Merge pull request #579 from zsloan/feature/rqtl_with_gn3

Use GN3 API for R/qtl

3 files changed, 46 insertions, 45 deletions

diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
index b094294a..159c982b 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -58,7 +58,7 @@ class TestMapping(unittest.TestCase):
 
         self.assertEqual(results_2, expected_results)
 
-    @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno")
+    @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl")
     @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
     @mock.patch("wqflask.api.mapping.initialize_parameters")
     @mock.patch("wqflask.api.mapping.retrieve_sample_data")
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..9d13e943 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 +1,43 @@
 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 dataclasses import dataclass
 
+from wqflask.marker_regression.rqtl_mapping import run_rqtl
 
-class TestRqtlMapping(unittest.TestCase):
+@dataclass
+class MockGroup:
+    name: str
+    genofile: str
+
+@dataclass
+class MockDataset:
+    group: MockGroup
 
-    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)
+class TestRqtlMapping(unittest.TestCase):
+    """Tests for functions in rqtl_mapping.py"""
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post")
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.locate")
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
+    def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post):
+        """Test for run_rqtl with permutations > 0"""
+        dataset_group = MockGroup("GP1", "file_geno")
+        dataset = MockDataset(dataset_group)
+
+        mock_write_pheno_file.return_value = "pheno_filename"
+        mock_locate.return_value = "geno_filename"
+        mock_post.return_value = mock.Mock(ok=True)
+        mock_post.return_value.json.return_value = {"perm_results": [],
+                                                    "suggestive": 3,
+                                                    "significant": 4,
+                                                    "results" : []}
+
+        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()
+
+        self.assertEqual(results, ([], 3, 4, []))
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index 78cd3be9..c220a072 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -229,20 +229,20 @@ class TestRunMapping(unittest.TestCase):
         used_samples = ["S1", "S2"]
         sample_list = AttributeSetter({"sample_attribute_values": {
             "S1": {
-                "C1": "c1_value",
-                "C2": "c2_value",
-                "W1": "w1_value"
+                "c1": "c1_value",
+                "c2": "c2_value",
+                "w1": "w1_value"
 
             },
             "S2": {
-                "W1": "w2_value",
-                "W2": "w2_value"
+                "w1": "w2_value",
+                "w2": "w2_value"
 
             },
             "S3": {
 
-                "C1": "c1_value",
-                "C2": "c2_value"
+                "c1": "c1_value",
+                "c2": "c2_value"
 
             },