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

Example 1 with PartData

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

the class EntryLinks method getParents.

/**
     * Retrieves list of this entry's parents that user has read access to
     *
     * @return list of parents of entry
     */
public List<PartData> getParents() {
    List<Entry> parents = this.entryDAO.getParents(this.entry.getId());
    List<PartData> parentData = new ArrayList<>(parents.size());
    for (Entry parent : parents) {
        if (!entryAuthorization.canRead(this.userId, parent))
            continue;
        parentData.add(parent.toDataTransferObject());
    }
    return parentData;
}

Example 2 with PartData

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

the class EntryCreator method copyPart.

/**
     * Creates a copy of
     *
     * @param userId   identifier for user making request
     * @param sourceId unique identifier for part acting as source of copy. Can be the part id, uuid or id
     * @return wrapper around the id and record id of the newly created entry
     * @throws IllegalArgumentException if the source part for the copy cannot be located using the identifier
     */
public PartData copyPart(String userId, String sourceId) {
    Entry entry = getEntry(sourceId);
    if (entry == null)
        throw new IllegalArgumentException("Could not retrieve entry \"" + sourceId + "\" for copy");
    // check permission (expecting read permission)
    entryAuthorization.expectRead(userId, entry);
    Sequence sequence = null;
    if (sequenceDAO.hasSequence(entry.getId())) {
        sequence = sequenceDAO.getByEntry(entry);
    }
    // copy to data model and back ??
    PartData partData = ModelToInfoFactory.getInfo(entry);
    entry = InfoToModelFactory.infoToEntry(partData);
    // create entry
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    entry.setName(entry.getName() + " (copy)");
    entry.setRecordId(Utils.generateUUID());
    entry.setVersionId(entry.getRecordId());
    entry.setOwnerEmail(account.getEmail());
    entry.setOwner(account.getFullName());
    entry = createEntry(account, entry, new ArrayList<>());
    // check sequence
    if (sequence != null) {
        SequenceController sequenceController = new SequenceController();
        FeaturedDNASequence dnaSequence = sequenceController.sequenceToDNASequence(sequence);
        sequence = SequenceController.dnaSequenceToSequence(dnaSequence);
        sequence.setEntry(entry);
        sequenceDAO.saveSequence(sequence);
        BlastPlus.scheduleBlastIndexRebuildTask(true);
    }
    PartData copy = new PartData(EntryType.nameToType(entry.getRecordType()));
    copy.setId(entry.getId());
    copy.setRecordId(entry.getRecordId());
    return copy;
}

Example 3 with PartData

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

the class RemoteEntries method getPublicEntries.

public PartnerEntries getPublicEntries(long remoteId, int offset, int limit, String sort, boolean asc) {
    if (!hasRemoteAccessEnabled())
        return null;
    RemotePartner partner = this.remotePartnerDAO.get(remoteId);
    if (partner == null)
        return null;
    FolderDetails details;
    try {
        final String restPath = "rest/folders/public/entries";
        HashMap<String, Object> queryParams = new HashMap<>();
        queryParams.put("offset", offset);
        queryParams.put("limit", limit);
        queryParams.put("asc", asc);
        queryParams.put("sort", sort);
        details = this.remoteContact.getFolderEntries(partner.getUrl(), restPath, queryParams, partner.getApiKey());
        if (details == null)
            return null;
    } catch (Exception e) {
        Logger.error(e);
        return null;
    }
    Results<PartData> results = new Results<>();
    results.setData(details.getEntries());
    results.setResultCount(details.getCount());
    return new PartnerEntries(partner.toDataTransferObject(), results);
}

Example 4 with PartData

use of org.jbei.ice.lib.dto.entry.PartData 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 5 with PartData

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

the class WebEntries method getPart.

/**
     * Checks the local database for the entry with id <code>recordId</code>
     * If it exists locally and is public, it returns it. Otherwise it checks the
     * other ICE instances that it partners with, in turn, to see if it exists on there
     *
     * @param recordId unique record identifier for the desired entry
     * @return entry details if found, else null
     * @throws PermissionException if the entry exists locally but is not a public entry
     */
public PartData getPart(String recordId) {
    // check local first
    Entry entry = this.entryDAO.getByRecordId(recordId);
    if (entry != null && entry.getVisibility() != Visibility.REMOTE.getValue()) {
        PermissionsController permissionsController = new PermissionsController();
        if (permissionsController.isPubliclyVisible(entry))
            return ModelToInfoFactory.getInfo(entry);
    }
    List<RemotePartner> partners = this.remotePartnerDAO.getRegistryPartners();
    for (RemotePartner partner : partners) {
        if (partner.getPartnerStatus() != RemotePartnerStatus.APPROVED)
            continue;
        PartData partData = this.remoteContact.getPublicEntry(partner.getUrl(), recordId, partner.getApiKey());
        // if the part is just a remote then the main one is on some other ICE instance
        if (partData == null || partData.getVisibility() == Visibility.REMOTE)
            continue;
        return partData;
    }
    return null;
}