From 65fc51b4f997048990954fa5a7940d47f93d363c Mon Sep 17 00:00:00 2001
From: korikuzma <korikuzma@gmail.com>
Date: Mon, 1 Apr 2024 09:12:15 -0400
Subject: [PATCH] cleanup + fix test dir

---
 src/metakb/transform/moa.py                | 20 ++++++++++++--------
 tests/conftest.py                          |  3 +++
 tests/unit/transform/test_moa_transform.py |  4 ++--
 3 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/metakb/transform/moa.py b/src/metakb/transform/moa.py
index 5a8ac310..7abfb4ef 100644
--- a/src/metakb/transform/moa.py
+++ b/src/metakb/transform/moa.py
@@ -364,15 +364,14 @@ async def _get_variation_members(
             representation, if variation-normalizer was able to successfully normalize
         """
         members = None
-        chromosome = moa_rep_coord["chromosome"]
-        pos = moa_rep_coord["start_position"]
-        ref = moa_rep_coord["reference_allele"]
-        alt = moa_rep_coord["alternate_allele"]
-
-        if all(
-            (chromosome is not None, pos is not None, ref is not None, alt is not None)
-        ):
+        chromosome = moa_rep_coord.get("chromosome")
+        pos = moa_rep_coord.get("start_position")
+        ref = moa_rep_coord.get("reference_allele")
+        alt = moa_rep_coord.get("alternate_allele")
+
+        if all((chromosome, pos is not None, ref and ref != "-", alt and alt != "-")):
             gnomad_vcf = f"{chromosome}-{pos}-{ref}-{alt}"
+
             vrs_genomic_variation = await self.vicc_normalizers.normalize_variation(
                 [gnomad_vcf]
             )
@@ -386,6 +385,11 @@ async def _get_variation_members(
                     "Variation Normalizer unable to normalize genomic representation: %s",
                     gnomad_vcf,
                 )
+        else:
+            logger.debug(
+                "MOA does not provide enough information to create genomic representation: %s",
+                moa_rep_coord,
+            )
 
         return members
 
diff --git a/tests/conftest.py b/tests/conftest.py
index ae92289f..775d15d7 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,11 +1,14 @@
 """Module for pytest fixtures."""
 import json
 from copy import deepcopy
+from pathlib import Path
 
 import pytest
 
 from metakb.normalizers import ViccNormalizers
 
+TEST_DATA_DIR = Path(__file__).resolve().parents[0] / "data"
+
 
 @pytest.fixture(scope="session")
 def cetuximab_extensions():
diff --git a/tests/unit/transform/test_moa_transform.py b/tests/unit/transform/test_moa_transform.py
index c3c3e977..26c47be6 100644
--- a/tests/unit/transform/test_moa_transform.py
+++ b/tests/unit/transform/test_moa_transform.py
@@ -3,11 +3,11 @@
 
 import pytest
 import pytest_asyncio
+from tests.conftest import TEST_DATA_DIR
 
-from metakb import PROJECT_ROOT
 from metakb.transform.moa import MoaTransform
 
-DATA_DIR = PROJECT_ROOT / "tests" / "data" / "transform"
+DATA_DIR = TEST_DATA_DIR / "transform"
 FILENAME = "moa_cdm.json"