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

Example 1 with Strain

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

the class TestEntryCreator method createTestStrain.

public static Strain createTestStrain(Account account) throws Exception {
    Strain strain = new Strain();
    strain.setName("sTrain");
    strain = (Strain) new EntryCreator().createEntry(account, strain, null);
    return strain;
}

Example 2 with Strain

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

the class TestEntryCreator method createTestAccountAndStrain.

public static Strain createTestAccountAndStrain(String userId) throws Exception {
    Account account = AccountCreator.createTestAccount(userId, false);
    Assert.assertNotNull(account);
    Strain strain = new Strain();
    strain.setName("sTrain");
    strain.setBioSafetyLevel(BioSafetyOption.LEVEL_ONE.ordinal());
    strain.setShortDescription("test strain");
    strain = (Strain) new EntryCreator().createEntry(account, strain, null);
    return strain;
}

Example 3 with Strain

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

the class TransferredPartsTest method createStrainObject.

private Strain createStrainObject(Account owner) {
    Strain strain = new Strain();
    strain.setName("sTrain");
    strain.setOwner(owner.getFullName());
    strain.setOwnerEmail(owner.getEmail());
    strain.setCreator(strain.getOwner());
    strain.setCreatorEmail(strain.getOwnerEmail());
    strain.setCreationTime(new Date());
    return strain;
}

Example 4 with Strain

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

the class TransferredPartsTest method testReceiveTransferredEntry.

@Test
public void testReceiveTransferredEntry() throws Exception {
    Account account = AccountCreator.createTestAccount("testReceivedTransferredEntry", false);
    Strain strain = createStrainObject(account);
    Plasmid plasmid = createPlasmidObject(account);
    // link the two
    PartData strainData = strain.toDataTransferObject();
    PartData plasmidData = plasmid.toDataTransferObject();
    strainData.getLinkedParts().add(plasmidData);
    strainData = parts.receiveTransferredEntry(strainData);
    Assert.assertNotNull(strainData);
    strain = (Strain) DAOFactory.getEntryDAO().get(strainData.getId());
    Assert.assertNotNull(strain);
    Assert.assertTrue(strain.getVisibility() == Visibility.TRANSFERRED.getValue());
    plasmid = (Plasmid) DAOFactory.getEntryDAO().get(strainData.getLinkedParts().get(0).getId());
    Assert.assertNotNull(plasmid);
    Assert.assertTrue(plasmid.getVisibility() == Visibility.TRANSFERRED.getValue());
    Assert.assertTrue(strain.getLinkedEntries().contains(plasmid));
    // create new plasmid
    Plasmid plasmid2 = createPlasmidObject(account);
    strainData.getLinkedParts().add(plasmid2.toDataTransferObject());
    Assert.assertEquals(2, strainData.getLinkedParts().size());
    // transfer strain (with 2 linked plasmids)
    PartData received = parts.receiveTransferredEntry(strainData);
    Assert.assertNotNull(received);
    // check return
    strain = (Strain) DAOFactory.getEntryDAO().get(strainData.getId());
    Assert.assertNotNull(strain);
    plasmid = (Plasmid) DAOFactory.getEntryDAO().get(strainData.getLinkedParts().get(0).getId());
    Assert.assertNotNull(plasmid);
    Assert.assertTrue(strain.getLinkedEntries().contains(plasmid));
    plasmid2 = (Plasmid) DAOFactory.getEntryDAO().get(strainData.getLinkedParts().get(1).getId());
    Assert.assertNotNull(plasmid2);
    Assert.assertTrue(strain.getLinkedEntries().contains(plasmid2));
}

Example 5 with Strain

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

the class EntryLinksTest method testAddLink.

@Test
public void testAddLink() throws Exception {
    Account account = AccountCreator.createTestAccount("testAddLink", false);
    String userId = account.getEmail();
    Account differentAccount = AccountCreator.createTestAccount("testAddLink2", false);
    //create strain and plasmid
    Strain strain = TestEntryCreator.createTestStrain(account);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(differentAccount);
    // give each account read permissions
    AccessPermission accessPermission = new AccessPermission(AccessPermission.Article.ACCOUNT, account.getId(), AccessPermission.Type.READ_ENTRY, plasmid.getId(), "");
    PermissionsController permissionsController = new PermissionsController();
    Assert.assertNotNull(permissionsController.addPermission(differentAccount.getEmail(), accessPermission));
    accessPermission = new AccessPermission(AccessPermission.Article.ACCOUNT, differentAccount.getId(), AccessPermission.Type.READ_ENTRY, strain.getId(), "");
    Assert.assertNotNull(permissionsController.addPermission(account.getEmail(), accessPermission));
    // add plasmid links to strain
    EntryLinks entryLinks = new EntryLinks(userId, Long.toString(strain.getId()));
    // attempt to add as a parent (expected to fail)
    Assert.assertFalse(entryLinks.addLink(plasmid.toDataTransferObject(), LinkType.PARENT));
    // now add as a child
    Assert.assertTrue(entryLinks.addLink(plasmid.toDataTransferObject(), LinkType.CHILD));
    // add second plasmid
    Plasmid plasmid2 = TestEntryCreator.createTestPlasmid(account);
    Assert.assertTrue(entryLinks.addLink(plasmid2.toDataTransferObject(), LinkType.CHILD));
}