def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = request.referrer
manual_rank = request.form.get('manual_rank')
if manual_rank:
new_manual_rank = int(manual_rank) if manual_rank != '-1' else None
store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj,
new_manual_rank)
if new_manual_rank:
flash("updated variant tag: {}".format(new_manual_rank), 'info')
else:
flash("reset variant tag: {}".format(variant_obj.get('manual_rank', 'NA')), 'info')
elif request.form.get('acmg_classification'):
new_acmg = request.form['acmg_classification']
acmg_classification = variant_obj.get('acmg_classification')
if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]):
new_acmg = None
store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg)
flash("updated ACMG classification: {}".format(new_acmg), 'info')
new_dismiss = request.form.getlist('dismiss_variant')
if request.form.getlist('dismiss_variant'):
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
if new_dismiss:
flash("Dismissed variant: {}".format(new_dismiss), 'info')
if variant_obj.get('dismiss_variant') and not new_dismiss:
if 'dismiss' in request.form:
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
flash("Reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
else:
log.debug("DO NOT reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
mosaic_tags = request.form.getlist('mosaic_tags')
if mosaic_tags:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
if new_dismiss:
flash("Added mosaic tags: {}".format(mosaic_tags), 'info')
if variant_obj.get('mosaic_tags') and not mosaic_tags:
if 'mosaic' in request.form:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
flash("Reset mosaic tags: {}".format(variant_obj.get('mosaic_tags')), 'info')
return redirect(request.referrer)
def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = request.referrer
manual_rank = request.form.get('manual_rank')
if manual_rank:
new_manual_rank = int(manual_rank) if manual_rank != '-1' else None
store.update_manual_rank(institute_obj, case_obj, user_obj, link, variant_obj,
new_manual_rank)
if new_manual_rank:
flash("updated variant tag: {}".format(new_manual_rank), 'info')
else:
flash("reset variant tag: {}".format(variant_obj.get('manual_rank', 'NA')), 'info')
elif request.form.get('acmg_classification'):
new_acmg = request.form['acmg_classification']
acmg_classification = variant_obj.get('acmg_classification')
if isinstance(acmg_classification, int) and (new_acmg == ACMG_MAP[acmg_classification]):
new_acmg = None
store.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, new_acmg)
flash("updated ACMG classification: {}".format(new_acmg), 'info')
new_dismiss = request.form.getlist('dismiss_variant')
if request.form.getlist('dismiss_variant'):
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
if new_dismiss:
flash("Dismissed variant: {}".format(new_dismiss), 'info')
if variant_obj.get('dismiss_variant') and not new_dismiss:
if 'dismiss' in request.form:
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link, variant_obj,
new_dismiss)
flash("Reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
else:
log.debug("DO NOT reset variant dismissal: {}".format(variant_obj.get('dismiss_variant')), 'info')
mosaic_tags = request.form.getlist('mosaic_tags')
if mosaic_tags:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
if new_dismiss:
flash("Added mosaic tags: {}".format(mosaic_tags), 'info')
if variant_obj.get('mosaic_tags') and not mosaic_tags:
if 'mosaic' in request.form:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link, variant_obj,
mosaic_tags)
flash("Reset mosaic tags: {}".format(variant_obj.get('mosaic_tags')), 'info')
return redirect(request.referrer)
def variant_update(institute_id, case_name, variant_id):
"""Update user-defined information about a variant: manual rank & ACMG."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
link = request.referrer
manual_rank = request.form.get("manual_rank")
cancer_tier = request.form.get("cancer_tier")
if manual_rank:
try:
new_manual_rank = int(manual_rank) if manual_rank != "-1" else None
except ValueError:
LOG.warning(
"Attempt to update manual rank with invalid value {}".format(
manual_rank))
manual_rank = "-1"
new_manual_rank = -1
store.update_manual_rank(institute_obj, case_obj, user_obj, link,
variant_obj, new_manual_rank)
if new_manual_rank:
flash("updated variant tag: {}".format(new_manual_rank), "info")
else:
flash(
"reset variant tag: {}".format(
variant_obj.get("manual_rank", "NA")),
"info",
)
elif cancer_tier:
try:
new_cancer_tier = cancer_tier if cancer_tier != "-1" else None
except ValueError:
LOG.warning(
"Attempt to update cancer tier with invalid value {}".format(
cancer_tier))
cancer_tier = "-1"
new_cancer_tier = "-1"
store.update_cancer_tier(institute_obj, case_obj, user_obj, link,
variant_obj, new_cancer_tier)
if new_cancer_tier:
flash("updated variant tag: {}".format(new_cancer_tier), "info")
else:
flash(
"reset variant tag: {}".format(
variant_obj.get("cancer_tier", "NA")),
"info",
)
elif request.form.get("acmg_classification"):
new_acmg = request.form["acmg_classification"]
acmg_classification = variant_obj.get("acmg_classification")
# If there already is a classification and the same one is sent again this means that
# We want to remove the classification
if isinstance(acmg_classification,
int) and (new_acmg == ACMG_MAP[acmg_classification]):
new_acmg = None
store.submit_evaluation(
variant_obj=variant_obj,
user_obj=user_obj,
institute_obj=institute_obj,
case_obj=case_obj,
link=link,
classification=new_acmg,
)
flash("updated ACMG classification: {}".format(new_acmg), "info")
new_dismiss = request.form.getlist("dismiss_variant")
if new_dismiss:
store.update_dismiss_variant(institute_obj, case_obj, user_obj, link,
variant_obj, new_dismiss)
flash("Dismissed variant: {}".format(new_dismiss), "info")
variant_dismiss = variant_obj.get("dismiss_variant")
if variant_dismiss and not new_dismiss:
if "dismiss" in request.form:
store.update_dismiss_variant(institute_obj, case_obj, user_obj,
link, variant_obj, new_dismiss)
flash(
"Reset variant dismissal: {}".format(
variant_obj.get("dismiss_variant")),
"info",
)
else:
LOG.debug("DO NOT reset variant dismissal: {}".format(
",".join(variant_dismiss), "info"))
mosaic_tags = request.form.getlist("mosaic_tags")
if mosaic_tags:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link,
variant_obj, mosaic_tags)
flash("Added mosaic tags: {}".format(mosaic_tags), "info")
variant_mosaic = variant_obj.get("mosaic_tags")
if variant_mosaic and not mosaic_tags:
if "mosaic" in request.form:
store.update_mosaic_tags(institute_obj, case_obj, user_obj, link,
variant_obj, mosaic_tags)
flash("Reset mosaic tags: {}".format(",".join(variant_mosaic),
"info"))
return redirect(request.referrer)