add tests for snp browser

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)
+
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