refactor - Organise lims samples fixtures (#2841)(patch)

This is the first step of #2842. Refactor the fixtures returning lists of `FlowCellSample` to only use elements from the 7 canonical flow cells in demultiplexing


### Added

- Raw sample file `tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_bcl2fastq_raw.json`  with anonymised names and projects

### Changed

- Renamed `novaseq_6000_pre_1_5_kits_lims_samples` and `novaseq_6000_post_1_5_kits_lims_samples` to explicitly include the bcl converter in their name

### Fixed

- Removed fixture `lims_novaseq_6000_bcl2fastq_samples`, replaced usages with `novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples`.
- Removed fixture `lims_novaseq_bcl_convert_samples`, replaced usages with `novaseq_x_lims_samples`
- Removed paths to lims sample files that were used only once. Instantiated Path in the fixture where they were used instead.

tests/apps/demultiplex/conftest.py

@@ -47,12 +47,12 @@ def bcl_convert_samples_similar_index2() -> list[FlowCellSampleBCLConvert]:
 @pytest.fixture
 def bcl2fastq_sample_sheet_creator(
     novaseq_flow_cell_demultiplexed_with_bcl2fastq: FlowCellDirectoryData,
-    lims_novaseq_6000_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq],
+    novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq],
 ) -> SampleSheetCreatorBcl2Fastq:
     """Returns a sample sheet creator for version 1 sample sheets with bcl2fastq format."""
     return SampleSheetCreatorBcl2Fastq(
         flow_cell=novaseq_flow_cell_demultiplexed_with_bcl2fastq,
-        lims_samples=lims_novaseq_6000_bcl2fastq_samples,
+        lims_samples=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples,
     )
 
 

tests/apps/demultiplex/test_sample_models.py

@@ -321,8 +321,14 @@ def test_update_barcode_mismatches_2(
     "run_parameters_fixture, raw_lims_samples_fixture",
     [
         ("novaseq_x_run_parameters", "novaseq_x_lims_samples"),
-        ("novaseq_6000_run_parameters_pre_1_5_kits", "novaseq_6000_pre_1_5_kits_lims_samples"),
-        ("novaseq_6000_run_parameters_post_1_5_kits", "novaseq_6000_post_1_5_kits_lims_samples"),
+        (
+            "novaseq_6000_run_parameters_pre_1_5_kits",
+            "novaseq_6000_pre_1_5_kits_bcl_convert_lims_samples",
+        ),
+        (
+            "novaseq_6000_run_parameters_post_1_5_kits",
+            "novaseq_6000_post_1_5_kits_bcl_convert_lims_samples",
+        ),
         ("hiseq_x_single_index_run_parameters", "hiseq_x_single_index_bcl_convert_lims_samples"),
         ("hiseq_x_dual_index_run_parameters", "hiseq_x_dual_index_bcl_convert_lims_samples"),
         ("hiseq_2500_dual_index_run_parameters", "hiseq_2500_dual_index_bcl_convert_lims_samples"),

tests/apps/demultiplex/test_sample_sheet_creator.py

@@ -21,7 +21,7 @@
 
 def test_bcl_convert_sample_sheet_fails_with_bcl2fastq(
     novaseq_x_flow_cell: FlowCellDirectoryData,
-    lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert],
+    novaseq_x_lims_samples: list[FlowCellSampleBCLConvert],
 ):
     """Test that creating a BCL Convert sample sheet fails if the bcl converter is Bcl2fastq."""
     # GIVEN a NovaSeqX flow cell and samples and the bcl converter is Bcl2fastq
@@ -31,7 +31,7 @@ def test_bcl_convert_sample_sheet_fails_with_bcl2fastq(
     with pytest.raises(SampleSheetError) as exc_info:
         SampleSheetCreatorBCLConvert(
             flow_cell=novaseq_x_flow_cell,
-            lims_samples=lims_novaseq_bcl_convert_samples,
+            lims_samples=novaseq_x_lims_samples,
         )
         # THEN an error is raised
         assert (

tests/apps/demultiplex/test_sample_sheet_creator_factory.py

@@ -17,7 +17,7 @@
 
 def test_sample_sheet_creator_factory_novaseq_6000(
     novaseq_flow_cell_demultiplexed_with_bcl2fastq: FlowCellDirectoryData,
-    lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq],
+    novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq],
 ):
     """Test that a sample sheet creator defined with NovaSeq6000 data is V1."""
     # GIVEN a NovaSeq6000 flow cell and a list of NovaSeq6000 samples
@@ -28,26 +28,26 @@ def test_sample_sheet_creator_factory_novaseq_6000(
     # WHEN defining the sample sheet creator
     sample_sheet_creator: SampleSheetCreator = get_sample_sheet_creator(
         flow_cell=novaseq_flow_cell_demultiplexed_with_bcl2fastq,
-        lims_samples=lims_novaseq_bcl2fastq_samples,
+        lims_samples=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples,
         force=False,
     )
 
     # THEN no error is raised and the sample sheet creator is a Bcl2Fastq sample sheet creator
     assert isinstance(sample_sheet_creator, SampleSheetCreatorBcl2Fastq)
 
 
-def test_sample_sheet_creator_factory_BCL_convert(
+def test_sample_sheet_creator_factory_bcl_convert(
     novaseq_x_flow_cell: FlowCellDirectoryData,
-    lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert],
+    novaseq_x_lims_samples: list[FlowCellSampleBCLConvert],
 ):
     """Test that a sample sheet creator defined with BCL convert data is BCL Convert."""
-    # GIVEN a NovaSeqX flow cell and a list of NovaSeqX samples that is demultiplexed wit BCL Convert
+    # GIVEN a NovaSeqX flow cell and a list of NovaSeqX BCL Convert samples
     assert novaseq_x_flow_cell.bcl_converter == BclConverter.DRAGEN
 
     # WHEN defining the sample sheet creator
     sample_sheet_creator: SampleSheetCreator = get_sample_sheet_creator(
         flow_cell=novaseq_x_flow_cell,
-        lims_samples=lims_novaseq_bcl_convert_samples,
+        lims_samples=novaseq_x_lims_samples,
         force=False,
     )
 

tests/cli/demultiplex/test_create_sample_sheet.py

@@ -23,7 +23,7 @@ def test_create_sample_sheet_no_run_parameters_fails(
     cli_runner: testing.CliRunner,
     tmp_flow_cells_directory_no_run_parameters: Path,
     sample_sheet_context: CGConfig,
-    lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq],
+    novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq],
     caplog,
     mocker,
 ):
@@ -36,7 +36,7 @@ def test_create_sample_sheet_no_run_parameters_fails(
     # GIVEN flow cell samples
     mocker.patch(
         FLOW_CELL_FUNCTION_NAME,
-        return_value=lims_novaseq_bcl2fastq_samples,
+        return_value=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples,
     )
 
     # GIVEN that the context's flow cell directory holds the given flow cell
@@ -60,7 +60,7 @@ def test_create_bcl2fastq_sample_sheet(
     cli_runner: testing.CliRunner,
     tmp_flow_cells_directory_no_sample_sheet: Path,
     sample_sheet_context: CGConfig,
-    lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq],
+    novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq],
     mocker,
 ):
     """Test that creating a Bcl2fastq sample sheet works."""
@@ -82,7 +82,7 @@ def test_create_bcl2fastq_sample_sheet(
     # GIVEN flow cell samples
     mocker.patch(
         FLOW_CELL_FUNCTION_NAME,
-        return_value=lims_novaseq_bcl2fastq_samples,
+        return_value=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples,
     )
     # GIVEN a lims api that returns some samples
 
@@ -116,14 +116,14 @@ class SampleSheetScenario(BaseModel):
     "scenario",
     [
         SampleSheetScenario(
-            flow_cell_directory="novaseq_6000_pre_1_5_kits_flow_cell",
-            lims_samples="novaseq_6000_pre_1_5_kits_lims_samples",
-            correct_sample_sheet="novaseq_6000_pre_1_5_kits_correct_sample_sheet",
+            flow_cell_directory="novaseq_6000_pre_1_5_kits_flow_cell_path",
+            lims_samples="novaseq_6000_pre_1_5_kits_bcl_convert_lims_samples",
+            correct_sample_sheet="novaseq_6000_pre_1_5_kits_correct_sample_sheet_path",
         ),
         SampleSheetScenario(
-            flow_cell_directory="novaseq_6000_post_1_5_kits_flow_cell",
-            lims_samples="novaseq_6000_post_1_5_kits_lims_samples",
-            correct_sample_sheet="novaseq_6000_post_1_5_kits_correct_sample_sheet",
+            flow_cell_directory="novaseq_6000_post_1_5_kits_flow_cell_path",
+            lims_samples="novaseq_6000_post_1_5_kits_bcl_convert_lims_samples",
+            correct_sample_sheet="novaseq_6000_post_1_5_kits_correct_sample_sheet_path",
         ),
         SampleSheetScenario(
             flow_cell_directory="novaseq_x_flow_cell_directory",
@@ -137,7 +137,6 @@ def test_create_dragen_sample_sheet(
     cli_runner: testing.CliRunner,
     scenario: SampleSheetScenario,
     sample_sheet_context: CGConfig,
-    lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert],
     mocker,
     request: FixtureRequest,
 ):
@@ -193,7 +192,7 @@ def test_incorrect_bcl2fastq_headers_samplesheet(
     cli_runner: testing.CliRunner,
     tmp_flow_cells_directory_malformed_sample_sheet: Path,
     sample_sheet_context: CGConfig,
-    lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq],
+    novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq],
     mocker,
     caplog,
 ):
@@ -207,7 +206,7 @@ def test_incorrect_bcl2fastq_headers_samplesheet(
     # GIVEN flow cell samples
     mocker.patch(
         FLOW_CELL_FUNCTION_NAME,
-        return_value=lims_novaseq_bcl2fastq_samples,
+        return_value=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples,
     )
     # GIVEN a lims api that returns some samples
 

tests/fixture_plugins/demultiplex_fixtures/flow_cell_fixtures.py

@@ -92,10 +92,10 @@ def novaseq_6000_flow_cell(bcl_convert_flow_cell: FlowCellDirectoryData) -> Flow
 
 
 @pytest.fixture(scope="function")
-def novaseq_x_flow_cell(novaseq_x_flow_cell_dir: Path) -> FlowCellDirectoryData:
+def novaseq_x_flow_cell(novaseq_x_flow_cell_directory: Path) -> FlowCellDirectoryData:
     """Create a NovaSeqX flow cell object with flow cell that is demultiplexed."""
     return FlowCellDirectoryData(
-        flow_cell_path=novaseq_x_flow_cell_dir, bcl_converter=BclConverter.DRAGEN
+        flow_cell_path=novaseq_x_flow_cell_directory, bcl_converter=BclConverter.DRAGEN
     )
 
 

tests/fixture_plugins/demultiplex_fixtures/path_fixtures.py

@@ -202,39 +202,27 @@ def demux_results_not_finished_dir(demultiplex_fixtures: Path) -> Path:
 
 
 @pytest.fixture
-def novaseq_6000_post_1_5_kits_flow_cell(tmp_flow_cells_directory: Path) -> Path:
+def novaseq_6000_post_1_5_kits_flow_cell_path(tmp_flow_cells_directory: Path) -> Path:
     return Path(tmp_flow_cells_directory, "230912_A00187_1009_AHK33MDRX3")
 
 
 @pytest.fixture
-def novaseq_6000_post_1_5_kits_correct_sample_sheet(
-    novaseq_6000_post_1_5_kits_flow_cell: Path,
+def novaseq_6000_post_1_5_kits_correct_sample_sheet_path(
+    novaseq_6000_post_1_5_kits_flow_cell_path: Path,
 ) -> Path:
-    return Path(novaseq_6000_post_1_5_kits_flow_cell, CORRECT_SAMPLE_SHEET)
+    return Path(novaseq_6000_post_1_5_kits_flow_cell_path, CORRECT_SAMPLE_SHEET)
 
 
 @pytest.fixture
-def novaseq_6000_post_1_5_kits_raw_lims_samples(
-    novaseq_6000_post_1_5_kits_flow_cell: Path,
-) -> Path:
-    return Path(novaseq_6000_post_1_5_kits_flow_cell, "HK33MDRX3_raw.json")
-
-
-@pytest.fixture
-def novaseq_6000_pre_1_5_kits_flow_cell(tmp_flow_cells_directory: Path) -> Path:
+def novaseq_6000_pre_1_5_kits_flow_cell_path(tmp_flow_cells_directory: Path) -> Path:
     return Path(tmp_flow_cells_directory, "190927_A00689_0069_BHLYWYDSXX")
 
 
 @pytest.fixture
-def novaseq_6000_pre_1_5_kits_correct_sample_sheet(
-    novaseq_6000_pre_1_5_kits_flow_cell: Path,
+def novaseq_6000_pre_1_5_kits_correct_sample_sheet_path(
+    novaseq_6000_pre_1_5_kits_flow_cell_path: Path,
 ) -> Path:
-    return Path(novaseq_6000_pre_1_5_kits_flow_cell, CORRECT_SAMPLE_SHEET)
-
-
-@pytest.fixture
-def novaseq_6000_pre_1_5_kits_raw_lims_samples(novaseq_6000_pre_1_5_kits_flow_cell: Path) -> Path:
-    return Path(novaseq_6000_pre_1_5_kits_flow_cell, "HLYWYDSXX_raw.json")
+    return Path(novaseq_6000_pre_1_5_kits_flow_cell_path, CORRECT_SAMPLE_SHEET)
 
 
 @pytest.fixture
@@ -247,11 +235,6 @@ def novaseq_x_correct_sample_sheet(novaseq_x_flow_cell_directory: Path) -> Path:
     return Path(novaseq_x_flow_cell_directory, CORRECT_SAMPLE_SHEET)
 
 
-@pytest.fixture
-def novaseq_x_raw_lims_samples(novaseq_x_flow_cell_directory: Path) -> Path:
-    return Path(novaseq_x_flow_cell_directory, "22F52TLT3_raw.json")
-
-
 @pytest.fixture(scope="session")
 def novaseq_x_manifest_file(novaseq_x_flow_cell_dir: Path) -> Path:
     """Return the path to a NovaSeqX manifest file."""
@@ -374,22 +357,22 @@ def novaseq_6000_run_parameters_path(bcl2fastq_flow_cell_dir: Path) -> Path:
 
 @pytest.fixture
 def novaseq_6000_run_parameters_pre_1_5_kits_path(
-    novaseq_6000_pre_1_5_kits_flow_cell: Path,
+    novaseq_6000_pre_1_5_kits_flow_cell_path: Path,
 ) -> Path:
     """Return the path to a NovaSeq6000 pre 1.5 kit run parameters file."""
     return Path(
-        novaseq_6000_pre_1_5_kits_flow_cell,
+        novaseq_6000_pre_1_5_kits_flow_cell_path,
         DemultiplexingDirsAndFiles.RUN_PARAMETERS_PASCAL_CASE,
     )
 
 
 @pytest.fixture
 def novaseq_6000_run_parameters_post_1_5_kits_path(
-    novaseq_6000_post_1_5_kits_flow_cell: Path,
+    novaseq_6000_post_1_5_kits_flow_cell_path: Path,
 ) -> Path:
     """Return the path to a NovaSeq6000 post 1.5 kit run parameters file."""
     return Path(
-        novaseq_6000_post_1_5_kits_flow_cell,
+        novaseq_6000_post_1_5_kits_flow_cell_path,
         DemultiplexingDirsAndFiles.RUN_PARAMETERS_PASCAL_CASE,
     )