update test

cancervariants · Jan 3, 2025 · 0718a49 · 0718a49
1 parent a4d09f9
commit 0718a49
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Showing 3 changed files with 21 additions and 7 deletions.
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -0,0 +1,5 @@
+"""Provide utilities for tests."""
+
+from pathlib import Path
+
+DATA_DIR = Path(__file__).resolve().parents[1] / "evidence" / "data"
diff --git a/tests/data_sources/test_cancer_hotspots.py b/tests/data_sources/test_cancer_hotspots.py
@@ -2,12 +2,14 @@
 
 import pytest
 from evidence.data_sources import CancerHotspots
+from tests.conftest import DATA_DIR
 
 
 @pytest.fixture(scope="module")
 def cancer_hotspots():
     """Create test fixture for cancer hotspots class"""
-    return CancerHotspots()
+    globbed = (DATA_DIR / "cancer_hotspots").glob("cancer_hotspots_*.json")
+    return CancerHotspots(transformed_data_path=sorted(globbed)[-1])
 
 
 @pytest.fixture(scope="module")
@@ -32,7 +34,7 @@ def check_source_meta(response):
 def test_mutation_hotspots(cancer_hotspots, braf_v600e):
     """Test that mutation_hotspots method works correctly."""
     resp = cancer_hotspots.mutation_hotspots(
-        "ga4gh:VA.mo-SCo1oC_8rUioVymmrlDjwewWzJUdt"
+        "ga4gh:VA.urVNVupVvzqE57gZFBu6vsAFScIBNojG"
     )
     assert resp.data == {
         "variation": "BRAF N486_A489delinsK",
@@ -44,7 +46,7 @@ def test_mutation_hotspots(cancer_hotspots, braf_v600e):
     }
 
     resp = cancer_hotspots.mutation_hotspots(
-        "ga4gh:VA.qiBmeiaWQpVa-NQbBk-tRb29arFXHlII"
+        "ga4gh:VA.iKBIyhCE-3Cnh5XJpVNZ4t0Ju8Ov8Ine"
     )
     assert resp.data == {
         "variation": "BRAF N486_P490del",
@@ -56,7 +58,7 @@ def test_mutation_hotspots(cancer_hotspots, braf_v600e):
     }
 
     resp = cancer_hotspots.mutation_hotspots(
-        "ga4gh:VA.4Wr6-Pw1TiTDxvYTSthJHz0sl52wb7Hq"
+        "ga4gh:VA.uIzxca0MnfZ1ni3NYNkvNh6Isw-5QXG9"
     )
     assert resp.data == {
         "variation": "TP53 I255del",
@@ -68,7 +70,7 @@ def test_mutation_hotspots(cancer_hotspots, braf_v600e):
     }
 
     resp = cancer_hotspots.mutation_hotspots(
-        "ga4gh:VA.0rVaYwX7S_-NenW_WQ5e7JoHQFkscWUS"
+        "ga4gh:VA.AM5oy_X7xBxJmWyUPJ0ZSLpRaTgu2kHt"
     )
     assert resp.data == {
         "variation": "CEBPA T310_Q311insKQNP",
@@ -80,7 +82,7 @@ def test_mutation_hotspots(cancer_hotspots, braf_v600e):
     }
 
     resp = cancer_hotspots.mutation_hotspots(
-        vrs_variation_id="ga4gh:VA.4XBXAxSAk-WyAu5H0S1-plrk_SCTW1PO"
+        vrs_variation_id="ga4gh:VA.j4XnsLZcdzDIYa5pvvXM7t1wn9OITr0L"
     ).model_dump(by_alias=True)
     assert resp["_id"] == "normalize.evidence:92f3db383a79d855323a71d65d860ec3"
     assert resp["data"] == braf_v600e

diff --git a/tests/data_sources/test_cbioportal.py b/tests/data_sources/test_cbioportal.py
@@ -2,12 +2,19 @@
 
 import pytest
 from evidence.data_sources import CBioPortal
+from tests.conftest import DATA_DIR
 
 
 @pytest.fixture(scope="module")
 def cbioportal():
     """Create test fixture for cbioportal class"""
-    return CBioPortal()
+    cbioportal_data_dir = DATA_DIR / "cbioportal"
+    return CBioPortal(
+        transformed_mutations_data_path=cbioportal_data_dir
+        / "msk_impact_2017_mutations.csv",
+        transformed_case_lists_data_path=cbioportal_data_dir
+        / "msk_impact_2017_case_lists.csv",
+    )
 
 
 @pytest.fixture(scope="module")