Examples with PartSample org.jbei.ice.lib.dto.sample.PartSample used on opensource projects

Example 1 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class SampleService method retrieveEntrySamples.

public List<PartSample> retrieveEntrySamples(String userId, String entryId) {
    Entry entry = super.getEntry(entryId);
    if (entry == null)
        return null;
    entryAuthorization.expectRead(userId, entry);
    // samples
    List<Sample> entrySamples = dao.getSamplesByEntry(entry);
    ArrayList<PartSample> samples = new ArrayList<>();
    if (entrySamples == null)
        return samples;
    boolean inCart = false;
    if (userId != null) {
        Account userAccount = accountDAO.getByEmail(userId);
        inCart = DAOFactory.getRequestDAO().getSampleRequestInCart(userAccount, entry) != null;
    }
    ArrayList<Sample> siblingSamples = new ArrayList<>();
    for (Sample sample : entrySamples) {
        Storage storage = sample.getStorage();
        if (storage == null)
            continue;
        if (storage.getParent() != null && storage.getParent().getParent() != null) {
            siblingSamples.addAll(dao.getSamplesByStorage(storage.getParent().getParent()));
        }
    }
    entrySamples.addAll(siblingSamples);
    Set<Sample> unique = new HashSet<>(entrySamples);
    entrySamples = new ArrayList<>(unique);
    for (Sample sample : entrySamples) {
        // convert sample to info
        Storage storage = sample.getStorage();
        if (storage == null) {
            // dealing with sample with no storage
            PartSample generic = sample.toDataTransferObject();
            StorageLocation location = new StorageLocation();
            location.setType(SampleType.GENERIC);
            location.setDisplay(sample.getLabel());
            generic.setLocation(location);
            generic = setAccountInfo(generic, sample.getDepositor());
            samples.add(generic);
            continue;
        }
        StorageLocation storageLocation = storage.toDataTransferObject();
        while (storage.getParent() != null) {
            storage = storage.getParent();
            StorageLocation parentLocation = storage.toDataTransferObject();
            parentLocation.setChild(storageLocation);
            storageLocation = parentLocation;
            boolean isParent = (storageLocation.getType() != null && storageLocation.getType().isTopLevel());
            if (isParent)
                break;
        }
        // get specific sample type and details about it
        PartSample partSample = new PartSample();
        partSample.setId(sample.getId());
        partSample.setPartId(sample.getEntry().getId());
        partSample.setLocation(storageLocation);
        partSample.setPartName(sample.getEntry().getName());
        partSample.setLabel(sample.getLabel());
        if (sample.getEntry().getId() == entry.getId()) {
            partSample.setCreationTime(sample.getCreationTime().getTime());
            partSample.setInCart(inCart);
            partSample.setCanEdit(sampleAuthorization.canWrite(userId, sample));
            if (sample.getComments() != null) {
                for (Comment comment : sample.getComments()) {
                    UserComment userComment = new UserComment();
                    userComment.setId(comment.getId());
                    userComment.setMessage(comment.getBody());
                    partSample.getComments().add(userComment);
                }
            }
        } else {
            partSample.setCanEdit(false);
        }
        partSample = setAccountInfo(partSample, sample.getDepositor());
        samples.add(partSample);
    }
    return samples;
}

Example 2 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class Sample method toDataTransferObject.

@Override
public PartSample toDataTransferObject() {
    PartSample sample = new PartSample();
    sample.setLabel(label);
    if (entry != null)
        sample.setPartId(entry.getId());
    sample.setCreationTime(creationTime.getTime());
    if (this.getStorage() != null)
        sample.setLocation(this.getStorage().toDataTransferObject());
    return sample;
}

Example 3 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class SampleServiceTest method testGetSamplesByBarcode.

@Test
public void testGetSamplesByBarcode() throws Exception {
    Account account = AccountCreator.createTestAccount("SampleServiceTest.testGetSamplesByBarcode", false);
    String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    PartSample partSample = new PartSample();
    partSample.setLabel("test");
    StorageLocation location = new StorageLocation();
    location.setDisplay("tube");
    location.setType(SampleType.TUBE);
    partSample.setLocation(location);
    partSample = service.createSample(userId, Long.toString(strain.getId()), partSample, null);
    Assert.assertNotNull(partSample);
    List<PartSample> partSamples = service.getSamplesByBarcode(userId, location.getDisplay());
    Assert.assertNotNull(partSamples);
    Assert.assertEquals(1, partSamples.size());
}

Example 4 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class SampleServiceTest method testCreateSample.

@Test
public void testCreateSample() throws Exception {
    Account account = AccountCreator.createTestAccount("SampleServiceTest.testCreateSample", false);
    String userId = account.getEmail();
    // create 96 strains
    Map<Long, String> idPartNumberMap = new HashMap<>();
    for (int i = 0; i < 96; i += 1) {
        Strain strain = TestEntryCreator.createTestStrain(account);
        Assert.assertNotNull(strain);
        idPartNumberMap.put(strain.getId(), strain.getPartNumber());
    }
    Assert.assertEquals(96, idPartNumberMap.size());
    String mainPlate = "0000000001";
    // create main plate
    createPlateSamples(userId, mainPlate, idPartNumberMap);
    List<Storage> storageList = DAOFactory.getStorageDAO().retrieveStorageByIndex(mainPlate, SampleType.PLATE96);
    Assert.assertNotNull(storageList);
    Assert.assertEquals(1, storageList.size());
    // retrieve samples for entries
    int i = 0;
    for (String partNumber : idPartNumberMap.values()) {
        List<PartSample> samples = service.retrieveEntrySamples(userId, partNumber);
        Assert.assertNotNull(samples);
        Assert.assertTrue(samples.size() == 1);
        verifyMainPlate(samples.get(0), i, mainPlate);
        i += 1;
    }
    // create backup 1
    String backUp1Plate = "0000000002";
    createPlateSamples(userId, backUp1Plate, idPartNumberMap);
    storageList = DAOFactory.getStorageDAO().retrieveStorageByIndex(backUp1Plate, SampleType.PLATE96);
    Assert.assertNotNull(storageList);
    Assert.assertEquals(1, storageList.size());
    // retrieve samples for entries
    i = 0;
    for (String partNumber : idPartNumberMap.values()) {
        List<PartSample> samples = service.retrieveEntrySamples(userId, partNumber);
        Assert.assertNotNull(samples);
        Assert.assertTrue(samples.size() == 2);
        verifyMainPlate(samples.get(0), i, mainPlate, backUp1Plate);
        verifyMainPlate(samples.get(1), i, mainPlate, backUp1Plate);
        i += 1;
    }
    // create backup 2
    String backUp2Plate = "0000000003";
    createPlateSamples(userId, backUp2Plate, idPartNumberMap);
    storageList = DAOFactory.getStorageDAO().retrieveStorageByIndex(backUp1Plate, SampleType.PLATE96);
    Assert.assertNotNull(storageList);
    Assert.assertEquals(1, storageList.size());
    // retrieve samples for entries
    i = 0;
    for (String partNumber : idPartNumberMap.values()) {
        List<PartSample> samples = service.retrieveEntrySamples(userId, partNumber);
        Assert.assertNotNull(samples);
        Assert.assertTrue(samples.size() == 3);
        verifyMainPlate(samples.get(0), i, mainPlate, backUp1Plate, backUp2Plate);
        verifyMainPlate(samples.get(1), i, mainPlate, backUp1Plate, backUp2Plate);
        verifyMainPlate(samples.get(2), i, mainPlate, backUp1Plate, backUp2Plate);
        i += 1;
    }
}

Example 5 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class SampleServiceTest method createPlateSamples.

protected void createPlateSamples(String userId, String plate, Map<Long, String> idPartNumberMap) {
    int i = 0;
    for (Long entryId : idPartNumberMap.keySet()) {
        // for each entry
        PartSample partSample = new PartSample();
        StorageLocation plateLocation = new StorageLocation();
        plateLocation.setType(SampleType.PLATE96);
        plateLocation.setDisplay(plate);
        StorageLocation well = new StorageLocation();
        well.setType(SampleType.WELL);
        String wellDisplay = numberToPosition(i);
        Assert.assertNotNull(wellDisplay);
        // e.g. "AO1"
        well.setDisplay(wellDisplay);
        plateLocation.setChild(well);
        StorageLocation tube = new StorageLocation();
        tube.setType(SampleType.TUBE);
        String index = UUID.randomUUID().toString().split("-")[0];
        tube.setDisplay(index);
        well.setChild(tube);
        partSample.setLocation(plateLocation);
        String partNumber = idPartNumberMap.get(entryId);
        Assert.assertNotNull(partNumber);
        // part number of part_number_backup 1/2
        partSample.setLabel(partNumber);
        partSample = service.createSample(userId, partNumber, partSample, null);
        Assert.assertNotNull(partSample);
        Assert.assertNotNull(partSample.getLabel());
        i += 1;
    }
}