diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/tests/unit/wqflask/snp_browser/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py | 84 |
2 files changed, 84 insertions, 0 deletions
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..e8751778 --- /dev/null +++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py @@ -0,0 +1,84 @@ +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() + + + @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 " + results = get_gene_id( + species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR") + mock_db.db.execute.assert_called_once_with(called_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,{}) + + @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,"") + + @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_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) + + + + + + + + + + + + + + + |