def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
level = "phenotype" if "phenotype" in request.form else "gene"
omim_id = request.form["omim_term"].split("|")[0]
if not "OMIM:" in omim_id: # Could be an omim number provided by user
omim_id = ":".join(["OMIM", omim_id])
# Make sure omim term exists in database:
omim_obj = store.disease_term(omim_id.strip())
if not omim_obj:
flash("Couldn't find any disease term with id: {}".format(omim_id),
"warning")
remove = True if request.args.get("remove") == "yes" else False
store.diagnose(
institute_obj,
case_obj,
user_obj,
link,
level=level,
omim_id=omim_id,
remove=remove,
)
return redirect(request.referrer)
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
omim_id = request.form["omim_term"].split("|")[0]
omim_inds = request.form.getlist(
"omim_inds") # Individual-level phenotypes
if not "OMIM:" in omim_id: # Could be an omim number provided by user
omim_id = ":".join(["OMIM", omim_id])
# Make sure omim term exists in database:
omim_obj = store.disease_term(omim_id.strip())
if omim_obj is None:
flash("Couldn't find any disease term with id: {}".format(omim_id),
"warning")
return redirect(request.referrer)
remove = True if request.args.get("remove") == "yes" else False
store.diagnose(institute_obj, case_obj, user_obj, link, omim_obj,
omim_inds, remove)
return redirect("#".join([link, "omim_assign"]))
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
level = 'phenotype' if 'phenotype' in request.form else 'gene'
omim_id = request.form['omim_id']
remove = True if request.args.get('remove') == 'yes' else False
store.diagnose(institute_obj, case_obj, user_obj, link, level=level,
omim_id=omim_id, remove=remove)
return redirect(request.referrer)
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
user_obj = store.user(current_user.email)
link = url_for('.case', institute_id=institute_id, case_name=case_name)
level = 'phenotype' if 'phenotype' in request.form else 'gene'
omim_id = request.form['omim_id']
remove = True if request.args.get('remove') == 'yes' else False
store.diagnose(institute_obj, case_obj, user_obj, link, level=level,
omim_id=omim_id, remove=remove)
return redirect(request.referrer)
def case_diagnosis(institute_id, case_name):
"""Add or remove a diagnosis for a case."""
institute_obj, case_obj = institute_and_case(store, institute_id,
case_name)
user_obj = store.user(current_user.email)
link = url_for(".case", institute_id=institute_id, case_name=case_name)
level = "phenotype" if "phenotype" in request.form else "gene"
omim_id = request.form["omim_id"]
remove = True if request.args.get("remove") == "yes" else False
store.diagnose(
institute_obj,
case_obj,
user_obj,
link,
level=level,
omim_id=omim_id,
remove=remove,
)
return redirect(request.referrer)