From 4817ba35c1ca48ac1afa22ddc6ff6f167c6ee1cf Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 17 Mar 2022 16:36:22 +0300
Subject: Lint some test files
---
wqflask/tests/unit/wqflask/api/test_correlation.py | 163 ++++++++++--------
.../unit/wqflask/snp_browser/test_snp_browser.py | 183 +++++++++++++++------
2 files changed, 223 insertions(+), 123 deletions(-)
(limited to 'wqflask/tests/unit')
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 50df2bb4..53e1b9a2 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -20,12 +20,7 @@ class MockDataset(AttributeSetter):
return None
def retrieve_genes(self, id=None):
- return {
- "TT-1": "GH-1",
- "TT-2": "GH-2",
- "TT-3": "GH-3"
-
- }
+ return {"TT-1": "GH-1", "TT-2": "GH-2", "TT-3": "GH-3"}
class TestCorrelations(unittest.TestCase):
@@ -37,18 +32,10 @@ class TestCorrelations(unittest.TestCase):
self.app_context.pop()
def test_init_corr_params(self):
- start_vars = {
- "return_count": "3",
- "type": "T1",
- "method": "spearman"
- }
+ 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"
- }
+ expected_results = {"return_count": 3, "type": "T1", "method": "spearman"}
self.assertEqual(corr_params_results, expected_results)
@@ -57,74 +44,100 @@ class TestCorrelations(unittest.TestCase):
conn = mock.MagicMock()
mock_db.return_value.__enter__.return_value = conn
with conn.cursor() as cursor:
- cursor.fetchone.side_effect = [
- ("MG-1",), ("MG-2",)]
-
- self.assertEqual(convert_to_mouse_gene_id(
- species="Other", gene_id=""), None)
- 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")
+ cursor.fetchone.side_effect = [("MG-1",), ("MG-2",)]
+
+ self.assertEqual(
+ convert_to_mouse_gene_id(species="Other", gene_id=""), None
+ )
+ 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.database_connection")
@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"
+ 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"}
conn = mock.MagicMock()
mock_db.return_value.__enter__.return_value = conn
with conn.cursor() as cursor:
- cursor.fetchone.side_effect = [
- ("V1", ), ("V2", ), ("V3", )]
+ cursor.fetchone.side_effect = [("V1",), ("V2",), ("V3",)]
this_trait = AttributeSetter({"geneid": "GH-1"})
target_dataset = AttributeSetter(
- {"group": AttributeSetter({"species": "rat"})})
+ {"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']}
+ 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"]})
+ {"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})}
+ 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")
+ 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):
@@ -137,18 +150,26 @@ class TestCorrelations(unittest.TestCase):
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]}
+ "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_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]}
+ 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/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index 46a74231..a09d1538 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -17,48 +17,110 @@ 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"}
+ 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'])
+ 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)
+ 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=[])
+ 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'])
+ [
+ "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.database_connection")
def test_get_gene_id(self, mock_db):
- db_query_value = ("SELECT geneId FROM GeneList WHERE "
- "SpeciesId = %s AND geneSymbol = %s")
+ db_query_value = (
+ "SELECT geneId FROM GeneList WHERE " "SpeciesId = %s AND geneSymbol = %s"
+ )
conn = mock.MagicMock()
mock_db.return_value.__enter__.return_value = conn
with conn.cursor() as cursor:
- cursor.fetchone.return_value = (("517d729f-aa13-4413"
- "-a885-40a3f7ff768a"),)
+ cursor.fetchone.return_value = (
+ ("517d729f-aa13-4413" "-a885-40a3f7ff768a"),
+ )
results = get_gene_id(
- species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83",
- gene_name="INSR")
+ species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR"
+ )
cursor.execute.assert_called_once_with(
- db_query_value,
- ("c9c0f59e-1259-4cba-91e6-831ef1a99c83",
- "INSR"))
- self.assertEqual(results,
- "517d729f-aa13-4413-a885-40a3f7ff768a")
+ db_query_value, ("c9c0f59e-1259-4cba-91e6-831ef1a99c83", "INSR")
+ )
+ self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
@mock.patch("wqflask.snp_browser.snp_browser.database_connection")
def test_gene_id_name_dict(self, mock_db):
@@ -68,25 +130,37 @@ class TestSnpBrowser(unittest.TestCase):
with conn.cursor() as cursor:
cursor.fetchall.side_effect = [
[],
- [("fsdf43-fseferger-f22", "GH1"),
- ("1sdf43-fsewferger-f22", "GH2"),
- ("fwdj43-fstferger-f22", "GH3")]]
- self.assertEqual("", get_gene_id_name_dict(
- species_id="fregb343bui43g4",
- gene_name_list=no_gene_names))
+ [
+ ("fsdf43-fseferger-f22", "GH1"),
+ ("1sdf43-fsewferger-f22", "GH2"),
+ ("fwdj43-fstferger-f22", "GH3"),
+ ],
+ ]
+ self.assertEqual(
+ "",
+ get_gene_id_name_dict(
+ species_id="fregb343bui43g4", gene_name_list=no_gene_names
+ ),
+ )
gene_name_list = ["GH1", "GH2", "GH3"]
no_results = get_gene_id_name_dict(
- species_id="ret3-32rf32", gene_name_list=gene_name_list)
+ 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'}
+ 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 = %s AND geneSymbol in (%s, %s, %s)")
+ "SpeciesId = %s AND geneSymbol in (%s, %s, %s)"
+ )
cursor.execute.assert_called_with(
- db_query_value, ("ret3-32rf32", "GH1", "GH2", "GH3"))
+ db_query_value, ("ret3-32rf32", "GH1", "GH2", "GH3")
+ )
self.assertEqual(results_found, expected_found)
self.assertEqual(no_results, {})
@@ -95,26 +169,31 @@ class TestSnpBrowser(unittest.TestCase):
conn = mock.MagicMock()
mock_db.return_value.__enter__.return_value = conn
with conn.cursor() as cursor:
- cursor.fetchone.side_effect = [
- ("fsdf-232sdf-sdf", "GHA"), ""]
+ cursor.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)
+ species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr_="CH1", mb=12.09
+ )
self.assertEqual(results_found, ["fsdf-232sdf-sdf", "GHA"])
db_query_value = (
"SELECT geneId, geneSymbol FROM GeneList "
"WHERE SpeciesId = %s AND chromosome = %s "
- "AND (txStart < %s AND txEnd > %s)")
+ "AND (txStart < %s AND txEnd > %s)"
+ )
gene_not_found = check_if_in_gene(
- species_id="517d729f-aa13-4413-a885-40a3f7ff768a",
- chr_="CH1", mb=12.09)
+ species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr_="CH1", mb=12.09
+ )
cursor.execute.assert_has_calls(
- [mock.call(db_query_value,
- ("517d729f-aa13-4413-a885-40a3f7ff768a",
- "CH1", 12.09, 12.09)),
- mock.call(db_query_value,
- ("517d729f-aa13-4413-a885-40a3f7ff768a",
- "CH1", 12.09, 12.09))])
+ [
+ mock.call(
+ db_query_value,
+ ("517d729f-aa13-4413-a885-40a3f7ff768a", "CH1", 12.09, 12.09),
+ ),
+ mock.call(
+ db_query_value,
+ ("517d729f-aa13-4413-a885-40a3f7ff768a", "CH1", 12.09, 12.09),
+ ),
+ ]
+ )
self.assertEqual(gene_not_found, "")
@mock.patch("wqflask.snp_browser.snp_browser.database_connection")
@@ -124,4 +203,4 @@ class TestSnpBrowser(unittest.TestCase):
with conn.cursor() as cursor:
cursor.execute.return_value.fetchall.return_value = []
results = get_browser_sample_lists(species_id="12")
- self.assertEqual(results, {'mouse': [], 'rat': []})
+ self.assertEqual(results, {"mouse": [], "rat": []})
--
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