification is null", amplification);
    DefinedTerm dnaMarker = amplification.getDnaMarker();
    assertNotNull(dnaMarker);
    assertEquals("ITS (ITS1, 5.8S rRNA, ITS2)", dnaMarker.getLabel());
    // amplification primers
    Primer forwardPrimer = amplification.getForwardPrimer();
    assertNotNull(forwardPrimer);
    assertEquals("PIpetB1411F", forwardPrimer.getLabel());
    assertEquals("5´-GCCGTMTTTATGTTAATGC-3´", forwardPrimer.getSequence().getString());
    assertNotNull(forwardPrimer.getPublishedIn());
    assertEquals("Löhne & Borsch 2005", forwardPrimer.getPublishedIn().getTitle());
    Primer reversePrimer = amplification.getReversePrimer();
    assertNotNull(reversePrimer);
    assertEquals("PIpetD738R", reversePrimer.getLabel());
    assertEquals("5´-AATTTAGCYCTTAATACAGG-3´", reversePrimer.getSequence().getString());
    // sequencing
    Set<Sequence> sequences = dnaSample.getSequences();
    assertNotNull(sequences);
    assertEquals(1, sequences.size());
    Sequence sequence = sequences.iterator().next();
    SequenceString consensusSequence = sequence.getConsensusSequence();
    assertNotNull(consensusSequence);
    assertEquals("TTTCGGGTCC TTTATAGTGA AGATATAGCA TAGATAGTTG TAATCCATTA" + " TGTATCATTG GGGAAGGAAG GAGAATATTT TTTTGATAGA ATACAAGTAT" + " GGATTATTGA AACTAATACG CCATGTATTT GGATATTTCC CTTGAACTGC" + " ATAATATTCT TTATTTTCCA TGAATAGTGT AAGGGAATTT TTCGAAGAGA" + " AAATGGATTA TGGGAGTGTG TGACTTGAGC TATTGATTGG TCTGTGCAGA" + " TACGGGCTTT TATCTATCTG CCACATTGTA ATTCACAAAC CAATGTGTCT" + " TTGTTCCAAC CATCGCGTAA GCCCCATACA GAAGATAGGC TGGTTCGCTT" + " GAAGAGAATC TTTTCTATGA TCAGATCCGA ATTATGTCGT ACATGAGCAG" + " GCTCCGTAAG ATCTAGTTGA CTTAAGTCAA ACTTCAATAG TATAAAAATG" + " CACTCATTTC CTCTGCATTG ACACGAGCTA TGAGACTATC GGAGTGAAAG" + " AAAGGGTCTA AAGAAGAAGA AAGCTTGGGC TAGATTAGTA ACAAGTAAAT" + " CCTTTGTGTG TGTGTTTGTA ATTAGTAAAT GGGCTCTCAA TATTTTGGGG" + " CTAATTACTG ATCCTAAGGT TTGAGACGAC CCAGAAAGCA CTTGATCATA" + " TCACGATTGA CTTTGTAAGC CTACTTGGGT ATTGAGTATT TACTTGTAAG" + " AACCGAATTC TTTGGGGGAT AGTTGCAAAA AGAATCCAGT CAATTGTTCT" + " TACGTAAAAC CATTCATATC TCGTATATGG ATATGTCTAG ATAGGCTATC" + " GATTTTCGAT GGATTCGTTT GGTTCTTTTG ATTATTGCTC GAGCTGGATG" + " ATGAAAAATT ATCATGTCCG GTTCCTTCG", consensusSequence.getString());
    // assertEquals((Integer)912, consensusSequence.getLength());
    assertNotNull(sequence.getContigFile());
    assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_Campa_drabifolia.pde"), MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile()).getUri());
    assertEquals(1, sequence.getCitations().size());
    Reference reference = sequence.getCitations().iterator().next();
    assertEquals("Gemeinholzer,B., Bachmann,K. (2005): Examining morphological " + "and molecular diagnostic character states in " + "Cichorium intybus L. (Asteraceae) and Cichorium spinosum L." + " Plant Systematics and Evolution 253 (1-3): 105-123.", reference.getTitle());
    // single reads
    Set<SingleRead> singleReads = sequence.getSingleReads();
    assertNotNull(singleReads);
    assertEquals(2, singleReads.size());
    for (SingleRead singleRead : singleReads) {
        if (singleRead.getDirection().equals(SequenceDirection.Forward)) {
            assertNotNull(singleRead.getPherogram());
            assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_F.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());
        } else {
            assertNotNull(singleRead.getPherogram());
            assertEquals(URI.create("http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&path=%2FCAM385_GM312-petD_R.ab1"), MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri());
        }
    }
    assertNotNull(amplificationResult.getSingleReads());
    assertEquals(amplificationResult.getSingleReads(), singleReads);
}

Example 2 with FindOccurrencesConfigurator

use of eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator in project cdmlib by cybertaxonomy.

the class TaxonController method doCountSpecimensOrObservations.

@RequestMapping(value = "specimensOrObservationsCount", method = RequestMethod.GET)
public StringResultDTO doCountSpecimensOrObservations(@PathVariable("uuid") UUID uuid, HttpServletRequest request, HttpServletResponse response) {
    logger.info("doListSpecimensOrObservations() - " + request.getRequestURI());
    List<OrderHint> orderHints = new ArrayList<>();
    orderHints.add(new OrderHint("titleCache", SortOrder.DESCENDING));
    FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
    config.setAssociatedTaxonUuid(uuid);
    long countSpecimen = occurrenceService.countOccurrences(config);
    return new StringResultDTO(String.valueOf(countSpecimen));
}

Example 3 with FindOccurrencesConfigurator

use of eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator in project cdmlib by cybertaxonomy.

the class AbcdGgbnImportTest method testImportAssociatedSpecimenSamePopulation.

/**
 * Tests import of DNA unit which is associated to a specimen being its sibling
 * by having the same field unit
 */
@Test
@DataSet(value = "/eu/etaxonomy/cdm/database/ClearDBDataSet.xml", loadStrategy = CleanSweepInsertLoadStrategy.class)
public // @Ignore
void testImportAssociatedSpecimenSamePopulation() {
    String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6_sibling_association.xml";
    URL url = this.getClass().getResource(inputFile);
    assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
    Abcd206ImportConfigurator importConfigurator = null;
    try {
        importConfigurator = Abcd206ImportConfigurator.NewInstance(new URI(url), null, false);
    } catch (URISyntaxException e) {
        e.printStackTrace();
        Assert.fail();
    }
    assertNotNull("Configurator could not be created", importConfigurator);
    boolean result = defaultImport.invoke(importConfigurator).isSuccess();
    assertTrue("Return value for import.invoke should be true", result);
    assertEquals("Number of derived units is incorrect", 2, occurrenceService.count(DerivedUnit.class));
    assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
    assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));
    // associated specimen
    FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
    config.setSignificantIdentifier("B 10 0066577");
    List<SpecimenOrObservationBase> records = occurrenceService.findByTitle(config).getRecords();
    assertEquals(1, records.size());
    SpecimenOrObservationBase<?> derivedUnitSpecimen = records.iterator().next();
    assertEquals(DerivedUnit.class, derivedUnitSpecimen.getClass());
    DerivedUnit specimen = (DerivedUnit) derivedUnitSpecimen;
    assertEquals("Herbarium Berolinense", specimen.getCollection().getCode());
    assertTrue(SpecimenOrObservationType.DnaSample != specimen.getRecordBasis());
    // dna sample
    FindOccurrencesConfigurator dnaConfig = new FindOccurrencesConfigurator();
    dnaConfig.setSignificantIdentifier("DB 6");
    List<SpecimenOrObservationBase> dnaRecords = occurrenceService.findByTitle(dnaConfig).getRecords();
    assertEquals(1, dnaRecords.size());
    SpecimenOrObservationBase<?> dnaSpecimen = dnaRecords.iterator().next();
    assertEquals(DnaSample.class, dnaSpecimen.getClass());
    DnaSample dnaSample = (DnaSample) dnaSpecimen;
    DerivationEvent derivedFrom = dnaSample.getDerivedFrom();
    assertNotNull(derivedFrom);
    assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), derivedFrom.getType());
    assertEquals("Wrong number of originals", 1, derivedFrom.getOriginals().size());
    // TODO
    // assertTrue(derivedFrom.getOriginals().iterator().next() instanceof FieldUnit);
    assertEquals("DNA Bank", dnaSample.getCollection().getCode());
    assertEquals(SpecimenOrObservationType.DnaSample, dnaSample.getRecordBasis());
// TODO field unit
}

Example 4 with FindOccurrencesConfigurator

use of eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator in project cdmlib by cybertaxonomy.

the class OccurrenceServiceImpl method findByTitle.

@Override
public <S extends SpecimenOrObservationBase> Pager<S> findByTitle(IIdentifiableEntityServiceConfigurator<S> config) {
    if (config instanceof FindOccurrencesConfigurator) {
        FindOccurrencesConfigurator occurrenceConfig = (FindOccurrencesConfigurator) config;
        List<SpecimenOrObservationBase> occurrences = new ArrayList<>();
        Taxon taxon = null;
        if (occurrenceConfig.getAssociatedTaxonUuid() != null) {
            TaxonBase<?> taxonBase = taxonService.load(occurrenceConfig.getAssociatedTaxonUuid());
            if (taxonBase.isInstanceOf(Taxon.class)) {
                taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
            }
        }
        TaxonName taxonName = null;
        if (occurrenceConfig.getAssociatedTaxonNameUuid() != null) {
            taxonName = nameService.load(occurrenceConfig.getAssociatedTaxonNameUuid());
        }
        List<? extends SpecimenOrObservationBase> foundOccurrences = dao.findOccurrences(occurrenceConfig.getClazz(), occurrenceConfig.getTitleSearchString(), occurrenceConfig.getSignificantIdentifier(), occurrenceConfig.getSpecimenType(), taxon, taxonName, occurrenceConfig.getMatchMode(), null, null, occurrenceConfig.getOrderHints(), occurrenceConfig.getPropertyPaths());
        occurrences.addAll(foundOccurrences);
        occurrences = filterOccurencesByAssignmentAndHierarchy(occurrenceConfig, occurrences, taxon, taxonName);
        long count = Integer.valueOf(occurrences.size()).longValue();
        return new DefaultPagerImpl<>(config.getPageNumber(), count, config.getPageSize(), (List<S>) occurrences);
    }
    return super.findByTitle(config);
}

Example 5 with FindOccurrencesConfigurator

use of eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator in project cdmlib by cybertaxonomy.

the class AbcdGgbnImportTest method testImportAssociatedSpecimenSameIndividual.

/**
 * Tests import of DNA unit which is associated to a specimen being its parent derivative
 * @throws ParseException
 */
@Test
@DataSet(value = "/eu/etaxonomy/cdm/database/ClearDBDataSet.xml", loadStrategy = CleanSweepInsertLoadStrategy.class)
public void testImportAssociatedSpecimenSameIndividual() throws ParseException {
    String inputFile = "/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6_parent_child_association.xml";
    URL url = this.getClass().getResource(inputFile);
    assertNotNull("URL for the test file '" + inputFile + "' does not exist", url);
    Abcd206ImportConfigurator importConfigurator = null;
    try {
        importConfigurator = Abcd206ImportConfigurator.NewInstance(new URI(url), null, false);
    } catch (URISyntaxException e) {
        e.printStackTrace();
        Assert.fail();
    }
    assertNotNull("Configurator could not be created", importConfigurator);
    boolean result = defaultImport.invoke(importConfigurator).isSuccess();
    assertTrue("Return value for import.invoke should be true", result);
    assertEquals("Number of derived units is incorrect", 2, occurrenceService.count(DerivedUnit.class));
    assertEquals("Number of dna samples is incorrect", 1, occurrenceService.count(DnaSample.class));
    assertEquals("Number of field units is incorrect", 1, occurrenceService.count(FieldUnit.class));
    // associated specimen
    FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
    config.setSignificantIdentifier("B 10 0066577");
    List<SpecimenOrObservationBase> records = occurrenceService.findByTitle(config).getRecords();
    assertEquals(1, records.size());
    SpecimenOrObservationBase derivedUnitSpecimen = records.iterator().next();
    assertEquals(DerivedUnit.class, derivedUnitSpecimen.getClass());
    DerivedUnit specimen = (DerivedUnit) derivedUnitSpecimen;
    assertEquals("Herbarium Berolinense", specimen.getCollection().getCode());
    assertTrue(SpecimenOrObservationType.DnaSample != specimen.getRecordBasis());
    // dna sample
    FindOccurrencesConfigurator dnaConfig = new FindOccurrencesConfigurator();
    dnaConfig.setSignificantIdentifier("DB 6");
    List<SpecimenOrObservationBase> dnaRecords = occurrenceService.findByTitle(dnaConfig).getRecords();
    assertEquals(1, dnaRecords.size());
    SpecimenOrObservationBase dnaSpecimen = dnaRecords.iterator().next();
    assertEquals(DnaSample.class, dnaSpecimen.getClass());
    DnaSample dnaSample = (DnaSample) dnaSpecimen;
    DerivationEvent derivedFrom = dnaSample.getDerivedFrom();
    assertNotNull(derivedFrom);
    assertEquals("Wrong derivation type!", DerivationEventType.DNA_EXTRACTION(), derivedFrom.getType());
    assertEquals("Wrong number of originals", 1, derivedFrom.getOriginals().size());
    assertTrue(derivedFrom.getOriginals().iterator().next() instanceof DerivedUnit);
    assertEquals("DNA Bank", dnaSample.getCollection().getCode());
    assertEquals(SpecimenOrObservationType.DnaSample, dnaSample.getRecordBasis());
}