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

Example 1 with EntryField

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

the class RemoteEntriesAsCSV method writeDataEntries.

protected void writeDataEntries(RemotePartner partner, List<PartData> entries, List<EntryField> fields, CSVWriter writer, ZipOutputStream zos) {
    if (entries == null)
        return;
    for (PartData partData : entries) {
        String[] line = new String[fields.size() + 4];
        line[0] = partner.getUrl();
        line[1] = new Date(partData.getCreationTime()).toString();
        line[2] = partData.getPartId();
        int i = 2;
        for (EntryField field : fields) {
            line[i + 1] = PartDataUtil.entryFieldToValue(partData, field);
            i += 1;
        }
        // write sequence to zip file
        if (partData.isHasSequence()) {
            try {
                // get remote sequence
                FeaturedDNASequence featuredDNASequence = remoteEntries.getPublicEntrySequence(partner.getId(), Long.toString(partData.getId()));
                if (featuredDNASequence != null) {
                    String name = partData.getPartId() + ".gb";
                    // write sequence to zip
                    line[i + 1] = name;
                    Sequence sequence = SequenceController.dnaSequenceToSequence(featuredDNASequence);
                    GenbankFormatter genbankFormatter = new GenbankFormatter(name);
                    ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
                    genbankFormatter.format(sequence, byteStream);
                    ByteArrayWrapper wrapper = new ByteArrayWrapper(byteStream.toByteArray(), name);
                    putZipEntry(wrapper, zos);
                } else {
                    line[i + 1] = "";
                }
            } catch (Exception e) {
                line[i + 1] = "";
            }
        } else {
            line[i + 1] = "";
        }
        writer.writeNext(line);
    }
}

Example 2 with EntryField

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

the class RemoteEntriesAsCSV method getCSVHeaders.

protected String[] getCSVHeaders(List<EntryField> fields) {
    String[] headers = new String[fields.size() + 4];
    headers[0] = "Registry";
    headers[1] = "Created";
    headers[2] = "Part ID";
    int i = 2;
    for (EntryField field : fields) {
        i += 1;
        headers[i] = field.getLabel();
    }
    headers[i + 1] = "Sequence File";
    return headers;
}

Example 3 with EntryField

use of org.jbei.ice.lib.dto.entry.EntryField 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(sequenceFormats.toArray(new String[sequenceFormats.size()]));
    List<EntryField> entryFields = new ArrayList<>();
    try {
        if (fields != null) {
            entryFields.addAll(fields.stream().map(EntryField::fromString).collect(Collectors.toList()));
        }
    } catch (Exception e) {
        Logger.error(e);
    }
    boolean success = entriesAsCSV.setSelectedEntries(userId, selection, entryFields.toArray(new EntryField[entryFields.size()]));
    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 4 with EntryField

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

the class EntriesAsCSV method getEntryFields.

protected EntryField[] getEntryFields() {
    Set<String> recordTypes = new HashSet<>(dao.getRecordTypes(entries));
    List<EntryField> fields = EntryFields.getCommonFields();
    for (String recordType : recordTypes) {
        EntryType type = EntryType.nameToType(recordType);
        if (type == null) {
            Logger.error("Could not convert entry type " + recordType);
            continue;
        }
        switch(type) {
            case ARABIDOPSIS:
                EntryFields.addArabidopsisSeedHeaders(fields);
                break;
            case STRAIN:
                EntryFields.addStrainHeaders(fields);
                break;
            case PLASMID:
                EntryFields.addPlasmidHeaders(fields);
                break;
        }
    }
    return fields.toArray(new EntryField[(fields.size())]);
}

Example 5 with EntryField

use of org.jbei.ice.lib.dto.entry.EntryField 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();
    String csvFile = null;
    HashMap<String, InputStream> files = new HashMap<>();
    try {
        ZipFile zipFile = new ZipFile(zipFilePath.toFile());
        Enumeration<? extends ZipEntry> enumeration = zipFile.entries();
        // go through zip elements
        while (enumeration.hasMoreElements()) {
            ZipEntry zipEntry = enumeration.nextElement();
            // does not go into directories for now
            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;
            // 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;
                }
                csvFile = Utils.getString(zipFile.getInputStream(zipEntry));
            } else {
                InputStream inputStream = zipFile.getInputStream(zipEntry);
                files.put(name, inputStream);
            }
        }
    } 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 {
        ByteArrayInputStream inputStream = new ByteArrayInputStream(csvFile.getBytes(StandardCharsets.UTF_8));
        // retrieve the partData and validates
        List<PartWithSample> updates = super.getBulkUploadDataFromFile(inputStream);
        if (updates == null) {
            processedBulkUpload.setSuccess(false);
            processedBulkUpload.setUserMessage("Validation failed");
            for (EntryField field : invalidFields) {
                processedBulkUpload.getHeaders().add(new EntryHeaderValue(false, 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
        BulkEntryCreator creator = new BulkEntryCreator();
        long uploadId = creator.createBulkUpload(userId, addType);
        // create entries
        if (!creator.createEntries(userId, uploadId, 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;
    }
}