def project_page_data(request, project_guid):
"""Returns a JSON object containing information used by the project page:
::
json_response = {
'project': {..},
'familiesByGuid': {..},
'individualsByGuid': {..},
'samplesByGuid': {..},
}
Args:
project_guid (string): GUID of the Project to retrieve data for.
"""
project = get_project_and_check_permissions(project_guid, request.user)
update_project_from_json(project, {'last_accessed_date': timezone.now()})
response = _get_project_child_entities(project, request.user)
project_json = _get_json_for_project(project, request.user)
project_json['collaborators'] = get_json_for_project_collaborator_list(project)
project_json['locusListGuids'] = response['locusListsByGuid'].keys()
project_json['detailsLoaded'] = True
project_json.update(_get_json_for_variant_tag_types(project))
gene_ids = set()
for tag in project_json['discoveryTags']:
gene_ids.update(tag.get('transcripts', {}).keys())
response.update({
'projectsByGuid': {project_guid: project_json},
'genesById': get_genes(gene_ids),
})
return create_json_response(response)
def create_project_collaborator(request, project_guid):
project = get_project_and_check_permissions(project_guid,
request.user,
can_edit=True)
try:
user = _create_user(request)
except CreateUserException as e:
if e.existing_user:
return _update_existing_user(e.existing_user, project,
json.loads(request.body))
else:
return create_json_response({'error': str(e)},
status=e.status_code,
reason=str(e))
project.can_view_group.user_set.add(user)
return create_json_response({
'projectsByGuid': {
project_guid: {
'collaborators':
get_json_for_project_collaborator_list(project)
}
}
})
def _update_existing_user(user, project, request_json):
user.first_name = request_json.get('firstName') or ''
user.last_name = request_json.get('lastName') or ''
user.save()
project.can_view_group.user_set.add(user)
if request_json.get('hasEditPermissions'):
project.can_edit_group.user_set.add(user)
else:
project.can_edit_group.user_set.remove(user)
create_xbrowse_project_collaborator(
project,
user,
collaborator_type='manager'
if request_json.get('hasEditPermissions') else 'collaborator')
return create_json_response({
'projectsByGuid': {
project.guid: {
'collaborators':
get_json_for_project_collaborator_list(project)
}
}
})
def delete_project_collaborator(request, project_guid, username):
project = get_project_and_check_permissions(project_guid, request.user, permission_level=CAN_EDIT)
user = User.objects.get(username=username)
project.can_view_group.user_set.remove(user)
project.can_edit_group.user_set.remove(user)
return create_json_response({
'projectsByGuid': {project_guid: {'collaborators': get_json_for_project_collaborator_list(project)}}
})
def _update_existing_user(user, project, request_json):
project.can_view_group.user_set.add(user)
if request_json.get('hasEditPermissions'):
project.can_edit_group.user_set.add(user)
else:
project.can_edit_group.user_set.remove(user)
return create_json_response({
'projectsByGuid': {
project.guid: {
'collaborators':
get_json_for_project_collaborator_list(user, project)
}
}
})
def create_project_collaborator(request, project_guid):
project = get_project_and_check_permissions(project_guid,
request.user,
can_edit=True)
if project.workspace_name:
raise PermissionDenied(
'Adding collaborators directly in seqr is disabled. Users can be managed from the associated AnVIL workspace'
)
request_json = json.loads(request.body)
if not request_json.get('email'):
return create_json_response({'error': 'Email is required'}, status=400)
existing_user = User.objects.filter(
email__iexact=request_json['email']).first()
if existing_user:
return _update_existing_user(existing_user, project, request_json)
username = User.objects.make_random_password()
user = User.objects.create_user(
username,
email=request_json['email'],
first_name=request_json.get('firstName') or '',
last_name=request_json.get('lastName') or '',
)
logger.info('Created user {} (local)'.format(request_json['email']),
extra={'user': request.user})
try:
send_welcome_email(user, request.user)
except AnymailError as e:
return create_json_response({'error': str(e)},
status=getattr(e, 'status_code', None)
or 400,
reason=str(e))
project.can_view_group.user_set.add(user)
return create_json_response({
'projectsByGuid': {
project_guid: {
'collaborators':
get_json_for_project_collaborator_list(request.user, project)
}
}
})
