def delete(request, project_id, family_group_slug):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
return HttpResponse("Unauthorized")
family_group = get_object_or_404(FamilyGroup,
project=project,
slug=family_group_slug)
if request.method == 'POST':
if request.POST.get('confirm') == 'yes':
delete_xbrowse_model(family_group)
return redirect('family_groups', project_id)
return render(
request, 'family_group/delete.html', {
'project':
project,
'family_group':
family_group,
'new_page_url':
'/project/{}/analysis_group/{}'.format(
project.seqr_project.guid,
family_group.seqr_analysis_group.guid) if project.seqr_project
and family_group.seqr_analysis_group else None,
})
def delete_tag(request, project_id, tag_name, tag_title):
"""Deletes the tag with the given tag_name and tag_title.
Args:
request: Django HTTP request object
project_id: seqr project ID string
tag_name: name of the tag to edit
tag_title: title of the tag to edit
"""
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
tag_name = urllib.unquote(tag_name)
tag_title = urllib.unquote(tag_title)
try:
tag = ProjectTag.objects.get(project=project,
tag=tag_name,
title=tag_title)
delete_xbrowse_model(tag)
except ObjectDoesNotExist as e:
return HttpResponse(
"Error: tag not found: %s - %s. Maybe it's already been deleted? "
% (tag_name, tag_title))
else:
return redirect('project_home', project_id=project_id)
def delete_family(project_id, family_id):
"""
Delete a project and perform any cleanup (ie. deleting from datastore and removing temp files)
"""
family = Family.objects.get(project__project_id=project_id, family_id=family_id)
for individual in family.get_individuals():
update_xbrowse_model(individual, family=None)
get_mall(project_id).variant_store.delete_family(project_id, family_id)
delete_xbrowse_model(family)
def delete_family(project_id, family_id):
"""
Delete a project and perform any cleanup (ie. deleting from datastore and removing temp files)
"""
family = Family.objects.get(project__project_id=project_id, family_id=family_id)
for individual in family.get_individuals():
update_xbrowse_model(individual, family=None)
get_mall(project_id).variant_store.delete_family(project_id, family_id)
delete_xbrowse_model(family)
def delete(request, slug):
_gene_list = get_object_or_404(GeneList, slug=slug)
authorized = False
if _gene_list.owner == request.user:
authorized = True
if not authorized:
raise PermissionDenied
if request.method == 'POST':
delete_xbrowse_model(_gene_list)
return redirect('gene_lists_home')
return render(request, 'gene_lists/delete.html', {
'gene_list': _gene_list,
})
def delete(request, project_id, family_group_slug):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
return HttpResponse("Unauthorized")
family_group = get_object_or_404(FamilyGroup, project=project, slug=family_group_slug)
if request.method == 'POST':
if request.POST.get('confirm') == 'yes':
delete_xbrowse_model(family_group)
return redirect('family_groups', project_id)
return render(request, 'family_group/delete.html', {
'project': project,
'family_group': family_group,
'new_page_url': '/project/{}/analysis_group/{}'.format(project.seqr_project.guid, family_group.seqr_analysis_group.guid) if project.seqr_project and family_group.seqr_analysis_group else None,
})
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(request, slug):
_gene_list = get_object_or_404(GeneList, slug=slug)
authorized = False
if _gene_list.owner == request.user:
authorized = True
if not authorized:
raise PermissionDenied
if request.method == 'POST':
delete_xbrowse_model(_gene_list)
return redirect('gene_lists_home')
return render(request, 'gene_lists/delete.html', {
'gene_list': _gene_list,
'new_page_url': '/gene_lists/{}'.format(_gene_list.seqr_locus_list.guid) if _gene_list.seqr_locus_list else None,
})
def edit(request, slug):
gene_list = get_object_or_404(GeneList, slug=slug)
authorized = False
if gene_list.owner == request.user:
authorized = True
if not authorized:
raise PermissionDenied
if request.method == 'POST':
form = GeneListForm(request.POST)
if form.is_valid():
update_xbrowse_model(gene_list,
slug=form.cleaned_data['slug'],
name=form.cleaned_data['name'],
description=form.cleaned_data['description'],
is_public=form.cleaned_data['is_public'],
last_updated=datetime.datetime.now())
for gene_list_item in GeneListItem.objects.filter(
gene_list=gene_list):
delete_xbrowse_model(gene_list_item)
for gene_id in form.cleaned_data['gene_ids']:
create_xbrowse_model(GeneListItem,
gene_list=gene_list,
gene_id=gene_id)
return redirect('gene_list', slug=gene_list.slug)
else:
form = GeneListForm(
initial={
'name': gene_list.name,
'description': gene_list.description,
'is_public': gene_list.is_public,
'genes': '\n'.join(
[g['symbol'] for g in gene_list.get_genes()]),
})
return render(request, 'gene_lists/edit.html', {
'form': form,
'gene_list': gene_list,
})
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:
if not settings.DEBUG: 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 edit(request, slug):
gene_list = get_object_or_404(GeneList, slug=slug)
authorized = False
if gene_list.owner == request.user:
authorized = True
if not authorized:
raise PermissionDenied
if request.method == 'POST':
form = GeneListForm(request.POST)
if form.is_valid():
update_xbrowse_model(gene_list,
slug=form.cleaned_data['slug'],
name=form.cleaned_data['name'],
description=form.cleaned_data['description'],
is_public=form.cleaned_data['is_public'],
last_updated = datetime.datetime.now())
for gene_list_item in GeneListItem.objects.filter(gene_list=gene_list):
delete_xbrowse_model(gene_list_item)
for gene_id in form.cleaned_data['gene_ids']:
create_xbrowse_model(GeneListItem, gene_list=gene_list, gene_id=gene_id)
return redirect('gene_list', slug=gene_list.slug)
else:
form = GeneListForm(initial={
'name': gene_list.name,
'description': gene_list.description,
'is_public': gene_list.is_public,
'genes': '\n'.join([g['symbol'] for g in gene_list.get_genes()]),
})
return render(request, 'gene_lists/edit.html', {
'form': form,
'gene_list': gene_list,
'new_page_url': '/gene_lists/{}'.format(gene_list.seqr_locus_list.guid) if gene_list.seqr_locus_list else None,
})
def delete_tag(request, project_id, tag_name, tag_title):
"""Deletes the tag with the given tag_name and tag_title.
Args:
request: Django HTTP request object
project_id: seqr project ID string
tag_name: name of the tag to edit
tag_title: title of the tag to edit
"""
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
tag_name = urllib.unquote(tag_name)
tag_title = urllib.unquote(tag_title)
try:
tag = ProjectTag.objects.get(project=project, tag=tag_name, title=tag_title)
delete_xbrowse_model(tag)
except ObjectDoesNotExist as e:
return HttpResponse("Error: tag not found: %s - %s. Maybe it's already been deleted? " % (tag_name, tag_title))
else:
return redirect('project_home', project_id=project_id)
