def edit_family(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
return HttpResponse('unauthorized')
if request.method == 'POST':
form = EditFamilyForm(request.POST, request.FILES)
if form.is_valid():
family.short_description = form.cleaned_data['short_description']
family.about_family_content = form.cleaned_data['about_family_content']
family.analysis_status = form.cleaned_data['analysis_status']
if 'pedigree_image' in request.FILES:
family.pedigree_image = request.FILES['pedigree_image']
family.save()
return redirect('family_home', project_id=project.project_id, family_id=family.family_id)
else:
form = EditFamilyForm(initial={'short_description': family.short_description, 'about_family_content': family.about_family_content})
return render(request, 'family_edit.html', {
'project': project,
'family': family,
'error': error,
'form': form,
'analysis_statuses': ANALYSIS_STATUS_CHOICES
})
def edit_family(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
return HttpResponse('unauthorized')
if request.method == 'POST':
form = EditFamilyForm(request.POST, request.FILES)
if form.is_valid():
family.short_description = form.cleaned_data['short_description']
family.about_family_content = form.cleaned_data['about_family_content']
family.analysis_status = form.cleaned_data['analysis_status']
if 'pedigree_image' in request.FILES:
family.pedigree_image = request.FILES['pedigree_image']
family.save()
return redirect('family_home', project_id=project.project_id, family_id=family.family_id)
else:
form = EditFamilyForm(initial={'short_description': family.short_description, 'about_family_content': family.about_family_content})
return render(request, 'family_edit.html', {
'project': project,
'family': family,
'error': error,
'form': form,
})
def edit_family(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
raise PermissionDenied
if request.method == 'POST':
form = EditFamilyForm(request.POST, request.FILES)
if form.is_valid():
update_xbrowse_model(
family,
coded_phenotype=form.cleaned_data['coded_phenotype'],
short_description=form.cleaned_data['short_description'],
about_family_content=form.cleaned_data['about_family_content'],
analysis_summary_content=form.cleaned_data['analysis_summary_content'],
post_discovery_omim_number=form.cleaned_data['post_discovery_omim_number'])
if family.analysis_status != form.cleaned_data['analysis_status']:
if family.analysis_status not in ('Q', 'I'):
if not settings.DEBUG: settings.EVENTS_COLLECTION.insert({
'event_type': 'family_analysis_status_changed', 'project_id': project_id, 'family_id': family_id, 'date': timezone.now(),
'username': request.user.username, 'email': request.user.email,
'from': family.analysis_status, 'to': form.cleaned_data['analysis_status'] })
update_xbrowse_model(
family,
analysis_status=form.cleaned_data['analysis_status'],
analysis_status_date_saved=timezone.now(),
analysis_status_saved_by=request.user)
if 'pedigree_image' in request.FILES:
update_xbrowse_model(
family,
pedigree_image = request.FILES['pedigree_image'])
return redirect('family_home', project_id=project.project_id, family_id=family.family_id)
else:
form = EditFamilyForm(initial={
'coded_phenotype': family.coded_phenotype,
'short_description': family.short_description,
'about_family_content': family.about_family_content,
'analysis_summary_content': family.analysis_summary_content,
'post_discovery_omim_number': family.post_discovery_omim_number,
})
return render(request, 'family_edit.html', {
'user': request.user,
'project': project,
'family': family,
'error': error,
'form': form,
'analysis_statuses': ANALYSIS_STATUS_CHOICES,
'new_page_url': '/project/{0}/family_page/{1}'.format(
family.seqr_family.project.guid, family.seqr_family.guid) if family.seqr_family else None,
})
def edit_family(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
raise PermissionDenied
if request.method == 'POST':
form = EditFamilyForm(request.POST, request.FILES)
if form.is_valid():
update_xbrowse_model(
family,
coded_phenotype=form.cleaned_data['coded_phenotype'],
short_description=form.cleaned_data['short_description'],
about_family_content=form.cleaned_data['about_family_content'],
analysis_summary_content=form.cleaned_data['analysis_summary_content'],
post_discovery_omim_number=form.cleaned_data['post_discovery_omim_number'])
if family.analysis_status != form.cleaned_data['analysis_status']:
if family.analysis_status not in ('Q', 'I'):
if not settings.DEBUG: settings.EVENTS_COLLECTION.insert({
'event_type': 'family_analysis_status_changed', 'project_id': project_id, 'family_id': family_id, 'date': timezone.now(),
'username': request.user.username, 'email': request.user.email,
'from': family.analysis_status, 'to': form.cleaned_data['analysis_status'] })
update_xbrowse_model(
family,
analysis_status=form.cleaned_data['analysis_status'],
analysis_status_date_saved=timezone.now(),
analysis_status_saved_by=request.user)
if 'pedigree_image' in request.FILES:
update_xbrowse_model(
family,
pedigree_image = request.FILES['pedigree_image'])
return redirect('family_home', project_id=project.project_id, family_id=family.family_id)
else:
form = EditFamilyForm(initial={
'coded_phenotype': family.coded_phenotype,
'short_description': family.short_description,
'about_family_content': family.about_family_content,
'analysis_summary_content': family.analysis_summary_content,
'post_discovery_omim_number': family.post_discovery_omim_number,
})
return render(request, 'family_edit.html', {
'user': request.user,
'project': project,
'family': family,
'error': error,
'form': form,
'analysis_statuses': ANALYSIS_STATUS_CHOICES,
'new_page_url': '/project/{0}/family_page/{1}'.format(
family.seqr_family.project.guid, family.seqr_family.guid) if family.seqr_family else None,
})
def edit_family_cause(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
raise PermissionDenied
causal_variants = list(CausalVariant.objects.filter(family=family))
if request.GET.get('variant'):
xpos, ref, alt = request.GET['variant'].split('|')
c = CausalVariant.objects.get_or_create(
family=family,
xpos=int(xpos),
ref=ref,
alt=alt,
)[0]
causal_variants = list(CausalVariant.objects.filter(family=family))
if request.method == 'POST':
form = EditFamilyCauseForm(family, request.POST)
if form.is_valid():
CausalVariant.objects.filter(family=family).delete()
for v_str in request.POST.getlist('variants'):
xpos, ref, alt = v_str.split('|')
CausalVariant.objects.create(
family=family,
xpos=int(xpos),
ref=ref,
alt=alt,
)
update_xbrowse_model(family,
analysis_status='S',
causal_inheritance_mode=form.
cleaned_data['inheritance_mode'])
return redirect('family_home',
project_id=project.project_id,
family_id=family.family_id)
else:
error = server_utils.form_error_string(form)
else:
form = EditFamilyForm(family)
variants = []
for c in causal_variants:
variants.append(
get_datastore(project).get_single_variant(project_id, family_id,
c.xpos, c.ref, c.alt))
return render(
request, 'family/edit_cause.html', {
'project': project,
'family': family,
'error': error,
'form': form,
'variants': [v.toJSON() for v in variants],
})
def edit_family(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
raise PermissionDenied
if request.method == 'POST':
form = EditFamilyForm(request.POST, request.FILES)
if form.is_valid():
family.short_description = form.cleaned_data['short_description']
family.about_family_content = form.cleaned_data[
'about_family_content']
family.analysis_summary_content = form.cleaned_data[
'analysis_summary_content']
if family.analysis_status != form.cleaned_data['analysis_status']:
family.analysis_status = form.cleaned_data['analysis_status']
family.analysis_status_date_saved = timezone.now()
family.analysis_status_saved_by = request.user
if 'pedigree_image' in request.FILES:
family.pedigree_image = request.FILES['pedigree_image']
family.save()
return redirect('family_home',
project_id=project.project_id,
family_id=family.family_id)
else:
form = EditFamilyForm(
initial={
'short_description': family.short_description,
'about_family_content': family.about_family_content,
'analysis_summary_content': family.analysis_summary_content
})
return render(
request, 'family_edit.html', {
'project': project,
'family': family,
'error': error,
'form': form,
'analysis_statuses': ANALYSIS_STATUS_CHOICES,
})
def edit_family(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
raise PermissionDenied
if request.method == 'POST':
form = EditFamilyForm(request.POST, request.FILES)
if form.is_valid():
family.short_description = form.cleaned_data['short_description']
family.about_family_content = form.cleaned_data['about_family_content']
family.analysis_summary_content = form.cleaned_data['analysis_summary_content']
if family.analysis_status != form.cleaned_data['analysis_status']:
print("Analysis status changed to: %s" % form.cleaned_data['analysis_status'])
if family.analysis_status not in ('Q', 'I'):
settings.EVENTS_COLLECTION.insert({
'event_type': 'family_analysis_status_changed', 'project_id': project_id, 'family_id': family_id, 'date': timezone.now(),
'username': request.user.username, 'email': request.user.email,
'from': family.analysis_status, 'to': form.cleaned_data['analysis_status'] })
family.analysis_status = form.cleaned_data['analysis_status']
family.analysis_status_date_saved = timezone.now()
family.analysis_status_saved_by = request.user
if 'pedigree_image' in request.FILES:
family.pedigree_image = request.FILES['pedigree_image']
family.save()
return redirect('family_home', project_id=project.project_id, family_id=family.family_id)
else:
form = EditFamilyForm(initial={'short_description': family.short_description, 'about_family_content': family.about_family_content, 'analysis_summary_content': family.analysis_summary_content})
return render(request, 'family_edit.html', {
'project': project,
'family': family,
'error': error,
'form': form,
'analysis_statuses': ANALYSIS_STATUS_CHOICES,
})
def edit_family(request, project_id, family_id):
error = None
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_admin(request.user):
raise PermissionDenied
if request.method == 'POST':
form = EditFamilyForm(request.POST, request.FILES)
if form.is_valid():
family.short_description = form.cleaned_data['short_description']
family.about_family_content = form.cleaned_data['about_family_content']
family.analysis_summary_content = form.cleaned_data['analysis_summary_content']
family.analysis_status = form.cleaned_data['analysis_status']
if 'pedigree_image' in request.FILES:
family.pedigree_image = request.FILES['pedigree_image']
family.save()
analysis_status, created = AnalysisStatus.objects.get_or_create(family=family)
if created or analysis_status.status != form.cleaned_data['analysis_status']:
analysis_status.user = request.user
analysis_status.date_saved = datetime.datetime.now()
analysis_status.status = form.cleaned_data['analysis_status']
analysis_status.save()
return redirect('family_home', project_id=project.project_id, family_id=family.family_id)
else:
form = EditFamilyForm(initial={'short_description': family.short_description, 'about_family_content': family.about_family_content, 'analysis_summary_content': family.analysis_summary_content})
return render(request, 'family_edit.html', {
'project': project,
'family': family,
'error': error,
'form': form,
'analysis_statuses': ANALYSIS_STATUS_CHOICES,
})