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-rw-r--r--tests/unit/db/test_datasets.py133
-rw-r--r--tests/unit/db/test_traits.py193
2 files changed, 269 insertions, 57 deletions
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py
new file mode 100644
index 0000000..38de0e2
--- /dev/null
+++ b/tests/unit/db/test_datasets.py
@@ -0,0 +1,133 @@
+"""Tests for gn3/db/datasets.py"""
+
+from unittest import mock, TestCase
+from gn3.db.datasets import (
+ retrieve_dataset_name,
+ retrieve_riset_fields,
+ retrieve_geno_riset_fields,
+ retrieve_publish_riset_fields,
+ retrieve_probeset_riset_fields)
+
+class TestDatasetsDBFunctions(TestCase):
+ """Test cases for datasets functions."""
+
+ def test_retrieve_dataset_name(self):
+ """Test that the function is called correctly."""
+ for trait_type, thresh, trait_name, dataset_name, columns, table in [
+ ["ProbeSet", 9, "probesetTraitName", "probesetDatasetName",
+ "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"],
+ ["Geno", 3, "genoTraitName", "genoDatasetName",
+ "Id, Name, FullName, ShortName", "GenoFreeze"],
+ ["Publish", 6, "publishTraitName", "publishDatasetName",
+ "Id, Name, FullName, ShortName", "PublishFreeze"],
+ ["Temp", 4, "tempTraitName", "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 = {}
+ self.assertEqual(
+ retrieve_dataset_name(
+ trait_type, thresh, trait_name, dataset_name, db_mock),
+ {})
+ cursor.execute.assert_called_once_with(
+ "SELECT {cols} "
+ "FROM {table} "
+ "WHERE public > %(threshold)s AND "
+ "(Name = %(name)s "
+ "OR FullName = %(name)s "
+ "OR ShortName = %(name)s)".format(
+ table=table, cols=columns),
+ {"threshold": thresh, "name": dataset_name})
+
+ def test_retrieve_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(
+ retrieve_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_retrieve_riset_fields(self):
+ """
+ Test that the riset fields are set up correctly for the different trait
+ types.
+ """
+ for trait_type, trait_name, dataset_info, expected in [
+ ["Publish", "pubTraitName01", {"dataset_name": "pubDBName01"},
+ {"dataset_name": "pubDBName01", "riset": ""}],
+ ["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"},
+ {"dataset_name": "prbDBName01", "riset": ""}],
+ ["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"},
+ {"dataset_name": "genoDBName01", "riset": ""}],
+ ["Temp", "tempTraitName01", {}, {"riset": ""}],
+ ]:
+ db_mock = mock.MagicMock()
+ with self.subTest(
+ trait_type=trait_type, trait_name=trait_name,
+ dataset_info=dataset_info):
+ with db_mock.cursor() as cursor:
+ cursor.execute.return_value = ("riset_name", 0)
+ self.assertEqual(
+ retrieve_riset_fields(
+ trait_type, trait_name, dataset_info, db_mock),
+ expected)
+
+ def test_retrieve_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(
+ retrieve_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_retrieve_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(
+ retrieve_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 c8f28b5..ee98893 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -1,51 +1,20 @@
"""Tests for gn3/db/traits.py"""
from unittest import mock, TestCase
from gn3.db.traits import (
- GENO_TRAIT_INFO_QUERY,
- TEMP_TRAIT_INFO_QUERY,
- PUBLISH_TRAIT_INFO_QUERY,
- PROBESET_TRAIT_INFO_QUERY)
-from gn3.db.traits import (
+ build_trait_name,
+ 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_trait_dataset_name,
retrieve_publish_trait_info,
- retrieve_probeset_trait_info,
- update_sample_data)
-
+ 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 in [
- ["ProbeSet", 9, "testName",
- "Id, Name, FullName, ShortName, DataScale"],
- ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"],
- ["Publish", 6, "publishTraitName",
- "Id, Name, FullName, ShortName"],
- ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName"]]:
- 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 {cols} "
- "FROM {ttype}Freeze "
- "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})
-
def test_retrieve_publish_trait_info(self):
"""Test retrieval of type `Publish` traits."""
db_mock = mock.MagicMock()
@@ -54,12 +23,32 @@ class TestTraitsDBFunctions(TestCase):
trait_source = {
"trait_name": "PublishTraitName", "trait_dataset_id": 1}
self.assertEqual(
- retrieve_publish_trait_info(
- trait_source,
- db_mock),
- tuple())
+ retrieve_publish_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- PUBLISH_TRAIT_INFO_QUERY, trait_source)
+ ("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."""
@@ -70,9 +59,31 @@ class TestTraitsDBFunctions(TestCase):
"trait_name": "ProbeSetTraitName",
"trait_dataset_name": "ProbeSetDatasetTraitName"}
self.assertEqual(
- retrieve_probeset_trait_info(trait_source, db_mock), tuple())
+ retrieve_probeset_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- PROBESET_TRAIT_INFO_QUERY, trait_source)
+ (
+ "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."""
@@ -83,9 +94,19 @@ class TestTraitsDBFunctions(TestCase):
"trait_name": "GenoTraitName",
"trait_dataset_name": "GenoDatasetTraitName"}
self.assertEqual(
- retrieve_geno_trait_info(trait_source, db_mock), tuple())
+ retrieve_geno_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- GENO_TRAIT_INFO_QUERY, trait_source)
+ (
+ "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."""
@@ -94,26 +115,51 @@ class TestTraitsDBFunctions(TestCase):
cursor.fetchone.return_value = tuple()
trait_source = {"trait_name": "TempTraitName"}
self.assertEqual(
- retrieve_temp_trait_info(trait_source, db_mock), tuple())
+ retrieve_temp_trait_info(trait_source, db_mock), {})
cursor.execute.assert_called_once_with(
- TEMP_TRAIT_INFO_QUERY, trait_source)
+ "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 trait_type, trait_name, trait_dataset_id, trait_dataset_name, in [
- ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"],
- ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"],
- ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"],
- ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]:
+ 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_type=trait_type):
+ with self.subTest(trait_fullname=trait_fullname):
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),
- tuple())
+ 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
@@ -143,3 +189,36 @@ class TestTraitsDBFunctions(TestCase):
mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)),
mock.call(N_STRAIN_SQL, (2, 10, 8967049))]
)
+
+ 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)