def add_tag(request, project_id):
"""For HTTP GET requests, this view generates the html page for creating a tag.
For HTTP POST, it saves the submitted changes.
Args:
request: Django HTTP request object
project_id: seqr project ID string
"""
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
error = None
if request.method == 'POST':
form = AddTagForm(project, request.POST)
if form.is_valid():
create_xbrowse_model(ProjectTag,
project=project,
tag=form.cleaned_data['tag'],
title=form.cleaned_data['title'])
return redirect('project_home', project_id=project_id)
else:
error = server_utils.form_error_string(form)
else:
form = AddTagForm(project)
return render(request, 'project/add_or_edit_tag.html', {
'project': project,
'form': form,
'error': error,
})
def add_tag(request, project_id):
"""For HTTP GET requests, this view generates the html page for creating a tag.
For HTTP POST, it saves the submitted changes.
Args:
request: Django HTTP request object
project_id: seqr project ID string
"""
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
error = None
if request.method == 'POST':
form = AddTagForm(project, request.POST)
if form.is_valid():
create_xbrowse_model(
ProjectTag,
project=project,
tag=form.cleaned_data['tag'],
title=form.cleaned_data['title'])
return redirect('project_home', project_id=project_id)
else:
error = server_utils.form_error_string(form)
else:
form = AddTagForm(project)
return render(request, 'project/add_or_edit_tag.html', {
'project': project,
'form': form,
'error': error,
})
def add(request):
if request.method == 'POST':
form = GeneListForm(request.POST)
if form.is_valid():
unique_slug = form.cleaned_data['slug']
while GeneList.objects.filter(slug=unique_slug):
unique_slug += "_"
new_list = create_xbrowse_model(
GeneList,
slug=unique_slug,
name=form.cleaned_data['name'],
description=form.cleaned_data['description'],
is_public=form.cleaned_data['is_public'],
owner=request.user,
last_updated=datetime.datetime.now(),
)
for gene_id in form.cleaned_data['gene_ids']:
create_xbrowse_model(GeneListItem,
gene_list=new_list,
gene_id=gene_id)
return redirect('gene_list', slug=new_list.slug)
else:
form = GeneListForm()
return render(request, 'gene_lists/add.html', {
'form': form,
})
def handle(self, *args, **options):
if 'project_id' not in options:
print '\n'
print 'Creates a project in Seqr.\n'
print 'Please provide a project ID as an argument. Optionally, provide a more human-readable project name as a second argument. '
print 'Example: python manage.py add_project 1kg\n'
sys.exit()
project_id = options['project_id']
if "." in project_id:
sys.exit("ERROR: A '.' in the project ID is not supported")
if Project.objects.filter(project_id=project_id).exists():
print '\nSorry, I am unable to create that project since it exists already\n'
sys.exit()
project_name = options.get('project_name') or project_id
print(
'Creating project with id "%(project_id)s" and name "%(project_name)s"'
% locals())
try:
create_xbrowse_model(Project,
project_id=project_id,
project_name=project_name,
created_date=timezone.now())
except Exception as e:
print('\nError creating project:', e, '\n')
sys.exit()
def add(request):
if request.method == 'POST':
form = GeneListForm(request.POST)
if form.is_valid():
unique_slug = form.cleaned_data['slug']
while GeneList.objects.filter(slug=unique_slug):
unique_slug += "_"
new_list = create_xbrowse_model(GeneList,
slug=unique_slug,
name=form.cleaned_data['name'],
description=form.cleaned_data['description'],
is_public=form.cleaned_data['is_public'],
owner=request.user,
last_updated=datetime.datetime.now(),
)
for gene_id in form.cleaned_data['gene_ids']:
create_xbrowse_model(GeneListItem, gene_list=new_list, gene_id=gene_id)
return redirect('gene_list', slug=new_list.slug)
else:
form = GeneListForm()
return render(request, 'gene_lists/add.html', {
'form': form,
'new_page_url': '/gene_lists',
})
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 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:
create_xbrowse_model(Individual, 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 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:
create_xbrowse_model(Individual, 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 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 handle(self, *args, **options):
if 'project_id' not in options:
print '\n'
print 'Creates a project in Seqr.\n'
print 'Please provide a project ID as an argument. Optionally, provide a more human-readable project name as a second argument. '
print 'Example: python manage.py add_project 1kg\n'
sys.exit()
project_id = options['project_id']
if "." in project_id:
sys.exit("ERROR: A '.' in the project ID is not supported")
if Project.objects.filter(project_id=project_id).exists():
print '\nSorry, I am unable to create that project since it exists already\n'
sys.exit()
project_name = options.get('project_name') or project_id
print('Creating project with id "%(project_id)s" and name "%(project_name)s"' % locals())
try:
create_xbrowse_model(Project, project_id=project_id, project_name=project_name, created_date=timezone.now())
except Exception as e:
print('\nError creating project:', e, '\n')
sys.exit()