def show_interactive(request, username, project_slug):
project = get_project(username, project_slug)
view_key = request.GET.get('view_key')
if view_key is None:
view_key = "no_view_key"
if not check_view_permission(project, request.user, view_key):
raise Http404
return render(request, 'interactive.html', {'project': project, 'view_key': view_key})
def details_project(request, project_slug):
project = get_project(request.user.username, project_slug)
files = []
for f in os.listdir(project.get_path()):
files.append({'name': f, 'size': os.path.getsize(os.path.join(project.get_path(), f))})
context = {
'project': project,
'project_files': files
}
return render(request, 'projects/details.html', context)
def list_projects(request):
action = request.POST.get('action')
if action == 'delete':
project = get_project(request.user.username, request.POST.get('slug'))
if project:
project.delete_project_path()
project.delete()
else:
raise Http404
context = {
'projects': Project.objects.filter(user=request.user),
}
return render(request, 'projects/list.html', context)
def download_zip(request, username, project_slug):
project = get_project(username, project_slug)
view_key = request.GET.get('view_key')
if view_key is None:
view_key = "no_view_key"
if not check_view_permission(project, request.user, view_key):
raise Http404
zip_io = io.BytesIO()
with zipfile.ZipFile(zip_io, mode='w', compression=zipfile.ZIP_DEFLATED) as backup_zip:
for f in os.listdir(project.get_path()):
backup_zip.write(os.path.join(project.get_path(), f), f)
response = HttpResponse(zip_io.getvalue(), content_type='application/x-zip-compressed')
response['Content-Disposition'] = 'attachment; filename=%s' % project.slug + ".zip"
response['Content-Length'] = zip_io.tell()
return response
def show_inspect(request, username, project_slug, inspection_type):
project = get_project(username, project_slug)
view_key = request.GET.get('view_key')
if view_key is None:
view_key = "no_view_key"
if not check_view_permission(project, request.user, view_key):
raise Http404
html_page = ''
if inspection_type == 'inspect':
html_page = 'charts'
elif inspection_type == 'geneclusters':
html_page = 'geneclusters'
return render(request, 'inspect.html', {'project': project,
'view_key': view_key,
'id': request.GET.get('id'),
'html_page': html_page
})
def share_project(request, project_slug):
project = get_project(request.user.username, project_slug)
action = request.POST.get('action')
if action == 'generate_link':
newlink = ProjectLink(project=project, link=get_random_string(length=16))
newlink.save()
context = {
'status': 'ok'
}
return JsonResponse(context)
if action == 'delete_link':
link = ProjectLink.objects.filter(project=project, link=request.POST.get('link'))
if link:
link.delete()
context = {
'status': 'ok'
}
return JsonResponse(context)
if action == 'set_public':
project.is_public = True if request.POST.get('permission') == 'true' else False
project.save(update_fields=["is_public"])
context = {
'status': 'ok'
}
return JsonResponse(context)
shared_teams = ProjectTeam.objects.filter(project=project)
if action == 'share_with_team':
team_id = request.POST.get('team_id')
if team_id:
team = Team.objects.get(id=team_id)
is_member = TeamUser.objects.filter(user=request.user, team=team)
already_shared = ProjectTeam.objects.filter(project=project, team=team)
if not already_shared and is_member:
ProjectTeam(project=project, team=team).save()
if action == 'delete_team' or action == 'set_team_write_permission':
team_id = request.POST.get('team_id')
if team_id:
team = Team.objects.get(id=team_id)
sharing = ProjectTeam.objects.get(project=project, team=team)
if sharing:
if action == 'delete_team':
sharing.delete()
elif action == 'set_team_write_permission':
sharing.can_write = True if request.POST.get('permission') == 'true' else False
sharing.save()
teams = Team.objects.filter(teamuser__user=request.user)
context = {
'project': project,
'shared_teams': shared_teams,
'teams': teams
}
return render(request, 'projects/share.html', context)
def ajax_handler(request, username, project_slug, view_key, requested_url):
if not request.is_ajax():
raise Http404
project = get_project(username, project_slug)
if not check_view_permission(project, request.user, view_key):
raise Http404
read_only = not check_write_permission(project, request.user)
bottle_request = utils.MockBottleRequest(django_request=request)
bottle_response = utils.MockBottleResponse()
interactive = None
if not requested_url.startswith('data/news'):
interactive = project.get_interactive(read_only=read_only)
bottleapp = BottleApplication(interactive, bottle_request, bottle_response)
if requested_url.startswith('data/init'):
download_zip_url = reverse('download_zip', args=[username, project_slug])
if view_key != 'no_view_key':
download_zip_url += '?view_key=' + view_key
default_view = interactive.default_view
default_order = interactive.p_meta['default_item_order']
autodraw = False
state_dict = None
if interactive.state_autoload:
state_dict = json.loads(interactive.states_table.states[interactive.state_autoload]['content'])
if state_dict['current-view'] in interactive.views:
default_view = state_dict['current-view']
if state_dict['order-by'] in interactive.p_meta['item_orders']:
default_order = state_dict['order-by']
autodraw = True
collection_dict = None
if interactive.collection_autoload:
collection_dict = json.loads(bottleapp.get_collection_dict(interactive.collection_autoload))
functions_sources = []
if interactive.mode == 'full' or interactive.mode == 'gene':
functions_sources = list(interactive.gene_function_call_sources)
elif interactive.mode == 'pan':
functions_sources = list(interactive.gene_clusters_function_sources)
return JsonResponse({ "title": project.name,
"description": interactive.p_meta['description'],
"item_orders": (default_order, interactive.p_meta['item_orders'][default_order], list(interactive.p_meta['item_orders'].keys())),
"views": (default_view, interactive.views[default_view], list(interactive.views.keys())),
"item_lengths": dict([tuple((c, interactive.splits_basic_info[c]['length']),) for c in interactive.splits_basic_info]),
"server_mode": True,
"mode": interactive.mode,
"read_only": interactive.read_only,
"bin_prefix": "Bin_",
"session_id": 0,
"layers_order": interactive.layers_order_data_dict,
"layers_information": interactive.layers_additional_data_dict,
"layers_information_default_order": interactive.layers_additional_data_keys,
"check_background_process": False,
"autodraw": autodraw,
"inspection_available": interactive.auxiliary_profile_data_available,
"sequences_available": True if interactive.split_sequences else False,
"functions_initialized": interactive.gene_function_calls_initiated,
"functions_sources": functions_sources,
"state": (interactive.state_autoload, state_dict),
"collection": collection_dict,
"samples": interactive.p_meta['samples'] if interactive.mode in ['full', 'refine'] else [],
"load_full_state": True,
"project": {
'username': project.user.username,
'fullname': project.user.userprofile.fullname if project.user.userprofile.fullname else project.user.username,
'user_avatar': gravatar(project.user.email),
'download_zip_url': download_zip_url
}
})
elif requested_url.startswith('data/view/'):
param = requested_url.split('/')[-1]
return HttpResponse(bottleapp.get_view_data(param), content_type='application/json')
elif requested_url.startswith('tree/'):
param = requested_url.split('/')[-1]
return HttpResponse(bottleapp.get_items_order(param), content_type='application/json')
elif requested_url.startswith('data/collections'):
return HttpResponse(bottleapp.get_collections(), content_type='application/json')
elif requested_url.startswith('data/collection/'):
param = requested_url.split('/')[-1]
return HttpResponse(bottleapp.get_collection_dict(param), content_type='application/json')
elif requested_url.startswith('store_collection'):
if not check_write_permission(project, request.user):
raise Http404
ret = HttpResponse(bottleapp.store_collections_dict(), content_type='application/json')
project.synchronize_num_collections(save=True)
return ret
elif requested_url.startswith('data/contig/'):
param = requested_url.split('/')[-1]
return HttpResponse(bottleapp.get_sequence_for_split(param), content_type='application/json')
elif requested_url.startswith('store_description'):
if not check_write_permission(project, request.user):
raise Http404
return HttpResponse(bottleapp.store_description(), content_type='application/json')
elif requested_url.startswith('state/all'):
return HttpResponse(bottleapp.state_all(), content_type='application/json')
elif requested_url.startswith('state/get'):
param = requested_url.split('/')[-1]
return HttpResponse(bottleapp.get_state(param), content_type='application/json')
elif requested_url.startswith('state/save'):
if not check_write_permission(project, request.user):
raise Http404
param = requested_url.split('/')[-1]
ret = HttpResponse(bottleapp.save_state(param), content_type='application/json')
project.synchronize_num_states(save=True)
return ret
elif requested_url.startswith('data/charts/'):
order_name = requested_url.split('/')[-2]
item_name = requested_url.split('/')[-1]
return HttpResponse(bottleapp.charts(order_name, item_name), content_type='application/json')
elif requested_url.startswith('data/geneclusters/'):
order_name = requested_url.split('/')[-2]
item_name = requested_url.split('/')[-1]
return HttpResponse(bottleapp.inspect_gene_cluster(order_name, item_name), content_type='application/json')
elif requested_url.startswith('data/get_AA_sequences_for_gene_cluster/'):
param = requested_url.split('/')[-1]
return HttpResponse(bottleapp.get_AA_sequences_for_gene_cluster(param), content_type='application/json')
elif requested_url.startswith('data/news'):
return HttpResponse(bottleapp.get_news(), content_type='application/json')
elif requested_url.startswith('data/gene'):
param = requested_url.split('/')[-1]
return HttpResponse(bottleapp.get_sequence_for_gene_call(param), content_type='application/json')
elif requested_url.startswith('data/completeness'):
return HttpResponse(bottleapp.completeness(), content_type='application/json')
elif requested_url.startswith('data/reroot_tree'):
return HttpResponse(bottleapp.reroot_tree(), content_type='application/json')
raise Http404