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authorzsloan2021-05-22 22:31:51 +0000
committerzsloan2021-05-22 22:31:51 +0000
commit579ec56e488db19e7cd489b906ae6da7cd453239 (patch)
tree8840540ff2cc2f4fc9cffc78bff636ae792cc39e
parentd2edff1a05a81cd2ca703de940ea2bec5bd1dd10 (diff)
downloadgenenetwork2-579ec56e488db19e7cd489b906ae6da7cd453239.tar.gz
Rewrote test_rqtl_mapping.py, though haven't done tests for all functions yet
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py76
1 files changed, 40 insertions, 36 deletions
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 91d2c587..5c679c05 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -1,42 +1,46 @@
import unittest
from unittest import mock
-from wqflask import app
-from wqflask.marker_regression.rqtl_mapping import get_trait_data_type
-from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype
-from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names
+from wqflask.marker_regression.rqtl_mapping import run_rqtl
+class AttributeSetter:
+ def __init__(self, obj):
+ for key, val in obj.items():
+ setattr(self, key, val)
+
+class MockGroup(AttributeSetter):
+ def get_samplelist(self):
+ return None
class TestRqtlMapping(unittest.TestCase):
- def setUp(self):
- self.app_context = app.app_context()
- self.app_context.push()
-
- def tearDown(self):
- self.app_context.pop()
-
- @mock.patch("wqflask.marker_regression.rqtl_mapping.g")
- @mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
- def test_get_trait_data(self, mock_logger, mock_db):
- """test for getting trait data_type return True"""
- query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
- mock_db.db.execute.return_value.fetchone.return_value = [
- """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
- results = get_trait_data_type("traid_id")
- mock_db.db.execute.assert_called_with(query_value)
- self.assertEqual(results, "fer434f")
-
- def test_sanitize_rqtl_phenotype(self):
- """test for sanitizing rqtl phenotype"""
- vals = ['f', "x", "r", "x", "x"]
- results = sanitize_rqtl_phenotype(vals)
- expected_phenotype_string = 'c(f,NA,r,NA,NA)'
-
- self.assertEqual(results, expected_phenotype_string)
-
- def test_sanitize_rqtl_names(self):
- """test for sanitzing rqtl names"""
- vals = ['f', "x", "r", "x", "x"]
- expected_sanitized_name = "c('f',NA,'r',NA,NA)"
- results = sanitize_rqtl_names(vals)
- self.assertEqual(expected_sanitized_name, results)
+ @mock.patch("wqflask.marker_regression.rqtl_mapping.process_rqtl_results")
+ @mock.patch("wqflask.marker_regression.rqtl_mapping.process_perm_results")
+ @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post")
+ @mock.patch("wqflask.marker_regression.rqtl_mapping.locate")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.write_phenotype_file")
+ def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post, mock_process_perm, mock_process_rqtl):
+ """Test for run_rqtl with permutations > 0"""
+ dataset_group = MockGroup(
+ {"name": "GP1", "genofile": "file_geno"})
+
+ dataset = AttributeSetter({"group": dataset_group})
+
+ mock_write_pheno_file.return_value = "pheno_filename"
+ mock_locate.return_value = "geno_filename"
+
+ mock_post.return_value = "output_filename"
+
+ mock_process_perm.return_value = [[], 3, 4]
+ mock_process_rqtl.return_value = []
+
+ results = run_rqtl(trait_name="the_trait", vals=[], samples=[],
+ dataset=dataset, mapping_scale="cM", model="normal", method="hk",
+ num_perm=5, perm_strata_list=[], do_control="false", control_marker="",
+ manhattan_plot=True, cofactors="")
+
+ mock_write_pheno_file.assert_called_once()
+ mock_locate.assert_called_once()
+ mock_post.assert_called_once()
+ mock_process_perm.assert_called_once()
+ mock_process_rqtl.assert_called_once()
+ self.assertEqual(results, ([], 3, 4, [])) \ No newline at end of file