def create_variant_note_handler(request, variant_guids):
request_json = json.loads(request.body)
save_as_gene_note = request_json.get('saveAsGeneNote')
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
all_variant_guids = variant_guids.split(',')
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(', '.join(
[
guid for guid in all_variant_guids
if guid not in {sv.guid
for sv in saved_variants}
]))
return create_json_response({'error': error}, status=400, reason=error)
# update saved_variants
note = _create_variant_note(saved_variants, request_json, request.user)
note_json = get_json_for_variant_note(note, add_variant_guids=False)
note_json['variantGuids'] = all_variant_guids
response = {
'savedVariantsByGuid': {
saved_variant.guid: {
'noteGuids':
[n.guid for n in saved_variant.variantnote_set.all()]
}
for saved_variant in saved_variants
},
'variantNotesByGuid': {
note.guid: note_json
},
}
if save_as_gene_note:
main_transcript_id = saved_variants[
0].selected_main_transcript_id or saved_variants[
0].saved_variant_json['mainTranscriptId']
gene_id = next(
(gene_id for gene_id, transcripts in saved_variants[0].
saved_variant_json['transcripts'].items() if any(
t['transcriptId'] == main_transcript_id
for t in transcripts)), None) if main_transcript_id else None
GeneNote.objects.create(
note=request_json.get('note'),
gene_id=gene_id,
created_by=request.user,
)
response['genesById'] = {
gene_id: {
'notes':
get_json_for_gene_notes_by_gene_id([gene_id],
request.user)[gene_id],
}
}
return create_json_response(response)
def create_variant_note_handler(request, variant_guid):
request_json = json.loads(request.body)
save_as_gene_note = request_json.get('saveAsGeneNote')
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.family.project, request.user, CAN_VIEW)
if save_as_gene_note:
main_transcript_id = saved_variant.selected_main_transcript_id or saved_variant.saved_variant_json[
'mainTranscriptId']
gene_id = next(
(gene_id for gene_id, transcripts in
saved_variant.saved_variant_json['transcripts'].items() if any(
t['transcriptId'] == main_transcript_id
for t in transcripts)), None) if main_transcript_id else None
create_seqr_model(
GeneNote,
note=request_json.get('note'),
gene_id=gene_id,
created_by=request.user,
)
gene_note = {
gene_id: {
'notes':
get_json_for_gene_notes_by_gene_id([gene_id], request.user).get(
gene_id, [])
}
} if save_as_gene_note else {}
_create_variant_note(saved_variant, request_json, request.user)
variant_note = {
variant_guid: {
'notes': [
get_json_for_variant_note(tag)
for tag in saved_variant.variantnote_set.all()
]
},
}
return create_json_response({
'savedVariantsByGuid': variant_note,
'genesById': gene_note
})
def create_variant_note_handler(request, variant_guid):
request_json = json.loads(request.body)
save_as_gene_note = request_json.get('saveAsGeneNote')
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
if save_as_gene_note:
gene_id = json.loads(
saved_variant.saved_variant_json)['mainTranscript']['geneId']
create_seqr_model(
GeneNote,
note=request_json.get('note'),
gene_id=gene_id,
created_by=request.user,
)
gene_note = {
gene_id: {
'notes':
get_json_for_gene_notes_by_gene_id([gene_id], request.user).get(
gene_id, [])
}
} if save_as_gene_note else {}
_create_variant_note(saved_variant, request_json, request.user)
variant_note = {
variant_guid: {
'notes': [
get_json_for_variant_note(tag)
for tag in saved_variant.variantnote_set.all()
]
},
}
return create_json_response({
'savedVariantsByGuid': variant_note,
'genesById': gene_note
})
def _get_json_for_genes(genes, user=None, gene_fields=None):
if not gene_fields:
gene_fields = {}
total_gene_constraints = None
if CONSTRAINT in gene_fields:
total_gene_constraints = GeneConstraint.objects.count()
if NOTES in gene_fields:
gene_notes_json = get_json_for_gene_notes_by_gene_id(
[gene.gene_id for gene in genes], user)
def _add_total_constraint_count(result, *args):
result['totalGenes'] = total_gene_constraints
def _process_result(result, gene):
for field, (_, result_func) in gene_fields.items():
if field == NOTES:
updates = {'notes': gene_notes_json.get(result['geneId'], [])}
elif field == CONSTRAINT:
constraint = _get_gene_model(gene, 'geneconstraint')
updates = {
'constraints': _get_json_for_model(
constraint, process_result=_add_total_constraint_count)
if constraint else {}
}
else:
updates = result_func(gene)
result.update(updates)
for model, _ in gene_fields.values():
if model:
prefetch_related_objects(
genes,
Prefetch('{}_set'.format(model.__name__.lower()),
queryset=model.objects.only(
'gene__gene_id', *model._meta.json_fields)))
return _get_json_for_models(genes, process_result=_process_result)
def _get_gene_notes(gene_id, user):
return get_json_for_gene_notes_by_gene_id([gene_id], user).get(gene_id, [])
def _get_gene_notes(gene_id, user):
return get_json_for_gene_notes_by_gene_id([gene_id], user).get(gene_id, [])
