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

Example 31 with PartData

use of org.jbei.ice.lib.dto.entry.PartData 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 32 with PartData

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

the class EntryDAOTest method testGetByUniqueName.

@Test
public void testGetByUniqueName() throws Exception {
    Account account = AccountCreator.createTestAccount("testGetByUniqueName", false);
    PartData data = new PartData(EntryType.PART);
    data.setShortDescription("summary for test");
    String uniqueName = "pTest" + account.getEmail();
    data.setName(uniqueName);
    data.setBioSafetyLevel(1);
    EntryCreator creator = new EntryCreator();
    creator.createPart(account.getEmail(), data);
    List<Entry> entries = entryDAO.getByName("pTest");
    Assert.assertTrue(entries == null || entries.isEmpty());
    entries = entryDAO.getByName(uniqueName);
    Assert.assertNotNull(entries);
}

Example 33 with PartData

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

the class BulkUploadControllerTest method testApproveBulkImport.

@Test
public void testApproveBulkImport() throws Exception {
    Account account = AccountCreator.createTestAccount("testApproveBulkImport", true);
    //
    // test strain with plasmid
    //
    // create bulk upload draft
    String userId = account.getEmail();
    BulkUploadInfo testInfo = new BulkUploadInfo();
    testInfo.setName("testing");
    testInfo.setType(EntryType.STRAIN.getName());
    testInfo = controller.create(userId, testInfo);
    Assert.assertNotNull(testInfo);
    // create entry for upload
    BulkEntryCreator creator = new BulkEntryCreator();
    PartData strainData = new PartData(EntryType.STRAIN);
    strainData.setName("testStrain");
    ArrayList<String> selectionMarkers = new ArrayList<>();
    selectionMarkers.add("Spectinomycin");
    strainData.setSelectionMarkers(selectionMarkers);
    strainData.setBioSafetyLevel(1);
    strainData.setStatus("Complete");
    strainData.setShortDescription("testing bulk upload");
    strainData.setCreator(account.getFullName());
    strainData.setCreatorEmail(account.getEmail());
    strainData.setPrincipalInvestigator("PI");
    PartData plasmidData = new PartData(EntryType.PLASMID);
    plasmidData.setName("testPlasmid");
    selectionMarkers.clear();
    selectionMarkers.add("Spectinomycin");
    plasmidData.setSelectionMarkers(selectionMarkers);
    plasmidData.setBioSafetyLevel(1);
    //        plasmidData.setStatus("In Progress");
    plasmidData.setShortDescription("testing bulk upload with strain with plasmid");
    plasmidData.setCreator(account.getFullName());
    plasmidData.setCreatorEmail(account.getEmail());
    plasmidData.setPrincipalInvestigator("PI");
    strainData.getLinkedParts().add(plasmidData);
    PartData returnStrainData = creator.createEntry(userId, testInfo.getId(), strainData);
    Assert.assertNotNull(returnStrainData);
    plasmidData.setStatus("In Progress");
    plasmidData = creator.updateEntry(userId, testInfo.getId(), returnStrainData.getLinkedParts().get(0).getId(), plasmidData);
    Assert.assertNotNull(plasmidData);
//        testInfo = controller.submitBulkImportDraft(userId, testInfo.getId());
//        Assert.assertNotNull(testInfo);
//        Assert.assertEquals(testInfo.getStatus(), BulkUploadStatus.PENDING_APPROVAL);
}

Example 34 with PartData

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

the class EntryCreator method createPart.

/**
     * Creates a new entry using the passed data
     *
     * @param userId unique identifier for user creating entry
     * @param part   data used to create new part
     * @return new part data id and record id information
     */
public PartData createPart(String userId, PartData part) {
    Entry entry = InfoToModelFactory.infoToEntry(part);
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    // linked entries can be a combination of new and existing parts
    if (part.getLinkedParts() != null) {
        for (PartData data : part.getLinkedParts()) {
            Entry linked;
            if (data.getId() > 0) {
                linked = dao.get(data.getId());
                if (linked == null || !entryAuthorization.canRead(userId, linked)) {
                    continue;
                }
                // TODO : may contain new information e.g. if the sequence is uploaded before
                // TODO : this entry was created then the general information is added here
                linked = InfoToModelFactory.updateEntryField(data, linked);
                linked.setVisibility(Visibility.OK.getValue());
                if (entryAuthorization.canWrite(userId, linked)) {
                // then update
                }
            } else {
                // create new linked (can only do one deep)
                Entry linkedEntry = InfoToModelFactory.infoToEntry(data);
                linked = createEntry(account, linkedEntry, data.getAccessPermissions());
            }
            entry.getLinkedEntries().add(linked);
        }
    }
    entry = createEntry(account, entry, part.getAccessPermissions());
    PartData partData = new PartData(part.getType());
    partData.setId(entry.getId());
    partData.setRecordId(entry.getRecordId());
    return partData;
}

Example 35 with PartData

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

the class PartDefaults method get.

/**
     * Retrieves and sets the default values for the entry. Some of these values (e.g. PI, and Funding Source)
     * are set by individual users as part of their personal preferences
     *
     * @param type entry type
     * @return PartData object with the retrieve part defaults
     */
public PartData get(EntryType type) {
    PartData partData = new PartData(type);
    PreferencesController preferencesController = new PreferencesController();
    // pi defaults
    String value = preferencesController.getPreferenceValue(userId, PreferenceKey.PRINCIPAL_INVESTIGATOR.name());
    if (value != null) {
        Account piAccount = this.accountDAO.getByEmail(value);
        if (piAccount == null) {
            partData.setPrincipalInvestigator(value);
        } else {
            partData.setPrincipalInvestigator(piAccount.getFullName());
            partData.setPrincipalInvestigatorEmail(piAccount.getEmail());
            partData.setPrincipalInvestigatorId(piAccount.getId());
        }
    }
    // funding source defaults
    value = preferencesController.getPreferenceValue(userId, PreferenceKey.FUNDING_SOURCE.name());
    if (value != null) {
        partData.setFundingSource(value);
    }
    // owner and creator details
    Account account = this.accountDAO.getByEmail(userId);
    if (account != null) {
        partData.setOwner(account.getFullName());
        partData.setOwnerEmail(account.getEmail());
        partData.setCreator(partData.getOwner());
        partData.setCreatorEmail(partData.getOwnerEmail());
    }
    // set the entry type defaults
    return EntryUtil.setPartDefaults(partData);
}