def case_phenotype(institute_id, case_id, phenotype_id=None):
"""Add a new HPO term to the case.
TODO: validate ID and fetch phenotype description before adding to case.
"""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
case_url = url_for(".case", institute_id=institute_id, case_id=case_id)
if phenotype_id:
# DELETE a phenotype from the list
store.remove_phenotype(institute, case_model, current_user, case_url, phenotype_id)
else:
try:
# POST a new phenotype to the list
phenotype_term = request.form["hpo_term"]
if phenotype_term.startswith("HP:") or len(phenotype_term) == 7:
store.add_phenotype(institute, case_model, current_user, case_url, hpo_term=phenotype_term)
else:
# assume omim id
store.add_phenotype(institute, case_model, current_user, case_url, omim_term=phenotype_term)
except ValueError:
return abort(400, ("unable to add phenotype term: {}".format(phenotype_id)))
# fetch genes to update dynamic gene list
genes = hpo_genes(case_model.phenotype_terms)
store.update_dynamic_gene_list(case_model, genes)
return redirect(case_url)
def case_phenotype(institute_id, case_id, phenotype_id=None):
"""Add a new HPO term to the case.
TODO: validate ID and fetch phenotype description before adding to case.
"""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
case_url = url_for('.case', institute_id=institute_id, case_id=case_id)
if phenotype_id:
# DELETE a phenotype from the list
store.remove_phenotype(institute, case_model, current_user, case_url,
phenotype_id)
else:
# POST a new phenotype to the list
hpo_term = request.form['hpo_term']
store.add_phenotype(institute, case_model, current_user, case_url,
hpo_term)
# fetch genes to update dynamic gene list
genes = hpo_genes(case_model.phenotype_terms)
store.update_dynamic_gene_list(case_model, genes)
return redirect(case_url)
def case_phenotype(institute_id, case_id, phenotype_id=None):
"""Add a new HPO term to the case.
TODO: validate ID and fetch phenotype description before adding to case.
"""
institute = validate_user(current_user, institute_id)
case_model = store.case(institute_id, case_id)
case_url = url_for('.case', institute_id=institute_id, case_id=case_id)
if phenotype_id:
# DELETE a phenotype from the list
store.remove_phenotype(institute, case_model, current_user, case_url, phenotype_id)
else:
# POST a new phenotype to the list
hpo_term = request.form['hpo_term']
store.add_phenotype(institute, case_model, current_user, case_url, hpo_term)
# fetch genes to update dynamic gene list
genes = hpo_genes(case_model.phenotype_terms)
store.update_dynamic_gene_list(case_model, genes)
return redirect(case_url)
