def test_remove_phenomodel(app, user_obj, institute_obj, mocker,
mock_redirect):
"""Testing the endpoint to remove an existing phenotype model for an institute"""
mocker.patch("scout.server.blueprints.institutes.views.redirect",
return_value=mock_redirect)
# GIVEN an institute with a phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Test model",
"Model description")
model_obj = store.phenomodel_collection.find_one()
assert model_obj
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
form_data = {"model_id": model_obj["_id"]}
# WHEN the user removes the model via the remove_phenomodel endpoint
resp = client.post(
url_for("overview.remove_phenomodel",
institute_id=institute_obj["internal_id"]),
data=form_data,
)
# THEN the phenotype model should be deleted from the database
assert store.phenomodel_collection.find_one() is None
def test_phenomodel_POST_rename_model(app, user_obj, institute_obj):
"""Test the phenomodel endpoing, POST request for updating model info"""
# GIVEN an institute with a phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Old model", "Old description")
model_obj = store.phenomodel_collection.find_one()
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
# WHEN the user updates model info using a POST request
form_data = dict(
update_model="update", model_name="New model", model_desc="New description"
)
resp = client.post(
url_for(
"overview.phenomodel",
institute_id=institute_obj["internal_id"],
model_id=model_obj["_id"],
),
data=form_data,
)
# THEN the model in the database should be updated
updated_model = store.phenomodel_collection.find_one()
assert updated_model["name"] == "New model"
def test_phenomodel_POST_remove_subpanel_checkbox(app, user_obj, institute_obj):
"""Test removing a single checkbox from a phenotype model subpanel"""
# GIVEN an institute with a phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Test model", "Model description")
model_obj = store.phenomodel_collection.find_one()
# containing a subpanel with a checkbox
TEST_SUBPANEL["checkboxes"] = {"HP:000001": {"name": "HP:000001"}}
model_obj["subpanels"] = {"subpanel_x": TEST_SUBPANEL}
store.update_phenomodel(model_obj["_id"], model_obj)
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
# WHEN the user removes the checkbox using the endpoint, POST request
form_data = dict(checkgroup_remove="#".join(["HP:000001", "subpanel_x"]))
resp = client.post(
url_for(
"overview.checkbox_edit",
institute_id=institute_obj["internal_id"],
model_id=model_obj["_id"],
),
data=form_data,
)
# THEN the checkbox should be removed from the subpanel
updated_model = store.phenomodel_collection.find_one()
assert updated_model["subpanels"]["subpanel_x"]["checkboxes"] == {}
def test_phenomodel_unlock(app, user_obj, institute_obj, mocker,
mock_redirect):
"""Test the endpoint to unlock a phenomodel and make it editable only by all users"""
mocker.patch("scout.server.blueprints.institutes.views.redirect",
return_value=mock_redirect)
# GIVEN an institute with phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Test model",
"Model description")
model = store.phenomodel_collection.find_one()
# GIVEN an initialized app
with app.test_client() as client:
# GIVEN that the user could be logged in
client.get(url_for("auto_login"))
# Given that the phenomodel is locked and current user is admin
model["admins"] = [current_user.email]
store.update_phenomodel(model["_id"], model)
locked_model = store.phenomodel_collection.find_one()
assert locked_model["admins"] == [current_user.email]
# When the test_phenomodel_lock endpoint is used to unlock the model
form_data = dict(model_id=model["_id"], )
resp = client.post(
url_for("overview.lock_phenomodel"),
data=form_data,
)
# Then the page should redirect
assert resp.status_code == 302
# And the model will have no admins
unlocked_model = store.phenomodel_collection.find_one()
assert unlocked_model["admins"] == []
def test_phenomodel_lock(app, user_obj, institute_obj, mocker, mock_redirect):
"""Test the endpoint to lock a phenomodel and make it editable only by admins"""
mocker.patch("scout.server.blueprints.institutes.views.redirect",
return_value=mock_redirect)
# GIVEN an institute with a phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Test model",
"Model description")
model = store.phenomodel_collection.find_one()
assert "admins" not in model
admins = ["user1@email", "user2@email"]
# GIVEN an initialized app
with app.test_client() as client:
# GIVEN that the user could be logged in
client.get(url_for("auto_login"))
# WHEN the user locks model up using two admins
form_data = dict(model_id=model["_id"], lock="", user_admins=admins)
resp = client.post(
url_for("overview.lock_phenomodel"),
data=form_data,
)
# Then the page should redirect
assert resp.status_code == 302
# And current user + admins emails will be registered as the emails of the admins
locked_model = store.phenomodel_collection.find_one()
assert locked_model["admins"] == [current_user.email] + admins
def advanced_phenotypes(institute_id):
"""Show institute-level advanced phenotypes"""
institute_obj = institute_and_case(store, institute_id)
# Get a list of all users which are registered to this institute or collaborate with it
collaborators = set()
for inst_id in [institute_id] + institute_obj.get("collaborators", []):
for user in store.users(institute=inst_id):
if (user["email"] == current_user.email
): # Do not include current user among collaborators
continue
collaborators.add((user["email"], user["name"], inst_id))
if request.form.get("create_model"): # creating a new phenomodel
store.create_phenomodel(institute_id, request.form.get("model_name"),
request.form.get("model_desc"))
pheno_form = PhenoModelForm(request.form or None)
phenomodels = list(store.phenomodels(institute_id=institute_id))
data = {
"institute": institute_obj,
"collaborators": collaborators,
"pheno_form": pheno_form,
"phenomodels": phenomodels,
}
return data
def test_phenomodel_POST_add_hpo_checkbox_to_subpanel(app, user_obj,
institute_obj,
hpo_checkboxes):
"""Test adding an HPO checkbox with its children to a subpanel of a phenotype model via POST request"""
# GIVEN an institute with a phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Test model",
"Model description")
model_obj = store.phenomodel_collection.find_one()
# containing a subpanel
model_obj["subpanels"] = {"subpanel_x": TEST_SUBPANEL}
store.update_phenomodel(model_obj["_id"], model_obj)
# GIVEN a database with the required HPO terms (one parent term and one child term)
store.hpo_term_collection.insert_many(hpo_checkboxes)
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
# WHEN the user creates an HPO checkbox using the endpoint
form_data = dict(
hpo_subpanel_id="subpanel_x",
hpoHasTitle="on",
hpoTermTitle="Title for term",
hpo_term=" | ".join(
[hpo_checkboxes[0]["_id"], hpo_checkboxes[0]["description"]]),
hpo_custom_name="Alternative HPO name",
add_hpo="",
includeChildren="on",
)
resp = client.post(
url_for(
"overview.checkbox_edit",
institute_id=institute_obj["internal_id"],
model_id=model_obj["_id"],
),
data=form_data,
)
# THEN the term should have been added to the subpanel checkboxes
updated_model = store.phenomodel_collection.find_one()
checkbox = updated_model["subpanels"]["subpanel_x"]["checkboxes"][
"HP:0025190"]
assert checkbox["name"] == "HP:0025190"
assert checkbox["checkbox_type"] == "hpo"
assert checkbox[
"description"] == "Bilateral tonic-clonic seizure with generalized onset"
assert checkbox["term_title"] == form_data["hpoTermTitle"]
assert checkbox["custom_name"] == form_data["hpo_custom_name"]
# Additionally, the HPO term checkbox should contain a nested HPO term:
nested_hpo_term = {
"name": hpo_checkboxes[1]["_id"],
"description": hpo_checkboxes[1]["description"],
}
assert checkbox["children"] == [nested_hpo_term]
def test_phenomodel_POST_add_omim_checkbox_to_subpanel(app, user_obj,
institute_obj,
omim_checkbox):
"""Test adding an OMIM checkbox to a subpanel of a phenotype model via POST request"""
# GIVEN an institute with a phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Test model",
"Model description")
model_obj = store.phenomodel_collection.find_one()
# containing a subpanel
model_obj["subpanels"] = {"subpanel_x": TEST_SUBPANEL}
store.update_phenomodel(model_obj["_id"], model_obj)
model_obj = store.phenomodel_collection.find_one()
assert model_obj["subpanels"]["subpanel_x"]
# GIVEN that database contains the HPO term to add to the subopanel
store.disease_term_collection.insert_one(omim_checkbox)
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
# WHEN the user creates an OMIM checkbox using the endpoint
form_data = dict(
omim_subpanel_id="subpanel_x",
omimHasTitle="on",
omimTermTitle="Title for term",
omim_term=" | ".join(
[omim_checkbox["_id"], omim_checkbox["description"]]),
omim_custom_name="Alternative OMIM name",
add_omim="",
)
resp = client.post(
url_for(
"overview.checkbox_edit",
institute_id=institute_obj["internal_id"],
model_id=model_obj["_id"],
),
data=form_data,
)
# THEN the term should have been added to the subpanel checkboxe
updated_model = store.phenomodel_collection.find_one()
checkbox = updated_model["subpanels"]["subpanel_x"]["checkboxes"][
"OMIM:121210"]
assert checkbox["name"] == "OMIM:121210"
assert checkbox["checkbox_type"] == "omim"
assert checkbox["description"] == "Febrile seizures familial 1"
assert checkbox["term_title"] == form_data["omimTermTitle"]
assert checkbox["custom_name"] == form_data["omim_custom_name"]
def test_phenomodel_POST_add_delete_subpanel(app, user_obj, institute_obj):
"""Test the phenomodel endpoint, by sending requests for adding and deleting a subpanel"""
# GIVEN an institute with a phenotype model having no subpanels
store.create_phenomodel(institute_obj["internal_id"], "Test model",
"Model description")
model_obj = store.phenomodel_collection.find_one()
assert model_obj["subpanels"] == {}
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
form_data = dict(
title="Phenotype subpanel title",
subtitle="Phenotype subpanel subtitle",
add_subpanel="Save phenotype subpanel",
)
# WHEN the user creates subpanel in phenotype model via POST request
resp = client.post(
url_for(
"overview.phenomodel",
institute_id=institute_obj["internal_id"],
model_id=model_obj["_id"],
),
data=form_data,
)
# Then the subpanel dictionary should be added to model subpanels
updated_model = store.phenomodel_collection.find_one()
subpanel_id = list(updated_model["subpanels"].keys())[0]
assert updated_model["subpanels"][subpanel_id][
"title"] == "Phenotype subpanel title"
assert updated_model["subpanels"][subpanel_id][
"subtitle"] == "Phenotype subpanel subtitle"
# WHEN the user sends a POST request to remove the subpanel
form_data = dict(subpanel_delete=subpanel_id)
resp = client.post(
url_for(
"overview.phenomodel",
institute_id=institute_obj["internal_id"],
model_id=model_obj["_id"],
),
data=form_data,
)
# THEN the model should be removed from models subpanels
updated_model = store.phenomodel_collection.find_one()
assert updated_model["subpanels"] == {}
def advanced_phenotypes(institute_id):
"""Show institute-level advanced phenotypes"""
institute_obj = institute_and_case(store, institute_id)
if request.form.get("create_model"): # creating a new phenomodel
store.create_phenomodel(institute_id, request.form.get("model_name"),
request.form.get("model_desc"))
pheno_form = PhenoModelForm(request.form or None)
phenomodels = store.phenomodels(institute_id=institute_id)
data = {
"institute": institute_obj,
"pheno_form": pheno_form,
"phenomodels": phenomodels,
}
return data
def test_phenomodel_GET(app, user_obj, institute_obj):
"""test the phenomodel page endpoint, GET request"""
# GIVEN an institute with a phenotype model
store.create_phenomodel(institute_obj["internal_id"], "Test model", "Model description")
model_obj = store.phenomodel_collection.find_one()
# GIVEN an initialized app
# GIVEN a valid user and institute
with app.test_client() as client:
# GIVEN that the user could be logged in
resp = client.get(url_for("auto_login"))
# THEN the phenomodel endpoint should shown phenotype model info
resp = client.get(
url_for(
"overview.phenomodel",
institute_id=institute_obj["internal_id"],
model_id=model_obj["_id"],
)
)
assert "Test model" in str(resp.data)