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-rw-r--r--tests/unit/db/data/genotypes/genotype_sample1.geno23
-rw-r--r--tests/unit/db/test_datasets.py42
-rw-r--r--tests/unit/db/test_genotypes.py170
-rw-r--r--tests/unit/db/test_traits.py16
4 files changed, 224 insertions, 27 deletions
diff --git a/tests/unit/db/data/genotypes/genotype_sample1.geno b/tests/unit/db/data/genotypes/genotype_sample1.geno
new file mode 100644
index 0000000..2a55964
--- /dev/null
+++ b/tests/unit/db/data/genotypes/genotype_sample1.geno
@@ -0,0 +1,23 @@
+# File name: genotype_sample for testing
+
+# Metadata: Please retain this header information with file.
+
+
+@name: BXD
+@type: riset
+@mat: B
+@pat: D
+@het:H
+@unk: U
+
+
+
+
+
+
+Chr Locus cM Mb BXD1 BXD2 BXD5 BXD6 BXD8 BXD9
+1 rs31443144 1.50 3.010274 B B D D D B
+1 rs6269442 1.50 3.492195 B B D D H Y
+1 rs32285189 1.63 3.511204 B U D D D B
+2 rs31443144 1.50 3.010274 B B D D D B
+2 rs6269442 1.50 3.492195 B B D D H Y \ No newline at end of file
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py
index 38de0e2..39f4af9 100644
--- a/tests/unit/db/test_datasets.py
+++ b/tests/unit/db/test_datasets.py
@@ -3,10 +3,10 @@
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)
+ retrieve_group_fields,
+ retrieve_geno_group_fields,
+ retrieve_publish_group_fields,
+ retrieve_probeset_group_fields)
class TestDatasetsDBFunctions(TestCase):
"""Test cases for datasets functions."""
@@ -40,9 +40,9 @@ class TestDatasetsDBFunctions(TestCase):
table=table, cols=columns),
{"threshold": thresh, "name": dataset_name})
- def test_retrieve_probeset_riset_fields(self):
+ def test_retrieve_probeset_group_fields(self):
"""
- Test that the `riset` and `riset_id` fields are retrieved appropriately
+ Test that the `group` and `group_id` fields are retrieved appropriately
for the 'ProbeSet' trait type.
"""
for trait_name, expected in [
@@ -52,7 +52,7 @@ class TestDatasetsDBFunctions(TestCase):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
- retrieve_probeset_riset_fields(trait_name, db_mock),
+ retrieve_probeset_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
@@ -63,34 +63,34 @@ class TestDatasetsDBFunctions(TestCase):
" AND ProbeSetFreeze.Name = %(name)s"),
{"name": trait_name})
- def test_retrieve_riset_fields(self):
+ def test_retrieve_group_fields(self):
"""
- Test that the riset fields are set up correctly for the different trait
+ Test that the group 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": ""}],
+ {"dataset_name": "pubDBName01", "group": ""}],
["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"},
- {"dataset_name": "prbDBName01", "riset": ""}],
+ {"dataset_name": "prbDBName01", "group": ""}],
["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"},
- {"dataset_name": "genoDBName01", "riset": ""}],
- ["Temp", "tempTraitName01", {}, {"riset": ""}],
+ {"dataset_name": "genoDBName01", "group": ""}],
+ ["Temp", "tempTraitName01", {}, {"group": ""}],
]:
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)
+ cursor.execute.return_value = ("group_name", 0)
self.assertEqual(
- retrieve_riset_fields(
+ retrieve_group_fields(
trait_type, trait_name, dataset_info, db_mock),
expected)
- def test_retrieve_publish_riset_fields(self):
+ def test_retrieve_publish_group_fields(self):
"""
- Test that the `riset` and `riset_id` fields are retrieved appropriately
+ Test that the `group` and `group_id` fields are retrieved appropriately
for the 'Publish' trait type.
"""
for trait_name, expected in [
@@ -100,7 +100,7 @@ class TestDatasetsDBFunctions(TestCase):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
- retrieve_publish_riset_fields(trait_name, db_mock),
+ retrieve_publish_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
@@ -110,9 +110,9 @@ class TestDatasetsDBFunctions(TestCase):
" AND PublishFreeze.Name = %(name)s"),
{"name": trait_name})
- def test_retrieve_geno_riset_fields(self):
+ def test_retrieve_geno_group_fields(self):
"""
- Test that the `riset` and `riset_id` fields are retrieved appropriately
+ Test that the `group` and `group_id` fields are retrieved appropriately
for the 'Geno' trait type.
"""
for trait_name, expected in [
@@ -122,7 +122,7 @@ class TestDatasetsDBFunctions(TestCase):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
- retrieve_geno_riset_fields(trait_name, db_mock),
+ retrieve_geno_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py
new file mode 100644
index 0000000..c125224
--- /dev/null
+++ b/tests/unit/db/test_genotypes.py
@@ -0,0 +1,170 @@
+"""Tests gn3.db.genotypes"""
+from unittest import TestCase
+from gn3.db.genotypes import (
+ parse_genotype_file,
+ parse_genotype_labels,
+ parse_genotype_header,
+ parse_genotype_marker,
+ build_genotype_chromosomes)
+
+class TestGenotypes(TestCase):
+ """Tests for functions in `gn3.db.genotypes`."""
+
+ def test_parse_genotype_labels(self):
+ """Test that the genotype labels are parsed correctly."""
+ self.assertEqual(
+ parse_genotype_labels([
+ "@name: test_group\t", "@filler: test_filler ",
+ "@type:test_type", "@mat:test_mat \t", "@pat:test_pat ",
+ "@het: test_het ", "@unk: test_unk", "@other: test_other",
+ "@brrr: test_brrr "]),
+ (("group", "test_group"), ("filler", "test_filler"),
+ ("type", "test_type"), ("mat", "test_mat"), ("pat", "test_pat"),
+ ("het", "test_het"), ("unk", "test_unk")))
+
+ def test_parse_genotype_header(self):
+ """Test that the genotype header is parsed correctly."""
+ for header, expected in [
+ [("Chr\tLocus\tcM\tMb\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\t"
+ "BXD11\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18\tBXD19"),
+ (("Mbmap", True), ("cm_column", 2), ("mb_column", 3),
+ ("prgy",
+ ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11",
+ "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18",
+ "BXD19")),
+ ("nprgy", 14))],
+ [("Chr\tLocus\tcM\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\tBXD11"
+ "\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18"),
+ (("Mbmap", False), ("cm_column", 2), ("mb_column", None),
+ ("prgy",
+ ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11",
+ "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18")),
+ ("nprgy", 13))]]:
+ with self.subTest(header=header):
+ self.assertEqual(parse_genotype_header(header), expected)
+
+ def test_parse_genotype_data_line(self):
+ """Test parsing of data lines."""
+ for line, geno_obj, parlist, expected in [
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB",
+ {"mat": "test_mat", "pat": "test_pat", "het": "test_het",
+ "unk": "test_unk", "cm_column": 2, "Mbmap": True,
+ "mb_column": 3},
+ tuple(),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype",
+ ("U", "U", "U", "U", "U", "U", "U", "U", "U", "U")))],
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB",
+ {"mat": "test_mat", "pat": "test_pat", "het": "test_het",
+ "unk": "test_unk", "cm_column": 2, "Mbmap": True,
+ "mb_column": 3},
+ ("some", "parlist", "content"),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype",
+ (-1, 1, "U", "U", "U", "U", "U", "U", "U", "U")))],
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tH\tD\tB\tU\tD\tB\tB",
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": True, "mb_column": 3},
+ tuple(),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)))]]:
+ with self.subTest(line=line):
+ self.assertEqual(
+ parse_genotype_marker(line, geno_obj, parlist),
+ expected)
+
+ def test_build_genotype_chromosomes(self):
+ """
+ Given `markers` and `geno_obj`, test that `build_genotype_chromosomes`
+ builds a sequence of chromosomes with the given markers ordered
+ according to the `chr` value."""
+ for markers, geno_obj, expected in [
+ [[(("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1))),
+ (("chr", "2"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)))],
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": True, "mb_column": 3},
+ ((("name", "1"), ("mb_exists", True), ("cm_column", 2),
+ ("mb_column", 3),
+ ("loci",
+ ({"chr": "1", "name": "rs31443144", "cM": 2.0, "Mb": 3.0,
+ "genotype": (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)},))),
+ (("name", "2"), ("mb_exists", True), ("cm_column", 2),
+ ("mb_column", 3),
+ ("loci",
+ ({"chr": "2", "name": "rs31443144", "cM": 2.0, "Mb": 3.0,
+ "genotype": (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)},))))],
+ [[(("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", None),
+ ("genotype", (-1, 1, 1, 0, 1, -1, "U", 1, -1, -1)))],
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": False, "mb_column": None},
+ ((("name", "1"), ("mb_exists", False), ("cm_column", 2),
+ ("mb_column", None),
+ ("loci",
+ ({"chr": "1", "name": "rs31443144", "cM": 2.0, "Mb": None,
+ "genotype": (-1, 1, 1, 0, 1, -1, "U", 1, -1, -1)},))),)]]:
+ with self.subTest(markers=markers):
+ self.assertEqual(
+ build_genotype_chromosomes(geno_obj, markers),
+ expected)
+
+ def test_parse_genotype_file(self):
+ """Test the parsing of genotype files. """
+ self.assertEqual(
+ parse_genotype_file(
+ "tests/unit/db/data/genotypes/genotype_sample1.geno"),
+ {"group": "BXD",
+ "type": "riset",
+ "mat": "B",
+ "pat": "D",
+ "het": "H",
+ "unk": "U",
+ "Mbmap": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "prgy": ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9"),
+ "nprgy": 6,
+ "chromosomes": (
+ {"name": "1",
+ "mb_exists": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "loci": (
+ {"chr": "1",
+ "name": "rs31443144",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 1, -1)
+ },
+ {"chr": "1",
+ "name": "rs6269442",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 0, "U")},
+ {"chr": "1",
+ "name": "rs32285189",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, "U", 1, 1, 1, -1)})},
+ {"name": "2",
+ "mb_exists": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "loci": (
+ {"chr": "2",
+ "name": "rs31443144",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 1, -1)},
+ {"chr": "2",
+ "name": "rs6269442",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 0, "U")})})})
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index ee98893..8af8e82 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -166,15 +166,19 @@ class TestTraitsDBFunctions(TestCase):
the right calls.
"""
+ # pylint: disable=C0103
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")
+ 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 01:02:14 +0000