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

Example 51 with PartData

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

the class EntryControllerTest method testMoveEntriesToTrash.

@Test
public void testMoveEntriesToTrash() throws Exception {
    Account account = AccountCreator.createTestAccount("testMoveEntriesToTrash", false);
    String email = account.getEmail();
    long id1 = TestEntryCreator.createTestPart(email);
    Entry entry1 = controller.getEntry(Long.toString(id1));
    Assert.assertNotNull(entry1);
    PartData partData1 = ModelToInfoFactory.getInfo(entry1);
    Assert.assertNotNull(partData1);
    ArrayList<PartData> toTrash1 = new ArrayList<>();
    toTrash1.add(partData1);
    Assert.assertNotNull(toTrash1);
    Assert.assertEquals(toTrash1.size(), 1);
    Assert.assertTrue(controller.moveEntriesToTrash(email, toTrash1));
    long id2 = TestEntryCreator.createTestPart(email);
    Entry entry2 = controller.getEntry(Long.toString(id2));
    Assert.assertNotNull(entry2);
    PartData partData2 = ModelToInfoFactory.getInfo(entry2);
    Assert.assertNotNull(partData2);
    long id3 = TestEntryCreator.createTestPart(email);
    Entry entry3 = controller.getEntry(Long.toString(id3));
    Assert.assertNotNull(entry3);
    PartData partData3 = ModelToInfoFactory.getInfo(entry3);
    Assert.assertNotNull(partData3);
    ArrayList<PartData> toTrash2 = new ArrayList<>();
    toTrash2.add(partData2);
    toTrash2.add(partData3);
    Assert.assertNotNull(toTrash2);
    Assert.assertEquals(toTrash2.size(), 2);
    Assert.assertTrue(controller.moveEntriesToTrash(email, toTrash2));
}

Example 52 with PartData

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

the class EntryControllerTest method testUpdatePart.

@Test
public void testUpdatePart() throws Exception {
    Account account = AccountCreator.createTestAccount("testUpdatePart", false);
    String email = account.getEmail();
    long id = TestEntryCreator.createTestPart(email);
    Entry entry = controller.getEntry(Long.toString(id));
    Assert.assertNotNull(entry);
    PartData partData = ModelToInfoFactory.getInfo(entry);
    Assert.assertNotNull(partData);
    partData.setAlias("testUpdatePartAlias");
    long updated = controller.updatePart(email, id, partData);
    Assert.assertEquals(id, updated);
    entry = controller.getEntry(Long.toString(id));
    Assert.assertEquals("testUpdatePartAlias", entry.getAlias());
    // add links
    partData.getLinks().add("a");
    partData.getLinks().add("b");
    controller.updatePart(email, id, partData);
    entry = controller.getEntry(Long.toString(id));
    Assert.assertNotNull(entry);
    Assert.assertEquals(2, entry.getLinks().size());
}

Example 53 with PartData

use of org.jbei.ice.lib.dto.entry.PartData 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 54 with PartData

use of org.jbei.ice.lib.dto.entry.PartData 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 55 with PartData

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

the class Entries method validateEntries.

/**
     * @param stream csv file input stream
     */
public List<ParsedEntryId> validateEntries(InputStream stream) throws IOException {
    List<ParsedEntryId> accepted = new ArrayList<>();
    EntryAuthorization authorization = new EntryAuthorization();
    try (CSVReader reader = new CSVReader(new InputStreamReader(stream, StandardCharsets.UTF_8))) {
        List<String[]> results = reader.readAll();
        for (String[] result : results) {
            if (result[0].isEmpty())
                continue;
            Entry entry = dao.getByPartNumber(result[0]);
            if (entry == null || !authorization.canRead(this.userId, entry)) {
                accepted.add(new ParsedEntryId(result[0], null));
                continue;
            }
            PartData partData = new PartData(EntryType.nameToType(entry.getRecordType()));
            partData.setPartId(entry.getPartNumber());
            partData.setId(entry.getId());
            accepted.add(new ParsedEntryId(result[0], partData));
        }
    }
    return accepted;
}