def _get_project_child_entities(project, user, is_analyst):
has_case_review_perm = has_case_review_permissions(project, user)
families_by_guid = _retrieve_families(project.guid, is_analyst, has_case_review_perm)
individuals_by_guid, individual_models = _retrieve_individuals(project.guid, is_analyst, has_case_review_perm)
for individual_guid, individual in individuals_by_guid.items():
families_by_guid[individual['familyGuid']]['individualGuids'].add(individual_guid)
samples_by_guid = _retrieve_samples(
project.guid, individuals_by_guid, Sample.objects.filter(individual__in=individual_models))
igv_samples_by_guid = _retrieve_samples(
project.guid, individuals_by_guid, IgvSample.objects.filter(individual__in=individual_models),
sample_guid_key='igvSampleGuids')
mme_submissions_by_guid = _retrieve_mme_submissions(individuals_by_guid, individual_models)
analysis_groups_by_guid = _retrieve_analysis_groups(project)
locus_lists = get_json_for_locus_lists(LocusList.objects.filter(projects__id=project.id), user, is_analyst=is_analyst)
locus_lists_by_guid = {locus_list['locusListGuid']: locus_list for locus_list in locus_lists}
return {
'familiesByGuid': families_by_guid,
'individualsByGuid': individuals_by_guid,
'samplesByGuid': samples_by_guid,
'igvSamplesByGuid': igv_samples_by_guid,
'locusListsByGuid': locus_lists_by_guid,
'analysisGroupsByGuid': analysis_groups_by_guid,
'mmeSubmissionsByGuid': mme_submissions_by_guid,
}
def _get_case_review_fields(model, project, user):
if not (user and has_case_review_permissions(project, user)):
return []
return [
field.name for field in type(model)._meta.fields
if field.name.startswith('case_review')
]
def _get_case_review_fields(model, has_case_review_perm, user, get_project):
if has_case_review_perm is None:
has_case_review_perm = user and has_case_review_permissions(
get_project(model), user)
if not has_case_review_perm:
return []
return [
field.name for field in type(model)._meta.fields
if field.name.startswith('case_review')
]
def _update_case_review(model,
project,
request,
field,
get_response_json,
additional_updates=None):
if not has_case_review_permissions(project, request.user):
raise PermissionDenied('User cannot edit case review for this project')
update_json = {field: json.loads(request.body).get(field)}
if additional_updates:
update_json.update(additional_updates)
update_model_from_json(model, update_json, user=request.user)
return create_json_response(
{model.guid: get_response_json(model, request.user)})