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"""Tests for gn3/db/traits.py"""
from unittest import mock, TestCase
from gn3.db.traits import (
set_riset_fields,
set_haveinfo_field,
update_sample_data,
retrieve_trait_info,
set_geno_riset_fields,
set_confidential_field,
set_homologene_id_field,
retrieve_geno_trait_info,
retrieve_temp_trait_info,
set_publish_riset_fields,
set_probeset_riset_fields,
retrieve_trait_dataset_name,
retrieve_publish_trait_info,
retrieve_probeset_trait_info)
class TestTraitsDBFunctions(TestCase):
"Test cases for traits functions"
def test_retrieve_trait_dataset_name(self):
"""Test that the function is called correctly."""
for trait_type, thresh, trait_dataset_name, columns, table in [
["ProbeSet", 9, "testName",
"Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"],
["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName",
"GenoFreeze"],
["Publish", 6, "publishTraitName",
"Id, Name, FullName, ShortName", "PublishFreeze"],
["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName",
"TempFreeze"]]:
db_mock = mock.MagicMock()
with self.subTest(trait_type=trait_type):
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = (
"testName", "testNameFull", "testNameShort",
"dataScale")
self.assertEqual(
retrieve_trait_dataset_name(
trait_type, thresh, trait_dataset_name, db_mock),
("testName", "testNameFull", "testNameShort",
"dataScale"))
cursor.execute.assert_called_once_with(
"SELECT %(columns)s "
"FROM %(table)s "
"WHERE public > %(threshold)s AND "
"(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format(
cols=columns, ttype=trait_type),
{"threshold": thresh, "name": trait_dataset_name,
"table": table, "columns": columns})
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_retrieve_trait_info(self):
"""Test that information on traits is retrieved as appropriate."""
for trait_type, trait_name, trait_dataset_id, trait_dataset_name, expected in [
["Publish", "PublishTraitName", 1, "PublishDatasetTraitName",
{"haveinfo": 0, "homologeneid": None, "type": "Publish",
"confidential": 0}],
["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName",
{"haveinfo": 0, "homologeneid": None, "type": "ProbeSet"}],
["Geno", "GenoTraitName", 3, "GenoDatasetTraitName",
{"haveinfo": 0, "homologeneid": None, "type": "Geno"}],
["Temp", "TempTraitName", 4, "TempDatasetTraitName",
{"haveinfo": 0, "homologeneid": None, "type": "Temp"}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_type=trait_type):
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = tuple()
self.assertEqual(
retrieve_trait_info(
trait_type, trait_name, trait_dataset_id,
trait_dataset_name, 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.
"""
db_mock = mock.MagicMock()
STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s"
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
self.assertEqual(update_sample_data(
conn=db_mock, strain_name="BXD11",
strain_id=10, publish_data_id=8967049,
value=18.7, error=2.3, count=2),
(1, 1, 1, 1))
cursor.execute.assert_has_calls(
[mock.call(STRAIN_ID_SQL, ('BXD11', 10)),
mock.call(PUBLISH_DATA_SQL, (18.7, 10, 8967049)),
mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)),
mock.call(N_STRAIN_SQL, (2, 10, 8967049))]
)
def test_set_haveinfo_field(self):
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):
for trait_info, expected in [
[{"type": "Publish"},
{"type": "Publish", "homologeneid": None}],
[{"type": "ProbeSet"},
{"type": "ProbeSet", "homologeneid": None}],
[{"type": "Geno"}, {"type": "Geno", "homologeneid": None}],
[{"type": "Temp"}, {"type": "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_info, db_mock), expected)
def test_set_confidential_field(self):
for trait_info, expected in [
[{"type": "Publish"}, {"type": "Publish", "confidential": 0}],
[{"type": "ProbeSet"}, {"type": "ProbeSet"}],
[{"type": "Geno"}, {"type": "Geno"}],
[{"type": "Temp"}, {"type": "Temp"}]]:
with self.subTest(trait_info=trait_info, expected=expected):
self.assertEqual(
set_confidential_field(trait_info), expected)
def test_set_geno_riset_fields(self):
"""
Test that the `riset` and `riset_id` fields are retrieved appropriately
for the 'Geno' trait type.
"""
for trait_name, expected in [
["testGenoName", ()]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
set_geno_riset_fields(trait_name, db_mock), expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, GenoFreeze"
" WHERE GenoFreeze.InbredSetId = InbredSet.Id"
" AND GenoFreeze.Name = %(name)s"),
{"name": trait_name})
def test_set_publish_riset_fields(self):
"""
Test that the `riset` and `riset_id` fields are retrieved appropriately
for the 'Publish' trait type.
"""
for trait_name, expected in [
["testPublishName", ()]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
set_publish_riset_fields(trait_name, db_mock), expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, PublishFreeze"
" WHERE PublishFreeze.InbredSetId = InbredSet.Id"
" AND PublishFreeze.Name = %(name)s"),
{"name": trait_name})
def test_set_probeset_riset_fields(self):
"""
Test that the `riset` and `riset_id` fields are retrieved appropriately
for the 'ProbeSet' trait type.
"""
for trait_name, expected in [
["testProbeSetName", ()]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
set_probeset_riset_fields(trait_name, db_mock), expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, ProbeSetFreeze, ProbeFreeze"
" WHERE ProbeFreeze.InbredSetId = InbredSet.Id"
" AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId"
" AND ProbeSetFreeze.Name = %(name)s"),
{"name": trait_name})
def test_set_riset_fields(self):
"""
Test that the riset fields are set up correctly for the different trait
types.
"""
for trait_info, expected in [
[{}, {}],
[{"haveinfo": 0, "type": "Publish"},
{"haveinfo": 0, "type": "Publish"}],
[{"haveinfo": 0, "type": "ProbeSet"},
{"haveinfo": 0, "type": "ProbeSet"}],
[{"haveinfo": 0, "type": "Geno"},
{"haveinfo": 0, "type": "Geno"}],
[{"haveinfo": 0, "type": "Temp"},
{"haveinfo": 0, "type": "Temp"}],
[{"haveinfo": 1, "type": "Publish", "name": "test"},
{"haveinfo": 1, "type": "Publish", "name": "test",
"riset": "riset_name", "risetid": 0}],
[{"haveinfo": 1, "type": "ProbeSet", "name": "test"},
{"haveinfo": 1, "type": "ProbeSet", "name": "test",
"riset": "riset_name", "risetid": 0}],
[{"haveinfo": 1, "type": "Geno", "name": "test"},
{"haveinfo": 1, "type": "Geno", "name": "test",
"riset": "riset_name", "risetid": 0}],
[{"haveinfo": 1, "type": "Temp", "name": "test"},
{"haveinfo": 1, "type": "Temp", "name": "test", "riset": None,
"risetid": None}]
]:
db_mock = mock.MagicMock()
with self.subTest(trait_info=trait_info, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ("riset_name", 0)
self.assertEqual(
set_riset_fields(trait_info, db_mock), expected)
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