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-rw-r--r--tests/integration/test_correlation.py118
1 files changed, 80 insertions, 38 deletions
diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py
index 33e0de9..488a8a4 100644
--- a/tests/integration/test_correlation.py
+++ b/tests/integration/test_correlation.py
@@ -1,57 +1,99 @@
-"""Integration tests for correlation api"""
-
-import os
-import json
-import unittest
+"""module contains integration tests for correlation"""
+from unittest import TestCase
from unittest import mock
-
from gn3.app import create_app
-def file_path(relative_path):
- """getting abs path for file """
- dir_name = os.path.dirname(os.path.abspath(__file__))
- split_path = relative_path.split("/")
- new_path = os.path.join(dir_name, *split_path)
- return new_path
+class CorrelationIntegrationTest(TestCase):
+ """class for correlation integration tests"""
-
-class CorrelationAPITest(unittest.TestCase):
- # currently disable
- """Test cases for the Correlation API"""
def setUp(self):
self.app = create_app().test_client()
- with open(file_path("correlation_data.json")) as json_file:
- self.correlation_data = json.load(json_file)
+ def test_fail(self):
+ """initial method for class that fails"""
+ self.assertEqual(2, 2)
+
+ @mock.patch("gn3.api.correlation.compute_all_sample_correlation")
+ def test_sample_r_correlation(self, mock_compute_samples):
+ """Test /api/correlation/sample_r/{method}"""
+ this_trait_data = {
+ "trait_id": "1455376_at",
+ "trait_sample_data": {
+ "C57BL/6J": "6.138",
+ "DBA/2J": "6.266",
+ "B6D2F1": "6.434",
+ "D2B6F1": "6.55",
+ "BXS2": "6.7"
+ }}
+
+ traits_dataset = [
+ {
+ "trait_id": "14192_at",
+ "trait_sample_data": {
+ "DBA/2J": "7.13",
+ "D2B6F1": "5.65",
+ "BXD2": "1.46"
+ }
+ }
+ ]
+
+ correlation_input_data = {"corr_method": "pearson",
+ "this_trait": this_trait_data,
+ "target_dataset": traits_dataset}
+
+ expected_results = [
+ {
+ "sample_r": "-0.407",
+ "p_value": "6.234e-04"
+ },
+ {
+ "sample_r": "0.398",
+ "sample_p": "8.614e-04"
+ }
+ ]
+
+ mock_compute_samples.return_value = expected_results
+
+ api_response = {
+ "corr_results": expected_results
+ }
+
+ response = self.app.post("/api/correlation/sample_r/pearson",
+ json=correlation_input_data, follow_redirects=True)
- with open(file_path("expected_corr_results.json")) as results_file:
- self.correlation_results = json.load(results_file)
+ self.assertEqual(response.status_code, 200)
+ self.assertEqual(response.get_json(), api_response)
- def tearDown(self):
- self.correlation_data = ""
+ @mock.patch("gn3.api.correlation.compute_all_lit_correlation")
+ def test_lit_correlation(self, mock_compute_corr):
+ """Test api/correlation/lit_corr/{species}/{gene_id}"""
- self.correlation_results = ""
+ mock_compute_corr.return_value = []
- @mock.patch("gn3.api.correlation.compute_correlation")
- def test_corr_compute(self, compute_corr):
- """Test that the correct response in correlation"""
+ post_data = [{"gene_id": 8, "lit_corr": 1}, {
+ "gene_id": 12, "lit_corr": 0.3}]
- compute_corr.return_value = self.correlation_results
- response = self.app.post("/api/correlation/corr_compute",
- json=self.correlation_data,
- follow_redirects=True)
+ response = self.app.post(
+ "/api/correlation/lit_corr/mouse/16", json=post_data, follow_redirects=True)
+ self.assertEqual(mock_compute_corr.call_count, 1)
self.assertEqual(response.status_code, 200)
- @mock.patch("gn3.api.correlation.compute_correlation")
- def test_corr_compute_failed_request(self, compute_corr):
- """test taht cormpute requests fails """
+ @mock.patch("gn3.api.correlation.compute_all_tissue_correlation")
+ def test_tissue_correlation(self, mock_tissue_corr):
+ """Test api/correlation/tissue_corr/{corr_method}"""
+ mock_tissue_corr.return_value = {}
- compute_corr.return_value = self.correlation_results
+ primary_dict = {"trait_id": "1449593_at", "tissue_values": [1, 2, 3]}
- response = self.app.post("/api/correlation/corr_compute",
- json=None,
- follow_redirects=True)
+ target_tissue_dict_list = [
+ {"trait_id": "1449593_at", "tissue_values": [1, 2, 3]}]
- self.assertEqual(response.status_code, 400)
+ tissue_corr_input_data = {"primary_tissue": primary_dict,
+ "target_tissues": target_tissue_dict_list}
+
+ response = self.app.post("/api/correlation/tissue_corr/spearman",
+ json=tissue_corr_input_data, follow_redirects=True)
+
+ self.assertEqual(response.status_code, 200)