test: update tests based on changes

Author: JoshLoecker

tests/fixtures/collect_files.py

@@ -81,13 +81,13 @@ def como_input_data_directory(request: SubRequest) -> Path:
 
 
 @pytest.fixture(params=["naiveB", "smB"])
-def packed_filepaths(sample_name: str) -> PackedFilepaths:
+def packed_filepaths(request: SubRequest) -> PackedFilepaths:
     return PackedFilepaths(
-        sample_name=sample_name,
-        fragment_size=Path(f"main/data/COMO_input/{sample_name}/fragmentSizes/{sample_name}_fragment_size.txt"),
-        gene_count=Path(f"main/data/COMO_input/{sample_name}/geneCounts/{sample_name}.tab"),
-        insert_size=Path(f"main/data/COMO_input/{sample_name}/insertSizes/{sample_name}_insert_size.txt"),
-        layout=Path(f"main/data/COMO_input/{sample_name}/layouts/{sample_name}_layout.txt"),
-        preparation_method=Path(f"main/data/COMO_input/{sample_name}/prepMethods/{sample_name}_prep_method.txt"),
-        strandedness=Path(f"main/data/COMO_input/{sample_name}/strandedness/{sample_name}_strandedness.txt"),
+        sample_name=request.param,
+        fragment_size=Path(f"main/data/COMO_input/{request.param}/fragmentSizes/{request.param}_fragment_size.txt"),
+        gene_count=Path(f"main/data/COMO_input/{request.param}/geneCounts/{request.param}.tab"),
+        insert_size=Path(f"main/data/COMO_input/{request.param}/insertSizes/{request.param}_insert_size.txt"),
+        layout=Path(f"main/data/COMO_input/{request.param}/layouts/{request.param}_layout.txt"),
+        preparation_method=Path(f"main/data/COMO_input/{request.param}/prepMethods/{request.param}_prep_method.txt"),
+        strandedness=Path(f"main/data/COMO_input/{request.param}/strandedness/{request.param}_strandedness.txt"),
     )

tests/unit/test_rnaseq_preprocess.py

@@ -24,8 +24,8 @@
 
 
 class TestSTARInformation:
-    valid_data = Path("main/data/COMO_input/naiveB/geneCounts/S1/naiveB_S1R1.tab").absolute()
-    invalid_data = Path("main/data/COMO_input/naiveB/fragmentSizes/S1/naiveB_S1R1_fragment_size.txt").absolute()
+    valid_data = Path("main/data/COMO_input/naiveB/geneCounts/S1/naiveB_S1R1.tab").resolve()
+    invalid_data = Path("main/data/COMO_input/naiveB/fragmentSizes/S1/naiveB_S1R1_fragment_size.txt").resolve()
 
     @pytest.mark.asyncio
     async def test_build_from_tab_valid_file(self):
@@ -40,7 +40,7 @@ async def test_build_from_tab_valid_file(self):
     @pytest.mark.asyncio
     async def test_build_from_tab_invalid_file(self):
         """Validate error on invalid file."""
-        with pytest.raises(ValueError, match="Invalid file format"):
+        with pytest.raises(ValueError, match="Building STAR information requires a '.tab' file"):
             await _STARinformation.build_from_tab(TestSTARInformation.invalid_data)
 
 
@@ -80,12 +80,3 @@ def test_pack_filepaths(packed_filepaths: PackedFilepaths):
     assert packed_filepaths.sample_name in packed_filepaths.layout.as_posix()
     assert packed_filepaths.sample_name in packed_filepaths.preparation_method.as_posix()
     assert packed_filepaths.sample_name in packed_filepaths.strandedness.as_posix()
-
-
-@pytest.mark.asyncio
-async def test_process_standard_replicate(packed_filepaths: PackedFilepaths):
-    await _process_standard_replicate(
-        counts_file=packed_filepaths.gene_count,
-        strand_file=packed_filepaths.strandedness,
-        sample_name=packed_filepaths.sample_name,
-    )