def phenotypes(institute_id, case_name, phenotype_id=None):
"""Handle phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
is_group = request.args.get('is_group') == 'yes'
user_obj = store.user(current_user.email)
if phenotype_id:
# DELETE a phenotype item/group from case
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
phenotype_id, is_group=is_group)
else:
try:
# add a new phenotype item/group to the case
phenotype_term = request.form['hpo_term']
if phenotype_term.startswith('HP:') or len(phenotype_term) == 7:
hpo_term = phenotype_term.split(' | ', 1)[0]
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_term=hpo_term, is_group=is_group)
else:
# assume omim id
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
omim_term=phenotype_term)
except ValueError:
return abort(400, ("unable to add phenotype: {}".format(phenotype_term)))
return redirect(case_url)
def phenotypes(institute_id, case_name, phenotype_id=None):
"""Handle phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
case_url = url_for('.case', institute_id=institute_id, case_name=case_name)
is_group = request.args.get('is_group') == 'yes'
user_obj = store.user(current_user.email)
if phenotype_id:
# DELETE a phenotype item/group from case
store.remove_phenotype(institute_obj, case_obj, user_obj, case_url,
phenotype_id, is_group=is_group)
else:
try:
# add a new phenotype item/group to the case
phenotype_term = request.form['hpo_term']
if phenotype_term.startswith('HP:') or len(phenotype_term) == 7:
hpo_term = phenotype_term.split(' | ', 1)[0]
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
hpo_term=hpo_term, is_group=is_group)
else:
# assume omim id
store.add_phenotype(institute_obj, case_obj, user_obj, case_url,
omim_term=phenotype_term)
except ValueError:
return abort(400, ("unable to add phenotype: {}".format(phenotype_term)))
return redirect(case_url)
def phenotypes(institute_id, case_name, phenotype_id=None):
"""Handle phenotypes."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
case_url = url_for(".case", institute_id=institute_id, case_name=case_name)
is_group = request.args.get("is_group") == "yes"
user_obj = store.user(current_user.email)
if phenotype_id:
# DELETE a phenotype item/group from case
store.remove_phenotype(institute_obj,
case_obj,
user_obj,
case_url,
phenotype_id,
is_group=is_group)
else:
try:
# add a new phenotype item/group to the case
hpo_term = None
omim_term = None
phenotype_term = request.form["hpo_term"]
phenotype_inds = request.form.getlist(
"phenotype_inds") # Individual-level phenotypes
if phenotype_term.startswith("HP:") or len(phenotype_term) == 7:
hpo_term = phenotype_term.split(" | ", 1)[0]
else:
omim_term = phenotype_term
store.add_phenotype(
institute=institute_obj,
case=case_obj,
user=user_obj,
link=case_url,
hpo_term=hpo_term,
omim_term=omim_term,
is_group=is_group,
phenotype_inds=phenotype_inds,
)
except ValueError:
flash(
f"Unable to add phenotype for the given terms:{phenotype_term}",
"warning",
)
return redirect(case_url)
return redirect("#".join([case_url, "phenotypes_panel"]))