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-rw-r--r--wqflask/tests/unit/base/test_data_set.py17
-rw-r--r--wqflask/tests/unit/base/test_species.py116
-rw-r--r--wqflask/tests/unit/base/test_webqtl_case_data.py9
-rw-r--r--wqflask/tests/unit/utility/test_authentication_tools.py3
-rw-r--r--wqflask/tests/unit/utility/test_chunks.py1
-rw-r--r--wqflask/tests/unit/wqflask/api/test_correlation.py12
-rw-r--r--wqflask/tests/unit/wqflask/api/test_gen_menu.py401
-rw-r--r--wqflask/tests/unit/wqflask/api/test_mapping.py2
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py2
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py14
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py5
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py29
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py3
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py37
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py79
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py17
-rw-r--r--wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py16
-rw-r--r--wqflask/tests/unit/wqflask/test_collect.py2
-rw-r--r--wqflask/tests/unit/wqflask/test_server_side.py13
19 files changed, 465 insertions, 313 deletions
diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index 96563a16..66ad361d 100644
--- a/wqflask/tests/unit/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -31,14 +31,12 @@ class TestDataSetTypes(unittest.TestCase):
def tearDown(self):
self.app_context.pop()
- @mock.patch('base.data_set.g')
- def test_data_set_type(self, db_mock):
+ def test_data_set_type(self):
"""Test that DatasetType returns correctly if the Redis Instance is not empty
and the name variable exists in the dictionary
"""
with app.app_context():
- db_mock.get = mock.Mock()
redis_mock = mock.Mock()
redis_mock.get.return_value = self.test_dataset
self.assertEqual(DatasetType(redis_mock)
@@ -89,10 +87,9 @@ class TestDataSetTypes(unittest.TestCase):
'"B139_K_1206_M": "ProbeSet", '
'"B139_K_1206_R": "ProbeSet", '
'"Test": "ProbeSet"}'))
-
- db_mock.db.execute.assert_called_with(
- ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
- "WHERE ProbeSetFreeze.Name = \"Test\" ")
+ db_mock.db.execute.assert_called_once_with(
+ ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze "
+ + "WHERE ProbeSetFreeze.Name = \"Test\" ")
)
@mock.patch('base.data_set.g')
@@ -148,9 +145,9 @@ class TestDataSetTypes(unittest.TestCase):
'"Test": "Publish"}'))
db_mock.db.execute.assert_called_with(
- ("SELECT PublishFreeze.Name " +
- "FROM PublishFreeze, InbredSet " +
- "WHERE InbredSet.Name = 'Test' AND "
+ ("SELECT PublishFreeze.Name "
+ + "FROM PublishFreeze, InbredSet "
+ + "WHERE InbredSet.Name = 'Test' AND "
"PublishFreeze.InbredSetId = InbredSet.Id")
)
diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py
new file mode 100644
index 00000000..9b5c023c
--- /dev/null
+++ b/wqflask/tests/unit/base/test_species.py
@@ -0,0 +1,116 @@
+"""Tests wqflask/base/species.py"""
+
+import unittest
+from unittest import mock
+from base.species import TheSpecies
+from base.species import IndChromosome
+from base.species import Chromosomes
+from collections import OrderedDict
+from wqflask import app
+from dataclasses import dataclass
+
+
+@dataclass
+class MockChromosome:
+ OrderId: int
+ Name: str
+ Length: int
+
+
+@dataclass
+class MockGroup:
+ name: str
+
+
+@dataclass
+class MockDataset:
+ group: MockGroup
+
+
+class TestTheSpecies(unittest.TestCase):
+ """Tests for TheSpecies class"""
+ @mock.patch('base.species.Chromosomes')
+ def test_create_species_with_null_species_name(self, mock_chromosome):
+ """Test that TheSpecies is instantiated correctly when the
+species_name is provided."""
+ mock_chromosome.return_value = 1
+ test_species = TheSpecies(dataset="random_dataset", species_name="a")
+ self.assertEqual(test_species.name, "a")
+ self.assertEqual(test_species.chromosomes, 1)
+
+ @mock.patch('base.species.Chromosomes')
+ def test_create_species_with_species_name(self, mock_chromosome):
+ """Test that TheSpecies is instantiated correctly when the
+species_name is not provided."""
+ mock_chromosome.return_value = 1
+ test_species = TheSpecies(dataset="random_dataset")
+ self.assertEqual(test_species.dataset, "random_dataset")
+ self.assertEqual(test_species.chromosomes, 1)
+ mock_chromosome.assert_called_once_with(dataset="random_dataset")
+
+
+class TestIndChromosome(unittest.TestCase):
+ """Tests for IndChromosome class"""
+
+ def test_create_ind_chromosome(self):
+ """Test that IndChromosome is instantiated correctly"""
+ test_ind_chromosome = IndChromosome(name="Test", length=10000000)
+ self.assertEqual(test_ind_chromosome.name, "Test")
+ self.assertEqual(test_ind_chromosome.length, 10000000)
+ self.assertEqual(test_ind_chromosome.mb_length, 10)
+
+
+class TestChromosomes(unittest.TestCase):
+ """Tests for Chromosomes class"""
+ maxDiff = None
+
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ @mock.patch("base.species.g")
+ def test_create_chromosomes_with_no_species(self, mock_db):
+ """Test instantiating a chromosome without a species"""
+ mock_db.db.execute.return_value.fetchall.return_value = [
+ MockChromosome(1, "X", 100),
+ MockChromosome(2, "Y", 1000),
+ MockChromosome(3, "Z", 10000),
+ ]
+ mock_dataset = MockDataset(MockGroup("Random"))
+ test_chromosomes = Chromosomes(dataset=mock_dataset)
+ self.assertEqual(
+ list(test_chromosomes.chromosomes.keys()),
+ [1, 2, 3]
+ )
+ self.assertEqual(test_chromosomes.dataset, mock_dataset)
+ mock_db.db.execute.assert_called_with(
+ "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
+ "FROM Chr_Length, InbredSet WHERE "
+ "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
+ "InbredSet.Name = 'Random' ORDER BY OrderId"
+ )
+
+ @mock.patch("base.species.g")
+ def test_create_chromosomes_with_species(self, mock_db):
+ """Test instantiating a chromosome with a species"""
+ mock_db.db.execute.return_value.fetchall.return_value = [
+ MockChromosome(1, "X", 100),
+ MockChromosome(2, "Y", 1000),
+ MockChromosome(3, "Z", 10000),
+ ]
+ mock_dataset = MockDataset(MockGroup("Random"))
+ test_chromosomes = Chromosomes(dataset=mock_dataset,
+ species="testSpecies")
+ self.assertEqual(
+ list(test_chromosomes.chromosomes.keys()),
+ [1, 2, 3]
+ )
+ mock_db.db.execute.assert_called_with(
+ "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
+ "FROM Chr_Length, Species WHERE "
+ "Chr_Length.SpeciesId = Species.SpeciesId AND "
+ "Species.Name = 'Testspecies' ORDER BY OrderId"
+ )
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index 8e8ba482..e1555cb4 100644
--- a/wqflask/tests/unit/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -4,15 +4,16 @@ import unittest
from wqflask import app # Required because of utility.tools in webqtlCaseData.py
from base.webqtlCaseData import webqtlCaseData
+
class TestWebqtlCaseData(unittest.TestCase):
"""Tests for WebqtlCaseData class"""
def setUp(self):
self.w = webqtlCaseData(name="Test",
- value=0,
- variance=0.0,
- num_cases=10,
- name2="Test2")
+ value=0,
+ variance=0.0,
+ num_cases=10,
+ name2="Test2")
def test_webqtl_case_data_repr(self):
self.assertEqual(
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
index fff5fd8f..024ab43f 100644
--- a/wqflask/tests/unit/utility/test_authentication_tools.py
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
@@ -5,6 +5,7 @@ from unittest import mock
from utility.authentication_tools import check_resource_availability
from utility.authentication_tools import add_new_resource
+
class TestResponse:
"""Mock Test Response after a request"""
@property
@@ -18,7 +19,7 @@ class TestUser:
@property
def user_id(self):
"""Mockes user id. Used in Flask.g.user_session.user_id"""
- return "Jane"
+ return b"Jane"
class TestUserSession:
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
index 8d90a1ec..1d349193 100644
--- a/wqflask/tests/unit/utility/test_chunks.py
+++ b/wqflask/tests/unit/utility/test_chunks.py
@@ -7,6 +7,7 @@ from utility.chunks import divide_into_chunks
class TestChunks(unittest.TestCase):
"Test Utility method for chunking"
+
def test_divide_into_chunks(self):
"Check that a list is chunked correctly"
self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index d0264b87..1089a36f 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -105,10 +105,10 @@ class TestCorrelations(unittest.TestCase):
target_dataset = AttributeSetter({"group": group})
target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
- trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
- "S3": AttributeSetter(
- {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
- "S6": AttributeSetter({"value": 5.0})}
+ trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
+ "S3": AttributeSetter(
+ {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
+ "S6": AttributeSetter({"value": 5.0})}
this_trait = AttributeSetter({"data": trait_data})
mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
[3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6)
@@ -127,9 +127,9 @@ class TestCorrelations(unittest.TestCase):
expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6]
expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6]
for i, val in enumerate(expected_pearsonr):
- self.assertAlmostEqual(val, results_pearsonr[i],4)
+ self.assertAlmostEqual(val, results_pearsonr[i], 4)
for i, val in enumerate(expected_spearmanr):
- self.assertAlmostEqual(val, results_spearmanr[i],4)
+ self.assertAlmostEqual(val, results_spearmanr[i], 4)
self.assertEqual(results_num_overlap, None)
@mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index 57eb1650..7e477da2 100644
--- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
@@ -2,9 +2,7 @@
import unittest
from unittest import mock
-from wqflask import app
from wqflask.api.gen_menu import gen_dropdown_json
-from wqflask.api.gen_menu import get_species
from wqflask.api.gen_menu import get_groups
from wqflask.api.gen_menu import get_types
from wqflask.api.gen_menu import get_datasets
@@ -18,8 +16,6 @@ class TestGenMenu(unittest.TestCase):
"""Tests for the gen_menu module"""
def setUp(self):
- self.app_context = app.app_context()
- self.app_context.push()
self.test_group = {
'mouse': [
['H_T1',
@@ -70,212 +66,225 @@ class TestGenMenu(unittest.TestCase):
}
}
- def tearDown(self):
- self.app_context.pop()
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_get_species(self, db_mock):
- """Test that assertion is raised when dataset and dataset_name
- are defined"""
- db_mock.db.execute.return_value.fetchall.return_value = (
- ('human', 'Human'),
- ('mouse', 'Mouse'))
- self.assertEqual(get_species(),
- [['human', 'Human'], ['mouse', 'Mouse']])
- db_mock.db.execute.assert_called_once_with(
- "SELECT Name, MenuName FROM Species ORDER BY OrderId"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_get_groups(self, db_mock):
+ def test_get_groups(self):
"""Test that species groups are grouped correctly"""
- db_mock.db.execute.return_value.fetchall.side_effect = [
- # Mouse
- (('BXD', 'BXD', None),
- ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)',
- 'Test')),
- # Human
- (('H_T1', "H_T", "DescriptionA"),
- ('H_T2', "H_T'", None))
- ]
-
- self.assertEqual(get_groups([["human", "Human"], ["mouse", "Mouse"]]),
- self.test_group)
-
- for name in ["mouse", "human"]:
- db_mock.db.execute.assert_any_call(
- ("SELECT InbredSet.Name, InbredSet.FullName, " +
- "IFNULL(InbredSet.Family, 'None') " +
- "FROM InbredSet, Species WHERE Species.Name " +
- "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " +
- "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " +
- "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " +
- "InbredSet.FullName) ASC, InbredSet.FullName ASC, " +
- "InbredSet.MenuOrderId ASC").format(name)
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.side_effect = [
+ # Mouse
+ (('BXD', 'BXD', None),
+ ('HLC', ('Liver: Normal Gene Expression '
+ 'with Genotypes (Merck)'),
+ 'Test')),
+ # Human
+ (('H_T1', "H_T", "DescriptionA"),
+ ('H_T2', "H_T'", None))
+ ]
+ self.assertEqual(get_groups([["human", "Human"],
+ ["mouse", "Mouse"]],
+ db_mock),
+ self.test_group)
+
+ for name in ["mouse", "human"]:
+ cursor.execute.assert_any_call(
+ ("SELECT InbredSet.Name, InbredSet.FullName, "
+ "IFNULL(InbredSet.Family, 'None') "
+ "FROM InbredSet, Species WHERE Species.Name "
+ "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by "
+ "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+ "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+ "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+ "InbredSet.MenuOrderId ASC").format(name)
+ )
+
+ def test_phenotypes_exist_called_with_correct_query(self):
+ """Test that phenotypes_exist is called with the correct query"""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = None
+ phenotypes_exist("test", db_mock)
+ cursor.execute.assert_called_with(
+ "SELECT Name FROM PublishFreeze "
+ "WHERE PublishFreeze.Name = 'testPublish'"
)
- @mock.patch('wqflask.api.gen_menu.g')
- def test_phenotypes_exist_called_with_correct_query(self, db_mock):
- """Test that phenotypes_exist is called with the correct query"""
- db_mock.db.execute.return_value.fetchone.return_value = None
- phenotypes_exist("test")
- db_mock.db.execute.assert_called_with(
- "SELECT Name FROM PublishFreeze "
- "WHERE PublishFreeze.Name = 'testPublish'"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_phenotypes_exist_with_falsy_values(self, db_mock):
+ def test_phenotypes_exist_with_falsy_values(self):
"""Test that phenotype check returns correctly when given
a None value"""
- for x in [None, False, (), [], ""]:
- db_mock.db.execute.return_value.fetchone.return_value = x
- self.assertFalse(phenotypes_exist("test"))
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_phenotypes_exist_with_truthy_value(self, db_mock):
- """Test that phenotype check returns correctly when given Truthy """
- for x in ["x", ("result"), ["result"], [1]]:
- db_mock.db.execute.return_value.fetchone.return_value = (x)
- self.assertTrue(phenotypes_exist("test"))
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_genotypes_exist_called_with_correct_query(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ for x in [None, False, (), [], ""]:
+ cursor.fetchone.return_value = x
+ self.assertFalse(phenotypes_exist("test", db_mock))
+
+ def test_phenotypes_exist_with_truthy_value(self):
+ """Test that phenotype check returns correctly when given Truthy"""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as conn:
+ with conn.cursor() as cursor:
+ for x in ["x", ("result"), ["result"], [1]]:
+ cursor.fetchone.return_value = (x)
+ self.assertTrue(phenotypes_exist("test", db_mock))
+
+ def test_genotypes_exist_called_with_correct_query(self):
"""Test that genotypes_exist is called with the correct query"""
- db_mock.db.execute.return_value.fetchone.return_value = None
- genotypes_exist("test")
- db_mock.db.execute.assert_called_with(
- "SELECT Name FROM GenoFreeze WHERE GenoFreeze.Name = 'testGeno'"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_genotypes_exist_with_falsy_values(self, db_mock):
- """Test that genotype check returns correctly when given
- a None value"""
- for x in [None, False, (), [], ""]:
- db_mock.db.execute.return_value.fetchone.return_value = x
- self.assertFalse(genotypes_exist("test"))
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = None
+ genotypes_exist("test", db_mock)
+ cursor.execute.assert_called_with(
+ "SELECT Name FROM GenoFreeze WHERE "
+ "GenoFreeze.Name = 'testGeno'"
+ )
+
+ def test_genotypes_exist_with_falsy_values(self):
+ """Test that genotype check returns correctly when given a None value
- @mock.patch('wqflask.api.gen_menu.g')
- def test_genotypes_exist_with_truthy_value(self, db_mock):
+ """
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ for x in [None, False, (), [], ""]:
+ cursor.fetchone.return_value = x
+ self.assertFalse(genotypes_exist("test", db_mock))
+
+ def test_genotypes_exist_with_truthy_value(self):
"""Test that genotype check returns correctly when given Truthy """
- for x in ["x", ("result"), ["result"], [1]]:
- db_mock.db.execute.return_value.fetchone.return_value = (x)
- self.assertTrue(phenotypes_exist("test"))
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ for x in ["x", ("result"), ["result"], [1]]:
+ cursor.fetchone.return_value = (x)
+ self.assertTrue(phenotypes_exist("test", db_mock))
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_phenotypes(self, db_mock):
+ def test_build_datasets_with_type_phenotypes(self):
"""Test that correct dataset is returned for a phenotype type"""
- db_mock.db.execute.return_value.fetchall.return_value = (
- (602, "BXDPublish", "BXD Published Phenotypes"),
- )
- self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
- [['602', "BXDPublish", "BXD Published Phenotypes"]])
- db_mock.db.execute.assert_called_with(
- "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " +
- "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " +
- "InbredSet WHERE InbredSet.Name = 'BXD' AND " +
- "PublishFreeze.InbredSetId = InbredSet.Id AND " +
- "InfoFiles.InfoPageName = PublishFreeze.Name " +
- "ORDER BY PublishFreeze.CreateTime ASC"
- )
- self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
- [['602', "BXDPublish", "Mouse Phenome Database"]])
-
- db_mock.db.execute.return_value.fetchall.return_value = ()
- db_mock.db.execute.return_value.fetchone.return_value = (
- "BXDPublish", "Mouse Phenome Database"
- )
- self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
- [["None", "BXDPublish", "Mouse Phenome Database"]])
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.return_value = (
+ (602, "BXDPublish", "BXD Published Phenotypes"),
+ )
+ self.assertEqual(build_datasets("Mouse", "BXD",
+ "Phenotypes", db_mock),
+ [['602', "BXDPublish",
+ "BXD Published Phenotypes"]])
+ cursor.execute.assert_called_with(
+ "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, "
+ + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, "
+ + "InbredSet WHERE InbredSet.Name = 'BXD' AND "
+ + "PublishFreeze.InbredSetId = InbredSet.Id AND "
+ + "InfoFiles.InfoPageName = PublishFreeze.Name "
+ + "ORDER BY PublishFreeze.CreateTime ASC"
+ )
+ self.assertEqual(build_datasets("Mouse", "MDP",
+ "Phenotypes", db_mock),
+ [['602', "BXDPublish",
+ "Mouse Phenome Database"]])
+
+ cursor.fetchall.return_value = ()
+ cursor.fetchone.return_value = (
+ "BXDPublish", "Mouse Phenome Database"
+ )
+ self.assertEqual(build_datasets("Mouse", "MDP",
+ "Phenotypes", db_mock),
+ [["None", "BXDPublish",
+ "Mouse Phenome Database"]])
+
+ def test_build_datasets_with_type_phenotypes_and_no_results(self):
"""Test that correct dataset is returned for a phenotype type with no
results
"""
- db_mock.db.execute.return_value.fetchall.return_value = None
- db_mock.db.execute.return_value.fetchone.return_value = (121,
- "text value")
- self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
- [["None", "121", "text value"]])
- db_mock.db.execute.assert_called_with(
- "SELECT PublishFreeze.Name, PublishFreeze.FullName "
- "FROM PublishFreeze, InbredSet "
- "WHERE InbredSet.Name = 'BXD' AND "
- "PublishFreeze.InbredSetId = InbredSet.Id "
- "ORDER BY PublishFreeze.CreateTime ASC"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_genotypes(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.return_value = None
+ cursor.fetchone.return_value = (121,
+ "text value")
+ self.assertEqual(build_datasets("Mouse", "BXD",
+ "Phenotypes", db_mock),
+ [["None", "121",
+ "text value"]])
+ cursor.execute.assert_called_with(
+ "SELECT PublishFreeze.Name, PublishFreeze.FullName "
+ "FROM PublishFreeze, InbredSet "
+ "WHERE InbredSet.Name = 'BXD' AND "
+ "PublishFreeze.InbredSetId = InbredSet.Id "
+ "ORDER BY PublishFreeze.CreateTime ASC"
+ )
+
+ def test_build_datasets_with_type_genotypes(self):
"""Test that correct dataset is returned for a phenotype type"""
- db_mock.db.execute.return_value.fetchone.return_value = (
- 635, "HLCPublish", "HLC Published Genotypes"
- )
-
- self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
- [["635", "HLCGeno", "HLC Genotypes"]])
- db_mock.db.execute.assert_called_with(
- "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
- "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
- "GenoFreeze.InbredSetId = InbredSet.Id AND "
- "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
- "ORDER BY GenoFreeze.CreateTime DESC"
- )
- db_mock.db.execute.return_value.fetchone.return_value = ()
- self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
- [["None", "HLCGeno", "HLC Genotypes"]])
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_mrna(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = (
+ 635, "HLCPublish", "HLC Published Genotypes"
+ )
+ self.assertEqual(build_datasets("Mouse", "HLC",
+ "Genotypes", db_mock),
+ [["635", "HLCGeno", "HLC Genotypes"]])
+ cursor.execute.assert_called_with(
+ "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
+ "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
+ "GenoFreeze.InbredSetId = InbredSet.Id AND "
+ "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+ "ORDER BY GenoFreeze.CreateTime DESC"
+ )
+ cursor.fetchone.return_value = ()
+ self.assertEqual(build_datasets("Mouse", "HLC",
+ "Genotypes", db_mock),
+ [["None", "HLCGeno", "HLC Genotypes"]])
+
+ def test_build_datasets_with_type_mrna(self):
"""Test that correct dataset is returned for a mRNA
expression/ Probeset"""
- db_mock.db.execute.return_value.fetchall.return_value = (
- (112, "HC_M2_0606_P",
- "Hippocampus Consortium M430v2 (Jun06) PDNN"), )
- self.assertEqual(build_datasets("Mouse", "HLC", "mRNA"), [[
- "112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"
- ]])
- db_mock.db.execute.assert_called_once_with(
- "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " +
- "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " +
- "ProbeFreeze, InbredSet, Tissue, Species WHERE " +
- "Species.Name = 'Mouse' AND Species.Id = " +
- "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " +
- "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " +
- "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " +
- "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " +
- "ProbeSetFreeze.public > 0 " +
- "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.return_value = (
+ (112, "HC_M2_0606_P",
+ "Hippocampus Consortium M430v2 (Jun06) PDNN"), )
+ self.assertEqual(build_datasets("Mouse",
+ "HLC", "mRNA", db_mock),
+ [["112", 'HC_M2_0606_P',
+ "Hippocampus Consortium M430v2 (Jun06) PDNN"
+ ]])
+ cursor.execute.assert_called_once_with(
+ "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+ "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+ "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+ "Species.Name = 'Mouse' AND Species.Id = "
+ "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND "
+ "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
+ "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = "
+ "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND "
+ "ProbeSetFreeze.public > 0 "
+ "ORDER BY -ProbeSetFreeze.OrderList DESC, "
+ "ProbeSetFreeze.CreateTime DESC")
@mock.patch('wqflask.api.gen_menu.build_datasets')
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_types(self, db_mock, datasets_mock):
+ def test_build_types(self, datasets_mock):
"""Test that correct tissue metadata is returned"""
+ db_mock = mock.MagicMock()
datasets_mock.return_value = [
["112", 'HC_M2_0606_P',
"Hippocampus Consortium M430v2 (Jun06) PDNN"]
]
- db_mock.db.execute.return_value.fetchall.return_value = (
- ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
- )
- self.assertEqual(build_types('mouse', 'random group'),
- [['M', 'M', 'Molecular Traits'],
- ['H', 'H', 'Molecular Traits'],
- ['R', 'R', 'Molecular Traits']])
- db_mock.db.execute.assert_called_once_with(
- "SELECT DISTINCT Tissue.Name " +
- "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " +
- "Tissue, Species WHERE Species.Name = 'mouse' " +
- "AND Species.Id = InbredSet.SpeciesId AND " +
- "InbredSet.Name = 'random group' AND " +
- "ProbeFreeze.TissueId = Tissue.Id AND " +
- "ProbeFreeze.InbredSetId = InbredSet.Id AND " +
- "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " +
- "ORDER BY Tissue.Name"
- )
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.return_value = (
+ ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
+ )
+ self.assertEqual(build_types('mouse', 'random group', db_mock),
+ [['M', 'M', 'Molecular Traits'],
+ ['H', 'H', 'Molecular Traits'],
+ ['R', 'R', 'Molecular Traits']])
+ cursor.execute.assert_called_once_with(
+ "SELECT DISTINCT Tissue.Name "
+ "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+ "Tissue, Species WHERE Species.Name = 'mouse' "
+ "AND Species.Id = InbredSet.SpeciesId AND "
+ "InbredSet.Name = 'random group' AND "
+ "ProbeFreeze.TissueId = Tissue.Id AND "
+ "ProbeFreeze.InbredSetId = InbredSet.Id AND "
+ "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+ "ORDER BY Tissue.Name"
+ )
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -297,7 +306,9 @@ class TestGenMenu(unittest.TestCase):
build_types_mock.return_value = [
['M', 'M', 'Molecular Trait Datasets']
]
- self.assertEqual(get_types(self.test_group), expected_result)
+ self.assertEqual(get_types(self.test_group,
+ mock.MagicMock()),
+ expected_result)
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -315,10 +326,8 @@ class TestGenMenu(unittest.TestCase):
genotypes_exist_mock.return_value = False
build_types_mock.return_value = []
- self.assertEqual(get_types(self.test_group), {
- 'mouse': {},
- 'human': {}
- })
+ self.assertEqual(get_types(self.test_group, mock.MagicMock()),
+ {'mouse': {}, 'human': {}})
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -345,7 +354,7 @@ class TestGenMenu(unittest.TestCase):
'human': {
'HLC': [['M', 'M', 'Molecular Trait Datasets']],
'BXD': [['M', 'M', 'Molecular Trait Datasets']]}}
- self.assertEqual(get_types(self.test_group),
+ self.assertEqual(get_types(self.test_group, mock.MagicMock()),
expected_result)
@mock.patch('wqflask.api.gen_menu.build_datasets')
@@ -367,7 +376,7 @@ class TestGenMenu(unittest.TestCase):
'BXD': {'Genotypes': 'Test',
'M': 'Test',
'Phenotypes': 'Test'}}}
- self.assertEqual(get_datasets(self.test_type),
+ self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
expected_result)
@mock.patch('wqflask.api.gen_menu.build_datasets')
@@ -381,13 +390,13 @@ class TestGenMenu(unittest.TestCase):
'H_T1': {}},
'human': {'HLC': {},
'BXD': {}}}
- self.assertEqual(get_datasets(self.test_type),
+ self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
expected_result)
@mock.patch('wqflask.api.gen_menu.get_datasets')
@mock.patch('wqflask.api.gen_menu.get_types')
@mock.patch('wqflask.api.gen_menu.get_groups')
- @mock.patch('wqflask.api.gen_menu.get_species')
+ @mock.patch('wqflask.api.gen_menu.get_all_species')
def test_gen_dropdown_json(self,
species_mock,
groups_mock,
@@ -411,4 +420,4 @@ class TestGenMenu(unittest.TestCase):
'groups': ['groupA', 'groupB', 'groupC', 'groupD'],
'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']}
- self.assertEqual(gen_dropdown_json(), expected_result)
+ self.assertEqual(gen_dropdown_json(mock.MagicMock()), expected_result)
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/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index 44d2e0fc..2bbeab1f 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -5,7 +5,7 @@ from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_ti
class TestCorrelationFunctions(unittest.TestCase):
-
+
@mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
def test_get_trait_symbol_and_tissue_values(self, mock_class):
"""test for getting trait symbol and tissue_values"""
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py
new file mode 100644
index 00000000..e1bd6d86
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py
@@ -0,0 +1,14 @@
+"""this module contains tests for code used in integrating to gn3 api"""
+from unittest import TestCase
+from base.data_set import create_dataset
+
+class TestCorrelation(TestCase):
+
+ def test_create_dataset(self):
+ """test for creating datasets"""
+
+ pass
+ def test_fetch_dataset_info(self):
+ """test for fetching dataset info data"""
+
+ pass
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 8ae0f09f..f4869c45 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -9,6 +9,7 @@ from wqflask.marker_regression.display_mapping_results import (
class TestDisplayMappingResults(unittest.TestCase):
"""Basic Methods to test Mapping Results"""
+
def test_pil_colors(self):
"""Test that colors use PILLOW color format"""
self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
@@ -17,6 +18,7 @@ class TestDisplayMappingResults(unittest.TestCase):
class TestHtmlGenWrapper(unittest.TestCase):
"""Test Wrapper around HTMLGen"""
+
def test_create_image(self):
"""Test HT.Image method"""
self.assertEqual(
@@ -37,7 +39,8 @@ class TestHtmlGenWrapper(unittest.TestCase):
cgi="/testing/",
enctype='multipart/form-data',
name="formName",
- submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name')
+ submit=HtmlGenWrapper.create_input_tag(
+ type_='hidden', name='Default_Name')
)
test_image = HtmlGenWrapper.create_image_tag(
src="test.png",
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index fe2569b8..4003d68f 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -47,11 +47,11 @@ class TestGemmaMapping(unittest.TestCase):
@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):
+ 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={}
+ this_chromosomes = {}
for i in range(1, 5):
- this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"}))
+ this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"}))
chromosomes = AttributeSetter({"chromosomes": this_chromosomes})
dataset_group = MockGroup(
@@ -68,9 +68,10 @@ class TestGemmaMapping(unittest.TestCase):
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)
+ 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_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)
@@ -102,7 +103,8 @@ class TestGemmaMapping(unittest.TestCase):
create_trait_side_effect = []
for i in range(4):
- create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'}))
+ create_dataset_side_effect.append(
+ AttributeSetter({"name": f'name_{i}'}))
create_trait_side_effect.append(
AttributeSetter({"data": [f'data_{i}']}))
@@ -144,7 +146,7 @@ class TestGemmaMapping(unittest.TestCase):
"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
+ 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"""
@@ -159,11 +161,14 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
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}]
+ 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)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
index 5eec93f1..fd21a825 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -12,9 +12,10 @@ class AttributeSetter:
def __init__(self, obj):
for key, val in obj.items():
setattr(self, key, val)
-class TestPlinkMapping(unittest.TestCase):
+class TestPlinkMapping(unittest.TestCase):
+
def test_build_line_list(self):
"""test for building line list"""
line_1 = "this is line one test"
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index b47f877a..8b4337ec 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -1,21 +1,24 @@
import unittest
-from unittest import mock
-from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
+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
-#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)
+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
index c585f1df..9d13e943 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -1,48 +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
-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)
-
-
-
-
+from wqflask.marker_regression.rqtl_mapping import run_rqtl
+@dataclass
+class MockGroup:
+ name: str
+ genofile: str
+@dataclass
+class MockDataset:
+ group: MockGroup
+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 a29d8cfb..c220a072 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -187,7 +187,8 @@ class TestRunMapping(unittest.TestCase):
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('N Samples: 100\n'), mock.call('Transform - Quantile Normalized\n'),
+ mock.call('N Samples: 100\n'), mock.call(
+ 'Transform - Quantile Normalized\n'),
mock.call('Gene Symbol: IGFI\n'), mock.call(
'Location: X1 @ 123313 Mb\n'),
mock.call('Cofactors (dataset - trait):\n'),
@@ -228,20 +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"
},
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index ce3e7b83..89442c47 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -21,11 +21,11 @@ class TestSnpBrowser(unittest.TestCase):
"transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
- 'Domain 1', 'Domain 2', 'Details'],
- ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
- ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
- 'conservation_score', 'domain_1', 'domain_2',
- 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
+ 'Domain 1', 'Domain 2', 'Details'],
+ ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
+ ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
+ 'conservation_score', 'domain_1', 'domain_2',
+ 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
results_with_snp = get_header_list(
variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
@@ -33,9 +33,9 @@ class TestSnpBrowser(unittest.TestCase):
variant_type="InDel", strains=strains, species="rat", empty_columns=[])
expected_results_with_indel = (
['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
- 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
- ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
- 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
+ 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
+ ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
+ 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
self.assertEqual(expected_results, results_with_snp)
self.assertEqual(expected_results_with_indel, results_with_indel)
diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
index 9a36132d..2a914fb2 100644
--- a/wqflask/tests/unit/wqflask/test_collect.py
+++ b/wqflask/tests/unit/wqflask/test_collect.py
@@ -11,6 +11,7 @@ app = Flask(__name__)
class MockSession:
"""Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+
def __init__(self, is_logged_in=False):
self.is_logged_in = is_logged_in
@@ -21,6 +22,7 @@ class MockSession:
class MockFlaskG:
"""Helper class for mocking wqflask.collect.g.user_session"""
+
def __init__(self, is_logged_in=False):
self.is_logged_in = is_logged_in
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
index 4f91d8ca..be7ca2df 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -17,15 +17,18 @@ class TestServerSideTableTests(unittest.TestCase):
def test_get_page(self):
rows_count = 3
table_rows = [
- {'first': 'd', 'second': 4, 'third': 'zz'},
- {'first': 'b', 'second': 2, 'third': 'aa'},
+ {'first': 'd', 'second': 4, 'third': 'zz'},
+ {'first': 'b', 'second': 2, 'third': 'aa'},
{'first': 'c', 'second': 1, 'third': 'ss'},
]
headers = ['first', 'second', 'third']
- request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
+ request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1',
+ 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
- test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page()
+ test_page = ServerSideTable(
+ rows_count, table_rows, headers, request_args).get_page()
self.assertEqual(test_page['sEcho'], '1')
self.assertEqual(test_page['iTotalRecords'], 'nan')
self.assertEqual(test_page['iTotalDisplayRecords'], '3')
- self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
+ self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {
+ 'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])