Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

9 files changed, 788 insertions, 0 deletions

diff --git a/gn2/tests/unit/wqflask/marker_regression/__init__.py b/gn2/tests/unit/wqflask/marker_regression/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/__init__.py
diff --git a/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt
diff --git a/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
new file mode 100644
index 00000000..580d79cf
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -0,0 +1,159 @@
+import unittest
+
+import htmlgen as HT
+from gn2.wqflask.marker_regression.display_mapping_results import (
+    DisplayMappingResults,
+    HtmlGenWrapper
+)
+
+
+class TestDisplayMappingResults(unittest.TestCase):
+    """Basic Methods to test Mapping Results"""
+
+    def test_pil_colors(self):
+        """Test that colors use PILLOW color format"""
+        self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
+                         (245, 211, 211))
+
+
+class TestHtmlGenWrapper(unittest.TestCase):
+    """Test Wrapper around HTMLGen"""
+
+    def test_create_image(self):
+        """Test HT.Image method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_image_tag(src="test.png",
+                                                alt="random",
+                                                border="0",
+                                                width="10",
+                                                height="13",
+                                                usemap="#webqtlmap")),
+            ("""<img alt="random" border="0" height="13" """
+             """src="test.png" usemap="#webqtlmap" """
+             """width="10"/>""")
+        )
+
+    def test_create_form(self):
+        """Test HT.Form method"""
+        test_form = HtmlGenWrapper.create_form_tag(
+            cgi="/testing/",
+            enctype='multipart/form-data',
+            name="formName",
+            submit=HtmlGenWrapper.create_input_tag(
+                type_='hidden', name='Default_Name')
+        )
+        test_image = HtmlGenWrapper.create_image_tag(
+            src="test.png",
+            alt="random",
+            border="0",
+            width="10",
+            height="13",
+            usemap="#webqtlmap"
+        )
+        self.assertEqual(
+            str(test_form).replace("\n", ""),
+            ("""<form action="/testing/" enctype="multipart/form-data" """
+             """method="POST" """
+             """name="formName"><input name="Default_Name" """
+             """type="hidden"/></form>"""))
+        hddn = {
+            'FormID': 'showDatabase',
+            'ProbeSetID': '_',
+            'database': "TestGeno",
+            'CellID': '_',
+            'RISet': "Test",
+            'incparentsf1': 'ON'
+        }
+        for key in hddn.keys():
+            test_form.append(
+                HtmlGenWrapper.create_input_tag(
+                    name=key,
+                    value=hddn[key],
+                    type_='hidden'))
+        test_form.append(test_image)
+
+        self.assertEqual(str(test_form).replace("\n", ""), (
+            """<form action="/testing/" enctype="multipart/form-data" """
+            """method="POST" name="formName">"""
+            """<input name="Default_Name" type="hidden"/>"""
+            """<input name="FormID" type="hidden" value="showDatabase"/>"""
+            """<input name="ProbeSetID" type="hidden" value="_"/>"""
+            """<input name="database" type="hidden" value="TestGeno"/>"""
+            """<input name="CellID" type="hidden" value="_"/>"""
+            """<input name="RISet" type="hidden" value="Test"/>"""
+            """<input name="incparentsf1" type="hidden" value="ON"/>"""
+            """<img alt="random" border="0" height="13" src="test.png" """
+            """usemap="#webqtlmap" width="10"/>"""
+            """</form>"""))
+
+    def test_create_paragraph(self):
+        """Test HT.Paragraph method"""
+        test_p_element = HtmlGenWrapper.create_p_tag(id="smallSize")
+        par_text = (
+            "Mapping using genotype data as "
+            "a trait will result in infinity LRS at one locus. "
+            "In order to display the result properly, all LRSs "
+            "higher than 100 are capped at 100."
+        )
+        self.assertEqual(
+            str(test_p_element),
+            """<p id="smallSize"></p>"""
+        )
+        test_p_element.append(HtmlGenWrapper.create_br_tag())
+        test_p_element.append(par_text)
+        self.assertEqual(
+            str(test_p_element),
+            """<p id="smallSize"><br/>{}</p>""".format(par_text)
+        )
+
+    def test_create_br_tag(self):
+        """Test HT.BR() method"""
+        self.assertEqual(str(HtmlGenWrapper.create_br_tag()),
+                         "<br/>")
+
+    def test_create_input_tag(self):
+        """Test HT.Input method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_input_tag(
+                type_="hidden",
+                name="name",
+                value="key",
+                Class="trait trait_")).replace("\n", ""),
+            ("""<input class="trait trait_" name="name" """
+             """type="hidden" value="key"/>"""))
+
+    def test_create_map_tag(self):
+        """Test HT.Map method"""
+        self.assertEqual(str(HtmlGenWrapper.create_map_tag(
+            name="WebqTLImageMap")).replace("\n", ""),
+            """<map name="WebqTLImageMap"></map>""")
+        gifmap = HtmlGenWrapper.create_map_tag(name="test")
+        gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect",
+                                                     coords='1 2 3', href='#area1'))
+        gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect",
+                                                     coords='1 2 3', href='#area2'))
+        self.assertEqual(
+            str(gifmap).replace("\n", ""),
+            ("""<map name="test">"""
+             """<area coords="1 2 3" """
+             """href="#area1" shape="rect"/>"""
+             """<area coords="1 2 3" href="#area2" shape="rect"/>"""
+             """</map>"""))
+
+    def test_create_area_tag(self):
+        """Test HT.Area method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_area_tag(
+                shape="rect",
+                coords="1 2",
+                href="http://test.com",
+                title="Some Title")).replace("\n", ""),
+            ("""<area coords="1 2" href="http://test.com" """
+             """shape="rect" title="Some Title"/>"""))
+
+    def test_create_link_tag(self):
+        """Test HT.HREF method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_link_tag(
+                "www.test.com", "test", target="_blank")).replace("\n", ""),
+            """<a href="www.test.com" target="_blank">test</a>""")
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
new file mode 100644
index 00000000..26f0c50a
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -0,0 +1,188 @@
+# test for wqflask/marker_regression/gemma_mapping.py
+import os
+import unittest
+import random
+from unittest import mock
+from gn2.wqflask.marker_regression.gemma_mapping import run_gemma
+from gn2.wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file
+from gn2.wqflask.marker_regression.gemma_mapping import gen_covariates_file
+from gn2.wqflask.marker_regression.gemma_mapping import parse_loco_output
+
+
+class AttributeSetter:
+    def __init__(self, obj):
+        for key, val in obj.items():
+            setattr(self, key, val)
+
+
+class MockGroup(AttributeSetter):
+    def get_samplelist(self, redis_conn):
+        return None
+
+
+class TestGemmaMapping(unittest.TestCase):
+
+    @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
+    def test_run_gemma_firstrun_set_false(self, mock_parse_loco):
+        """add tests for gemma function where  first run is set to false"""
+        dataset = AttributeSetter(
+            {"group": AttributeSetter({"genofile": "genofile.geno"})})
+
+        output_file = "file1"
+        mock_parse_loco.return_value = []
+        this_trait = AttributeSetter({"name": "t1"})
+
+        result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[
+        ], covariates="", use_loco=True, first_run=False, output_files=output_file)
+
+        expected_results = ([], "file1")
+        self.assertEqual(expected_results, result)
+
+    @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR",
+                os.path.join(os.path.dirname(__file__), "user/data"))
+    @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
+    @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
+    def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco):
+        """add tests for run_gemma where first run is set to true"""
+        this_chromosomes = {}
+        for i in range(1, 5):
+            this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"}))
+        chromosomes = AttributeSetter({"chromosomes": lambda cursor: this_chromosomes})
+
+        dataset_group = MockGroup(
+            {"name": "GP1", "genofile": "file_geno"})
+        dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name",
+                                   "species": AttributeSetter({"chromosomes": chromosomes})})
+        trait = AttributeSetter({"name": "trait1"})
+        samples = []
+        mock_gen_pheno_txt.return_value = None
+        mock_os.path.isfile.return_value = True
+        mock_gen_covar.return_value = None
+        mock_choice.return_value = "R"
+        mock_flat_files.return_value = os.path.join(
+            os.path.dirname(__file__), "genotype/bimbam")
+        mock_parse_loco.return_value = []
+        results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
+        ], vals=[], covariates="", use_loco=True)
+        mock_gen_pheno_txt.assert_called_once()
+        mock_parse_loco.assert_called_once_with(
+            dataset, "GP1_GWA_RRRRRR", True)
+        mock_os.path.isfile.assert_called_once_with(
+            ('/home/user/imgfile_output.assoc.txt'))
+        self.assertEqual(results, ([], "GP1_GWA_RRRRRR"))
+
+    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data")
+    def test_gen_pheno_txt_file(self):
+        """add tests for generating pheno txt file"""
+        with mock.patch("builtins.open", mock.mock_open())as mock_open:
+            gen_pheno_txt_file(
+                this_dataset=AttributeSetter({"name": "A"}),
+                genofile_name="", vals=[
+                    "x", "w", "q", "we", "R"])
+            mock_open.assert_called_once_with(
+                '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w')
+            filehandler = mock_open()
+            values = ["x", "w", "q", "we", "R"]
+            write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call(
+                'q\n'), mock.call('we\n'), mock.call('R\n')]
+
+            filehandler.write.assert_has_calls(write_calls)
+
+    @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset")
+    def test_gen_covariates_file(self, create_dataset, create_trait, flat_files):
+        """add tests for generating covariates files"""
+        covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2"
+        samplelist = ["X1", "X2", "X3", "X4"]
+        create_dataset_side_effect = []
+        create_trait_side_effect = []
+
+        for i in range(4):
+            create_dataset_side_effect.append(
+                AttributeSetter({"name": f'name_{i}'}))
+            create_trait_side_effect.append(
+                AttributeSetter({"data": [f'data_{i}']}))
+
+        create_dataset.side_effect = create_trait_side_effect
+        create_trait.side_effect = create_trait_side_effect
+
+        group = MockGroup({"name": "group_X", "samplelist": samplelist})
+        this_dataset = AttributeSetter({"group": group, "name": "dataset1_name"})
+        flat_files.return_value = "Home/Genenetwork"
+
+        with mock.patch("builtins.open", mock.mock_open())as mock_open:
+            gen_covariates_file(this_dataset=this_dataset, covariates=covariates,
+                                samples=["x1", "x2", "X3"])
+
+            create_dataset.assert_has_calls(
+                [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')])
+            mock_calls = []
+            trait_names = ["X1", "Y1", "M1", "V1"]
+
+            for i, trait in enumerate(create_trait_side_effect):
+                mock_calls.append(
+                    mock.call(dataset=trait, name=trait_names[i], cellid=None))
+
+            create_trait.assert_has_calls(mock_calls)
+
+            flat_files.assert_called_once_with('mapping')
+            mock_open.assert_called_once_with(
+                'Home/Genenetwork/COVAR_npKxIOnq3azWdgYixtd9IQ.txt', 'w')
+            filehandler = mock_open()
+            filehandler.write.assert_has_calls([mock.call(
+                '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
+
+    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.json")
+    def test_parse_loco_outputfile_found(self, mock_json, mock_os):
+        """add tests for parse loco output file found"""
+        mock_json.load.return_value = {
+            "files": [["file_name", "user", "~/file1"],
+                      ["file_name", "user", "~/file2"]]
+        }
+        return_file = """X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
+chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5
+Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7
+X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
+
+        return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5\t0.4"""
+        mock_os.path.isfile.return_value = True
+        file_to_write = """{"files":["file_1","file_2"]}"""
+        with mock.patch("builtins.open") as mock_open:
+
+            handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open(
+                read_data=return_file).return_value, mock.mock_open(read_data=return_file_2).return_value)
+            mock_open.side_effect = handles
+            results = parse_loco_output(
+                this_dataset={}, gwa_output_filename=".xw/")
+            expected_results = [
+                {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85,
+                 'additive': -11.65, 'lod_score': 0.07058107428570727},
+                {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5,
+                 'additive': -12.0, 'lod_score': 0.3010299956639812},
+                {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7,
+                 'additive': -5.8, 'lod_score': 0.1549019599857432},
+                {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': -10.55, 'lod_score': 0.22184874961635637}]
+            self.assertEqual(expected_results, results)
+
+    @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
+    @mock.patch("wqflask.marker_regression.gemma_mapping.os")
+    def test_parse_loco_outputfile_not_found(self, mock_os):
+        """add tests for parse loco output where  output file not found"""
+
+        mock_os.path.isfile.return_value = False
+        file_to_write = """{"files":["file_1","file_2"]}"""
+
+        with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open:
+            results = parse_loco_output(
+                this_dataset={}, gwa_output_filename=".xw/")
+            self.assertEqual(results, [])
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py
new file mode 100644
index 00000000..4c13b907
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -0,0 +1,86 @@
+# test for wqflask/marker_regression/plink_mapping.py
+import unittest
+from unittest import mock
+from gn2.wqflask.marker_regression.plink_mapping import build_line_list
+from gn2.wqflask.marker_regression.plink_mapping import get_samples_from_ped_file
+from gn2.wqflask.marker_regression.plink_mapping import flat_files
+from gn2.wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink
+from gn2.wqflask.marker_regression.plink_mapping import parse_plink_output
+
+
+class AttributeSetter:
+    def __init__(self, obj):
+        for key, val in obj.items():
+            setattr(self, key, val)
+
+
+class TestPlinkMapping(unittest.TestCase):
+
+    def test_build_line_list(self):
+        """test for building line list"""
+        line_1 = "this is line one test"
+        irregular_line = "  this     is an, irregular line     "
+        exp_line1 = ["this", "is", "line", "one", "test"]
+
+        results = build_line_list(irregular_line)
+        self.assertEqual(exp_line1, build_line_list(line_1))
+        self.assertEqual([], build_line_list())
+        self.assertEqual(["this", "is", "an,", "irregular", "line"], results)
+
+    @mock.patch("wqflask.marker_regression.plink_mapping.flat_files")
+    def test_get_samples_from_ped_file(self, mock_flat_files):
+        """test for getting samples from ped file"""
+        dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
+        file_sample = """Expected_1\tline test
+Expected_2\there
+  Expected_3\tthree"""
+        mock_flat_files.return_value = "/home/user/"
+        with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open:
+            results = get_samples_from_ped_file(dataset)
+            mock_flat_files.assert_called_once_with("mapping")
+            mock_open.assert_called_once_with("/home/user/n_1.ped", "r")
+            self.assertEqual(
+                ["Expected_1", "Expected_2", "Expected_3"], results)
+
+    @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+    @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file")
+    def test_gen_pheno_txt_file_plink(self, mock_samples):
+        """test for getting gen_pheno txt file"""
+        mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"]
+
+        trait = AttributeSetter({"name": "TX"})
+        dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})})
+        vals = ["value=K1", "value=K2", "value=K3"]
+        with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+            results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset,
+                                               vals=vals, pheno_filename="ph_file")
+            mock_open.assert_called_once_with(
+                "/home/user/data/ph_file.txt", "wb")
+            filehandler = mock_open()
+            calls_expected = [mock.call('FID\tIID\tTX\n'),
+                              mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')]
+
+            filehandler.write.assert_has_calls(calls_expected)
+
+            filehandler.close.assert_called_once()
+
+    @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/")
+    @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list")
+    def test_parse_plink_output(self, mock_line_list):
+        """test for parsing plink output"""
+        chromosomes = [0, 34, 110, 89, 123, 23, 2]
+        species = AttributeSetter(
+            {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})})
+
+        fake_file = """0 AACCAT T98.6  0.89\n2  AATA  B45  0.3\n121  ACG  B56.4 NA"""
+
+        mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [
+            "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]]
+        with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open:
+            parse_results = parse_plink_output(
+                output_filename="P1_file", species=species)
+            mock_open.assert_called_once_with(
+                "/home/user/data/P1_file.qassoc", "rb")
+            expected = (2, {'AACCAT': 0.89, 'AATA': 0.3})
+
+            self.assertEqual(parse_results, expected)
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
new file mode 100644
index 00000000..2268f4cb
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -0,0 +1,24 @@
+import unittest
+from unittest import mock
+from gn2.wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
+
+# issues some methods in genofile object are not defined
+# modify samples should equal to vals
+
+
+class TestQtlReaperMapping(unittest.TestCase):
+    @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
+    def test_gen_pheno_txt_file(self):
+        vals = ["V1", "x", "V4", "V3", "x"]
+        samples = ["S1", "S2", "S3", "S4", "S5"]
+        trait_filename = "trait_file"
+        with mock.patch("builtins.open", mock.mock_open())as mock_open:
+            gen_pheno_txt_file(samples=samples, vals=vals,
+                               trait_filename=trait_filename)
+            mock_open.assert_called_once_with(
+                "/home/user/data/gn2/trait_file.txt", "w")
+            filehandler = mock_open()
+            write_calls = [mock.call('Trait\t'), mock.call(
+                'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
+
+            filehandler.write.assert_has_calls(write_calls)
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
new file mode 100644
index 00000000..5cfce28c
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -0,0 +1,43 @@
+import unittest
+from unittest import mock
+from dataclasses import dataclass
+
+from gn2.wqflask.marker_regression.rqtl_mapping import run_rqtl
+
+@dataclass
+class MockGroup:
+    name: str
+    genofile: str
+
+@dataclass
+class MockDataset:
+    group: MockGroup
+
+class TestRqtlMapping(unittest.TestCase):
+    """Tests for functions in rqtl_mapping.py"""
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post")
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.locate")
+    @mock.patch("wqflask.marker_regression.rqtl_mapping.write_phenotype_file")
+    def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post):
+        """Test for run_rqtl with permutations > 0"""
+        dataset_group = MockGroup("GP1", "file_geno")
+        dataset = MockDataset(dataset_group)
+
+        mock_write_pheno_file.return_value = "pheno_filename"
+        mock_locate.return_value = "geno_filename"
+        mock_post.return_value = mock.Mock(ok=True)
+        mock_post.return_value.json.return_value = {"perm_results": [],
+                                                    "suggestive": 3,
+                                                    "significant": 4,
+                                                    "results" : []}
+
+        results = run_rqtl(trait_name="the_trait", vals=[], samples=[],
+        dataset=dataset, pair_scan=False, mapping_scale="cM", model="normal", method="hk",
+        num_perm=5, perm_strata_list=[], do_control="false", control_marker="",
+        manhattan_plot=True, cofactors="")
+
+        mock_write_pheno_file.assert_called_once()
+        mock_locate.assert_called_once()
+        mock_post.assert_called_once()
+
+        self.assertEqual(results, ([], 3, 4, []))
diff --git a/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py
new file mode 100644
index 00000000..dd67ce49
--- /dev/null
+++ b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -0,0 +1,288 @@
+import unittest
+import datetime
+from unittest import mock
+
+from gn2.wqflask.marker_regression.run_mapping import get_genofile_samplelist
+from gn2.wqflask.marker_regression.run_mapping import geno_db_exists
+from gn2.wqflask.marker_regression.run_mapping import write_input_for_browser
+from gn2.wqflask.marker_regression.run_mapping import export_mapping_results
+from gn2.wqflask.marker_regression.run_mapping import trim_markers_for_figure
+from gn2.wqflask.marker_regression.run_mapping import get_perm_strata
+from gn2.wqflask.marker_regression.run_mapping import get_chr_lengths
+
+
+class AttributeSetter:
+    def __init__(self, obj):
+        for k, v in obj.items():
+            setattr(self, k, v)
+
+
+class MockGroup(AttributeSetter):
+
+    def get_genofiles(self):
+        return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}]
+
+
+class TestRunMapping(unittest.TestCase):
+    def setUp(self):
+
+        self.group = MockGroup(
+            {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"})
+        chromosomes = {
+            "3": AttributeSetter({
+                "name": "C1",
+                "length": "0.04"
+            }),
+            "4": AttributeSetter({
+                "name": "C2",
+                "length": "0.03"
+            }),
+            "5": AttributeSetter({
+                "name": "C4",
+                "length": "0.01"
+            })
+        }
+        self.dataset = AttributeSetter(
+            {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"})
+
+        self.chromosomes = AttributeSetter({"chromosomes": lambda cur: chromosomes})
+        self.trait = AttributeSetter(
+            {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"})
+
+    def tearDown(self):
+        self.dataset = AttributeSetter(
+            {"group": {"location": "~/genofiles/g1_file"}})
+
+    def test_get_genofile_samplelist(self):
+
+        results_1 = get_genofile_samplelist(self.dataset)
+        self.assertEqual(results_1, ["S1", "S2", "S3", "S4"])
+        self.group.genofile = "~/genofiles/g2_file"
+        result_2 = get_genofile_samplelist(self.dataset)
+        self.assertEqual(result_2, [])
+
+    @mock.patch("wqflask.marker_regression.run_mapping.data_set")
+    def test_if_geno_db_exists(self, mock_data_set):
+        mock_data_set.create_dataset.side_effect = [
+            AttributeSetter({}), Exception()]
+        results_no_error = geno_db_exists(self.dataset)
+        results_with_error = geno_db_exists(self.dataset)
+
+        self.assertEqual(mock_data_set.create_dataset.call_count, 2)
+        self.assertEqual(results_with_error, "False")
+        self.assertEqual(results_no_error, "True")
+
+    def test_trim_markers_for_figure(self):
+
+        markers = [{
+            "name": "MK1",
+            "chr": "C1",
+            "cM": "1",
+            "Mb": "12000",
+            "genotypes": [],
+            "dominance":"TT",
+            "additive":"VA",
+            "lod_score":0.5
+        },
+            {
+            "name": "MK2",
+            "chr": "C2",
+            "cM": "15",
+            "Mb": "10000",
+            "genotypes": [],
+            "lod_score":0.7
+        },
+            {
+            "name": "MK1",
+            "chr": "C3",
+            "cM": "45",
+            "Mb": "1",
+            "genotypes": [],
+            "dominance":"Tt",
+            "additive":"VE",
+            "lod_score":1
+        }]
+
+        marker_2 = [{
+            "name": "MK1",
+            "chr": "C1",
+            "cM": "1",
+            "Mb": "12000",
+            "genotypes": [],
+            "dominance":"TT",
+            "additive":"VA",
+            "p_wald":4.6
+        }]
+        results = trim_markers_for_figure(markers)
+        result_2 = trim_markers_for_figure(marker_2)
+        expected = [
+            {
+                "name": "MK1",
+                "chr": "C1",
+                "cM": "1",
+                "Mb": "12000",
+                "genotypes": [],
+                "dominance":"TT",
+                "additive":"VA",
+                "lod_score":0.5
+            },
+            {
+                "name": "MK1",
+                "chr": "C3",
+                "cM": "45",
+                "Mb": "1",
+                "genotypes": [],
+                "dominance":"Tt",
+                "additive":"VE",
+                "lod_score":1
+            }
+
+        ]
+        self.assertEqual(results, expected)
+        self.assertEqual(result_2, marker_2)
+
+    def test_export_mapping_results(self):
+        """test for exporting mapping results"""
+        datetime_mock = mock.Mock(wraps=datetime.datetime)
+        datetime_mock.now.return_value = datetime.datetime(
+            2019, 9, 1, 10, 12, 12)
+
+        markers = [{
+            "name": "MK1",
+            "chr": "C1",
+            "cM": "1",
+            "Mb": "12000",
+            "genotypes": [],
+            "dominance":"TT",
+            "additive":"VA",
+            "lod_score":3
+        },
+            {
+            "name": "MK2",
+            "chr": "C2",
+            "cM": "15",
+            "Mb": "10000",
+            "genotypes": [],
+            "lod_score":7
+        },
+            {
+            "name": "MK1",
+            "chr": "C3",
+            "cM": "45",
+            "Mb": "1",
+            "genotypes": [],
+            "dominance":"Tt",
+            "additive":"VE",
+            "lod_score":7
+        }]
+
+        with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+
+            with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
+                export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
+                                       results_path="~/results", mapping_method="gemma", mapping_scale="physic",
+                                       score_type="-logP", transform="qnorm",
+                                       covariates="Dataset1:Trait1,Dataset2:Trait2",
+                                       n_samples="100", vals_hash="")
+
+                write_calls = [
+                    mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
+                    mock.call('Population: Human GP1_\n'), mock.call(
+                        'Data Set: dataset_1\n'),
+                    mock.call('Trait: Test Name\n'),
+                    mock.call('Trait Hash: \n'),
+                    mock.call('N Samples: 100\n'),
+                    mock.call('Mapping Tool: gemma\n'),
+                    mock.call('Transform - Quantile Normalized\n'),
+                    mock.call('Gene Symbol: IGFI\n'), mock.call(
+                        'Location: X1 @ 123313 Mb\n'),
+                    mock.call('Cofactors (dataset - trait):\n'),
+                    mock.call('Trait1 - Dataset1\n'),
+                    mock.call('Trait2 - Dataset2\n'),
+                    mock.call('\n'), mock.call('Name,Chr,'),
+                    mock.call('Mb,-logP'),
+                    mock.call(',Additive'), mock.call(',Dominance'),
+                    mock.call('\n'), mock.call('MK1,C1,'),
+                    mock.call('12000,'), mock.call('3'),
+                    mock.call(',VA'), mock.call(',TT'),
+                    mock.call('\n'), mock.call('MK2,C2,'),
+                    mock.call('10000,'), mock.call('7'),
+                    mock.call('\n'), mock.call('MK1,C3,'),
+                    mock.call('1,'), mock.call('7'),
+                    mock.call(',VE'), mock.call(',Tt')
+                ]
+                mock_open.assert_called_once_with("~/results", "w+")
+                filehandler = mock_open()
+                filehandler.write.assert_has_calls(write_calls)
+
+    @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+    def test_write_input_for_browser(self, mock_choice):
+        """test for writing input for browser"""
+        mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"]
+        with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+            expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT']
+
+            results = write_input_for_browser(
+                this_dataset=self.dataset, gwas_results={}, annotations={})
+            self.assertEqual(results, expected)
+
+    def test_get_perm_strata(self):
+        categorical_vars = ["C1", "C2", "W1"]
+        used_samples = ["S1", "S2"]
+        sample_list = AttributeSetter({"sample_attribute_values": {
+            "S1": {
+                "c1": "c1_value",
+                "c2": "c2_value",
+                "w1": "w1_value"
+            },
+            "S2": {
+                "w1": "w2_value",
+                "w2": "w2_value"
+            },
+            "S3": {
+
+                "c1": "c1_value",
+                "c2": "c2_value"
+            },
+        }})
+        results = get_perm_strata(this_trait={}, sample_list=sample_list,
+                                  categorical_vars=categorical_vars, used_samples=used_samples)
+        self.assertEqual(results, [1, 1])
+
+    def test_get_chr_length(self):
+        """test for getting chromosome length"""
+        cursor = mock.MagicMock()
+        chromosomes = AttributeSetter({"chromosomes": self.chromosomes})
+        dataset = AttributeSetter({"species": chromosomes})
+        results = get_chr_lengths(
+            mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[])
+        chr_lengths = []
+        for key, chromo in self.chromosomes.chromosomes(cursor).items():
+            chr_lengths.append({"chr": chromo.name, "size": chromo.length})
+
+        self.assertEqual(chr_lengths, results)
+
+        qtl_results = [{
+            "chr": "16",
+            "cM": "0.2"
+        },
+            {
+            "chr": "12",
+            "cM": "0.5"
+        },
+            {
+            "chr": "18",
+            "cM": "0.1"
+        },
+            {
+            "chr": "22",
+            "cM": "0.4"
+        },
+        ]
+
+        result_with_other_mapping_scale = get_chr_lengths(
+            mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results)
+        expected_value = [{'chr': '1', 'size': '0'}, {
+            'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}]
+
+        self.assertEqual(result_with_other_mapping_scale, expected_value)