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authorFrederick Muriuki Muriithi2021-10-18 12:27:32 +0300
committerFrederick Muriuki Muriithi2021-10-18 12:27:32 +0300
commit94ca79045baf978d6aab964c7c70b84911c1124f (patch)
tree35627e25d9d7073c9c06258e3fafb114b69e9dd4 /tests/unit
parent157df453cdb84591cb44af9f1d2677cd0b2c0380 (diff)
downloadgenenetwork3-94ca79045baf978d6aab964c7c70b84911c1124f.tar.gz
Move `export_informative` function to `gn3.db.traits` module
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/traits.py: Move `export_informative` function here * gn3/partial_correlations.py: Remove `export_informative` function * tests/unit/db/test_traits.py: Move `export_informative` function tests here * tests/unit/test_partial_correlations.py: Remove `export_informative` function tests The `export_informative` function relates more to the traits than to the partial correlations, and could find use in more than just the partial correlations stuff. This commit moves the function to the more traits-specific `gn3.db.traits` module.
Diffstat (limited to 'tests/unit')
-rw-r--r--tests/unit/db/test_traits.py86
-rw-r--r--tests/unit/test_partial_correlations.py87
2 files changed, 87 insertions, 86 deletions
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 0c4ef78..67f0c6f 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -3,6 +3,7 @@ from unittest import mock, TestCase
from gn3.db.traits import (
build_trait_name,
export_trait_data,
+ export_informative,
set_haveinfo_field,
update_sample_data,
retrieve_trait_info,
@@ -315,3 +316,88 @@ class TestTraitsDBFunctions(TestCase):
trait_data, samplelist, dtype=dtype, var_exists=vflag,
n_exists=nflag),
expected)
+
+ def test_export_informative(self):
+ """Test that the function exports appropriate data."""
+ for trait_data, inc_var, expected in [
+ [{"data": {
+ "sample1": {
+ "sample_name": "sample1", "value": 9, "variance": None,
+ "ndata": 13
+ },
+ "sample2": {
+ "sample_name": "sample2", "value": 8, "variance": None,
+ "ndata": 13
+ },
+ "sample3": {
+ "sample_name": "sample3", "value": 7, "variance": None,
+ "ndata": 13
+ },
+ "sample4": {
+ "sample_name": "sample4", "value": 6, "variance": None,
+ "ndata": 13
+ },
+ }}, 0, (
+ ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
+ (None, None, None, None))],
+ [{"data": {
+ "sample1": {
+ "sample_name": "sample1", "value": 9, "variance": None,
+ "ndata": 13
+ },
+ "sample2": {
+ "sample_name": "sample2", "value": 8, "variance": None,
+ "ndata": 13
+ },
+ "sample3": {
+ "sample_name": "sample3", "value": None, "variance": None,
+ "ndata": 13
+ },
+ "sample4": {
+ "sample_name": "sample4", "value": 6, "variance": None,
+ "ndata": 13
+ },
+ }}, 0, (
+ ("sample1", "sample2", "sample4"), (9, 8, 6),
+ (None, None, None))],
+ [{"data": {
+ "sample1": {
+ "sample_name": "sample1", "value": 9, "variance": None,
+ "ndata": 13
+ },
+ "sample2": {
+ "sample_name": "sample2", "value": 8, "variance": None,
+ "ndata": 13
+ },
+ "sample3": {
+ "sample_name": "sample3", "value": 7, "variance": None,
+ "ndata": 13
+ },
+ "sample4": {
+ "sample_name": "sample4", "value": 6, "variance": None,
+ "ndata": 13
+ },
+ }}, True, (tuple(), tuple(), tuple())],
+ [{"data": {
+ "sample1": {
+ "sample_name": "sample1", "value": 9, "variance": None,
+ "ndata": 13
+ },
+ "sample2": {
+ "sample_name": "sample2", "value": 8, "variance": 0.657,
+ "ndata": 13
+ },
+ "sample3": {
+ "sample_name": "sample3", "value": 7, "variance": None,
+ "ndata": 13
+ },
+ "sample4": {
+ "sample_name": "sample4", "value": 6, "variance": None,
+ "ndata": 13
+ },
+ }}, 0, (
+ ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
+ (None, 0.657, None, None))]]:
+ with self.subTest(trait_data=trait_data):
+ self.assertEqual(
+ export_informative(trait_data, inc_var), expected)
diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py
index 6eea078..f204d4f 100644
--- a/tests/unit/test_partial_correlations.py
+++ b/tests/unit/test_partial_correlations.py
@@ -1,92 +1,7 @@
"""Module contains tests for gn3.partial_correlations"""
from unittest import TestCase
-from gn3.partial_correlations import export_informative
+
class TestPartialCorrelations(TestCase):
"""Class for testing partial correlations computation functions"""
-
- def test_export_informative(self):
- """Test that the function exports appropriate data."""
- for trait_data, inc_var, expected in [
- [{"data": {
- "sample1": {
- "sample_name": "sample1", "value": 9, "variance": None,
- "ndata": 13
- },
- "sample2": {
- "sample_name": "sample2", "value": 8, "variance": None,
- "ndata": 13
- },
- "sample3": {
- "sample_name": "sample3", "value": 7, "variance": None,
- "ndata": 13
- },
- "sample4": {
- "sample_name": "sample4", "value": 6, "variance": None,
- "ndata": 13
- },
- }}, 0, (
- ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
- (None, None, None, None))],
- [{"data": {
- "sample1": {
- "sample_name": "sample1", "value": 9, "variance": None,
- "ndata": 13
- },
- "sample2": {
- "sample_name": "sample2", "value": 8, "variance": None,
- "ndata": 13
- },
- "sample3": {
- "sample_name": "sample3", "value": None, "variance": None,
- "ndata": 13
- },
- "sample4": {
- "sample_name": "sample4", "value": 6, "variance": None,
- "ndata": 13
- },
- }}, 0, (
- ("sample1", "sample2", "sample4"), (9, 8, 6),
- (None, None, None))],
- [{"data": {
- "sample1": {
- "sample_name": "sample1", "value": 9, "variance": None,
- "ndata": 13
- },
- "sample2": {
- "sample_name": "sample2", "value": 8, "variance": None,
- "ndata": 13
- },
- "sample3": {
- "sample_name": "sample3", "value": 7, "variance": None,
- "ndata": 13
- },
- "sample4": {
- "sample_name": "sample4", "value": 6, "variance": None,
- "ndata": 13
- },
- }}, True, (tuple(), tuple(), tuple())],
- [{"data": {
- "sample1": {
- "sample_name": "sample1", "value": 9, "variance": None,
- "ndata": 13
- },
- "sample2": {
- "sample_name": "sample2", "value": 8, "variance": 0.657,
- "ndata": 13
- },
- "sample3": {
- "sample_name": "sample3", "value": 7, "variance": None,
- "ndata": 13
- },
- "sample4": {
- "sample_name": "sample4", "value": 6, "variance": None,
- "ndata": 13
- },
- }}, 0, (
- ("sample1", "sample2", "sample3", "sample4"), (9, 8, 7, 6),
- (None, 0.657, None, None))]]:
- with self.subTest(trait_data=trait_data):
- self.assertEqual(
- export_informative(trait_data, inc_var), expected)