diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/unit/utility/test_type_checking.py | 93 | ||||
| -rw-r--r-- | wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py | 120 |
2 files changed, 112 insertions, 101 deletions
diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py index 1ea11695..48d110c7 100644 --- a/wqflask/tests/unit/utility/test_type_checking.py +++ b/wqflask/tests/unit/utility/test_type_checking.py @@ -5,53 +5,50 @@ 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=["1sdf",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") - - +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/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py index 9ec32c78..496d228f 100644 --- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py +++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py @@ -7,6 +7,7 @@ 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() @@ -16,70 +17,83 @@ class TestSnpBrowser(unittest.TestCase): 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) - - 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) - - self.assertEqual(expected_results,results_with_snp) - self.assertEqual(results_with_indel,expected_results_with_indel) - + 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) + + 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) + + self.assertEqual(expected_results, results_with_snp) + self.assertEqual(results_with_indel, expected_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" - called_value="\n SELECT\n geneId\n FROM\n GeneList\n WHERE\n SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'\n " + 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(called_value) + 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="\n SELECT\n geneId, geneSymbol\n FROM\n GeneList\n WHERE\n SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')\n " - mock_db.db.execute.assert_called_with(db_query_value) - self.assertEqual(results_found,expected_found) - self.assertEqual(no_results,{}) + 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\n FROM GeneList\n WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND\n (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,"") + 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': []}) - - - - - - - - - - - - - - - + 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': []}) |