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

Example 56 with Account

use of org.jbei.ice.storage.model.Account 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 57 with Account

use of org.jbei.ice.storage.model.Account 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 58 with Account

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

the class BulkUploadControllerTest method testAutoUpdateBulkUpload.

@Test
public void testAutoUpdateBulkUpload() throws Exception {
    EntryType type = EntryType.STRAIN;
    Account account = AccountCreator.createTestAccount("testAutoUpdateBulkUpload", false);
    BulkUploadAutoUpdate autoUpdate = new BulkUploadAutoUpdate(EntryType.STRAIN);
    autoUpdate.getKeyValue().put(EntryField.LINKS, "google");
    // first auto update. expect it to create a new bulk upload and entry
    autoUpdate = controller.autoUpdateBulkUpload(account.getEmail(), autoUpdate, type);
    Assert.assertNotNull(autoUpdate);
    long entryId = autoUpdate.getEntryId();
    long bulkId = autoUpdate.getBulkUploadId();
    Assert.assertTrue(entryId > 0);
    Assert.assertTrue(bulkId > 0);
    BulkUploadInfo bulkUploadInfo = controller.getBulkImport(account.getEmail(), bulkId, 0, 1000);
    Assert.assertNotNull(bulkUploadInfo);
    EntryDAO dao = DAOFactory.getEntryDAO();
    Entry entry = dao.get(entryId);
    Assert.assertNotNull(entry);
    Assert.assertNotNull(entry.getLinks());
    Assert.assertEquals(1, entry.getLinks().size());
    autoUpdate = new BulkUploadAutoUpdate(EntryType.PLASMID);
    // auto update: expect plasmid and bulk upload with no fields set
    autoUpdate = controller.autoUpdateBulkUpload(account.getEmail(), autoUpdate, type);
    Assert.assertNotNull(autoUpdate);
    entryId = autoUpdate.getEntryId();
    bulkId = autoUpdate.getBulkUploadId();
    Assert.assertTrue(entryId > 0);
    Assert.assertTrue(bulkId > 0);
    entry = dao.get(entryId);
    Assert.assertNotNull(entry);
}

Example 59 with Account

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

the class BulkUploadControllerTest method testRevertSubmitted.

@Test
public void testRevertSubmitted() throws Exception {
    Account account = AccountCreator.createTestAccount("testRevertSubmitted", false);
    Account admin = AccountCreator.createTestAccount("testRevertSubmitted+Admin", true);
    BulkUploadAutoUpdate autoUpdate = new BulkUploadAutoUpdate(EntryType.ARABIDOPSIS);
    autoUpdate.getKeyValue().put(EntryField.NAME, "JBEI-0001");
    autoUpdate.getKeyValue().put(EntryField.SUMMARY, "this is a test");
    autoUpdate.getKeyValue().put(EntryField.PI, "test");
    autoUpdate.getKeyValue().put(EntryField.STATUS, StatusType.COMPLETE.toString());
    autoUpdate.getKeyValue().put(EntryField.BIO_SAFETY_LEVEL, BioSafetyOption.LEVEL_TWO.getValue());
    autoUpdate.getKeyValue().put(EntryField.SELECTION_MARKERS, "test");
    autoUpdate = controller.autoUpdateBulkUpload(account.getEmail(), autoUpdate, EntryType.ARABIDOPSIS);
    Assert.assertNotNull(autoUpdate);
    Assert.assertTrue(autoUpdate.getEntryId() > 0);
    Assert.assertTrue(autoUpdate.getBulkUploadId() > 0);
    Assert.assertTrue(autoUpdate.getLastUpdate() != null);
    Assert.assertNotNull(controller.getBulkImport(account.getEmail(), autoUpdate.getBulkUploadId(), 0, 0));
    // try to revert. not submitted
    Assert.assertFalse(controller.revertSubmitted(admin, autoUpdate.getBulkUploadId()));
    // actual submission (update status)
    BulkEntryCreator bulkEntryCreator = new BulkEntryCreator();
    bulkEntryCreator.updateStatus(account.getEmail(), autoUpdate.getBulkUploadId(), BulkUploadStatus.PENDING_APPROVAL);
    BulkUploadInfo info = controller.getBulkImport(account.getEmail(), autoUpdate.getBulkUploadId(), 0, 0);
    Assert.assertNotNull(info);
    Assert.assertTrue(controller.revertSubmitted(admin, autoUpdate.getBulkUploadId()));
}

Example 60 with Account

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