diff options
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/db/test_traits.py | 89 | ||||
| -rw-r--r-- | tests/unit/test_heatmaps.py | 87 |
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. |