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

Example 11 with Strain

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

Example 12 with Strain

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

the class CustomFieldsTest method testGetFieldsForPart.

@Test
public void testGetFieldsForPart() throws Exception {
    Account account = AccountCreator.createTestAccount("testGetFieldsForPart", false);
    Assert.assertNotNull(account);
    final String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    Assert.assertNotNull(strain);
    HashSet<Long> ids = new HashSet<>();
    for (int i = 1; i <= 10; i += 1) {
        CustomField field = new CustomField(strain.getId(), "name" + i, "value" + i);
        long id = fields.createField(userId, strain.getId(), field).getId();
        ids.add(id);
    }
    List<CustomField> result = fields.getFieldsForPart(userId, strain.getId());
    Assert.assertNotNull(result);
    Assert.assertTrue(result.size() == 10);
    for (CustomField field : result) {
        Assert.assertTrue(ids.contains(field.getId()));
    }
}

Example 13 with Strain

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

the class FolderContentsTest method testGetContents.

@Test
public void testGetContents() throws Exception {
    FolderContents folderContents = new FolderContents();
    // test with null id
    folderContents.getContents(null, 0, new PageParameters(0, 10, ColumnField.PART_ID, false, null));
    Account account = AccountCreator.createTestAccount("testRetrieveFolderContents", false);
    String userId = account.getEmail();
    FolderDetails folderDetails = new FolderDetails();
    folderDetails.setName("test");
    // create folder
    FolderDetails folder = createPersonalFolder(userId, folderDetails);
    Assert.assertNotNull(folder);
    final short size = 105;
    // create 100 test strains
    HashMap<String, Entry> parts = new HashMap<>();
    List<Long> entryList = new ArrayList<>();
    for (int i = 0; i < size; i += 1) {
        Strain strain = TestEntryCreator.createTestStrain(account);
        Assert.assertNotNull(strain);
        parts.put(strain.getPartNumber(), strain);
        entryList.add(strain.getId());
    }
    Assert.assertEquals(size, parts.size());
    // add to folder
    List<FolderDetails> foldersToAdd = new ArrayList<>();
    foldersToAdd.add(folder);
    foldersToAdd = folderContents.addEntriesToFolders(account.getEmail(), entryList, foldersToAdd);
    Assert.assertNotNull(foldersToAdd);
    // keep track to find duplicates
    HashSet<Long> set = new HashSet<>();
    // retrieve (supported sort types created, status, name, part_id, type)
    FolderDetails details = folderContents.getContents(account.getEmail(), folder.getId(), new PageParameters(0, 15, ColumnField.PART_ID, false, null));
    Assert.assertNotNull(details);
    short pageSize = 15;
    int it = 1;
    while (!details.getEntries().isEmpty()) {
        Assert.assertEquals(pageSize, details.getEntries().size());
        for (PartData partData : details.getEntries()) {
            Assert.assertNotNull(parts.remove(partData.getPartId()));
            Assert.assertFalse(set.contains(partData.getId()));
            set.add(partData.getId());
        }
        // check remaining
        Assert.assertEquals((size - (it * pageSize)), parts.size());
        details = folderContents.getContents(account.getEmail(), folder.getId(), new PageParameters(pageSize * it, pageSize, ColumnField.PART_ID, false, null));
        it += 1;
    }
}

Example 14 with Strain

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

the class PartSequenceTest method testGet.

@Test
public void testGet() throws Exception {
    Account account = AccountCreator.createTestAccount("PartSequenceTest.testGet", false);
    Strain strain = TestEntryCreator.createTestStrain(account);
    PartSequence partSequence = new PartSequence(account.getEmail(), strain.getRecordId());
    FeaturedDNASequence sequence = partSequence.get();
    Assert.assertNull(sequence);
    ByteArrayInputStream inputStream = new ByteArrayInputStream(genbank.getBytes());
    SequenceInfo sequenceInfo = partSequence.parseSequenceFile(inputStream, "testFile.gb");
    Assert.assertNotNull(sequenceInfo);
    FeaturedDNASequence featuredDNASequence = (FeaturedDNASequence) sequenceInfo.getSequence();
    Assert.assertNotNull(featuredDNASequence);
    Assert.assertEquals(1, featuredDNASequence.getFeatures().size());
    sequence = partSequence.get();
    Assert.assertNotNull(sequence);
    Assert.assertEquals(234, sequence.getSequence().length());
    Assert.assertEquals(1, sequence.getFeatures().size());
}

Example 15 with Strain

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

the class SelectionMarkerDAOTest method testGetMatchingSelectionMarkers.

@Test
public void testGetMatchingSelectionMarkers() throws Exception {
    String email = "testGetMatchingSelectionMarkers";
    Account account = AccountCreator.createTestAccount(email, false);
    Assert.assertNotNull(account);
    Strain strain = new Strain();
    strain.setName("sTrain");
    strain.setBioSafetyLevel(BioSafetyOption.LEVEL_ONE.ordinal());
    strain.setShortDescription("test strain");
    SelectionMarker marker = new SelectionMarker();
    marker.setName("xkcd");
    SelectionMarker marker2 = new SelectionMarker();
    marker2.setName("test");
    Set<SelectionMarker> markerSet = new HashSet<>();
    markerSet.add(marker);
    markerSet.add(marker2);
    strain.setSelectionMarkers(markerSet);
    EntryCreator creator = new EntryCreator();
    strain = (Strain) creator.createEntry(account, strain, null);
    Assert.assertNotNull(strain);
    Assert.assertEquals(2, strain.getSelectionMarkers().size());
    List<String> results = dao.getMatchingSelectionMarkers("xkcd", 5);
    Assert.assertEquals(1, results.size());
    List<String> res = dao.getMatchingSelectionMarkers("tes", 5);
    Assert.assertEquals(1, res.size());
    Assert.assertEquals("test", res.get(0));
}