Merge master

tests/conftest.py

@@ -1087,6 +1087,21 @@ def fixture_populated_stats_api(
     return stats_api
 
 
+@pytest.fixture(name="novaseq6000_bcl_convert_sample_sheet_path")
+def fixture_novaseq6000_sample_sheet_path() -> Path:
+    """Return the path to a NovaSeq 6000 BCL convert sample sheet."""
+    return Path(
+        "tests",
+        "fixtures",
+        "apps",
+        "sequencing_metrics_parser",
+        "230622_A00621_0864_AHY7FFDRX2",
+        "Unaligned",
+        "Reports",
+        "SampleSheet.csv",
+    )
+
+
 @pytest.fixture(name="demultiplex_fixtures", scope="session")
 def fixture_demultiplex_fixtures(apps_dir: Path) -> Path:
     """Return the path to the demultiplex fixture directory."""
@@ -2688,8 +2703,8 @@ def fixture_store_with_sequencing_metrics(
     yield store
 
 
-@pytest.fixture
-def demultiplexed_flow_cells_directory(tmp_path) -> Path:
+@pytest.fixture(name="demultiplexed_flow_cells_tmp_directory")
+def fixture_demultiplexed_flow_cells_tmp_directory(tmp_path) -> Path:
     original_dir = Path(
         Path(__file__).parent, "fixtures", "apps", "demultiplexing", "demultiplexed-runs"
     )

tests/meta/demultiplex/test_demux_post_processing.py

@@ -715,7 +715,7 @@ def test_update_sample_read_count(demultiplex_context: CGConfig):
     "demux_type",
     ["BCL2FASTQ_TREE", "BCLCONVERT_TREE", "BCLCONVERT_FLAT"],
 )
-def test_post_processing_of_flow_cell_demultiplexed_with_bclconvert(
+def test_post_processing_of_flow_cell(
     demux_type: str,
     demultiplex_context: CGConfig,
     flow_cell_info_map: Dict[str, FlowCellInfo],
@@ -785,22 +785,48 @@ def test_post_processing_of_flow_cell_demultiplexed_with_bclconvert(
     assert delivery_path.exists()
 
 
-def test_copy_sample_sheet(demultiplex_context: CGConfig):
+def test_add_demux_logs_to_housekeeper(
+    demultiplex_context: CGConfig, dragen_flow_cell: FlowCellDirectoryData
+):
     # GIVEN a DemuxPostProcessing API
     demux_post_processing_api = DemuxPostProcessingAPI(demultiplex_context)
 
-    # GIVEN a sample sheet in the run directory
-    sample_sheet_path = Path(
-        demux_post_processing_api.demux_api.run_dir,
-        DemultiplexingDirsAndFiles.SAMPLE_SHEET_FILE_NAME,
-    )
-    sample_sheet_path.touch()
+    # GIVEN a bundle and flow cell version exists in housekeeper
+    demux_post_processing_api.add_bundle_and_version_if_non_existent(
+        bundle_name=dragen_flow_cell.id
+    )
+
+    # GIVEN a demux log in the run directory
+    demux_log_file_paths: List[Path] = [
+        Path(
+            demux_post_processing_api.demux_api.run_dir,
+            f"{dragen_flow_cell.full_name}",
+            f"{dragen_flow_cell.id}_demultiplex.stdout",
+        ),
+        Path(
+            demux_post_processing_api.demux_api.run_dir,
+            f"{dragen_flow_cell.full_name}",
+            f"{dragen_flow_cell.id}_demultiplex.stderr",
+        ),
+    ]
+    for file_path in demux_log_file_paths:
+        file_path.parent.mkdir(parents=True, exist_ok=True)
+        file_path.touch()
+
+    # WHEN adding the demux logs to housekeeper
+    demux_post_processing_api.add_demux_logs_to_housekeeper(flow_cell=dragen_flow_cell)
+
+    # THEN the demux log was added to housekeeper
+    files = demux_post_processing_api.hk_api.get_files(
+        tags=[SequencingFileTag.DEMUX_LOG],
+        bundle=dragen_flow_cell.id,
+    ).all()
 
-    # WHEN copying the sample sheet
-    demux_post_processing_api.copy_sample_sheet()
+    expected_file_names: List[str] = []
+    for file_path in demux_log_file_paths:
+        expected_file_names.append(file_path.name.split("/")[-1])
 
-    # THEN the sample sheet was copied to the out directory
-    assert Path(
-        demux_post_processing_api.demux_api.out_dir,
-        DemultiplexingDirsAndFiles.SAMPLE_SHEET_FILE_NAME,
-    ).exists()
+    # THEN the demux logs were added to housekeeper with the correct names
+    assert len(files) == 2
+    for file in files:
+        assert file.path.split("/")[-1] in expected_file_names