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-rw-r--r--tests/unit/db/test_traits.py89
-rw-r--r--tests/unit/test_heatmaps.py87
2 files changed, 89 insertions, 87 deletions
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 8af8e82..0c4ef78 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -2,6 +2,7 @@
from unittest import mock, TestCase
from gn3.db.traits import (
build_trait_name,
+ export_trait_data,
set_haveinfo_field,
update_sample_data,
retrieve_trait_info,
@@ -12,6 +13,38 @@ from gn3.db.traits import (
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"
@@ -226,3 +259,59 @@ class TestTraitsDBFunctions(TestCase):
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)
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
index 7b66688..03fd4a6 100644
--- a/tests/unit/test_heatmaps.py
+++ b/tests/unit/test_heatmaps.py
@@ -4,43 +4,12 @@ from gn3.heatmaps import (
cluster_traits,
get_loci_names,
get_lrs_from_chr,
- export_trait_data,
compute_traits_order,
retrieve_samples_and_values,
process_traits_data_for_heatmap)
from tests.unit.sample_test_data import organised_trait_1, organised_trait_2
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}}}
slinked = (
(((0, 2, 0.16381088984330505),
@@ -55,62 +24,6 @@ slinked = (
class TestHeatmap(TestCase):
"""Class for testing heatmap computation functions"""
- 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_cluster_traits(self):
"""
Test that the clustering is working as expected.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 13:42:07 +0000