import unittest
from unittest import mock
from gn2.wqflask import app
from gn2.wqflask.snp_browser.snp_browser import get_gene_id
from gn2.wqflask.snp_browser.snp_browser import get_gene_id_name_dict
from gn2.wqflask.snp_browser.snp_browser import check_if_in_gene
from gn2.wqflask.snp_browser.snp_browser import get_browser_sample_lists
from gn2.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()
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,
[
"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,
)
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,
[
"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("gn2.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"
)
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"),
)
results = get_gene_id(
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")
@mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
def test_gene_id_name_dict(self, mock_db):
no_gene_names = []
conn = mock.MagicMock()
mock_db.return_value.__enter__.return_value = conn
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
),
)
gene_name_list = ["GH1", "GH2", "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 = %s AND geneSymbol in (%s, %s, %s)"
)
cursor.execute.assert_called_with(
db_query_value, ("ret3-32rf32", "GH1", "GH2", "GH3")
)
self.assertEqual(results_found, expected_found)
self.assertEqual(no_results, {})
@mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
def test_check_if_in_gene(self, mock_db):
conn = mock.MagicMock()
mock_db.return_value.__enter__.return_value = conn
with conn.cursor() as cursor:
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
)
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)"
)
gene_not_found = check_if_in_gene(
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),
),
]
)
self.assertEqual(gene_not_found, "")
@mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection")
def test_get_browser_sample_lists(self, mock_db):
conn = mock.MagicMock()
mock_db.return_value.__enter__.return_value = conn
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": []})
