def add_family_group_submit(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
return HttpResponse('unauthorized')
error = None
form = AddFamilyGroupForm(project, request.POST)
if form.is_valid():
# todo: move to sample_anagement
family_group = FamilyGroup.objects.create(
project=project,
slug=form.cleaned_data['family_group_slug'],
name=form.cleaned_data['name'],
description=form.cleaned_data['description'],
)
for family in form.cleaned_data['families']:
family_group.families.add(family)
else:
error = server_utils.form_error_string(form)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return server_utils.JSONResponse({
'is_error':
False,
'new_url':
reverse('family_group_home',
args=(project.project_id, family_group.slug))
})
def add_family_group(request, project_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
form = AddFamilyGroupForm(project, request.POST)
if form.is_valid():
# todo: move to sample_anagement
family_group = FamilyGroup.objects.create(
project=project,
slug=form.cleaned_data['family_group_slug'],
name=form.cleaned_data['name'],
description=form.cleaned_data['description'],
)
for family in form.cleaned_data['families']:
family_group.families.add(family)
else:
error = server_utils.form_error_string(form)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return redirect('family_group_home', project.project_id,
family_group.slug)
def add_phenotype(request, project_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
form = AddPhenotypeForm(project, request.POST)
if form.is_valid():
phenotype = ProjectPhenotype(
project=project,
slug=form.cleaned_data['slug'],
name=form.cleaned_data['name'],
category=form.cleaned_data['category'],
datatype=form.cleaned_data['datatype'],
)
phenotype.save()
return redirect('edit_individuals', project.project_id)
else:
error = server_utils.form_error_string(form)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return redirect('edit_individuals', project.project_id)
def delete_individuals(request, project_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
indiv_id_list = request.POST.get('to_delete').split('|')
to_delete = []
for indiv_id in indiv_id_list:
i = Individual.objects.get(project=project, indiv_id=indiv_id)
to_delete.append(i)
for individual in to_delete:
individual.delete()
try:
settings.EVENTS_COLLECTION.insert({
'event_type': 'delete_individuals',
'date': timezone.now(),
'project_id': project_id,
'individuals': ", ".join([i.indiv_id for i in to_delete]),
'username': request.user.username,
'email': request.user.email,
})
except Exception as e:
logging.error("Error while logging add_variant_tag event: %s" % e)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return redirect('edit_individuals', project.project_id)
def save_one_individual(request, project_id):
error = None
project = Project.objects.get(project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
indiv_json = json.loads(request.POST.get('individual_json'))
save_individual_from_json_dict(project, indiv_json)
if not error:
ret = {
'is_error': False,
}
return server_utils.JSONResponse(ret)
else:
ret = {'is_error': True, 'error': error}
return server_utils.JSONResponse(ret)
def add_individuals(request, project_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
indiv_id_list = json.loads(request.POST.get('indiv_id_list'), '[]')
for indiv_id in indiv_id_list:
if Individual.objects.filter(project=project, indiv_id=indiv_id).exists():
error = "Indiv ID %s already exists" % indiv_id
if not error:
for indiv_id in indiv_id_list:
Individual.objects.create(project=project, indiv_id=indiv_id)
if True:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return server_utils.JSONResponse({'is_error': False})
def save_all_individuals(request, project_id):
error = None
# todo: validation
project = Project.objects.get(project_id=project_id)
if not project.can_admin(request.user):
return HttpResponse('unauthorized')
individuals_json = json.loads(request.POST.get('individuals_json'))
for indiv_obj in individuals_json:
save_individual_from_json_dict(project, indiv_obj)
if not error:
ret = {
'is_error': False,
}
return server_utils.JSONResponse(ret)
else:
ret = {'is_error': True, 'error': error}
return server_utils.JSONResponse(ret)
def add_family_group_submit(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
error = None
form = AddFamilyGroupForm(project, request.POST)
if form.is_valid():
# todo: move to sample_anagement
family_group, created = get_or_create_xbrowse_model(
FamilyGroup,
project=project,
slug=form.cleaned_data['family_group_slug'],
)
update_xbrowse_model(family_group,
name=form.cleaned_data['name'],
description=form.cleaned_data['description'])
seqr_analysis_group = find_matching_seqr_model(family_group)
for family in form.cleaned_data['families']:
family_group.families.add(family)
seqr_analysis_group.families.add(find_matching_seqr_model(family))
else:
error = server_utils.form_error_string(form)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return server_utils.JSONResponse({
'is_error':
False,
'new_url':
reverse('family_group_home',
args=(project.project_id, family_group.slug))
})
def delete_individuals(request, project_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
indiv_id_list = request.POST.get('to_delete').split('|')
to_delete = []
for indiv_id in indiv_id_list:
for i in Individual.objects.filter(project=project, indiv_id=indiv_id):
to_delete.append(i)
family_ids = set()
for individual in to_delete:
family_ids.add(individual.family.family_id)
delete_xbrowse_model(individual)
for family_id in family_ids:
if len(Individual.objects.filter(family__family_id=family_id)) == 0:
families = Family.objects.filter(family_id=family_id)
if families:
delete_xbrowse_model(families[0])
try:
settings.EVENTS_COLLECTION.insert({
'event_type':
'delete_individuals',
'date':
timezone.now(),
'project_id':
project_id,
'individuals':
", ".join([i.indiv_id for i in to_delete]),
'username':
request.user.username,
'email':
request.user.email,
})
except Exception as e:
logging.error("Error while logging add_variant_tag event: %s" % e)
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return redirect('edit_individuals', project.project_id)
def delete_individuals(request, project_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
indiv_id_list = request.POST.get('to_delete').split('|')
to_delete = []
for indiv_id in indiv_id_list:
i = Individual.objects.get(project=project, indiv_id=indiv_id)
to_delete.append(i)
for individual in to_delete:
individual.delete()
if error:
return server_utils.JSONResponse({'is_error': True, 'error': error})
else:
return redirect('edit_individuals', project.project_id)
def update_project_from_fam(request, project_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
form = FAMFileForm(request.POST, request.FILES)
if form.is_valid():
sample_management.update_project_from_individuals(project, form.cleaned_data['individuals'])
return redirect('edit_individuals', project.project_id)
else:
error = "File error"
if error:
ret = {'is_error': True, 'error': error}
else:
ret = {'is_error': False}
return server_utils.JSONResponse(ret)
