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

Example 41 with PartData

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

the class CollectionEntriesTest method testGetEntriesByVisibility.

@Test
public void testGetEntriesByVisibility() throws Exception {
    Account account = AccountCreator.createTestAccount("CollectionEntriesTest.testGetEntriesByVisibility", false);
    Assert.assertNotNull(account);
    long id = TestEntryCreator.createTestPart(account.getEmail());
    Entry entry = DAOFactory.getEntryDAO().get(id);
    entry.setVisibility(Visibility.DRAFT.getValue());
    DAOFactory.getEntryDAO().update(entry);
    CollectionEntries collectionEntries = new CollectionEntries(account.getEmail(), CollectionType.DRAFTS);
    Results<PartData> results = collectionEntries.getEntries(ColumnField.CREATED, true, 0, 13);
    Assert.assertNotNull(results);
    Assert.assertEquals(1, results.getData().size());
    Assert.assertEquals(1, results.getResultCount());
}

Example 42 with PartData

use of org.jbei.ice.lib.dto.entry.PartData 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 43 with PartData

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

the class BulkEntryCreator method doUpdate.

protected PartData doUpdate(String userId, Entry entry, PartData data) {
    if (entry == null)
        return null;
    entry = InfoToModelFactory.updateEntryField(data, entry);
    if (entry == null)
        return null;
    entry.setModificationTime(new Date());
    entry = entryDAO.update(entry);
    data.setModificationTime(entry.getModificationTime().getTime());
    // check if there is any linked parts. update if so (expect a max of 1)
    if (data.getLinkedParts() == null || data.getLinkedParts().size() == 0)
        return data;
    // retrieve the entry (this is the only time you can create another entry on update)
    // bulk upload can only link 1
    PartData linkedPartData = data.getLinkedParts().get(0);
    Entry linkedEntry = entryDAO.get(linkedPartData.getId());
    if (linkedEntry == null && !StringUtils.isEmpty(linkedPartData.getPartId())) {
        // try partId
        linkedEntry = entryDAO.getByPartNumber(linkedPartData.getPartId());
        linkedPartData.setId(linkedEntry.getId());
    }
    if (linkedEntry == null) {
        linkedEntry = InfoToModelFactory.infoToEntry(linkedPartData);
        if (linkedEntry != null) {
            linkedEntry.setVisibility(Visibility.DRAFT.getValue());
            Account account = accountController.getByEmail(userId);
            linkedEntry.setOwner(account.getFullName());
            linkedEntry.setOwnerEmail(account.getEmail());
            linkedEntry = entryDAO.create(linkedEntry);
            entry.getLinkedEntries().add(linkedEntry);
            entryDAO.update(linkedEntry);
        }
    } else {
        // linking to existing
        EntryLinks entryLinks = new EntryLinks(userId, Long.toString(entry.getId()));
        entryLinks.addLink(linkedPartData, LinkType.CHILD);
    }
    // recursively update
    PartData linked = doUpdate(userId, linkedEntry, linkedPartData);
    data.getLinkedParts().clear();
    if (linked != null)
        data.getLinkedParts().add(linked);
    return data;
}

Example 44 with PartData

use of org.jbei.ice.lib.dto.entry.PartData 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;
}

Example 45 with PartData

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

the class BulkEntryCreator method createEntryForUpload.

protected PartData createEntryForUpload(String userId, PartData data, BulkUpload upload) {
    Entry entry = InfoToModelFactory.infoToEntry(data);
    if (entry == null)
        return null;
    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.
    if (data.getLinkedParts() != null && data.getLinkedParts().size() > 0) {
        PartData linked = data.getLinkedParts().get(0);
        // check if linking to existing
        if (StringUtils.isEmpty(linked.getPartId())) {
            // create new
            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());
                data.getLinkedParts().clear();
                data.getLinkedParts().add(linked);
                // link to main entry in the database
                entry.getLinkedEntries().add(linkedEntry);
            }
        } else {
            // link existing
            Entry linkedEntry = entryDAO.getByPartNumber(linked.getPartId());
            if (!entry.getLinkedEntries().contains(linkedEntry)) {
                entry.getLinkedEntries().add(linkedEntry);
            }
        }
    }
    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);
    upload.getContents().add(entry);
    dao.update(upload);
    data.setId(entry.getId());
    data.setModificationTime(entry.getModificationTime().getTime());
    return data;
}