Merge branch 'testing' into feature/add_location_type_correlation_option

32 files changed, 1007 insertions, 264 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 eab6afe6..fe2569b8 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -144,21 +144,26 @@ class TestGemmaMapping(unittest.TestCase):
             "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_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'}])
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index f15b17e2..6b029317 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -23,20 +23,20 @@ def is_str(value):
     except:
         return False
 
-def get_float(vars,name,default=None):
-    if name in vars:
-        if is_float(vars[name]):
-            return float(vars[name])
+def get_float(vars_obj,name,default=None):
+    if name in vars_obj:
+        if is_float(vars_obj[name]):
+            return float(vars_obj[name])
     return default
 
-def get_int(vars,name,default=None):
-    if name in vars:
-        if is_int(vars[name]):
-            return float(vars[name])
+def get_int(vars_obj,name,default=None):
+    if name in vars_obj:
+        if is_int(vars_obj[name]):
+            return float(vars_obj[name])
     return default
 
-def get_string(vars,name,default=None):
-    if name in vars:
-        if not vars[name] is None:
-            return str(vars[name])
+def get_string(vars_obj,name,default=None):
+    if name in vars_obj:
+        if not vars_obj[name] is None:
+            return str(vars_obj[name])
     return default
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index b883e361..fd7691d4 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -71,34 +71,6 @@ def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pears
     return corr_result
 
 
-###########################################################################
-#Input: cursor, symbolList (list), dataIdDict(Dict)
-#output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
-#        key is symbol, value is one list of expression values of one probeSet;
-#function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
-#Attention! All keys are lower case!
-###########################################################################
-def get_symbol_value_pairs(tissue_data):
-    id_list = [tissue_data[symbol.lower()].data_id for item in tissue_data]
-
-    symbol_value_pairs = {}
-    value_list=[]
-
-    query = """SELECT value, id
-               FROM TissueProbeSetData
-               WHERE Id IN {}""".format(create_in_clause(id_list))
-
-    try :
-        results = g.db.execute(query).fetchall()
-        for result in results:
-            value_list.append(result.value)
-        symbol_value_pairs[symbol] = value_list
-    except:
-        symbol_value_pairs[symbol] = None
-
-    return symbol_value_pairs
-
-
 ########################################################################################################
 #input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
 #output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 6175dc7e..fb4dc4f4 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -86,8 +86,6 @@ class CorrelationResults(object):
             else:
                 helper_functions.get_species_dataset_trait(self, start_vars)
 
-            #self.dataset.group.read_genotype_file()
-
             corr_samples_group = start_vars['corr_samples_group']
 
             self.sample_data = {}
@@ -462,13 +460,13 @@ class CorrelationResults(object):
         if not excluded_samples:
             excluded_samples = ()
 
+        sample_val_dict = json.loads(start_vars['sample_vals'])
         for sample in sample_names:
             if sample not in excluded_samples:
-                # print("Looking for",sample,"in",start_vars)
-                value = start_vars.get('value:' + sample)
-                if value:
-                    if not value.strip().lower() == 'x':
-                        self.sample_data[str(sample)] = float(value)
+                value = sample_val_dict[sample]
+                if not value.strip().lower() == 'x':
+                    self.sample_data[str(sample)] = float(value)
+
 
 def do_bicor(this_trait_vals, target_trait_vals):
     r_library = ro.r["library"]             # Map the library function
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 08c2d750..9f1b050d 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -270,8 +270,9 @@ class DisplayMappingResults(object):
 
         # Needing for form submission when doing single chr
         # mapping or remapping after changing options
-        self.samples = start_vars['samples']
-        self.vals = start_vars['vals']
+        self.sample_vals = start_vars['sample_vals']
+        self.sample_vals_dict = json.loads(self.sample_vals)
+
         self.transform = start_vars['transform']
         self.mapping_method = start_vars['mapping_method']
         self.mapping_results_path = start_vars['mapping_results_path']
@@ -492,11 +493,10 @@ class DisplayMappingResults(object):
 ## count the amount of individuals to be plotted, and increase self.graphHeight
         if self.haplotypeAnalystChecked and self.selectedChr > -1:
             thisTrait = self.this_trait
-            _strains, _vals, _vars, _aliases = thisTrait.export_informative()
             smd=[]
-            for ii, _val in enumerate(self.vals):
-                if _val != "x":
-                    temp = GeneralObject(name=self.samples[ii], value=float(_val))
+            for sample in self.sample_vals_dict.keys():
+                if self.sample_vals_dict[sample] != "x":
+                    temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
                     smd.append(temp)
                 else:
                     continue
@@ -1464,12 +1464,11 @@ class DisplayMappingResults(object):
         yPaddingTop = yTopOffset
 
         thisTrait = self.this_trait
-        _strains, _vals, _vars, _aliases = thisTrait.export_informative()
 
         smd=[]
-        for ii, _val in enumerate(self.vals):
-            if _val != "x":
-                temp = GeneralObject(name=self.samples[ii], value=float(_val))
+        for sample in self.sample_vals_dict.keys():
+            if self.sample_vals_dict[sample] != "x":
+                temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
                 smd.append(temp)
             else:
                 continue
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 0a5758af..4117a0e5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -94,9 +94,6 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
         ro.r('all_covars <- cbind(marker_covars, trait_covars)')
     else:
         ro.r('all_covars <- marker_covars')
-    #logger.info("Saving");
-    #ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")')
-    #logger.info("Saving Done");
     covars = ro.r['all_covars']
     #DEBUG to save the session object to file
     if pair_scan:
@@ -159,7 +156,7 @@ def generate_cross_from_geno(dataset, scale_units):        # TODO: Need to figur
          toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1                            # Major hack to skip the geno headers
          type <- getGenoCode(header, 'type')
          if(type == '4-way'){
-            genocodes <- c('1','2','3','4')
+            genocodes <- NULL
          } else {
             genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat'))             # Get the genotype codes
          }
@@ -174,7 +171,7 @@ def generate_cross_from_geno(dataset, scale_units):        # TODO: Need to figur
          require(qtl)
          if(type == '4-way'){
            cat('Loading in as 4-WAY\n')
-           cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE)                 # Load the created cross file using R/qtl read.cross
+           cross = read.cross(file=out, 'csvr', genotypes=NULL, crosstype="4way")                                         # Load the created cross file using R/qtl read.cross
          }else if(type == 'f2'){
            cat('Loading in as F2\n')
            cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="f2")                                       # Load the created cross file using R/qtl read.cross
@@ -332,8 +329,6 @@ def add_cofactors(cross, this_dataset, covariates, samples):
                         covar_name_string += '"' + col_name + '", '
                     else:
                         covar_name_string += '"' + col_name + '"'
-
-                logger.info("covar_name_string:" + covar_name_string)
         else:
             col_name = "covar_" + str(i)
             cross = add_phenotype(cross, covar_as_string, col_name)
@@ -343,7 +338,6 @@ def add_cofactors(cross, this_dataset, covariates, samples):
                 covar_name_string += '"' + col_name + '"'
 
     covar_name_string += ")"
-    logger.info("covar_name_string:" + covar_name_string); 
     covars_ob = pull_var("trait_covars", cross, covar_name_string)
     return cross, covars_ob
 
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 891fcc66..a1f87b61 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -71,56 +71,22 @@ class RunMapping(object):
         all_samples_ordered = self.dataset.group.all_samples_ordered()
 
         self.vals = []
-        if 'samples' in start_vars:
-            self.samples = start_vars['samples'].split(",")
-            if (len(genofile_samplelist) != 0):
-                for sample in genofile_samplelist:
-                    if sample in self.samples:
-                        value = start_vars.get('value:' + sample)
-                        if value:
-                            self.vals.append(value)
-                    else:
-                        self.vals.append("x")
-            else:
-                for sample in self.samples:
-                    value = start_vars.get('value:' + sample)
-                    if value:
-                        self.vals.append(value)
+        self.samples = []
+        self.sample_vals = start_vars['sample_vals']
+        sample_val_dict = json.loads(self.sample_vals)
+        samples = sample_val_dict.keys()
+        if (len(genofile_samplelist) != 0):
+            for sample in genofile_samplelist:
+                self.samples.append(sample)
+                if sample in samples:
+                    self.vals.append(sample_val_dict[sample])
+                else:
+                    self.vals.append("x")
         else:
-            self.samples = []
-            if (len(genofile_samplelist) != 0):
-                for sample in genofile_samplelist:
-                    if sample in self.dataset.group.samplelist:
-                        in_trait_data = False
-                        for item in self.this_trait.data:
-                            if self.this_trait.data[item].name == sample:
-                                value = start_vars['value:' + self.this_trait.data[item].name]
-                                self.samples.append(self.this_trait.data[item].name)
-                                self.vals.append(value)
-                                in_trait_data = True
-                                break
-                        if not in_trait_data:
-                            value = start_vars.get('value:' + sample)
-                            if value:
-                                self.samples.append(sample)
-                                self.vals.append(value)
-                    else:
-                        self.vals.append("x")
-            else:
-                for sample in self.dataset.group.samplelist: # sample is actually the name of an individual
-                    in_trait_data = False
-                    for item in self.this_trait.data:
-                        if self.this_trait.data[item].name == sample:
-                            value = start_vars['value:' + self.this_trait.data[item].name]
-                            self.samples.append(self.this_trait.data[item].name)
-                            self.vals.append(value)
-                            in_trait_data = True
-                            break
-                    if not in_trait_data:
-                        value = start_vars.get('value:' + sample)
-                        if value:
-                            self.samples.append(sample)
-                            self.vals.append(value)
+            for sample in self.dataset.group.samplelist:
+                if sample in samples:
+                    self.vals.append(sample_val_dict[sample])
+                    self.samples.append(sample)
 
         if 'n_samples' in start_vars:
             self.n_samples = start_vars['n_samples']
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 0d0894a4..c4ea2921 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -28,9 +28,9 @@ class SearchResultPage(object):
     #maxReturn = 3000
 
     def __init__(self, kw):
-        """This class gets invoked after hitting submit on the main menu (in
-views.py).
-
+        """
+            This class gets invoked after hitting submit on the main menu (in
+            views.py).
         """
 
         ###########################################
@@ -86,7 +86,6 @@ views.py).
             else:
                 self.gen_search_result()
 
-
     def gen_search_result(self):
         """
         Get the info displayed in the search result table from the set of results computed in
@@ -161,7 +160,14 @@ views.py).
                         trait_dict[key] = trait_dict[key].decode('utf-8')
                 trait_list.append(trait_dict)
 
-        self.trait_list = json.dumps(trait_list)
+        self.trait_list = trait_list
+
+        if this_trait.dataset.type == "ProbeSet":
+            self.header_data_names = ['index', 'display_name', 'symbol', 'description', 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
+        elif this_trait.dataset.type == "Publish":
+            self.header_data_names = ['index', 'display_name', 'description', 'mean', 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
+        elif this_trait.dataset.type == "Geno":
+            self.header_data_names = ['index', 'display_name', 'location']
 
     def search(self):
         """
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
new file mode 100644
index 00000000..5f764767
--- /dev/null
+++ b/wqflask/wqflask/server_side.py
@@ -0,0 +1,93 @@
+# handles server side table processing
+
+
+
+class ServerSideTable(object):
+    """
+        This class is used to do server-side processing
+        on the DataTables table such as paginating, sorting,
+        filtering(not implemented) etc. This takes the load off
+        the client-side and reduces the size of data interchanged.
+
+        Usage:
+            ServerSideTable(table_data, request_values)
+        where,
+            `table_data` must have data members
+            `rows_count` as number of rows in the table,
+            `table_rows` as data rows of the table,
+            `header_data_names` as headers names of the table.
+
+            `request_values` must have request arguments values
+            including the DataTables server-side processing arguments.
+
+        Have a look at snp_browser_table() function in 
+        wqflask/wqflask/views.py for reference use.
+    """
+
+    def __init__(self, rows_count, table_rows, header_data_names, request_values):
+        self.request_values = request_values
+        self.sEcho = self.request_values['sEcho']
+
+        self.rows_count = rows_count
+        self.table_rows = table_rows
+        self.header_data_names = header_data_names
+        
+        self.sort_rows()
+        self.paginate_rows()
+
+    def sort_rows(self):
+        """
+        Sorts the rows taking in to account the column (or columns) that the
+        user has selected.
+        """
+        def is_reverse(str_direction):
+            """ Maps the 'desc' and 'asc' words to True or False. """
+            return True if str_direction == 'desc' else False
+
+        if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0):
+            for i in range(0, int(self.request_values['iSortingCols'])):
+                column_number = int(self.request_values['iSortCol_' + str(i)])
+                column_name = self.header_data_names[column_number - 1]
+                sort_direction = self.request_values['sSortDir_' + str(i)]
+                self.table_rows = sorted(self.table_rows,
+                              key=lambda x: x[column_name],
+                              reverse=is_reverse(sort_direction))
+
+    def paginate_rows(self):
+        """
+        Selects a subset of the filtered and sorted data based on if the table
+        has pagination, the current page and the size of each page.
+        """
+        def requires_pagination():
+            """ Check if the table is going to be paginated """
+            if self.request_values['iDisplayStart'] != "":
+                if int(self.request_values['iDisplayLength']) != -1:
+                    return True
+            return False
+
+        if not requires_pagination():
+            return
+
+        start = int(self.request_values['iDisplayStart'])
+        length = int(self.request_values['iDisplayLength'])
+
+        # if search returns only one page
+        if len(self.table_rows) <= length:
+            # display only one page
+            self.table_rows = self.table_rows[start:]
+        else:
+            limit = -len(self.table_rows) + start + length
+            if limit < 0:
+                # display pagination
+                self.table_rows = self.table_rows[start:limit]
+            else:
+                # display last page of pagination
+                self.table_rows = self.table_rows[start:]
+
+    def get_page(self):
+        output = {}
+        output['sEcho'] = str(self.sEcho)
+        output['iTotalRecords'] = str(float('Nan'))
+        output['iTotalDisplayRecords'] = str(self.rows_count)
+        output['data'] = self.table_rows
+        return output
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 6c3fcf53..a52399a2 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -4,7 +4,7 @@ import string
 from PIL import (Image)
 
 from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
 
 from base import species
 from base import webqtlConfig
@@ -14,21 +14,21 @@ class SnpBrowser(object):
     def __init__(self, start_vars):
         self.strain_lists = get_browser_sample_lists()
         self.initialize_parameters(start_vars)
-        self.limit_number = 10000
 
         if self.first_run == "false":
             self.filtered_results = self.get_browser_results()
+            self.table_rows = self.get_table_rows()
+            self.rows_count = len(self.table_rows)
 
-            if len(self.filtered_results) <= self.limit_number:
-                self.table_rows = self.get_table_rows()
-            else:
-                self.empty_columns = None
+            del self.filtered_results
+
+            if 'sEcho' not in start_vars:
                 self.table_rows = []
 
             if self.limit_strains == "true":
-                self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
+                self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
             else:
-                self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+                self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
 
     def initialize_parameters(self, start_vars):
         if 'first_run' in start_vars:
@@ -368,19 +368,19 @@ class SnpBrowser(object):
 
         #ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
         self.empty_columns = {
-                    "snp_source": "false",
-                    "conservation_score": "false",
-                    "gene_name": "false",
-                    "transcript": "false",
-                    "exon": "false",
-                    "domain_2": "false",
-                    "function": "false", 
-                    "function_details": "false"
-            }
+            "snp_source": "false",
+            "conservation_score": "false",
+            "gene_name": "false",
+            "transcript": "false",
+            "exon": "false",
+            "domain_2": "false",
+            "function": "false",
+            "function_details": "false"
+        }
 
         the_rows = []
         for i, result in enumerate(self.filtered_results):
-            this_row = []
+            this_row = {}
             if self.variant_type == "SNP":
                 snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
                 allele_value_list = result[14:]
@@ -520,13 +520,10 @@ class SnpBrowser(object):
                     "source_name": str(source_name)
                 }
                 #this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
-            else:
-                this_row = {}
 
             the_rows.append(this_row)
 
         return the_rows
-                
 
     def include_record(self, domain, function, snp_source, conservation_score):
         """ Decide whether to add this record """
@@ -674,9 +671,13 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
     empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this
 
     header_fields = []
+    header_data_names = []
     if variant_type == "SNP":
         header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
+        header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
+
         header_fields.append(strain_list)
+        header_data_names += strain_list
 
         if empty_columns != None:
             if empty_columns['snp_source'] == "false":
@@ -703,11 +704,16 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
             if empty_columns['function_details'] == "false":
                 empty_field_count += 1
                 header_fields[0].remove('Details')
+        
+        for col in empty_columns.keys():
+            if empty_columns[col] == "false":
+                header_data_names.remove(col)
 
     elif variant_type == "InDel":
         header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
+        header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
 
-    return header_fields, empty_field_count
+    return header_fields, empty_field_count, header_data_names
 
 def get_effect_details_by_category(effect_name = None, effect_value = None):
     gene_list = []
@@ -868,8 +874,6 @@ def get_gene_id_name_dict(species_id, gene_name_list):
     if len(results) > 0:
         for item in results:
             gene_id_name_dict[item[1]] = item[0]
-    else:
-        pass
 
     return gene_id_name_dict
 
@@ -883,7 +887,7 @@ def check_if_in_gene(species_id, chr, mb):
         query = """SELECT geneId,geneSymbol
                    FROM GeneList
                    WHERE chromosome = '{0}' AND
-                        (txStart < {1} AND txEnd > {1}); """.format(species_id, chr, mb)
+                        (txStart < {1} AND txEnd > {1}); """.format(chr, mb)
 
     result = g.db.execute(query).fetchone()
 
diff --git a/wqflask/wqflask/static/new/css/snp_browser.css b/wqflask/wqflask/static/new/css/snp_browser.css
index 30fe9a59..a7942d2a 100644
--- a/wqflask/wqflask/static/new/css/snp_browser.css
+++ b/wqflask/wqflask/static/new/css/snp_browser.css
@@ -6,6 +6,10 @@ table.dataTable thead th {
   vertical-align: bottom;
 }
 
+table.dataTable tbody tr.selected {
+  background-color: #ffee99;
+}
+
 table.dataTable thead .sorting,
 table.dataTable thead .sorting_asc,
 table.dataTable thead .sorting_desc,
@@ -18,7 +22,7 @@ table.dataTable thead .sorting_desc_disabled {
 table.dataTable thead th{
   border-right: 1px solid white;
   color: white;
-  background-color: royalblue;
+  background-color: #369;
 }
 
 table.dataTable tbody td {
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index 3d756303..1b944d4f 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -118,7 +118,6 @@
           };
         };
         data = [make_data('samples_primary'), make_data('samples_other')];
-        console.log("THE DATA IS:", data);
         d3.select("#prob_plot_container svg").datum(data).call(chart);
         if (js_data.trait_symbol != null) {
             $("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>");
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index 2552fb04..508f5bf2 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -1,5 +1,3 @@
-console.log("THE FILES:", js_data.browser_files)
-
 snps_filename = "/browser_input?filename=" + js_data.browser_files[0]
 annot_filename = "/browser_input?filename=" + js_data.browser_files[1]
 
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 9ffef4f8..05dcfda5 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -1,4 +1,4 @@
-change_buttons = function() {
+change_buttons = function(check_node = 0) {
   var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2;
   buttons = ["#add", "#remove"];
 
@@ -6,7 +6,7 @@ change_buttons = function() {
   table_api = $('#trait_table').DataTable();
   check_cells = table_api.column(0).nodes().to$();
   for (let i = 0; i < check_cells.length; i++) {
-    if (check_cells[i].childNodes[0].checked){
+    if (check_cells[i].childNodes[check_node].checked){
       num_checked += 1
     }
   }
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 83d4f193..2ec9d6d5 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -94,25 +94,7 @@ add = function() {
 $('#add_to_collection').click(add);
 sample_lists = js_data.sample_lists;
 sample_group_types = js_data.sample_group_types;
-d3.select("#select_compare_trait").on("click", (function(_this) {
-  return function() {
-    $('.scatter-matrix-container').remove();
-    return open_trait_selection();
-  };
-})(this));
 
-$(".select_covariates").click(function () {
-  open_covariate_selection();
-});
-$(".remove_covariates").click(function () {
-  $("input[name=covariates]").val("")
-  $(".selected-covariates").val("")
-});
-d3.select("#clear_compare_trait").on("click", (function(_this) {
-  return function() {
-    return $('.scatter-matrix-container').remove();
-  };
-})(this));
 open_trait_selection = function() {
   return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
     return function() {
@@ -225,6 +207,8 @@ update_histogram = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   Plotly.newPlot('histogram', root.histogram_data, root.histogram_layout, root.modebar_options);
@@ -273,6 +257,8 @@ update_bar_chart = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   root.bar_data[0]['y'] = trait_vals
@@ -314,6 +300,8 @@ update_box_plot = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   Plotly.newPlot('box_plot', root.box_data, root.box_layout, root.modebar_options)
@@ -345,6 +333,8 @@ update_violin_plot = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   Plotly.newPlot('violin_plot', root.violin_data, root.violin_layout, root.modebar_options)
@@ -419,6 +409,25 @@ process_id = function() {
   }
   return processed;
 };
+
+fetch_sample_values = function() {
+  // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster)
+  sample_val_dict = {};
+
+  table = 'samples_primary';
+  if ($('#' + table).length){
+    table_api = $('#' + table).DataTable();
+    val_nodes = table_api.column(3).nodes().to$();
+    for (_j = 0; _j < val_nodes.length; _j++){
+      sample_name = val_nodes[_j].childNodes[0].name.split(":")[1]
+      sample_val = val_nodes[_j].childNodes[0].value
+      sample_val_dict[sample_name] = sample_val
+    }
+  }
+
+  return sample_val_dict;
+}
+
 edit_data_change = function() {
   var already_seen, checkbox, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
   already_seen = {};
@@ -448,15 +457,15 @@ edit_data_change = function() {
         if (is_number(sample_val) && sample_val !== "") {
           sample_val = parseFloat(sample_val);
           sample_sets[table].add_value(sample_val);
-          if (typeof var_nodes === 'undefined'){
-            sample_var = null;
-          } else {
+          try {
             sample_var = var_nodes[_j].childNodes[0].value
             if (is_number(sample_var)) {
               sample_var = parseFloat(sample_var)
             } else {
               sample_var = null;
             }
+          } catch {
+            sample_var = null;
           }
           sample_dict = {
             value: sample_val,
@@ -541,7 +550,7 @@ $('select[name=corr_dataset]').change(on_dataset_change);
 $('select[name=location_type]').change(on_dataset_change);
 
 submit_special = function(url) {
-  get_table_contents_for_form_submit("trait_data_form");
+  $("input[name=sample_vals]").val(JSON.stringify(fetch_sample_values()))
   $("#trait_data_form").attr("action", url);
   $("#trait_data_form").submit();
 };
@@ -565,7 +574,7 @@ get_table_contents_for_form_submit = function(form_id) {
  });
 }
 
-var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+var corr_input_list = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
                         'corr_return_results', 'location_type', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
 
 $(".corr_compute").on("click", (function(_this) {
@@ -818,6 +827,7 @@ reset_samples_table = function() {
 };
 $('.reset').click(function() {
   reset_samples_table();
+  $('input[name="transform"]').val("");
   edit_data_change();
 });
 
@@ -1307,7 +1317,7 @@ if (js_data.num_values < 256) {
     margin: {
         l: left_margin,
         r: 30,
-        t: 30,
+        t: 100,
         b: bottom_margin
     }
   };
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 34582f21..3ae52975 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -141,7 +141,7 @@ $('input[name=display_all]').change((function(_this) {
 })(this));
 
 //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
                           'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
                           'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
                           'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index 4df03412..6c443ab3 100644
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -91,8 +91,6 @@ Stats = (function() {
   Stats.prototype.interquartile = function() {
     var iq, length, q1, q3;
     length = this.the_values.length;
-    console.log("in interquartile the_values are:", this.the_values);
-    console.log("length is:", length);
     if (js_data.dataset_type == "ProbeSet" && js_data.data_scale == "linear_positive") {
       q1 = Math.log2(this.the_values[Math.floor(length * .25)]);
       q3 = Math.log2(this.the_values[Math.floor(length * .75)]);
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 1a76ef7a..c2256e47 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -31,10 +31,7 @@
         {% endif %}
         <input type="hidden" name="results_path" value="{{ mapping_results_path }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
-        <input type="hidden" name="samples" value="{{ samples|join(",") }}">
-        {% for sample in samples %}
-        <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
-        {% endfor %}
+        <input type="hidden" name="sample_vals" value="{{ sample_vals }}">
         <input type="hidden" name="n_samples" value="{{ n_samples }}">
         <input type="hidden" name="maf" value="{{ maf }}">
         <input type="hidden" name="use_loco" value="{{ use_loco }}">
@@ -248,7 +245,7 @@
         <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
         <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
         <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
-        <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
+        {% if geno_db_exists == "True" %}<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>{% endif %}
         <br />
         <br />
           <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
@@ -375,6 +372,20 @@
             console.time("Creating table");
             {% if selectedChr == -1 %}
             $('#trait_table').DataTable( {
+                "drawCallback": function( settings ) {
+                  $('#trait_table tr').off().on("click", function(event) {
+                    if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
+                      var obj =$(this).find('input');
+                      obj.prop('checked', !obj.is(':checked'));
+                    }
+                    if ($(this).hasClass("selected")){
+                      $(this).removeClass("selected")
+                    } else {
+                      $(this).addClass("selected")
+                    }
+                    {% if geno_db_exists == "True" %}change_buttons(check_node=1){% endif %}
+                  });
+                },
                 "columns": [
                     { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "8%" },
@@ -450,7 +461,7 @@
 
         });
 
-        var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+        var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
                             'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
                             'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
                             'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index f2334512..411a6628 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -3,7 +3,7 @@
 {% block css %}
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" />
-    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scroller/css/scroller.dataTables.min.css') }}">
+    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scrollerStyle/css/scroller.dataTables.min.css') }}">
     <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
     <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css">
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
@@ -160,6 +160,16 @@
 
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
+
+            var getParams = function(url) {
+                let parser = document.createElement('a');
+                parser.href = url;
+                let params = parser.search.substring(1);
+                if(params.length > 0) {
+                    return ('?'+params);
+                }
+                return params;
+            };
             
             $('#trait_table tr').click(function(event) {
                 if (event.target.type !== 'checkbox') {
@@ -225,7 +235,7 @@
                       'data': null,
                       'width': "25px",
                       'orderDataType': "dom-checkbox",
-                      'orderSequence': [ "desc", "asc"],
+                      'orderable': false,
                       'render': function(data, type, row, meta) {
                         return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '">'
                       }
@@ -373,15 +383,33 @@
                     }{% endif %}
                 ],
                 "order": [[1, "asc" ]],
-                'sDom': "itirp",
+                {% if dataset.type != 'Geno' %}
+                buttons: [
+                    {
+                        extend: 'columnsToggle',
+                        columns: function( idx, data, node ) {
+                          if (idx != 0) {
+                            return true;
+                          } else {
+                            return false;
+                          }
+                        },
+                        postfixButtons: [ 'colvisRestore' ]
+                    }
+                ],
+                'sDom': "Bpitirp",
+                {% else %}
+                'sDom': "pitirp",
+                {% endif %}
                 'iDisplayLength': 500,
                 'deferRender': true,
                 'paging': true,
                 'orderClasses': true,
                 'processing': true,
-                'language': {
-                  'loadingRecords': '&nbsp;',
-                  'processing': 'Loading...'
+                'bServerSide': true,
+                'sAjaxSource': '/search_table'+getParams(window.location.href),
+                'infoCallback': function(settings, start, end, max, total, pre) {
+                  return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
                 }
             } );
             
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index c881eb76..77fc9342 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -35,6 +35,7 @@
         <input type="hidden" name="genofile" value="">
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
+        <input type="hidden" name="sample_vals" value="">
 
         <div class="container showtrait-main-div">
             <div class="panel-group" id="accordion">
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 4f347d4e..865959b1 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -21,9 +21,6 @@
             <li>
                 <a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
             </li>
-            <li>
-                <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
-            </li>
         </ul>
         <div class="tab-content">
             <div class="tab-pane active" id="stats_tab">
@@ -116,19 +113,6 @@
                     <div id="violin_plot"></div>
                 </div>
             </div>
-            <div class="tab-pane" id="scatterplot_matrix">
-                <div class="btn-group scatterplot-btn-div">
-                    <button type="button" class="btn btn-default" id="select_compare_trait">
-                        <i class="icon-th-large"></i> Select Traits
-                    </button>
-                    <button type="button" class="btn btn-default" id="clear_compare_trait">
-                        <i class="icon-trash"></i> Clear
-                    </button>
-                </div>
-                <div id="scatterplot_container">
-                    <div id="comparison_scatterplot" class="qtlcharts"></div>
-                </div>
-            </div>
         </div>
     </div>
     <div id="collections_holder_wrapper" style="display:none;">
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index a96b8e3b..b9aea570 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -15,7 +15,7 @@
         <input type="hidden" name="first_run" value="{{ first_run }}">
         <input type="hidden" name="chosen_strains_mouse" value="{{ chosen_strains_mouse|join(",") }}">
         <input type="hidden" name="chosen_strains_rat" value="{{ chosen_strains_rat|join(",") }}">
-        <div class="col-xs-4" style="padding-left: 0px;">
+        <div class="col-xs-4" style="width: 260px; padding-left: 30px; padding-right: 0px;">
           <div class="form-group row" style="margin-bottom: 5px;">
             <label for="snp_or_indel" style="text-align: right;" class="col-xs-4 col-form-label"><b>Type:</b></label>
             <div class="col-xs-8">
@@ -74,7 +74,7 @@
             </div>
           </div>
         </div>
-        <div class="col-xs-4" style="padding-left: 0px;">
+        <div class="col-xs-4" style="width: 310px; padding-left: 0px; padding-right: 20px;">
           <div class="form-group row" style="margin-bottom: 10px;">
             <label for="strains" style="text-align: right;" class="col-xs-4 col-form-label"><b>Strains:</b></label>
             <div class="col-xs-8">
@@ -107,8 +107,14 @@
               </div>
             </div>
           </div>
+          <div class="form-group row">
+            <label class="col-xs-4 col-form-label"></label>
+            <div class="col-xs-8" style="margin-top: 65px;">
+              <input class="btn btn-primary" type="button" name="export_csv" value="Export to CSV">
+            </div>
+          </div>
         </div>
-        <div class="col-xs-4" style="padding-left: 20px;">
+        <div class="col-xs-4" style="width: 310px; padding-left: 20px;">
           <div class="form-group row" style="margin-bottom: 5px;">
             <label for="domain" style="text-align: right;" class="col-xs-4 col-form-label"><b>Domain:</b></label>
             <div class="col-xs-8">
@@ -182,24 +188,21 @@
     </div>
 
     <div style="margin-top: 20px;">
-    {% if filtered_results is defined %}
-    {% if filtered_results|length > limit_number %}
-    There are more than 10000 results. Consider limiting your search to a smaller range.
-    {% else %}
+    {% if table_rows is defined %}
     <table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
       <thead>
         <tr>
           <th></th>
           {% if header_fields|length == 2 %}
           {% for header in header_fields[0] %}
-          <th data-export="{{ header }}">{{ header }}</th>
+          <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
           {% endfor %}
           {% for strain in header_fields[1] %}
-          <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 15px;">{% for letter in strain %}<div style="transform: rotate(90deg);">{{ letter }}</div>{% endfor %}</th>
+          <th data-export="{{ strain }}" name="{{ strain }}" style="align: center; text-align: center; line-height: 12px;">{% for letter in strain|reverse %}<div style="transform: rotate(270deg);">{{ letter }}</div>{% endfor %}</th>
           {% endfor %}
           {% else %}
           {% for header in header_fields %}
-          <th data-export="{{ header }}">{{ header }}</th>
+          <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
           {% endfor %}
           {% endif %}
         </tr>
@@ -208,7 +211,6 @@
       <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
       </tbody>
     </table>
-    {% endif %}
     {% endif %}     
     </div>
   </div>
@@ -222,12 +224,24 @@
   <script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script>
 
   <script type='text/javascript'>
-      var json_rows = {{ table_rows|safe }};
       var empty_columns = {{ empty_columns|safe }};
+
+      var remain_field_count = 15 - {{ empty_field_count|safe }};
+      var total_field_count = 15 - {{ empty_field_count|safe }} + {{ allele_list|safe|length }};
   </script>
 
   <script language="javascript">
 
+    var getParams = function(url) {
+      let parser = document.createElement('a');
+      parser.href = url;
+      let params = parser.search.substring(1);
+      if(params.length > 0) {
+        return ('?'+params);
+      }
+      return params;
+    };
+
     var substringMatcher = function(strs) {
       return function findMatches(q, cb) {
         var matches, substringRegex;
@@ -260,19 +274,20 @@
       source: substringMatcher(rat_genes)
     });
 
-    {% if filtered_results is defined %}
+    {% if table_rows is defined %}
     $("#results_table").DataTable( {
-      'data': json_rows,
       {% if variant_type == "SNP" %}
       'columns': [
         {
           'data': null,
+          'className': 'dt-body-center',
           'orderable': false,
           'render': function(data, type, row, meta) {
-            return '<input type="checkbox" name="trait_check">'
+            return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
           }
         }, {
-          'data': 'index'
+          'data': 'index',
+          'className': 'dt-body-right'
         }, {
           'data': null,
           'render': function(data, type, row, meta) {
@@ -283,27 +298,30 @@
             }
           }
         }, {
-          'data': 'chr'
+          'data': 'chr',
+          'className': 'dt-body-center'
         }, {
-          'data': 'mb_formatted'
+          'data': 'mb_formatted',
+          'className': 'dt-body-right'
         }, {
           'data': 'alleles'
         }, {% if empty_columns['snp_source'] == "true" %}{
           'data': null,
           'render': function(data, type, row, meta) {
             if (data.snp_source == "Sanger/UCLA") {
-              return '<a href="' + data.source_urls[0] + '">Sanger</a><a href="' + data.source_urls[1] + '">UCLA</a>'
+              return '<a href="' + data.source_urls[0] + '">Sanger</a>, <a href="' + data.source_urls[1] + '">UCLA</a>'
             } else {
               return data.snp_source
             }
           }
         }, {% endif %} {% if empty_columns['conservation_score'] == "true" %}{
-          'data': 'conservation_score'
+          'data': 'conservation_score',
+          'className': 'dt-body-right'
         }, {% endif %} {% if empty_columns['gene_name'] == "true" %}{
           'data': null,
           'render': function(data, type, row, meta) {
             if (data.gene_name != "") {
-              return '<i>' + data.gene_name + '</i><br><a href="' + data.gene_link + '">NCBI</a>'
+              return '<i>' + data.gene_name + '</i>, <a href="' + data.gene_link + '">NCBI</a>'
             } else {
               return data.gene_name
             }
@@ -330,6 +348,7 @@
         }, {% endif %} {% for item in allele_list %} {
           'data': null,
           'orderable': false,
+          'className': 'dt-body-center',
           'render': function(data, type, row, meta) {
             if (typeof data.allele_value_list[{{ loop.index - 1 }}][0] !== "undefined") {
               return data.allele_value_list[{{ loop.index - 1 }}][0]
@@ -339,12 +358,9 @@
           }
         }{% if loop.index < allele_list|length %},{% endif %}{% endfor %}
       ],
-      'createdRow': function( row, data, dataIndex) {
-        $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
-        $('td', row).eq(1).attr("align", "right");
-        for (i = {{ 15 - empty_field_count }}; i < ({{ 15 - empty_field_count }} + {{ allele_list|length }}); i++) {
+      'createdRow': function(row, data, dataIndex) {
+        for (i = remain_field_count; i < total_field_count; i++) {
           var this_allele = $('td', row).eq(i).text();
-          $('td', row).eq(i).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
           switch (this_allele) {
             case "A":
               $('td', row).eq(i).addClass('A_allele_color');
@@ -380,24 +396,29 @@
         {
           'data': null,
           'render': function(data, type, row, meta) {
-            return '<input type="checkbox" name="trait_check">'
+            return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
           }
         }, {
-          'data': 'index'
+          'data': 'index',
+          'className': 'dt-body-right'
         }, {
           'data': 'indel_name'
         }, {
           'data': 'indel_type'
         }, {
-          'data': 'indel_chr'
+          'data': 'indel_chr',
+          'className': 'dt-body-center'
         }, {
-          'data': 'indel_mb_s'
+          'data': 'indel_mb_s',
+          'className': 'dt-body-right'
         }, {
-          'data': 'indel_mb_e'
+          'data': 'indel_mb_e',
+          'className': 'dt-body-right'
         }, {
           'data': 'indel_strand'
         }, {
-          'data': 'indel_size'
+          'data': 'indel_size',
+          'className': 'dt-body-right'
         }, {
           'data': 'indel_sequence'
         }, {
@@ -407,15 +428,28 @@
       {% endif %}
       'order': [[1, "asc" ]],
       'sDom': "rtip",
-      'iDisplayLength': 500,
-      'processing': true,
-      'language': {
-        'loadingRecords': '&nbsp;',
-        'processing': 'Loading...'
+      'iDisplayLength': 100,
+      'bServerSide': true,
+      'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
+      'infoCallback': function(settings, start, end, max, total, pre) {
+        return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
       }
     });
     {% endif %}
 
+    function onVarinatCheck(checkboxElem) {
+        if (checkboxElem.checked) {
+            if (!checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+                checkboxElem.parentElement.parentElement.classList.add('selected')
+            }
+        }
+        else {
+            if (checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+                checkboxElem.parentElement.parentElement.classList.remove('selected')
+            }
+        }
+    }
+
     $("#species_select").change(function() {
         this_species = $(this).val();
         $("#strain_select").empty()
@@ -509,6 +543,40 @@
       });
       $("input[name=chosen_strains]").val(strain_list.join(","));
     });
+
+    
+
+    $("input[name=export_csv]").click(function() {
+      var csv = [];
+      var rows = document.querySelectorAll("table tr");
+
+      var headers = [];
+      var col_header = rows[0].querySelectorAll("th");
+      for(let i = 1; i < col_header.length; i++) {
+        headers.push(col_header[i].getAttribute("name"));
+      }
+      csv.push(headers.join(","));
+
+      for (let i = 1; i < rows.length; i++) {
+        var row = [], cols = rows[i].querySelectorAll("td");
+        var checkBox = rows[i].querySelector("input");
+
+        if(checkBox.checked == true) {
+          for (let j = 1; j < cols.length; j++)
+            row.push(cols[j].innerText);
+
+            csv.push(row.join(","));
+        }
+      }
+
+      var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
+      var downloadLink = document.createElement("a");
+      downloadLink.download = "variant_data.csv";
+      downloadLink.href = window.URL.createObjectURL(csvFile);
+      downloadLink.style.display = "none";
+      document.body.appendChild(downloadLink);
+      downloadLink.click();
+    });
   </script>
 {% endblock %}
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 25563e86..e4834d53 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -26,6 +26,15 @@ import sqlalchemy
 from wqflask import app
 from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
 
+from wqflask import group_manager
+from wqflask import resource_manager
+from wqflask import search_results
+from wqflask import export_traits
+from wqflask import gsearch
+from wqflask import update_search_results
+from wqflask import docs
+from wqflask import news
+from wqflask import server_side
 from wqflask.submit_bnw import get_bnw_input
 from base.data_set import create_dataset, DataSet    # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
@@ -220,6 +229,26 @@ def search_page():
     else:
         return render_template("search_error.html")
 
+@app.route("/search_table", methods=('GET',))
+def search_page_table():
+    logger.info("in search_page table")
+    logger.info(request.url)
+
+    logger.info("request.args is", request.args)
+    the_search = search_results.SearchResultPage(request.args)
+
+    logger.info(type(the_search.trait_list))
+    logger.info(the_search.trait_list)
+    
+    current_page = server_side.ServerSideTable(
+        len(the_search.trait_list),
+        the_search.trait_list,
+        the_search.header_data_names,
+        request.args,
+    ).get_page()
+
+    return flask.jsonify(current_page)
+
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
     logger.info(request.url)
@@ -621,12 +650,13 @@ def loading_page():
         wanted = initial_start_vars['wanted_inputs'].split(",")
         start_vars = {}
         for key, value in list(initial_start_vars.items()):
-            if key in wanted or key.startswith(('value:')):
+            if key in wanted:
                 start_vars[key] = value
 
         if 'n_samples' in start_vars:
             n_samples = int(start_vars['n_samples'])
         else:
+            sample_vals_dict = json.loads(start_vars['sample_vals'])
             if 'group' in start_vars:
                 dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
             else:
@@ -642,9 +672,9 @@ def loading_page():
                         samples = genofile_samples
 
             for sample in samples:
-                value = start_vars.get('value:' + sample)
-                if value != "x":
-                    n_samples += 1
+                if sample in sample_vals_dict:
+                    if sample_vals_dict[sample] != "x":
+                        n_samples += 1
 
         start_vars['n_samples'] = n_samples
         start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
@@ -660,7 +690,6 @@ def loading_page():
 @app.route("/run_mapping", methods=('POST',))
 def mapping_results_page():
     initial_start_vars = request.form
-    #logger.debug("Mapping called with initial_start_vars:", initial_start_vars.items())
     logger.info(request.url)
     temp_uuid = initial_start_vars['temp_uuid']
     wanted = (
@@ -670,6 +699,7 @@ def mapping_results_page():
         'species',
         'samples',
         'vals',
+        'sample_vals',
         'first_run',
         'output_files',
         'geno_db_exists',
@@ -723,13 +753,11 @@ def mapping_results_page():
     )
     start_vars = {}
     for key, value in list(initial_start_vars.items()):
-        if key in wanted or key.startswith(('value:')):
+        if key in wanted:
             start_vars[key] = value
-    #logger.debug("Mapping called with start_vars:", start_vars)
 
     version = "v3"
     key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
-    #logger.info("key is:", pf(key))
     with Bench("Loading cache"):
         result = None # Just for testing
         #result = Redis.get(key)
@@ -751,10 +779,9 @@ def mapping_results_page():
                     rendered_template = render_template("mapping_error.html")
                     return rendered_template
             except:
-                rendered_template = render_template("mapping_error.html")
-                return rendered_template
+               rendered_template = render_template("mapping_error.html")
+               return rendered_template
 
-            #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
             template_vars.js_data = json.dumps(template_vars.js_data,
                                                     default=json_default_handler,
                                                     indent="   ")
@@ -775,10 +802,6 @@ def mapping_results_page():
                     rendered_template = render_template("pair_scan_results.html", **result)
             else:
                 gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
-                #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
-                #logger.info("pickled result length:", len(pickled_result))
-                #Redis.set(key, pickled_result)
-                #Redis.expire(key, 1*60)
 
                 with Bench("Rendering template"):
                     #if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
@@ -896,6 +919,19 @@ def db_info_page():
 
     return render_template("info_page.html", **template_vars.__dict__)
 
+@app.route("/snp_browser_table", methods=('GET',))
+def snp_browser_table():
+    logger.info(request.url)
+    snp_table_data = snp_browser.SnpBrowser(request.args)
+    current_page = server_side.ServerSideTable(
+        snp_table_data.rows_count,
+        snp_table_data.table_rows,
+        snp_table_data.header_data_names,
+        request.args,
+    ).get_page()
+
+    return flask.jsonify(current_page)
+
 @app.route("/tutorial/WebQTLTour", methods=('GET',))
 def tutorial_page():
     #ZS: Currently just links to GN1