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

Example 16 with Plasmid

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

the class EntryHistoryTest method testAdd.

@Test
public void testAdd() throws Exception {
    Account account = AccountCreator.createTestAccount("EntryHistoryTest.testAdd", false);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    Account reader = AccountCreator.createTestAccount("EntryHistoryTest.testAddReader", false);
    EntryHistory entryHistory = new EntryHistory(reader.getEmail(), plasmid.getId());
    Assert.assertTrue(entryHistory.add());
}

Example 17 with Plasmid

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

the class EntryLinksTest method testGetParents.

@Test
public void testGetParents() throws Exception {
    Account account = AccountCreator.createTestAccount("testGetParents", false);
    String userId = account.getEmail();
    // add plasmid links to strain
    Strain strain = TestEntryCreator.createTestStrain(account);
    EntryLinks entryLinks = new EntryLinks(userId, Long.toString(strain.getId()));
    Assert.assertEquals(0, entryLinks.getParents().size());
    // attempt to add as a parent (expected to fail)
    Plasmid plasmid1 = TestEntryCreator.createTestPlasmid(account);
    Assert.assertFalse(entryLinks.addLink(plasmid1.toDataTransferObject(), LinkType.PARENT));
    // now add as a child
    Assert.assertTrue(entryLinks.addLink(plasmid1.toDataTransferObject(), LinkType.CHILD));
    // add second plasmid
    Plasmid plasmid2 = TestEntryCreator.createTestPlasmid(account);
    Assert.assertTrue(entryLinks.addLink(plasmid2.toDataTransferObject(), LinkType.CHILD));
    List<PartData> children = entryLinks.getChildren();
    Assert.assertEquals(2, children.size());
    EntryLinks plasmidLinks = new EntryLinks(userId, Long.toString(plasmid1.getId()));
    Assert.assertEquals(1, plasmidLinks.getParents().size());
    EntryLinks plasmid2Links = new EntryLinks(userId, Long.toString(plasmid2.getId()));
    Assert.assertEquals(1, plasmid2Links.getParents().size());
}

Example 18 with Plasmid

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

the class EntryLinksTest method testGetChildren.

@Test
public void testGetChildren() throws Exception {
    Account account = AccountCreator.createTestAccount("testGetChildren", false);
    String userId = account.getEmail();
    // create alternate account
    Account account2 = AccountCreator.createTestAccount("testGetChildren2", true);
    // add plasmid links to strain
    Strain strain = TestEntryCreator.createTestStrain(account);
    EntryLinks entryLinks = new EntryLinks(userId, Long.toString(strain.getId()));
    Assert.assertEquals(0, entryLinks.getChildren().size());
    // attempt to add as a parent (expected to fail)
    Plasmid plasmid1 = TestEntryCreator.createTestPlasmid(account);
    Assert.assertFalse(entryLinks.addLink(plasmid1.toDataTransferObject(), LinkType.PARENT));
    // now add as a child
    Assert.assertTrue(entryLinks.addLink(plasmid1.toDataTransferObject(), LinkType.CHILD));
    // add second plasmid
    Plasmid plasmid2 = TestEntryCreator.createTestPlasmid(account);
    Assert.assertTrue(entryLinks.addLink(plasmid2.toDataTransferObject(), LinkType.CHILD));
    List<PartData> children = entryLinks.getChildren();
    Assert.assertEquals(2, children.size());
    // create plasmid for alternate account
    Strain alternateStrain = TestEntryCreator.createTestStrain(account2);
    // add as child to account's strain
    EntryLinks alternateLinks = new EntryLinks(account2.getEmail(), Long.toString(strain.getId()));
    Assert.assertTrue(alternateLinks.addLink(alternateStrain.toDataTransferObject(), LinkType.CHILD));
    // account2 should see three children (since it is an admin)
    Assert.assertEquals(3, alternateLinks.getChildren().size());
    // but account should still see 2 since it does not have read permissions on account2's entry
    Assert.assertEquals(2, entryLinks.getChildren().size());
}

Example 19 with Plasmid

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

the class RemoteTransferTest method testGetPartsForTransfer.

@Test
public void testGetPartsForTransfer() throws Exception {
    EntryDAO dao = DAOFactory.getEntryDAO();
    Account account = AccountCreator.createTestAccount("testGetPartsForTransfer", false);
    Strain strain = TestEntryCreator.createTestStrain(account);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    strain.getLinkedEntries().add(plasmid);
    DAOFactory.getEntryDAO().update(strain);
    strain = (Strain) DAOFactory.getEntryDAO().get(strain.getId());
    Assert.assertTrue(strain.getLinkedEntries().size() == 1);
    Plasmid plasmid2 = TestEntryCreator.createTestPlasmid(account);
    strain.getLinkedEntries().add(plasmid2);
    dao.update(strain);
    Plasmid plasmid3 = TestEntryCreator.createTestPlasmid(account);
    Strain strain2 = TestEntryCreator.createTestStrain(account);
    strain2.getLinkedEntries().add(plasmid2);
    strain2.getLinkedEntries().add(plasmid3);
    dao.update(strain2);
    ArrayList<Long> ids = new ArrayList<>();
    ids.add(plasmid.getId());
    ids.add(plasmid2.getId());
    ids.add(plasmid3.getId());
    ids.add(strain.getId());
    ids.add(strain2.getId());
    List<PartData> data = transfer.getPartsForTransfer(ids);
    TransferredParts parts = new TransferredParts();
    Assert.assertEquals(data.size(), 2);
    for (PartData datum : data) {
        // both should have 2 linked entries with 1 in common
        Assert.assertEquals(datum.getLinkedParts().size(), 2);
        // transfer
        datum.setRecordId("");
        PartData transferred = parts.receiveTransferredEntry(datum);
        Assert.assertNotNull(transferred);
    }
}

Example 20 with Plasmid

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

the class SequenceDAOTest method testSequenceString.

@Test
public void testSequenceString() throws Exception {
    Account account = AccountCreator.createTestAccount("SequenceDAOTest.testSequenceString", 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);
    // get
    Optional<String> result = sequenceDAO.getSequenceString(plasmid);
    Assert.assertTrue(result.isPresent());
    Assert.assertEquals(result.get(), dnaSequence.getSequence());
}