def modify_managed_variant(store, managed_variant_id, edit_form):
"""Modify a managed variant."""
managed_variant = store.find_managed_variant(managed_variant_id)
if managed_variant is None:
return
original_obj_id = managed_variant["_id"]
managed_variant.update({
"chromosome": edit_form["chromosome"].data,
"position": edit_form["position"].data,
"end": edit_form["end"].data,
"reference": edit_form["reference"].data,
"alternative": edit_form["alternative"].data,
"category": edit_form["category"].data,
"sub_category": edit_form["sub_category"].data,
"description": edit_form["description"].data,
})
# new ids must be built upon update
updated_variant = build_managed_variant(managed_variant)
LOG.debug(
"Updated variant has mvid %s and old id is %s.",
updated_variant["managed_variant_id"],
original_obj_id,
)
result = store.upsert_managed_variant(updated_variant, original_obj_id)
return result
def upload_managed_variants(store, lines, institutes, current_user_id):
"""Add managed variants from a CSV file"""
total_variant_lines = 0
new_managed_variants = 0
for managed_variant_info in parse_managed_variant_lines(lines):
total_variant_lines += 1
if not validate_managed_variant(managed_variant_info):
flash(
f"Managed variant info line {total_variant_lines} has errors ({managed_variant_info})",
"warning",
)
continue
managed_variant_info.update({
"maintainer": [current_user_id],
"institutes": institutes
})
managed_variant_obj = build_managed_variant(managed_variant_info)
if store.upsert_managed_variant(managed_variant_obj):
new_managed_variants += 1
return new_managed_variants, total_variant_lines
def add_managed_variant(request):
"""Add a managed variant.
Args:
request(werkzeug.local.LocalProxy): request containing form data
"""
add_form = ManagedVariantAddForm(request.form)
institutes = list(user_institutes(store, current_user))
current_user_id = current_user._id
managed_variant_obj = build_managed_variant(
dict(
chromosome=add_form["chromosome"].data,
position=add_form["position"].data,
end=add_form["end"].data,
reference=add_form["reference"].data,
alternative=add_form["alternative"].data,
institutes=institutes,
maintainer=[current_user_id],
category=add_form["category"].data,
sub_category=add_form["sub_category"].data,
description=add_form["description"].data,
))
return store.upsert_managed_variant(managed_variant_obj)
def upload_managed_variants(store, lines, institutes, current_user_id):
"""Add managed variants from a CSV file"""
total_variant_lines = 0
new_managed_variants = 0
for managed_variant_info in parse_managed_variant_lines(lines):
total_variant_lines += 1
managed_variant_info.update({"maintainer": [current_user_id], "institutes": institutes})
managed_variant_obj = build_managed_variant(managed_variant_info)
if store.upsert_managed_variant(managed_variant_obj):
new_managed_variants += 1
return new_managed_variants, total_variant_lines
def add_managed_variant(store, add_form, institutes, current_user_id):
"""Add a managed variant."""
managed_variant_obj = build_managed_variant(
dict(
chromosome=add_form["chromosome"].data,
position=add_form["position"].data,
end=add_form["end"].data,
reference=add_form["reference"].data,
alternative=add_form["alternative"].data,
institutes=institutes,
maintainer=[current_user_id],
category=add_form["category"].data,
sub_category=add_form["sub_category"].data,
description=add_form["description"].data,
))
return store.upsert_managed_variant(managed_variant_obj)