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-rw-r--r--wqflask/tests/integration/__init__.py (renamed from wqflask/tests/base/__init__.py)0
-rw-r--r--wqflask/tests/integration/test_markdown_routes.py21
-rw-r--r--wqflask/tests/unit/__init__.py (renamed from wqflask/tests/utility/__init__.py)0
-rw-r--r--wqflask/tests/unit/base/__init__.py (renamed from wqflask/tests/wqflask/__init__.py)0
-rw-r--r--wqflask/tests/unit/base/data.py (renamed from wqflask/tests/base/data.py)0
-rw-r--r--wqflask/tests/unit/base/test_data_set.py (renamed from wqflask/tests/base/test_data_set.py)0
-rw-r--r--wqflask/tests/unit/base/test_general_object.py (renamed from wqflask/tests/base/test_general_object.py)0
-rw-r--r--wqflask/tests/unit/base/test_trait.py (renamed from wqflask/tests/base/test_trait.py)0
-rw-r--r--wqflask/tests/unit/base/test_webqtl_case_data.py (renamed from wqflask/tests/base/test_webqtl_case_data.py)0
-rw-r--r--wqflask/tests/unit/utility/__init__.py (renamed from wqflask/tests/wqflask/api/__init__.py)0
-rw-r--r--wqflask/tests/unit/utility/test_authentication_tools.py (renamed from wqflask/tests/utility/test_authentication_tools.py)0
-rw-r--r--wqflask/tests/unit/utility/test_chunks.py (renamed from wqflask/tests/utility/test_chunks.py)0
-rw-r--r--wqflask/tests/unit/utility/test_corestats.py (renamed from wqflask/tests/utility/test_corestats.py)0
-rw-r--r--wqflask/tests/unit/utility/test_corr_result_helpers.py (renamed from wqflask/tests/utility/test_corr_result_helpers.py)0
-rw-r--r--wqflask/tests/unit/utility/test_formatting.py (renamed from wqflask/tests/utility/test_formatting.py)0
-rw-r--r--wqflask/tests/unit/utility/test_hmac.py (renamed from wqflask/tests/utility/test_hmac.py)1
-rw-r--r--wqflask/tests/unit/wqflask/__init__.py (renamed from wqflask/tests/wqflask/marker_regression/__init__.py)0
-rw-r--r--wqflask/tests/unit/wqflask/api/__init__.py (renamed from wqflask/tests/wqflask/show_trait/__init__.py)0
-rw-r--r--wqflask/tests/unit/wqflask/api/test_gen_menu.py (renamed from wqflask/tests/wqflask/api/test_gen_menu.py)0
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/__init__.py0
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py (renamed from wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py)0
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py181
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py85
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py21
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py48
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py284
-rw-r--r--wqflask/tests/unit/wqflask/show_trait/__init__.py0
-rw-r--r--wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py (renamed from wqflask/tests/wqflask/show_trait/test_export_trait_data.py)0
-rw-r--r--wqflask/tests/unit/wqflask/test_collect.py (renamed from wqflask/tests/wqflask/test_collect.py)0
-rw-r--r--wqflask/tests/unit/wqflask/test_markdown_routes.py54
-rw-r--r--wqflask/tests/unit/wqflask/test_pbkdf2.py (renamed from wqflask/tests/wqflask/test_pbkdf2.py)0
-rw-r--r--wqflask/tests/unit/wqflask/test_user_login.py (renamed from wqflask/tests/wqflask/test_user_login.py)0
-rw-r--r--wqflask/tests/unit/wqflask/test_user_session.py (renamed from wqflask/tests/wqflask/test_user_session.py)0
-rw-r--r--wqflask/tests/wqflask/show_trait/testSampleList.py16
-rw-r--r--wqflask/tests/wqflask/show_trait/test_show_trait.py278
35 files changed, 988 insertions, 1 deletions
diff --git a/wqflask/tests/base/__init__.py b/wqflask/tests/integration/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/base/__init__.py
+++ b/wqflask/tests/integration/__init__.py
diff --git a/wqflask/tests/integration/test_markdown_routes.py b/wqflask/tests/integration/test_markdown_routes.py
new file mode 100644
index 00000000..5e3e5045
--- /dev/null
+++ b/wqflask/tests/integration/test_markdown_routes.py
@@ -0,0 +1,21 @@
+"Integration tests for markdown routes"
+import unittest
+
+from bs4 import BeautifulSoup
+
+from wqflask import app
+
+
+class TestGenMenu(unittest.TestCase):
+ """Tests for glossary"""
+
+ def setUp(self):
+ self.app = app.test_client()
+
+ def tearDown(self):
+ pass
+
+ def test_glossary_page(self):
+ """Test that the glossary page is rendered properly"""
+ response = self.app.get('/glossary', follow_redirects=True)
+ pass
diff --git a/wqflask/tests/utility/__init__.py b/wqflask/tests/unit/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/utility/__init__.py
+++ b/wqflask/tests/unit/__init__.py
diff --git a/wqflask/tests/wqflask/__init__.py b/wqflask/tests/unit/base/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/__init__.py
+++ b/wqflask/tests/unit/base/__init__.py
diff --git a/wqflask/tests/base/data.py b/wqflask/tests/unit/base/data.py
index 06a5a989..06a5a989 100644
--- a/wqflask/tests/base/data.py
+++ b/wqflask/tests/unit/base/data.py
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index 96563a16..96563a16 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
diff --git a/wqflask/tests/base/test_general_object.py b/wqflask/tests/unit/base/test_general_object.py
index 00fd3c72..00fd3c72 100644
--- a/wqflask/tests/base/test_general_object.py
+++ b/wqflask/tests/unit/base/test_general_object.py
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/unit/base/test_trait.py
index 826ccefd..826ccefd 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/unit/base/test_trait.py
diff --git a/wqflask/tests/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index 8e8ba482..8e8ba482 100644
--- a/wqflask/tests/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
diff --git a/wqflask/tests/wqflask/api/__init__.py b/wqflask/tests/unit/utility/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/api/__init__.py
+++ b/wqflask/tests/unit/utility/__init__.py
diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
index 5c391be5..5c391be5 100644
--- a/wqflask/tests/utility/test_authentication_tools.py
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
diff --git a/wqflask/tests/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
index 8d90a1ec..8d90a1ec 100644
--- a/wqflask/tests/utility/test_chunks.py
+++ b/wqflask/tests/unit/utility/test_chunks.py
diff --git a/wqflask/tests/utility/test_corestats.py b/wqflask/tests/unit/utility/test_corestats.py
index cf91a248..cf91a248 100644
--- a/wqflask/tests/utility/test_corestats.py
+++ b/wqflask/tests/unit/utility/test_corestats.py
diff --git a/wqflask/tests/utility/test_corr_result_helpers.py b/wqflask/tests/unit/utility/test_corr_result_helpers.py
index e196fbdf..e196fbdf 100644
--- a/wqflask/tests/utility/test_corr_result_helpers.py
+++ b/wqflask/tests/unit/utility/test_corr_result_helpers.py
diff --git a/wqflask/tests/utility/test_formatting.py b/wqflask/tests/unit/utility/test_formatting.py
index 9d3033d1..9d3033d1 100644
--- a/wqflask/tests/utility/test_formatting.py
+++ b/wqflask/tests/unit/utility/test_formatting.py
diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/unit/utility/test_hmac.py
index 4e3652f8..13d6261d 100644
--- a/wqflask/tests/utility/test_hmac.py
+++ b/wqflask/tests/unit/utility/test_hmac.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
"""Test hmac utility functions"""
import unittest
diff --git a/wqflask/tests/wqflask/marker_regression/__init__.py b/wqflask/tests/unit/wqflask/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/marker_regression/__init__.py
+++ b/wqflask/tests/unit/wqflask/__init__.py
diff --git a/wqflask/tests/wqflask/show_trait/__init__.py b/wqflask/tests/unit/wqflask/api/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/wqflask/show_trait/__init__.py
+++ b/wqflask/tests/unit/wqflask/api/__init__.py
diff --git a/wqflask/tests/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index 84898bd1..84898bd1 100644
--- a/wqflask/tests/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
diff --git a/wqflask/tests/unit/wqflask/marker_regression/__init__.py b/wqflask/tests/unit/wqflask/marker_regression/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/__init__.py
diff --git a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 8ae0f09f..8ae0f09f 100644
--- a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
new file mode 100644
index 00000000..fe2569b8
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -0,0 +1,181 @@
+# test for wqflask/marker_regression/gemma_mapping.py
+import unittest
+import random
+from unittest import mock
+from wqflask.marker_regression.gemma_mapping import run_gemma
+from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file
+from wqflask.marker_regression.gemma_mapping import gen_covariates_file
+from wqflask.marker_regression.gemma_mapping import parse_loco_output
+
+
+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 TestGemmaMapping(unittest.TestCase):
+
+ @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
+ def test_run_gemma_firstrun_set_false(self, mock_parse_loco):
+ """add tests for gemma function where first run is set to false"""
+ dataset = AttributeSetter(
+ {"group": AttributeSetter({"genofile": "genofile.geno"})})
+
+ output_file = "file1"
+ mock_parse_loco.return_value = []
+ this_trait = AttributeSetter({"name": "t1"})
+
+ result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[
+ ], covariates="", use_loco=True, first_run=False, output_files=output_file)
+
+ expected_results = ([], "file1")
+ self.assertEqual(expected_results, result)
+
+ @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
+ @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
+ def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco):
+ """add tests for run_gemma where first run is set to true"""
+ this_chromosomes={}
+ for i in range(1, 5):
+ this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"}))
+ chromosomes = AttributeSetter({"chromosomes": this_chromosomes})
+
+ dataset_group = MockGroup(
+ {"name": "GP1", "genofile": "file_geno"})
+ dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name",
+ "species": AttributeSetter({"chromosomes": chromosomes})})
+ trait = AttributeSetter({"name": "trait1"})
+ samples = []
+ mock_gen_pheno_txt.return_value = None
+ mock_os.path.isfile.return_value = True
+ mock_gen_covar.return_value = None
+ mock_choice.return_value = "R"
+ mock_flat_files.return_value = "/home/genotype/bimbam"
+ mock_parse_loco.return_value = []
+ results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
+ ], vals=[], covariates="", use_loco=True)
+ self.assertEqual(mock_os.system.call_count,2)
+ mock_gen_pheno_txt.assert_called_once()
+ mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True)
+ mock_os.path.isfile.assert_called_once_with(
+ ('/home/user/imgfile_output.assoc.txt'))
+ self.assertEqual(mock_flat_files.call_count, 4)
+ self.assertEqual(results, ([], "GP1_GWA_RRRRRR"))
+
+ @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data")
+ def test_gen_pheno_txt_file(self):
+ """add tests for generating pheno txt file"""
+ with mock.patch("builtins.open", mock.mock_open())as mock_open:
+ gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[
+ "x", "w", "q", "we", "R"], trait_filename="fitr.re")
+ mock_open.assert_called_once_with(
+ '/home/user/data/gn2/fitr.re.txt', 'w')
+ filehandler = mock_open()
+ values = ["x", "w", "q", "we", "R"]
+ write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call(
+ 'q\n'), mock.call('we\n'), mock.call('R\n')]
+
+ filehandler.write.assert_has_calls(write_calls)
+
+ @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset")
+ def test_gen_covariates_file(self, create_dataset, create_trait, flat_files):
+ """add tests for generating covariates files"""
+ covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2"
+ samplelist = ["X1", "X2", "X3", "X4"]
+ create_dataset_side_effect = []
+ create_trait_side_effect = []
+
+ for i in range(4):
+ create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'}))
+ create_trait_side_effect.append(
+ AttributeSetter({"data": [f'data_{i}']}))
+
+ create_dataset.side_effect = create_trait_side_effect
+ create_trait.side_effect = create_trait_side_effect
+
+ group = MockGroup({"name": "group_X", "samplelist": samplelist})
+ this_dataset = AttributeSetter({"group": group})
+ flat_files.return_value = "Home/Genenetwork"
+
+ with mock.patch("builtins.open", mock.mock_open())as mock_open:
+ gen_covariates_file(this_dataset=this_dataset, covariates=covariates,
+ samples=["x1", "x2", "X3"])
+
+ create_dataset.assert_has_calls(
+ [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')])
+ mock_calls = []
+ trait_names = ["X1", "Y1", "M1", "V1"]
+
+ for i, trait in enumerate(create_trait_side_effect):
+ mock_calls.append(
+ mock.call(dataset=trait, name=trait_names[i], cellid=None))
+
+ create_trait.assert_has_calls(mock_calls)
+
+ flat_files.assert_called_once_with('mapping')
+ mock_open.assert_called_once_with(
+ 'Home/Genenetwork/group_X_covariates.txt', 'w')
+ filehandler = mock_open()
+ filehandler.write.assert_has_calls([mock.call(
+ '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
+
+ @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.json")
+ def test_parse_loco_outputfile_found(self, mock_json, mock_os):
+ """add tests for parse loco output file found"""
+ mock_json.load.return_value = {
+ "files": [["file_name", "user", "~/file1"],
+ ["file_name", "user", "~/file2"]]
+ }
+ return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
+chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5
+Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7
+X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
+
+ return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5\t0.4"""
+ mock_os.path.isfile.return_value = True
+ file_to_write = """{"files":["file_1","file_2"]}"""
+ with mock.patch("builtins.open") as mock_open:
+
+ handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open(
+ read_data=return_file).return_value, mock.mock_open(read_data=return_file_2).return_value)
+ mock_open.side_effect = handles
+ results = parse_loco_output(
+ this_dataset={}, gwa_output_filename=".xw/")
+ expected_results= [
+ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727},
+ {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812},
+ {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432},
+ {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
+
+ self.assertEqual(expected_results, results)
+
+ @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+ @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+ def test_parse_loco_outputfile_not_found(self, mock_os):
+ """add tests for parse loco output where output file not found"""
+
+ mock_os.path.isfile.return_value = False
+ file_to_write = """{"files":["file_1","file_2"]}"""
+
+ with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open:
+ results = parse_loco_output(
+ this_dataset={}, gwa_output_filename=".xw/")
+ self.assertEqual(results, [])
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
new file mode 100644
index 00000000..5eec93f1
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -0,0 +1,85 @@
+# test for wqflask/marker_regression/plink_mapping.py
+import unittest
+from unittest import mock
+from wqflask.marker_regression.plink_mapping import build_line_list
+from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file
+from wqflask.marker_regression.plink_mapping import flat_files
+from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink
+from wqflask.marker_regression.plink_mapping import parse_plink_output
+
+
+class AttributeSetter:
+ def __init__(self, obj):
+ for key, val in obj.items():
+ setattr(self, key, val)
+class TestPlinkMapping(unittest.TestCase):
+
+
+ def test_build_line_list(self):
+ """test for building line list"""
+ line_1 = "this is line one test"
+ irregular_line = " this is an, irregular line "
+ exp_line1 = ["this", "is", "line", "one", "test"]
+
+ results = build_line_list(irregular_line)
+ self.assertEqual(exp_line1, build_line_list(line_1))
+ self.assertEqual([], build_line_list())
+ self.assertEqual(["this", "is", "an,", "irregular", "line"], results)
+
+ @mock.patch("wqflask.marker_regression.plink_mapping.flat_files")
+ def test_get_samples_from_ped_file(self, mock_flat_files):
+ """test for getting samples from ped file"""
+ dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
+ file_sample = """Expected_1\tline test
+Expected_2\there
+ Expected_3\tthree"""
+ mock_flat_files.return_value = "/home/user/"
+ with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open:
+ results = get_samples_from_ped_file(dataset)
+ mock_flat_files.assert_called_once_with("mapping")
+ mock_open.assert_called_once_with("/home/user/n_1.ped", "r")
+ self.assertEqual(
+ ["Expected_1", "Expected_2", "Expected_3"], results)
+
+ @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+ @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file")
+ def test_gen_pheno_txt_file_plink(self, mock_samples):
+ """test for getting gen_pheno txt file"""
+ mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"]
+
+ trait = AttributeSetter({"name": "TX"})
+ dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
+ vals = ["value=K1", "value=K2", "value=K3"]
+ with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+ results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset,
+ vals=vals, pheno_filename="ph_file")
+ mock_open.assert_called_once_with(
+ "/home/user/data/ph_file.txt", "wb")
+ filehandler = mock_open()
+ calls_expected = [mock.call('FID\tIID\tTX\n'),
+ mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')]
+
+ filehandler.write.assert_has_calls(calls_expected)
+
+ filehandler.close.assert_called_once()
+
+ @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+ @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list")
+ def test_parse_plink_output(self, mock_line_list):
+ """test for parsing plink output"""
+ chromosomes = [0, 34, 110, 89, 123, 23, 2]
+ species = AttributeSetter(
+ {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})})
+
+ fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA"""
+
+ mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [
+ "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]]
+ with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open:
+ parse_results = parse_plink_output(
+ output_filename="P1_file", species=species)
+ mock_open.assert_called_once_with(
+ "/home/user/data/P1_file.qassoc", "rb")
+ expected = (2, {'AACCAT': 0.89, 'AATA': 0.3})
+
+ self.assertEqual(parse_results, expected)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
new file mode 100644
index 00000000..b47f877a
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -0,0 +1,21 @@
+import unittest
+from unittest import mock
+from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
+
+#issues some methods in genofile object are not defined
+#modify samples should equal to vals
+class TestQtlReaperMapping(unittest.TestCase):
+ @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
+ def test_gen_pheno_txt_file(self):
+ vals=["V1","x","V4","V3","x"]
+ samples=["S1","S2","S3","S4","S5"]
+ trait_filename="trait_file"
+ with mock.patch("builtins.open", mock.mock_open())as mock_open:
+ gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename)
+ mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w")
+ filehandler=mock_open()
+ write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')]
+
+ filehandler.write.assert_has_calls(write_calls)
+
+
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
new file mode 100644
index 00000000..c585f1df
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -0,0 +1,48 @@
+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
+
+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)
+
+
+
+
+
+
+
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
new file mode 100644
index 00000000..4129cc0c
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -0,0 +1,284 @@
+import unittest
+import datetime
+from unittest import mock
+
+from wqflask.marker_regression.run_mapping import get_genofile_samplelist
+from wqflask.marker_regression.run_mapping import geno_db_exists
+from wqflask.marker_regression.run_mapping import write_input_for_browser
+from wqflask.marker_regression.run_mapping import export_mapping_results
+from wqflask.marker_regression.run_mapping import trim_markers_for_figure
+from wqflask.marker_regression.run_mapping import get_perm_strata
+from wqflask.marker_regression.run_mapping import get_chr_lengths
+
+
+class AttributeSetter:
+ def __init__(self, obj):
+ for k, v in obj.items():
+ setattr(self, k, v)
+
+
+class MockGroup(AttributeSetter):
+
+ def get_genofiles(self):
+ return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}]
+
+
+class TestRunMapping(unittest.TestCase):
+ def setUp(self):
+
+ self.group = MockGroup(
+ {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"})
+ chromosomes = {
+ "3": AttributeSetter({
+ "name": "C1",
+ "length": "0.04"
+ }),
+ "4": AttributeSetter({
+ "name": "C2",
+ "length": "0.03"
+ }),
+ "5": AttributeSetter({
+ "name": "C4",
+ "length": "0.01"
+ })
+ }
+ self.dataset = AttributeSetter(
+ {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+
+ self.chromosomes = AttributeSetter({"chromosomes": chromosomes})
+ self.trait = AttributeSetter(
+ {"symbol": "IGFI", "chr": "X1", "mb": 123313})
+
+ def tearDown(self):
+ self.dataset = AttributeSetter(
+ {"group": {"location": "~/genofiles/g1_file"}})
+
+ def test_get_genofile_samplelist(self):
+
+ results_1 = get_genofile_samplelist(self.dataset)
+ self.assertEqual(results_1, ["S1", "S2", "S3", "S4"])
+ self.group.genofile = "~/genofiles/g2_file"
+ result_2 = get_genofile_samplelist(self.dataset)
+ self.assertEqual(result_2, [])
+
+ @mock.patch("wqflask.marker_regression.run_mapping.data_set")
+ def test_if_geno_db_exists(self, mock_data_set):
+ mock_data_set.create_dataset.side_effect = [
+ AttributeSetter({}), Exception()]
+ results_no_error = geno_db_exists(self.dataset)
+ results_with_error = geno_db_exists(self.dataset)
+
+ self.assertEqual(mock_data_set.create_dataset.call_count, 2)
+ self.assertEqual(results_with_error, "False")
+ self.assertEqual(results_no_error, "True")
+
+ def test_trim_markers_for_figure(self):
+
+ markers = [{
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "lod_score":0.5
+ },
+ {
+ "name": "MK2",
+ "chr": "C2",
+ "cM": "15",
+ "Mb": "10000",
+ "genotypes": [],
+ "lod_score":0.7
+ },
+ {
+ "name": "MK1",
+ "chr": "C3",
+ "cM": "45",
+ "Mb": "1",
+ "genotypes": [],
+ "dominance":"Tt",
+ "additive":"VE",
+ "lod_score":1
+ }]
+
+ marker_2 = [{
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "p_wald":4.6
+ }]
+ results = trim_markers_for_figure(markers)
+ result_2 = trim_markers_for_figure(marker_2)
+ expected = [
+ {
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "lod_score":0.5
+ },
+ {
+ "name": "MK1",
+ "chr": "C3",
+ "cM": "45",
+ "Mb": "1",
+ "genotypes": [],
+ "dominance":"Tt",
+ "additive":"VE",
+ "lod_score":1
+ }
+
+ ]
+ self.assertEqual(results, expected)
+ self.assertEqual(result_2, marker_2)
+
+ def test_export_mapping_results(self):
+ """test for exporting mapping results"""
+ datetime_mock = mock.Mock(wraps=datetime.datetime)
+ datetime_mock.now.return_value = datetime.datetime(
+ 2019, 9, 1, 10, 12, 12)
+
+ markers = [{
+ "name": "MK1",
+ "chr": "C1",
+ "cM": "1",
+ "Mb": "12000",
+ "genotypes": [],
+ "dominance":"TT",
+ "additive":"VA",
+ "lod_score":3
+ },
+ {
+ "name": "MK2",
+ "chr": "C2",
+ "cM": "15",
+ "Mb": "10000",
+ "genotypes": [],
+ "lod_score":7
+ },
+ {
+ "name": "MK1",
+ "chr": "C3",
+ "cM": "45",
+ "Mb": "1",
+ "genotypes": [],
+ "dominance":"Tt",
+ "additive":"VE",
+ "lod_score":7
+ }]
+
+ with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+
+ with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
+ export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
+ results_path="~/results", mapping_scale="physic", score_type="-log(p)")
+
+ write_calls = [
+ mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
+ mock.call('Population: Human GP1_\n'), mock.call(
+ 'Data Set: dataser_1\n'),
+ mock.call('Gene Symbol: IGFI\n'), mock.call(
+ 'Location: X1 @ 123313 Mb\n'),
+ mock.call('\n'), mock.call('Name,Chr,'),
+ mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
+ mock.call(',Additive'), mock.call(',Dominance'),
+ mock.call('\n'), mock.call('MK1,C1,'),
+ mock.call('12000,'), mock.call('1,'),
+ mock.call('3'), mock.call(',VA'),
+ mock.call(',TT'), mock.call('\n'),
+ mock.call('MK2,C2,'), mock.call('10000,'),
+ mock.call('15,'), mock.call('7'),
+ mock.call('\n'), mock.call('MK1,C3,'),
+ mock.call('1,'), mock.call('45,'),
+ mock.call('7'), mock.call(',VE'),
+ mock.call(',Tt')
+
+ ]
+ mock_open.assert_called_once_with("~/results", "w+")
+ filehandler = mock_open()
+ filehandler.write.assert_has_calls(write_calls)
+
+ @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+ def test_write_input_for_browser(self, mock_choice):
+ """test for writing input for browser"""
+ mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"]
+ with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+ expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT']
+
+ results = write_input_for_browser(
+ this_dataset=self.dataset, gwas_results={}, annotations={})
+ self.assertEqual(results, expected)
+
+ def test_get_perm_strata(self):
+ categorical_vars = ["C1", "C2", "W1"]
+ used_samples = ["S1", "S2"]
+ sample_list = AttributeSetter({"sample_attribute_values": {
+ "S1": {
+ "C1": "c1_value",
+ "C2": "c2_value",
+ "W1": "w1_value"
+
+ },
+ "S2": {
+ "W1": "w2_value",
+ "W2": "w2_value"
+
+ },
+ "S3": {
+
+ "C1": "c1_value",
+ "C2": "c2_value"
+
+ },
+
+ }})
+
+ results = get_perm_strata(this_trait={}, sample_list=sample_list,
+ categorical_vars=categorical_vars, used_samples=used_samples)
+ self.assertEqual(results, [2, 1])
+
+ def test_get_chr_length(self):
+ """test for getting chromosome length"""
+ chromosomes = AttributeSetter({"chromosomes": self.chromosomes})
+ dataset = AttributeSetter({"species": chromosomes})
+ results = get_chr_lengths(
+ mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[])
+ chr_lengths = []
+ for key, chromo in self.chromosomes.chromosomes.items():
+ chr_lengths.append({"chr": chromo.name, "size": chromo.length})
+
+ self.assertEqual(chr_lengths, results)
+
+ qtl_results = [{
+ "chr": "16",
+ "cM": "0.2"
+ },
+ {
+ "chr": "12",
+ "cM": "0.5"
+ },
+ {
+ "chr": "18",
+ "cM": "0.1"
+ },
+ {
+ "chr": "22",
+ "cM": "0.4"
+ },
+ ]
+
+ result_with_other_mapping_scale = get_chr_lengths(
+ mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results)
+ expected_value = [{'chr': '1', 'size': '0'}, {
+ 'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}]
+
+ self.assertEqual(result_with_other_mapping_scale, expected_value)
diff --git a/wqflask/tests/unit/wqflask/show_trait/__init__.py b/wqflask/tests/unit/wqflask/show_trait/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/show_trait/__init__.py
diff --git a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
index 41761944..41761944 100644
--- a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py
+++ b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
index 9a36132d..9a36132d 100644
--- a/wqflask/tests/wqflask/test_collect.py
+++ b/wqflask/tests/unit/wqflask/test_collect.py
diff --git a/wqflask/tests/unit/wqflask/test_markdown_routes.py b/wqflask/tests/unit/wqflask/test_markdown_routes.py
new file mode 100644
index 00000000..90e0f17c
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_markdown_routes.py
@@ -0,0 +1,54 @@
+"""Test functions in markdown utils"""
+
+import unittest
+from unittest import mock
+
+from dataclasses import dataclass
+from wqflask.markdown_routes import render_markdown
+
+
+@dataclass
+class MockRequests404:
+ status_code: int = 404
+
+
+@dataclass
+class MockRequests200:
+ status_code: int = 200
+ content: str = b"""
+# Glossary
+This is some content
+
+## Sub-heading
+This is another sub-heading"""
+
+
+class TestMarkdownRoutesFunctions(unittest.TestCase):
+ """Test cases for functions in markdown_routes"""
+
+ @mock.patch('wqflask.markdown_routes.requests.get')
+ def test_render_markdown_when_fetching_locally(self, requests_mock):
+ requests_mock.return_value = MockRequests404()
+ markdown_content = render_markdown("general/glossary/glossary.md")
+ requests_mock.assert_called_with(
+ "https://raw.githubusercontent.com"
+ "/genenetwork/gn-docs/"
+ "master/general/"
+ "glossary/glossary.md")
+ self.assertRegexpMatches(markdown_content,
+ "Content for general/glossary/glossary.md not available.")
+
+ @mock.patch('wqflask.markdown_routes.requests.get')
+ def test_render_markdown_when_fetching_remotely(self, requests_mock):
+ requests_mock.return_value = MockRequests200()
+ markdown_content = render_markdown("general/glossary/glossary.md")
+ requests_mock.assert_called_with(
+ "https://raw.githubusercontent.com"
+ "/genenetwork/gn-docs/"
+ "master/general/"
+ "glossary/glossary.md")
+ self.assertEqual("""<h1>Glossary</h1>
+<p>This is some content</p>
+<h2>Sub-heading</h2>
+<p>This is another sub-heading</p>""",
+ markdown_content)
diff --git a/wqflask/tests/wqflask/test_pbkdf2.py b/wqflask/tests/unit/wqflask/test_pbkdf2.py
index a33fbd4f..a33fbd4f 100644
--- a/wqflask/tests/wqflask/test_pbkdf2.py
+++ b/wqflask/tests/unit/wqflask/test_pbkdf2.py
diff --git a/wqflask/tests/wqflask/test_user_login.py b/wqflask/tests/unit/wqflask/test_user_login.py
index 61cd9ab9..61cd9ab9 100644
--- a/wqflask/tests/wqflask/test_user_login.py
+++ b/wqflask/tests/unit/wqflask/test_user_login.py
diff --git a/wqflask/tests/wqflask/test_user_session.py b/wqflask/tests/unit/wqflask/test_user_session.py
index ebb0334a..ebb0334a 100644
--- a/wqflask/tests/wqflask/test_user_session.py
+++ b/wqflask/tests/unit/wqflask/test_user_session.py
diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py
new file mode 100644
index 00000000..34c51e3e
--- /dev/null
+++ b/wqflask/tests/wqflask/show_trait/testSampleList.py
@@ -0,0 +1,16 @@
+import unittest
+import re
+from unittest import mock
+from wqflask.show_trait.SampleList import natural_sort
+
+
+class TestSampleList(unittest.TestCase):
+ def test_natural_sort(self):
+ "Sort the list into natural alphanumeric order."
+
+ characters_list = ["z", "f", "q", "s", "t", "a", "g"]
+ names_list = ["temp1", "publish", "Sample", "Dataset"]
+ sorted_list_a=natural_sort(characters_list)
+ sorted_list_b=natural_sort(names_list)
+ self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"])
+ self.assertEqual(sorted_list_b,["Dataset", "Sample", "publish", "temp1"])
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
new file mode 100644
index 00000000..8c866874
--- /dev/null
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -0,0 +1,278 @@
+"""test for wqflask/show_trait/test_show_trait.py"""
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.show_trait.show_trait import check_if_attr_exists
+from wqflask.show_trait.show_trait import get_ncbi_summary
+from wqflask.show_trait.show_trait import has_num_cases
+from wqflask.show_trait.show_trait import get_table_widths
+from wqflask.show_trait.show_trait import get_categorical_variables
+from wqflask.show_trait.show_trait import get_trait_units
+from wqflask.show_trait.show_trait import get_nearest_marker
+from wqflask.show_trait.show_trait import get_genotype_scales
+from wqflask.show_trait.show_trait import requests
+from wqflask.show_trait.show_trait import get_scales_from_genofile
+
+
+class TraitObject:
+ def __init__(self, obj):
+ for key, value in obj.items():
+ setattr(self, key, value)
+
+
+class TestTraits(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ def test_check_if_attr_exists_truthy(self):
+ """"test if attributes exists with true return"""
+ trait_obj = TraitObject({"id_type": "id"})
+ trait_obj2 = TraitObject({"sample_name": ['samp1']})
+ results = check_if_attr_exists(trait_obj, "id_type")
+ result2 = check_if_attr_exists(trait_obj2, "sample_name")
+ self.assertIsInstance(trait_obj, TraitObject)
+ self.assertTrue(results)
+ self.assertTrue(result2)
+
+ def test_check_if_attr_exists_empty_attr(self):
+ """test if attributes exists with false return"""
+ trait_obj = TraitObject({"sample": ""})
+ trait_obj2 = TraitObject({"group": None})
+ result = check_if_attr_exists(trait_obj, "sample")
+ result2 = check_if_attr_exists(trait_obj, "group")
+ self.assertFalse(result)
+ self.assertFalse(result2)
+
+ def test_check_if_attr_exists_falsey(self):
+ """check if attribute exists with empty attributes"""
+ trait_obj = TraitObject({})
+ results = check_if_attr_exists(trait_obj, "any")
+ self.assertFalse(results)
+
+ @mock.patch("wqflask.show_trait.show_trait.requests.get")
+ @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+ def test_get_ncbi_summary_request_success(self, mock_exists, mock_get):
+ """test for getting ncbi summary with
+ successful request"""
+ trait = TraitObject({"geneid": "id"})
+ mock_exists.return_value = True
+ content_json_string = """{
+ "result":{
+ "id":{
+ "summary":"this is a summary of the geneid"
+ }
+ }
+ }
+ """
+ get_return_obj = TraitObject({"content": content_json_string})
+ mock_get.return_value = get_return_obj
+ results = get_ncbi_summary(trait)
+ mock_exists.assert_called_once()
+ mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json")
+
+ self.assertEqual(results, "this is a summary of the geneid")
+
+ @mock.patch("wqflask.show_trait.show_trait.requests.get")
+ @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+ def test_get_ncbi_summary_request_fail(self, mock_exists, mock_get_fail):
+ """test for getting ncbi summary with request fail"""
+ trait = TraitObject({"geneid": "id"})
+ mock_exists.return_value = True
+ mock_get_fail.side_effect = Exception("an error occurred")
+ content_json_string = """{
+ "result":{
+ "id":{
+ "summary":"this is a summary of the geneid"
+ }
+ }
+ }
+ """
+ results = get_ncbi_summary(trait)
+ self.assertEqual(results, None)
+
+ def test_hash_num_cases_is_probeset(self):
+ """test for hash num_cases with dataset.type set to Probeset"""
+ create_dataset = TraitObject({"type": "ProbeSet"})
+ create_trait = TraitObject({"dataset": create_dataset})
+ self.assertFalse(has_num_cases(create_trait))
+
+ def test_hash_num_cases_no_probeset(self):
+ """test for hash num cases with dataset.type not Probeset"""
+ create_dataset = TraitObject({"type": "Temp"})
+ construct_data = {
+ "nm1": TraitObject({"num_cases": False}),
+ "nm2": TraitObject({"num_cases": True}),
+ "nm3": TraitObject({"num_cases": False})
+ }
+ construct_data2 = {
+ "nm1": TraitObject({"num_cases": False}),
+ "nm2": TraitObject({"num_cases": False}),
+ "nm3": TraitObject({"num_cases": False})
+ }
+ create_trait = TraitObject(
+ {"dataset": create_dataset, "data": construct_data})
+ create_trait2 = TraitObject(
+ {"dataset": create_dataset, "data": construct_data2})
+
+ results = has_num_cases(create_trait)
+ self.assertTrue(has_num_cases(create_trait))
+ self.assertFalse(has_num_cases(create_trait2))
+
+ def test_get_table_widths(self):
+ """test for getting table widths"""
+ sample_groups = [TraitObject({'se_exists': True, "attributes": ["attr1", "attr2", "attr3"]}
+ ), TraitObject(
+ {"se_exists": False, "attributes": ["at1", "at2"]
+ })]
+
+ results_with_numcase = get_table_widths(sample_groups, True)
+ result_no_numcase = get_table_widths(sample_groups, False)
+
+ results_one_sample = get_table_widths(
+ [TraitObject({"se_exists": True, "attributes": []})], True)
+ expected_with_numcase = (450, "750px")
+ expected_no_numcase = (450, "670px")
+ expected_one_sample = (250, "540px")
+ self.assertEqual(results_with_numcase, expected_with_numcase)
+ self.assertEqual(result_no_numcase, expected_no_numcase)
+ self.assertEqual(results_one_sample,
+ expected_one_sample)
+
+ def test_get_categorical_variables_no_sample_attributes(self):
+ """test for getting categorical variable names with no samples"""
+ trait = TraitObject({})
+ sample_list = TraitObject({"se_exists": True, "attributes": []})
+ self.assertEqual(get_categorical_variables(trait, sample_list), [])
+
+ def test_get_categorical_variables_with_sample_attributes(self):
+ """test for getting categorical variable names with no samples"""
+ this_trait = TraitObject({"data": {
+ "Gene1": TraitObject({"extra_attributes": {"ex1": "ex1value"}}),
+ "Gene2": TraitObject({"extra_attributes": {"ex2": "ex2value"}}),
+ "Gene3": TraitObject({"extra_attributes": {"ex3": "ex3value"}})
+ }})
+ sample_list = TraitObject({"attributes": {
+ "sample_attribute_1": TraitObject({"name": "ex1"}),
+ "sample_attribute_2": TraitObject({"name": "ex2"}),
+ "sample_attribute_3": TraitObject({"name": "ex3"}),
+ "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"})
+ }})
+ results = get_categorical_variables(this_trait, sample_list)
+ self.assertEqual(
+ ["ex1", "ex2", "ex3", "not_in_extra_attributes"], results)
+
+ def test_get_trait_units(self):
+ """test for getting trait units"""
+ trait = TraitObject(
+ {"description_fmt": "[this is a description] another test [N/A]"})
+ trait_no_unit_type = TraitObject({"description_fmt": ""})
+ results = get_trait_units(trait)
+ results_no_unit = get_trait_units(trait_no_unit_type)
+ self.assertEqual(results, "this is a descriptionN/A")
+ self.assertEqual(results_no_unit, "Value")
+
+ @mock.patch("wqflask.show_trait.show_trait.g")
+ def test_get_nearest_marker(self, mock_db):
+ """test for getting nearest marker with non-empty db"""
+
+ mock_db.db.execute.return_value.fetchall.return_value = [
+ ["Geno1", "Geno2"], ["Geno3"]]
+
+ trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+ group_name = TraitObject({"name": "group_name"})
+ this_db = TraitObject({"group": group_name})
+ results_with_item_db = get_nearest_marker(trait, this_db)
+ called_with_value = """SELECT Geno.Name
+ FROM Geno, GenoXRef, GenoFreeze
+ WHERE Geno.Chr = 'test_chr' AND
+ GenoXRef.GenoId = Geno.Id AND
+ GenoFreeze.Id = GenoXRef.GenoFreezeId AND
+ GenoFreeze.Name = 'group_nameGeno'
+ ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1"""
+
+ mock_db.db.execute.assert_called_with(called_with_value)
+
+ self.assertEqual(results_with_item_db, "Geno1")
+
+ @mock.patch("wqflask.show_trait.show_trait.g")
+ def test_get_nearest_marker_empty_db(self, mock_db):
+ """test for getting nearest marker with empty db"""
+ mock_db.db.execute.return_value.fetchall.return_value = []
+ trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+ group_name = TraitObject({"name": "group_name"})
+ this_db = TraitObject({"group": group_name})
+ results_empty_db = get_nearest_marker(trait, this_db)
+ mock_db.db.execute.assert_called_once()
+ self.assertEqual(results_empty_db, "")
+
+ @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+ def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales):
+ """test for getting genotype scales with genofile as list """
+ # where genofile is instance of list
+ genofiles_list = [{"filename": "file1", "location": "~/data/files/f1"},
+ {"filename": "file2", "location": "~/data/files/f2"},
+ {"filename": "file3", "location": "~/data/files/f3"}]
+
+ mock_get_scales.side_effect = [[["morgan", "cM"]],
+ [["morgan", "cM"]],
+ [["physic", "Mb"]]]
+
+ results = get_genotype_scales(genofiles_list)
+ expected_results = {
+ "~/data/files/f1": [["morgan", "cM"]],
+ "~/data/files/f2": [["morgan", "cM"]],
+ "~/data/files/f3": [["physic", "Mb"]]
+ }
+
+ multiple_calls = [mock.call('~/data/files/f1'), mock.call('~/data/files/f2'),
+ mock.call('~/data/files/f3')]
+ mock_get_scales.assert_has_calls(multiple_calls)
+ self.assertEqual(results, expected_results)
+
+ @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+ def test_genotype_scales_with_genofile_other(self, mock_get_scales):
+ """test for getting genotype scales with genofile as a string"""
+ file_location = "~/another_file_location"
+ mock_get_scales.return_value = [["physic", "Mb"]]
+ expected_results = {f"{file_location}": [["physic", "Mb"]]}
+ self.assertEqual(get_genotype_scales(file_location), expected_results)
+ mock_get_scales.assert_called_once_with(file_location)
+
+
+ @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
+ def test_get_scales_from_genofile_found(self, mock_ignore_location):
+ """"add test for get scales from genofile where file is found"""
+ mock_ignore_location.return_value = True
+ geno_file = """
+ #sample line with no @scales:other\n
+ #sample line @scales and :separated by semicolon\n
+ This attempts to check whether\n
+ """
+
+ geno_file_string = "@line start with @ and has @scale:morgan"
+
+ file_location = "~/data/file.geno"
+
+ mock_open_geno_file = mock.mock_open(read_data=geno_file)
+ with mock.patch("builtins.open", mock_open_geno_file):
+ results = get_scales_from_genofile(file_location)
+ self.assertEqual(results, [["morgan", "cM"]])
+
+ mock_open_string = mock.mock_open(read_data=geno_file_string)
+
+ with mock.patch("builtins.open", mock_open_string):
+ result2 = get_scales_from_genofile(file_location)
+ self.assertEqual([['morgan', 'cM']], result2)
+
+ @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
+ def test_get_scales_from_genofile_not_found(self, mock_location_ignore):
+ mock_location_ignore.return_value = False
+
+ expected_results = [["physic", "Mb"]]
+ results = get_scales_from_genofile("~/data/file")
+ mock_location_ignore.assert_called_once_with("~/data/file", "genotype")
+ self.assertEqual(results, expected_results)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 07:46:50 +0000