views.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (C) 2008-2016 University of Dundee & Open Microscopy Environment.
# All rights reserved.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

''' A view functions is simply a Python function that takes a Web request and
returns a Web response. This response can be the HTML contents of a Web page,
or a redirect, or the 404 and 500 error, or an XML document, or an image...
or anything.'''

import copy
import os
import datetime
import Ice
from Ice import Exception as IceException
import logging
import traceback
import json
import re
import sys
import warnings

from time import time

from omero_version import build_year
from omero_version import omero_version

import omero
import omero.scripts
from omero.rtypes import wrap, unwrap

from omero.gateway.utils import toBoolean

from django.conf import settings
from django.template import loader as template_loader
from django.http import Http404, HttpResponse, HttpResponseRedirect, \
    JsonResponse
from django.http import HttpResponseServerError, HttpResponseBadRequest
from django.template import RequestContext as Context
from django.utils.http import urlencode
from django.core.urlresolvers import reverse
from django.utils.encoding import smart_str
from django.core.servers.basehttp import FileWrapper
from django.views.decorators.cache import never_cache
from django.views.decorators.http import require_POST

from webclient_utils import _formatReport, _purgeCallback
from forms import GlobalSearchForm, ContainerForm
from forms import ShareForm, BasketShareForm
from forms import ContainerNameForm, ContainerDescriptionForm
from forms import CommentAnnotationForm, TagsAnnotationForm
from forms import MetadataFilterForm, MetadataDetectorForm
from forms import MetadataChannelForm, MetadataEnvironmentForm
from forms import MetadataObjectiveForm, MetadataObjectiveSettingsForm
from forms import MetadataStageLabelForm, MetadataLightSourceForm
from forms import MetadataDichroicForm, MetadataMicroscopeForm
from forms import FilesAnnotationForm, WellIndexForm, NewTagsAnnotationFormSet

from controller.container import BaseContainer
from controller.history import BaseCalendar
from controller.search import BaseSearch
from controller.share import BaseShare

from omeroweb.webadmin.forms import LoginForm

from omeroweb.webgateway import views as webgateway_views
from omeroweb.webgateway.marshal import chgrpMarshal
from omeroweb.webgateway.util import get_longs as webgateway_get_longs

from omeroweb.feedback.views import handlerInternalError

from omeroweb.webclient.decorators import login_required
from omeroweb.webclient.decorators import render_response
from omeroweb.webclient.show import Show, IncorrectMenuError, \
    paths_to_object, paths_to_tag
from omeroweb.decorators import ConnCleaningHttpResponse, parse_url
from omeroweb.webgateway.util import getIntOrDefault

from omero.model import ProjectI, DatasetI, ImageI, \
    ScreenI, PlateI, \
    ProjectDatasetLinkI, DatasetImageLinkI, \
    ScreenPlateLinkI, AnnotationAnnotationLinkI, TagAnnotationI
from omero import ApiUsageException, ServerError, CmdError
from omero.rtypes import rlong, rlist
from omeroweb.webgateway.views import LoginView

import tree

logger = logging.getLogger(__name__)

logger.info("INIT '%s'" % os.getpid())


def get_long_or_default(request, name, default):
    """
    Retrieves a parameter from the request. If the parameter is not present
    the default is returned

    This does not catch exceptions as it makes sense to throw exceptions if
    the arguments provided do not pass basic type validation
    """
    val = None
    val_raw = request.GET.get(name, default)
    if val_raw is not None:
        val = long(val_raw)
    return val


def get_longs(request, name):
    warnings.warn(
        "Deprecated. Use omeroweb.webgateway.util.get_longs()",
        DeprecationWarning)
    return webgateway_get_longs(request, name)


def get_bool_or_default(request, name, default):
    """
    Retrieves a parameter from the request. If the parameter is not present
    the default is returned

    This does not catch exceptions as it makes sense to throw exceptions if
    the arguments provided do not pass basic type validation
    """
    return toBoolean(request.GET.get(name, default))

##############################################################################
# custom index page


@never_cache
@render_response()
def custom_index(request, conn=None, **kwargs):
    context = {"version": omero_version, 'build_year': build_year}

    if settings.INDEX_TEMPLATE is not None:
        try:
            template_loader.get_template(settings.INDEX_TEMPLATE)
            context['template'] = settings.INDEX_TEMPLATE
        except Exception:
            context['template'] = 'webclient/index.html'
            context["error"] = traceback.format_exception(*sys.exc_info())[-1]
    else:
        context['template'] = 'webclient/index.html'

    return context


##############################################################################
# views


class WebclientLoginView(LoginView):
    """
    Webclient Login - Customises the superclass LoginView
    for webclient. Also can be used by other Apps to log in to OMERO. Uses
    the 'server' id from request to lookup the server-id (index), host and
    port from settings. E.g. "localhost", 4064. Stores these details, along
    with username, password etc in the request.session. Resets other data
    parameters in the request.session. Tries to get connection to OMERO and
    if this works, then we are redirected to the 'index' page or url
    specified in REQUEST. If we can't connect, the login page is returned
    with appropriate error messages.
    """

    template = "webclient/login.html"
    useragent = 'OMERO.web'

    def get(self, request):
        """
        GET simply returns the login page
        """
        return self.handle_not_logged_in(request)

    def handle_logged_in(self, request, conn, connector):
        """
        We override this to provide webclient-specific functionality
        such as cleaning up any previous sessions (if user didn't logout)
        and redirect to specified url or webclient index page.
        """

        # webclient has various state that needs cleaning up...
        # if 'active_group' remains in session from previous
        # login, check it's valid for this user
        if request.session.get('active_group'):
            if (request.session.get('active_group') not in
                    conn.getEventContext().memberOfGroups):
                del request.session['active_group']
        if request.session.get('user_id'):
            # always want to revert to logged-in user
            del request.session['user_id']
        if request.session.get('server_settings'):
            # always clean when logging in
            del request.session['server_settings']
        # do we ned to display server version ?
        # server_version = conn.getServerVersion()
        if request.POST.get('noredirect'):
            return HttpResponse('OK')
        url = request.GET.get("url")
        if url is None or len(url) == 0:
            try:
                url = parse_url(settings.LOGIN_REDIRECT)
            except:
                url = reverse("webindex")
        return HttpResponseRedirect(url)

    def handle_not_logged_in(self, request, error=None, form=None):
        """
        Returns a response for failed login.
        Reason for failure may be due to server 'error' or because
        of form validation errors.

        @param request:     http request
        @param error:       Error message
        @param form:        Instance of Login Form, populated with data
        """
        if form is None:
            server_id = request.GET.get('server', request.POST.get('server'))
            if server_id is not None:
                initial = {'server': unicode(server_id)}
                form = LoginForm(initial=initial)
            else:
                form = LoginForm()
        context = {
            'version': omero_version,
            'build_year': build_year,
            'error': error,
            'form': form}
        url = request.GET.get("url")
        if url is not None and len(url) != 0:
            context['url'] = urlencode({'url': url})

        if hasattr(settings, 'LOGIN_LOGO'):
            context['LOGIN_LOGO'] = settings.LOGIN_LOGO

        t = template_loader.get_template(self.template)
        c = Context(request, context)
        rsp = t.render(c)
        return HttpResponse(rsp)


@login_required(ignore_login_fail=True)
def keepalive_ping(request, conn=None, **kwargs):
    """ Keeps the OMERO session alive by pinging the server """

    # login_required handles ping, timeout etc, so we don't need to do
    # anything else
    return HttpResponse("OK")


@login_required()
def change_active_group(request, conn=None, url=None, **kwargs):
    """
    Simply changes the request.session['active_group'] which is then used by
    the @login_required decorator to configure conn for any group-based
    queries.
    Finally this redirects to the 'url'.
    """
    switch_active_group(request)
    url = url or reverse("webindex")
    return HttpResponseRedirect(url)


def switch_active_group(request, active_group=None):
    """
    Simply changes the request.session['active_group'] which is then used by
    the @login_required decorator to configure conn for any group-based
    queries.
    """
    if active_group is None:
        active_group = request.GET.get('active_group')
    active_group = int(active_group)
    if ('active_group' not in request.session or
            active_group != request.session['active_group']):
        request.session.modified = True
        request.session['active_group'] = active_group


def fake_experimenter(request, default_name='All members'):
    """
    Marshal faked experimenter when id is -1
    Load omero.client.ui.menu.dropdown.everyone.label as username
    """
    label = request.session.get('server_settings').get('ui', {}) \
        .get('menu', {}).get('dropdown', {}).get('everyone', {}) \
        .get('label', default_name)
    return {
        'id': -1,
        'omeName': label,
        'firstName': label,
        'lastName': '',
    }


@login_required(login_redirect='webindex')
def logout(request, conn=None, **kwargs):
    """
    Logout of the session and redirects to the homepage (will redirect to
    login first)
    """

    if request.method == "POST":
        try:
            try:
                conn.close()
            except:
                logger.error('Exception during logout.', exc_info=True)
        finally:
            request.session.flush()
        return HttpResponseRedirect(reverse("webindex"))
    else:
        context = {
            'url': reverse('weblogout'),
            'submit': "Do you want to log out?"}
        t = template_loader.get_template(
            'webgateway/base/includes/post_form.html')
        c = Context(request, context)
        return HttpResponse(t.render(c))


###########################################################################
def _load_template(request, menu, conn=None, url=None, **kwargs):

    """
    This view handles most of the top-level pages, as specified by 'menu' E.g.
    userdata, usertags, history, search etc.
    Query string 'path' that specifies an object to display in the data tree
    is parsed.
    We also prepare the list of users in the current group, for the
    switch-user form. Change-group form is also prepared.
    """
    request.session.modified = True

    template = kwargs.get('template', None)
    if template is None:
        if menu == 'userdata':
            template = "webclient/data/containers.html"
        elif menu == 'usertags':
            template = "webclient/data/containers.html"
        else:
            # E.g. search/search.html
            template = "webclient/%s/%s.html" % (menu, menu)

    # tree support
    show = kwargs.get('show', Show(conn, request, menu))
    # Constructor does no loading.  Show.first_selected must be called first
    # in order to set up our initial state correctly.
    try:
        first_sel = show.first_selected
    except IncorrectMenuError, e:
        return HttpResponseRedirect(e.uri)
    # We get the owner of the top level object, E.g. Project
    # Actual api_paths_to_object() is retrieved by jsTree once loaded
    initially_open_owner = show.initially_open_owner

    # need to be sure that tree will be correct omero.group
    if first_sel is not None:
        switch_active_group(request, first_sel.details.group.id.val)

    # search support
    init = {}
    global_search_form = GlobalSearchForm(data=request.POST.copy())
    if menu == "search":
        if global_search_form.is_valid():
            init['query'] = global_search_form.cleaned_data['search_query']

    # get url without request string - used to refresh page after switch
    # user/group etc
    url = kwargs.get('load_template_url', None)
    if url is None:
        url = reverse(viewname="load_template", args=[menu])

    # validate experimenter is in the active group
    active_group = (request.session.get('active_group') or
                    conn.getEventContext().groupId)
    # prepare members of group...
    leaders, members = conn.getObject(
        "ExperimenterGroup", active_group).groupSummary()
    userIds = [u.id for u in leaders]
    userIds.extend([u.id for u in members])

    # check any change in experimenter...
    user_id = request.GET.get('experimenter')
    if initially_open_owner is not None:
        if (request.session.get('user_id', None) != -1):
            # if we're not already showing 'All Members'...
            user_id = initially_open_owner
    try:
        user_id = long(user_id)
    except:
        user_id = None
    # check if user_id is in a currnt group
    if user_id is not None:
        if (user_id not in
            (set(map(lambda x: x.id, leaders))
             | set(map(lambda x: x.id, members))) and user_id != -1):
            # All users in group is allowed
            user_id = None
    if user_id is None:
        # ... or check that current user is valid in active group
        user_id = request.session.get('user_id', None)
        if user_id is None or int(user_id) not in userIds:
            if user_id != -1:           # All users in group is allowed
                user_id = conn.getEventContext().userId

    request.session['user_id'] = user_id

    myGroups = list(conn.getGroupsMemberOf())
    myGroups.sort(key=lambda x: x.getName().lower())
    groups = myGroups

    new_container_form = ContainerForm()

    # colleagues required for search.html page only.
    myColleagues = {}
    if menu == "search":
        for g in groups:
            g.loadLeadersAndMembers()
            for c in g.leaders + g.colleagues:
                myColleagues[c.id] = c
        myColleagues = myColleagues.values()
        myColleagues.sort(key=lambda x: x.getLastName().lower())

    context = {
        'menu': menu,
        'init': init,
        'myGroups': myGroups,
        'new_container_form': new_container_form,
        'global_search_form': global_search_form}
    context['groups'] = groups
    context['myColleagues'] = myColleagues
    context['active_group'] = conn.getObject(
        "ExperimenterGroup", long(active_group))
    context['active_user'] = conn.getObject("Experimenter", long(user_id))
    context['initially_select'] = show.initially_select
    context['initially_open'] = show.initially_open
    context['isLeader'] = conn.isLeader()
    context['current_url'] = url
    context['page_size'] = settings.PAGE
    context['template'] = template
    context['thumbnails_batch'] = settings.THUMBNAILS_BATCH

    return context


@login_required()
@render_response()
def load_template(request, menu, conn=None, url=None, **kwargs):
    return _load_template(request=request, menu=menu, conn=conn,
                          url=url, **kwargs)


@login_required()
@render_response()
def group_user_content(request, url=None, conn=None, **kwargs):
    """
    Loads html content of the Groups/Users drop-down menu on main webclient
    pages.
    Url should be supplied in request, as target for redirect after switching
    group.
    """

    myGroups = list(conn.getGroupsMemberOf())
    myGroups.sort(key=lambda x: x.getName().lower())
    if conn.isAdmin():  # Admin can see all groups
        system_groups = [
            conn.getAdminService().getSecurityRoles().userGroupId,
            conn.getAdminService().getSecurityRoles().guestGroupId]
        groups = [g for g in conn.getObjects("ExperimenterGroup")
                  if g.getId() not in system_groups]
        groups.sort(key=lambda x: x.getName().lower())
    else:
        groups = myGroups

    for g in groups:
        g.loadLeadersAndMembers()  # load leaders / members

    context = {
        'template': 'webclient/base/includes/group_user_content.html',
        'current_url': url,
        'groups': groups,
        'myGroups': myGroups}
    return context


@login_required()
def api_group_list(request, conn=None, **kwargs):
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        member_id = get_long_or_default(request, 'member', -1)
    except ValueError as e:
        return HttpResponseBadRequest('Invalid parameter value')

    try:
        # Get the groups
        groups = tree.marshal_groups(conn=conn,
                                     member_id=member_id,
                                     page=page,
                                     limit=limit)
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse({'groups': groups})


@login_required()
def api_experimenter_list(request, conn=None, **kwargs):
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        group_id = get_long_or_default(request, 'group', -1)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    try:
        # Get the experimenters
        experimenters = tree.marshal_experimenters(conn=conn,
                                                   group_id=group_id,
                                                   page=page,
                                                   limit=limit)
        return JsonResponse({'experimenters': experimenters})
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)


@login_required()
def api_experimenter_detail(request, experimenter_id, conn=None, **kwargs):
    # Validate parameter
    try:
        experimenter_id = long(experimenter_id)
    except ValueError:
        return HttpResponseBadRequest('Invalid experimenter id')

    try:
        # Get the experimenter
        if experimenter_id < 0:
            experimenter = fake_experimenter(request)
        else:
            # Get the experimenter
            experimenter = tree.marshal_experimenter(
                conn=conn, experimenter_id=experimenter_id)
        return JsonResponse({'experimenter': experimenter})

    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)


@login_required()
def api_container_list(request, conn=None, **kwargs):
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        group_id = get_long_or_default(request, 'group', -1)
        experimenter_id = get_long_or_default(request, 'id', -1)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    # While this interface does support paging, it does so in a
    # very odd way. The results per page is enforced per query so this
    # will actually get the limit for projects, datasets (without
    # parents), screens and plates (without parents). This is fine for
    # the first page, but the second page may not be what is expected.

    r = dict()
    try:
        # Get the projects
        r['projects'] = tree.marshal_projects(
            conn=conn,
            group_id=group_id,
            experimenter_id=experimenter_id,
            page=page,
            limit=limit)

        # Get the orphaned datasets (without project parents)
        r['datasets'] = tree.marshal_datasets(
            conn=conn,
            orphaned=True,
            group_id=group_id,
            experimenter_id=experimenter_id,
            page=page,
            limit=limit)

        # Get the screens for the current user
        r['screens'] = tree.marshal_screens(
            conn=conn,
            group_id=group_id,
            experimenter_id=experimenter_id,
            page=page,
            limit=limit)

        # Get the orphaned plates (without project parents)
        r['plates'] = tree.marshal_plates(
            conn=conn,
            orphaned=True,
            group_id=group_id,
            experimenter_id=experimenter_id,
            page=page,
            limit=limit)
        # Get the orphaned images container
        try:
            orph_t = request \
                .session['server_settings']['ui']['tree']['orphans']
        except:
            orph_t = {'enabled': True}
        if (conn.isAdmin() or
                conn.isLeader(gid=request.session.get('active_group')) or
                experimenter_id == conn.getUserId() or
                orph_t.get('enabled', True)):

            orphaned = tree.marshal_orphaned(
                conn=conn,
                group_id=group_id,
                experimenter_id=experimenter_id,
                page=page,
                limit=limit)
            orphaned['name'] = orph_t.get('name', "Orphaned Images")
            r['orphaned'] = orphaned
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse(r)


@login_required()
def api_dataset_list(request, conn=None, **kwargs):
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        group_id = get_long_or_default(request, 'group', -1)
        project_id = get_long_or_default(request, 'id', None)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    try:
        # Get the datasets
        datasets = tree.marshal_datasets(conn=conn,
                                         project_id=project_id,
                                         group_id=group_id,
                                         page=page,
                                         limit=limit)
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse({'datasets': datasets})


@login_required()
def api_image_list(request, conn=None, **kwargs):
    ''' Get a list of images
        Specifiying dataset_id will return only images in that dataset
        Specifying experimenter_id will return orpahned images for that
        user
        The orphaned images will include images which belong to the user
        but are not in any dataset belonging to the user
        Currently specifying both, experimenter_id will be ignored

    '''
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        group_id = get_long_or_default(request, 'group', -1)
        dataset_id = get_long_or_default(request, 'id', None)
        orphaned = get_bool_or_default(request, 'orphaned', False)
        load_pixels = get_bool_or_default(request, 'sizeXYZ', False)
        thumb_version = get_bool_or_default(request, 'thumbVersion', False)
        date = get_bool_or_default(request, 'date', False)
        experimenter_id = get_long_or_default(request,
                                              'experimenter_id', -1)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    # Share ID is in kwargs from api/share_images/<id>/ which will create
    # a share connection in @login_required.
    # We don't support ?share_id in query string since this would allow a
    # share connection to be created for ALL urls, instead of just this one.
    share_id = 'share_id' in kwargs and long(kwargs['share_id']) or None

    try:
        # Get the images
        images = tree.marshal_images(conn=conn,
                                     orphaned=orphaned,
                                     experimenter_id=experimenter_id,
                                     dataset_id=dataset_id,
                                     share_id=share_id,
                                     load_pixels=load_pixels,
                                     group_id=group_id,
                                     page=page,
                                     date=date,
                                     thumb_version=thumb_version,
                                     limit=limit)
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse({'images': images})


@login_required()
def api_plate_list(request, conn=None, **kwargs):
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        group_id = get_long_or_default(request, 'group', -1)
        screen_id = get_long_or_default(request, 'id', None)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    try:
        # Get the plates
        plates = tree.marshal_plates(conn=conn,
                                     screen_id=screen_id,
                                     group_id=group_id,
                                     page=page,
                                     limit=limit)
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse({'plates': plates})


@login_required()
def api_plate_acquisition_list(request, conn=None, **kwargs):
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        plate_id = get_long_or_default(request, 'id', None)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    # Orphaned PlateAcquisitions are not possible so querying without a
    # plate is an error
    if plate_id is None:
        return HttpResponseBadRequest('id (plate) must be specified')

    try:
        # Get the plate acquisitions
        plate_acquisitions = tree.marshal_plate_acquisitions(
            conn=conn, plate_id=plate_id, page=page, limit=limit)
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse({'acquisitions': plate_acquisitions})


def get_object_links(conn, parent_type, parent_id, child_type, child_ids):
    """ This is just used internally by api_link DELETE below """
    if parent_type == 'orphaned':
        return None
    link_type = None
    if parent_type == 'experimenter':
        if child_type in ['dataset', 'plate', 'tag']:
            # This will be a requested link if a dataset or plate is
            # moved from the de facto orphaned datasets/plates, it isn't
            # an error, but no link actually needs removing
            return None
    elif parent_type == 'project':
        if child_type == 'dataset':
            link_type = 'ProjectDatasetLink'
    elif parent_type == 'dataset':
        if child_type == 'image':
            link_type = 'DatasetImageLink'
    elif parent_type == 'screen':
        if child_type == 'plate':
            link_type = 'ScreenPlateLink'
    elif parent_type == 'tagset':
        if child_type == 'tag':
            link_type = 'AnnotationAnnotationLink'
    if not link_type:
        raise Http404("json data needs 'parent_type' and 'child_type'")

    params = omero.sys.ParametersI()
    params.addIds(child_ids)

    qs = conn.getQueryService()
    # Need to fetch child and parent, otherwise
    # AnnotationAnnotationLink is not loaded
    q = """
        from %s olink join fetch olink.child join fetch olink.parent
        where olink.child.id in (:ids)
        """ % link_type
    if parent_id:
        params.add('pid', rlong(parent_id))
        q += " and olink.parent.id = :pid"

    res = qs.findAllByQuery(q, params, conn.SERVICE_OPTS)

    if parent_id is not None and len(res) == 0:
        raise Http404("No link found for %s-%s to %s-%s"
                      % (parent_type, parent_id, child_type, child_ids))
    return link_type, res


def create_link(parent_type, parent_id, child_type, child_id):
    """ This is just used internally by api_link DELETE below """
    if parent_type == 'experimenter':
        if child_type == 'dataset' or child_type == 'plate':
            # This is actually not a link that needs creating, this
            # dataset/plate is an orphan
            return 'orphan'
    if parent_type == 'project':
        project = ProjectI(long(parent_id), False)
        if child_type == 'dataset':
            dataset = DatasetI(long(child_id), False)
            l = ProjectDatasetLinkI()
            l.setParent(project)
            l.setChild(dataset)
            return l
    elif parent_type == 'dataset':
        dataset = DatasetI(long(parent_id), False)
        if child_type == 'image':
            image = ImageI(long(child_id), False)
            l = DatasetImageLinkI()
            l.setParent(dataset)
            l.setChild(image)
            return l
    elif parent_type == 'screen':
        screen = ScreenI(long(parent_id), False)
        if child_type == 'plate':
            plate = PlateI(long(child_id), False)
            l = ScreenPlateLinkI()
            l.setParent(screen)
            l.setChild(plate)
            return l
    elif parent_type == 'tagset':
        if child_type == 'tag':
            l = AnnotationAnnotationLinkI()
            l.setParent(TagAnnotationI(long(parent_id), False))
            l.setChild(TagAnnotationI(long(child_id), False))
            return l
    return None


@login_required()
def api_links(request, conn=None, **kwargs):
    """
    Entry point for the api_links methods.
    We delegate depending on request method to
    create or delete links between objects.
    """
    # Handle link creation/deletion
    json_data = json.loads(request.body)

    if request.method == 'POST':
        return _api_links_POST(conn, json_data)
    elif request.method == 'DELETE':
        return _api_links_DELETE(conn, json_data)


def _api_links_POST(conn, json_data, **kwargs):
    """ Creates links between objects specified by a json
    blob in the request body.
    e.g. {"dataset":{"10":{"image":[1,2,3]}}}
    When creating a link, fails silently if ValidationException
    (E.g. adding an image to a Dataset that already has that image).
    """

    response = {'success': False}

    # json is [parent_type][parent_id][child_type][childIds]
    # e.g. {"dataset":{"10":{"image":[1,2,3]}}}

    linksToSave = []
    for parent_type, parents in json_data.items():
        if parent_type == "orphaned":
            continue
        for parent_id, children in parents.items():
            for child_type, child_ids in children.items():
                for child_id in child_ids:
                    parent_id = int(parent_id)
                    link = create_link(parent_type, parent_id,
                                       child_type, child_id)
                    if link and link != 'orphan':
                        linksToSave.append(link)

    if len(linksToSave) > 0:
        # Need to set context to correct group (E.g parent group)
        ptype = parent_type.title()
        if ptype in ["Tagset", "Tag"]:
            ptype = "TagAnnotation"
        p = conn.getQueryService().get(ptype, parent_id,
                                       conn.SERVICE_OPTS)
        conn.SERVICE_OPTS.setOmeroGroup(p.details.group.id.val)
        logger.info("api_link: Saving %s links" % len(linksToSave))

        try:
            # We try to save all at once, for speed.
            conn.saveArray(linksToSave)
            response['success'] = True
        except:
            logger.info("api_link: Exception on saveArray with %s links"
                        % len(linksToSave))
            # If this fails, e.g. ValidationException because link
            # already exists, try to save individual links
            for l in linksToSave:
                try:
                    conn.saveObject(l)
                except:
                    pass
            response['success'] = True

    return JsonResponse(response)


def _api_links_DELETE(conn, json_data):
    """ Deletes links between objects specified by a json
    blob in the request body.
    e.g. {"dataset":{"10":{"image":[1,2,3]}}}
    """

    response = {'success': False}

    # json is [parent_type][parent_id][child_type][childIds]
    # e.g. {"dataset":{"10":{"image":[1,2,3]}}}
    for parent_type, parents in json_data.items():
        if parent_type == "orphaned":
            continue
        for parent_id, children in parents.items():
            for child_type, child_ids in children.items():
                objLnks = get_object_links(conn, parent_type,
                                           parent_id,
                                           child_type,
                                           child_ids)
                if objLnks is None:
                    continue
                linkType, links = objLnks
                linkIds = [r.id.val for r in links]
                logger.info("api_link: Deleting %s links" % len(linkIds))
                conn.deleteObjects(linkType, linkIds, wait=True)
                # webclient needs to know what is orphaned
                linkType, remainingLinks = get_object_links(conn,
                                                            parent_type,
                                                            None,
                                                            child_type,
                                                            child_ids)
                # return remaining links in same format as json above
                # e.g. {"dataset":{"10":{"image":[1,2,3]}}}
                for rl in remainingLinks:
                    pid = rl.parent.id.val
                    cid = rl.child.id.val
                    # Deleting links still in progress above - ignore these
                    if pid == int(parent_id):
                        continue
                    if parent_type not in response:
                        response[parent_type] = {}
                    if pid not in response[parent_type]:
                        response[parent_type][pid] = {child_type: []}
                    response[parent_type][pid][child_type].append(cid)

    # If we got here, DELETE was OK
    response['success'] = True

    return JsonResponse(response)


@login_required()
def api_paths_to_object(request, conn=None, **kwargs):
    """
    This finds the paths to objects in the hierarchy. It returns only
    the path, not the object hierarchy itself.

    An example usage is for the 'show' functionality
    Example to go to the image with id 1 somewhere in the tree.
    http://localhost:8000/webclient/?show=image-1

    This method can tell the webclient exactly what needs to be
    dynamically loaded to display this in the jstree.
    """

    try:
        experimenter_id = get_long_or_default(request, 'experimenter', None)
        project_id = get_long_or_default(request, 'project', None)
        dataset_id = get_long_or_default(request, 'dataset', None)
        image_id = get_long_or_default(request, 'image', None)
        screen_id = get_long_or_default(request, 'screen', None)
        plate_id = get_long_or_default(request, 'plate', None)
        acquisition_id = get_long_or_default(request, 'run', None)
        # acquisition will override 'run' if both are specified as they are
        # the same thing
        acquisition_id = get_long_or_default(request, 'acquisition',
                                             acquisition_id)
        well_id = request.GET.get('well', None)
        tag_id = get_long_or_default(request, 'tag', None)
        tagset_id = get_long_or_default(request, 'tagset', None)
        group_id = get_long_or_default(request, 'group', None)
        page_size = get_long_or_default(request, 'page_size', settings.PAGE)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    if tag_id is not None or tagset_id is not None:
        paths = paths_to_tag(conn, experimenter_id, tagset_id, tag_id)

    else:
        paths = paths_to_object(conn, experimenter_id, project_id,
                                dataset_id, image_id, screen_id, plate_id,
                                acquisition_id, well_id, group_id,
                                page_size=page_size)
    return JsonResponse({'paths': paths})


@login_required()
def api_tags_and_tagged_list(request, conn=None, **kwargs):
    if request.method == 'GET':
        return api_tags_and_tagged_list_GET(request, conn, **kwargs)
    elif request.method == 'DELETE':
        return api_tags_and_tagged_list_DELETE(request, conn, **kwargs)


def api_tags_and_tagged_list_GET(request, conn=None, **kwargs):
    ''' Get a list of tags
        Specifiying tag_id will return any sub-tags, sub-tagsets and
        objects tagged with that id
        If no tagset_id is specifed it will return tags which have no
        parent
    '''
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        group_id = get_long_or_default(request, 'group', -1)
        tag_id = get_long_or_default(request, 'id', None)
        experimenter_id = get_long_or_default(request, 'experimenter_id', -1)
        orphaned = get_bool_or_default(request, 'orphaned', False)
        load_pixels = get_bool_or_default(request, 'sizeXYZ', False)
        date = get_bool_or_default(request, 'date', False)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    try:
        # Get ALL data (all owners) under specified tags
        if tag_id is not None:
            tagged = tree.marshal_tagged(conn=conn,
                                         experimenter_id=experimenter_id,
                                         tag_id=tag_id,
                                         group_id=group_id,
                                         page=page,
                                         load_pixels=load_pixels,
                                         date=date,
                                         limit=limit)
        else:
            tagged = {}

        # Get 'tags' under tag_id
        tagged['tags'] = tree.marshal_tags(conn=conn,
                                           orphaned=orphaned,
                                           experimenter_id=experimenter_id,
                                           tag_id=tag_id,
                                           group_id=group_id,
                                           page=page,
                                           limit=limit)
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse(tagged)


def api_tags_and_tagged_list_DELETE(request, conn=None, **kwargs):
    ''' Delete the listed tags by ids

    '''
    # Get parameters
    try:
        tag_ids = get_longs(request, 'id')
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    dcs = list()

    handle = None
    try:
        for tag_id in tag_ids:
            dcs.append(omero.cmd.Delete('/Annotation', tag_id))
        doall = omero.cmd.DoAll()
        doall.requests = dcs
        handle = conn.c.sf.submit(doall, conn.SERVICE_OPTS)

        try:
            conn._waitOnCmd(handle)
        finally:
            handle.close()

    except CmdError as e:
        return HttpResponseBadRequest(e.message)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse('')


@login_required()
def api_annotations(request, conn=None, **kwargs):

    r = request.GET
    image_ids = r.getlist('image')
    dataset_ids = r.getlist('dataset')
    project_ids = r.getlist('project')
    screen_ids = r.getlist('screen')
    plate_ids = r.getlist('plate')
    run_ids = r.getlist('acquisition')
    well_ids = r.getlist('well')
    page = get_long_or_default(request, 'page', 1)
    limit = get_long_or_default(request, 'limit', settings.PAGE)

    ann_type = r.get('type', None)

    anns, exps = tree.marshal_annotations(conn, project_ids=project_ids,
                                          dataset_ids=dataset_ids,
                                          image_ids=image_ids,
                                          screen_ids=screen_ids,
                                          plate_ids=plate_ids,
                                          run_ids=run_ids,
                                          well_ids=well_ids,
                                          ann_type=ann_type,
                                          page=page,
                                          limit=limit)

    return JsonResponse({'annotations': anns, 'experimenters': exps})


@login_required()
def api_share_list(request, conn=None, **kwargs):
    # Get parameters
    try:
        page = get_long_or_default(request, 'page', 1)
        limit = get_long_or_default(request, 'limit', settings.PAGE)
        member_id = get_long_or_default(request, 'member_id', -1)
        owner_id = get_long_or_default(request, 'owner_id', -1)
    except ValueError:
        return HttpResponseBadRequest('Invalid parameter value')

    # Like with api_container_list, this is a combination of
    # results which will each be able to return up to the limit in page
    # size

    try:
        # Get the shares
        shares = tree.marshal_shares(conn=conn,
                                     member_id=member_id,
                                     owner_id=owner_id,
                                     page=page,
                                     limit=limit)
        # Get the discussions
        discussions = tree.marshal_discussions(conn=conn,
                                               member_id=member_id,
                                               owner_id=owner_id,
                                               page=page,
                                               limit=limit)
    except ApiUsageException as e:
        return HttpResponseBadRequest(e.serverStackTrace)
    except ServerError as e:
        return HttpResponseServerError(e.serverStackTrace)
    except IceException as e:
        return HttpResponseServerError(e.message)

    return JsonResponse({'shares': shares, 'discussions': discussions})


@login_required()
@render_response()
def load_plate(request, o1_type=None, o1_id=None, conn=None, **kwargs):
    """
    This loads data for the center panel, via AJAX calls.
    Used for Datasets, Plates & Orphaned Images.
    """

    # get index of the plate
    index = getIntOrDefault(request, 'index', 0)

    # prepare data. E.g. kw = {}  or  {'plate': 301L}  or
    # 'acquisition': 301L}
    kw = dict()
    if o1_type is not None:
        if o1_id is not None and o1_id > 0:
            kw[str(o1_type)] = long(o1_id)

    try:
        manager = BaseContainer(conn, **kw)
    except AttributeError, x:
        return handlerInternalError(request, x)

    # prepare forms
    form_well_index = None

    context = {
        'manager': manager,
        'form_well_index': form_well_index,
        'index': index}

    # load data & template
    template = None
    if 'plate' in kw or 'acquisition' in kw:
        fields = manager.getNumberOfFields()
        if fields is not None:
            form_well_index = WellIndexForm(
                initial={'index': index, 'range': fields})
            if index == 0:
                index = fields[0]

        # Show parameter will be well-1|well-2
        show = request.REQUEST.get('show')
        if show is not None:
            wells_to_select = []
            for w in show.split("|"):
                if 'well-' in w:
                    wells_to_select.append(w.replace('well-', ''))
            context['select_wells'] = ','.join(wells_to_select)

        context['baseurl'] = reverse('webgateway').rstrip('/')
        context['form_well_index'] = form_well_index
        context['index'] = index
        context['thumbnails_batch'] = settings.THUMBNAILS_BATCH
        template = "webclient/data/plate.html"
        if o1_type == 'acquisition':
            context['acquisition'] = o1_id

    context['isLeader'] = conn.isLeader()
    context['template'] = template
    return context


@login_required()
@render_response()
def load_chgrp_groups(request, conn=None, **kwargs):
    """
    Get the potential groups we can move selected data to.
    These will be groups that the owner(s) of selected objects is a member of.
    Objects are specified by query string like: ?Image=1,2&Dataset=3
    If no selected objects are specified, simply list the groups that the
    current user is a member of.
    Groups list will exclude the 'current' group context.
    """

    ownerIds = []
    currentGroups = set()
    groupSets = []
    groups = {}
    owners = {}
    for dtype in ("Project", "Dataset", "Image", "Screen", "Plate"):
        oids = request.GET.get(dtype, None)
        if oids is not None:
            for o in conn.getObjects(dtype, oids.split(",")):
                ownerIds.append(o.getDetails().owner.id.val)
                currentGroups.add(o.getDetails().group.id.val)
    ownerIds = list(set(ownerIds))
    # In case we were passed no objects or they weren't found
    if len(ownerIds) == 0:
        ownerIds = [conn.getUserId()]
    for owner in conn.getObjects("Experimenter", ownerIds):
        # Each owner has a set of groups
        gids = []
        owners[owner.id] = owner.getFullName()
        for group in owner.copyGroupExperimenterMap():
            groups[group.parent.id.val] = group.parent
            gids.append(group.parent.id.val)
        groupSets.append(set(gids))

    # Can move to groups that all owners are members of...
    targetGroupIds = set.intersection(*groupSets)
    # ...but not 'user' group
    userGroupId = conn.getAdminService().getSecurityRoles().userGroupId
    targetGroupIds.remove(userGroupId)

    # if all the Objects are in a single group, exclude it from the target
    # groups
    if len(currentGroups) == 1:
        targetGroupIds.remove(currentGroups.pop())

    def getPerms(group):
        p = group.getDetails().permissions
        return {
            'write': p.isGroupWrite(),
            'annotate': p.isGroupAnnotate(),
            'read': p.isGroupRead()}

    # From groupIds, create a list of group dicts for json
    targetGroups = []
    for gid in targetGroupIds:
        targetGroups.append({
            'id': gid,
            'name': groups[gid].name.val,
            'perms': getPerms(groups[gid])
        })
    targetGroups.sort(key=lambda x: x['name'])

    owners = [[k, v] for k, v in owners.items()]

    return {'owners': owners, 'groups': targetGroups}


@login_required()
@render_response()
def load_chgrp_target(request, group_id, target_type, conn=None, **kwargs):
    """ Loads a tree for user to pick target Project, Dataset or Screen """

    # filter by group (not switching group)
    conn.SERVICE_OPTS.setOmeroGroup(int(group_id))
    owner = getIntOrDefault(request, 'owner', None)

    manager = BaseContainer(conn)
    manager.listContainerHierarchy(owner)
    template = 'webclient/data/chgrp_target_tree.html'

    context = {
        'manager': manager,
        'target_type': target_type,
        'template': template}
    return context


@login_required()
@render_response()
def load_searching(request, form=None, conn=None, **kwargs):
    """
    Handles AJAX calls to search
    """
    manager = BaseSearch(conn)

    foundById = []
    # form = 'form' if we are searching. Get query from request...
    r = request.GET or request.POST
    if form is not None:
        query_search = r.get('query').replace("+", " ")
        template = "webclient/search/search_details.html"

        onlyTypes = r.getlist("datatype")
        fields = r.getlist("field")
        searchGroup = r.get('searchGroup', None)
        ownedBy = r.get('ownedBy', None)

        useAcquisitionDate = toBoolean(r.get('useAcquisitionDate'))
        startdate = r.get('startdateinput', None)
        startdate = startdate is not None and smart_str(startdate) or None
        enddate = r.get('enddateinput', None)
        enddate = enddate is not None and smart_str(enddate) or None
        date = None
        if startdate is not None:
            if enddate is None:
                n = datetime.datetime.now()
                enddate = "%s-%02d-%02d" % (n.year, n.month, n.day)
            date = "%s_%s" % (startdate, enddate)

        # by default, if user has not specified any types:
        if len(onlyTypes) == 0:
            onlyTypes = ['images']

        # search is carried out and results are stored in
        # manager.containers.images etc.
        manager.search(query_search, onlyTypes, fields, searchGroup, ownedBy,
                       useAcquisitionDate, date)

        # if the query is only numbers (separated by commas or spaces)
        # we search for objects by ID
        isIds = re.compile('^[\d ,]+$')
        if isIds.search(query_search) is not None:
            conn.SERVICE_OPTS.setOmeroGroup(-1)
            idSet = set()
            for queryId in re.split(' |,', query_search):
                if len(queryId) == 0:
                    continue
                try:
                    searchById = long(queryId)
                    if searchById in idSet:
                        continue
                    idSet.add(searchById)
                    for t in onlyTypes:
                        t = t[0:-1]  # remove 's'
                        if t in ('project', 'dataset', 'image', 'screen',
                                 'plate', 'well'):
                            obj = conn.getObject(t, searchById)
                            if obj is not None:
                                foundById.append({'otype': t, 'obj': obj})
                except ValueError:
                    pass

    else:
        # simply display the search home page.
        template = "webclient/search/search.html"

    context = {
        'manager': manager,
        'foundById': foundById,
        'resultCount': manager.c_size + len(foundById)}
    context['template'] = template
    context['thumbnails_batch'] = settings.THUMBNAILS_BATCH
    return context


@login_required()
@render_response()
def load_metadata_details(request, c_type, c_id, conn=None, share_id=None,
                          **kwargs):
    """
    This page is the right-hand panel 'general metadata', first tab only.
    Shown for Projects, Datasets, Images, Screens, Plates, Wells, Tags etc.
    The data and annotations are loaded by the manager. Display of appropriate
    data is handled by the template.
    """

    # the index of a field within a well
    index = getIntOrDefault(request, 'index', 0)

    context = dict()

    # we only expect a single object, but forms can take multiple objects
    images = (c_type == "image" and
              list(conn.getObjects("Image", [c_id])) or
              list())
    datasets = (c_type == "dataset" and
                list(conn.getObjects("Dataset", [c_id])) or list())
    projects = (c_type == "project" and
                list(conn.getObjects("Project", [c_id])) or list())
    screens = (c_type == "screen" and
               list(conn.getObjects("Screen", [c_id])) or
               list())
    plates = (c_type == "plate" and
              list(conn.getObjects("Plate", [c_id])) or list())
    acquisitions = (c_type == "acquisition" and
                    list(conn.getObjects("PlateAcquisition", [c_id])) or
                    list())
    shares = ((c_type == "share" or c_type == "discussion") and
              [conn.getShare(c_id)] or list())
    wells = (c_type == "well" and
             list(conn.getObjects("Well", [c_id])) or list())

    # we simply set up the annotation form, passing the objects to be
    # annotated.
    selected = {
        'images': c_type == "image" and [c_id] or [],
        'datasets': c_type == "dataset" and [c_id] or [],
        'projects': c_type == "project" and [c_id] or [],
        'screens': c_type == "screen" and [c_id] or [],
        'plates': c_type == "plate" and [c_id] or [],
        'acquisitions': c_type == "acquisition" and [c_id] or [],
        'wells': c_type == "well" and [c_id] or [],
        'shares': ((c_type == "share" or c_type == "discussion") and [c_id] or
                   [])}

    initial = {
        'selected': selected, 'images': images,  'datasets': datasets,
        'projects': projects, 'screens': screens, 'plates': plates,
        'acquisitions': acquisitions, 'wells': wells, 'shares': shares}

    form_comment = None
    figScripts = None
    if c_type in ("share", "discussion"):
        template = "webclient/annotations/annotations_share.html"
        manager = BaseShare(conn, c_id)
        manager.getAllUsers(c_id)
        manager.getComments(c_id)
        form_comment = CommentAnnotationForm(initial=initial)
    else:
        try:
            manager = BaseContainer(
                conn, **{str(c_type): long(c_id), 'index': index})
        except AttributeError, x:
            return handlerInternalError(request, x)
        if share_id is not None:
            template = "webclient/annotations/annotations_share.html"
            context['share'] = BaseShare(conn, share_id)
        else:
            template = "webclient/annotations/metadata_general.html"
            context['canExportAsJpg'] = manager.canExportAsJpg(request)
            context['annotationCounts'] = manager.getAnnotationCounts()
            figScripts = manager.listFigureScripts()
    context['manager'] = manager

    if c_type in ("tag", "tagset"):
        context['insight_ns'] = omero.rtypes.rstring(
            omero.constants.metadata.NSINSIGHTTAGSET).val
    if form_comment is not None:
        context['form_comment'] = form_comment

    context['figScripts'] = figScripts
    context['template'] = template
    context['webclient_path'] = reverse('webindex')
    return context


@login_required()
@render_response()
def load_metadata_preview(request, c_type, c_id, conn=None, share_id=None,
                          **kwargs):
    """
    This is the image 'Preview' tab for the right-hand panel.
    """
    context = {}

    # the index of a field within a well
    index = getIntOrDefault(request, 'index', 0)

    manager = BaseContainer(conn, **{str(c_type): long(c_id)})
    if share_id:
        context['share'] = BaseShare(conn, share_id)
    if c_type == "well":
        manager.image = manager.well.getImage(index)

    allRdefs = manager.image.getAllRenderingDefs()
    rdefs = {}
    rdefId = manager.image.getRenderingDefId()
    # remove duplicates per user
    for r in allRdefs:
        ownerId = r['owner']['id']
        r['current'] = r['id'] == rdefId
        # if duplicate rdefs for user, pick one with highest ID
        if ownerId not in rdefs or rdefs[ownerId]['id'] < r['id']:
            rdefs[ownerId] = r
    rdefs = rdefs.values()
    # format into rdef strings,
    # E.g. {c: '1|3118:35825$FF0000,2|2086:18975$FFFF00', m: 'c'}
    rdefQueries = []
    for r in rdefs:
        chs = []
        for i, c in enumerate(r['c']):
            act = "-"
            if c['active']:
                act = ""
            color = c['lut'] if 'lut' in c else c['color']
            reverse = 'r' if c['reverseIntensity'] else '-r'
            chs.append('%s%s|%d:%d%s$%s'
                       % (act, i+1, c['start'], c['end'], reverse, color))
        rdefQueries.append({
            'id': r['id'],
            'owner': r['owner'],
            'c': ",".join(chs),
            'm': r['model'] == 'greyscale' and 'g' or 'c'
            })
    max_w, max_h = conn.getMaxPlaneSize()
    size_x = manager.image.getSizeX()
    size_y = manager.image.getSizeY()

    context['tiledImage'] = (size_x * size_y) > (max_w * max_h)
    context['manager'] = manager
    context['rdefsJson'] = json.dumps(rdefQueries)
    context['rdefs'] = rdefs
    context['template'] = "webclient/annotations/metadata_preview.html"
    return context


@login_required()
@render_response()
def load_metadata_hierarchy(request, c_type, c_id, conn=None, **kwargs):
    """
    This loads the ancestors of the specified object and displays them in a
    static tree.
    Used by an AJAX call from the metadata_general panel.
    """
    manager = BaseContainer(conn, **{str(c_type): long(c_id)})

    context = {'manager': manager}
    context['template'] = "webclient/annotations/metadata_hierarchy.html"
    return context


@login_required()
@render_response()
def load_metadata_acquisition(request, c_type, c_id, conn=None, share_id=None,
                              **kwargs):
    """
    The acquisition tab of the right-hand panel. Only loaded for images.
    TODO: urls regex should make sure that c_type is only 'image' OR 'well'
    """
    try:
        if c_type in ("share", "discussion"):
            template = "webclient/annotations/annotations_share.html"
            manager = BaseShare(conn, c_id)
            manager.getAllUsers(c_id)
            manager.getComments(c_id)
        else:
            template = "webclient/annotations/metadata_acquisition.html"
            manager = BaseContainer(
                conn, **{str(c_type): long(c_id)})
    except AttributeError, x:
        return handlerInternalError(request, x)

    form_environment = None
    form_objective = None
    form_microscope = None
    form_instrument_objectives = list()
    form_stageLabel = None
    form_filters = list()
    form_dichroics = list()
    form_detectors = list()
    form_channels = list()
    form_lasers = list()

    lasertypes = list(conn.getEnumerationEntries("LaserType"))
    arctypes = list(conn.getEnumerationEntries("ArcType"))
    filamenttypes = list(conn.getEnumerationEntries("FilamentType"))

    # various enums we need for the forms (don't load unless needed)
    mediums = None
    immersions = None
    corrections = None

    if c_type == 'image':
        if share_id is None:
            manager.companionFiles()
        manager.channelMetadata()
        for theC, ch in enumerate(manager.channel_metadata):
            logicalChannel = ch.getLogicalChannel()
            if logicalChannel is not None:
                channel = dict()
                channel['form'] = MetadataChannelForm(initial={
                    'logicalChannel': logicalChannel,
                    'exWave': ch.getExcitationWave(units=True),
                    'emWave': ch.getEmissionWave(units=True),
                    'illuminations': list(conn.getEnumerationEntries(
                        "IlluminationI")),
                    'contrastMethods': list(conn.getEnumerationEntries(
                        "ContrastMethodI")),
                    'modes': list(conn.getEnumerationEntries(
                        "AcquisitionModeI"))})
                # 9853 Much metadata is not available to 'shares'
                if share_id is None:
                    lightPath = logicalChannel.getLightPath()
                    if lightPath is not None:
                        channel['form_dichroic'] = None
                        channel['form_excitation_filters'] = list()
                        channel['form_emission_filters'] = list()
                        lightPathDichroic = lightPath.getDichroic()
                        if lightPathDichroic is not None:
                            channel['form_dichroic'] = MetadataDichroicForm(
                                initial={'dichroic': lightPathDichroic})
                        filterTypes = list(conn.getEnumerationEntries(
                            "FilterTypeI"))
                        for f in lightPath.getEmissionFilters():
                            channel['form_emission_filters'].append(
                                MetadataFilterForm(initial={
                                    'filter': f, 'types': filterTypes}))
                        for f in lightPath.getExcitationFilters():
                            channel['form_excitation_filters'].append(
                                MetadataFilterForm(initial={
                                    'filter': f, 'types': filterTypes}))

                    detectorSettings = logicalChannel.getDetectorSettings()
                    if (detectorSettings._obj is not None and
                            detectorSettings.getDetector()):
                        channel['form_detector_settings'] = \
                            MetadataDetectorForm(initial={
                                'detectorSettings': detectorSettings,
                                'detector': detectorSettings.getDetector(),
                                'types': list(conn.getEnumerationEntries(
                                    "DetectorTypeI")),
                                'binnings': list(conn.getEnumerationEntries(
                                    "Binning"))})

                    lightSourceSettings = \
                        logicalChannel.getLightSourceSettings()
                    if (lightSourceSettings is not None and
                            lightSourceSettings._obj is not None):
                        lightSrc = lightSourceSettings.getLightSource()
                        if lightSrc is not None:
                            lstypes = lasertypes
                            if lightSrc.OMERO_CLASS == "Arc":
                                lstypes = arctypes
                            elif lightSrc.OMERO_CLASS == "Filament":
                                lstypes = filamenttypes
                            channel['form_light_source'] = \
                                MetadataLightSourceForm(initial={
                                    'lightSource': lightSrc,
                                    'lightSourceSettings': lightSourceSettings,
                                    'lstypes': lstypes,
                                    'mediums': list(
                                        conn.getEnumerationEntries(
                                            "LaserMediumI")),
                                    'pulses': list(conn.getEnumerationEntries(
                                        "PulseI"))})
                # TODO: We don't display filter sets here yet since they are
                # not populated on Import by BioFormats.
                channel['label'] = ch.getLabel()
                color = ch.getColor()
                channel['color'] = (color is not None and color.getHtml() or
                                    None)
                planeInfo = (
                    manager.image and
                    manager.image.getPrimaryPixels().copyPlaneInfo(
                        theC=theC, theZ=0))
                plane_info = []

                for pi in planeInfo:
                    deltaT = pi.getDeltaT(units="SECOND")
                    exposure = pi.getExposureTime(units="SECOND")
                    if deltaT is None and exposure is None:
                        continue
                    if deltaT is not None:
                        deltaT = deltaT.getValue()
                    if exposure is not None:
                        exposure = exposure.getValue()
                    plane_info.append({
                        'theT': pi.theT,
                        'deltaT': deltaT,
                        'exposureTime': exposure})
                channel['plane_info'] = plane_info

                form_channels.append(channel)

        try:
            image = manager.well.getWellSample().image()
        except:
            image = manager.image

        if share_id is None:    # 9853
            if image.getObjectiveSettings() is not None:
                # load the enums if needed and create our Objective Form
                if mediums is None:
                    mediums = list(conn.getEnumerationEntries("MediumI"))
                if immersions is None:
                    immersions = list(
                        conn.getEnumerationEntries("ImmersionI"))
                if corrections is None:
                    corrections = list(
                        conn.getEnumerationEntries("CorrectionI"))
                form_objective = MetadataObjectiveSettingsForm(initial={
                    'objectiveSettings': image.getObjectiveSettings(),
                    'objective': image.getObjectiveSettings().getObjective(),
                    'mediums': mediums,
                    'immersions': immersions,
                    'corrections': corrections})
            if image.getImagingEnvironment() is not None:
                form_environment = MetadataEnvironmentForm(initial={
                    'image': image})
            if image.getStageLabel() is not None:
                form_stageLabel = MetadataStageLabelForm(initial={
                    'image': image})

            instrument = image.getInstrument()
            if instrument is not None:
                if instrument.getMicroscope() is not None:
                    form_microscope = MetadataMicroscopeForm(initial={
                        'microscopeTypes': list(
                            conn.getEnumerationEntries("MicroscopeTypeI")),
                        'microscope': instrument.getMicroscope()})

                objectives = instrument.getObjectives()
                for o in objectives:
                    # load the enums if needed and create our Objective Form
                    if mediums is None:
                        mediums = list(conn.getEnumerationEntries("MediumI"))
                    if immersions is None:
                        immersions = list(
                            conn.getEnumerationEntries("ImmersionI"))
                    if corrections is None:
                        corrections = list(
                            conn.getEnumerationEntries("CorrectionI"))
                    obj_form = MetadataObjectiveForm(initial={
                        'objective': o,
                        'mediums': mediums,
                        'immersions': immersions,
                        'corrections': corrections})
                    form_instrument_objectives.append(obj_form)
                filters = list(instrument.getFilters())
                if len(filters) > 0:
                    for f in filters:
                        form_filter = MetadataFilterForm(initial={
                            'filter': f, 'types': list(
                                conn.getEnumerationEntries("FilterTypeI"))})
                        form_filters.append(form_filter)

                dichroics = list(instrument.getDichroics())
                for d in dichroics:
                    form_dichroic = MetadataDichroicForm(
                        initial={'dichroic': d})
                    form_dichroics.append(form_dichroic)

                detectors = list(instrument.getDetectors())
                if len(detectors) > 0:
                    for d in detectors:
                        form_detector = MetadataDetectorForm(initial={
                            'detectorSettings': None,
                            'detector': d,
                            'types': list(
                                conn.getEnumerationEntries("DetectorTypeI"))})
                        form_detectors.append(form_detector)

                lasers = list(instrument.getLightSources())
                if len(lasers) > 0:
                    for l in lasers:
                        lstypes = lasertypes
                        if l.OMERO_CLASS == "Arc":
                            lstypes = arctypes
                        elif l.OMERO_CLASS == "Filament":
                            lstypes = filamenttypes
                        form_laser = MetadataLightSourceForm(initial={
                            'lightSource': l,
                            'lstypes': lstypes,
                            'mediums': list(
                                conn.getEnumerationEntries("LaserMediumI")),
                            'pulses': list(
                                conn.getEnumerationEntries("PulseI"))})
                        form_lasers.append(form_laser)

    # TODO: remove this 'if' since we should only have c_type = 'image'?
    context = {'manager': manager, "share_id": share_id}
    if c_type not in ("share", "discussion", "tag"):
        context['form_channels'] = form_channels
        context['form_environment'] = form_environment
        context['form_objective'] = form_objective
        context['form_microscope'] = form_microscope
        context['form_instrument_objectives'] = form_instrument_objectives
        context['form_filters'] = form_filters
        context['form_dichroics'] = form_dichroics
        context['form_detectors'] = form_detectors
        context['form_lasers'] = form_lasers
        context['form_stageLabel'] = form_stageLabel
    context['template'] = template
    return context


@login_required()
@render_response()
def load_original_metadata(request, imageId, conn=None, share_id=None,
                           **kwargs):

    image = conn.getObject("Image", imageId)
    if image is None:
        raise Http404("No Image found with ID %s" % imageId)

    context = {
        'template': 'webclient/annotations/original_metadata.html',
        'imageId': image.getId()}
    try:
        om = image.loadOriginalMetadata()
        if om is not None:
            context['original_metadata'] = om[0]
            context['global_metadata'] = om[1]
            context['series_metadata'] = om[2]
    except omero.LockTimeout:
        # 408 is Request Timeout
        return HttpResponse(content='LockTimeout', status=408)
    return context

###########################################################################
# ACTIONS

# Annotation in the right-hand panel is handled the same way for single
# objects (metadata_general.html)
# AND for batch annotation (batch_annotate.html) by 4 forms:
# Comment (this is loaded in the initial page)
# Tags (the empty form is in the initial page but fields are loaded via AJAX)
# Local File (this is loaded in the initial page)
# Existing File (the empty form is in the initial page but field is loaded via
# AJAX)
#
# In each case, the form itself contains hidden fields to specify the
# object(s) being annotated
# All forms inherit from a single form that has these fields.


def getObjects(request, conn=None):
    """
    Prepare objects for use in the annotation forms.
    These objects are required by the form superclass to populate hidden
    fields, so we know what we're annotating on submission
    """
    r = request.GET or request.POST
    images = (
        len(r.getlist('image')) > 0 and
        list(conn.getObjects("Image", r.getlist('image'))) or
        list())
    datasets = (
        len(r.getlist('dataset')) > 0 and
        list(conn.getObjects(
            "Dataset", r.getlist('dataset'))) or
        list())
    projects = (
        len(r.getlist('project')) > 0 and
        list(conn.getObjects(
            "Project", r.getlist('project'))) or
        list())
    screens = (
        len(r.getlist('screen')) > 0 and
        list(conn.getObjects("Screen", r.getlist('screen'))) or
        list())
    plates = (
        len(r.getlist('plate')) > 0 and
        list(conn.getObjects("Plate", r.getlist('plate'))) or
        list())
    acquisitions = (
        len(r.getlist('acquisition')) > 0 and
        list(conn.getObjects(
            "PlateAcquisition", r.getlist('acquisition'))) or
        list())
    shares = (len(r.getlist('share')) > 0 and
              [conn.getShare(r.getlist('share')[0])] or list())
    wells = (len(r.getlist('well')) > 0 and
             list(conn.getObjects("Well", r.getlist('well'))) or list())
    return {
        'image': images, 'dataset': datasets, 'project': projects,
        'screen': screens, 'plate': plates, 'acquisition': acquisitions,
        'well': wells, 'share': shares}


def getIds(request):
    """
    Used by forms to indicate the currently selected objects prepared above
    """
    r = request.GET or request.POST
    selected = {
        'images': r.getlist('image'),
        'datasets': r.getlist('dataset'),
        'projects': r.getlist('project'),
        'screens': r.getlist('screen'),
        'plates': r.getlist('plate'),
        'acquisitions': r.getlist('acquisition'),
        'wells': r.getlist('well'),
        'shares': r.getlist('share')}
    return selected


@login_required()
@render_response()
def batch_annotate(request, conn=None, **kwargs):
    """
    This page gives a form for batch annotation.
    Local File form and Comment form are loaded. Other forms are loaded via
    AJAX
    """

    objs = getObjects(request, conn)

    # get groups for selected objects - setGroup() and create links
    obj_ids = []
    obj_labels = []
    groupIds = set()
    annotationBlocked = False
    for key in objs:
        obj_ids += ["%s=%s" % (key, o.id) for o in objs[key]]
        for o in objs[key]:
            groupIds.add(o.getDetails().group.id.val)
            if not o.canAnnotate():
                annotationBlocked = ("Can't add annotations because you don't"
                                     " have permissions")
            obj_labels.append({
                'type': key.title(), 'id': o.id, 'name': o.getName()})
    obj_string = "&".join(obj_ids)
    link_string = "|".join(obj_ids).replace("=", "-")
    if len(groupIds) == 0:
        # No supported objects found.
        # If multiple tags / tagsets selected, return placeholder
        if (len(request.GET.getlist('tag')) > 0 or
                len(request.GET.getlist('tagset')) > 0):
            return HttpResponse("<h2>Can't batch annotate tags</h2>")
        else:
            return handlerInternalError(request, "No objects found")
    groupId = list(groupIds)[0]
    conn.SERVICE_OPTS.setOmeroGroup(groupId)

    manager = BaseContainer(conn)
    figScripts = manager.listFigureScripts(objs)
    canExportAsJpg = manager.canExportAsJpg(request, objs)
    filesetInfo = None
    iids = []
    if 'image' in objs and len(objs['image']) > 0:
        iids = [i.getId() for i in objs['image']]
    if len(iids) > 0:
        filesetInfo = conn.getFilesetFilesInfo(iids)
        archivedInfo = conn.getArchivedFilesInfo(iids)
        filesetInfo['count'] += archivedInfo['count']
        filesetInfo['size'] += archivedInfo['size']

    context = {
        'iids': iids,
        'obj_string': obj_string,
        'link_string': link_string,
        'obj_labels': obj_labels,
        'batch_ann': True,
        'figScripts': figScripts,
        'canExportAsJpg': canExportAsJpg,
        'filesetInfo': filesetInfo,
        'annotationBlocked': annotationBlocked,
        'differentGroups': False}
    if len(groupIds) > 1:
        context['annotationBlocked'] = ("Can't add annotations because"
                                        " objects are in different groups")
        context['differentGroups'] = True       # E.g. don't run scripts etc
    context['canDownload'] = manager.canDownload(objs)
    context['template'] = "webclient/annotations/batch_annotate.html"
    context['webclient_path'] = reverse('webindex')
    context['annotationCounts'] = manager.getBatchAnnotationCounts(
        getObjects(request, conn))
    return context


@login_required()
@render_response()
def annotate_file(request, conn=None, **kwargs):
    """
    On 'POST', This handles attaching an existing file-annotation(s) and/or
    upload of a new file to one or more objects
    Otherwise it generates the form for choosing file-annotations & local
    files.
    """
    oids = getObjects(request, conn)
    selected = getIds(request)
    initial = {
        'selected': selected,
        'images': oids['image'],
        'datasets': oids['dataset'],
        'projects': oids['project'],
        'screens': oids['screen'],
        'plates': oids['plate'],
        'acquisitions': oids['acquisition'],
        'wells': oids['well']}

    # Use the first object we find to set context (assume all objects are in
    # same group!)
    for obs in oids.values():
        if len(obs) > 0:
            conn.SERVICE_OPTS.setOmeroGroup(obs[0].getDetails().group.id.val)
            break

    obj_count = sum([len(selected[types]) for types in selected])

    # Get appropriate manager, either to list available Files to add to single
    # object, or list ALL Files (multiple objects)
    manager = None
    if obj_count == 1:
        for t in selected:
            if len(selected[t]) > 0:
                o_type = t[:-1]         # "images" -> "image"
                o_id = selected[t][0]
                break
        if o_type in ("dataset", "project", "image", "screen", "plate",
                      "acquisition", "well", "comment", "file", "tag",
                      "tagset"):
            if o_type == 'tagset':
                # TODO: this should be handled by the BaseContainer
                o_type = 'tag'
            kw = {}
            if o_type is not None and o_id > 0:
                kw[str(o_type)] = long(o_id)
            try:
                manager = BaseContainer(conn, **kw)
            except AttributeError, x:
                return handlerInternalError(request, x)

    if manager is not None:
        files = manager.getFilesByObject()
    else:
        manager = BaseContainer(conn)
        for dtype, objs in oids.items():
            if len(objs) > 0:
                # NB: we only support a single data-type now. E.g. 'image' OR
                # 'dataset' etc.
                files = manager.getFilesByObject(
                    parent_type=dtype, parent_ids=[o.getId() for o in objs])
                break

    initial['files'] = files

    if request.method == 'POST':
        # handle form submission
        form_file = FilesAnnotationForm(
            initial=initial, data=request.POST.copy())
        if form_file.is_valid():
            # Link existing files...
            files = form_file.cleaned_data['files']
            added_files = []
            if files is not None and len(files) > 0:
                added_files = manager.createAnnotationsLinks(
                    'file', files, oids)
            # upload new file
            fileupload = ('annotation_file' in request.FILES and
                          request.FILES['annotation_file'] or None)
            if fileupload is not None and fileupload != "":
                newFileId = manager.createFileAnnotations(
                    fileupload, oids)
                added_files.append(newFileId)
            return JsonResponse({'fileIds': added_files})
        else:
            return HttpResponse(form_file.errors)

    else:
        form_file = FilesAnnotationForm(initial=initial)
        context = {'form_file': form_file}
        template = "webclient/annotations/files_form.html"
    context['template'] = template
    return context


@login_required()
@render_response()
def annotate_rating(request, conn=None, **kwargs):
    """
    Handle adding Rating to one or more objects
    """
    rating = getIntOrDefault(request, 'rating', 0)
    oids = getObjects(request, conn)

    # add / update rating
    for otype, objs in oids.items():
        for o in objs:
            o.setRating(rating)

    # return a summary of ratings
    return JsonResponse({'success': True})


@login_required()
@render_response()
def annotate_comment(request, conn=None, **kwargs):
    """ Handle adding Comments to one or more objects
    Unbound instance of Comment form not available.
    If the form has been submitted, a bound instance of the form
    is created using request.POST"""

    if request.method != 'POST':
        raise Http404("Unbound instance of form not available.")

    oids = getObjects(request, conn)
    selected = getIds(request)
    initial = {
        'selected': selected,
        'images': oids['image'],
        'datasets': oids['dataset'],
        'projects': oids['project'],
        'screens': oids['screen'],
        'plates': oids['plate'],
        'acquisitions': oids['acquisition'],
        'wells': oids['well'],
        'shares': oids['share']}

    # Use the first object we find to set context (assume all objects are in
    # same group!) this does not aplly to share
    if len(oids['share']) < 1:
        for obs in oids.values():
            if len(obs) > 0:
                conn.SERVICE_OPTS.setOmeroGroup(
                    obs[0].getDetails().group.id.val)
                break

    # Handle form submission...
    form_multi = CommentAnnotationForm(initial=initial,
                                       data=request.POST.copy())
    if form_multi.is_valid():
        # In each case below, we pass the {'object_type': [ids]} map
        content = form_multi.cleaned_data['comment']
        if content is not None and content != "":
            if oids['share'] is not None and len(oids['share']) > 0:
                sid = oids['share'][0].id
                manager = BaseShare(conn, sid)
                host = "%s?server=%i" % (
                    request.build_absolute_uri(
                        reverse("load_template", args=["public"])),
                    int(conn.server_id))
                textAnn = manager.addComment(host, content)
                # For shares we need to return html for display...
                context = {
                    'tann': textAnn,
                    'added_by': conn.getUserId(),
                    'template': "webclient/annotations/comment.html"}
            else:
                # ...otherwise Comments are re-loaded by AJAX json
                # so we don't *need* to return anything
                manager = BaseContainer(conn)
                annId = manager.createCommentAnnotations(
                    content, oids)
                context = {
                    'annId': annId,
                    'added_by': conn.getUserId()}
            return context
    else:
        # TODO: handle invalid form error
        return HttpResponse(str(form_multi.errors))


@login_required()
@render_response()
def annotate_map(request, conn=None, **kwargs):
    """
        Handle adding Map Annotations to one or more objects
        POST data "mapAnnotation" should be list of ['key':'value'] pairs.
    """

    if request.method != 'POST':
        raise Http404("Need to POST map annotation data as list of"

                      " ['key', 'value'] pairs")

    oids = getObjects(request, conn)

    # Use the first object we find to set context (assume all objects are in
    # same group!)
    # this does not aplly to share
    if len(oids['share']) < 1:
        for obs in oids.values():
            if len(obs) > 0:
                conn.SERVICE_OPTS.setOmeroGroup(
                    obs[0].getDetails().group.id.val)
                break

    data = request.POST.get('mapAnnotation')
    data = json.loads(data)

    annId = request.POST.get('annId')
    # Create a new annotation
    if annId is None and len(data) > 0:
        ann = omero.gateway.MapAnnotationWrapper(conn)
        ann.setValue(data)
        ann.setNs(omero.constants.metadata.NSCLIENTMAPANNOTATION)
        ann.save()
        for k, objs in oids.items():
            for obj in objs:
                obj.linkAnnotation(ann)
        annId = ann.getId()
    # Or update existing annotation
    elif annId is not None:
        ann = conn.getObject("MapAnnotation", annId)
        if len(data) > 0:
            ann.setValue(data)
            ann.save()
            annId = ann.getId()
        else:
            # Delete if no data
            handle = conn.deleteObjects('/Annotation', [annId])
            try:
                conn._waitOnCmd(handle)
            finally:
                handle.close()
            annId = None

    return {"annId": annId}


@login_required()
@render_response()
def marshal_tagging_form_data(request, conn=None, **kwargs):
    """
    Provides json data to ome.tagging_form.js
    """

    group = get_long_or_default(request, 'group', -1)
    conn.SERVICE_OPTS.setOmeroGroup(str(group))
    try:
        offset = int(request.GET.get('offset'))
        limit = int(request.GET.get('limit', 1000))
    except:
        offset = limit = None

    jsonmode = request.GET.get('jsonmode')
    if jsonmode == 'tagcount':
        tag_count = conn.getTagCount()
        return dict(tag_count=tag_count)

    manager = BaseContainer(conn)
    manager.loadTagsRecursive(eid=-1, offset=offset, limit=limit)
    all_tags = manager.tags_recursive
    all_tags_owners = manager.tags_recursive_owners

    if jsonmode == 'tags':
        # send tag information without descriptions
        r = list((i, t, o, s) for i, d, t, o, s in all_tags)
        return r

    elif jsonmode == 'desc':
        # send descriptions for tags
        return dict((i, d) for i, d, t, o, s in all_tags)

    elif jsonmode == 'owners':
        # send owner information
        return all_tags_owners

    return HttpResponse()


@login_required()
@render_response()
def annotate_tags(request, conn=None, **kwargs):
    """
    This handles creation AND submission of Tags form, adding new AND/OR
    existing tags to one or more objects
    """

    oids = getObjects(request, conn)
    selected = getIds(request)
    obj_count = sum([len(selected[types]) for types in selected])

    # Get appropriate manager, either to list available Tags to add to single
    # object, or list ALL Tags (multiple objects)
    manager = None
    self_id = conn.getEventContext().userId

    tags = []

    # Use the first object we find to set context (assume all objects are
    # in same group!)
    for obs in oids.values():
        if len(obs) > 0:
            conn.SERVICE_OPTS.setOmeroGroup(
                obs[0].getDetails().group.id.val)
            break

    # Make a list of all current tags
    # As would be on right column of tagging dialog...
    taglist, users = tree.marshal_annotations(
        conn,
        project_ids=selected['projects'],
        dataset_ids=selected['datasets'],
        image_ids=selected['images'],
        screen_ids=selected['screens'],
        plate_ids=selected['plates'],
        run_ids=selected['acquisitions'],
        well_ids=selected['wells'],
        ann_type='tag',
        # If we reach this limit we'll get some tags not removed
        limit=100000)

    userMap = {}
    for exp in users:
        userMap[exp['id']] = exp

    # For batch annotate, only include tags that user has added to all objects
    if obj_count > 1:
        # count my links
        myLinkCount = {}
        for t in taglist:
            tid = t['id']
            if tid not in myLinkCount:
                myLinkCount[tid] = 0
            if t['link']['owner']['id'] == self_id:
                myLinkCount[tid] += 1
        # filter
        taglist = [t for t in taglist if myLinkCount[t['id']] == obj_count]

    selected_tags = []
    for tag in taglist:
        linkOwnerId = tag['link']['owner']['id']
        owner = userMap[linkOwnerId]
        ownerName = "%s %s" % (
            owner['firstName'],
            owner['lastName'])
        canDelete = True
        created = tag['link']['date']
        linkOwned = linkOwnerId == self_id
        selected_tags.append(
            (tag['id'], self_id, ownerName, canDelete, created, linkOwned))

    # selected_tags is really a list of tag LINKS.
    # May be several links per tag.id
    selected_tags.sort(key=lambda x: x[0])

    initial = {
        'selected': selected,
        'images': oids['image'],
        'datasets': oids['dataset'],
        'projects': oids['project'],
        'screens': oids['screen'],
        'plates': oids['plate'],
        'acquisitions': oids['acquisition'],
        'wells': oids['well']}

    if request.method == 'POST':
        # handle form submission
        form_tags = TagsAnnotationForm(
            initial=initial, data=request.POST.copy())
        newtags_formset = NewTagsAnnotationFormSet(
            prefix='newtags', data=request.POST.copy())
        # Create new tags or Link existing tags...
        if form_tags.is_valid() and newtags_formset.is_valid():
            # filter down previously selected tags to the ones linked by
            # current user
            selected_tag_ids = [stag[0] for stag in selected_tags if stag[5]]
            # Remove duplicates from tag IDs
            selected_tag_ids = list(set(selected_tag_ids))
            post_tags = form_tags.cleaned_data['tags']
            tags = [tag for tag in post_tags
                    if tag not in selected_tag_ids]
            removed = [tag for tag in selected_tag_ids
                       if tag not in post_tags]
            manager = BaseContainer(conn)
            if tags:
                manager.createAnnotationsLinks(
                    'tag',
                    tags,
                    oids
                )
            new_tags = []
            for form in newtags_formset.forms:
                new_tags.append(manager.createTagAnnotations(
                    form.cleaned_data['tag'],
                    form.cleaned_data['description'],
                    oids,
                    tag_group_id=form.cleaned_data['tagset'],
                ))
            # only remove Tags where the link is owned by self_id
            for remove in removed:
                tag_manager = BaseContainer(conn, tag=remove)
                tag_manager.remove([
                    "%s-%s" % (dtype, obj.id)
                    for dtype, objs in oids.items()
                    for obj in objs], tag_owner_id=self_id)
            return JsonResponse({'added': tags,
                                 'removed': removed,
                                 'new': new_tags})
        else:
            # TODO: handle invalid form error
            return HttpResponse(str(form_tags.errors))

    else:
        form_tags = TagsAnnotationForm(initial=initial)
        newtags_formset = NewTagsAnnotationFormSet(prefix='newtags')
        context = {
            'form_tags': form_tags,
            'newtags_formset': newtags_formset,
            'selected_tags': selected_tags,
        }
        template = "webclient/annotations/tags_form.html"
    context['template'] = template
    return context


@require_POST
@login_required()
@render_response()
def edit_channel_names(request, imageId, conn=None, **kwargs):
    """
    Edit and save channel names
    """
    image = conn.getObject("Image", imageId)
    sizeC = image.getSizeC()
    channelNames = {}
    nameDict = {}
    for i in range(sizeC):
        cname = request.POST.get("channel%d" % i, None)
        if cname is not None:
            cname = smart_str(cname)[:255]      # Truncate to fit in DB
            channelNames["channel%d" % i] = cname
            nameDict[i+1] = cname
    # If the 'Apply to Dataset' button was used to submit...
    if request.POST.get('confirm_apply', None) is not None:
        # plate-123 OR dataset-234
        parentId = request.POST.get('parentId', None)
        if parentId is not None:
            ptype = parentId.split("-")[0].title()
            pid = long(parentId.split("-")[1])
            counts = conn.setChannelNames(
                ptype, [pid], nameDict, channelCount=sizeC)
    else:
        counts = conn.setChannelNames("Image", [image.getId()], nameDict)
    rv = {"channelNames": channelNames}
    if counts:
        rv['imageCount'] = counts['imageCount']
        rv['updateCount'] = counts['updateCount']
        return rv
    else:
        return {"error": "No parent found to apply Channel Names"}


@login_required(setGroupContext=True)
@render_response()
def manage_action_containers(request, action, o_type=None, o_id=None,
                             conn=None, **kwargs):
    """
    Handles many different actions on various objects.

    @param action:      "addnewcontainer", (creates a new Project, Dataset,
                        Screen), "editname", "savename", "editdescription",
                        "savedescription",  (used as GET and POST for in-line
                        editing),
                        "removefromshare", (tree P/D/I moving etc)
                        "delete", "deletemany"      (delete objects)
                        "remove" (remove tag/comment from object)
    @param o_type:      "dataset", "project", "image", "screen", "plate",
                        "acquisition", "well","comment", "file", "tag",
                        "tagset","share", "sharecomment"
    """
    template = None

    manager = None
    if o_type in ("dataset", "project", "image", "screen", "plate",
                  "acquisition", "well", "comment", "file", "tag", "tagset"):
        kw = {}
        if o_type is not None and o_id > 0:
            kw[str(o_type)] = long(o_id)
        try:
            manager = BaseContainer(conn, **kw)
        except AttributeError, x:
            return handlerInternalError(request, x)
    elif o_type in ("share", "sharecomment", "chat"):
        manager = BaseShare(conn, o_id)
    else:
        manager = BaseContainer(conn)

    form = None
    if action == 'addnewcontainer':
        # Used within the jsTree to add a new Project, Dataset, Tag,
        # Tagset etc under a specified parent OR top-level
        if not request.method == 'POST':
            return HttpResponseRedirect(reverse("manage_action_containers",
                                        args=["edit", o_type, o_id]))
        if o_type == "project" and hasattr(manager, o_type) and o_id > 0:
            # If Parent o_type is 'project'...
            form = ContainerForm(data=request.POST.copy())
            if form.is_valid():
                logger.debug(
                    "Create new in %s: %s" % (o_type, str(form.cleaned_data)))
                name = form.cleaned_data['name']
                description = form.cleaned_data['description']
                oid = manager.createDataset(name, description)
                rdict = {'bad': 'false', 'id': oid}
                return JsonResponse(rdict)
            else:
                d = dict()
                for e in form.errors.iteritems():
                    d.update({e[0]: unicode(e[1])})
                rdict = {'bad': 'true', 'errs': d}
                return JsonResponse(rdict)
        elif o_type == "tagset" and o_id > 0:
            form = ContainerForm(data=request.POST.copy())
            if form.is_valid():
                name = form.cleaned_data['name']
                description = form.cleaned_data['description']
                oid = manager.createTag(name, description)
                rdict = {'bad': 'false', 'id': oid}
                return JsonResponse(rdict)
            else:
                d = dict()
                for e in form.errors.iteritems():
                    d.update({e[0]: unicode(e[1])})
                rdict = {'bad': 'true', 'errs': d}
                return JsonResponse(rdict)
        elif request.POST.get('folder_type') in ("project", "screen",
                                                 "dataset", "tag", "tagset"):
            # No parent specified. We can create orphaned 'project', 'dataset'
            # etc.
            form = ContainerForm(data=request.POST.copy())
            if form.is_valid():
                logger.debug("Create new: %s" % (str(form.cleaned_data)))
                name = form.cleaned_data['name']
                description = form.cleaned_data['description']
                folder_type = request.POST.get('folder_type')
                if folder_type == "dataset":
                    oid = manager.createDataset(
                        name, description,
                        img_ids=request.POST.getlist('image', None))
                else:
                    # lookup method, E.g. createTag, createProject etc.
                    oid = getattr(manager, "create" +
                                  folder_type.capitalize())(name, description)
                rdict = {'bad': 'false', 'id': oid}
                return JsonResponse(rdict)
            else:
                d = dict()
                for e in form.errors.iteritems():
                    d.update({e[0]: unicode(e[1])})
                rdict = {'bad': 'true', 'errs': d}
                return JsonResponse(rdict)
        else:
            return HttpResponseServerError("Object does not exist")
    elif action == 'add':
        template = "webclient/public/share_form.html"
        experimenters = list(conn.getExperimenters())
        experimenters.sort(key=lambda x: x.getOmeName().lower())
        if o_type == "share":
            img_ids = request.GET.getlist('image',
                                          request.POST.getlist('image'))
            images_to_share = list(conn.getObjects("Image", img_ids))
            if request.method == 'POST':
                form = BasketShareForm(
                    initial={'experimenters': experimenters,
                             'images': images_to_share},
                    data=request.POST.copy())
                if form.is_valid():
                    images = form.cleaned_data['image']
                    message = form.cleaned_data['message']
                    expiration = form.cleaned_data['expiration']
                    members = form.cleaned_data['members']
                    # guests = request.POST['guests']
                    enable = form.cleaned_data['enable']
                    host = "%s?server=%i" % (request.build_absolute_uri(
                        reverse("load_template", args=["public"])),
                        int(conn.server_id))
                    shareId = manager.createShare(
                        host, images, message, members, enable, expiration)
                    return HttpResponse("shareId:%s" % shareId)
            else:
                initial = {
                    'experimenters': experimenters,
                    'images': images_to_share,
                    'enable': True,
                    'selected': request.GET.getlist('image')
                }
                form = BasketShareForm(initial=initial)
        template = "webclient/public/share_form.html"
        context = {'manager': manager, 'form': form}

    elif action == 'edit':
        # form for editing an Object. E.g. Project etc. TODO: not used now?
        if o_type == "share" and o_id > 0:
            template = "webclient/public/share_form.html"
            manager.getMembers(o_id)
            manager.getComments(o_id)
            experimenters = list(conn.getExperimenters())
            experimenters.sort(key=lambda x: x.getOmeName().lower())
            initial = {
                'message': manager.share.message,
                'expiration': "",
                'shareMembers': manager.membersInShare,
                'enable': manager.share.active,
                'experimenters': experimenters}
            if manager.share.getExpireDate() is not None:
                initial['expiration'] = \
                    manager.share.getExpireDate().strftime("%Y-%m-%d")
            form = ShareForm(initial=initial)  # 'guests':share.guestsInShare,
            context = {'manager': manager, 'form': form}
        elif hasattr(manager, o_type) and o_id > 0:
            obj = getattr(manager, o_type)
            template = "webclient/data/container_form.html"
            form = ContainerForm(
                initial={'name': obj.name, 'description': obj.description})
            context = {'manager': manager, 'form': form}
    elif action == 'save':
        # Handles submission of the 'edit' form above. TODO: not used now?
        if not request.method == 'POST':
            return HttpResponseRedirect(reverse("manage_action_containers",
                                        args=["edit", o_type, o_id]))
        if o_type == "share":
            experimenters = list(conn.getExperimenters())
            experimenters.sort(key=lambda x: x.getOmeName().lower())
            form = ShareForm(initial={'experimenters': experimenters},
                             data=request.POST.copy())
            if form.is_valid():
                logger.debug("Update share: %s" % (str(form.cleaned_data)))
                message = form.cleaned_data['message']
                expiration = form.cleaned_data['expiration']
                members = form.cleaned_data['members']
                # guests = request.POST['guests']
                enable = form.cleaned_data['enable']
                host = "%s?server=%i" % (request.build_absolute_uri(
                    reverse("load_template", args=["public"])),
                    int(conn.server_id))
                manager.updateShareOrDiscussion(
                    host, message, members, enable, expiration)
                r = "enable" if enable else "disable"
                return HttpResponse(r)
            else:
                template = "webclient/public/share_form.html"
                context = {'share': manager, 'form': form}
        else:
            return HttpResponseServerError("Object does not exist")
    elif action == 'editname':
        # start editing 'name' in-line
        if hasattr(manager, o_type) and o_id > 0:
            obj = getattr(manager, o_type)
            template = "webclient/ajax_form/container_form_ajax.html"
            if o_type == "tag":
                txtValue = obj.textValue
            else:
                txtValue = obj.getName()
            form = ContainerNameForm(initial={'name': txtValue})
            context = {'manager': manager, 'form': form}
        else:
            return HttpResponseServerError("Object does not exist")
    elif action == 'savename':
        # Save name edit in-line
        if not request.method == 'POST':
            return HttpResponseRedirect(reverse("manage_action_containers",
                                        args=["edit", o_type, o_id]))
        if hasattr(manager, o_type) and o_id > 0:
            form = ContainerNameForm(data=request.POST.copy())
            if form.is_valid():
                logger.debug("Update name form:" + str(form.cleaned_data))
                name = form.cleaned_data['name']
                rdict = {'bad': 'false', 'o_type': o_type}
                manager.updateName(o_type, name)
                return JsonResponse(rdict)
            else:
                d = dict()
                for e in form.errors.iteritems():
                    d.update({e[0]: unicode(e[1])})
                rdict = {'bad': 'true', 'errs': d}
                return JsonResponse(rdict)
        else:
            return HttpResponseServerError("Object does not exist")
    elif action == 'editdescription':
        # start editing description in-line
        if hasattr(manager, o_type) and o_id > 0:
            obj = getattr(manager, o_type)
            template = "webclient/ajax_form/container_form_ajax.html"
            form = ContainerDescriptionForm(
                initial={'description': obj.description})
            context = {'manager': manager, 'form': form}
        else:
            return HttpResponseServerError("Object does not exist")
    elif action == 'savedescription':
        # Save editing of description in-line
        if not request.method == 'POST':
            return HttpResponseServerError(
                "Action '%s' on the '%s' id:%s cannot be complited"
                % (action, o_type, o_id))
        if hasattr(manager, o_type) and o_id > 0:
            form = ContainerDescriptionForm(data=request.POST.copy())
            if form.is_valid():
                logger.debug("Update name form:" + str(form.cleaned_data))
                description = form.cleaned_data['description']
                manager.updateDescription(o_type, description)
                rdict = {'bad': 'false'}
                return JsonResponse(rdict)
            else:
                d = dict()
                for e in form.errors.iteritems():
                    d.update({e[0]: unicode(e[1])})
                rdict = {'bad': 'true', 'errs': d}
                return JsonResponse(rdict)
        else:
            return HttpResponseServerError("Object does not exist")
    elif action == 'remove':
        # Handles removal of comment, tag from
        # Object etc.
        # E.g. image-123  or image-1|image-2
        parents = request.POST['parent']
        try:
            manager.remove(parents.split('|'))
        except Exception, x:
            logger.error(traceback.format_exc())
            rdict = {'bad': 'true', 'errs': str(x)}
            return JsonResponse(rdict)

        rdict = {'bad': 'false'}
        return JsonResponse(rdict)
    elif action == 'removefromshare':
        image_id = request.POST.get('source')
        try:
            manager.removeImage(image_id)
        except Exception, x:
            logger.error(traceback.format_exc())
            rdict = {'bad': 'true', 'errs': str(x)}
            return JsonResponse(rdict)
        rdict = {'bad': 'false'}
        return JsonResponse(rdict)
    elif action == 'delete':
        # Handles delete of a file attached to object.
        child = toBoolean(request.POST.get('child'))
        anns = toBoolean(request.POST.get('anns'))
        try:
            handle = manager.deleteItem(child, anns)
            request.session['callback'][str(handle)] = {
                'job_type': 'delete',
                'delmany': False,
                'did': o_id,
                'dtype': o_type,
                'status': 'in progress',
                'error': 0,
                'dreport': _formatReport(handle),
                'start_time': datetime.datetime.now()}
            request.session.modified = True
        except Exception, x:
            logger.error(
                'Failed to delete: %r' % {'did': o_id, 'dtype': o_type},
                exc_info=True)
            rdict = {'bad': 'true', 'errs': str(x)}
        else:
            rdict = {'bad': 'false'}
        return JsonResponse(rdict)
    elif action == 'deletemany':
        # Handles multi-delete from jsTree.
        object_ids = {
            'Image': request.POST.getlist('image'),
            'Dataset': request.POST.getlist('dataset'),
            'Project': request.POST.getlist('project'),
            'Annotation': request.POST.getlist('tag'),
            'Screen': request.POST.getlist('screen'),
            'Plate': request.POST.getlist('plate'),
            'Well': request.POST.getlist('well'),
            'PlateAcquisition': request.POST.getlist('acquisition')}
        child = toBoolean(request.POST.get('child'))
        anns = toBoolean(request.POST.get('anns'))
        logger.debug(
            "Delete many: child? %s anns? %s object_ids %s"
            % (child, anns, object_ids))
        try:
            for key, ids in object_ids.iteritems():
                if ids is not None and len(ids) > 0:
                    handle = manager.deleteObjects(key, ids, child, anns)
                    if key == "PlateAcquisition":
                        key = "Plate Run"      # for nicer user message
                    dMap = {
                        'job_type': 'delete',
                        'start_time': datetime.datetime.now(),
                        'status': 'in progress',
                        'error': 0,
                        'dreport': _formatReport(handle),
                        'dtype': key}
                    if len(ids) > 1:
                        dMap['delmany'] = len(ids)
                        dMap['did'] = ids
                    else:
                        dMap['delmany'] = False
                        dMap['did'] = ids[0]
                    request.session['callback'][str(handle)] = dMap
            request.session.modified = True
        except Exception, x:
            logger.error(
                'Failed to delete: %r' % {'did': ids, 'dtype': key},
                exc_info=True)
            # Ajax error handling will allow user to submit bug report
            raise
        else:
            rdict = {'bad': 'false'}
        return JsonResponse(rdict)
    context['template'] = template
    return context


@login_required(doConnectionCleanup=False)
def get_original_file(request, fileId, download=False, conn=None, **kwargs):
    """
    Returns the specified original file as an http response. Used for
    displaying text or png/jpeg etc files in browser
    """

    # May be viewing results of a script run in a different group.
    conn.SERVICE_OPTS.setOmeroGroup(-1)

    orig_file = conn.getObject("OriginalFile", fileId)
    if orig_file is None:
        return handlerInternalError(
            request, "Original File does not exists (id:%s)." % (fileId))

    rsp = ConnCleaningHttpResponse(
        orig_file.getFileInChunks(buf=settings.CHUNK_SIZE))
    rsp.conn = conn
    mimetype = orig_file.mimetype
    if mimetype == "text/x-python":
        mimetype = "text/plain"  # allows display in browser
    rsp['Content-Type'] = mimetype
    rsp['Content-Length'] = orig_file.getSize()

    if download:
        downloadName = orig_file.name.replace(" ", "_")
        downloadName = downloadName.replace(",", ".")
        rsp['Content-Disposition'] = 'attachment; filename=%s' % downloadName
    return rsp


@login_required()
def image_as_map(request, imageId, conn=None, **kwargs):
    """
    Converts OMERO image into mrc.map file (using tiltpicker utils) and
    returns the file
    """
    warnings.warn(
        "This module is deprecated as of OMERO 5.3.0", DeprecationWarning)

    from omero_ext.tiltpicker.pyami import mrc
    from numpy import dstack, zeros, int8

    image = conn.getObject("Image", imageId)
    if image is None:
        message = "Image ID %s not found in image_as_map" % imageId
        logger.error(message)
        return handlerInternalError(request, message)

    imageName = image.getName()
    downloadName = (imageName.endswith(".map") and imageName or
                    "%s.map" % imageName)
    pixels = image.getPrimaryPixels()

    # get a list of numpy planes and make stack
    zctList = [(z, 0, 0) for z in range(image.getSizeZ())]
    npList = list(pixels.getPlanes(zctList))
    npStack = dstack(npList)
    logger.info(
        "Numpy stack for image_as_map: dtype: %s, range %s-%s"
        % (npStack.dtype.name, npStack.min(), npStack.max()))

    # OAV only supports 'float' and 'int8'. Convert anything else to int8
    if (pixels.getPixelsType().value != 'float' or
            ('8bit' in kwargs and kwargs['8bit'])):
        # scale from -127 -> 128 and conver to 8 bit integer
        npStack = npStack - npStack.min()  # start at 0
        # range - 127 -> 128
        npStack = (npStack * 255.0 / npStack.max()) - 127
        a = zeros(npStack.shape, dtype=int8)
        npStack = npStack.round(out=a)

    if "maxSize" in kwargs and int(kwargs["maxSize"]) > 0:
        sz = int(kwargs["maxSize"])
        targetSize = sz * sz * sz
        # if available, use scipy.ndimage to resize
        if npStack.size > targetSize:
            try:
                import scipy.ndimage
                from numpy import round
                factor = float(targetSize) / npStack.size
                factor = pow(factor, 1.0/3)
                logger.info(
                    "Resizing numpy stack %s by factor of %s"
                    % (npStack.shape, factor))
                npStack = round(
                    scipy.ndimage.interpolation.zoom(npStack, factor), 1)
            except ImportError:
                logger.info(
                    "Failed to import scipy.ndimage for interpolation of"
                    " 'image_as_map'. Full size: %s" % str(npStack.shape))
                pass

    header = {}
    # Sometimes causes scaling issues in OAV.
    # header["xlen"] = pixels.physicalSizeX * image.getSizeX()
    # header["ylen"] = pixels.physicalSizeY * image.getSizeY()
    # header["zlen"] = pixels.physicalSizeZ * image.getSizeZ()
    # if header["xlen"] == 0 or header["ylen"] == 0 or header["zlen"] == 0:
    #     header = {}

    # write mrc.map to temp file
    import tempfile
    temp = tempfile.NamedTemporaryFile(suffix='.map')
    try:
        mrc.write(npStack, temp.name, header)
        logger.debug(
            "download file: %r" % {'name': temp.name, 'size': temp.tell()})
        originalFile_data = FileWrapper(temp)
        rsp = HttpResponse(originalFile_data)
        rsp['Content-Type'] = 'application/force-download'
        # rsp['Content-Length'] = temp.tell()
        rsp['Content-Length'] = os.path.getsize(temp.name)
        rsp['Content-Disposition'] = 'attachment; filename=%s' % downloadName
        temp.seek(0)
    except Exception:
        temp.close()
        logger.error(traceback.format_exc())
        return handlerInternalError(
            request, "Cannot generate map (id:%s)." % (imageId))
    return rsp


@login_required(doConnectionCleanup=False)
def download_annotation(request, annId, conn=None, **kwargs):
    """ Returns the file annotation as an http response for download """
    ann = conn.getObject("Annotation", annId)
    if ann is None:
        return handlerInternalError(
            request, "Annotation does not exist (id:%s)." % (annId))

    rsp = ConnCleaningHttpResponse(
        ann.getFileInChunks(buf=settings.CHUNK_SIZE))
    rsp.conn = conn
    rsp['Content-Type'] = 'application/force-download'
    rsp['Content-Length'] = ann.getFileSize()
    rsp['Content-Disposition'] = ('attachment; filename=%s'
                                  % (ann.getFileName().replace(" ", "_")))
    return rsp


@login_required()
def download_orig_metadata(request, imageId, conn=None, **kwargs):
    """ Downloads the 'Original Metadata' as a text file """

    image = conn.getObject("Image", imageId)
    if image is None:
        raise Http404("No Image found with ID %s" % imageId)

    om = image.loadOriginalMetadata()

    txtLines = ["[Global Metadata]"]
    txtLines.extend(["%s=%s" % (kv[0], kv[1]) for kv in om[1]])

    txtLines.append("[Series Metadata]")
    txtLines.extend(["%s=%s" % (kv[0], kv[1]) for kv in om[2]])
    rspText = "\n".join(txtLines)

    rsp = HttpResponse(rspText)
    rsp['Content-Type'] = 'application/force-download'
    rsp['Content-Length'] = len(rspText)
    rsp['Content-Disposition'] = 'attachment; filename=Original_Metadata.txt'
    return rsp


@login_required()
@render_response()
def download_placeholder(request, conn=None, **kwargs):
    """
    Page displays a simple "Preparing download..." message and redirects to
    the 'url'.
    We construct the url and query string from request: 'url' and 'ids'.
    """

    format = request.GET.get('format', None)
    if format is not None:
        download_url = reverse('download_as')
        zipName = 'Export_as_%s' % format
    else:
        download_url = reverse('archived_files')
        zipName = 'OriginalFileDownload'
    targetIds = request.GET.get('ids')      # E.g. image-1|image-2
    defaultName = request.GET.get('name', zipName)  # default zip name
    defaultName = os.path.basename(defaultName)         # remove path

    if targetIds is None:
        raise Http404("No IDs specified. E.g. ?ids=image-1|image-2")

    ids = targetIds.split("|")

    fileLists = []
    fileCount = 0
    # If we're downloading originals, list original files so user can
    # download individual files.
    if format is None:
        imgIds = []
        wellIds = []
        for i in ids:
            if i.split("-")[0] == "image":
                imgIds.append(i.split("-")[1])
            elif i.split("-")[0] == "well":
                wellIds.append(i.split("-")[1])

        images = []
        # Get images...
        if imgIds:
            images = list(conn.getObjects("Image", imgIds))

        if len(images) == 0:
            raise Http404("No images found.")

        # Have a list of files per fileset (or per image without fileset)
        fsIds = set()
        fileIds = set()
        for image in images:
            fs = image.getFileset()
            if fs is not None:
                # Make sure we've not processed this fileset before.
                if fs.id in fsIds:
                    continue
                fsIds.add(fs.id)
            files = list(image.getImportedImageFiles())
            fList = []
            for f in files:
                if f.id in fileIds:
                    continue
                fileIds.add(f.id)
                fList.append({'id': f.id,
                              'name': f.name,
                              'size': f.getSize()})
            if len(fList) > 0:
                fileLists.append(fList)
        fileCount = sum([len(l) for l in fileLists])
    else:
        # E.g. JPEG/PNG - 1 file per image
        fileCount = len(ids)

    query = "&".join([i.replace("-", "=") for i in ids])
    download_url = download_url + "?" + query
    if format is not None:
        download_url = (download_url + "&format=%s"
                        % format)

    context = {
        'template': "webclient/annotations/download_placeholder.html",
        'url': download_url,
        'defaultName': defaultName,
        'fileLists': fileLists,
        'fileCount': fileCount
        }
    return context


@login_required(setGroupContext=True)
@render_response()
def load_calendar(request, year=None, month=None, conn=None, **kwargs):
    """
    Loads the calendar which is displayed in the left panel of the history
    page.
    Shows current month by default. Filter by experimenter
    """

    template = "webclient/history/calendar.html"
    filter_user_id = request.session.get('user_id')

    if year is not None and month is not None:
        controller = BaseCalendar(
            conn=conn, year=year, month=month, eid=filter_user_id)
    else:
        today = datetime.datetime.today()
        controller = BaseCalendar(
            conn=conn, year=today.year, month=today.month, eid=filter_user_id)
    controller.create_calendar()

    context = {'controller': controller}

    context['template'] = template
    return context


@login_required(setGroupContext=True)
@render_response()
def load_history(request, year, month, day, conn=None, **kwargs):
    """ The data for a particular date that is loaded into the center panel """

    template = "webclient/history/history_details.html"

    # get page
    page = int(request.GET.get('page', 1))

    filter_user_id = request.session.get('user_id')
    controller = BaseCalendar(
        conn=conn, year=year, month=month, day=day, eid=filter_user_id)
    controller.get_items(page)

    context = {'controller': controller}
    context['template'] = template
    return context


def getObjectUrl(conn, obj):
    """
    This provides a url to browse to the specified omero.model.ObjectI P/D/I,
    S/P, FileAnnotation etc. used to display results from the scripting
    service
    E.g webclient/userdata/?path=image-12601
    If the object is a file annotation, try to browse to the parent P/D/I
    """
    base_url = reverse(viewname="load_template", args=['userdata'])

    # if we have a File Annotation, then we want our URL to be for the parent
    # object...
    if isinstance(obj, omero.model.FileAnnotationI):
        fa = conn.getObject("Annotation", obj.id.val)
        for ptype in ['project', 'dataset', 'image']:
            links = list(fa.getParentLinks(ptype))
            if len(links) > 0:
                obj = links[0].parent
                break

    if obj.__class__.__name__ in (
            "ImageI", "DatasetI", "ProjectI", "ScreenI", "PlateI", "WellI"):
        otype = obj.__class__.__name__[:-1].lower()
        base_url += "?show=%s-%s" % (otype, obj.id.val)
        return base_url


######################
# Activities window & Progressbar
def update_callback(request, cbString, **kwargs):
    """Update a callback handle with  key/value pairs"""
    for key, value in kwargs.iteritems():
        request.session['callback'][cbString][key] = value


@login_required()
@render_response()
def activities(request, conn=None, **kwargs):
    """
    This refreshes callback handles (delete, scripts, chgrp etc) and provides
    html to update Activities window & Progressbar.
    The returned html contains details for ALL callbacks in web session,
    regardless of their status.
    We also add counts of jobs, failures and 'in progress' to update status
    bar.
    """

    in_progress = 0
    failure = 0
    new_results = []
    _purgeCallback(request)

    # If we have a jobId, just process that (Only chgrp supported)
    jobId = request.GET.get('jobId', None)
    if jobId is not None:
        jobId = str(jobId)
        prx = omero.cmd.HandlePrx.checkedCast(conn.c.ic.stringToProxy(jobId))
        rsp = prx.getResponse()
        if rsp is not None:
            rv = chgrpMarshal(conn, rsp)
            rv['finished'] = True
        else:
            rv = {'finished': False}
        return rv

    # test each callback for failure, errors, completion, results etc
    for cbString in request.session.get('callback').keys():
        callbackDict = request.session['callback'][cbString]
        job_type = callbackDict['job_type']

        status = callbackDict['status']
        if status == "failed":
            failure += 1

        request.session.modified = True

        # update chgrp
        if job_type == 'chgrp':
            if status not in ("failed", "finished"):
                rsp = None
                try:
                    prx = omero.cmd.HandlePrx.checkedCast(
                        conn.c.ic.stringToProxy(cbString))
                    rsp = prx.getResponse()
                    close_handle = False
                    try:
                        # if response is None, then we're still in progress,
                        # otherwise...
                        if rsp is not None:
                            close_handle = True
                            new_results.append(cbString)
                            if isinstance(rsp, omero.cmd.ERR):
                                rsp_params = ", ".join(
                                    ["%s: %s" % (k, v) for k, v in
                                     rsp.parameters.items()])
                                logger.error("chgrp failed with: %s"
                                             % rsp_params)
                                update_callback(
                                    request, cbString,
                                    status="failed",
                                    report="%s %s" % (rsp.name, rsp_params),
                                    error=1)
                            elif isinstance(rsp, omero.cmd.OK):
                                update_callback(
                                    request, cbString,
                                    status="finished")
                        else:
                            in_progress += 1
                    finally:
                        prx.close(close_handle)
                except:
                    logger.info(
                        "Activities chgrp handle not found: %s" % cbString)
                    continue
        elif job_type == 'send_email':
            if status not in ("failed", "finished"):
                rsp = None
                try:
                    prx = omero.cmd.HandlePrx.checkedCast(
                        conn.c.ic.stringToProxy(cbString))
                    callback = omero.callbacks.CmdCallbackI(
                        conn.c, prx, foreground_poll=True)
                    rsp = callback.getResponse()
                    close_handle = False
                    try:
                        # if response is None, then we're still in progress,
                        # otherwise...
                        if rsp is not None:
                            close_handle = True
                            new_results.append(cbString)

                            if isinstance(rsp, omero.cmd.ERR):
                                rsp_params = ", ".join(
                                    ["%s: %s" % (k, v)
                                     for k, v in rsp.parameters.items()])
                                logger.error("send_email failed with: %s"
                                             % rsp_params)
                                update_callback(
                                    request, cbString,
                                    status="failed",
                                    report={'error': rsp_params},
                                    error=1)
                            else:
                                total = (rsp.success + len(rsp.invalidusers) +
                                         len(rsp.invalidemails))
                                update_callback(
                                    request, cbString,
                                    status="finished",
                                    rsp={'success': rsp.success,
                                         'total': total})
                                if (len(rsp.invalidusers) > 0 or
                                        len(rsp.invalidemails) > 0):
                                    invalidusers = [
                                        e.getFullName() for e in list(
                                            conn.getObjects(
                                                "Experimenter",
                                                rsp.invalidusers))]
                                    update_callback(
                                        request, cbString,
                                        report={
                                            'invalidusers': invalidusers,
                                            'invalidemails': rsp.invalidemails
                                        })
                        else:
                            in_progress += 1
                    finally:
                        callback.close(close_handle)
                except:
                    logger.error(traceback.format_exc())
                    logger.info("Activities send_email handle not found: %s"
                                % cbString)

        # update delete
        elif job_type == 'delete':
            if status not in ("failed", "finished"):
                try:
                    handle = omero.cmd.HandlePrx.checkedCast(
                        conn.c.ic.stringToProxy(cbString))
                    cb = omero.callbacks.CmdCallbackI(
                        conn.c, handle, foreground_poll=True)
                    rsp = cb.getResponse()
                    close_handle = False
                    try:
                        if not rsp:  # Response not available
                            update_callback(
                                request, cbString,
                                error=0,
                                status="in progress",
                                dreport=_formatReport(handle))
                            in_progress += 1
                        else:  # Response available
                            close_handle = True
                            new_results.append(cbString)
                            rsp = cb.getResponse()
                            err = isinstance(rsp, omero.cmd.ERR)
                            if err:
                                update_callback(
                                    request, cbString,
                                    error=1,
                                    status="failed",
                                    dreport=_formatReport(handle))
                                failure += 1
                            else:
                                update_callback(
                                    request, cbString,
                                    error=0,
                                    status="finished",
                                    dreport=_formatReport(handle))
                    finally:
                        cb.close(close_handle)
                except Ice.ObjectNotExistException:
                    update_callback(
                        request, cbString,
                        error=0,
                        status="finished",
                        dreport=None)
                except Exception, x:
                    logger.error(traceback.format_exc())
                    logger.error("Status job '%s'error:" % cbString)
                    update_callback(
                        request, cbString,
                        error=1,
                        status="failed",
                        dreport=str(x))
                    failure += 1

        # update scripts
        elif job_type == 'script':
            # if error on runScript, the cbString is not a ProcessCallback...
            if not cbString.startswith('ProcessCallback'):
                continue  # ignore
            if status not in ("failed", "finished"):
                logger.info("Check callback on script: %s" % cbString)
                proc = omero.grid.ScriptProcessPrx.checkedCast(
                    conn.c.ic.stringToProxy(cbString))
                cb = omero.scripts.ProcessCallbackI(conn.c, proc)
                # check if we get something back from the handle...
                if cb.block(0):  # ms.
                    cb.close()
                    try:
                        # we can only retrieve this ONCE - must save results
                        results = proc.getResults(0, conn.SERVICE_OPTS)
                        update_callback(request, cbString, status="finished")
                        new_results.append(cbString)
                    except Exception, x:
                        logger.error(traceback.format_exc())
                        continue
                    # value could be rstring, rlong, robject
                    rMap = {}
                    for key, value in results.items():
                        v = value.getValue()
                        if key in ("stdout", "stderr", "Message"):
                            if key in ('stderr', 'stdout'):
                                # just save the id of original file
                                v = v.id.val
                            update_kwargs = {key: v}
                            update_callback(request, cbString, **update_kwargs)
                        else:
                            if hasattr(v, "id"):
                                # do we have an object (ImageI,
                                # FileAnnotationI etc)
                                obj_data = {
                                    'id': v.id.val,
                                    'type': v.__class__.__name__[:-1]}
                                obj_data['browse_url'] = getObjectUrl(conn, v)
                                if v.isLoaded() and hasattr(v, "file"):
                                    # try:
                                    mimetypes = {
                                        'image/png': 'png',
                                        'image/jpeg': 'jpeg',
                                        'text/plain': 'text'}
                                    if v.file.mimetype.val in mimetypes:
                                        obj_data['fileType'] = mimetypes[
                                            v.file.mimetype.val]
                                        obj_data['fileId'] = v.file.id.val
                                    obj_data['name'] = v.file.name.val
                                    # except:
                                    #    pass
                                if v.isLoaded() and hasattr(v, "name"):
                                    # E.g Image, OriginalFile etc
                                    name = unwrap(v.name)
                                    if name is not None:
                                        # E.g. FileAnnotation has null name
                                        obj_data['name'] = name
                                rMap[key] = obj_data
                            else:
                                rMap[key] = v
                    update_callback(request, cbString, results=rMap)
                else:
                    in_progress += 1

    # having updated the request.session, we can now prepare the data for http
    # response
    rv = {}
    for cbString in request.session.get('callback').keys():
        # make a copy of the map in session, so that we can replace non
        # json-compatible objects, without modifying session
        rv[cbString] = copy.copy(request.session['callback'][cbString])

    # return json (used for testing)
    if 'template' in kwargs and kwargs['template'] == 'json':
        for cbString in request.session.get('callback').keys():
            rv[cbString]['start_time'] = str(
                request.session['callback'][cbString]['start_time'])
        rv['inprogress'] = in_progress
        rv['failure'] = failure
        rv['jobs'] = len(request.session['callback'])
        return JsonResponse(rv)  # json

    jobs = []
    new_errors = False
    for key, data in rv.items():
        # E.g. key: ProcessCallback/39f77932-c447-40d8-8f99-910b5a531a25 -t:tcp -h 10.211.55.2 -p 54727:tcp -h 10.37.129.2 -p 54727:tcp -h 10.12.2.21 -p 54727  # noqa
        # create id we can use as html id,
        # E.g. 39f77932-c447-40d8-8f99-910b5a531a25
        if len(key.split(" ")) > 0:
            htmlId = key.split(" ")[0]
            if len(htmlId.split("/")) > 1:
                htmlId = htmlId.split("/")[1]
        rv[key]['id'] = htmlId
        rv[key]['key'] = key
        if key in new_results:
            rv[key]['new'] = True
            if 'error' in data and data['error'] > 0:
                new_errors = True
        jobs.append(rv[key])

    jobs.sort(key=lambda x: x['start_time'], reverse=True)
    context = {
        'sizeOfJobs': len(request.session['callback']),
        'jobs': jobs,
        'inprogress': in_progress,
        'new_results': len(new_results),
        'new_errors': new_errors,
        'failure': failure}

    context['template'] = "webclient/activities/activitiesContent.html"
    return context


@login_required()
def activities_update(request, action, **kwargs):
    """
    If the above 'action' == 'clean' then we clear jobs from
    request.session['callback'] either a single job (if 'jobKey' is specified
    in POST) or all jobs (apart from those in progress)
    """

    request.session.modified = True

    if action == "clean":
        if 'jobKey' in request.POST:
            jobId = request.POST.get('jobKey')
            rv = {}
            if jobId in request.session['callback']:
                del request.session['callback'][jobId]
                request.session.modified = True
                rv['removed'] = True
            else:
                rv['removed'] = False
            return JsonResponse(rv)
        else:
            for key, data in request.session['callback'].items():
                if data['status'] != "in progress":
                    del request.session['callback'][key]
    return HttpResponse("OK")

##############################################################################
# User Photo


@login_required()
def avatar(request, oid=None, conn=None, **kwargs):
    """ Returns the experimenter's photo """
    photo = conn.getExperimenterPhoto(oid)
    return HttpResponse(photo, content_type='image/jpeg')

##############################################################################
# webgateway extention


@login_required()
def image_viewer(request, iid, share_id=None, **kwargs):
    """ Delegates to webgateway, using share connection if appropriate """
    kwargs['viewport_server'] = (
        share_id is not None and reverse("webindex")+share_id or
        reverse("webindex"))
    # remove any trailing slash
    kwargs['viewport_server'] = kwargs['viewport_server'].rstrip('/')
    return webgateway_views.full_viewer(request, iid, **kwargs)


##############################################################################
# scripting service....
@login_required()
@render_response()
def list_scripts(request, conn=None, **kwargs):
    """ List the available scripts - Just officical scripts for now """
    scriptService = conn.getScriptService()
    scripts = scriptService.getScripts()

    # group scripts into 'folders' (path), named by parent folder name
    scriptMenu = {}
    scripts_to_ignore = request.session.get('server_settings') \
                                       .get('scripts_to_ignore').split(",")
    for s in scripts:
        scriptId = s.id.val
        path = s.path.val
        name = s.name.val
        fullpath = os.path.join(path, name)
        if fullpath in scripts_to_ignore:
            logger.info('Ignoring script %r' % fullpath)
            continue

        # We want to build a hierarchical <ul> <li> structure
        # Each <ul> is a {}, each <li> is either a script 'name': <id> or
        # directory 'name': {ul}

        ul = scriptMenu
        dirs = fullpath.split(os.path.sep)
        for l, d in enumerate(dirs):
            if len(d) == 0:
                continue
            if d not in ul:
                # if last component in path:
                if l+1 == len(dirs):
                    ul[d] = scriptId
                else:
                    ul[d] = {}
            ul = ul[d]

    # convert <ul> maps into lists and sort

    def ul_to_list(ul):
        dir_list = []
        for name, value in ul.items():
            if isinstance(value, dict):
                # value is a directory
                dir_list.append({'name': name, 'ul': ul_to_list(value)})
            else:
                dir_list.append({'name': name, 'id': value})
        dir_list.sort(key=lambda x: x['name'].lower())
        return dir_list

    scriptList = ul_to_list(scriptMenu)

    # If we have a single top-level directory, we can skip it
    if len(scriptList) == 1:
        scriptList = scriptList[0]['ul']

    return scriptList


@login_required()
@render_response()
def script_ui(request, scriptId, conn=None, **kwargs):
    """
    Generates an html form for the parameters of a defined script.
    """
    scriptService = conn.getScriptService()

    try:
        params = scriptService.getParams(long(scriptId))
    except Exception, ex:
        if ex.message.lower().startswith("no processor available"):
            return {'template': 'webclient/scripts/no_processor.html',
                    'scriptId': scriptId}
        raise ex
    if params is None:
        return HttpResponse()

    paramData = {}

    paramData["id"] = long(scriptId)
    paramData["name"] = params.name.replace("_", " ")
    paramData["description"] = params.description
    paramData["authors"] = ", ".join([a for a in params.authors])
    paramData["contact"] = params.contact
    paramData["version"] = params.version
    paramData["institutions"] = ", ".join([i for i in params.institutions])

    inputs = []     # use a list so we can sort by 'grouping'
    Data_TypeParam = None
    IDsParam = None
    for key, param in params.inputs.items():
        i = {}
        i["name"] = key.replace("_", " ")
        i["key"] = key
        if not param.optional:
            i["required"] = True
        i["description"] = param.description
        if param.min:
            i["min"] = str(param.min.getValue())
        if param.max:
            i["max"] = str(param.max.getValue())
        if param.values:
            i["options"] = [v.getValue() for v in param.values.getValue()]
        if param.useDefault:
            i["default"] = unwrap(param.prototype)
            if isinstance(i["default"], omero.model.IObject):
                i["default"] = None
        pt = unwrap(param.prototype)
        if pt.__class__.__name__ == 'dict':
            i["map"] = True
        elif pt.__class__.__name__ == 'list':
            i["list"] = True
            if "default" in i:
                i["default"] = i["default"][0]
        elif isinstance(pt, bool):
            i["boolean"] = True
        elif isinstance(pt, int) or isinstance(pt, long):
            # will stop the user entering anything other than numbers.
            i["number"] = "number"
        elif isinstance(pt, float):
            i["number"] = "float"

        # if we got a value for this key in the page request, use this as
        # default
        if request.GET.get(key, None) is not None:
            i["default"] = request.GET.get(key, None)

        # E.g  ""  (string) or [0] (int list) or 0.0 (float)
        i["prototype"] = unwrap(param.prototype)
        i["grouping"] = param.grouping
        inputs.append(i)

        if key == "IDs":
            IDsParam = i           # remember these...
        if key == "Data_Type":
            Data_TypeParam = i
    inputs.sort(key=lambda i: i["grouping"])

    # if we have Data_Type param - use the request parameters to populate IDs
    if (Data_TypeParam is not None and IDsParam is not None and
            "options" in Data_TypeParam):
        IDsParam["default"] = ""
        for dtype in Data_TypeParam["options"]:
            if request.GET.get(dtype, None) is not None:
                Data_TypeParam["default"] = dtype
                IDsParam["default"] = request.GET.get(dtype, "")
                break       # only use the first match
        # if we've not found a match, check whether we have "Well" selected
        if (len(IDsParam["default"]) == 0 and
                request.GET.get("Well", None) is not None):
            if "Image" in Data_TypeParam["options"]:
                wellIds = [long(j) for j in request.GET.get(
                           "Well", None).split(",")]
                wellIdx = 0
                try:
                    wellIdx = int(request.GET.get("Index", 0))
                except:
                    pass
                wells = conn.getObjects("Well", wellIds)
                imgIds = [str(w.getImage(wellIdx).getId()) for w in wells]
                Data_TypeParam["default"] = "Image"
                IDsParam["default"] = ",".join(imgIds)

    # try to determine hierarchies in the groupings - ONLY handle 1 hierarchy
    # level now (not recursive!)
    for i in range(len(inputs)):
        if len(inputs) <= i:
            # we may remove items from inputs as we go - need to check
            break
        param = inputs[i]
        grouping = param["grouping"]    # E.g  03
        param['children'] = list()
        while len(inputs) > i+1:
            nextGrp = inputs[i+1]["grouping"]  # E.g. 03.1
            if nextGrp.split(".")[0] == grouping:
                param['children'].append(inputs[i+1])
                inputs.pop(i+1)
            else:
                break

    paramData["inputs"] = inputs

    return {
        'template': 'webclient/scripts/script_ui.html',
        'paramData': paramData,
        'scriptId': scriptId}


@login_required()
@render_response()
def figure_script(request, scriptName, conn=None, **kwargs):
    """
    Show a UI for running figure scripts
    """

    imageIds = request.GET.get('Image', None)    # comma - delimited list
    datasetIds = request.GET.get('Dataset', None)
    wellIds = request.GET.get('Well', None)

    if wellIds is not None:
        wellIds = [long(i) for i in wellIds.split(",")]
        wells = conn.getObjects("Well", wellIds)
        wellIdx = getIntOrDefault(request, 'Index', 0)
        imageIds = [str(w.getImage(wellIdx).getId()) for w in wells]
        imageIds = ",".join(imageIds)
    if imageIds is None and datasetIds is None:
        return HttpResponse(
            "Need to specify /?Image=1,2 or /?Dataset=1,2 or /?Well=1,2")

    def validateIds(dtype, ids):
        ints = [int(oid) for oid in ids.split(",")]
        validObjs = {}
        for obj in conn.getObjects(dtype, ints):
            validObjs[obj.id] = obj
        filteredIds = [iid for iid in ints if iid in validObjs.keys()]
        if len(filteredIds) == 0:
            raise Http404("No %ss found with IDs %s" % (dtype, ids))
        else:
            # Now we can specify group context - All should be same group
            gid = validObjs.values()[0].getDetails().group.id.val
            conn.SERVICE_OPTS.setOmeroGroup(gid)
        return filteredIds, validObjs

    context = {}

    if imageIds is not None:
        imageIds, validImages = validateIds("Image", imageIds)
        context['idString'] = ",".join([str(i) for i in imageIds])
        context['dtype'] = "Image"
    if datasetIds is not None:
        datasetIds, validDatasets = validateIds("Dataset", datasetIds)
        context['idString'] = ",".join([str(i) for i in datasetIds])
        context['dtype'] = "Dataset"

    if scriptName == "SplitView":
        scriptPath = "/omero/figure_scripts/Split_View_Figure.py"
        template = "webclient/scripts/split_view_figure.html"
        # Lookup Tags & Datasets (for row labels)
        imgDict = []    # A list of data about each image.
        for iId in imageIds:
            data = {'id': iId}
            img = validImages[iId]
            data['name'] = img.getName()
            tags = [ann.getTextValue() for ann in img.listAnnotations()
                    if ann._obj.__class__ == omero.model.TagAnnotationI]
            data['tags'] = tags
            data['datasets'] = [d.getName() for d in img.listParents()]
            imgDict.append(data)

        # Use the first image as a reference
        image = validImages[imageIds[0]]
        context['imgDict'] = imgDict
        context['image'] = image
        context['channels'] = image.getChannels()

    elif scriptName == "Thumbnail":
        scriptPath = "/omero/figure_scripts/Thumbnail_Figure.py"
        template = "webclient/scripts/thumbnail_figure.html"

        def loadImageTags(imageIds):
            tagLinks = conn.getAnnotationLinks("Image", parent_ids=imageIds)
            linkMap = {}    # group tags. {imageId: [tags]}
            tagMap = {}
            for iId in imageIds:
                linkMap[iId] = []
            for l in tagLinks:
                c = l.getChild()
                if c._obj.__class__ == omero.model.TagAnnotationI:
                    tagMap[c.id] = c
                    linkMap[l.getParent().id].append(c)
            imageTags = []
            for iId in imageIds:
                imageTags.append({'id': iId, 'tags': linkMap[iId]})
            tags = []
            for tId, t in tagMap.items():
                tags.append(t)
            return imageTags, tags

        thumbSets = []  # multiple collections of images
        tags = []
        figureName = "Thumbnail_Figure"
        if datasetIds is not None:
            for d in conn.getObjects("Dataset", datasetIds):
                imgIds = [i.id for i in d.listChildren()]
                imageTags, ts = loadImageTags(imgIds)
                thumbSets.append({
                    'name': d.getName(), 'imageTags': imageTags})
                tags.extend(ts)
            figureName = thumbSets[0]['name']
        else:
            imageTags, ts = loadImageTags(imageIds)
            thumbSets.append({'name': 'images', 'imageTags': imageTags})
            tags.extend(ts)
            parent = conn.getObject("Image", imageIds[0]).getParent()
            figureName = parent.getName() or "Thumbnail Figure"
            context['parent_id'] = parent.getId()
        uniqueTagIds = set()      # remove duplicates
        uniqueTags = []
        for t in tags:
            if t.id not in uniqueTagIds:
                uniqueTags.append(t)
                uniqueTagIds.add(t.id)
        uniqueTags.sort(key=lambda x: x.getTextValue().lower())
        context['thumbSets'] = thumbSets
        context['tags'] = uniqueTags
        context['figureName'] = figureName.replace(" ", "_")

    elif scriptName == "MakeMovie":
        scriptPath = "/omero/export_scripts/Make_Movie.py"
        template = "webclient/scripts/make_movie.html"

        # expect to run on a single image at a time
        image = conn.getObject("Image", imageIds[0])
        # remove extension (if 3 chars or less)
        movieName = image.getName().rsplit(".", 1)
        if len(movieName) > 1 and len(movieName[1]) > 3:
            movieName = ".".join(movieName)
        else:
            movieName = movieName[0]
        # make sure name is not a path
        context['movieName'] = os.path.basename(movieName)
        chs = []
        for c in image.getChannels():
            chs.append({
                'active': c.isActive(),
                'color': c.getColor().getHtml(),
                'label': c.getLabel()
                })
        context['channels'] = chs
        context['sizeT'] = image.getSizeT()
        context['sizeZ'] = image.getSizeZ()

    scriptService = conn.getScriptService()
    scriptId = scriptService.getScriptID(scriptPath)
    if (scriptId < 0):
        raise AttributeError("No script found for path '%s'" % scriptPath)

    context['template'] = template
    context['scriptId'] = scriptId
    return context


@login_required()
@render_response()
def fileset_check(request, action, conn=None, **kwargs):
    """
    Check whether Images / Datasets etc contain partial Multi-image filesets.
    Used by chgrp or delete dialogs to test whether we can perform this
    'action'.
    """
    dtypeIds = {}
    for dtype in ("Image", "Dataset", "Project"):
        ids = request.GET.get(dtype, None)
        if ids is not None:
            dtypeIds[dtype] = [int(i) for i in ids.split(",")]
    splitFilesets = conn.getContainerService().getImagesBySplitFilesets(
        dtypeIds, None, conn.SERVICE_OPTS)

    splits = []
    for fsId, splitIds in splitFilesets.items():
        splits.append({
            'id': fsId,
            'attempted_iids': splitIds[True],
            'blocking_iids': splitIds[False]})

    context = {"split_filesets": splits}
    context['action'] = action
    if action == 'chgrp':
        context['action'] = 'move'
    context['template'] = ("webclient/activities/"
                           "fileset_check_dialog_content.html")

    return context


def getAllObjects(conn, project_ids, dataset_ids, image_ids, screen_ids,
                  plate_ids, experimenter_id):
    """
    Given a list of containers and images, calculate all the descendants
    and necessary siblings (for any filesets)
    """
    # TODO Handle None inputs, maybe add defaults
    params = omero.sys.ParametersI()
    qs = conn.getQueryService()

    project_ids = set(project_ids)
    dataset_ids = set(dataset_ids)
    image_ids = set(image_ids)
    fileset_ids = set([])
    plate_ids = set(plate_ids)
    screen_ids = set(screen_ids)

    # Get any datasets for projects
    if project_ids:
        params.map = {}
        params.map['pids'] = rlist([rlong(x) for x in list(project_ids)])
        q = '''
            select pdlink.child.id
            from ProjectDatasetLink pdlink
            where pdlink.parent.id in (:pids)
            '''
        for e in qs.projection(q, params, conn.SERVICE_OPTS):
            dataset_ids.add(e[0].val)

    # Get any plates for screens
    if screen_ids:
        params.map = {}
        params.map['sids'] = rlist([rlong(x) for x in screen_ids])
        q = '''
            select splink.child.id
            from ScreenPlateLink splink
            where splink.parent.id in (:sids)
            '''
        for e in qs.projection(q, params, conn.SERVICE_OPTS):
            plate_ids.add(e[0].val)

    # Get any images for datasets
    if dataset_ids:
        params.map = {}
        params.map['dids'] = rlist([rlong(x) for x in dataset_ids])
        q = '''
            select dilink.child.id,
                   dilink.child.fileset.id
            from DatasetImageLink dilink
            where dilink.parent.id in (:dids)
            '''
        for e in qs.projection(q, params, conn.SERVICE_OPTS):
            image_ids.add(e[0].val)
            # Some images in Dataset may not have fileset
            if e[1] is not None:
                fileset_ids.add(e[1].val)

    # Get any images for plates
    # TODO Seemed no need to add the filesets for plates as it isn't possible
    # to link it from outside of its plate. This may be true for the client,
    # but it certainly isn't true for the model so maybe allow this to also get
    # filesets
    if plate_ids:
        params.map = {}
        params.map['plids'] = rlist([rlong(x) for x in plate_ids])
        q = '''
            select ws.image.id
            from WellSample ws
            join ws.plateAcquisition pa
            where pa.plate.id in (:plids)
            '''
        for e in qs.projection(q, params, conn.SERVICE_OPTS):
            image_ids.add(e[0].val)

    # Get any extra images due to filesets
    if fileset_ids:
        params.map = {}
        params.map['fsids'] = rlist([rlong(x) for x in fileset_ids])
        q = '''
            select image.id
            from Image image
            left outer join image.datasetLinks dilink
            where image.fileset.id in (select fs.id
                                       from Image im
                                       join im.fileset fs
                                       where fs.id in (:fsids)
                                       group by fs.id
                                       having count(im.id)>1)
            '''
        for e in qs.projection(q, params, conn.SERVICE_OPTS):
            image_ids.add(e[0].val)

    # Get any additional datasets that may need updating as their children have
    # been snatched.
    # TODO Need to differentiate which orphaned directories need refreshing
    extra_dataset_ids = set([])
    extra_orphaned = False
    if image_ids:
        params.map = {
            'iids': rlist([rlong(x) for x in image_ids]),
        }

        exclude_datasets = ''
        if dataset_ids:
            params.map['dids'] = rlist([rlong(x) for x in dataset_ids])
            # Make sure to allow parentless results as well as those
            # that do not match a dataset being removed
            exclude_datasets = '''
                               and (
                                    dilink.parent.id not in (:dids)
                                    or dilink.parent.id = null
                                   )
                               '''

        q = '''
            select distinct dilink.parent.id
            from Image image
            left outer join image.datasetLinks dilink
            where image.id in (:iids)
            %s
            and (select count(dilink2.child.id)
                 from DatasetImageLink dilink2
                 where dilink2.parent.id = dilink.parent.id
                 and dilink2.child.id not in (:iids)) = 0
            ''' % exclude_datasets

        for e in qs.projection(q, params, conn.SERVICE_OPTS):
            if e:
                extra_dataset_ids.add(e[0].val)
            else:
                extra_orphaned = True

    # Get any additional projects that may need updating as their children have
    # been snatched. There is no need to check for orphans because if a dataset
    # is being removed from somewhere else, it can not exist as an orphan.
    extra_project_ids = set([])
    if dataset_ids:
        params.map = {
            'dids': rlist([rlong(x) for x in dataset_ids])
        }

        exclude_projects = ''
        if project_ids:
            params.map['pids'] = rlist([rlong(x) for x in project_ids])
            exclude_projects = 'and pdlink.parent.id not in (:pids)'

        q = '''
            select distinct pdlink.parent.id
            from ProjectDatasetLink pdlink
            where pdlink.child.id in (:dids)
            %s
            and (select count(pdlink2.child.id)
                 from ProjectDatasetLink pdlink2
                 where pdlink2.parent.id = pdlink.parent.id
                 and pdlink2.child.id not in (:dids)) = 0
            ''' % exclude_projects

        for e in qs.projection(q, params, conn.SERVICE_OPTS):
            extra_project_ids.add(e[0].val)

    # We now have the complete list of objects that will change group
    # We also have an additional list of datasets/projects that may have had
    # snatched children and thus may need updating in the client if the
    # dataset/project has gone from N to 0 children

    result = {
        # These objects are completely removed
        'remove': {
            'project': list(project_ids),
            'dataset': list(dataset_ids),
            'screen': list(screen_ids),
            'plate': list(plate_ids),
            'image': list(image_ids)
        },
        # These objects now have no children
        'childless': {
            'project': list(extra_project_ids),
            'dataset': list(extra_dataset_ids),
            'orphaned': extra_orphaned
        }
    }
    return result


@require_POST
@login_required()
def chgrpDryRun(request, conn=None, **kwargs):

    group_id = getIntOrDefault(request, 'group_id', None)
    targetObjects = {}
    dtypes = ["Project", "Dataset", "Image", "Screen", "Plate", "Fileset"]
    for dtype in dtypes:
        oids = request.POST.get(dtype, None)
        if oids is not None:
            obj_ids = [int(oid) for oid in oids.split(",")]
            targetObjects[dtype] = obj_ids

    handle = conn.chgrpDryRun(targetObjects, group_id)
    jobId = str(handle)
    return HttpResponse(jobId)


@login_required()
def chgrp(request, conn=None, **kwargs):
    """
    Moves data to a new group, using the chgrp queue.
    Handles submission of chgrp form: all data in POST.
    Adds the callback handle to the request.session['callback']['jobId']
    """
    # Get the target group_id
    group_id = getIntOrDefault(request, 'group_id', None)
    if group_id is None:
        raise AttributeError("chgrp: No group_id specified")
    group_id = long(group_id)

    def getObjectOwnerId(r):
        for t in ["Dataset", "Image", "Plate"]:
            ids = r.POST.get(t, None)
            if ids is not None:
                for o in list(conn.getObjects(t, ids.split(","))):
                    return o.getDetails().owner.id.val

    group = conn.getObject("ExperimenterGroup", group_id)
    new_container_name = request.POST.get('new_container_name', None)
    new_container_type = request.POST.get('new_container_type', None)
    container_id = None

    # Context must be set to owner of data, E.g. to create links.
    ownerId = getObjectOwnerId(request)
    conn.SERVICE_OPTS.setOmeroUser(ownerId)
    if (new_container_name is not None and len(new_container_name) > 0 and
            new_container_type is not None):
        conn.SERVICE_OPTS.setOmeroGroup(group_id)
        container_id = conn.createContainer(
            new_container_type, new_container_name)
    # No new container, check if target is specified
    if container_id is None:
        # E.g. "dataset-234"
        target_id = request.POST.get('target_id', None)
        container_id = (target_id is not None and target_id.split("-")[1] or
                        None)
    dtypes = ["Project", "Dataset", "Image", "Screen", "Plate"]
    for dtype in dtypes:
        # Get all requested objects of this type
        oids = request.POST.get(dtype, None)
        if oids is not None:
            obj_ids = [int(oid) for oid in oids.split(",")]
            # TODO Doesn't the filesets only apply to images?
            # if 'filesets' are specified, make sure we move ALL Fileset Images
            fsIds = request.POST.getlist('fileset')
            if len(fsIds) > 0:
                # If a dataset is being moved and there is a split fileset
                # then those images need to go somewhere in the new
                if dtype == 'Dataset':
                    conn.regroupFilesets(dsIds=obj_ids, fsIds=fsIds)
                else:
                    for fs in conn.getObjects("Fileset", fsIds):
                        obj_ids.extend([i.id for i in fs.copyImages()])
                    obj_ids = list(set(obj_ids))    # remove duplicates
            logger.debug(
                "chgrp to group:%s %s-%s" % (group_id, dtype, obj_ids))
            handle = conn.chgrpObjects(dtype, obj_ids, group_id, container_id)
            jobId = str(handle)
            request.session['callback'][jobId] = {
                'job_type': "chgrp",
                'group': group.getName(),
                'to_group_id': group_id,
                'dtype': dtype,
                'obj_ids': obj_ids,
                'job_name': "Change group",
                'start_time': datetime.datetime.now(),
                'status': 'in progress'}
            request.session.modified = True

    # Update contains a list of images/containers that need to be
    # updated.

    project_ids = request.POST.get('Project', [])
    dataset_ids = request.POST.get('Dataset', [])
    image_ids = request.POST.get('Image', [])
    screen_ids = request.POST.get('Screen', [])
    plate_ids = request.POST.get('Plate', [])

    if project_ids:
        project_ids = [long(x) for x in project_ids.split(',')]
    if dataset_ids:
        dataset_ids = [long(x) for x in dataset_ids.split(',')]
    if image_ids:
        image_ids = [long(x) for x in image_ids.split(',')]
    if screen_ids:
        screen_ids = [long(x) for x in screen_ids.split(',')]
    if plate_ids:
        plate_ids = [long(x) for x in plate_ids.split(',')]

    # TODO Change this user_id to be an experimenter_id in the request as it
    # is possible that a user is chgrping data from another user so it is
    # that users orphaned that will need updating. Or maybe all orphaned
    # directories could potentially need updating?

    # Create a list of objects that have been changed by this operation. This
    # can be used by the client to visually update.
    update = getAllObjects(conn, project_ids, dataset_ids, image_ids,
                           screen_ids, plate_ids,
                           request.session.get('user_id'))

    # return HttpResponse("OK")
    return JsonResponse({'update': update})


@login_required(setGroupContext=True)
def script_run(request, scriptId, conn=None, **kwargs):
    """
    Runs a script using values in a POST
    """
    scriptService = conn.getScriptService()

    inputMap = {}

    sId = long(scriptId)

    try:
        params = scriptService.getParams(sId)
    except Exception, x:
        if x.message and x.message.startswith("No processor available"):
            # Delegate to run_script() for handling 'No processor available'
            rsp = run_script(
                request, conn, sId, inputMap, scriptName='Script')
            return JsonResponse(rsp)
        else:
            raise
    params = scriptService.getParams(sId)
    scriptName = params.name.replace("_", " ").replace(".py", "")

    logger.debug("Script: run with request.POST: %s" % request.POST)

    for key, param in params.inputs.items():
        prototype = param.prototype
        pclass = prototype.__class__

        # handle bool separately, since unchecked checkbox will not be in
        # request.POST
        if pclass == omero.rtypes.RBoolI:
            value = key in request.POST
            inputMap[key] = pclass(value)
            continue

        if pclass.__name__ == 'RMapI':
            keyName = "%s_key0" % key
            valueName = "%s_value0" % key
            row = 0
            paramMap = {}
            while keyName in request.POST:
                # the key and value don't have any data-type defined by
                # scripts - just use string
                k = str(request.POST[keyName])
                v = request.POST[valueName]
                if len(k) > 0 and len(v) > 0:
                    paramMap[str(k)] = v.encode('utf8')
                row += 1
                keyName = "%s_key%d" % (key, row)
                valueName = "%s_value%d" % (key, row)
            if len(paramMap) > 0:
                inputMap[key] = wrap(paramMap)
            continue

        if key in request.POST:
            if pclass == omero.rtypes.RListI:
                values = request.POST.getlist(key)
                if len(values) == 0:
                    continue
                if len(values) == 1:     # process comma-separated list
                    if len(values[0]) == 0:
                        continue
                    values = values[0].split(",")

                # try to determine 'type' of values in our list
                listClass = omero.rtypes.RStringI
                l = prototype.val     # list
                # check if a value type has been set (first item of prototype
                # list)
                if len(l) > 0:
                    listClass = l[0].__class__
                    if listClass == int(1).__class__:
                        listClass = omero.rtypes.rint
                    if listClass == long(1).__class__:
                        listClass = omero.rtypes.rlong

                # construct our list, using appropriate 'type'
                valueList = []
                for v in values:
                    try:
                        # RStringI() will encode any unicode
                        obj = listClass(v.strip())
                    except:
                        logger.debug("Invalid entry for '%s' : %s" % (key, v))
                        continue
                    if isinstance(obj, omero.model.IObject):
                        valueList.append(omero.rtypes.robject(obj))
                    else:
                        valueList.append(obj)
                inputMap[key] = omero.rtypes.rlist(valueList)

            # Handle other rtypes: String, Long, Int etc.
            else:
                value = request.POST[key]
                if len(value) == 0:
                    continue
                try:
                    inputMap[key] = pclass(value)
                except:
                    logger.debug("Invalid entry for '%s' : %s" % (key, value))
                    continue

    # If we have objects specified via 'IDs' and 'DataType', try to pick
    # correct group
    if 'IDs' in inputMap.keys() and 'Data_Type' in inputMap.keys():
        gid = conn.SERVICE_OPTS.getOmeroGroup()
        conn.SERVICE_OPTS.setOmeroGroup('-1')
        try:
            firstObj = conn.getObject(
                inputMap['Data_Type'].val, unwrap(inputMap['IDs'])[0])
            newGid = firstObj.getDetails().group.id.val
            conn.SERVICE_OPTS.setOmeroGroup(newGid)
        except Exception, x:
            logger.debug(traceback.format_exc())
            # if inputMap values not as expected or firstObj is None
            conn.SERVICE_OPTS.setOmeroGroup(gid)

    try:
        # Try/except in case inputs are not serializable, e.g. unicode
        logger.debug("Running script %s with "
                     "params %s" % (scriptName, inputMap))
    except:
        pass
    rsp = run_script(request, conn, sId, inputMap, scriptName)
    return JsonResponse(rsp)


@require_POST
@login_required()
def ome_tiff_script(request, imageId, conn=None, **kwargs):
    """
    Uses the scripting service (Batch Image Export script) to generate
    OME-TIFF for an image and attach this as a file annotation to the image.
    Script will show up in the 'Activities' for users to monitor and download
    result etc.
    """

    scriptService = conn.getScriptService()
    sId = scriptService.getScriptID(
        "/omero/export_scripts/Batch_Image_Export.py")

    image = conn.getObject("Image", imageId)
    if image is not None:
        gid = image.getDetails().group.id.val
        conn.SERVICE_OPTS.setOmeroGroup(gid)
    imageIds = [long(imageId)]
    inputMap = {'Data_Type': wrap('Image'), 'IDs': wrap(imageIds)}
    inputMap['Format'] = wrap('OME-TIFF')
    rsp = run_script(
        request, conn, sId, inputMap, scriptName='Create OME-TIFF')
    return JsonResponse(rsp)


def run_script(request, conn, sId, inputMap, scriptName='Script'):
    """
    Starts running a script, adding details to the request.session so that it
    shows up in the webclient Activities panel and results are available there
    etc.
    """
    request.session.modified = True
    scriptService = conn.getScriptService()
    try:
        handle = scriptService.runScript(
            sId, inputMap, None, conn.SERVICE_OPTS)
        # E.g. ProcessCallback/4ab13b23-22c9-4b5f-9318-40f9a1acc4e9 -t:tcp -h  10.37.129.2 -p 53154:tcp -h 10.211.55.2 -p 53154:tcp -h 10.12.1.230 -p 53154 # noqa
        jobId = str(handle)
        status = 'in progress'
        request.session['callback'][jobId] = {
            'job_type': "script",
            'job_name': scriptName,
            'start_time': datetime.datetime.now(),
            'status': status}
        request.session.modified = True
    except Exception, x:
        jobId = str(time())      # E.g. 1312803670.6076391
        if x.message and x.message.startswith("No processor available"):
            # omero.ResourceError
            logger.info(traceback.format_exc())
            error = "No Processor Available"
            status = 'no processor available'
            message = ""  # template displays message and link
        else:
            logger.error(traceback.format_exc())
            error = traceback.format_exc()
            status = 'failed'
            message = x.message
        # save the error to http session, for display in 'Activities' window
        request.session['callback'][jobId] = {
            'job_type': "script",
            'job_name': scriptName,
            'start_time': datetime.datetime.now(),
            'status': status,
            'Message': message,
            'error': error}
        return {'status': status, 'error': error}

    return {'jobId': jobId, 'status': status}


@login_required()
@render_response()
def ome_tiff_info(request, imageId, conn=None, **kwargs):
    """
    Query to see if we have an OME-TIFF attached to the image (assume only 1,
    since Batch Image Export will delete old ones)
    """
    # Any existing OME-TIFF will appear in list
    links = list(conn.getAnnotationLinks(
        "Image", [imageId], ns=omero.constants.namespaces.NSOMETIFF))
    rv = {}
    if len(links) > 0:
        # use highest ID === most recent
        links.sort(key=lambda x: x.getId(), reverse=True)
        annlink = links[0]
        created = annlink.creationEventDate()
        annId = annlink.getChild().getId()
        from omeroweb.webgateway.templatetags.common_filters import ago
        download = reverse("download_annotation", args=[annId])
        rv = {"created": str(created), "ago": ago(created), "id": annId,
              "download": download}
    return rv       # will get returned as json by default