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

Example 21 with Plasmid

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

the class SequenceDAOTest method testGetSequence.

@Test
public void testGetSequence() throws Exception {
    Account account = AccountCreator.createTestAccount("SequenceDAOTest.testGetSequence", false);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    Assert.assertNotNull(plasmid);
    // parse sequence and associate with plasmid
    FeaturedDNASequence dnaSequence = GeneralParser.parse(sequenceString);
    Sequence sequence = SequenceUtil.dnaSequenceToSequence(dnaSequence);
    Assert.assertNotNull(sequence);
    sequence.setEntry(plasmid);
    sequence = sequenceDAO.create(sequence);
    Assert.assertNotNull(sequence);
    Assert.assertNotNull(sequenceDAO.getSequence(0));
}

Example 22 with Plasmid

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

the class TransferredPartsTest method createPlasmidObject.

private Plasmid createPlasmidObject(Account owner) {
    Plasmid plasmid = new Plasmid();
    plasmid.setBackbone("plasmid backone");
    plasmid.setOriginOfReplication("None");
    plasmid.setBioSafetyLevel(1);
    plasmid.setShortDescription("plasmid description");
    plasmid.setName("pLasmid");
    plasmid.setOwner(owner.getFullName());
    plasmid.setOwnerEmail(owner.getEmail());
    plasmid.setCreator(plasmid.getOwner());
    plasmid.setCreatorEmail(plasmid.getOwnerEmail());
    plasmid.setCreationTime(new Date());
    return plasmid;
}

Example 23 with Plasmid

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

the class AuditDAOTest method testDeleteAll.

@Test
public void testDeleteAll() throws Exception {
    Account account = AccountCreator.createTestAccount("AuditDAOTest.testDeleteAll", false);
    Assert.assertNotNull(account);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    Random random = new Random();
    final long amount = random.nextInt(20);
    for (int i = 0; i < amount; i += 1) {
        Audit audit = new Audit();
        audit.setUserId(account.getEmail());
        audit.setEntry(plasmid);
        audit.setTime(new Date());
        audit.setAction("-r");
        Assert.assertNotNull(dao.create(audit));
    }
    Assert.assertEquals(amount, dao.getAuditsForEntryCount(plasmid));
    // create for second plasmid
    Strain strain = TestEntryCreator.createTestStrain(account);
    int amount2 = random.nextInt(20);
    for (int i = 0; i < amount2; i += 1) {
        Audit audit = new Audit();
        audit.setUserId(account.getEmail());
        audit.setEntry(strain);
        audit.setTime(new Date());
        audit.setAction("-r");
        Assert.assertNotNull(dao.create(audit));
    }
    Assert.assertEquals(amount2, dao.getAuditsForEntryCount(strain));
    // delete all for first
    Assert.assertEquals(amount, dao.deleteAll(plasmid));
    // verify that second remains while first is empty
    Assert.assertEquals(amount2, dao.getAuditsForEntryCount(strain));
    Assert.assertEquals(0, dao.getAuditsForEntryCount(plasmid));
    // delete for second
    Assert.assertEquals(amount2, dao.deleteAll(strain));
    // verify
    Assert.assertEquals(0, dao.getAuditsForEntryCount(strain));
    Assert.assertEquals(0, dao.getAuditsForEntryCount(plasmid));
}

Example 24 with Plasmid

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

the class TestEntryCreator method createTestPlasmid.

public static Plasmid createTestPlasmid(Account account) {
    PartData plasmid = new PartData(EntryType.PLASMID);
    PlasmidData plasmidData = new PlasmidData();
    plasmidData.setBackbone("plasmid backone");
    plasmidData.setOriginOfReplication("None");
    plasmid.setPlasmidData(plasmidData);
    plasmid.setBioSafetyLevel(1);
    plasmid.setShortDescription("plasmid description");
    plasmid.setName("pLasmid");
    plasmid = new Entries(account.getEmail()).create(plasmid);
    return (Plasmid) DAOFactory.getEntryDAO().get(plasmid.getId());
}