def fetch_project_individuals_data(project_id):
"""
Notes:
1. ONLY project-authorized user has access to this individual
"""
project = get_object_or_404(Project, project_id=project_id)
variants = get_causal_variants_for_project(project)
variants = sorted(variants, key=lambda v: (v.extras['family_id'], v.xpos))
grouped_variants = itertools.groupby(variants, key=lambda v: v.extras['family_id'])
for family_id, family_variants in grouped_variants:
family = Family.objects.get(project=project, family_id=family_id)
family_variants = list(family_variants)
add_extra_info_to_variants_family(get_reference(), family, family_variants)
family_data = [v.toJSON() for v in variants]
variant_data = {family.family_id: family.get_json_obj() for family in project.get_families()}
phenotype_entry_counts = gather_phenotype_data_for_project(project_id, variant_data)
status_description_map = {}
for abbrev, details in ANALYSIS_STATUS_CHOICES:
status_description_map[abbrev] = details[0]
families_json = json_displays.family_list(project.get_families())
family_statuses = {}
for f in families_json:
family_statuses[f['family_id']] = status_description_map[f['analysis_status']['status']]
return family_data, variant_data, phenotype_entry_counts, family_statuses
def family_group_home(request, project_id, family_group_slug):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_view(request.user):
raise PermissionDenied
family_group = get_object_or_404(FamilyGroup,
project=project,
slug=family_group_slug)
return render(
request, 'family_group/family_group_home.html', {
'project':
project,
'family_group':
family_group,
'families_json':
json.dumps(json_displays.family_list(family_group.get_families())),
'analysis_statuses':
json.dumps(dict(ANALYSIS_STATUS_CHOICES)),
'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 add_family_group(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
return HttpResponse('unauthorized')
families_json = json_displays.family_list(project.get_families())
return render(request, 'family_group/add_family_group.html', {
'project': project,
'families_json': json.dumps(families_json),
})
def add_family_group(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
return HttpResponse('unauthorized')
families_json = json_displays.family_list(project.get_families())
return render(request, 'family_group/add_family_group.html', {
'project': project,
'families_json': json.dumps(families_json),
})
def add_family_group(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
families_json = json_displays.family_list(project.get_families())
return render(request, 'family_group/add_family_group.html', {
'project': project,
'families_json': json.dumps(families_json),
})
def family_group_home(request, project_id, family_group_slug):
project = get_object_or_404(Project, project_id=project_id)
family_group = get_object_or_404(FamilyGroup, project=project, slug=family_group_slug)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
return render(request, 'family_group/family_group_home.html', {
'project': project,
'family_group': family_group,
'families_json': json.dumps(json_displays.family_list(family_group.get_families())),
})
def families(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
families_json = json_displays.family_list(project.get_families())
return render(request, 'family/families.html', {
'project': project,
'families_json': json.dumps(families_json),
'analysis_statuses': json.dumps(dict(ANALYSIS_STATUS_CHOICES)),
})
def add_family_group(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
families_json = json_displays.family_list(project.get_families())
return render(request, 'family_group/add_family_group.html', {
'project': project,
'families_json': json.dumps(families_json),
'new_page_url': '/project/{}/project_page'.format(project.seqr_project.guid) if project.seqr_project else None,
})
def families(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_view(request.user):
raise PermissionDenied
families_json = json_displays.family_list(project.get_families())
return render(request, 'family/families.html', {
'project': project,
'families_json': json.dumps(families_json),
'analysis_statuses': json.dumps(dict(ANALYSIS_STATUS_CHOICES)),
'is_manager': 'true' if project.can_admin(request.user) else 'false',
})
def families(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_view(request.user):
raise PermissionDenied
families_json = json_displays.family_list(project.get_families())
return render(request, 'family/families.html', {
'project': project,
'families_json': json.dumps(families_json),
'analysis_statuses': json.dumps(dict(ANALYSIS_STATUS_CHOICES)),
'is_manager': 'true' if project.can_admin(request.user) else 'false',
})
def family_group_home(request, project_id, family_group_slug):
project = get_object_or_404(Project, project_id=project_id)
family_group = get_object_or_404(FamilyGroup, project=project, slug=family_group_slug)
if not project.can_view(request.user):
raise PermissionDenied
return render(request, 'family_group/family_group_home.html', {
'project': project,
'family_group': family_group,
'families_json': json.dumps(json_displays.family_list(family_group.get_families())),
'analysis_statuses': json.dumps(dict(ANALYSIS_STATUS_CHOICES)),
})
def family_group_home(request, project_id, family_group_slug):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_view(request.user):
raise PermissionDenied
family_group = get_object_or_404(FamilyGroup, project=project, slug=family_group_slug)
return render(request, 'family_group/family_group_home.html', {
'project': project,
'family_group': family_group,
'families_json': json.dumps(json_displays.family_list(family_group.get_families())),
'analysis_statuses': json.dumps(dict(ANALYSIS_STATUS_CHOICES)),
'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 add_family_group(request, project_id):
project = get_object_or_404(Project, project_id=project_id)
if not project.can_admin(request.user):
raise PermissionDenied
families_json = json_displays.family_list(project.get_families())
return render(
request, 'family_group/add_family_group.html', {
'project':
project,
'families_json':
json.dumps(families_json),
'new_page_url':
'/project/{}/project_page'.format(project.seqr_project.guid)
if project.seqr_project else None,
})
def family_group_home(request, project_id, family_group_slug):
project = get_object_or_404(Project, project_id=project_id)
family_group = get_object_or_404(FamilyGroup,
project=project,
slug=family_group_slug)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
return render(
request, 'family_group/family_group_home.html', {
'project':
project,
'family_group':
family_group,
'families_json':
json.dumps(json_displays.family_list(family_group.get_families())),
})
