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-rw-r--r--wqflask/tests/unit/wqflask/api/test_mapping.py154
1 files changed, 75 insertions, 79 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
index 5455b215..b094294a 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -5,108 +5,104 @@ from wqflask.api.mapping import do_mapping_for_api
class AttributeSetter:
- def __init__(self,obj):
- for key,value in obj.items():
- setattr(self,key,value)
+ def __init__(self, obj):
+ for key, value in obj.items():
+ setattr(self, key, value)
+
class MockGroup(AttributeSetter):
def get_marker(self):
- self.markers=[]
+ self.markers = []
+
+
class TestMapping(unittest.TestCase):
-
+
def test_initialize_parameters(self):
- expected_results={
- "format":"json",
- "limit_to":False,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":True,
- "num_perm":0,
- "perm_check":False
+ expected_results = {
+ "format": "json",
+ "limit_to": False,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": True,
+ "num_perm": 0,
+ "perm_check": False
}
- results=initialize_parameters(start_vars={},dataset={},this_trait={})
- self.assertEqual(results,expected_results)
+ results = initialize_parameters(
+ start_vars={}, dataset={}, this_trait={})
+ self.assertEqual(results, expected_results)
- start_vars={
- "format":"F1",
- "limit_to":"1",
- "mapping_method":"rqtl",
- "control_marker":True,
- "pair_scan":"true",
- "interval_mapping":"true",
- "use_loco":"true",
- "num_perm":"14"
+ start_vars = {
+ "format": "F1",
+ "limit_to": "1",
+ "mapping_method": "rqtl",
+ "control_marker": True,
+ "pair_scan": "true",
+ "interval_mapping": "true",
+ "use_loco": "true",
+ "num_perm": "14"
}
- results_2=initialize_parameters(start_vars=start_vars,dataset={},this_trait={})
- expected_results={
- "format":"F1",
- "limit_to":1,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":True,
- "num_perm":14,
- "perm_check":"ON"
+ results_2 = initialize_parameters(
+ start_vars=start_vars, dataset={}, this_trait={})
+ expected_results = {
+ "format": "F1",
+ "limit_to": 1,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": True,
+ "num_perm": 14,
+ "perm_check": "ON"
}
- self.assertEqual(results_2,expected_results)
+ self.assertEqual(results_2, expected_results)
-
@mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno")
@mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
@mock.patch("wqflask.api.mapping.initialize_parameters")
@mock.patch("wqflask.api.mapping.retrieve_sample_data")
@mock.patch("wqflask.api.mapping.create_trait")
@mock.patch("wqflask.api.mapping.data_set.create_dataset")
- def test_do_mapping_for_api(self,mock_create_dataset,mock_trait,mock_retrieve_sample,mock_param,run_gemma
- ,run_rqtl_geno):
- start_vars={
- "db":"Temp",
- "trait_id":"dewf3232rff2",
- "format":"F1",
- "mapping_method":"gemma",
- "use_loco":True
+ def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno):
+ start_vars = {
+ "db": "Temp",
+ "trait_id": "dewf3232rff2",
+ "format": "F1",
+ "mapping_method": "gemma",
+ "use_loco": True
}
- sampleList=["S1","S2","S3","S4"]
- samplelist=["S1","S2","S4"]
- dataset=AttributeSetter({"group":samplelist})
- this_trait=AttributeSetter({})
- trait_data=AttributeSetter({
- "data":{
- "item1":AttributeSetter({"name":"S1","value":"S1_value"}),
- "item2":AttributeSetter({"name":"S2","value":"S2_value"}),
- "item3":AttributeSetter({"name":"S3","value":"S3_value"}),
+ sampleList = ["S1", "S2", "S3", "S4"]
+ samplelist = ["S1", "S2", "S4"]
+ dataset = AttributeSetter({"group": samplelist})
+ this_trait = AttributeSetter({})
+ trait_data = AttributeSetter({
+ "data": {
+ "item1": AttributeSetter({"name": "S1", "value": "S1_value"}),
+ "item2": AttributeSetter({"name": "S2", "value": "S2_value"}),
+ "item3": AttributeSetter({"name": "S3", "value": "S3_value"}),
}
- })
- trait=AttributeSetter({
- "data":trait_data
- })
-
- dataset.return_value=dataset
- mock_trait.return_value=this_trait
-
- mock_retrieve_sample.return_value=trait
- mock_param.return_value={
- "format":"F1",
- "limit_to":False,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":"True",
- "num_perm":14,
- "perm_check":"ON"
+ })
+ trait = AttributeSetter({
+ "data": trait_data
+ })
+
+ dataset.return_value = dataset
+ mock_trait.return_value = this_trait
+
+ mock_retrieve_sample.return_value = trait
+ mock_param.return_value = {
+ "format": "F1",
+ "limit_to": False,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": "True",
+ "num_perm": 14,
+ "perm_check": "ON"
}
- run_gemma.return_value=["results"]
- results=do_mapping_for_api(start_vars=start_vars)
- self.assertEqual(results,("results",None))
-
-
-
-
-
-
-
+ run_gemma.return_value = ["results"]
+ results = do_mapping_for_api(start_vars=start_vars)
+ self.assertEqual(results, ("results", None))