def sv_variant(institute_id, case_name, variant_id):
"""Display a specific structural variant."""
data = variant_controller(store, institute_id, case_name, variant_id, add_other=False)
if current_app.config.get("LOQUSDB_SETTINGS"):
LOG.debug("Fetching loqusdb information for %s", variant_id)
data["observations"] = observations(store, loqusdb, data["case"], data["variant"])
return data
def variant(institute_id, case_name, variant_id):
"""Display a specific SNV variant."""
LOG.debug("Variants view requesting data for variant %s", variant_id)
data = variant_controller(store, institute_id, case_name, variant_id=variant_id)
if data is None:
LOG.warning(
"An error occurred: variants view requesting data for variant {}".format(variant_id)
)
flash("An error occurred while retrieving variant object", "danger")
return redirect(request.referrer)
if current_app.config.get("LOQUSDB_SETTINGS"):
LOG.debug("Fetching loqusdb information for %s", variant_id)
data["observations"] = observations(store, loqusdb, data["case"], data["variant"])
return data
def test_observations_controller(app, real_variant_database, case_obj, loqusdb):
## GIVEN a database and a loqusdb mock with one variant from the database
var_obj = real_variant_database.variant_collection.find_one()
assert var_obj
loqusdb._add_variant(var_obj)
## WHEN updating the case_id for the variant
var_obj["case_id"] = "internal_id2"
data = None
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
data = observations(real_variant_database, loqusdb, case_obj, var_obj)
## THEN assert that the data was found
assert data
def test_observations_controller_non_existing(app, real_variant_database, case_obj, loqusdb):
## GIVEN a database and a loqusdb mock without the variant
var_obj = real_variant_database.variant_collection.find_one()
assert var_obj
## WHEN updating the case_id for the variant
var_obj["case_id"] = "internal_id2"
data = None
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
data = observations(real_variant_database, loqusdb, case_obj, var_obj)
## THEN assert that the number of cases is still returned
assert data["total"] == loqusdb.nr_cases
## THEN assert the cases variable is in data
assert "cases" in data
## THEN assert there are no case information returned
assert data["cases"] == []
def test_observations_controller_sv(app, sv_variant_obj, institute_obj, loqusdburl):
"""Testing observations controller to retrieve observations for one SV variant.
Test that SV variant similar to a given one from another case is returned
"""
case_obj = store.case_collection.find_one()
# GIVEN an app with a connected loqusdb instance
loqus_id = "test"
assert app.config["LOQUSDB_SETTINGS"][loqus_id]
# GIVEN that the institute is associated to the same loqusdb instance
store.institute_collection.find_one_and_update(
{"_id": institute_obj["_id"]}, {"$set": {"loqusdb_id": loqus_id}}
)
# GIVEN a database with a case with a specific SV variant
store.variant_collection.insert_one(sv_variant_obj)
## GIVEN patched request to the loqusdbapi instance
req_url = f"{loqusdburl}/svs/?chrom={sv_variant_obj['chromosome']}&end_chrom={sv_variant_obj['end_chrom']}&pos={sv_variant_obj['position']}&end={sv_variant_obj['end']}&sv_type={sv_variant_obj['sub_category'].upper()}"
responses.add(
responses.GET,
req_url,
json={"families": [sv_variant_obj["case_id"]], "observations": 1},
status=200,
)
# WHEN the same variant is in another case
sv_variant_obj["case_id"] = "internal_id2"
# And has a different variant_id
sv_variant_obj["variant_id"] = "someOtherVarID"
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
# THEN the observation of the original case should be found
data = observations(store, loqusdb, case_obj, sv_variant_obj)
## THEN loqus should return the occurrence from the first case
assert case_obj["_id"] in data[loqus_id]["families"]
assert data[loqus_id]["cases"][0]["case"] == case_obj
assert data[loqus_id]["cases"][0]["variant"]["_id"] == sv_variant_obj["_id"]
def sv_variant(institute_id, case_name, variant_id):
"""Display a specific structural variant."""
data = variant_controller(store,
institute_id,
case_name,
variant_id,
add_other=False)
if data is None:
flash("An error occurred while retrieving variant object", "danger")
return redirect(
url_for("variants.sv_variants",
institute_id=institute_id,
case_name=case_name))
if current_app.config.get("LOQUSDB_SETTINGS"):
LOG.debug("Fetching loqusdb information for %s", variant_id)
data["observations"] = observations(store, loqusdb, data["case"],
data["variant"])
return data
def test_observations_controller_snv(app, institute_obj, loqusdburl):
"""Testing observation controller to retrieve observations for one SNV variant"""
case_obj = store.case_collection.find_one()
# GIVEN an app with a connected loqusdb instance
loqus_id = "test"
assert app.config["LOQUSDB_SETTINGS"][loqus_id]
var_obj = store.variant_collection.find_one()
assert var_obj["category"] == "snv"
assert var_obj
## GIVEN patched request to the loqusdbapi instance
var_name = f"{var_obj['chromosome']}_{var_obj['position']}_{var_obj['reference']}_{var_obj['alternative']}"
responses.add(
responses.GET,
f"{loqusdburl}/variants/{var_name}",
json={"families": [var_obj["case_id"]], "observations": 1},
status=200,
)
# GIVEN that the institute is associated to the same loqusdb instance
store.institute_collection.find_one_and_update(
{"_id": institute_obj["_id"]}, {"$set": {"loqusdb_id": loqus_id}}
)
## WHEN updating the case_id for the variant
var_obj["case_id"] = "internal_id2"
data = None
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
data = observations(store, loqusdb, case_obj, var_obj)
## THEN loqus should return the occurrence from the first case
assert case_obj["_id"] in data[loqus_id]["families"]
assert data[loqus_id]["cases"][0]["case"] == case_obj
assert data[loqus_id]["cases"][0]["variant"]["_id"] == var_obj["_id"]
def test_observations_controller_non_existing(app, institute_obj, case_obj, loqusdburl):
# GIVEN an app with a connected loqusdb instance
loqus_id = "test"
assert app.config["LOQUSDB_SETTINGS"][loqus_id]
var_obj = store.variant_collection.find_one()
assert var_obj
## GIVEN patched request to the loqusdbapi instance
n_cases = 102
var_name = f"{var_obj['chromosome']}_{var_obj['position']}_{var_obj['reference']}_{var_obj['alternative']}"
responses.add(
responses.GET,
f"{loqusdburl}/variants/{var_name}",
json={"total": n_cases, "cases": []},
status=200,
)
# GIVEN that the institute is associated to the same loqusdb instance
store.institute_collection.find_one_and_update(
{"_id": institute_obj["_id"]}, {"$set": {"loqusdb_id": loqus_id}}
)
## WHEN updating the case_id for the variant
var_obj["case_id"] = "internal_id2"
data = None
with app.test_client() as client:
resp = client.get(url_for("auto_login"))
data = observations(store, loqusdb, case_obj, var_obj)
## THEN assert that the number of cases is still returned
assert data[loqus_id]["total"] == n_cases
## THEN assert the cases variable is in data but it's an empty list
assert data[loqus_id]["cases"] == []