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authorFrederick Muriuki Muriithi2021-10-25 15:13:05 +0300
committerFrederick Muriuki Muriithi2021-10-25 15:13:05 +0300
commit5a472ebab04c68cd5228f253cc98d0ae22a520d7 (patch)
tree3d6b1a5a8933896a6e7fdc98f473ef069accd348 /tests/unit/computations/test_wgcna.py
parent0814eea6b57e45d4337424e63c164d204d03b64d (diff)
parent5440bfcd6940db08c4479a39ba66dbc802b2c426 (diff)
downloadgenenetwork3-5a472ebab04c68cd5228f253cc98d0ae22a520d7.tar.gz
Merge branch 'main' of github.com:genenetwork/genenetwork3 into partial-correlations
Diffstat (limited to 'tests/unit/computations/test_wgcna.py')
-rw-r--r--tests/unit/computations/test_wgcna.py14
1 files changed, 10 insertions, 4 deletions
diff --git a/tests/unit/computations/test_wgcna.py b/tests/unit/computations/test_wgcna.py
index ec81d94..5f23a86 100644
--- a/tests/unit/computations/test_wgcna.py
+++ b/tests/unit/computations/test_wgcna.py
@@ -10,13 +10,16 @@ from gn3.computations.wgcna import call_wgcna_script
class TestWgcna(TestCase):
"""test class for wgcna"""
+ @mock.patch("gn3.computations.wgcna.process_image")
@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):
+ mock_run_cmd,
+ mock_img,
+ ):
"""test for calling wgcna script"""
# pylint: disable = line-too-long
@@ -50,7 +53,7 @@ class TestWgcna(TestCase):
"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\":[]}}"
+ json_output = "{\"inputdata\":{\"trait_sample_data \":{},\"minModuleSize\":30,\"TOMtype\":\"unsigned\"},\"output\":{\"eigengenes\":[],\"imageLoc\":[],\"colors\":[]}}"
expected_output = {
@@ -61,9 +64,11 @@ class TestWgcna(TestCase):
"TOMtype": "unsigned"
},
- "outputdata": {
+ "output": {
"eigengenes": [],
- "colors": []
+ "imageLoc": [],
+ "colors": [],
+ "image_data": "AFDSFNBSDGJJHH"
}
},
@@ -74,6 +79,7 @@ class TestWgcna(TestCase):
with mock.patch("builtins.open", mock.mock_open(read_data=json_output)):
mock_run_cmd.return_value = mock_run_cmd_results
+ mock_img.return_value = b"AFDSFNBSDGJJHH"
results = call_wgcna_script(
"Rscript/GUIX_PATH/scripts/r_file.R", request_data)