def mme_details(request):
submissions = MatchmakerSubmission.objects.filter(
deleted_date__isnull=True)
hpo_terms_by_id, genes_by_id, gene_symbols_to_ids = get_mme_genes_phenotypes_for_submissions(
submissions)
submission_json = get_json_for_matchmaker_submissions(
submissions, additional_model_fields=['label'], all_parent_guids=True)
submissions_by_guid = {s['submissionGuid']: s for s in submission_json}
for submission in submissions:
gene_variants = parse_mme_gene_variants(submission.genomic_features,
gene_symbols_to_ids)
submissions_by_guid[submission.guid].update({
'phenotypes':
parse_mme_features(submission.features, hpo_terms_by_id),
'geneVariants':
gene_variants,
'geneSymbols':
','.join({
genes_by_id.get(gv['geneId'], {}).get('geneSymbol')
for gv in gene_variants
})
})
return create_json_response({
'metrics': get_mme_metrics(),
'submissions': submissions_by_guid.values(),
'genesById': genes_by_id,
})
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)