Use pytest's "mark" feature to categorise tests

Use pytest's `mark` feature to explicitly categorise the tests and run them
per category

4 files changed, 28 insertions, 1 deletions

diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py
index bdd9bce..cf63c17 100644
--- a/tests/integration/test_correlation.py
+++ b/tests/integration/test_correlation.py
@@ -1,6 +1,7 @@
 """module contains integration tests for correlation"""
 from unittest import TestCase
 from unittest import mock
+import pytest
 from gn3.app import create_app
 
 
@@ -10,6 +11,7 @@ class CorrelationIntegrationTest(TestCase):
     def setUp(self):
         self.app = create_app().test_client()
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.correlation.compute_all_sample_correlation")
     def test_sample_r_correlation(self, mock_compute_samples):
         """Test /api/correlation/sample_r/{method}"""
@@ -61,6 +63,7 @@ class CorrelationIntegrationTest(TestCase):
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response.get_json(), api_response)
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.correlation.compute_all_lit_correlation")
     @mock.patch("gn3.api.correlation.database_connector")
     def test_lit_correlation(self, database_connector, mock_compute_corr):
@@ -80,6 +83,7 @@ class CorrelationIntegrationTest(TestCase):
         self.assertEqual(mock_compute_corr.call_count, 1)
         self.assertEqual(response.status_code, 200)
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.correlation.compute_tissue_correlation")
     def test_tissue_correlation(self, mock_tissue_corr):
         """Test api/correlation/tissue_corr/{corr_method}"""
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index f871173..0515539 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -7,6 +7,8 @@ from dataclasses import dataclass
 from typing import Callable
 from unittest import mock
 
+import pytest
+
 from gn3.app import create_app
 
 
@@ -30,6 +32,7 @@ class GemmaAPITest(unittest.TestCase):
             "TMPDIR": "/tmp"
         }).test_client()
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.run_cmd")
     def test_get_version(self, mock_run_cmd):
         """Test that the correct response is returned"""
@@ -38,6 +41,7 @@ class GemmaAPITest(unittest.TestCase):
         self.assertEqual(response.get_json(), {"status": 0, "output": "v1.9"})
         self.assertEqual(response.status_code, 200)
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.redis.Redis")
     def test_check_cmd_status(self, mock_redis):
         """Test that you can check the status of a given command"""
@@ -52,6 +56,7 @@ class GemmaAPITest(unittest.TestCase):
             name="cmd::2021-02-1217-3224-3224-1234", key="status")
         self.assertEqual(response.get_json(), {"status": "test"})
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -94,6 +99,7 @@ class GemmaAPITest(unittest.TestCase):
                 "unique_id": "my-unique-id"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -137,6 +143,7 @@ class GemmaAPITest(unittest.TestCase):
                 "unique_id": "my-unique-id"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -187,6 +194,7 @@ class GemmaAPITest(unittest.TestCase):
                 "output_file": "hash-output.json"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -240,6 +248,7 @@ class GemmaAPITest(unittest.TestCase):
                 "output_file": "hash-output.json"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -292,6 +301,7 @@ class GemmaAPITest(unittest.TestCase):
                 "output_file": "hash-output.json"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -346,6 +356,7 @@ class GemmaAPITest(unittest.TestCase):
                 "output_file": "hash-output.json"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -401,6 +412,7 @@ class GemmaAPITest(unittest.TestCase):
                 "output_file": "hash-output.json"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -465,6 +477,7 @@ class GemmaAPITest(unittest.TestCase):
                 "output_file": "hash-output.json"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
@@ -530,6 +543,7 @@ class GemmaAPITest(unittest.TestCase):
                 "output_file": "hash-output.json"
             })
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.gemma.queue_cmd")
     @mock.patch("gn3.computations.gemma.get_hash_of_files")
     @mock.patch("gn3.api.gemma.jsonfile_to_dict")
diff --git a/tests/integration/test_general.py b/tests/integration/test_general.py
index 8fc2b43..9d87449 100644
--- a/tests/integration/test_general.py
+++ b/tests/integration/test_general.py
@@ -1,8 +1,10 @@
 """Integration tests for some 'general' API endpoints"""
 import os
 import unittest
-
 from unittest import mock
+
+import pytest
+
 from gn3.app import create_app
 
 
@@ -11,6 +13,7 @@ class GeneralAPITest(unittest.TestCase):
     def setUp(self):
         self.app = create_app().test_client()
 
+    @pytest.mark.integration_test
     def test_metadata_endpoint_exists(self):
         """Test that /metadata/upload exists"""
         response = self.app.post("/api/metadata/upload/d41d86-e4ceEo")
@@ -19,6 +22,7 @@ class GeneralAPITest(unittest.TestCase):
                          {"status": 128,
                           "error": "Please provide a file!"})
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.general.extract_uploaded_file")
     def test_metadata_file_upload(self, mock_extract_upload):
         """Test correct upload of file"""
@@ -37,6 +41,7 @@ class GeneralAPITest(unittest.TestCase):
                          {"status": 0,
                           "token": "d41d86-e4ceEo"})
 
+    @pytest.mark.integration_test
     def test_metadata_file_wrong_upload(self):
         """Test that incorrect upload return correct status code"""
         response = self.app.post("/api/metadata/upload/d41d86-e4ceEo",
@@ -47,6 +52,7 @@ class GeneralAPITest(unittest.TestCase):
                          {"status": 128,
                           "error": "gzip failed to unpack file"})
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.general.run_cmd")
     def test_run_r_qtl(self, mock_run_cmd):
         """Test correct upload of file"""
diff --git a/tests/integration/test_wgcna.py b/tests/integration/test_wgcna.py
index 078449d..5880b40 100644
--- a/tests/integration/test_wgcna.py
+++ b/tests/integration/test_wgcna.py
@@ -3,6 +3,8 @@
 from unittest import TestCase
 from unittest import mock
 
+import pytest
+
 from gn3.app import create_app
 
 
@@ -12,6 +14,7 @@ class WgcnaIntegrationTest(TestCase):
     def setUp(self):
         self.app = create_app().test_client()
 
+    @pytest.mark.integration_test
     @mock.patch("gn3.api.wgcna.call_wgcna_script")
     def test_wgcna_endpoint(self, mock_wgcna_script):
         """test /api/wgcna/run_wgcna endpoint"""