def update_variant_tags_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)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')]
new_tags = [tag for tag in updated_tags if not tag.get('tagGuid')]
for tag in saved_variant.varianttag_set.exclude(guid__in=existing_tag_guids):
delete_seqr_model(tag)
for tag in new_tags:
variant_tag_type = VariantTagType.objects.get(
Q(name=tag['name']),
Q(project=saved_variant.project) | Q(project__isnull=True)
)
create_seqr_model(
VariantTag,
saved_variant=saved_variant,
variant_tag_type=variant_tag_type,
search_parameters=request_json.get('searchParameters'),
created_by=request.user,
)
# Update functional data
existing_functional_guids = [tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')]
for tag in saved_variant.variantfunctionaldata_set.exclude(guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant
)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_parameters=request_json.get('searchParameters'),
created_by=request.user,
)
return create_json_response({
variant_guid: {
'tags': [get_json_for_variant_tag(tag) for tag in saved_variant.varianttag_set.all()],
'functionalData': [get_json_for_variant_functional_data(tag) for tag in saved_variant.variantfunctionaldata_set.all()]
}
})
def _update_locus_list_items(locus_list, new_genes, existing_gene_ids, new_intervals, existing_interval_guids, request_json, user):
# Update genes
for locus_list_gene in locus_list.locuslistgene_set.exclude(gene_id__in=existing_gene_ids):
delete_seqr_model(locus_list_gene)
for gene_id in new_genes.keys():
create_seqr_model(
LocusListGene,
locus_list=locus_list,
gene_id=gene_id,
created_by=user,
)
# Update intervals
genome_version = request_json.get('intervalGenomeVersion') or GENOME_VERSION_GRCh37
locus_list.locuslistinterval_set.exclude(guid__in=existing_interval_guids).delete()
for existing_interval in locus_list.locuslistinterval_set.all():
update_model_from_json(existing_interval, {'genomeVersion': genome_version})
for interval in new_intervals:
LocusListInterval.objects.create(
locus_list=locus_list,
chrom=interval['chrom'].lstrip('chr'),
start=interval['start'],
end=interval['end'],
genome_version=genome_version,
)
def _create_variant_note(saved_variant, note_json, user):
create_seqr_model(
VariantNote,
saved_variant=saved_variant,
note=note_json.get('note'),
submit_to_clinvar=note_json.get('submitToClinvar') or False,
search_hash=note_json.get('searchHash'),
created_by=user,
)
def _create_variant_note(saved_variant, note_json, user):
create_seqr_model(
VariantNote,
saved_variant=saved_variant,
note=note_json.get('note'),
submit_to_clinvar=note_json.get('submitToClinvar') or False,
search_hash=note_json.get('searchHash'),
created_by=user,
)
def create_gene_note_handler(request, gene_id):
request_json = json.loads(request.body)
create_seqr_model(
GeneNote,
note=request_json.get('note'),
gene_id=gene_id,
created_by=request.user,
)
return create_json_response({'genesById': {gene_id: {
'notes': _get_gene_notes(gene_id, request.user)
}}})
def create_gene_note_handler(request, gene_id):
request_json = json.loads(request.body)
create_seqr_model(
GeneNote,
note=request_json.get('note'),
gene_id=gene_id,
created_by=request.user,
)
return create_json_response(
{gene_id: {
'notes': _get_gene_notes(gene_id, request.user)
}})
def _create_new_tags(saved_variant, tags_json, user):
tags = tags_json.get('tags', [])
new_tags = [tag for tag in tags if not tag.get('tagGuid')]
for tag in new_tags:
variant_tag_type = VariantTagType.objects.get(
Q(name=tag['name']),
Q(project=saved_variant.family.project) | Q(project__isnull=True))
create_seqr_model(
VariantTag,
saved_variant=saved_variant,
variant_tag_type=variant_tag_type,
search_hash=tags_json.get('searchHash'),
created_by=user,
)
def handle(self, *args, **options):
project_name = options['project']
tag_options = {
k: options[k] or ''
for k in ['name', 'order', 'category', 'description', 'color']
}
project = Project.objects.get(
Q(name=project_name) | Q(guid=project_name))
if VariantTagType.objects.filter(name__iexact=options['name']).filter(
Q(project=project) | Q(project__isnull=True)):
raise CommandError('Tag "{}" already exists for project {}'.format(
options['name'], project_name))
create_seqr_model(VariantTagType, project=project, **tag_options)
def update_family_analysed_by(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_EDIT)
create_seqr_model(FamilyAnalysedBy, family=family, created_by=request.user)
return create_json_response(
{family.guid: _get_json_for_family(family, request.user)})
def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.project, request.user, CAN_VIEW)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')]
for tag in saved_variant.varianttag_set.exclude(guid__in=existing_tag_guids):
delete_seqr_model(tag)
_create_new_tags(saved_variant, request_json, request.user)
# Update functional data
existing_functional_guids = [tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')]
for tag in saved_variant.variantfunctionaldata_set.exclude(guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant
)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_hash=request_json.get('searchHash'),
created_by=request.user,
)
return create_json_response({'savedVariantsByGuid': {
variant_guid: {
'tags': [get_json_for_variant_tag(tag) for tag in saved_variant.varianttag_set.all()],
'functionalData': [get_json_for_variant_functional_data(tag) for tag in saved_variant.variantfunctionaldata_set.all()]
}
}})
def _create_new_tags(saved_variant, tags_json, user):
tags = tags_json.get('tags', [])
new_tags = [tag for tag in tags if not tag.get('tagGuid')]
for tag in new_tags:
variant_tag_type = VariantTagType.objects.get(
Q(name=tag['name']),
Q(project=saved_variant.project) | Q(project__isnull=True)
)
create_seqr_model(
VariantTag,
saved_variant=saved_variant,
variant_tag_type=variant_tag_type,
search_hash=tags_json.get('searchHash'),
created_by=user,
)
def update_family_analysed_by(request, family_guid):
"""Updates the specified field in the Family model.
Args:
family_guid (string): GUID of the family.
field_name (string): Family model field name to update
"""
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_EDIT)
create_seqr_model(FamilyAnalysedBy, family=family, created_by=request.user)
return create_json_response({
family.guid: _get_json_for_family(family, request.user)
})
def create_locus_list_handler(request):
request_json = json.loads(request.body)
if not request_json.get('name'):
return create_json_response({},
status=400,
reason='"Name" is required')
genes_by_id, intervals, invalid_items = parse_locus_list_items(
request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items},
status=400,
reason=INVALID_ITEMS_ERROR)
locus_list = create_seqr_model(
LocusList,
name=request_json['name'],
description=request_json.get('description') or '',
is_public=request_json.get('isPublic') or False,
created_by=request.user,
)
_update_locus_list_items(locus_list, genes_by_id, intervals, request_json,
request.user)
add_locus_list_user_permissions(locus_list)
return create_json_response({
'locusListsByGuid': {
locus_list.guid: get_json_for_locus_list(locus_list, request.user)
},
'genesById': genes_by_id,
})
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 update_analysis_group_handler(request, project_guid, analysis_group_guid=None):
project = get_project_and_check_permissions(project_guid, request.user, permission_level=CAN_EDIT)
request_json = json.loads(request.body)
missing_fields = [field for field in REQUIRED_FIELDS.keys() if not request_json.get(field)]
if missing_fields:
return create_json_response(
{}, status=400, reason='Missing required field(s): {missing_field_names}'.format(
missing_field_names=', '.join([REQUIRED_FIELDS[field] for field in missing_fields])
))
families = Family.objects.filter(guid__in=request_json['familyGuids']).only('guid')
if len(families) != len(request_json['familyGuids']):
return create_json_response(
{}, status=400, reason='The following families do not exist: {missing_families}'.format(
missing_families=', '.join(set(request_json['familyGuids']) - set([family.guid for family in families]))
))
if analysis_group_guid:
analysis_group = AnalysisGroup.objects.get(guid=analysis_group_guid, project=project)
update_model_from_json(analysis_group, request_json, allow_unknown_keys=True)
else:
try:
analysis_group = create_seqr_model(
AnalysisGroup,
project=project,
name=request_json['name'],
description=request_json.get('description'),
created_by=request.user,
)
except IntegrityError:
return create_json_response(
{}, status=400, reason='An analysis group named "{name}" already exists for project "{project}"'.format(
name=request_json['name'], project=project.name
))
analysis_group.families.set(families)
base_family_group = find_matching_xbrowse_model(analysis_group)
if base_family_group:
base_family_group.families.set(BaseFamily.objects.filter(seqr_family__in=families))
return create_json_response({
'analysisGroupsByGuid': {
analysis_group.guid: get_json_for_analysis_group(analysis_group, project_guid=project_guid)
},
})
def update_analysis_group_handler(request, project_guid, analysis_group_guid=None):
project = get_project_and_check_permissions(project_guid, request.user, permission_level=CAN_EDIT)
request_json = json.loads(request.body)
missing_fields = [field for field in REQUIRED_FIELDS.keys() if not request_json.get(field)]
if missing_fields:
return create_json_response(
{}, status=400, reason='Missing required field(s): {missing_field_names}'.format(
missing_field_names=', '.join([REQUIRED_FIELDS[field] for field in missing_fields])
))
families = Family.objects.filter(guid__in=request_json['familyGuids']).only('guid')
if len(families) != len(request_json['familyGuids']):
return create_json_response(
{}, status=400, reason='The following families do not exist: {missing_families}'.format(
missing_families=', '.join(set(request_json['familyGuids']) - set([family.guid for family in families]))
))
if analysis_group_guid:
analysis_group = AnalysisGroup.objects.get(guid=analysis_group_guid, project=project)
update_model_from_json(analysis_group, request_json, allow_unknown_keys=True)
else:
try:
analysis_group = create_seqr_model(
AnalysisGroup,
project=project,
name=request_json['name'],
description=request_json.get('description'),
created_by=request.user,
)
except IntegrityError:
return create_json_response(
{}, status=400, reason='An analysis group named "{name}" already exists for project "{project}"'.format(
name=request_json['name'], project=project.name
))
analysis_group.families.set(families)
update_xbrowse_family_group_families(analysis_group, families)
return create_json_response({
'analysisGroupsByGuid': {
analysis_group.guid: get_json_for_analysis_group(analysis_group, project_guid=project_guid)
},
})
def create_locus_list_handler(request):
request_json = json.loads(request.body)
if not request_json.get('name'):
return create_json_response({}, status=400, reason='"Name" is required')
genes_by_id, intervals, invalid_items = parse_locus_list_items(request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items}, status=400, reason=INVALID_ITEMS_ERROR)
locus_list = create_seqr_model(
LocusList,
name=request_json['name'],
description=request_json.get('description') or '',
is_public=request_json.get('isPublic') or False,
created_by=request.user,
)
_update_locus_list_items(locus_list, genes_by_id, intervals, request_json, request.user)
add_locus_list_user_permissions(locus_list)
return create_json_response({
'locusListsByGuid': {locus_list.guid: get_json_for_locus_list(locus_list, request.user)},
'genesById': genes_by_id,
})
def update_variant_tags_handler(request, variant_guid):
saved_variant = SavedVariant.objects.get(guid=variant_guid)
check_permissions(saved_variant.family.project, request.user, CAN_VIEW)
request_json = json.loads(request.body)
updated_tags = request_json.get('tags', [])
updated_functional_data = request_json.get('functionalData', [])
# Update tags
existing_tag_guids = [
tag['tagGuid'] for tag in updated_tags if tag.get('tagGuid')
]
for tag in saved_variant.varianttag_set.exclude(
guid__in=existing_tag_guids):
delete_seqr_model(tag)
_create_new_tags(saved_variant, request_json, request.user)
# Update functional data
existing_functional_guids = [
tag['tagGuid'] for tag in updated_functional_data if tag.get('tagGuid')
]
for tag in saved_variant.variantfunctionaldata_set.exclude(
guid__in=existing_functional_guids):
delete_seqr_model(tag)
for tag in updated_functional_data:
if tag.get('tagGuid'):
tag_model = VariantFunctionalData.objects.get(
guid=tag.get('tagGuid'),
functional_data_tag=tag.get('name'),
saved_variant=saved_variant)
update_model_from_json(tag_model, tag, allow_unknown_keys=True)
else:
create_seqr_model(
VariantFunctionalData,
saved_variant=saved_variant,
functional_data_tag=tag.get('name'),
metadata=tag.get('metadata'),
search_hash=request_json.get('searchHash'),
created_by=request.user,
)
return create_json_response({
'savedVariantsByGuid': {
variant_guid: {
'tags': [
get_json_for_variant_tag(tag)
for tag in saved_variant.varianttag_set.all()
],
'functionalData': [
get_json_for_variant_functional_data(tag)
for tag in saved_variant.variantfunctionaldata_set.all()
]
}
}
})
