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

Example 1 with EntryFieldLabel

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

the class RemoteEntriesAsCSV method writeLocalEntries.

protected void writeLocalEntries(List<Long> entries, List<EntryFieldLabel> fields, CSVWriter writer, ZipOutputStream zos) {
    if (entries == null)
        return;
    SequenceDAO sequenceDAO = DAOFactory.getSequenceDAO();
    Configuration configuration = DAOFactory.getConfigurationDAO().get(ConfigurationKey.URI_PREFIX);
    String thisUrl = configuration == null ? "" : configuration.getValue();
    for (Long id : entries) {
        Entry entry = DAOFactory.getEntryDAO().get(id);
        String[] line = new String[fields.size() + 4];
        line[0] = thisUrl;
        line[1] = entry.getCreationTime().toString();
        line[2] = entry.getPartNumber();
        int i = 2;
        for (EntryFieldLabel field : fields) {
            line[i + 1] = EntryUtil.entryFieldToValue(entry, field);
            i += 1;
        }
        // write sequence to zip file
        long entryId = entry.getId();
        if (sequenceDAO.hasSequence(entryId)) {
            String name = entry.getPartNumber() + ".gb";
            try {
                Sequence sequence = sequenceDAO.getByEntry(entry);
                line[i + 1] = name;
                GenbankFormatter genbankFormatter = new GenbankFormatter(name);
                ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
                genbankFormatter.format(sequence, byteStream);
                ByteArrayInputStream inputStream = new ByteArrayInputStream(byteStream.toByteArray());
                InputStreamWrapper wrapper = new InputStreamWrapper(inputStream, name);
                putZipEntry(wrapper, zos);
            } catch (Exception e) {
                line[i + 1] = "";
            }
        } else {
            line[i + 1] = "";
        }
        writer.writeNext(line);
    }
}

Example 2 with EntryFieldLabel

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

the class FileResource method downloadCSV.

/**
 * Extracts the csv information and writes it to the temp dir and returns the file uuid. Then
 * the client is expected to make another rest call with the uuid in a separate window. This
 * workaround is due to not being able to download files using XHR or sumsuch
 */
@POST
@Path("csv")
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
public Response downloadCSV(@QueryParam("sequenceFormats") final List<String> sequenceFormats, @QueryParam("entryFields") final List<String> fields, EntrySelection selection) {
    String userId = super.requireUserId();
    EntriesAsCSV entriesAsCSV = new EntriesAsCSV(userId, sequenceFormats.toArray(new String[0]));
    List<EntryFieldLabel> entryFieldLabels = new ArrayList<>();
    try {
        if (fields != null && !fields.isEmpty()) {
            entryFieldLabels.addAll(fields.stream().map(EntryFieldLabel::fromString).collect(Collectors.toList()));
        }
    } catch (Exception e) {
        Logger.error(e);
    }
    boolean success = entriesAsCSV.setSelectedEntries(selection, entryFieldLabels.toArray(new EntryFieldLabel[0]));
    if (!success)
        return super.respond(false);
    final File file = entriesAsCSV.getFilePath().toFile();
    if (file.exists()) {
        return Response.ok(new Setting("key", file.getName())).build();
    }
    return Response.serverError().build();
}

Example 3 with EntryFieldLabel

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

the class BulkUploadEntries method submitBulkImportDraft.

/**
 * Submits a bulk import that has been saved. This action is restricted to the owner of the
 * draft or to administrators.
 */
private ProcessedBulkUpload submitBulkImportDraft(String userId, BulkUpload draft, ProcessedBulkUpload processedBulkUpload) throws PermissionException {
    // validate entries
    BulkUploadValidation validation = new BulkUploadValidation(draft);
    if (!validation.isValid()) {
        processedBulkUpload.setSuccess(false);
        for (EntryFieldLabel entryFieldLabel : validation.getFailedFields()) {
            processedBulkUpload.getHeaders().add(new EntryHeaderValue(entryFieldLabel));
        }
        processedBulkUpload.setUserMessage("Cannot submit your bulk upload due to a validation failure");
        return processedBulkUpload;
    }
    draft.setStatus(BulkUploadStatus.PENDING_APPROVAL);
    draft.setLastUpdateTime(new Date());
    draft.setName(userId);
    BulkUpload bulkUpload = dao.update(draft);
    if (bulkUpload != null) {
        // convert entries to pending
        dao.setEntryStatus(bulkUpload, Visibility.PENDING);
        String email = Utils.getConfigValue(ConfigurationKey.BULK_UPLOAD_APPROVER_EMAIL);
        if (email != null && !email.isEmpty()) {
            String subject = Utils.getConfigValue(ConfigurationKey.PROJECT_NAME) + " Bulk Upload Notification";
            String body = "A bulk upload has been submitted and is pending verification.\n\n";
            body += "Please login to the registry at:\n\n";
            body += Utils.getConfigValue(ConfigurationKey.URI_PREFIX);
            body += "\n\nand use the \"Pending Approval\" menu item to approve it\n\nThanks.";
            EmailFactory.getEmail().send(email, subject, body);
        }
        return processedBulkUpload;
    }
    return null;
}

Example 4 with EntryFieldLabel

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

the class BulkUploadEntries method createOrUpdateEntry.

/**
 * Creates (or updates) entry based on information in parameters
 *
 * @param autoUpdate wrapper for information used to create entry
 * @return updated wrapper for information used to create entry. Will contain additional information
 * such as the unique identifier for the part, if one was created
 */
BulkUploadAutoUpdate createOrUpdateEntry(BulkUploadAutoUpdate autoUpdate) {
    Account account = accountController.getByEmail(userId);
    // for bulk edit, drafts will not exist
    if (autoUpdate.getEditMode() != EditMode.BULK_EDIT) {
        autoUpdate.setBulkUploadId(this.upload.getId());
    }
    // for strain with plasmid this is the strain
    Entry entry = entryDAO.get(autoUpdate.getEntryId());
    // if entry is null, create entry
    if (entry == null) {
        PartData partData = new PartData(autoUpdate.getType());
        partData.setOwner(account.getFullName());
        partData.setOwnerEmail(account.getEmail());
        partData.setCreator(account.getFullName());
        partData.setCreatorEmail(account.getEmail());
        partData = entries.create(partData);
        entry = entryDAO.get(partData.getId());
        autoUpdate.setEntryId(entry.getId());
        if (this.upload != null) {
            this.upload.getContents().add(entry);
        }
    }
    // now update the values (for strain with plasmid, some values are for both
    for (Map.Entry<EntryFieldLabel, String> set : autoUpdate.getKeyValue().entrySet()) {
        String value = set.getValue();
        EntryFieldLabel field = set.getKey();
        InfoToModelFactory.infoToEntryForField(entry, new String[] { value }, field);
    }
    // if (this.upload != null && this.upload.getStatus() != BulkUploadStatus.PENDING_APPROVAL) {
    // if (otherEntry != null && autoUpdate.getEditMode() != EditMode.BULK_EDIT) {
    // if (otherEntry.getVisibility() == null || otherEntry.getVisibility() != Visibility.DRAFT.getValue())
    // otherEntry.setVisibility(Visibility.DRAFT.getValue());
    // 
    // updateEntry(otherEntry);
    // }
    // 
    // if ((entry.getVisibility() == null || entry.getVisibility() != Visibility.DRAFT.getValue())
    // && autoUpdate.getEditMode() != EditMode.BULK_EDIT)
    // entry.setVisibility(Visibility.DRAFT.getValue());
    // }
    updateEntry(entry);
    // update bulk upload. even if no new entry was created, entries belonging to it was updated
    if (this.upload != null) {
        this.upload.setLastUpdateTime(new Date());
        autoUpdate.setLastUpdate(this.upload.getLastUpdateTime());
        dao.update(this.upload);
    }
    return autoUpdate;
}

Example 5 with EntryFieldLabel

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

the class BulkZipUpload method processUpload.

/**
 * Process the zip file. It expects that there is exactly one file with the .csv extension.
 * This means that a .csv cannot be used as an attachment
 * </p>
 * Also, all dot files are ignored
 */
public ProcessedBulkUpload processUpload() {
    ProcessedBulkUpload processedBulkUpload = new ProcessedBulkUpload();
    InputStream csvFile = null;
    HashMap<String, InputStream> files = new HashMap<>();
    try (BufferedInputStream bis = new BufferedInputStream(inputStream);
        ZipInputStream zis = new ZipInputStream(bis)) {
        ZipEntry zipEntry;
        while ((zipEntry = zis.getNextEntry()) != null) {
            if (zipEntry.isDirectory())
                continue;
            String name = zipEntry.getName();
            if (name.contains("/"))
                name = name.substring(name.lastIndexOf("/") + 1);
            // ignore all dot files
            if (name.startsWith("."))
                continue;
            int len;
            ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
            byte[] buffer = new byte[1024];
            while ((len = zis.read(buffer)) > 0) {
                byteArrayOutputStream.write(buffer, 0, len);
            }
            zis.closeEntry();
            // get main csv
            if (name.endsWith(".csv")) {
                if (csvFile != null) {
                    processedBulkUpload.setSuccess(false);
                    processedBulkUpload.setUserMessage("Duplicate csv file in zip archive. It should only contain one.");
                    return processedBulkUpload;
                } else {
                    csvFile = new ByteArrayInputStream(byteArrayOutputStream.toByteArray());
                }
            } else {
                files.put(name, new ByteArrayInputStream(byteArrayOutputStream.toByteArray()));
            }
        }
    } catch (IOException e) {
        processedBulkUpload.setSuccess(false);
        processedBulkUpload.setUserMessage(e.getCause().getMessage());
        return processedBulkUpload;
    }
    if (csvFile == null) {
        processedBulkUpload.setSuccess(false);
        processedBulkUpload.setUserMessage("Could not find a csv file in the zip archive");
        return processedBulkUpload;
    }
    try {
        // retrieve the partData and validates
        List<PartWithSample> updates = super.getBulkUploadDataFromFile(csvFile);
        if (updates == null) {
            processedBulkUpload.setSuccess(false);
            processedBulkUpload.setUserMessage("Validation failed");
            for (EntryFieldLabel field : invalidFields) {
                processedBulkUpload.getHeaders().add(new EntryHeaderValue(field));
            }
            return processedBulkUpload;
        }
        // validate files to ensure that for each partData with a file, that the file is available
        for (PartWithSample partWithSample : updates) {
            // check sequences
            PartData data = partWithSample.getPartData();
            String sequenceFile = data.getSequenceFileName();
            if (StringUtils.isNotBlank(sequenceFile) && files.get(sequenceFile) == null) {
                processedBulkUpload.setSuccess(false);
                processedBulkUpload.setUserMessage("Sequence file \"" + sequenceFile + "\" not found in the zip archive");
                return processedBulkUpload;
            }
            // check attachments
            String attachmentFile;
            if (data.getAttachments() != null && !data.getAttachments().isEmpty()) {
                attachmentFile = data.getAttachments().get(0).getFilename();
                if (StringUtils.isNotBlank(attachmentFile) && files.get(attachmentFile) == null) {
                    processedBulkUpload.setSuccess(false);
                    processedBulkUpload.setUserMessage("Attachment file \"" + sequenceFile + "\" not found in the zip archive");
                    return processedBulkUpload;
                }
            }
        // todo : trace sequences
        }
        // create actual registry parts
        BulkUploadEntries creator = new BulkUploadEntries(userId, this.uploadId);
        // create entries
        if (!creator.createEntries(updates, files)) {
            String errorMsg = "Error creating entries for upload";
            throw new IOException(errorMsg);
        // todo: delete upload id
        }
        processedBulkUpload.setUploadId(uploadId);
        return processedBulkUpload;
    } catch (IOException e) {
        Logger.error(e);
        processedBulkUpload.setSuccess(false);
        processedBulkUpload.setUserMessage(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
        return processedBulkUpload;
    }
}