Examples with PartSample org.jbei.ice.lib.dto.sample.PartSample used on opensource projects

Example 6 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class SampleServiceTest method testRetrieveEntrySamples.

@Test
public void testRetrieveEntrySamples() throws Exception {
    Account account = AccountCreator.createTestAccount("SampleServiceTest.testRetrieveEntrySamples", false);
    String userId = account.getEmail();
    Strain strain = TestEntryCreator.createTestStrain(account);
    long entryId = strain.getId();
    List<PartSample> samplesList = service.retrieveEntrySamples(userId, Long.toString(entryId));
    Assert.assertNotNull(samplesList);
    for (PartSample partSample : samplesList) {
        Assert.assertNotNull(partSample.getId());
        Assert.assertNotNull(partSample.getCreationTime());
        Assert.assertNotNull(partSample.getLabel());
        Assert.assertNotNull(partSample.getLocation());
        Assert.assertNotNull(partSample.getDepositor());
        Assert.assertNotNull(partSample.getId());
        Assert.assertNotNull(partSample.isCanEdit());
        StorageLocation location = partSample.getLocation();
        while (location.getChild() != null) {
            location = location.getChild();
            Assert.assertNotNull(location.getType());
            Assert.assertNotNull(location.getId());
            Assert.assertNotNull(location.getDisplay());
            Assert.assertNotNull(location.getName());
        }
        if (partSample.getComments() != null) {
            for (UserComment comment : partSample.getComments()) {
                Assert.assertNotNull(comment.getId());
                Assert.assertNotNull(comment.getMessage());
            }
        }
    }
}

Example 7 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class SampleServiceTest method testDelete.

@Test
public void testDelete() throws Exception {
    Account account = AccountCreator.createTestAccount("testDelete", false);
    String userId = account.getEmail();
    // ----- CASE #1 -----
    Strain strain1 = TestEntryCreator.createTestStrain(account);
    PartSample partSample1 = new PartSample();
    partSample1.setLabel("testForShelfScheme1");
    // well
    StorageLocation well = new StorageLocation();
    well.setDisplay("well");
    well.setType(SampleType.WELL);
    // box
    StorageLocation box = new StorageLocation();
    box.setDisplay("box");
    box.setType(SampleType.BOX_INDEXED);
    box.setChild(well);
    // shelf
    StorageLocation shelf = new StorageLocation();
    shelf.setDisplay("shelf");
    shelf.setType(SampleType.SHELF);
    shelf.setChild(box);
    partSample1.setLocation(shelf);
    partSample1 = service.createSample(userId, strain1.getRecordId(), partSample1, null);
    Assert.assertNotNull(partSample1);
    // fetch
    List<PartSample> samples1 = service.retrieveEntrySamples(userId, Long.toString(strain1.getId()));
    Assert.assertEquals(1, samples1.size());
    StorageLocation location1 = samples1.get(0).getLocation();
    // delete
    Assert.assertTrue(service.delete(userId, strain1.getId(), samples1.get(0).getId()));
    Assert.assertNull(DAOFactory.getStorageDAO().get(location1.getId()));
    // ----- CASE 2 -----
    Strain strain2 = TestEntryCreator.createTestStrain(account);
    PartSample partSample2 = new PartSample();
    partSample2.setLabel("testForPlateScheme2");
    // tube2
    StorageLocation tube2 = new StorageLocation();
    tube2.setDisplay("tube2");
    tube2.setType(SampleType.TUBE);
    // well
    StorageLocation well2 = new StorageLocation();
    well2.setDisplay("well2");
    well2.setType(SampleType.WELL);
    well2.setChild(tube2);
    // plate2
    StorageLocation plate2 = new StorageLocation();
    plate2.setDisplay("plate2");
    plate2.setType(SampleType.PLATE96);
    plate2.setChild(well2);
    partSample2.setLocation(plate2);
    partSample2 = service.createSample(userId, Long.toString(strain2.getId()), partSample2, null);
    Assert.assertNotNull(partSample2);
    // ----- CASE 3 -----
    PartSample partSample3 = new PartSample();
    partSample3.setLabel("testForPlateScheme3");
    // tube2
    StorageLocation tube3 = new StorageLocation();
    tube3.setDisplay("tube3");
    tube3.setType(SampleType.TUBE);
    // well
    StorageLocation well3 = new StorageLocation();
    well3.setDisplay("well3");
    well3.setType(SampleType.WELL);
    well3.setChild(tube3);
    // plate2
    StorageLocation plate3 = new StorageLocation();
    plate3.setDisplay("plate3");
    plate3.setType(SampleType.PLATE96);
    plate3.setChild(well3);
    partSample3.setLocation(plate3);
    partSample3 = service.createSample(userId, Long.toString(strain2.getId()), partSample3, null);
    Assert.assertNotNull(partSample3);
    // fetch
    List<PartSample> samples3 = service.retrieveEntrySamples(userId, Long.toString(strain2.getId()));
    Assert.assertEquals(2, samples3.size());
    StorageLocation location3 = samples3.get(1).getLocation();
    // delete #2 and #3 consequently
    Assert.assertTrue(service.delete(userId, strain2.getId(), samples3.get(1).getId()));
    Assert.assertNull(DAOFactory.getStorageDAO().get(location3.getId()));
    List<PartSample> samples2 = service.retrieveEntrySamples(userId, Long.toString(strain2.getId()));
    Assert.assertEquals(1, samples2.size());
    StorageLocation location2 = samples2.get(0).getLocation();
    Assert.assertTrue(service.delete(userId, strain2.getId(), samples2.get(0).getId()));
    Assert.assertNull(DAOFactory.getStorageDAO().get(location2.getId()));
    List<PartSample> samplesEmpty = service.retrieveEntrySamples(userId, Long.toString(strain2.getId()));
    Assert.assertEquals(0, samplesEmpty.size());
}

Example 8 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class EntryController method createEntryComment.

public UserComment createEntryComment(String userId, long partId, UserComment newComment) {
    Entry entry = dao.get(partId);
    if (entry == null)
        return null;
    authorization.canRead(userId, entry);
    Account account = accountController.getByEmail(userId);
    Comment comment = new Comment();
    comment.setAccount(account);
    comment.setEntry(entry);
    comment.setBody(newComment.getMessage());
    comment.setCreationTime(new Date());
    comment = commentDAO.create(comment);
    if (newComment.getSamples() != null) {
        SampleDAO sampleDAO = DAOFactory.getSampleDAO();
        for (PartSample partSample : newComment.getSamples()) {
            Sample sample = sampleDAO.get(partSample.getId());
            if (sample == null)
                continue;
            comment.getSamples().add(sample);
            sample.getComments().add(comment);
        }
    }
    comment = commentDAO.update(comment);
    return comment.toDataTransferObject();
}

Example 9 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class BulkCSVUpload method getBulkUploadDataFromFile.

// NOTE: this also validates the part data (with the exception of the actual files)
List<PartWithSample> getBulkUploadDataFromFile(InputStream inputStream) throws IOException {
    List<PartWithSample> partDataList = new LinkedList<>();
    // initialize parser to null; when not-null in the loop below, then the header has been parsed
    CSVParser parser = null;
    HashMap<Integer, HeaderValue> headers = null;
    // parse CSV file
    try {
        LineIterator it = IOUtils.lineIterator(inputStream, "UTF-8");
        int index = 0;
        while (it.hasNext()) {
            String line = it.nextLine().trim();
            // check if first time parsing (first line)
            if (parser == null) {
                // to indicate the type of parser to use (tab or comma separated)
                if (line.contains("\t") && !line.contains(","))
                    parser = new CSVParser('\t');
                else
                    parser = new CSVParser();
                // get column headers
                String[] fieldStrArray = parser.parseLine(line);
                headers = processColumnHeaders(fieldStrArray);
                continue;
            }
            // skip any empty lines (holes) in the csv file
            if (StringUtils.isBlank(line) || line.replaceAll(",", "").trim().isEmpty())
                continue;
            // at this point we must have headers since that should be the first item in the file
            if (headers == null)
                throw new IOException("Could not parse file headers");
            // parser != null; process line contents with available headers
            String[] valuesArray = parser.parseLine(line);
            PartData partData = new PartData(addType);
            PartSample partSample = null;
            if (subType != null) {
                partData.getLinkedParts().add(new PartData(subType));
            }
            // for each column
            for (int i = 0; i < valuesArray.length; i += 1) {
                HeaderValue headerForColumn = headers.get(i);
                // process sample information
                if (headerForColumn.isSampleField()) {
                    // todo : move to another method
                    if (partSample == null)
                        partSample = new PartSample();
                    setPartSampleData(((SampleHeaderValue) headerForColumn).getSampleField(), partSample, valuesArray[i]);
                } else {
                    EntryHeaderValue entryHeaderValue = (EntryHeaderValue) headerForColumn;
                    EntryField field = entryHeaderValue.getEntryField();
                    PartData data;
                    String value = valuesArray[i];
                    boolean isSubType = entryHeaderValue.isSubType();
                    if (isSubType)
                        data = partData.getLinkedParts().get(0);
                    else
                        data = partData;
                    // get the data for the field
                    switch(field) {
                        case ATT_FILENAME:
                            ArrayList<AttachmentInfo> attachments = data.getAttachments();
                            if (attachments == null) {
                                attachments = new ArrayList<>();
                                data.setAttachments(attachments);
                            }
                            attachments.clear();
                            attachments.add(new AttachmentInfo(value));
                            break;
                        case SEQ_FILENAME:
                            data.setSequenceFileName(value);
                            break;
                        case SEQ_TRACE_FILES:
                            // todo
                            break;
                        case EXISTING_PART_NUMBER:
                            Entry entry = DAOFactory.getEntryDAO().getByPartNumber(value);
                            if (entry == null)
                                throw new IOException("Could not locate part number \"" + value + "\" for linking");
                            PartData toLink = entry.toDataTransferObject();
                            data.getLinkedParts().add(toLink);
                            break;
                        default:
                            partData = EntryUtil.setPartDataFromField(partData, value, field, isSubType);
                    }
                }
            }
            // validate
            List<EntryField> fields = EntryUtil.validates(partData);
            if (!fields.isEmpty()) {
                invalidFields.clear();
                invalidFields.addAll(fields);
                return null;
            }
            partData.setIndex(index);
            PartWithSample partWithSample = new PartWithSample(partSample, partData);
            partDataList.add(partWithSample);
            index += 1;
        }
    } finally {
        IOUtils.closeQuietly(inputStream);
    }
    return partDataList;
}

Example 10 with PartSample

use of org.jbei.ice.lib.dto.sample.PartSample in project ice by JBEI.

the class BulkEntryCreator method createEntries.

public boolean createEntries(String userId, long draftId, List<PartWithSample> data, HashMap<String, InputStream> files) {
    BulkUpload draft = dao.get(draftId);
    if (draft == null)
        return false;
    // check permissions
    authorization.expectWrite(userId, draft);
    SampleService sampleService = new SampleService();
    EntryAuthorization entryAuthorization = new EntryAuthorization();
    for (PartWithSample partWithSample : data) {
        if (partWithSample == null)
            continue;
        PartData partData = partWithSample.getPartData();
        if (partData == null)
            continue;
        Entry entry = InfoToModelFactory.infoToEntry(partData);
        if (entry == null)
            continue;
        entry.setVisibility(Visibility.DRAFT.getValue());
        Account account = accountController.getByEmail(userId);
        entry.setOwner(account.getFullName());
        entry.setOwnerEmail(account.getEmail());
        // check if there is any linked parts. create if so (expect a max of 1)
        if (partData.getLinkedParts() != null && partData.getLinkedParts().size() > 0) {
            // create linked
            PartData linked = partData.getLinkedParts().get(0);
            // for existing the link already....exists so just verify
            if (linked.getId() == 0) {
                Entry linkedEntry = InfoToModelFactory.infoToEntry(linked);
                if (linkedEntry != null) {
                    linkedEntry.setVisibility(Visibility.DRAFT.getValue());
                    linkedEntry.setOwner(account.getFullName());
                    linkedEntry.setOwnerEmail(account.getEmail());
                    linkedEntry = entryDAO.create(linkedEntry);
                    linked.setId(linkedEntry.getId());
                    linked.setModificationTime(linkedEntry.getModificationTime().getTime());
                    addWritePermission(account, linkedEntry);
                    // check for attachments and sequences for linked entry
                    saveFiles(linked, linkedEntry, files);
                    entry.getLinkedEntries().add(linkedEntry);
                }
            }
            entry = entryDAO.create(entry);
            // attempt to get linked entry and add
            if (linked.getId() != 0) {
                Entry linkedEntry = entryDAO.get(linked.getId());
                if (linkedEntry != null && entryAuthorization.canWrite(userId, entry)) {
                    EntryLinks links = new EntryLinks(userId, Long.toString(entry.getId()));
                    links.addLink(linked, LinkType.CHILD);
                }
            }
        } else {
            entry = entryDAO.create(entry);
        }
        // check for pi
        String piEmail = entry.getPrincipalInvestigatorEmail();
        if (StringUtils.isNotEmpty(piEmail)) {
            Account pi = DAOFactory.getAccountDAO().getByEmail(piEmail);
            if (pi != null) {
                // add write permission for the PI
                addWritePermission(pi, entry);
            }
        }
        // add write permissions for owner
        addWritePermission(account, entry);
        draft.getContents().add(entry);
        dao.update(draft);
        // save files
        saveFiles(partData, entry, files);
        // save sample, if available
        PartSample partSample = partWithSample.getPartSample();
        if (partSample == null)
            continue;
        sampleService.createSample(userId, Long.toString(entry.getId()), partSample, null);
    }
    return true;
}