Examples with GroupController org.jbei.ice.lib.group.GroupController used on opensource projects

Example 16 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class OwnerEntries method retrieveOwnerEntries.

public List<PartData> retrieveOwnerEntries(ColumnField sort, boolean asc, int start, int limit, String filter, List<String> fields) {
    List<Long> entries;
    if (this.isAdmin || this.isSelf) {
        entries = entryDAO.retrieveOwnerEntries(this.ownerAccount.getEmail(), sort, asc, start, limit, filter);
    } else {
        Set<Group> accountGroups = new HashSet<>(account.getGroups());
        GroupController controller = new GroupController();
        Group everybodyGroup = controller.createOrRetrievePublicGroup();
        accountGroups.add(everybodyGroup);
        // retrieve entries for user that can be read by others
        entries = entryDAO.retrieveUserEntries(account, this.ownerAccount.getEmail(), accountGroups, sort, asc, start, limit, filter);
    }
    ArrayList<PartData> data = new ArrayList<>();
    for (Long id : entries) {
        PartData info = ModelToInfoFactory.createTableView(id, fields);
        data.add(info);
    }
    return data;
}

Example 17 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class OwnerEntries method getNumberOfOwnerEntries.

public long getNumberOfOwnerEntries() {
    if (this.isAdmin || this.isSelf) {
        return entryDAO.ownerEntryCount(ownerAccount.getEmail());
    }
    Set<Group> accountGroups = new HashSet<>(account.getGroups());
    GroupController controller = new GroupController();
    Group everybodyGroup = controller.createOrRetrievePublicGroup();
    accountGroups.add(everybodyGroup);
    return entryDAO.ownerEntryCount(account, ownerAccount.getEmail(), accountGroups);
}

Example 18 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class Annotations method filter.

public Results<DNAFeature> filter(int offset, int limit, String filter) {
    Account account = accountDAO.getByEmail(userId);
    List<Group> groups = new GroupController().getAllGroups(account);
    List<SequenceFeature> features = sequenceFeatureDAO.getSequenceFeatures(this.userId, groups, filter, offset, limit);
    int count = sequenceFeatureDAO.getSequenceFeaturesCount(this.userId, groups, filter);
    Results<DNAFeature> results = new Results<>();
    results.setResultCount(count);
    for (SequenceFeature feature : features) {
        DNAFeature dnaFeature = feature.toDataTransferObject();
        Entry entry = feature.getSequence().getEntry();
        dnaFeature.setIdentifier(entry.getPartNumber());
        DNAFeatureLocation location = new DNAFeatureLocation();
        location.setGenbankStart(feature.getUniqueGenbankStart());
        location.setEnd(feature.getUniqueEnd());
        dnaFeature.getLocations().add(location);
        dnaFeature.getEntries().add(entry.getId());
        results.getData().add(dnaFeature);
    }
    return results;
}

Example 19 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class SharedEntries method getNumberOfEntries.

public long getNumberOfEntries(String filter) {
    GroupController groupController = new GroupController();
    Group publicGroup = groupController.createOrRetrievePublicGroup();
    Set<Group> accountGroups = account.getGroups();
    accountGroups.remove(publicGroup);
    return this.entryDAO.sharedEntryCount(account, accountGroups, filter);
}

Example 20 with GroupController

use of org.jbei.ice.lib.group.GroupController in project ice by JBEI.

the class SharedEntries method getEntries.

public List<PartData> getEntries(ColumnField field, boolean asc, int start, int limit, String filter, List<String> fields) {
    GroupController groupController = new GroupController();
    Group publicGroup = groupController.createOrRetrievePublicGroup();
    Set<Group> accountGroups = account.getGroups();
    accountGroups.remove(publicGroup);
    List<Long> entries = this.entryDAO.sharedWithUserEntries(account, accountGroups, field, asc, start, limit, filter);
    ArrayList<PartData> data = new ArrayList<>();
    for (Long id : entries) {
        PartData info = ModelToInfoFactory.createTableView(id, fields);
        data.add(info);
    }
    return data;
}