def _process_result(result, project):
result.update({
'projectCategoryGuids':
[c.guid for c in project.projectcategory_set.all()]
if add_project_category_guids_field else [],
'canEdit':
has_project_permissions(project, user, can_edit=True),
})
def _parse_mme_results(submission, saved_results, user, additional_genes=None, response_json=None):
results = []
contact_institutions = set()
prefetch_related_objects(saved_results, 'originating_submission__individual__family__project')
for result_model in saved_results:
result = result_model.result_data
result['matchStatus'] = _get_json_for_model(result_model)
if result_model.originating_submission:
originating_family = result_model.originating_submission.individual.family
if has_project_permissions(originating_family.project, user):
result['originatingSubmission'] = {
'originatingSubmissionGuid': result_model.originating_submission.guid,
'familyGuid': originating_family.guid,
'projectGuid': originating_family.project.guid,
}
results.append(result)
contact_institutions.add(result['patient']['contact'].get('institution', '').strip().lower())
additional_hpo_ids = {feature['id'] for feature in (submission.features or []) if feature.get('id')}
if not additional_genes:
additional_genes = set()
additional_genes.update({gene_feature['gene']['id'] for gene_feature in (submission.genomic_features or [])})
hpo_terms_by_id, genes_by_id, gene_symbols_to_ids = get_mme_genes_phenotypes_for_results(
results, additional_genes=additional_genes, additional_hpo_ids=additional_hpo_ids)
parsed_results = [_parse_mme_result(res, hpo_terms_by_id, gene_symbols_to_ids, submission.guid) for res in results]
parsed_results_gy_guid = {result['matchStatus']['matchmakerResultGuid']: result for result in parsed_results}
contact_notes = {note.institution: _get_json_for_model(note, user=user)
for note in MatchmakerContactNotes.objects.filter(institution__in=contact_institutions)}
submission_json = get_json_for_matchmaker_submission(
submission, individual_guid=submission.individual.guid,
additional_model_fields=['contact_name', 'contact_href', 'submission_id']
)
submission_json.update({
'mmeResultGuids': list(parsed_results_gy_guid.keys()),
'phenotypes': parse_mme_features(submission.features, hpo_terms_by_id),
'geneVariants': parse_mme_gene_variants(submission.genomic_features, gene_symbols_to_ids),
})
response = {
'mmeResultsByGuid': parsed_results_gy_guid,
'mmeContactNotes': contact_notes,
'mmeSubmissionsByGuid': {submission.guid: submission_json},
'individualsByGuid': {submission.individual.guid: {'mmeSubmissionGuid': submission.guid}},
'genesById': genes_by_id,
}
if response_json:
response.update(response_json)
return create_json_response(response)
def update_individual_handler(request, individual_guid):
"""Updates a single field in an Individual record.
Args:
request (object): Django HTTP Request object.
individual_guid (string): GUID of the Individual.
Request:
body should be a json dictionary like: { 'value': xxx }
Response:
json dictionary representing the updated individual like:
{
<individualGuid> : {
individualId: xxx,
sex: xxx,
affected: xxx,
...
}
}
"""
individual = Individual.objects.get(guid=individual_guid)
project = individual.family.project
check_project_permissions(project, request.user)
can_edit = has_project_permissions(project, request.user, can_edit=True)
request_json = json.loads(request.body)
update_json = request_json if can_edit else {
k: v
for k, v in request_json.items() if k in {'notes'}
}
update_individual_from_json(individual,
update_json,
user=request.user,
allow_unknown_keys=True)
return create_json_response(
{individual.guid: _get_json_for_individual(individual, request.user)})