aboutsummaryrefslogtreecommitdiff
path: root/tests/unit
diff options
context:
space:
mode:
Diffstat (limited to 'tests/unit')
-rw-r--r--tests/unit/db/test_datasets.py133
-rw-r--r--tests/unit/db/test_traits.py196
2 files changed, 161 insertions, 168 deletions
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py
new file mode 100644
index 0000000..34fe7f0
--- /dev/null
+++ b/tests/unit/db/test_datasets.py
@@ -0,0 +1,133 @@
+from unittest import mock, TestCase
+
+class TestDatasetsDBFunctions(TestCase):
+
+ 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_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)
+
+ 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_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})
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 39d7a31..7d161bf 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -2,55 +2,19 @@
from unittest import mock, TestCase
from gn3.db.traits import (
build_trait_name,
- 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()
@@ -159,10 +123,10 @@ class TestTraitsDBFunctions(TestCase):
def test_build_trait_name_with_good_fullnames(self):
for fullname, expected in [
["testdb::testname",
- {"trait_db": "testdb", "trait_name": "testname", "cellid": "",
- "trait_fullname": "testdb::testname"}],
+ {"db": {"dataset_name": "testdb"}, "trait_name": "testname",
+ "cellid": "", "trait_fullname": "testdb::testname"}],
["testdb::testname::testcell",
- {"trait_db": "testdb", "trait_name": "testname",
+ {"db": {"dataset_name": "testdb"}, "trait_name": "testname",
"cellid": "testcell",
"trait_fullname": "testdb::testname::testcell"}]]:
with self.subTest(fullname=fullname):
@@ -176,26 +140,26 @@ class TestTraitsDBFunctions(TestCase):
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", "pubDb::PublishTraitName::pubCell", 1,
- "PublishDatasetTraitName",
+ for trait_type, threshold, trait_fullname, expected in [
+ ["Publish", 9, "pubDb::PublishTraitName::pubCell",
{"haveinfo": 0, "homologeneid": None, "type": "Publish",
- "confidential": 0, "trait_db": "pubDb",
+ "confidential": 0, "db": {"dataset_name": "pubDb"},
"trait_name": "PublishTraitName", "cellid": "pubCell",
"trait_fullname": "pubDb::PublishTraitName::pubCell"}],
- ["ProbeSet", "prbDb::ProbeSetTraitName::prbCell", 2,
- "ProbeSetDatasetTraitName",
+ ["ProbeSet", 5, "prbDb::ProbeSetTraitName::prbCell",
{"haveinfo": 0, "homologeneid": None, "type": "ProbeSet",
"trait_fullname": "prbDb::ProbeSetTraitName::prbCell",
- "trait_db": "prbDb", "trait_name": "ProbeSetTraitName",
- "cellid": "prbCell"}],
- ["Geno", "genDb::GenoTraitName", 3, "GenoDatasetTraitName",
+ "db": {"dataset_name": "prbDb"},
+ "trait_name": "ProbeSetTraitName", "cellid": "prbCell"}],
+ ["Geno", 12, "genDb::GenoTraitName",
{"haveinfo": 0, "homologeneid": None, "type": "Geno",
- "trait_fullname": "genDb::GenoTraitName", "trait_db": "genDb",
+ "trait_fullname": "genDb::GenoTraitName",
+ "db": {"dataset_name": "genDb"},
"trait_name": "GenoTraitName", "cellid": ""}],
- ["Temp", "tmpDb::TempTraitName", 4, "TempDatasetTraitName",
+ ["Temp", 6, "tmpDb::TempTraitName",
{"haveinfo": 0, "homologeneid": None, "type": "Temp",
- "trait_fullname": "tmpDb::TempTraitName", "trait_db": "tmpDb",
+ "trait_fullname": "tmpDb::TempTraitName",
+ "db": {"dataset_name": "tmpDb"},
"trait_name": "TempTraitName", "cellid": ""}]]:
db_mock = mock.MagicMock()
with self.subTest(trait_type=trait_type):
@@ -203,8 +167,7 @@ class TestTraitsDBFunctions(TestCase):
cursor.fetchone.return_value = tuple()
self.assertEqual(
retrieve_trait_info(
- trait_type, trait_name, trait_dataset_id,
- trait_dataset_name, db_mock),
+ trait_type, threshold, trait_fullname, db_mock),
expected)
def test_update_sample_data(self):
@@ -246,128 +209,25 @@ class TestTraitsDBFunctions(TestCase):
def test_set_homologene_id_field(self):
"""Test that the `homologene_id` field is set up correctly"""
- 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}]]:
+ 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_info, db_mock), expected)
+ 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_info, expected in [
- [{"type": "Publish"}, {"type": "Publish", "confidential": 0}],
- [{"type": "ProbeSet"}, {"type": "ProbeSet"}],
- [{"type": "Geno"}, {"type": "Geno"}],
- [{"type": "Temp"}, {"type": "Temp"}]]:
+ 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_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)
+ set_confidential_field(trait_type, trait_info), expected)
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 12:37:57 +0000