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-rw-r--r--tests/integration/test_wgcna.py73
-rw-r--r--tests/unit/computations/test_wgcna.py160
2 files changed, 233 insertions, 0 deletions
diff --git a/tests/integration/test_wgcna.py b/tests/integration/test_wgcna.py
new file mode 100644
index 0000000..078449d
--- /dev/null
+++ b/tests/integration/test_wgcna.py
@@ -0,0 +1,73 @@
+"""integration tests for wgcna"""
+
+from unittest import TestCase
+from unittest import mock
+
+from gn3.app import create_app
+
+
+class WgcnaIntegrationTest(TestCase):
+ """class contains wgcna integration tests"""
+
+ def setUp(self):
+ self.app = create_app().test_client()
+
+ @mock.patch("gn3.api.wgcna.call_wgcna_script")
+ def test_wgcna_endpoint(self, mock_wgcna_script):
+ """test /api/wgcna/run_wgcna endpoint"""
+
+ wgcna_output_data = {
+ "code": 0,
+ "output": "run script successfully",
+ "data": {
+ "ModEigens": {
+ "MEturquoise": [
+ 0.0646677768085351,
+ 0.137200224277058,
+ 0.63451113720732,
+ -0.544002665501479,
+ -0.489487590361863,
+ 0.197111117570427
+ ]
+ },
+ "net_colors": {
+ "X1": "turquoise",
+ "X2": "turquoise",
+ "X3": "turquoise",
+ "X4": "turquoise"
+ },
+ "imageLoc": "/WGCNAoutput_1uujpTIpC.png"
+ }
+ }
+
+ request_data = {
+ "trait_names": [
+ "1455537_at",
+ "1425637_at"
+ ],
+ "trait_sample_data": [
+ {
+ "129S1/SvImJ": 6.142,
+ "A/J": 5.31,
+ "AKR/J": 3.49,
+ "B6D2F1": 2.899,
+ "BALB/cByJ": 1.172,
+ "BALB/cJ": 7.396
+ },
+ {
+ "129S1/SvImJ": 1.42,
+ "A/J": 2.31,
+ "AKR/J": 5.49,
+ "B6D2F1": 3.899,
+ "BALB/cByJ": 1.172,
+ "BALB/cJ": 7.396
+ }
+ ]
+ }
+ mock_wgcna_script.return_value = wgcna_output_data
+
+ response = self.app.post("/api/wgcna/run_wgcna",
+ json=request_data, follow_redirects=True)
+
+ self.assertEqual(response.status_code, 200)
+ self.assertEqual(response.get_json(), wgcna_output_data)
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
new file mode 100644
index 0000000..ec81d94
--- /dev/null
+++ b/tests/unit/computations/test_wgcna.py
@@ -0,0 +1,160 @@
+"""module contains python code for wgcna"""
+from unittest import TestCase
+from unittest import mock
+
+from gn3.computations.wgcna import dump_wgcna_data
+from gn3.computations.wgcna import compose_wgcna_cmd
+from gn3.computations.wgcna import call_wgcna_script
+
+
+class TestWgcna(TestCase):
+ """test class for wgcna"""
+
+ @mock.patch("gn3.computations.wgcna.run_cmd")
+ @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
+ @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
+ def test_call_wgcna_script(self,
+ mock_dumping_data,
+ mock_compose_wgcna,
+ mock_run_cmd):
+ """test for calling wgcna script"""
+
+ # pylint: disable = line-too-long
+ mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+ mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+ request_data = {
+ "trait_names": ["1455537_at", "1425637_at", "1449593_at", "1421945_a_at", "1450423_s_at", "1423841_at", "1451144_at"],
+ "trait_sample_data": [
+ {
+ "129S1/SvImJ": 7.142,
+ "A/J": 7.31,
+ "AKR/J": 7.49,
+ "B6D2F1": 6.899,
+ "BALB/cByJ": 7.172,
+ "BALB/cJ": 7.396
+ },
+ {
+ "129S1/SvImJ": 7.071,
+ "A/J": 7.05,
+ "AKR/J": 7.313,
+ "B6D2F1": 6.999,
+ "BALB/cByJ": 7.293,
+ "BALB/cJ": 7.117
+ }]}
+
+ mock_run_cmd_results = {
+
+ "code": 0,
+ "output": "Flagging genes and samples with too many missing values...\n ..step 1\nAllowing parallel execution with up to 3 working processes.\npickSoftThreshold: will use block size 7.\n pickSoftThreshold: calculating connectivity for given powers...\n ..working on genes 1 through 7 of 7\n Flagging genes and samples with too many missing values...\n ..step 1\n ..Working on block 1 .\n TOM calculation: adjacency..\n ..will not use multithreading.\nclustering..\n ....detecting modules..\n ....calculating module eigengenes..\n ....checking kME in modules..\n ..merging modules that are too close..\n mergeCloseModules: Merging modules whose distance is less than 0.15\n mergeCloseModules: less than two proper modules.\n ..color levels are turquoise\n ..there is nothing to merge.\n Calculating new MEs...\n"
+ }
+
+ json_output = "{\"inputdata\":{\"trait_sample_data \":{},\"minModuleSize\":30,\"TOMtype\":\"unsigned\"},\"outputdata\":{\"eigengenes\":[],\"colors\":[]}}"
+
+ expected_output = {
+
+ "data": {
+ "inputdata": {
+ "trait_sample_data ": {},
+ "minModuleSize": 30,
+ "TOMtype": "unsigned"
+ },
+
+ "outputdata": {
+ "eigengenes": [],
+ "colors": []
+ }
+ },
+
+ **mock_run_cmd_results
+
+ }
+
+ with mock.patch("builtins.open", mock.mock_open(read_data=json_output)):
+
+ mock_run_cmd.return_value = mock_run_cmd_results
+
+ results = call_wgcna_script(
+ "Rscript/GUIX_PATH/scripts/r_file.R", request_data)
+
+ mock_dumping_data.assert_called_once_with(request_data)
+
+ mock_compose_wgcna.assert_called_once_with(
+ "Rscript/GUIX_PATH/scripts/r_file.R",
+ "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
+
+ mock_run_cmd.assert_called_once_with(
+ "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json")
+
+ self.assertEqual(results, expected_output)
+
+ @mock.patch("gn3.computations.wgcna.run_cmd")
+ @mock.patch("gn3.computations.wgcna.compose_wgcna_cmd")
+ @mock.patch("gn3.computations.wgcna.dump_wgcna_data")
+ def test_call_wgcna_script_fails(self, mock_dumping_data, mock_compose_wgcna, mock_run_cmd):
+ """test for calling wgcna script\
+ fails and generates the expected error"""
+ # pylint: disable = line-too-long,
+ mock_dumping_data.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+ mock_compose_wgcna.return_value = "Rscript/GUIX_PATH/scripts/r_file.R /tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
+
+ expected_error = {
+ "code": 2,
+ "output": "could not read the json file"
+ }
+
+ with mock.patch("builtins.open", mock.mock_open(read_data="")):
+
+ mock_run_cmd.return_value = expected_error
+ self.assertEqual(call_wgcna_script(
+ "input_file.R", ""), expected_error)
+
+ def test_compose_wgcna_cmd(self):
+ """test for composing wgcna cmd"""
+ wgcna_cmd = compose_wgcna_cmd(
+ "wgcna.r", "/tmp/wgcna.json")
+ self.assertEqual(
+ wgcna_cmd, "Rscript ./scripts/wgcna.r /tmp/wgcna.json")
+
+ @mock.patch("gn3.computations.wgcna.TMPDIR", "/tmp")
+ @mock.patch("gn3.computations.wgcna.uuid.uuid4")
+ def test_create_json_file(self, file_name_generator):
+ """test for writing the data to a csv file"""
+ # # All the traits we have data for (should not contain duplicates)
+ # All the strains we have data for (contains duplicates)
+
+ trait_sample_data = {"1425642_at": {"129S1/SvImJ": 7.142,
+ "A/J": 7.31, "AKR/J": 7.49,
+ "B6D2F1": 6.899, "BALB/cByJ": 7.172,
+ "BALB/cJ": 7.396},
+ "1457784_at": {"129S1/SvImJ": 7.071, "A/J": 7.05,
+ "AKR/J": 7.313,
+ "B6D2F1": 6.999, "BALB/cByJ": 7.293,
+ "BALB/cJ": 7.117},
+ "1444351_at": {"129S1/SvImJ": 7.221, "A/J": 7.246,
+ "AKR/J": 7.754,
+ "B6D2F1": 6.866, "BALB/cByJ": 6.752,
+ "BALB/cJ": 7.269}
+
+ }
+
+ expected_input = {
+ "trait_sample_data": trait_sample_data,
+ "TOMtype": "unsigned",
+ "minModuleSize": 30
+ }
+
+ with mock.patch("builtins.open", mock.mock_open()) as file_handler:
+
+ file_name_generator.return_value = "facb73ff-7eef-4053-b6ea-e91d3a22a00c"
+
+ results = dump_wgcna_data(
+ expected_input)
+
+ file_handler.assert_called_once_with(
+ "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json", 'w')
+
+ self.assertEqual(
+ results, "/tmp/facb73ff-7eef-4053-b6ea-e91d3a22a00c.json")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 19:03:27 +0000