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 test_json_for_variant_note(self):
tag = VariantNote.objects.first()
json = get_json_for_variant_note(tag)
fields = {
'noteGuid', 'note', 'submitToClinvar', 'lastModifiedDate', 'createdBy'
}
self.assertSetEqual(set(json.keys()), fields)
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
delete_seqr_model(note)
return create_json_response({'savedVariantsByGuid': {variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}}})
def test_json_for_variant_note(self):
tag = VariantNote.objects.first()
json = get_json_for_variant_note(tag)
fields = {
'noteGuid', 'note', 'submitToClinvar', 'lastModifiedDate', 'createdBy'
}
self.assertSetEqual(set(json.keys()), fields)
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
delete_seqr_model(note)
return create_json_response({variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}})
def create_variant_note_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
_create_variant_note(saved_variant, json.loads(request.body), request.user)
return create_json_response({'savedVariantsByGuid': {variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}}})
def update_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
request_json = json.loads(request.body)
update_model_from_json(note, request_json, allow_unknown_keys=True)
return create_json_response({'savedVariantsByGuid': {variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}}})
def update_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
note = VariantNote.objects.get(guid=note_guid, saved_variant=saved_variant)
request_json = json.loads(request.body)
update_model_from_json(note, request_json, allow_unknown_keys=True)
return create_json_response({variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}})
def update_variant_note_handler(request, variant_guids, note_guid):
note = VariantNote.objects.get(guid=note_guid)
projects = {saved_variant.family.project for saved_variant in note.saved_variants.all()}
for project in projects:
check_project_permissions(project, request.user)
request_json = json.loads(request.body)
update_model_from_json(note, request_json, user=request.user, allow_unknown_keys=True)
note_json = get_json_for_variant_note(note, add_variant_guids=False)
note_json['variantGuids'] = variant_guids.split(',')
return create_json_response({
'variantNotesByGuid': {note.guid: note_json},
})
def delete_variant_note_handler(request, variant_guid, note_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.family.project, request.user, CAN_VIEW)
VariantNote.objects.get(guid=note_guid,
saved_variant=saved_variant).delete()
return create_json_response({
'savedVariantsByGuid': {
variant_guid: {
'notes': [
get_json_for_variant_note(tag)
for tag in saved_variant.variantnote_set.all()
]
}
}
})
def create_variant_note_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
_create_variant_note(saved_variant, json.loads(request.body), request.user)
return create_json_response({
'savedVariantsByGuid': {
variant_guid: {
'notes': [
get_json_for_variant_note(tag)
for tag in saved_variant.variantnote_set.all()
]
}
}
})
def create_variant_note_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_EDIT)
request_json = json.loads(request.body)
create_seqr_model(
VariantNote,
saved_variant=saved_variant,
note=request_json.get('note'),
submit_to_clinvar=request_json.get('submitToClinvar', False),
search_parameters=request_json.get('searchParameters'),
created_by=request.user,
)
return create_json_response({variant_guid: {
'notes': [get_json_for_variant_note(tag) for tag in saved_variant.variantnote_set.all()]
}})
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 test_json_for_variant_note(self):
tag = VariantNote.objects.first()
json = get_json_for_variant_note(tag)
self.assertSetEqual(set(json.keys()), VARIANT_NOTE_FIELDS)
