tests: fix test data dir + update param name change (#319)

tests/conftest.py

@@ -1,11 +1,16 @@
 """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"
+TEST_HARVESTERS_DIR = TEST_DATA_DIR / "harvesters"
+TEST_TRANSFORM_DIR = TEST_DATA_DIR / "transform"
+
 
 @pytest.fixture(scope="session")
 def cetuximab_extensions():

tests/unit/database/test_database.py

@@ -207,7 +207,7 @@ def test_gene_rules(
     """Verify property and relationship rules for Gene nodes."""
     check_unique_property("Gene", "id")
     check_relation_count(
-        "Gene", "Study", "HAS_GENE_CONTEXT", direction="in", min=1, max=None
+        "Gene", "Study", "HAS_GENE_CONTEXT", direction="in", min_rels=1, max_rels=None
     )
 
     expected_labels = [{"Gene"}]
@@ -244,15 +244,15 @@ def test_variation_rules(
         "CategoricalVariation",
         "HAS_DEFINING_CONTEXT",
         direction="in",
-        min=0,
-        max=None,
+        min_rels=0,
+        max_rels=None,
     )
     check_relation_count(
         "Variation",
         "CategoricalVariation",
         "HAS_MEMBERS",
-        min=0,
-        max=None,
+        min_rels=0,
+        max_rels=None,
         direction="in",
     )
 
@@ -315,10 +315,10 @@ def test_categorical_variation_rules(
     """Verify property and relationship rules for Categorical Variation nodes."""
     check_unique_property("CategoricalVariation", "id")
     check_relation_count(
-        "CategoricalVariation", "Variation", "HAS_DEFINING_CONTEXT", max=1
+        "CategoricalVariation", "Variation", "HAS_DEFINING_CONTEXT", max_rels=1
     )
     check_relation_count(
-        "CategoricalVariation", "Variation", "HAS_MEMBERS", min=0, max=None
+        "CategoricalVariation", "Variation", "HAS_MEMBERS", min_rels=0, max_rels=None
     )
 
     expected_node_labels = [{"CategoricalVariation", "ProteinSequenceConsequence"}]
@@ -369,7 +369,7 @@ def test_location_rules(
     """Verify property and relationship rules for Location nodes."""
     check_unique_property("Location", "id")
     check_relation_count(
-        "Location", "Variation", "HAS_LOCATION", direction="in", max=None
+        "Location", "Variation", "HAS_LOCATION", direction="in", max_rels=None
     )
 
     expected_labels = [{"Location", "SequenceLocation"}]
@@ -409,30 +409,33 @@ def test_therapeutic_procedure_rules(
 ):
     """Verify property and relationship rules for Therapeutic Procedure nodes."""
     check_unique_property("TherapeuticProcedure", "id")
-    # min is 0 because TherapeuticAgent may not be attached to study directly, but
+    # min_rels is 0 because TherapeuticAgent may not be attached to study directly, but
     # through CombinationTherapy and TherapeuticSubstituteGroup
     check_relation_count(
         "TherapeuticProcedure",
         "Study",
         "HAS_THERAPEUTIC",
-        min=0,
-        max=None,
+        min_rels=0,
+        max_rels=None,
         direction="in",
     )
     check_relation_count(
-        "CombinationTherapy", "TherapeuticAgent", "HAS_COMPONENTS", max=None
+        "CombinationTherapy", "TherapeuticAgent", "HAS_COMPONENTS", max_rels=None
     )
     check_relation_count(
-        "CombinationTherapy", "Study", "HAS_THERAPEUTIC", max=None, direction="in"
+        "CombinationTherapy", "Study", "HAS_THERAPEUTIC", max_rels=None, direction="in"
     )
     check_relation_count(
-        "TherapeuticSubstituteGroup", "TherapeuticAgent", "HAS_SUBSTITUTES", max=None
+        "TherapeuticSubstituteGroup",
+        "TherapeuticAgent",
+        "HAS_SUBSTITUTES",
+        max_rels=None,
     )
     check_relation_count(
         "TherapeuticSubstituteGroup",
         "Study",
         "HAS_THERAPEUTIC",
-        max=None,
+        max_rels=None,
         direction="in",
     )
 
@@ -485,7 +488,7 @@ def test_condition_rules(
     """Verify property and relationship rules for condition nodes."""
     check_unique_property("Condition", "id")
     check_relation_count(
-        "Condition", "Study", "HAS_TUMOR_TYPE", max=None, direction="in"
+        "Condition", "Study", "HAS_TUMOR_TYPE", max_rels=None, direction="in"
     )
 
     expected_node_labels = [{"Disease", "Condition"}]
@@ -514,8 +517,8 @@ def test_study_rules(
     check_relation_count("Study", "Condition", "HAS_TUMOR_TYPE")
     check_relation_count("Study", "TherapeuticProcedure", "HAS_THERAPEUTIC")
     check_relation_count("Study", "Coding", "HAS_STRENGTH")
-    check_relation_count("Study", "Method", "IS_SPECIFIED_BY", max=None)
-    check_relation_count("Study", "Gene", "HAS_GENE_CONTEXT", max=None)
+    check_relation_count("Study", "Method", "IS_SPECIFIED_BY", max_rels=None)
+    check_relation_count("Study", "Gene", "HAS_GENE_CONTEXT", max_rels=None)
 
     expected_node_labels = [{"Study", "VariantTherapeuticResponseStudy"}]
     check_node_labels("Study", expected_node_labels, 1)
@@ -560,7 +563,7 @@ def test_document_rules(
     """Verify property and relationship rules for Document nodes."""
     check_unique_property("Document", "id")
     check_relation_count(
-        "Document", "Study", "IS_REPORTED_IN", min=0, max=None, direction="in"
+        "Document", "Study", "IS_REPORTED_IN", min_rels=0, max_rels=None, direction="in"
     )
 
     expected_labels = [{"Document"}]
@@ -604,7 +607,9 @@ def test_method_rules(
 ):
     """Verify property and relationship rules for Method nodes."""
     check_unique_property("Method", "id")
-    check_relation_count("Method", "Study", "IS_SPECIFIED_BY", max=None, direction="in")
+    check_relation_count(
+        "Method", "Study", "IS_SPECIFIED_BY", max_rels=None, direction="in"
+    )
 
     expected_node_labels = [{"Method"}]
     check_node_labels("Method", expected_node_labels, 1)

tests/unit/harvesters/moa/test_moa_assertions.py

@@ -4,9 +4,9 @@
 from unittest.mock import patch
 
 import pytest
+from tests.conftest import TEST_HARVESTERS_DIR
 
-from metakb import PROJECT_ROOT
-from metakb.harvesters import MoaHarvester
+from metakb.harvesters.moa import MoaHarvester
 
 
 @pytest.fixture(scope="module")
@@ -54,13 +54,12 @@ def assertion165():
 @patch.object(MoaHarvester, "_get_all_assertions")
 def test_assertion_170(test_get_all_assertions, test_get_all_variants, assertion165):
     """Test moa harvester works correctly for assertions."""
-    with (
-        PROJECT_ROOT / "tests" / "data" / "harvesters/moa/assertions.json"
-    ).open() as f:
+    moa_harvester_test_dir = TEST_HARVESTERS_DIR / "moa"
+    with (moa_harvester_test_dir / "assertions.json").open() as f:
         data = json.load(f)
     test_get_all_assertions.return_value = data
 
-    with (PROJECT_ROOT / "tests" / "data" / "harvesters/moa/variants.json").open() as f:
+    with (moa_harvester_test_dir / "variants.json").open() as f:
         data = json.load(f)
     test_get_all_variants.return_value = data
 

tests/unit/harvesters/moa/test_moa_harvest.py

@@ -1,7 +1,7 @@
 """Test MOAlmanac Harvester."""
 
 from metakb import APP_ROOT
-from metakb.harvesters import MoaHarvester
+from metakb.harvesters.moa import MoaHarvester
 
 
 def test_harvest():

tests/unit/harvesters/moa/test_moa_source.py

@@ -3,9 +3,9 @@
 from unittest.mock import patch
 
 import pytest
+from tests.conftest import TEST_HARVESTERS_DIR
 
-from metakb import PROJECT_ROOT
-from metakb.harvesters import MoaHarvester
+from metakb.harvesters.moa import MoaHarvester
 
 
 @pytest.fixture(scope="module")
@@ -33,9 +33,7 @@ def source68():
 @patch.object(MoaHarvester, "_get_all_assertions")
 def test_source68(test_get_all_assertions, source68):
     """Test moa harvester works correctly for evidence."""
-    with (
-        PROJECT_ROOT / "tests" / "data" / "harvesters/moa/assertions.json"
-    ).open() as f:
+    with (TEST_HARVESTERS_DIR / "moa" / "assertions.json").open() as f:
         data = json.load(f)
     test_get_all_assertions.return_value = data
 

tests/unit/harvesters/test_civic_harvester.py

@@ -2,11 +2,12 @@
 import json
 
 import pytest
+from tests.conftest import TEST_HARVESTERS_DIR
 
-from metakb import APP_ROOT, PROJECT_ROOT
-from metakb.harvesters import CivicHarvester
+from metakb import APP_ROOT
+from metakb.harvesters.civic import CivicHarvester
 
-TEST_DATA_PATH = PROJECT_ROOT / "tests" / "data" / "harvesters" / "civic"
+TEST_DATA_PATH = TEST_HARVESTERS_DIR / "civic"
 TEST_CIVICPY_CACHE_PATH = sorted(TEST_DATA_PATH.glob("civicpy_cache_*.pkl"))[-1]
 
 

tests/unit/transform/test_civic_transform_diagnostic.py

@@ -3,11 +3,11 @@
 
 import pytest
 import pytest_asyncio
+from tests.conftest import TEST_TRANSFORM_DIR
 
-from metakb import PROJECT_ROOT
 from metakb.transform.civic import CivicTransform
 
-DATA_DIR = PROJECT_ROOT / "tests" / "data" / "transform" / "diagnostic"
+DATA_DIR = TEST_TRANSFORM_DIR / "diagnostic"
 FILENAME = "civic_cdm.json"
 
 

tests/unit/transform/test_civic_transform_prognostic.py

@@ -3,11 +3,11 @@
 
 import pytest
 import pytest_asyncio
+from tests.conftest import TEST_TRANSFORM_DIR
 
-from metakb import PROJECT_ROOT
 from metakb.transform.civic import CivicTransform
 
-DATA_DIR = PROJECT_ROOT / "tests" / "data" / "transform" / "prognostic"
+DATA_DIR = TEST_TRANSFORM_DIR / "prognostic"
 FILENAME = "civic_cdm.json"
 
 

tests/unit/transform/test_civic_transform_therapeutic.py

@@ -3,11 +3,11 @@
 
 import pytest
 import pytest_asyncio
+from tests.conftest import TEST_TRANSFORM_DIR
 
-from metakb import PROJECT_ROOT
 from metakb.transform.civic import CivicTransform
 
-DATA_DIR = PROJECT_ROOT / "tests" / "data" / "transform" / "therapeutic"
+DATA_DIR = TEST_TRANSFORM_DIR / "therapeutic"
 FILENAME = "civic_cdm.json"
 
 

tests/unit/transform/test_moa_transform.py

@@ -3,25 +3,26 @@
 
 import pytest
 import pytest_asyncio
+from tests.conftest import TEST_TRANSFORM_DIR
 
-from metakb import PROJECT_ROOT
 from metakb.transform.moa import MoaTransform
 
-DATA_DIR = PROJECT_ROOT / "tests" / "data" / "transform"
 FILENAME = "moa_cdm.json"
 
 
 @pytest_asyncio.fixture(scope="module")
 @pytest.mark.asyncio()
 async def data(normalizers):
     """Create a MOA Transform test fixture."""
-    harvester_path = DATA_DIR / "moa_harvester.json"
+    harvester_path = TEST_TRANSFORM_DIR / "moa_harvester.json"
     moa = MoaTransform(
-        data_dir=DATA_DIR, harvester_path=harvester_path, normalizers=normalizers
+        data_dir=TEST_TRANSFORM_DIR,
+        harvester_path=harvester_path,
+        normalizers=normalizers,
     )
     await moa.transform()
-    moa.create_json(transform_dir=DATA_DIR, filename=FILENAME)
-    with (DATA_DIR / FILENAME).open() as f:
+    moa.create_json(transform_dir=TEST_TRANSFORM_DIR, filename=FILENAME)
+    with (TEST_TRANSFORM_DIR / FILENAME).open() as f:
         return json.load(f)
 
 
@@ -196,4 +197,4 @@ def studies(moa_aid66_study, moa_aid155_study):
 
 def test_moa_cdm(data, studies, check_transformed_cdm):
     """Test that moa transform works correctly."""
-    check_transformed_cdm(data, studies, DATA_DIR / FILENAME)
+    check_transformed_cdm(data, studies, TEST_TRANSFORM_DIR / FILENAME)