def get_individual_mme_matches(request, submission_guid):
"""
Looks for matches for the given submission. Expects a single patient (MME spec) in the POST
data field under key "patient_data"
Args:
project_id,indiv_id and POST all data in POST under key "patient_data"
Returns:
Status code and results
"""
submission = MatchmakerSubmission.objects.get(guid=submission_guid)
check_mme_permissions(submission, request.user)
results = MatchmakerResult.objects.filter(submission=submission)
saved_variants = get_json_for_saved_variants(
SavedVariant.objects.filter(family=submission.individual.family),
add_tags=True,
add_details=True)
gene_ids = set()
for variant in saved_variants:
gene_ids.update(variant['transcripts'].keys())
return _parse_mme_results(
submission,
results,
request.user,
additional_genes=gene_ids,
response_json={
'savedVariantsByGuid':
{variant['variantGuid']: variant
for variant in saved_variants}
})
def delete_mme_submission(request, submission_guid):
"""
Create or update the submission for the given individual.
"""
submission = MatchmakerSubmission.objects.get(guid=submission_guid)
check_mme_permissions(submission, request.user)
if submission.deleted_date:
return create_json_response(
{},
status=402,
reason='Matchmaker submission has already been deleted for {}'.
format(submission.individual.individual_id),
)
deleted_date = datetime.now()
submission.deleted_date = deleted_date
submission.deleted_by = request.user
submission.save()
for saved_result in MatchmakerResult.objects.filter(submission=submission):
if not (saved_result.we_contacted or saved_result.host_contacted
or saved_result.comments):
saved_result.delete()
return create_json_response({
'mmeSubmissionsByGuid': {
submission.guid: {
'mmeDeletedDate': deleted_date
}
}
})
def update_mme_submission(request, submission_guid=None):
"""
Create or update the submission for the given individual.
"""
submission_json = json.loads(request.body)
phenotypes = submission_json.pop('phenotypes', [])
gene_variants = submission_json.pop('geneVariants', [])
if not phenotypes and not gene_variants:
return create_json_response({}, status=400, reason='Genotypes or phentoypes are required')
genomic_features = []
for gene_variant in gene_variants:
if not gene_variant.get('geneId'):
return create_json_response({}, status=400, reason='Gene id is required for genomic features')
feature = {'gene': {'id': gene_variant['geneId']}}
if 'numAlt' in gene_variant and gene_variant['numAlt'] > 0:
feature['zygosity'] = gene_variant['numAlt']
if gene_variant.get('pos'):
genome_version = gene_variant['genomeVersion']
feature['variant'] = {
'referenceName': gene_variant['chrom'],
'start': gene_variant['pos'],
'assembly': GENOME_VERSION_LOOKUP.get(genome_version, genome_version),
}
if gene_variant.get('alt'):
feature['variant'].update({
'alternateBases': gene_variant['alt'],
'referenceBases': gene_variant['ref'],
})
elif gene_variant.get('end'):
feature['variant']['end'] = gene_variant['end']
genomic_features.append(feature)
submission_json.update({
'features': phenotypes,
'genomicFeatures': genomic_features,
'deletedDate': None,
'deletedBy': None,
})
if submission_guid:
submission = MatchmakerSubmission.objects.get(guid=submission_guid)
check_mme_permissions(submission, request.user)
else:
individual_guid = submission_json.get('individualGuid')
if not individual_guid:
return create_json_response({}, status=400, reason='Individual is required for a new submission')
individual = Individual.objects.get(guid=individual_guid)
check_project_permissions(individual.family.project, request.user)
submission = MatchmakerSubmission.objects.create(
individual=individual,
submission_id=individual.guid,
label=individual.individual_id,
)
update_model_from_json(submission, submission_json, allow_unknown_keys=True)
# search for new matches
return _search_matches(submission, request.user)
def search_individual_mme_matches(request, submission_guid):
"""
Looks for matches for the given submission.
Returns:
Status code and results
"""
submission = MatchmakerSubmission.objects.get(guid=submission_guid)
check_mme_permissions(submission, request.user)
return _search_matches(submission, request.user)
def update_mme_result_status(request, matchmaker_result_guid):
"""
Looks for matches for the given individual. Expects a single patient (MME spec) in the POST
data field under key "patient_data"
Args:
project_id,indiv_id and POST all data in POST under key "patient_data"
Returns:
Status code and results
"""
result = MatchmakerResult.objects.get(guid=matchmaker_result_guid)
check_mme_permissions(result.submission, request.user)
request_json = json.loads(request.body)
update_model_from_json(result, request_json, allow_unknown_keys=True)
return create_json_response({
'mmeResultsByGuid': {matchmaker_result_guid: {'matchStatus': _get_json_for_model(result)}},
})
def send_mme_contact_email(request, matchmaker_result_guid):
"""
Sends the given email and updates the contacted status for the match
Args:
matchmaker_result_guid
Returns:
Status code and results
"""
result = MatchmakerResult.objects.get(guid=matchmaker_result_guid)
check_mme_permissions(result.submission, request.user)
request_json = json.loads(request.body)
email_message = EmailMessage(
subject=request_json['subject'],
body=request_json['body'],
to=map(lambda s: s.strip(), request_json['to'].split(',')),
from_email=MME_DEFAULT_CONTACT_EMAIL,
)
try:
email_message.send()
except Exception as e:
message = e.message
json_body = {}
if hasattr(e, 'response'):
message = e.response.content
try:
json_body = e.response.json()
except Exception:
json_body = {'message': message}
return create_json_response(json_body,
status=getattr(e, 'status_code', 400),
reason=message)
update_model_from_json(result, {'weContacted': True})
return create_json_response({
'mmeResultsByGuid': {
matchmaker_result_guid: {
'matchStatus': _get_json_for_model(result)
}
},
})
