def update_phenomodel(model_id, user_form):
"""Update a phenotype model according to the user form
Args:
model_id(ObjectId): document ID of the model to be updated
user_form(request.form): a POST request form object
"""
model_dict = store.phenomodel(model_id)
update_model = False
if model_dict is None:
return
if user_form.get(
"update_model"): # update either model name of description
update_model = True
model_dict["name"] = user_form.get("model_name")
model_dict["description"] = user_form.get("model_desc")
if user_form.get(
"subpanel_delete"): # Remove a phenotype submodel from phenomodel
subpanels = model_dict["subpanels"]
# remove panel from subpanels dictionary
subpanels.pop(user_form.get("subpanel_delete"), None)
model_dict["subpanels"] = subpanels
update_model = True
if user_form.get("add_subpanel"): # Add a new phenotype submodel
update_model = _add_subpanel(model_id, model_dict, user_form)
if user_form.get("model_save"
): # Save model according user preferences in the preview
update_model = phenomodel_checkgroups_filter(model_dict, user_form)
if update_model:
store.update_phenomodel(model_id=model_id, model_obj=model_dict)
def phenomodel(institute_id, model_id):
"""View/Edit an advanced phenotype model"""
institute_obj = institute_and_case(store, institute_id)
pheno_form = PhenoModelForm(request.form)
subpanel_form = PhenoSubPanelForm(request.form)
hide_subpanel = True
if request.method == "POST":
# update an existing phenotype model
controllers.update_phenomodel(model_id, request.form)
phenomodel_obj = store.phenomodel(model_id)
if phenomodel_obj is None:
flash(
f"Could not retrieve given phenotype model using the given key '{model_id}'",
"warning",
)
return redirect(request.referrer)
pheno_form.model_name.data = phenomodel_obj["name"]
pheno_form.model_desc.data = phenomodel_obj["description"]
return dict(
institute=institute_obj,
pheno_form=pheno_form,
phenomodel=phenomodel_obj,
subpanel_form=subpanel_form,
)
def lock_phenomodel():
"""Lock or unlock a specific phenomodel for editing"""
form = request.form
model_id = form.get("model_id")
phenomodel_obj = store.phenomodel(model_id)
if phenomodel_obj is None:
return redirect(request.referrer)
phenomodel_obj["admins"] = []
if (
"lock" in form
): # lock phenomodel for all users except current user and specified collaborators
phenomodel_obj["admins"] = [current_user.email
] + form.getlist("user_admins")
# update phenomodels admins:
store.update_phenomodel(model_id, phenomodel_obj)
return redirect(request.referrer)
def edit_subpanel_checkbox(model_id, user_form):
"""Update checkboxes from one or more panels according to the user form
Args:
model_id(ObjectId): document ID of the model to be updated
user_form(request.form): a POST request form object
"""
model_dict = store.phenomodel(model_id)
update_model = False
if model_dict is None:
return
if "add_hpo" in user_form: # add an HPO checkbox to subpanel
update_model = _subpanel_hpo_checkgroup_add(model_dict, user_form)
if "add_omim" in user_form: # add an OMIM checkbox to subpanel
update_model = _subpanel_omim_checkbox_add(model_dict, user_form)
if user_form.get("checkgroup_remove"
): # remove a checkbox of any type from subpanel
update_model = _subpanel_checkgroup_remove_one(model_dict, user_form)
if update_model:
store.update_phenomodel(model_id=model_id, model_obj=model_dict)