From 7e0229de746170458998e96abd9180450aac79df Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Wed, 7 Aug 2024 13:35:58 -0700
Subject: [PATCH] Fixed truthiness error that made the tsv writer ignore zero
 values

---
 src/koza/io/utils.py                       |  6 ++--
 tests/unit/test_io_utils.py                | 38 ++++++++++++++++++++++
 tests/unit/test_tsvwriter_node_and_edge.py | 30 +++++++++++++++--
 3 files changed, 69 insertions(+), 5 deletions(-)

diff --git a/src/koza/io/utils.py b/src/koza/io/utils.py
index b1b4ae3..c1b4455 100644
--- a/src/koza/io/utils.py
+++ b/src/koza/io/utils.py
@@ -144,7 +144,7 @@ def build_export_row(data: Dict, list_delimiter: str = None) -> Dict:
     tidy_data = {}
     for key, value in data.items():
         new_value = remove_null(value)
-        if new_value:
+        if new_value is not None:
             tidy_data[key] = _sanitize_export_property(key, new_value, list_delimiter)
     return tidy_data
 
@@ -221,14 +221,14 @@ def remove_null(input: Any) -> Any:
         new_value = []
         for v in input:
             x = remove_null(v)
-            if x:
+            if x is not None:
                 new_value.append(x)
     elif isinstance(input, dict):
         # value is a dict
         new_value = {}
         for k, v in input.items():
             x = remove_null(v)
-            if x:
+            if x is not None:
                 new_value[k] = x
     elif isinstance(input, str):
         # value is a str
diff --git a/tests/unit/test_io_utils.py b/tests/unit/test_io_utils.py
index c77c479..fe63168 100644
--- a/tests/unit/test_io_utils.py
+++ b/tests/unit/test_io_utils.py
@@ -96,3 +96,41 @@ def test_sanitize_export_property(query):
         assert query[1] == value
     else:
         assert query[1] in value
+
+
+@pytest.mark.parametrize(
+    "input, expected",
+    [
+        ([1, None, 2, "", 3, " "], [1, 2, 3]),
+        ({"a": 1, "b": None, "c": "", "d": 2, "e": " "}, {"a": 1, "d": 2}),
+        ({"a": [1, None, 2], "b": {"c": None, "d": 3}}, {"a": [1, 2], "b": {"d": 3}}),
+        ("test", "test"),
+        ("", None),
+        (None, None),
+        (5, 5),
+        (5.5, 5.5),
+        (True, True),
+        (False, False),
+        (0, 0),  # Ensure zeroes are not turned into None
+        ([0, None, 1], [0, 1]),  # Ensure zeroes in lists are not turned into None
+        ({"a": 0, "b": None}, {"a": 0}),  # Ensure zeroes in dicts are not turned into None
+    ],
+)
+def test_remove_null(input, expected):
+    assert remove_null(input) == expected
+
+
+@pytest.mark.parametrize(
+    "input, expected",
+    [
+        (None, True),
+        ("", True),
+        (" ", True),
+        ("non-empty string", False),
+        (0, False),
+        (False, False),
+        (True, False),
+    ],
+)
+def test_is_null(input, expected):
+    assert is_null(input) == expected
diff --git a/tests/unit/test_tsvwriter_node_and_edge.py b/tests/unit/test_tsvwriter_node_and_edge.py
index b0ac031..9456653 100644
--- a/tests/unit/test_tsvwriter_node_and_edge.py
+++ b/tests/unit/test_tsvwriter_node_and_edge.py
@@ -9,7 +9,7 @@ def test_tsv_writer():
     """
     Writes a test tsv file
     """
-    g = Gene(id="HGNC:11603", name="TBX4")
+    g = Gene(id="HGNC:11603", in_taxon=["NCBITaxon:9606"], symbol="TBX4")
     d = Disease(id="MONDO:0005002", name="chronic obstructive pulmonary disease")
     a = GeneToDiseaseAssociation(
         id="uuid:5b06e86f-d768-4cd9-ac27-abe31e95ab1e",
@@ -18,11 +18,23 @@ def test_tsv_writer():
         predicate="biolink:contributes_to",
         knowledge_level="not_provided",
         agent_type="not_provided",
+        has_count=0,
+        has_total=20,
     )
     ent = [g, d, a]
 
     node_properties = ["id", "category", "symbol", "in_taxon", "provided_by", "source"]
-    edge_properties = ["id", "subject", "predicate", "object", "category" "qualifiers", "publications", "provided_by"]
+    edge_properties = [
+        "id",
+        "subject",
+        "predicate",
+        "object",
+        "category" "qualifiers",
+        "has_count",
+        "has_total",
+        "publications",
+        "provided_by",
+    ]
 
     outdir = "output/tests"
     outfile = "tsvwriter-node-and-edge"
@@ -34,3 +46,17 @@ def test_tsv_writer():
     assert os.path.exists("{}/{}_nodes.tsv".format(outdir, outfile)) and os.path.exists(
         "{}/{}_edges.tsv".format(outdir, outfile)
     )
+
+    # read the node and edges tsv files and confirm the expected values
+    with open("{}/{}_nodes.tsv".format(outdir, outfile), "r") as f:
+        lines = f.readlines()
+        assert lines[1] == "HGNC:11603\tbiolink:Gene\t\tNCBITaxon:9606\t\tTBX4\n"
+        assert len(lines) == 3
+
+    with open("{}/{}_edges.tsv".format(outdir, outfile), "r") as f:
+        lines = f.readlines()
+        assert (
+            lines[1].strip()
+            == "uuid:5b06e86f-d768-4cd9-ac27-abe31e95ab1e\tHGNC:11603\tbiolink:contributes_to\tMONDO:0005002\t\t\t0\t20"
+        )
+        assert len(lines) == 2