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

Example 46 with PartData

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

the class FolderContents method addRemoteEntries.

/**
     * @param remoteEntries list of entries that map to entries on other ICE instances. It contains enough information
     *                      for the table view (as a cache)
     * @param folders       list of folders that the remote entries are to be added to
     * @return List of folders that the specified entries were added to
     */
protected List<FolderDetails> addRemoteEntries(String userId, List<PartData> remoteEntries, List<FolderDetails> folders) {
    // nothing adding to destination
    if (remoteEntries == null)
        return new ArrayList<>();
    // nothing to add
    if (remoteEntries.isEmpty())
        return folders;
    EntryDAO entryDAO = DAOFactory.getEntryDAO();
    List<Entry> entryModelList = new ArrayList<>(remoteEntries.size());
    for (PartData partData : remoteEntries) {
        Entry entry = entryDAO.getByRecordId(partData.getRecordId());
        if (entry == null) {
            switch(partData.getType()) {
                case PART:
                default:
                    entry = new Part();
                    break;
                case STRAIN:
                    entry = new Strain();
                    break;
                case PLASMID:
                    entry = new Plasmid();
                    break;
                case ARABIDOPSIS:
                    entry = new ArabidopsisSeed();
                    break;
            }
            entry.setRecordId(partData.getRecordId());
            entry.setVersionId(partData.getRecordId());
            entry.setRecordType(partData.getType().getDisplay());
            entry.setName(partData.getName());
            entry.setShortDescription(partData.getShortDescription());
            entry.setStatus(partData.getStatus());
            entry.setVisibility(Visibility.REMOTE.getValue());
            entry.setPartNumber(partData.getPartId());
            String sequence = partData.isHasSequence() ? "sequence" : "text";
            entry.setLongDescriptionType(sequence);
            entry.setBioSafetyLevel(partData.getBioSafetyLevel());
            entry.setCreationTime(new Date(partData.getCreationTime()));
            entry = entryDAO.create(entry);
        }
        entryModelList.add(entry);
    }
    for (FolderDetails details : folders) {
        Folder folder = folderDAO.get(details.getId());
        if (folder == null) {
            Logger.warn("Could not add entries to folder " + details.getId() + " which doesn't exist");
            continue;
        }
        if (!folderAuthorization.canWrite(userId, folder)) {
            Logger.warn(userId + " lacks write privileges on folder " + folder.getId());
            continue;
        }
        folderDAO.addFolderContents(folder, entryModelList);
        details.setCount(folderDAO.getFolderSize(folder.getId(), null, true));
    }
    return folders;
}

Example 47 with PartData

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

the class RemoteEntriesAsCSV method writeList.

private boolean writeList(List<RemotePartner> partners) throws IOException {
    Path tmpPath = Paths.get(Utils.getConfigValue(ConfigurationKey.TEMPORARY_DIRECTORY));
    File tmpFile = File.createTempFile("remote-ice-", ".csv", tmpPath.toFile());
    csvPath = tmpFile.toPath();
    FileWriter fileWriter = new FileWriter(tmpFile);
    List<EntryField> fields = getEntryFields();
    String[] headers = getCSVHeaders(fields);
    // csv file headers
    File tmpZip = File.createTempFile("zip-", ".zip", tmpPath.toFile());
    FileOutputStream fos = new FileOutputStream(tmpZip);
    try (CSVWriter writer = new CSVWriter(fileWriter);
        ZipOutputStream zos = new ZipOutputStream(fos)) {
        writer.writeNext(headers);
        // go through partners
        for (RemotePartner partner : partners) {
            try {
                Logger.info("Retrieving from " + partner.getUrl());
                PartnerEntries partnerEntries = remoteEntries.getPublicEntries(partner.getId(), 0, Integer.MAX_VALUE, null, true);
                Results<PartData> webEntries = partnerEntries.getEntries();
                if (webEntries == null || webEntries.getData() == null) {
                    Logger.error("Could not retrieve entries for " + partner.getUrl());
                    continue;
                }
                Logger.info("Obtained " + webEntries.getResultCount() + " from " + partner.getUrl());
                // go through entries for each partner and write to the zip file
                writeDataEntries(partner, webEntries.getData(), fields, writer, zos);
            } catch (Exception e) {
                Logger.warn("Exception retrieving entries " + e.getMessage());
            }
        }
        // write local entries
        if (this.includeLocal) {
            Logger.info("Retrieving local public entries");
            Group publicGroup = new GroupController().createOrRetrievePublicGroup();
            Set<Group> groups = new HashSet<>();
            groups.add(publicGroup);
            EntryDAO entryDAO = DAOFactory.getEntryDAO();
            List<Entry> results = entryDAO.retrieveVisibleEntries(null, groups, ColumnField.CREATED, true, 0, Integer.MAX_VALUE, null);
            writeLocalEntries(results, fields, writer, zos);
        }
        // write the csv file to the zip
        writeZip(tmpZip, zos);
    }
    return true;
}

Example 48 with PartData

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

the class RemoteTransfer method performTransfer.

/**
     * Transfers the sequence file for the part and any parts that are linked to it.
     * If the attached sequence was uploaded as a file or pasted, the system
     * transfers that. If not if attempts to convert the attached sequence to genbank format
     * and transfers that
     *
     * @param partner destination for the sequence transfer
     * @param data    data for part whose sequences are to be transferred
     */
protected void performTransfer(RemotePartner partner, PartData data) {
    String url = partner.getUrl();
    // check main entry for sequence
    if (sequenceDAO.hasSequence(data.getId())) {
        Entry entry = entryDAO.get(data.getId());
        Sequence sequence = sequenceDAO.getByEntry(entry);
        String sequenceString = sequence.getSequenceUser();
        if (StringUtils.isEmpty(sequenceString)) {
            GenbankFormatter genbankFormatter = new GenbankFormatter(entry.getName());
            genbankFormatter.setCircular(true);
            try {
                ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
                genbankFormatter.format(sequence, byteStream);
                sequenceString = byteStream.toString();
            } catch (Exception e) {
                Logger.error(e);
                sequenceString = sequence.getSequence();
            }
        }
        if (!StringUtils.isEmpty(sequenceString))
            remoteContact.transferSequence(url, data.getRecordId(), data.getType(), sequenceString);
    }
    // check child entries
    if (data.getLinkedParts() == null)
        return;
    for (PartData linked : data.getLinkedParts()) {
        performTransfer(partner, linked);
    }
}

Example 49 with PartData

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

the class RemoteTransfer method getPartsForTransfer.

/**
     * Using the list of entry Ids, populates a list of PartData objects that maintains the hierarchical
     * relationships
     *
     * @param entryIds list of ids for entries that are to be transferred
     * @return List of Part Data objects obtained using the list for transfer
     */
public List<PartData> getPartsForTransfer(List<Long> entryIds) {
    // for searching entries to be transferred
    HashSet<Long> forTransfer = new HashSet<>(entryIds);
    HashMap<Long, PartData> toTransfer = new LinkedHashMap<>();
    for (long entryId : entryIds) {
        // already being transferred; skip
        if (toTransfer.containsKey(entryId))
            continue;
        Entry entry = entryDAO.get(entryId);
        if (entry == null)
            continue;
        PartData data = ModelToInfoFactory.getInfo(entry);
        if (data == null) {
            Logger.error("Could not convert entry " + entry.getId() + " to data model");
            continue;
        }
        // check if the linked entries (if any) is in the list of entries to be transferred
        if (data.getLinkedParts() != null && !data.getLinkedParts().isEmpty()) {
            Iterator<PartData> iterator = data.getLinkedParts().iterator();
            while (iterator.hasNext()) {
                PartData linkedData = iterator.next();
                // make sure linked entry is among list to be transferred
                if (!forTransfer.contains(linkedData.getId())) {
                    iterator.remove();
                    continue;
                }
                // check if linked entry has already been transferred
                if (toTransfer.containsKey(linkedData.getId())) {
                    // part of this entry
                    if (toTransfer.remove(linkedData.getId()) == null)
                        Logger.warn("Entry " + linkedData.getId() + " being transferred twice");
                }
            }
        }
        toTransfer.put(data.getId(), data);
    }
    return new LinkedList<>(toTransfer.values());
}

Example 50 with PartData

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

the class HibernateSearch method executeSearchNoTerms.

public SearchResults executeSearchNoTerms(String userId, HashMap<String, SearchResult> blastResults, SearchQuery searchQuery) {
    ArrayList<EntryType> entryTypes = searchQuery.getEntryTypes();
    if (entryTypes == null || entryTypes.isEmpty()) {
        entryTypes = new ArrayList<>();
        entryTypes.addAll(Arrays.asList(EntryType.values()));
    }
    Session session = HibernateUtil.getSessionFactory().getCurrentSession();
    int resultCount;
    FullTextSession fullTextSession = Search.getFullTextSession(session);
    BooleanQuery.Builder builder = new BooleanQuery.Builder();
    QueryBuilder qb = fullTextSession.getSearchFactory().buildQueryBuilder().forEntity(Entry.class).get();
    ArrayList<Query> except = new ArrayList<>();
    for (EntryType type : EntryType.values()) {
        if (entryTypes.contains(type))
            continue;
        except.add(qb.keyword().onField("recordType").matching(type.getName()).createQuery());
    }
    // add terms for record types
    Query[] queries = new Query[] {};
    Query recordTypeQuery = qb.all().except(except.toArray(queries)).createQuery();
    builder.add(recordTypeQuery, BooleanClause.Occur.FILTER);
    // visibility
    Query visibilityQuery = qb.keyword().onField("visibility").matching(Visibility.OK.getValue()).createQuery();
    builder.add(visibilityQuery, BooleanClause.Occur.FILTER);
    // bio safety level
    BioSafetyOption option = searchQuery.getBioSafetyOption();
    if (option != null) {
        TermContext bslContext = qb.keyword();
        Query biosafetyQuery = bslContext.onField("bioSafetyLevel").ignoreFieldBridge().matching(option.getIntValue()).createQuery();
        builder.add(biosafetyQuery, BooleanClause.Occur.FILTER);
    }
    // check filter filters
    if (searchQuery.getFieldFilters() != null && !searchQuery.getFieldFilters().isEmpty()) {
        for (FieldFilter fieldFilter : searchQuery.getFieldFilters()) {
            String searchField = SearchFieldFactory.searchFieldForEntryField(fieldFilter.getField());
            if (StringUtils.isEmpty(searchField))
                continue;
            Query filterQuery = qb.keyword().onField(searchField).matching(fieldFilter.getFilter()).createQuery();
            builder.add(filterQuery, BooleanClause.Occur.MUST);
        }
    }
    // check if there is a blast results
    createBlastFilterQuery(fullTextSession, blastResults, builder);
    // wrap Lucene query in a org.hibernate.Query
    FullTextQuery fullTextQuery = fullTextSession.createFullTextQuery(builder.build(), Entry.class);
    // get sorting values
    Sort sort = getSort(searchQuery.getParameters().isSortAscending(), searchQuery.getParameters().getSortField());
    fullTextQuery.setSort(sort);
    // enable security filter if needed
    checkEnableSecurityFilter(userId, fullTextQuery);
    // enable has attachment/sequence/sample (if needed)
    checkEnableHasAttribute(fullTextQuery, searchQuery.getParameters());
    // set paging params
    fullTextQuery.setFirstResult(searchQuery.getParameters().getStart());
    fullTextQuery.setMaxResults(searchQuery.getParameters().getRetrieveCount());
    resultCount = fullTextQuery.getResultSize();
    List result = fullTextQuery.list();
    LinkedList<SearchResult> searchResults = new LinkedList<>();
    for (Object object : result) {
        Entry entry = (Entry) object;
        SearchResult searchResult;
        if (blastResults != null) {
            searchResult = blastResults.get(Long.toString(entry.getId()));
            if (// this should not really happen since we already filter
            searchResult == null)
                continue;
        } else {
            searchResult = new SearchResult();
            searchResult.setScore(1f);
            PartData info = ModelToInfoFactory.createTableViewData(userId, entry, true);
            searchResult.setEntryInfo(info);
        }
        searchResult.setMaxScore(1f);
        searchResults.add(searchResult);
    }
    SearchResults results = new SearchResults();
    results.setResultCount(resultCount);
    results.setResults(searchResults);
    Logger.info(userId + ": obtained " + resultCount + " results for empty query");
    return results;
}