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authorFrederick Muriuki Muriithi2021-10-18 12:27:32 +0300
committerBonfaceKilz2021-10-19 16:33:32 +0300
commit42c56d330fdb51820c0fdcbb0b4376ff568ea009 (patch)
treee529977fd89cd4e1daaea92cd0d4e4c3d22a7922 /tests
parent679c3edd08453d2f1ef09b3461fd8d0b038b3adf (diff)
downloadgenenetwork3-42c56d330fdb51820c0fdcbb0b4376ff568ea009.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')
-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)