Check that all distances are positive or zero

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

* gn3/computations/slink.py: check that all distances between the 'somethings'
  are all either zero or positive.

* tests/unit/computations/test_slink.py:
  * Remove data with all distances positive or zero, since it would fail the
    test
  * Change the expected message to more closely correspond to the business
    logic

2 files changed, 13 insertions, 3 deletions

diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index 928330d..7d13d91 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -46,6 +46,16 @@ If the two distances are different, throw an exception."""
                      "should be the same in both directions.").format(
                          lists[i][j], lists[j][i]))
 
+def raise_valueerror_on_negative_distances(lists):
+    """Check that distances between 'somethings' are all positive, otherwise,
+raise an exception."""
+    def zero_or_positive(val):
+        return val >= 0;
+    # flatten lists
+    flattened = [distance for child in lists for distance in child]
+    if not all(map(zero_or_positive, flattened)):
+        raise ValueError("Distances should be positive.")
+
 def nearest(lists, i, j):
     """Computes some form of distance.
 This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64.
@@ -58,5 +68,6 @@ This description should be updated once the form/type of 'distance' identified."
     raise_lengtherror_if_child_lists_are_not_same_as_parent(lists)
     raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists)
     raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists)
+    raise_valueerror_on_negative_distances(lists)
     #### END: Guard Functions ####
     return None
diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py
index 207debf..6be3f33 100644
--- a/tests/unit/computations/test_slink.py
+++ b/tests/unit/computations/test_slink.py
@@ -55,15 +55,14 @@ class TestSlink(TestCase):
     def test_nearest_expects_zero_or_positive_distances(self):
         # Based on:
         # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L87-L89
-        for lst in [[[0,1,2,3],[1,0,3,4],[2,3,0,5],[3,4,5,0]],
-                    [[0,-1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]],
+        for lst in [[[0,-1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]],
                     [[0,1,-2,3],[1,0,3,4],[-2,3,0,5],[3,4,5,0]],
                     [[0,1,2,3],[1,0,-3,4],[2,-3,0,5],[3,4,5,0]],
                     [[0,1,2,-3],[1,0,3,4],[2,3,0,5],[-3,4,5,0]],
                     [[0,1,2,3],[1,0,3,-4],[2,3,0,5],[3,-4,5,0]],
                     [[0,1,2,3],[1,0,3,4],[2,3,0,-5],[3,4,-5,0]]]:
             with self.subTest(lst=lst):
-                with self.assertRaises(ValueError, msg="Got an unexpected negative value!"):
+                with self.assertRaises(ValueError, msg="Distances should be positive."):
                     nearest(lst, 1, 1)
 
     def test_nearest_with_expected(self):