Examples with EntryCreator org.jbei.ice.lib.entry.EntryCreator used on opensource projects

Example 6 with EntryCreator

use of org.jbei.ice.lib.entry.EntryCreator in project ice by JBEI.

the class SBOLParser method createNewEntry.

protected long createNewEntry(TopLevel moduleDefinition, SBOLDocument document) {
    String identity = moduleDefinition.getIdentity().toString();
    String description = moduleDefinition.getDescription();
    String name = moduleDefinition.getName();
    Part part = new Part();
    part.setOwner(partData.getOwner());
    part.setOwnerEmail(partData.getOwnerEmail());
    part.setCreator(partData.getCreator());
    part.setCreatorEmail(partData.getCreatorEmail());
    part.setPrincipalInvestigator(partData.getPrincipalInvestigator());
    part.setPrincipalInvestigatorEmail(partData.getPrincipalInvestigatorEmail());
    part.setBioSafetyLevel(partData.getBioSafetyLevel());
    part.setStatus(partData.getStatus());
    description = StringUtils.isEmpty(description) ? partData.getShortDescription() : description;
    name = StringUtils.isEmpty(name) ? moduleDefinition.getDisplayId() : name;
    part.setShortDescription(description);
    part.setName(name);
    EntryCreator entryCreator = new EntryCreator();
    Account account = DAOFactory.getAccountDAO().getByEmail(part.getCreatorEmail());
    Entry entry = entryCreator.createEntry(account, part, null);
    parseToGenBank(document, entry.getName(), entry, moduleDefinition.getIdentity().toString());
    identityEntryMap.put(identity, entry.getId());
    return entry.getId();
}

Example 7 with EntryCreator

use of org.jbei.ice.lib.entry.EntryCreator in project ice by JBEI.

the class TestEntryCreator method createTestPlasmid.

public static Plasmid createTestPlasmid(Account account) throws Exception {
    Plasmid plasmid = new Plasmid();
    plasmid.setBackbone("plasmid backone");
    plasmid.setOriginOfReplication("None");
    plasmid.setBioSafetyLevel(1);
    plasmid.setShortDescription("plasmid description");
    plasmid.setName("pLasmid");
    plasmid = (Plasmid) new EntryCreator().createEntry(account, plasmid, null);
    return plasmid;
}

Example 8 with EntryCreator

use of org.jbei.ice.lib.entry.EntryCreator 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));
}

Example 9 with EntryCreator

use of org.jbei.ice.lib.entry.EntryCreator in project ice by JBEI.

the class FolderDAOTest method testRemoveFolderEntries.

@Test
public void testRemoveFolderEntries() throws Exception {
    Account account = AccountCreator.createTestAccount("testRemoveFolderEntries", false);
    String email = account.getEmail();
    // create test folder
    Folder folder = createFolderObject("testRemoveFolderEntries");
    folder = dao.create(folder);
    Assert.assertNotNull(folder);
    List<Entry> entries = new ArrayList<>();
    EntryCreator creator = new EntryCreator();
    // create 10 entries
    for (int i = 0; i < 10; i += 1) {
        Part part = new Part();
        part.setName("name" + i);
        part.setOwnerEmail(email);
        part.setAlias("alias" + i);
        part.setShortDescription("short description");
        Entry entry = creator.createEntry(account, part, null);
        entries.add(entry);
    }
    // add entries to folder
    folder = dao.addFolderContents(folder, entries);
    // remove entries from folder
    List<Long> entriesToRemove = new ArrayList<>();
    entriesToRemove.add(entries.get(2).getId());
    entriesToRemove.add(entries.get(8).getId());
    entriesToRemove.add(entries.get(1).getId());
    entriesToRemove.add(entries.get(3).getId());
    dao.removeFolderEntries(folder, entriesToRemove);
    folder = dao.get(folder.getId());
    Assert.assertNotNull(folder);
    Assert.assertEquals(6, folder.getContents().size());
}

Example 10 with EntryCreator

use of org.jbei.ice.lib.entry.EntryCreator in project ice by JBEI.

the class FolderDAOTest method testRetrieveFolderContents.

@Test
public void testRetrieveFolderContents() throws Exception {
    Account account = AccountCreator.createTestAccount("FolderDAOTest.testRetrieveFolderContents", false);
    String email = account.getEmail();
    Folder folder = createFolderObject(email);
    folder = dao.create(folder);
    Assert.assertNotNull(folder);
    // add entries to folder
    EntryCreator creator = new EntryCreator();
    List<Entry> entries = new ArrayList<>();
    for (int i = 1; i <= 9; i += 1) {
        Part part = new Part();
        part.setName("name" + i);
        part.setOwnerEmail(email);
        part.setAlias("alias" + i);
        part.setShortDescription("short description");
        Entry entry = creator.createEntry(account, part, null);
        entries.add(entry);
    }
    // add to folder
    folder = dao.addFolderContents(folder, entries);
    Assert.assertNotNull(folder);
    List<Entry> result = dao.retrieveFolderContents(folder.getId(), new PageParameters(0, 15, ColumnField.NAME, true, null), false);
    Assert.assertNotNull(result);
    for (int i = 1; i <= 9; i += 1) {
        Entry entry = result.get(i - 1);
        Assert.assertEquals(entry.getName(), "name" + i);
    }
}