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

Example 16 with Strain

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

the class PermissionDAOTest method makePrivateEntryIds.

public List<Long> makePrivateEntryIds(Account ownerAccount) throws Exception {
    List<Long> entryIds = new ArrayList<>(3);
    for (int i = 0; i < 3; i++) {
        Strain strain = TestEntryCreator.createTestStrain(ownerAccount);
        entryIds.add(strain.getId());
    }
    return entryIds;
}

Example 17 with Strain

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

the class CustomFieldsTest method testUpdateField.

@Test
public void testUpdateField() throws Exception {
    Account account = AccountCreator.createTestAccount("testUpdateField", false);
    Assert.assertNotNull(account);
    final String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    Assert.assertNotNull(strain);
    CustomField field = new CustomField(0, strain.getId(), "Afoo2", "Bbar2");
    long id = fields.createField(userId, strain.getId(), field).getId();
    // update
    field.setId(id);
    field.setName("foo2");
    field.setValue("bar2");
    field = fields.updateField(userId, id, field);
    // verify
    CustomField created = fields.getField(userId, id);
    Assert.assertEquals(created.getName(), field.getName());
    Assert.assertEquals(created.getValue(), field.getValue());
    Assert.assertEquals(created.getId(), id);
    // check what is associated with entry
    strain = (Strain) DAOFactory.getEntryDAO().get(strain.getId());
    Assert.assertNotNull(strain);
    Assert.assertTrue(strain.getParameters().size() == 1);
    created = strain.getParameters().get(0).toDataTransferObject();
    Assert.assertEquals(created.getName(), field.getName());
    Assert.assertEquals(created.getValue(), field.getValue());
    Assert.assertEquals(created.getId(), id);
}

Example 18 with Strain

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

the class CustomFieldsTest method testDeleteField.

@Test
public void testDeleteField() throws Exception {
    Account account = AccountCreator.createTestAccount("testDeleteField", false);
    Assert.assertNotNull(account);
    final String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    Assert.assertNotNull(strain);
    CustomField field = new CustomField(strain.getId(), "foo3", "bar3");
    long id = fields.createField(userId, strain.getId(), field).getId();
    // verify custom field creation
    strain = (Strain) DAOFactory.getEntryDAO().get(strain.getId());
    Assert.assertNotNull(strain);
    Assert.assertTrue(strain.getParameters().size() == 1);
    CustomField created = strain.getParameters().get(0).toDataTransferObject();
    Assert.assertEquals(created.getName(), field.getName());
    Assert.assertEquals(created.getValue(), field.getValue());
    Assert.assertEquals(created.getId(), id);
    // delete custom field
    Assert.assertTrue(fields.deleteField(userId, id));
    //verify deletion
    Assert.assertNull(DAOFactory.getParameterDAO().get(id));
    strain = (Strain) DAOFactory.getEntryDAO().get(strain.getId());
    Assert.assertNotNull(strain);
    Assert.assertTrue(strain.getParameters().isEmpty());
}

Example 19 with Strain

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

the class EntryCreatorTest method testCreatePart.

@Test
public void testCreatePart() throws Exception {
    Account account = AccountCreator.createTestAccount("testCreatePart", false);
    Assert.assertNotNull(account);
    String userId = account.getEmail();
    // create strain
    PartData strain = new PartData(EntryType.STRAIN);
    StrainData strainData = new StrainData();
    strainData.setGenotypePhenotype("genPhen");
    strainData.setHost("host");
    strain.setStrainData(strainData);
    strain.setOwner("Tester");
    strain.setOwnerEmail("tester");
    strain.setCreator(strain.getOwner());
    strain.setCreatorEmail(strain.getOwnerEmail());
    strain.setBioSafetyLevel(1);
    long id = creator.createPart(userId, strain).getId();
    Strain entry = (Strain) DAOFactory.getEntryDAO().get(id);
    Assert.assertNotNull(entry);
    Assert.assertEquals(entry.getOwnerEmail(), strain.getOwnerEmail());
    Assert.assertEquals(strainData.getGenotypePhenotype(), entry.getGenotypePhenotype());
    Assert.assertEquals(strainData.getHost(), entry.getHost());
    // create arabidopsis seed
    PartData seed = new PartData(EntryType.ARABIDOPSIS);
    ArabidopsisSeedData seedData = new ArabidopsisSeedData();
    seedData.setGeneration(Generation.F3);
    seedData.setPlantType(PlantType.OTHER);
    seedData.setHarvestDate("01/02/2014");
    seed.setBioSafetyLevel(2);
    seed.setArabidopsisSeedData(seedData);
    long seedId = creator.createPart(userId, seed).getId();
    ArabidopsisSeed entrySeed = (ArabidopsisSeed) DAOFactory.getEntryDAO().get(seedId);
    Assert.assertNotNull(entrySeed);
    Assert.assertEquals(seedData.getGeneration(), entrySeed.getGeneration());
    Assert.assertEquals(seedData.getPlantType(), entrySeed.getPlantType());
}

Example 20 with Strain

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

the class CustomFieldsTest method testCreateField.

@Test
public void testCreateField() throws Exception {
    Account account = AccountCreator.createTestAccount("testCreateField", false);
    Assert.assertNotNull(account);
    final String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    Assert.assertNotNull(strain);
    CustomField field = new CustomField(0, strain.getId(), "foo", "bar");
    long id = fields.createField(userId, strain.getId(), field).getId();
    strain = (Strain) DAOFactory.getEntryDAO().get(strain.getId());
    Assert.assertNotNull(strain);
    Assert.assertTrue(strain.getParameters().size() == 1);
    CustomField created = strain.getParameters().get(0).toDataTransferObject();
    Assert.assertEquals(created.getName(), field.getName());
    Assert.assertEquals(created.getValue(), field.getValue());
    Assert.assertEquals(created.getId(), id);
}