Migrate `export_informative` function

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi

* gn3/partial_correlations.py: Implement a mostly, bug-compatible
  `export_informative` function as part of migrating the partial correlations
  feature over to GN3 from GN1
* tests/unit/test_partial_correlations.py: Implement tests to ensure the code
  work in a similar manner as that one in GN1.

2 files changed, 124 insertions, 0 deletions

diff --git a/gn3/partial_correlations.py b/gn3/partial_correlations.py
new file mode 100644
index 0000000..8c37886
--- /dev/null
+++ b/gn3/partial_correlations.py
@@ -0,0 +1,32 @@
+"""
+This module deals with partial correlations.
+
+It is an attempt to migrate over the partial correlations feature from
+GeneNetwork1.
+"""
+
+from functools import reduce
+
+def export_informative(trait_data: dict, inc_var: bool = False) -> tuple:
+    """
+    Export informative strain
+
+    This is a migration of the `exportInformative` function in
+    web/webqtl/base/webqtlTrait.py module in GeneNetwork1.
+
+    There is a chance that the original implementation has a bug, especially
+    dealing with the `inc_var` value. It the `inc_var` value is meant to control
+    the inclusion of the `variance` value, then the current implementation, and
+    that one in GN1 have a bug.
+    """
+    def __exporter__(acc, data_item):
+        if not inc_var or data_item["variance"] is not None:
+            return (
+                acc[0] + (data_item["sample_name"],),
+                acc[1] + (data_item["value"],),
+                acc[2] + (data_item["variance"],))
+        return acc
+    return reduce(
+        __exporter__,
+        filter(lambda td: td["value"] is not None, trait_data["data"].values()),
+        (tuple(), tuple(), tuple()))
diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py
new file mode 100644
index 0000000..6eea078
--- /dev/null
+++ b/tests/unit/test_partial_correlations.py
@@ -0,0 +1,92 @@
+"""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)