def causatives(institute_obj, request):
"""Create content to be displayed on institute causatives page
Args:
institute_obj(dict) An institute object
request(flask.request) request sent by user's browser
Returns:
data(dict)
"""
# Retrieve variants grouped by case
query = request.args.get("query", "")
hgnc_id = None
if "|" in query:
# filter accepts an array of IDs. Provide an array with one ID element
try:
hgnc_id = [int(query.split(" | ", 1)[0])]
except ValueError:
flash("Provided gene info could not be parsed!", "warning")
variants = list(
store.check_causatives(institute_obj=institute_obj,
limit_genes=hgnc_id))
if variants:
variants = sorted(
variants,
key=lambda k: k.get("hgnc_symbols", [None])[0] or k.get("str_repid"
) or "",
)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj["category"] in ["snv", "cancer"]:
update_representative_gene(variant_obj, variant_obj.get(
"genes", [])) # required to display cDNA and protein change
if variant_obj["case_id"] not in all_cases:
case_obj = store.case(variant_obj["case_id"])
all_cases[variant_obj["case_id"]] = case_obj
else:
case_obj = all_cases[variant_obj["case_id"]]
if variant_obj["variant_id"] not in all_variants:
all_variants[variant_obj["variant_id"]] = []
all_variants[variant_obj["variant_id"]].append((case_obj, variant_obj))
data = dict(
institute=institute_obj,
variant_groups=all_variants,
acmg_map={
key: ACMG_COMPLETE_MAP[value]
for key, value in ACMG_MAP.items()
},
)
return data
def causatives(institute_id):
institute_obj = institute_and_case(store, institute_id)
query = request.args.get("query", "")
hgnc_id = None
if "|" in query:
# filter accepts an array of IDs. Provide an array with one ID element
try:
hgnc_id = [int(query.split(" | ", 1)[0])]
except ValueError:
flash("Provided gene info could not be parsed!", "warning")
variants = store.check_causatives(institute_obj=institute_obj,
limit_genes=hgnc_id)
if variants:
variants.sort("hgnc_symbols", pymongo.ASCENDING)
all_variants = {}
all_cases = {}
for variant_obj in variants:
if variant_obj["case_id"] not in all_cases:
case_obj = store.case(variant_obj["case_id"])
all_cases[variant_obj["case_id"]] = case_obj
else:
case_obj = all_cases[variant_obj["case_id"]]
if variant_obj["variant_id"] not in all_variants:
all_variants[variant_obj["variant_id"]] = []
all_variants[variant_obj["variant_id"]].append((case_obj, variant_obj))
acmg_map = {
key: ACMG_COMPLETE_MAP[value]
for key, value in ACMG_MAP.items()
}
return dict(institute=institute_obj,
variant_groups=all_variants,
acmg_map=acmg_map)
def update_variant_actions(self, institute_obj, case_obj, old_eval_variants):
"""Update existing variants of a case according to the tagged status
(manual_rank, dismiss_variant, mosaic_tags) of its previous variants
Accepts:
institute_obj(dict): an institute object
case_obj(dict): a case object
old_eval_variants(list(Variant))
Returns:
updated_variants(dict): a dictionary like this:
'manual_rank' : [list of variant ids],
'dismiss_variant' : [list of variant ids],
'mosaic_tags' : [list of variant ids],
'cancer_tier': [list of variant ids],
'acmg_classification': [list of variant ids]
'is_commented': [list of variant ids]
"""
updated_variants = {
"manual_rank": [],
"dismiss_variant": [],
"mosaic_tags": [],
"cancer_tier": [],
"acmg_classification": [],
"is_commented": [],
}
LOG.debug(
"Updating action status for {} variants in case:{}".format(
len(old_eval_variants), case_obj["_id"]
)
)
n_status_updated = 0
for old_var in old_eval_variants:
# search for the same variant in newly uploaded vars for this case
display_name = old_var["display_name"]
new_var = self.variant_collection.find_one(
{"case_id": case_obj["_id"], "display_name": display_name}
)
if new_var is None: # same var is no more among case variants, skip it
LOG.warning(
"Trying to propagate manual action from an old variant to a new, but couldn't find same variant any more"
)
continue
for action in list(
updated_variants.keys()
): # manual_rank, dismiss_variant, mosaic_tags
if (
old_var.get(action) is not None or action == "is_commented"
): # tag new variant accordingly
# collect only the latest associated event:
verb = action
if action == "acmg_classification":
verb = "acmg"
elif action == "is_commented":
verb = "comment"
old_event = self.event_collection.find_one(
{
"case": case_obj["_id"],
"verb": verb,
"variant_id": old_var["variant_id"],
"category": "variant",
},
sort=[("updated_at", pymongo.DESCENDING)],
)
if old_event is None:
continue
user_obj = self.user(old_event["user_id"])
if user_obj is None:
continue
# create a link to the new variant for the events
link = "/{0}/{1}/{2}".format(
new_var["institute"], case_obj["display_name"], new_var["_id"]
)
updated_variant = None
if action == "manual_rank":
updated_variant = self.update_manual_rank(
institute=institute_obj,
case=case_obj,
user=user_obj,
link=link,
variant=new_var,
manual_rank=old_var.get(action),
)
if action == "dismiss_variant":
updated_variant = self.update_dismiss_variant(
institute=institute_obj,
case=case_obj,
user=user_obj,
link=link,
variant=new_var,
dismiss_variant=old_var.get(action),
)
if action == "mosaic_tags":
updated_variant = self.update_mosaic_tags(
institute=institute_obj,
case=case_obj,
user=user_obj,
link=link,
variant=new_var,
mosaic_tags=old_var.get(action),
)
if action == "cancer_tier":
updated_variant = self.update_cancer_tier(
institute=institute_obj,
case=case_obj,
user=user_obj,
link=link,
variant=new_var,
cancer_tier=old_var.get(action),
)
if action == "acmg_classification":
str_classif = ACMG_MAP.get(old_var.get("acmg_classification"))
updated_variant = self.update_acmg(
institute_obj=institute_obj,
case_obj=case_obj,
user_obj=user_obj,
link=link,
variant_obj=new_var,
acmg_str=str_classif,
)
if action == "is_commented":
updated_comments = self.comments_reupload(
old_var, new_var, institute_obj, case_obj
)
if updated_comments > 0:
LOG.info(
"Created {} new comments for variant {} after reupload".format(
updated_comments, display_name
)
)
updated_variant = new_var
if updated_variant is not None:
n_status_updated += 1
updated_variants[action].append(updated_variant["_id"])
LOG.info("Variant actions updated {} times".format(n_status_updated))
return updated_variants