Examples with Strain org.jbei.ice.storage.model.Strain used on opensource projects

Example 6 with Strain

use of org.jbei.ice.storage.model.Strain 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 7 with Strain

use of org.jbei.ice.storage.model.Strain 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 8 with Strain

use of org.jbei.ice.storage.model.Strain in project ice by JBEI.

the class SampleServiceTest method testRetrieveEntrySamples.

@Test
public void testRetrieveEntrySamples() throws Exception {
    Account account = AccountCreator.createTestAccount("SampleServiceTest.testRetrieveEntrySamples", false);
    String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    long entryId = strain.getId();
    List<PartSample> samplesList = service.retrieveEntrySamples(userId, Long.toString(entryId));
    Assert.assertNotNull(samplesList);
    for (PartSample partSample : samplesList) {
        Assert.assertNotNull(partSample.getId());
        Assert.assertNotNull(partSample.getCreationTime());
        Assert.assertNotNull(partSample.getLabel());
        Assert.assertNotNull(partSample.getLocation());
        Assert.assertNotNull(partSample.getDepositor());
        Assert.assertNotNull(partSample.getId());
        Assert.assertNotNull(partSample.isCanEdit());
        StorageLocation location = partSample.getLocation();
        while (location.getChild() != null) {
            location = location.getChild();
            Assert.assertNotNull(location.getType());
            Assert.assertNotNull(location.getId());
            Assert.assertNotNull(location.getDisplay());
            Assert.assertNotNull(location.getName());
        }
        if (partSample.getComments() != null) {
            for (UserComment comment : partSample.getComments()) {
                Assert.assertNotNull(comment.getId());
                Assert.assertNotNull(comment.getMessage());
            }
        }
    }
}

Example 9 with Strain

use of org.jbei.ice.storage.model.Strain in project ice by JBEI.

the class CustomFieldsTest method testGetField.

@Test
public void testGetField() throws Exception {
    Account account = AccountCreator.createTestAccount("testGetField", false);
    Assert.assertNotNull(account);
    final String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    Assert.assertNotNull(strain);
    CustomField field = new CustomField(0, strain.getId(), "foo1", "bar1");
    long id = fields.createField(userId, strain.getId(), field).getId();
    CustomField created = fields.getField(userId, id);
    Assert.assertEquals(created.getName(), field.getName());
    Assert.assertEquals(created.getValue(), field.getValue());
    Assert.assertEquals(created.getId(), id);
}

Example 10 with Strain

use of org.jbei.ice.storage.model.Strain in project ice by JBEI.

the class CustomFieldsTest method testGetPartsByFields.

@Test
public void testGetPartsByFields() throws Exception {
    // create part
    Account account = AccountCreator.createTestAccount("testGetPartsByFields", false);
    final String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    Assert.assertNotNull(strain);
    // create fields for strain
    long strainId = strain.getId();
    fields.createField(userId, strainId, new CustomField(strainId, "type", "promoter"));
    fields.createField(userId, strainId, new CustomField(strainId, "strength", "weak"));
    // search for strength:weak
    List<CustomField> searchFields = new ArrayList<>();
    searchFields.add(new CustomField("strength", "weak"));
    List<PartData> results = fields.getPartsByFields(userId, searchFields);
    Assert.assertEquals(1, results.size());
    // create additional entry
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    Assert.assertNotNull(plasmid);
    long plasmidId = plasmid.getId();
    fields.createField(userId, plasmidId, new CustomField(plasmidId, "type", "promoter"));
    fields.createField(userId, plasmidId, new CustomField(plasmidId, "strength", "strong"));
    searchFields.clear();
    searchFields.add(new CustomField("strength", "strong"));
    results = fields.getPartsByFields(userId, searchFields);
    Assert.assertEquals(1, results.size());
    Assert.assertEquals(plasmid.getId(), results.get(0).getId());
    // search for type:promoter
    searchFields.clear();
    searchFields.add(new CustomField("type", "promoter"));
    results = fields.getPartsByFields(userId, searchFields);
    Assert.assertEquals(2, results.size());
    Assert.assertTrue(strain.getId() == results.get(0).getId() || results.get(1).getId() == strain.getId());
    // test two
    searchFields.clear();
    searchFields.add(new CustomField(strainId, "type", "promoter"));
    searchFields.add(new CustomField(strainId, "strength", "weak"));
    results = fields.getPartsByFields(userId, searchFields);
    Assert.assertNotNull(results);
    Assert.assertTrue(results.size() == 1);
    Assert.assertEquals(strain.getId(), results.get(0).getId());
}