Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into replace-bootstrap

11 files changed, 595 insertions, 49 deletions

diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py
new file mode 100644
index 00000000..48d110c7
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_type_checking.py
@@ -0,0 +1,54 @@
+import unittest
+from utility.type_checking import is_float
+from utility.type_checking import is_int
+from utility.type_checking import is_str
+from utility.type_checking import get_float
+from utility.type_checking import get_int
+from utility.type_checking import get_string
+
+
+class TestTypeChecking(unittest.TestCase):
+    def test_is_float(self):
+        floats = [2, 1.2, '3.1']
+        not_floats = ["String", None, [], ()]
+        for flt in floats:
+            results = is_float(flt)
+            self.assertTrue(results)
+        for nflt in not_floats:
+            results = is_float(nflt)
+            self.assertFalse(results)
+
+    def test_is_int(self):
+        int_values = [1, 1.1]
+        not_int_values = ["string", None, [], "1.1"]
+        for int_val in int_values:
+            results = is_int(int_val)
+            self.assertTrue(results)
+        for not_int in not_int_values:
+            results = is_int(not_int)
+            self.assertFalse(results)
+
+    def test_is_str(self):
+        string_values = [1, False, [], {}, "string_value"]
+        falsey_values = [None]
+        for string_val in string_values:
+            results = is_str(string_val)
+            self.assertTrue(results)
+        for non_string in falsey_values:
+            results = is_str(non_string)
+            self.assertFalse(results)
+
+    def test_get_float(self):
+        vars_object = {"min_value": "12"}
+        results = get_float(vars_object, "min_value")
+        self.assertEqual(results, 12.0)
+
+    def test_get_int(self):
+        vars_object = {"lx_value": "1"}
+        results = get_int(vars_object, "lx_value")
+        self.assertEqual(results, 1)
+
+    def test_get_string(self):
+        string_object = {"mx_value": 1}
+        results = get_string(string_object, "mx_value")
+        self.assertEqual(results, "1")
\ No newline at end of file
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
new file mode 100644
index 00000000..d0264b87
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -0,0 +1,153 @@
+import unittest
+from unittest import mock
+from wqflask import app
+from collections import OrderedDict
+from wqflask.api.correlation import init_corr_params
+from wqflask.api.correlation import convert_to_mouse_gene_id
+from wqflask.api.correlation import do_literature_correlation_for_all_traits
+from wqflask.api.correlation import get_sample_r_and_p_values
+from wqflask.api.correlation import calculate_results
+
+
+class AttributeSetter:
+    def __init__(self, obj):
+        for k, v in obj.items():
+            setattr(self, k, v)
+
+
+class MockDataset(AttributeSetter):
+    def get_trait_data(self):
+        return None
+
+    def retrieve_genes(self, id=None):
+        return {
+            "TT-1": "GH-1",
+            "TT-2": "GH-2",
+            "TT-3": "GH-3"
+
+        }
+
+
+class TestCorrelations(unittest.TestCase):
+    def setUp(self):
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    def test_init_corr_params(self):
+        start_vars = {
+            "return_count": "3",
+            "type": "T1",
+            "method": "spearman"
+        }
+
+        corr_params_results = init_corr_params(start_vars=start_vars)
+        expected_results = {
+            "return_count": 3,
+            "type": "T1",
+            "method": "spearman"
+        }
+
+        self.assertEqual(corr_params_results, expected_results)
+
+    @mock.patch("wqflask.api.correlation.g")
+    def test_convert_to_mouse_gene_id(self, mock_db):
+
+        results = convert_to_mouse_gene_id(species="Other", gene_id="")
+        self.assertEqual(results, None)
+
+        rat_species_results = convert_to_mouse_gene_id(
+            species="rat", gene_id="GH1")
+
+        mock_db.db.execute.return_value.fetchone.side_effect = [
+            AttributeSetter({"mouse": "MG-1"}), AttributeSetter({"mouse": "MG-2"})]
+
+        self.assertEqual(convert_to_mouse_gene_id(
+            species="mouse", gene_id="MG-4"), "MG-4")
+        self.assertEqual(convert_to_mouse_gene_id(
+            species="rat", gene_id="R1"), "MG-1")
+        self.assertEqual(convert_to_mouse_gene_id(
+            species="human", gene_id="H1"), "MG-2")
+
+    @mock.patch("wqflask.api.correlation.g")
+    @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
+    def test_do_literature_correlation_for_all_traits(self, mock_convert_to_mouse_geneid, mock_db):
+        mock_convert_to_mouse_geneid.side_effect = [
+            "MG-1", "MG-2;", "MG-3", "MG-4"]
+
+        trait_geneid_dict = {
+            "TT-1": "GH-1",
+            "TT-2": "GH-2",
+            "TT-3": "GH-3"
+
+        }
+        mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter(
+            {"value": "V1"}), AttributeSetter({"value": "V2"}), AttributeSetter({"value": "V3"})]
+
+        this_trait = AttributeSetter({"geneid": "GH-1"})
+
+        target_dataset = AttributeSetter(
+            {"group": AttributeSetter({"species": "rat"})})
+        results = do_literature_correlation_for_all_traits(
+            this_trait=this_trait, target_dataset=target_dataset, trait_geneid_dict=trait_geneid_dict, corr_params={})
+
+        expected_results = {'TT-1': ['GH-1', 0],
+                            'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
+        self.assertEqual(results, expected_results)
+
+    @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
+    def test_get_sample_r_and_p_values(self, mock_normalize):
+
+        group = AttributeSetter(
+            {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]})
+        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})}
+        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)
+        mock_normalize.side_effect = [([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),
+                                      ([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),
+                                      ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3)]
+
+        results_pearsonr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+        }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+        results_spearmanr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+        }, target_vals=target_vals, target_dataset=target_dataset, type="spearman")
+        results_num_overlap = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+        }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+        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)
+        for i, val in enumerate(expected_spearmanr):
+            self.assertAlmostEqual(val, results_spearmanr[i],4)
+        self.assertEqual(results_num_overlap, None)
+
+    @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
+    def test_calculate_results(self, literature_correlation):
+
+        literature_correlation.return_value = {
+            'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
+
+        this_dataset = MockDataset(
+            {"group": AttributeSetter({"species": "rat"})})
+        target_dataset = MockDataset(
+            {"group": AttributeSetter({"species": "rat"})})
+        this_trait = AttributeSetter({"geneid": "GH-1"})
+        corr_params = {"type": "literature"}
+        sorted_results = calculate_results(
+            this_trait=this_trait, this_dataset=this_dataset, target_dataset=target_dataset, corr_params=corr_params)
+        expected_results = {'TT-2': ['GH-2', 3],
+                            'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
+
+        self.assertTrue(isinstance(sorted_results, OrderedDict))
+        self.assertEqual(dict(sorted_results), expected_results)
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
new file mode 100644
index 00000000..b094294a
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -0,0 +1,108 @@
+import unittest
+from unittest import mock
+from wqflask.api.mapping import initialize_parameters
+from wqflask.api.mapping import do_mapping_for_api
+
+
+class AttributeSetter:
+    def __init__(self, obj):
+        for key, value in obj.items():
+            setattr(self, key, value)
+
+
+class MockGroup(AttributeSetter):
+    def get_marker(self):
+        self.markers = []
+
+
+class TestMapping(unittest.TestCase):
+
+    def test_initialize_parameters(self):
+        expected_results = {
+            "format": "json",
+            "limit_to": False,
+            "mapping_method": "gemma",
+            "maf": 0.01,
+            "use_loco": True,
+            "num_perm": 0,
+            "perm_check": False
+        }
+
+        results = initialize_parameters(
+            start_vars={}, dataset={}, this_trait={})
+        self.assertEqual(results, expected_results)
+
+        start_vars = {
+            "format": "F1",
+            "limit_to": "1",
+            "mapping_method": "rqtl",
+            "control_marker": True,
+            "pair_scan": "true",
+            "interval_mapping": "true",
+            "use_loco": "true",
+            "num_perm": "14"
+
+        }
+
+        results_2 = initialize_parameters(
+            start_vars=start_vars, dataset={}, this_trait={})
+        expected_results = {
+            "format": "F1",
+            "limit_to": 1,
+            "mapping_method": "gemma",
+            "maf": 0.01,
+            "use_loco": True,
+            "num_perm": 14,
+            "perm_check": "ON"
+        }
+
+        self.assertEqual(results_2, expected_results)
+
+    @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno")
+    @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
+    @mock.patch("wqflask.api.mapping.initialize_parameters")
+    @mock.patch("wqflask.api.mapping.retrieve_sample_data")
+    @mock.patch("wqflask.api.mapping.create_trait")
+    @mock.patch("wqflask.api.mapping.data_set.create_dataset")
+    def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno):
+        start_vars = {
+            "db": "Temp",
+            "trait_id": "dewf3232rff2",
+            "format": "F1",
+            "mapping_method": "gemma",
+            "use_loco": True
+
+        }
+        sampleList = ["S1", "S2", "S3", "S4"]
+        samplelist = ["S1", "S2", "S4"]
+        dataset = AttributeSetter({"group": samplelist})
+        this_trait = AttributeSetter({})
+        trait_data = AttributeSetter({
+            "data": {
+                "item1": AttributeSetter({"name": "S1", "value": "S1_value"}),
+                "item2": AttributeSetter({"name": "S2", "value": "S2_value"}),
+                "item3": AttributeSetter({"name": "S3", "value": "S3_value"}),
+
+            }
+        })
+        trait = AttributeSetter({
+            "data": trait_data
+        })
+
+        dataset.return_value = dataset
+        mock_trait.return_value = this_trait
+
+        mock_retrieve_sample.return_value = trait
+        mock_param.return_value = {
+            "format": "F1",
+            "limit_to": False,
+            "mapping_method": "gemma",
+            "maf": 0.01,
+            "use_loco": "True",
+            "num_perm": 14,
+            "perm_check": "ON"
+        }
+
+        run_gemma.return_value = ["results"]
+        results = do_mapping_for_api(start_vars=start_vars)
+        self.assertEqual(results, ("results", None))
diff --git a/wqflask/tests/unit/wqflask/correlation/__init__.py b/wqflask/tests/unit/wqflask/correlation/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/__init__.py
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
new file mode 100644
index 00000000..44d2e0fc
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -0,0 +1,20 @@
+import unittest
+from unittest import mock
+from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
+from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
+
+
+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"""
+        mock_class_instance = mock_class.return_value
+        mock_class_instance.gene_symbols = ["k1", "k2", "k3"]
+        mock_class_instance.get_symbol_values_pairs.return_value = {
+            "k1": ["v1", "v2", "v3"], "k2": ["v2", "v3"], "k3": ["k3"]}
+        results = get_trait_symbol_and_tissue_values(
+            symbol_list=["k1", "k2", "k3"])
+        mock_class.assert_called_with(gene_symbols=['k1', 'k2', 'k3'])
+        self.assertEqual({"k1": ["v1", "v2", "v3"], "k2": [
+                         "v2", "v3"], "k3": ["k3"]}, results)
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
new file mode 100644
index 00000000..33601990
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -0,0 +1,98 @@
+import unittest
+from unittest import mock
+from wqflask.correlation.show_corr_results import get_header_fields
+from wqflask.correlation.show_corr_results import generate_corr_json
+
+
+class AttributeSetter:
+    def __init__(self, trait_obj):
+        for key, value in trait_obj.items():
+            setattr(self, key, value)
+
+
+class TestShowCorrResults(unittest.TestCase):
+    def test_get_header_fields(self):
+        expected = [
+            ['Index',
+             'Record',
+             'Symbol',
+             'Description',
+             'Location',
+             'Mean',
+             'Sample rho',
+             'N',
+             'Sample p(rho)',
+             'Lit rho',
+             'Tissue rho',
+             'Tissue p(rho)',
+             'Max LRS',
+             'Max LRS Location',
+             'Additive Effect'],
+
+            ['Index',
+             'ID',
+             'Location',
+             'Sample r',
+             'N',
+             'Sample p(r)']
+
+        ]
+        result1 = get_header_fields("ProbeSet", "spearman")
+        result2 = get_header_fields("Other", "Other")
+        self.assertEqual(result1, expected[0])
+        self.assertEqual(result2, expected[1])
+
+    @mock.patch("wqflask.correlation.show_corr_results.hmac.data_hmac")
+    def test_generate_corr_json(self, mock_data_hmac):
+        mock_data_hmac.return_value = "hajsdiau"
+
+        dataset = AttributeSetter({"name": "the_name"})
+        this_trait = AttributeSetter(
+            {"name": "trait_test", "dataset": dataset})
+        target_dataset = AttributeSetter({"type": "Publish"})
+        corr_trait_1 = AttributeSetter({
+            "name": "trait_1",
+            "dataset": AttributeSetter({"name": "dataset_1"}),
+            "view": True,
+            "abbreviation": "T1",
+            "description_display": "Trait I description",
+            "authors": "JM J,JYEW",
+            "pubmed_id": "34n4nn31hn43",
+            "pubmed_text": "2016",
+            "pubmed_link": "https://www.load",
+            "lod_score": "",
+            "mean": "",
+            "LRS_location_repr": "BXBS",
+            "additive": "",
+            "sample_r": 10.5,
+            "num_overlap": 2,
+            "sample_p": 5
+
+
+
+
+        })
+        corr_results = [corr_trait_1]
+
+        dataset_type_other = {
+            "location": "cx-3-4",
+            "sample_4": 12.32,
+            "num_overlap": 3,
+            "sample_p": 10.34
+        }
+
+        expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
+
+        results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait,
+                                      dataset=dataset, target_dataset=target_dataset, for_api=True)
+        self.assertEqual(expected_results, results1)
+
+    def test_generate_corr_json_view_false(self):
+        trait = AttributeSetter({"view": False})
+        corr_results = [trait]
+        this_trait = AttributeSetter({"name": "trait_test"})
+        dataset = AttributeSetter({"name": "the_name"})
+
+        results_where_view_is_false = generate_corr_json(
+            corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False)
+        self.assertEqual(results_where_view_is_false, "[]")
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 b8c13ab4..fe2569b8 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -5,7 +5,6 @@ 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_gemma_output
 from wqflask.marker_regression.gemma_mapping import parse_loco_output
 
 
@@ -69,11 +68,9 @@ class TestGemmaMapping(unittest.TestCase):
         mock_parse_loco.return_value = []
         results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
         ], vals=[], covariates="", use_loco=True)
-        system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'),
-                        mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')]
-        mock_os.system.assert_has_calls(system_calls)
+        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")
+        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)
@@ -138,31 +135,6 @@ class TestGemmaMapping(unittest.TestCase):
             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.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/")
-    def test_parse_gemma_output(self):
-        """add test for generating gemma output with obj returned"""
-        file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7
-X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4
-125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67
-"""
-        with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open:
-            results = parse_gemma_output(genofile_name="gema_file")
-            expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812},
-                        {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}]
-            mock_open.assert_called_once_with(
-                "/home/user/img/gema_file_output.assoc.txt")
-            self.assertEqual(results, expected)
-
-    @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
-    def test_parse_gemma_output_with_empty_return(self):
-        """add tests for parse gemma output where nothing returned"""
-        output_file_results = """chr\t today"""
-        with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open:
-            results = parse_gemma_output(genofile_name="gema_file")
-            self.assertEqual(results, [])
-
     @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")
@@ -172,21 +144,26 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4
             "files": [["file_name", "user", "~/file1"],
                       ["file_name", "user", "~/file2"]]
         }
-        return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7"""
-        return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5"""
+        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_1).return_value, mock.mock_open(read_data=return_file_2).return_value)
+                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': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {
-                'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}]
+            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/snp_browser/__init__.py b/wqflask/tests/unit/wqflask/snp_browser/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/snp_browser/__init__.py
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
new file mode 100644
index 00000000..ce3e7b83
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -0,0 +1,105 @@
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.snp_browser.snp_browser import get_gene_id
+from wqflask.snp_browser.snp_browser import get_gene_id_name_dict
+from wqflask.snp_browser.snp_browser import check_if_in_gene
+from wqflask.snp_browser.snp_browser import get_browser_sample_lists
+from wqflask.snp_browser.snp_browser import get_header_list
+
+
+class TestSnpBrowser(unittest.TestCase):
+    def setUp(self):
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    def test_get_header_list(self):
+        empty_columns = {"snp_source": "false", "conservation_score": "true", "gene_name": "false",
+                         "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'])
+
+        results_with_snp = get_header_list(
+            variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
+        results_with_indel = get_header_list(
+            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'])
+
+        self.assertEqual(expected_results, results_with_snp)
+        self.assertEqual(expected_results_with_indel, results_with_indel)
+
+    @mock.patch("wqflask.snp_browser.snp_browser.g")
+    def test_get_gene_id(self, mock_db):
+        mock_db.db.execute.return_value.fetchone.return_value = "517d729f-aa13-4413-a885-40a3f7ff768a"
+        db_query_value = """
+                SELECT
+                        geneId
+                FROM
+                        GeneList
+                WHERE
+                        SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'
+            """
+        results = get_gene_id(
+            species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR")
+        mock_db.db.execute.assert_called_once_with(db_query_value)
+        self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
+
+    @mock.patch("wqflask.snp_browser.snp_browser.g")
+    def test_gene_id_name_dict(self, mock_db):
+        no_gene_names = []
+        self.assertEqual("", get_gene_id_name_dict(
+            species_id="fregb343bui43g4", gene_name_list=no_gene_names))
+        gene_name_list = ["GH1", "GH2", "GH3"]
+        mock_db.db.execute.return_value.fetchall.side_effect = [[], [("fsdf43-fseferger-f22", "GH1"), ("1sdf43-fsewferger-f22", "GH2"),
+                                                                     ("fwdj43-fstferger-f22", "GH3")]]
+        no_results = get_gene_id_name_dict(
+            species_id="ret3-32rf32", gene_name_list=gene_name_list)
+        results_found = get_gene_id_name_dict(
+            species_id="ret3-32rf32", gene_name_list=gene_name_list)
+        expected_found = {'GH1': 'fsdf43-fseferger-f22',
+                          'GH2': '1sdf43-fsewferger-f22', 'GH3': 'fwdj43-fstferger-f22'}
+        db_query_value = """
+                SELECT
+                        geneId, geneSymbol
+                FROM
+                        GeneList
+                WHERE
+                        SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')
+            """
+        mock_db.db.execute.assert_called_with(db_query_value)
+        self.assertEqual(results_found, expected_found)
+        self.assertEqual(no_results, {})
+
+    @mock.patch("wqflask.snp_browser.snp_browser.g")
+    def test_check_if_in_gene(self, mock_db):
+        mock_db.db.execute.return_value.fetchone.side_effect = [
+            ("fsdf-232sdf-sdf", "GHA"), ""]
+        results_found = check_if_in_gene(
+            species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+        db_query_value = """SELECT geneId, geneSymbol
+                   FROM GeneList
+                   WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND
+                        (txStart < 12.09 AND txEnd > 12.09); """
+        gene_not_found = check_if_in_gene(
+            species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+        mock_db.db.execute.assert_called_with(db_query_value)
+        self.assertEqual(gene_not_found, "")
+
+    @mock.patch("wqflask.snp_browser.snp_browser.g")
+    def test_get_browser_sample_lists(self, mock_db):
+        mock_db.db.execute.return_value.fetchall.return_value = []
+
+        results = get_browser_sample_lists(species_id="12")
+        self.assertEqual(results, {'mouse': [], 'rat': []})
diff --git a/wqflask/tests/unit/wqflask/test_pbkdf2.py b/wqflask/tests/unit/wqflask/test_pbkdf2.py
index a33fbd4f..7ad6c83e 100644
--- a/wqflask/tests/unit/wqflask/test_pbkdf2.py
+++ b/wqflask/tests/unit/wqflask/test_pbkdf2.py
@@ -11,43 +11,43 @@ class TestPbkdf2(unittest.TestCase):
         """
 
         for password, salt, iterations, keylen, expected_value in [
-                ('password', 'salt', 1, 20,
+                ('password', b'salt', 1, 20,
                  '0c60c80f961f0e71f3a9b524af6012062fe037a6'),
-                ('password', 'salt', 2, 20,
+                ('password', b'salt', 2, 20,
                  'ea6c014dc72d6f8ccd1ed92ace1d41f0d8de8957'),
-                ('password', 'salt', 4096, 20,
+                ('password', b'salt', 4096, 20,
                  '4b007901b765489abead49d926f721d065a429c1'),
                 ('passwordPASSWORDpassword',
-                 'saltSALTsaltSALTsaltSALTsaltSALTsalt',
+                 b'saltSALTsaltSALTsaltSALTsaltSALTsalt',
                  4096, 25,
                  '3d2eec4fe41c849b80c8d83662c0e44a8b291a964cf2f07038'),
-                ('pass\x00word', 'sa\x00lt', 4096, 16,
+                ('pass\x00word', b'sa\x00lt', 4096, 16,
                  '56fa6aa75548099dcc37d7f03425e0c3'),
-                ('password', 'ATHENA.MIT.EDUraeburn', 1, 16,
+                ('password', b'ATHENA.MIT.EDUraeburn', 1, 16,
                  'cdedb5281bb2f801565a1122b2563515'),
-                ('password', 'ATHENA.MIT.EDUraeburn', 1, 32,
+                ('password', b'ATHENA.MIT.EDUraeburn', 1, 32,
                  ('cdedb5281bb2f80'
                   '1565a1122b256351'
                   '50ad1f7a04bb9f3a33'
                   '3ecc0e2e1f70837')),
-                ('password', 'ATHENA.MIT.EDUraeburn', 2, 16,
+                ('password', b'ATHENA.MIT.EDUraeburn', 2, 16,
                  '01dbee7f4a9e243e988b62c73cda935d'),
-                ('password', 'ATHENA.MIT.EDUraeburn', 2, 32,
+                ('password', b'ATHENA.MIT.EDUraeburn', 2, 32,
                  ('01dbee7f4a9e243e9'
                   '88b62c73cda935da05'
                   '378b93244ec8f48a99'
                   'e61ad799d86')),
-                ('password', 'ATHENA.MIT.EDUraeburn', 1200, 32,
+                ('password', b'ATHENA.MIT.EDUraeburn', 1200, 32,
                  ('5c08eb61fdf71e'
                   '4e4ec3cf6ba1f55'
                   '12ba7e52ddbc5e51'
                   '42f708a31e2e62b1e13')),
-                ('X' * 64, 'pass phrase equals block size', 1200, 32,
+                ('X' * 64, b'pass phrase equals block size', 1200, 32,
                  ('139c30c0966bc32ba'
                   '55fdbf212530ac9c5'
                   'ec59f1a452f5cc9ad'
                   '940fea0598ed1')),
-                ('X' * 65, 'pass phrase exceeds block size', 1200, 32,
+                ('X' * 65, b'pass phrase exceeds block size', 1200, 32,
                  ('9ccad6d468770cd'
                   '51b10e6a68721be6'
                   '11a8b4d282601db3'
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
new file mode 100644
index 00000000..4f91d8ca
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -0,0 +1,31 @@
+import unittest
+
+from wqflask.server_side import ServerSideTable
+
+
+class TestServerSideTableTests(unittest.TestCase):
+    """
+    Test the ServerSideTable class
+
+    test table:
+        first, second, third
+        'd', 4, 'zz'
+        'b', 2, 'aa'
+        'c', 1, 'ss'
+    """
+
+    def test_get_page(self):
+        rows_count = 3
+        table_rows = [
+            {'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'}
+
+        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'}])