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authorFrederick Muriuki Muriithi2022-02-19 03:21:27 +0300
committerFrederick Muriuki Muriithi2022-02-19 03:21:27 +0300
commit058f6592d8815a64544f6721a9984b89ea92522a (patch)
tree2d2788432457ffda4570debed723b727057e3a7d
parentde56919183e7b86cd3e495c6274174720dd9ae3a (diff)
downloadgenenetwork3-058f6592d8815a64544f6721a9984b89ea92522a.tar.gz
Test partial corrs endpoint with non-existing control traits
Test that if the endpoint is queried and not a single one of the control traits exists in the database, then the endpoint will respond with a 404 (not-found) status code. Summary of changes: * gn3/computations/partial_correlations.py: Check whether any control trait is found. If none is found, return "not-found" message. * gn3/db/partial_correlations.py: Fix bug in Geno query. * tests/integration/test_partial_correlations.py: Add test for non-existing control traits. Rename function to make it clearer what it is testing for. Remove obsoleted comments.
-rw-r--r--gn3/computations/partial_correlations.py11
-rw-r--r--gn3/db/partial_correlations.py3
-rw-r--r--tests/integration/test_partial_correlations.py49
3 files changed, 54 insertions, 9 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 16cbbdb..1cc969c 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -621,14 +621,19 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911]
"status": "not-found",
"message": f"Could not find primary trait {primary_trait['trait_fullname']}"
}
+ cntrl_traits = tuple(
+ trait for trait in all_traits
+ if trait["trait_fullname"] != primary_trait_name)
+ if not any(trait["haveinfo"] for trait in cntrl_traits):
+ return {
+ "status": "not-found",
+ "message": "None of the requested control traits were found."}
+
group = primary_trait["db"]["group"]
primary_trait_data = all_traits_data[primary_trait["trait_name"]]
primary_samples, primary_values, _primary_variances = export_informative(
primary_trait_data)
- cntrl_traits = tuple(
- trait for trait in all_traits
- if trait["trait_fullname"] != primary_trait_name)
cntrl_traits_data = tuple(
data for trait_name, data in all_traits_data.items()
if trait_name != primary_trait["trait_name"])
diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py
index caf8d35..0931f09 100644
--- a/gn3/db/partial_correlations.py
+++ b/gn3/db/partial_correlations.py
@@ -197,13 +197,14 @@ def geno_traits_data(conn, traits):
"AND GenoXRef.DataId = GenoData.Id "
"AND GenoData.StrainId = Strain.Id "
"ORDER BY Strain.Name").format(
- species_ids=sp_ids,
+ species_ids=", ".join(["%s"] * len(sp_ids)),
trait_names=", ".join(["%s"] * len(traits)),
dataset_names=", ".join(["%s"] * len(dataset_names)))
if len(sp_ids) > 0 and len(dataset_names) > 0:
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
query,
+ sp_ids +
tuple(trait["trait_name"] for trait in traits) +
tuple(dataset_names))
return organise_trait_data_by_trait(cursor.fetchall())
diff --git a/tests/integration/test_partial_correlations.py b/tests/integration/test_partial_correlations.py
index 17ea539..ff6d771 100644
--- a/tests/integration/test_partial_correlations.py
+++ b/tests/integration/test_partial_correlations.py
@@ -92,7 +92,6 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data):
response.status_code == 400 and response.is_json and
response.json.get("status") == "error")
-
@pytest.mark.integration_test
@pytest.mark.slow
@pytest.mark.parametrize(
@@ -118,9 +117,7 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data):
{"dataset": "a_dataset2", "name": "a_name2"}],
"method": "a_method",
"target_db": "a_db"
- }, {# Temp -- Fails due to missing table. Remove this sample if it is
- # confirmed that the deletion of the database table is on purpose, and
- # that Temp traits are no longer a thing
+ }, {# Temp
"primary_trait": {"dataset": "a_Temp_dataset", "name": "a_name"},
"control_traits": [
{"dataset": "a_dataset", "name": "a_name"},
@@ -128,7 +125,7 @@ def test_partial_correlation_api_with_missing_request_data(client, post_data):
"method": "a_method",
"target_db": "a_db"
}))
-def test_partial_correlation_api_with_non_existent_traits(client, post_data):
+def test_partial_correlation_api_with_non_existent_primary_traits(client, post_data):
"""
Check that the system responds appropriately in the case where the user
makes a request with a non-existent primary trait.
@@ -137,3 +134,45 @@ def test_partial_correlation_api_with_non_existent_traits(client, post_data):
assert (
response.status_code == 404 and response.is_json and
response.json.get("status") != "error")
+
+@pytest.mark.integration_test
+@pytest.mark.slow
+@pytest.mark.parametrize(
+ "post_data",
+ ({# ProbeSet
+ "primary_trait": {
+ "dataset": "UCLA_BXDBXH_CARTILAGE_V2", "name": "ILM103710672"},
+ "control_traits": [
+ {"dataset": "a_dataset", "name": "a_name"},
+ {"dataset": "a_dataset2", "name": "a_name2"}],
+ "method": "a_method",
+ "target_db": "a_db"
+ }, {# Publish
+ "primary_trait": {"dataset": "BXDPublish", "name": "BXD_12557"},
+ "control_traits": [
+ {"dataset": "a_dataset", "name": "a_name"},
+ {"dataset": "a_dataset2", "name": "a_name2"}],
+ "method": "a_method",
+ "target_db": "a_db"
+ }, {# Geno
+ "primary_trait": {"dataset": "AKXDGeno", "name": "D4Mit16"},
+ "control_traits": [
+ {"dataset": "a_dataset", "name": "a_name"},
+ {"dataset": "a_dataset2", "name": "a_name2"}],
+ "method": "a_method",
+ "target_db": "a_db"
+ }
+ # Temp -- the data in the database for these is ephemeral, making it
+ # difficult to test for this
+ ))
+def test_partial_correlation_api_with_non_existent_control_traits(client, post_data):
+ """
+ Check that the system responds appropriately in the case where the user
+ makes a request with a non-existent control traits.
+
+ The code repetition here is on purpose - valuing clarity over succinctness.
+ """
+ response = client.post("/api/correlation/partial", json=post_data)
+ assert (
+ response.status_code == 404 and response.is_json and
+ response.json.get("status") != "error")