"""Tests for gn3/db/traits.py"""
from unittest import mock, TestCase
from gn3.db.traits import (
build_trait_name,
export_trait_data,
export_informative,
set_haveinfo_field,
update_sample_data,
retrieve_trait_info,
set_confidential_field,
set_homologene_id_field,
retrieve_geno_trait_info,
retrieve_temp_trait_info,
retrieve_publish_trait_info,
retrieve_probeset_trait_info)
samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
trait_data = {
"mysqlid": 36688172,
"data": {
"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
"BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
"BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
"BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
"BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
"BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
"BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
"BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
"BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
"BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
"BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
"BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
"BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
"BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
"BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
"BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
"BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
"BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
"BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
"BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
"BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
"BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
"BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
"BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
"C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
"C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
"DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
class TestTraitsDBFunctions(TestCase):
"Test cases for traits functions"
def test_retrieve_publish_trait_info(self):
"""Test retrieval of type `Publish` traits."""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = tuple()
trait_source = {
"trait_name": "PublishTraitName", "trait_dataset_id": 1}
self.assertEqual(
retrieve_publish_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
("SELECT "
"PublishXRef.Id, Publication.PubMed_ID,"
" Phenotype.Pre_publication_description,"
" Phenotype.Post_publication_description,"
" Phenotype.Original_description,"
" Phenotype.Pre_publication_abbreviation,"
" Phenotype.Post_publication_abbreviation,"
" Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner,"
" Phenotype.Authorized_Users,"
" CAST(Publication.Authors AS BINARY),"
" Publication.Title, Publication.Abstract,"
" Publication.Journal,"
" Publication.Volume, Publication.Pages, Publication.Month,"
" Publication.Year, PublishXRef.Sequence, Phenotype.Units,"
" PublishXRef.comments"
" FROM"
" PublishXRef, Publication, Phenotype, PublishFreeze"
" WHERE"
" PublishXRef.Id = %(trait_name)s"
" AND Phenotype.Id = PublishXRef.PhenotypeId"
" AND Publication.Id = PublishXRef.PublicationId"
" AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId"
" AND PublishFreeze.Id =%(trait_dataset_id)s"),
trait_source)
def test_retrieve_probeset_trait_info(self):
"""Test retrieval of type `Probeset` traits."""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = tuple()
trait_source = {
"trait_name": "ProbeSetTraitName",
"trait_dataset_name": "ProbeSetDatasetTraitName"}
self.assertEqual(
retrieve_probeset_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
(
"SELECT "
"ProbeSet.name, ProbeSet.symbol, ProbeSet.description, "
"ProbeSet.probe_target_description, ProbeSet.chr, "
"ProbeSet.mb, ProbeSet.alias, ProbeSet.geneid, "
"ProbeSet.genbankid, ProbeSet.unigeneid, ProbeSet.omim, "
"ProbeSet.refseq_transcriptid, ProbeSet.blatseq, "
"ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, "
"ProbeSet.strand_probe, ProbeSet.strand_gene, "
"ProbeSet.probe_set_target_region, ProbeSet.proteinid, "
"ProbeSet.probe_set_specificity, "
"ProbeSet.probe_set_blat_score, "
"ProbeSet.probe_set_blat_mb_start, "
"ProbeSet.probe_set_blat_mb_end, "
"ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, "
"ProbeSet.flag "
"FROM "
"ProbeSet, ProbeSetFreeze, ProbeSetXRef "
"WHERE "
"ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id "
"AND ProbeSetXRef.ProbeSetId = ProbeSet.Id "
"AND ProbeSetFreeze.Name = %(trait_dataset_name)s "
"AND ProbeSet.Name = %(trait_name)s"), trait_source)
def test_retrieve_geno_trait_info(self):
"""Test retrieval of type `Geno` traits."""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = tuple()
trait_source = {
"trait_name": "GenoTraitName",
"trait_dataset_name": "GenoDatasetTraitName"}
self.assertEqual(
retrieve_geno_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
(
"SELECT "
"Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence "
"FROM "
"Geno, GenoFreeze, GenoXRef "
"WHERE "
"GenoXRef.GenoFreezeId = GenoFreeze.Id "
"AND GenoXRef.GenoId = Geno.Id "
"AND GenoFreeze.Name = %(trait_dataset_name)s "
"AND Geno.Name = %(trait_name)s"),
trait_source)
def test_retrieve_temp_trait_info(self):
"""Test retrieval of type `Temp` traits."""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = tuple()
trait_source = {"trait_name": "TempTraitName"}
self.assertEqual(
retrieve_temp_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
"SELECT name, description FROM Temp WHERE Name = %(trait_name)s",
trait_source)
def test_build_trait_name_with_good_fullnames(self):
"""
Check that the name is built correctly.
"""
for fullname, expected in [
["testdb::testname",
{"db": {"dataset_name": "testdb", "dataset_type": "ProbeSet"},
"trait_name": "testname", "cellid": "",
"trait_fullname": "testdb::testname"}],
["testdb::testname::testcell",
{"db": {"dataset_name": "testdb", "dataset_type": "ProbeSet"},
"trait_name": "testname", "cellid": "testcell",
"trait_fullname": "testdb::testname::testcell"}]]:
with self.subTest(fullname=fullname):
self.assertEqual(build_trait_name(fullname), expected)
def test_build_trait_name_with_bad_fullnames(self):
"""
Check that an exception is raised if the full name format is wrong.
"""
for fullname in ["", "test", "test:test"]:
with self.subTest(fullname=fullname):
with self.assertRaises(AssertionError, msg="Name format error"):
build_trait_name(fullname)
def test_retrieve_trait_info(self):
"""Test that information on traits is retrieved as appropriate."""
for threshold, trait_fullname, expected in [
[9, "pubDb::PublishTraitName::pubCell", {"haveinfo": 0}],
[5, "prbDb::ProbeSetTraitName::prbCell", {"haveinfo": 0}],
[12, "genDb::GenoTraitName", {"haveinfo": 0}],
[6, "tmpDb::TempTraitName", {"haveinfo": 0}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_fullname=trait_fullname):
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = tuple()
self.assertEqual(
retrieve_trait_info(
threshold, trait_fullname, db_mock),
expected)
def test_update_sample_data(self):
"""Test that the SQL queries when calling update_sample_data are called with
the right calls.
"""
# pylint: disable=C0103
db_mock = mock.MagicMock()
PUBLISH_DATA_SQL: str = (
"UPDATE PublishData SET value = %s "
"WHERE StrainId = %s AND Id = %s")
PUBLISH_SE_SQL: str = (
"UPDATE PublishSE SET error = %s "
"WHERE StrainId = %s AND DataId = %s")
N_STRAIN_SQL: str = (
"UPDATE NStrain SET count = %s "
"WHERE StrainId = %s AND DataId = %s")
with db_mock.cursor() as cursor:
type(cursor).rowcount = 1
mock_fetchone = mock.MagicMock()
mock_fetchone.return_value = (1, 1)
type(cursor).fetchone = mock_fetchone
self.assertEqual(update_sample_data(
conn=db_mock, strain_name="BXD11",
trait_name="1",
phenotype_id=10, value=18.7,
error=2.3, count=2),
(1, 1, 1))
cursor.execute.assert_has_calls(
[mock.call('SELECT Strain.Id, PublishData.Id FROM'
' (PublishData, Strain, PublishXRef, '
'PublishFreeze) LEFT JOIN PublishSE ON '
'(PublishSE.DataId = PublishData.Id '
'AND PublishSE.StrainId = '
'PublishData.StrainId) LEFT JOIN NStrain ON '
'(NStrain.DataId = PublishData.Id AND '
'NStrain.StrainId = PublishData.StrainId) WHERE '
'PublishXRef.InbredSetId = '
'PublishFreeze.InbredSetId AND PublishData.Id = '
'PublishXRef.DataId AND PublishXRef.Id = 1 AND '
'PublishXRef.PhenotypeId = 10 AND '
'PublishData.StrainId = Strain.Id AND '
'Strain.Name = "BXD11"'),
mock.call(PUBLISH_DATA_SQL, (18.7, 1, 1)),
mock.call(PUBLISH_SE_SQL, (2.3, 1, 1)),
mock.call(N_STRAIN_SQL, (2, 1, 1))]
)
def test_set_haveinfo_field(self):
"""Test that the `haveinfo` field is set up correctly"""
for trait_info, expected in [
[{}, {"haveinfo": 0}],
[{"k1": "v1"}, {"k1": "v1", "haveinfo": 1}]]:
with self.subTest(trait_info=trait_info, expected=expected):
self.assertEqual(set_haveinfo_field(trait_info), expected)
def test_set_homologene_id_field(self):
"""Test that the `homologene_id` field is set up correctly"""
for trait_type, trait_info, expected in [
["Publish", {}, {"homologeneid": None}],
["ProbeSet", {}, {"homologeneid": None}],
["Geno", {}, {"homologeneid": None}],
["Temp", {}, {"homologeneid": None}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_info=trait_info, expected=expected):
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = ()
self.assertEqual(
set_homologene_id_field(trait_type, trait_info, db_mock), expected)
def test_set_confidential_field(self):
"""Test that the `confidential` field is set up correctly"""
for trait_type, trait_info, expected in [
["Publish", {}, {"confidential": 0}],
["ProbeSet", {}, {}],
["Geno", {}, {}],
["Temp", {}, {}]]:
with self.subTest(trait_info=trait_info, expected=expected):
self.assertEqual(
set_confidential_field(trait_type, trait_info), expected)
def test_export_trait_data_dtype(self):
"""
Test `export_trait_data` with different values for the `dtype` keyword
argument
"""
for dtype, expected in [
["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["var", (None, None, None, None, None, None)],
["N", (None, None, None, None, None, None)],
["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
with self.subTest(dtype=dtype):
self.assertEqual(
export_trait_data(trait_data, samplelist, dtype=dtype),
expected)
def test_export_trait_data_dtype_all_flags(self):
"""
Test `export_trait_data` with different values for the `dtype` keyword
argument and the different flags set up
"""
for dtype, vflag, nflag, expected in [
["val", False, False,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["val", False, True,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["val", True, False,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["val", True, True,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["var", False, False, (None, None, None, None, None, None)],
["var", False, True, (None, None, None, None, None, None)],
["var", True, False, (None, None, None, None, None, None)],
["var", True, True, (None, None, None, None, None, None)],
["N", False, False, (None, None, None, None, None, None)],
["N", False, True, (None, None, None, None, None, None)],
["N", True, False, (None, None, None, None, None, None)],
["N", True, True, (None, None, None, None, None, None)],
["all", False, False,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["all", False, True,
(7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
8.30401, None, 7.80944, None)],
["all", True, False,
(7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
8.30401, None, 7.80944, None)],
["all", True, True,
(7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
]:
with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
self.assertEqual(
export_trait_data(
trait_data, samplelist, dtype=dtype, var_exists=vflag,
n_exists=nflag),
expected)
def test_export_informative(self):
"""Test that the function exports appropriate data."""
# pylint: disable=W0621
for trait_data, inc_var, expected in [
[{"data": {
"sample1": {
"sample_name": "sample1", "value": 9, "variance": None,
"ndata": 13
},
"sample2": {
"sample_name": "sample2", "value": 8, "variance": None,
"ndata": 13
},
"sample3": {
"sample_name": "sample3", "value": 7, "variance": None,
"ndata": 13
},
"sample4": {
"sample_name": "sample4", "value": 6, "variance": None,
"ndata": 13
},
}}, 0, (
("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
(None, None, None, None))],
[{"data": {
"sample1": {
"sample_name": "sample1", "value": 9, "variance": None,
"ndata": 13
},
"sample2": {
"sample_name": "sample2", "value": 8, "variance": None,
"ndata": 13
},
"sample3": {
"sample_name": "sample3", "value": None, "variance": None,
"ndata": 13
},
"sample4": {
"sample_name": "sample4", "value": 6, "variance": None,
"ndata": 13
},
}}, 0, (
("sample1", "sample2", "sample4"), (9, 8, 6),
(None, None, None))],
[{"data": {
"sample1": {
"sample_name": "sample1", "value": 9, "variance": None,
"ndata": 13
},
"sample2": {
"sample_name": "sample2", "value": 8, "variance": None,
"ndata": 13
},
"sample3": {
"sample_name": "sample3", "value": 7, "variance": None,
"ndata": 13
},
"sample4": {
"sample_name": "sample4", "value": 6, "variance": None,
"ndata": 13
},
}}, True, (tuple(), tuple(), tuple())],
[{"data": {
"sample1": {
"sample_name": "sample1", "value": 9, "variance": None,
"ndata": 13
},
"sample2": {
"sample_name": "sample2", "value": 8, "variance": 0.657,
"ndata": 13
},
"sample3": {
"sample_name": "sample3", "value": 7, "variance": None,
"ndata": 13
},
"sample4": {
"sample_name": "sample4", "value": 6, "variance": None,
"ndata": 13
},
}}, 0, (
("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
(None, 0.657, None, None))]]:
with self.subTest(trait_data=trait_data):
self.assertEqual(
export_informative(trait_data, inc_var), expected)
