Python DBSession.flush方法代碼示例

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
def add_read_right(project, circle_id):    
    '''
    Add the ``read`` right to the project & circle specified. Flush the database
    '''
    _add_read_right(project, circle_id)
    DBSession.add(project)
    DBSession.flush()

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
def add_new_sequence(sequence):
    '''
    Method called when a new sequence is created on GDV.
    It should import fast from JBrowse
    '''
    print 'add new sequence'
    file_url = Assembly(sequence).get_sqlite_url()
    print file_url
    out = os.path.join(filemanager.temporary_directory(), 'Genes.sql')
    fileinfo = filemanager.FileInfo(inputtype='url',
        inpath=file_url, trackname='Genes', extension='sql', outpath=out, admin=True)
    print fileinfo
    user = DBSession.query(User).filter(User.key == constants.admin_user_key()).first()
    user_info = {'id': user.id, 'name': user.name, 'email': user.email}
    sequence_info = {'id': sequence.id, 'name': sequence.name}

    # track
    t = Track()
    t.name = fileinfo.trackname
    t.sequence_id = sequence.id
    t.user_id = user.id
    DBSession.add(t)
    DBSession.flush()
    # send task
    async = tasks.new_input.delay(user_info, fileinfo, sequence_info, t.id)
    t.task_id = async.task_id
    DBSession.add(t)

    sequence.default_tracks.append(t)
    DBSession.add(sequence)
    DBSession.flush()

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
 def delete_user(self, user_id, sequence_id):
     user = handler.user.get_user_in_session(request)
     s = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
     u = DBSession.query(User).filter(User.id == user_id).first()
     s.users.remove(u)
     DBSession.flush()
     raise redirect('/sequences/edit/%s' % sequence_id)

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
    def after_sha1(self, fname, sha1, force, callback_url, track_id, old_task_id, mail, key, sequence_id, extension, trackname):
        """
        Called after a sha1 where calculated on a file.
        If the sha1 already exist, only the databases operations are done.
        Else the input will go in the second part of the process.
        The input can be 'forced' to be recomputed
        """
        try:
            _input = DBSession.query(Input).filter(Input.sha1 == sha1).first()
            do_process = True
            if util.str2bool(force) and _input is not None:
                handler.track.delete_input(_input.sha1)
                DBSession.delete(_input)
                DBSession.flush()
            elif _input is not None:
                do_process = False
                handler.track.update(track_id=track_id,
                    params={'new_input_id': _input.id})
                handler.track.finalize_track_creation(track_id=track_id)

            if do_process:

                handler.track.update(track_id=track_id, params={'sha1': sha1})
                sequence = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
                async = tasks.track_process.delay(mail, key, old_task_id, fname, sha1, callback_url, track_id, sequence.name, extension, trackname, callback_url)

                handler.track.update(track_id=track_id,
                    params={'new_task_id': async.task_id})
            return {'success': 'to second process'}
        except Exception as e:
            etype, value, tb = sys.exc_info()
            traceback.print_exception(etype, value, tb)


            return {'error': str(e)}

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
def edit(project, name, user_id, sequence_id=None, tracks=None, isPublic=False, circles=None):
    '''
    Like create but edit an existing project.
    '''
    project.name=name
    if sequence_id is not None:
        project.sequence_id = sequence_id
    project.user_id = user_id
    project.is_public = isPublic
    DBSession.add(project)
    DBSession.flush()

    project.tracks = []
    if tracks is not None:
        for track_id in tracks :
            t = DBSession.query(Track).filter(Track.id == track_id).first()
            project.tracks.append(t)
    
   
    if circles is not None: # adding circle with the read permission by default
        project._circle_right = []
        for circle in circles : _add_read_right(project, circle.id)
    
    DBSession.add(project)
    DBSession.flush()
    return project

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
 def validation(*args, **kw):
     for arg in args_list:
         if arg not in kw:
             raise Exception('Missing args for the validation %s' % kw)
     user = DBSession.query(User).filter(User.email == str(kw['mail'])).first()
     if user.key != str(kw['key']):
         raise Exception('User not valid %s' % kw)
     project = DBSession.query(Project).filter(Project.id == int(kw['pid'])).first()
     if project.key != str(kw['pkey']):
         raise Exception('Project not valid %s' % kw)
     job = Job()
     job.user_id = user.id
     job.project_id = project.id
     job.status = 'PENDING'
     job.ext_task_id = kw['task_id']
     job.bioscript_url = handler.job.task_url(kw['task_id'])
     if 'plugin_info' in kw:
         info = json.loads(kw['plugin_info'])
         job.name = info['title']
         job.description = info['description']
     else:
         job.name = 'Job %s from bioscript' % kw['task_id']
         job.description = 'Description available at %s' % handler.job.task_url(kw['task_id'])
     DBSession.add(job)
     DBSession.flush()
     return {}

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
 def delete_track(self, sequence_id, track_id):
     user = handler.user.get_user_in_session(request)
     s = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
     t = DBSession.query(Track).filter(Track.id == track_id).first()
     s.default_tracks.remove(t)
     DBSession.flush()
     raise redirect('/sequences/edit/%s' % sequence_id)

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
def change_rights(project_id, circle_id, rights=None):
    '''
    Modify the right associated to a project to a group.
    If any right is added, automatically add read right.
    @param project_id : the project id
    @param circle_id : the circle id
    @param rights : the right to update
    '''
    project = DBSession.query(Project).filter(Project.id == project_id).first()
    rc_assocs = get_circle_right_assocs(circle_id, project_id)
    
    
    for rc in rc_assocs:
        if rc.circle.id == int(circle_id) :
            project._circle_right.remove(rc)
            DBSession.delete(rc)
            DBSession.flush()

    if rights is not None:
        _add_read_right(project, circle_id)
        for right_name in rights:
            if right_name != constants.right_read :
                right = DBSession.query(Right).filter(Right.name == right_name).first()
                cr_assoc = _get_circle_right_assoc(right, circle_id, project_id)
                project._circle_right.append(cr_assoc)

    DBSession.add(project)
    DBSession.flush()

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
def add_read_right_to_circles_ids(project, ids):
    '''
     Add the ``read`` right to the project & circles specified. Flush the database
    '''  
    for id in ids:
        _add_read_right(project, id)
    DBSession.add(project)
    DBSession.flush()

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
    def edit(self, *args, **kw):
        user = handler.user.get_user_in_session(request)

        # get circle id
        if request.method == 'GET':
            sequence_id = args[0]
        else :
            sequence_id = kw.get('cid')

        sequence_id=int(sequence_id)
        sequence = DBSession.query(Sequence).filter(Sequence.id == sequence_id).first()
        if not sequence:
            abort(404, 'Sequence with id %s not found' % sequence_id)

        if not sequence.public:
            add_user_widget = form.AddUser(action=url('/sequences/edit/%s' % sequence_id)).req()

            if request.method == 'POST':
                # add an user
                mail = kw.get('mail')
                try:
                    add_user_widget.validate({'cid' : sequence_id, 'mail' : mail})
                except twc.ValidationError as e:
                    users = ', '.join(['%s' % u.email for u in sequence.users])
                    default_tracks = ', '.join(['%s' % t.name for t in sequence.default_tracks])
                    kw['cid'] = sequence_id
                    users = sequence.users
                    for u in users:
                        u.__dict__['sid'] = sequence_id
                    widget = e.widget
                    widget.value = kw
                    return dict(page='sequences', users=users, add_user=add_user, add_user_widget=add_user_widget, default_tracks=default_tracks, au_error=True, seq_id=sequence_id)

                to_add = DBSession.query(User).filter(User.email == mail).first()
                if to_add is None:
                    to_add = handler.user.create_tmp_user(mail)
                sequence.users.append(to_add)
                DBSession.flush()

            kw['cid'] = sequence_id
            add_user_widget.value = kw

        else:
            add_user_widget = None

        users = sequence.users
        for u in users:
            u.__dict__['sid'] = sequence_id

        tracks = sequence.default_tracks
        for t in tracks:
            t.__dict__['sid'] = sequence_id

        add_user = util.to_datagrid(datagrid.sequence_user_grid, users, "Users", len(users)>0)

        def_tracks = util.to_datagrid(datagrid.sequence_default_tracks, tracks, "Default tracks", len(tracks)>0)

        return dict(page='sequences', users=users, add_user=add_user, add_user_widget=add_user_widget, default_tracks=def_tracks, au_error=False, seq_id=sequence_id)

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
def add_tracks(project, track_ids):
    '''
    Add a list of track to the project specified.
    '''
    for track_id in track_ids:
        track_ = DBSession.query(Track).filter(Track.id == track_id).first()
        project.tracks.append(track_)
    DBSession.add(project)
    DBSession.flush()

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
 def delete(self, circle_id, *args, **kw):
     user = handler.user.get_user_in_session(request)
     if not checker.user_own_circle(user.id, circle_id):
         flash('you have no right to delete this circle: you are not the creator of it')
         raise redirect('/circles')
     circle = DBSession.query(Circle).filter(Circle.id == circle_id).first()
     DBSession.delete(circle)
     DBSession.flush()
     raise redirect('/circles/')

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
 def after_process(self, mail, key, old_task_id, track_id, datatype):
     print '[x] after process [x] %s' % track_id
     task = DBSession.query(Task).filter(Task.task_id == old_task_id).first()
     if task is not None:
         DBSession.delete(task)
         DBSession.flush()
     if not track_id == 'None':
         handler.track.update(track_id=track_id, params={'datatype': datatype})
         handler.track.finalize_track_creation(track_id=track_id)
     return {'success': 'end'}

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
 def delete_user(self, id, user_id):
     user = handler.user.get_user_in_session(request)
     if not checker.user_own_circle(user.id, id):
         flash('you have no rights to delete users from this circle: you are not the creator of it')
         raise redirect('/circles')
     circle = DBSession.query(Circle).filter(Circle.id == id).first()
     to_delete = DBSession.query(User).filter(User.id == user_id).first()
     circle.users.remove(to_delete)
     DBSession.flush()
     raise redirect('/circles/edit/%s' % id)

# 需要導入模塊: from pygdv.model import DBSession [as 別名]
# 或者: from pygdv.model.DBSession import flush [as 別名]
def create_tmp_user(mail):
    user = User()
    user.name = constants.tmp_user_name
    user.email = mail
    user.firstname = ''
    user_group = DBSession.query(Group).filter(Group.id == constants.group_users_id).first()
    user_group.users.append(user)
    DBSession.add(user)
    DBSession.flush()
    return user