Examples with Entry org.jbei.ice.storage.model.Entry used on opensource projects

Example 1 with Entry

use of org.jbei.ice.storage.model.Entry in project ice by JBEI.

the class EntryLinks method removeLink.

/**
     * Removes link specified entry id based on the specified type
     *
     * @param partToRemove unique identifier for part to remove
     * @param linkType     type of relationship that exists
     * @return true, if entry is removed successfully.
     */
public boolean removeLink(long partToRemove, LinkType linkType) {
    entryAuthorization.expectWrite(userId, entry);
    Entry linkedEntry = entryDAO.get(partToRemove);
    switch(linkType) {
        case PARENT:
            return linkedEntry.getLinkedEntries().remove(entry) && entryDAO.update(linkedEntry) != null;
        case CHILD:
        default:
            return entry.getLinkedEntries().remove(linkedEntry) && entryDAO.update(entry) != null;
    }
}

Example 2 with Entry

use of org.jbei.ice.storage.model.Entry 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 3 with Entry

use of org.jbei.ice.storage.model.Entry in project ice by JBEI.

the class EntryPermissionTask method execute.

@Override
public void execute() {
    // check if user has write privileges on entries
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    List<Group> accountGroups = new GroupController().getAllGroups(account);
    boolean checkIndividual = false;
    if (account.getType() != AccountType.ADMIN && !permissionDAO.canWrite(account, accountGroups, entries)) {
        checkIndividual = true;
    }
    EntryDAO entryDAO = DAOFactory.getEntryDAO();
    EntryAuthorization entryAuthorization = new EntryAuthorization();
    for (long entryId : entries) {
        Entry entry = entryDAO.get(entryId);
        if (entry == null)
            continue;
        // check permission on individual entries
        if (checkIndividual && !entryAuthorization.canWrite(userId, entry)) {
            continue;
        }
        // add or remove permissions
        if (this.isAdd) {
            addPermissions(entry);
        } else {
            removePermissions(entry);
        }
    }
}

Example 4 with Entry

use of org.jbei.ice.storage.model.Entry in project ice by JBEI.

the class EntryLinks method addLink.

/**
     * Adds a link for the specified entry (or creates a new entry) of the type specified
     *
     * @param partData data for entry to be linked. If the id does not point to an existing entry, a new one will be
     *                 created and linked to this entry
     * @param type     type of link to create. If <code>CHILD</code> (default) is specified, then the entry in the parameter
     *                 is added as a child in the hierarchy; if <code>PARENT</code> is specified, then the entry is
     *                 add as a parent in the hierarchy.
     * @return true, if the two entries are successfully linked. false, if the specified hierarchy is not compatible
     * with the types of the link specified e.g. an plasmid cannot be added as a <code>PARENT</code> of a strain
     * @throws org.jbei.ice.lib.access.PermissionException if the user does not have write permissions
     *                                                     on at least one of the entries being linked
     */
public boolean addLink(PartData partData, LinkType type) {
    long linkId = partData.getId();
    Entry linkedEntry = this.entryDAO.get(linkId);
    if (linkedEntry == null) {
        // todo : create a new entry
        Logger.error("Could not retrieve entry for linking: " + linkId);
        return false;
    }
    if (linkedEntry.getId() == this.entry.getId())
        throw new IllegalArgumentException("Cannot link and entry to itself");
    // should have write permissions on the main entry but only read on the entry being linked
    entryAuthorization.expectRead(userId, linkedEntry);
    entryAuthorization.expectWrite(userId, entry);
    // add as parent
    switch(type) {
        case PARENT:
            return addParentEntry(linkedEntry);
        // add as child. default behavior
        case CHILD:
        default:
            return addChildEntry(linkedEntry);
    }
}

Example 5 with Entry

use of org.jbei.ice.storage.model.Entry in project ice by JBEI.

the class FileResource method getSBOLVisual.

@GET
@Produces("image/png")
@Path("sbolVisual/{rid}")
public Response getSBOLVisual(@PathParam("rid") String recordId) {
    final String tmpDir = Utils.getConfigValue(ConfigurationKey.TEMPORARY_DIRECTORY);
    final Entry entry = DAOFactory.getEntryDAO().getByRecordId(recordId);
    final Sequence sequence = entry.getSequence();
    final String hash = sequence.getFwdHash();
    final File png = Paths.get(tmpDir, hash + ".png").toFile();
    if (png.exists()) {
        return addHeaders(Response.ok(png), entry.getPartNumber() + ".png");
    }
    final URI uri = PigeonSBOLv.generatePigeonVisual(sequence);
    if (uri != null) {
        try (final InputStream in = uri.toURL().openStream();
            final OutputStream out = new FileOutputStream(png)) {
            ByteStreams.copy(in, out);
        } catch (IOException e) {
            Logger.error(e);
            return respond(false);
        }
        return addHeaders(Response.ok(png), entry.getPartNumber() + ".png");
    }
    return respond(false);
}