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

Example 1 with Plasmid

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

the class AnnotationsTest method testCurate.

@Test
public void testCurate() throws Exception {
    Account account = AccountCreator.createTestAccount("AnnotationsTest.testCurate", true);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    Assert.assertNotNull(plasmid);
    SequenceDAO sequenceDAO = new SequenceDAO();
    Assert.assertFalse(sequenceDAO.hasSequence(plasmid.getId()));
    FeaturedDNASequence dnaSequence = GeneralParser.parse(sequenceString);
    PartSequence partSequence = new PartSequence(account.getEmail(), plasmid.getRecordId());
    partSequence.save(dnaSequence);
    SequenceFeatureDAO sequenceFeatureDAO = new SequenceFeatureDAO();
    List<SequenceFeature> sequenceFeatures = sequenceFeatureDAO.getEntrySequenceFeatures(plasmid);
    Assert.assertEquals(1, sequenceFeatures.size());
    Feature feature = sequenceFeatures.get(0).getFeature();
    DNAFeature dnaFeature = feature.toDataTransferObject();
    Curation curation = new Curation();
    curation.setExclude(true);
    dnaFeature.setCuration(curation);
    List<DNAFeature> features = new ArrayList<>();
    features.add(dnaFeature);
    Annotations annotations = new Annotations(account.getEmail());
    annotations.curate(features);
    sequenceFeatures = sequenceFeatureDAO.getEntrySequenceFeatures(plasmid);
    feature = sequenceFeatures.get(0).getFeature();
    Assert.assertTrue(feature.getCuration().isExclude());
}

Example 2 with Plasmid

use of org.jbei.ice.storage.model.Plasmid 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 3 with Plasmid

use of org.jbei.ice.storage.model.Plasmid 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));
}

Example 4 with Plasmid

use of org.jbei.ice.storage.model.Plasmid 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.assertEquals(1, results.size());
    Assert.assertEquals(strain.getId(), results.get(0).getId());
}

Example 5 with Plasmid

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

the class EntryHistoryTest method testDeleteAll.

@Test
public void testDeleteAll() throws Exception {
    Account account = AccountCreator.createTestAccount("EntryHistoryTest.testDeleteAll", false);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    Account reader = AccountCreator.createTestAccount("EntryHistoryTest.testDeleteAllReader", false);
    EntryHistory entryHistory = new EntryHistory(reader.getEmail(), plasmid.getId());
    entryHistory.add();
    entryHistory = new EntryHistory(account.getEmail(), plasmid.getId());
    Results<History> history = entryHistory.get(20, 0, true, null);
    Assert.assertNotNull(history);
    Assert.assertEquals(1, entryHistory.deleteAll());
    history = entryHistory.get(20, 0, true, null);
    Assert.assertEquals(0, history.getResultCount());
}