feat - use fixture plugins instead of conftest files

tests/fixture_plugins/demultiplex_fixtures/flow_cell_fixtures.py

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+"""Fixtures for flow cell objects."""
+from pathlib import Path
+
+import pytest
+
+from cg.constants.demultiplexing import BclConverter, DemultiplexingDirsAndFiles
+from cg.models.flow_cell.flow_cell import FlowCellDirectoryData
+
+# Functional flow cells
+
+
+@pytest.fixture(scope="module")
+def hiseq_x_single_index_flow_cell(
+    hiseq_x_single_index_flow_cell_dir: Path,
+) -> FlowCellDirectoryData:
+    """Return a single-index HiSeqX flow cell."""
+    return FlowCellDirectoryData(flow_cell_path=hiseq_x_single_index_flow_cell_dir)
+
+
+@pytest.fixture(scope="module")
+def hiseq_x_dual_index_flow_cell(
+    hiseq_x_dual_index_flow_cell_dir: Path,
+) -> FlowCellDirectoryData:
+    """Return a dual-index HiSeqX flow cell."""
+    return FlowCellDirectoryData(flow_cell_path=hiseq_x_dual_index_flow_cell_dir)
+
+
+@pytest.fixture(scope="module")
+def hiseq_2500_dual_index_flow_cell(
+    hiseq_2500_dual_index_flow_cell_dir: Path,
+) -> FlowCellDirectoryData:
+    """Return a dual-index HiSeq2500 flow cell."""
+    return FlowCellDirectoryData(flow_cell_path=hiseq_2500_dual_index_flow_cell_dir)
+
+
+@pytest.fixture(scope="module")
+def hiseq_2500_custom_index_flow_cell(
+    hiseq_2500_custom_index_flow_cell_dir: Path,
+) -> FlowCellDirectoryData:
+    """Return a custom-index HiSeq2500 flow cell."""
+    return FlowCellDirectoryData(flow_cell_path=hiseq_2500_custom_index_flow_cell_dir)
+
+
+@pytest.fixture()
+def novaseq_6000_post_1_5_kits_flow_cell_data(flow_cells_dir: Path) -> FlowCellDirectoryData:
+    return FlowCellDirectoryData(Path(flow_cells_dir, "230912_A00187_1009_AHK33MDRX3"))
+
+
+@pytest.fixture()
+def novaseq_6000_pre_1_5_kits_flow_cell_data(flow_cells_dir: Path) -> FlowCellDirectoryData:
+    return FlowCellDirectoryData(Path(flow_cells_dir, "190927_A00689_0069_BHLYWYDSXX"))
+
+
+@pytest.fixture()
+def novaseq_x_flow_cell_data(flow_cells_dir: Path) -> FlowCellDirectoryData:
+    return FlowCellDirectoryData(Path(flow_cells_dir, "20231108_LH00188_0028_B22F52TLT3"))
+
+
+# Broken flow cells
+
+
+@pytest.fixture(scope="session")
+def bcl2fastq_flow_cell(bcl2fastq_flow_cell_dir: Path) -> FlowCellDirectoryData:
+    """Create a flow cell object with flow cell that is demultiplexed."""
+    return FlowCellDirectoryData(
+        flow_cell_path=bcl2fastq_flow_cell_dir, bcl_converter=BclConverter.BCL2FASTQ
+    )
+
+
+@pytest.fixture(scope="session")
+def novaseq_flow_cell_demultiplexed_with_bcl2fastq(
+    bcl_convert_flow_cell_dir: Path,
+) -> FlowCellDirectoryData:
+    """Return a Novaseq6000 flow cell object demultiplexed using Bcl2fastq."""
+    return FlowCellDirectoryData(
+        flow_cell_path=bcl_convert_flow_cell_dir, bcl_converter=BclConverter.BCL2FASTQ
+    )
+
+
+@pytest.fixture(scope="module")
+def bcl_convert_flow_cell(bcl_convert_flow_cell_dir: Path) -> FlowCellDirectoryData:
+    """Create a bcl_convert flow cell object with flow cell that is demultiplexed."""
+    return FlowCellDirectoryData(
+        flow_cell_path=bcl_convert_flow_cell_dir, bcl_converter=BclConverter.DRAGEN
+    )
+
+
+@pytest.fixture(scope="function")
+def novaseq_6000_flow_cell(bcl_convert_flow_cell: FlowCellDirectoryData) -> FlowCellDirectoryData:
+    """Return a NovaSeq6000 flow cell object."""
+    return bcl_convert_flow_cell
+
+
+@pytest.fixture(scope="function")
+def novaseq_x_flow_cell(novaseq_x_flow_cell_dir: 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
+    )
+
+
+@pytest.fixture()
+def novaseqx_flow_cell_with_sample_sheet_no_fastq(
+    novaseqx_flow_cell_directory: Path, novaseqx_demultiplexed_flow_cell: Path
+) -> FlowCellDirectoryData:
+    """Return a flow cell from a tmp dir with a sample sheet and no sample fastq files."""
+    novaseqx_flow_cell_directory.mkdir(parents=True, exist_ok=True)
+    flow_cell = FlowCellDirectoryData(novaseqx_flow_cell_directory)
+    sample_sheet_path = Path(
+        novaseqx_demultiplexed_flow_cell, DemultiplexingDirsAndFiles.SAMPLE_SHEET_FILE_NAME
+    )
+    flow_cell._sample_sheet_path_hk = sample_sheet_path
+    return flow_cell
+
+
+@pytest.fixture(name="tmp_bcl2fastq_flow_cell")
+def tmp_bcl2fastq_flow_cell(
+    tmp_demultiplexed_runs_bcl2fastq_directory: Path,
+) -> FlowCellDirectoryData:
+    """Create a flow cell object with flow cell that is demultiplexed."""
+    return FlowCellDirectoryData(
+        flow_cell_path=tmp_demultiplexed_runs_bcl2fastq_directory,
+        bcl_converter=BclConverter.BCL2FASTQ,
+    )
+
+
+@pytest.fixture
+def novaseq6000_flow_cell(
+    tmp_flow_cells_directory_malformed_sample_sheet: Path,
+) -> FlowCellDirectoryData:
+    """Return a NovaSeq6000 flow cell."""
+    return FlowCellDirectoryData(
+        flow_cell_path=tmp_flow_cells_directory_malformed_sample_sheet,
+        bcl_converter=BclConverter.BCLCONVERT,
+    )
+
+
+@pytest.fixture(name="tmp_bcl_convert_flow_cell")
+def tmp_bcl_convert_flow_cell(
+    tmp_flow_cell_directory_bclconvert: Path,
+) -> FlowCellDirectoryData:
+    """Create a flow cell object with flow cell that is demultiplexed."""
+    return FlowCellDirectoryData(
+        flow_cell_path=tmp_flow_cell_directory_bclconvert,
+        bcl_converter=BclConverter.DRAGEN,
+    )
+
+
+@pytest.fixture(name="tmp_unfinished_bcl2fastq_flow_cell")
+def unfinished_bcl2fastq_flow_cell(
+    demultiplexed_runs_unfinished_bcl2fastq_flow_cell_directory: Path,
+) -> FlowCellDirectoryData:
+    """Copy the content of a demultiplexed but not finished directory to a temporary location."""
+    return FlowCellDirectoryData(
+        flow_cell_path=demultiplexed_runs_unfinished_bcl2fastq_flow_cell_directory,
+        bcl_converter=BclConverter.BCL2FASTQ,
+    )
+
+
+# Flow cell attributes
+
+
+@pytest.fixture(scope="session")
+def bcl2fastq_flow_cell_id(bcl2fastq_flow_cell: FlowCellDirectoryData) -> str:
+    """Return flow cell id from bcl2fastq flow cell object."""
+    return bcl2fastq_flow_cell.id
+
+
+@pytest.fixture(scope="module")
+def bcl_convert_flow_cell_id(bcl_convert_flow_cell: FlowCellDirectoryData) -> str:
+    """Return flow cell id from bcl_convert flow cell object."""
+    return bcl_convert_flow_cell.id

tests/fixture_plugins/demultiplex_fixtures/name_fixtures.py

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+import pytest
+
+
+@pytest.fixture
+def tmp_flow_cell_name_no_run_parameters() -> str:
+    """This is the name of a flow cell directory with the run parameters missing."""
+    return "180522_A00689_0200_BHLCKNCCXY"
+
+
+@pytest.fixture
+def tmp_flow_cell_name_malformed_sample_sheet() -> str:
+    """ "Returns the name of a flow cell directory ready for demultiplexing with BCL convert.
+    Contains a sample sheet with malformed headers.
+    """
+    return "201203_A00689_0200_AHVKJCDRXY"
+
+
+@pytest.fixture
+def tmp_flow_cell_name_no_sample_sheet() -> str:
+    """Return the name of a flow cell directory with the run parameters and sample sheet missing."""
+    return "170407_A00689_0209_BHHKVCALXX"
+
+
+@pytest.fixture(name="tmp_flow_cell_name_ready_for_demultiplexing_bcl2fastq")
+def tmp_flow_cell_name_ready_for_demultiplexing_bcl2fastq() -> str:
+    """Returns the name of a flow cell directory ready for demultiplexing with bcl2fastq."""
+    return "211101_D00483_0615_AHLG5GDRXY"
+
+
+@pytest.fixture(scope="session")
+def flow_cell_name_demultiplexed_with_bcl2fastq() -> str:
+    """Return the name of a flow cell that has been demultiplexed with BCL2Fastq."""
+    return "HHKVCALXX"
+
+
+@pytest.fixture(scope="session")
+def flow_cell_directory_name_demultiplexed_with_bcl2fastq(
+    flow_cell_name_demultiplexed_with_bcl2fastq: str,
+) -> str:
+    """Return the name of a flow cell directory that has been demultiplexed with BCL2Fastq."""
+    return f"170407_ST-E00198_0209_B{flow_cell_name_demultiplexed_with_bcl2fastq}"
+
+
+@pytest.fixture(scope="session")
+def flow_cell_name_demultiplexed_with_bcl_convert() -> str:
+    return "HY7FFDRX2"
+
+
+@pytest.fixture(scope="session")
+def flow_cell_directory_name_demultiplexed_with_bcl_convert(
+    flow_cell_name_demultiplexed_with_bcl_convert: str,
+) -> str:
+    return f"230504_A00689_0804_B{flow_cell_name_demultiplexed_with_bcl_convert}"
+
+
+@pytest.fixture(scope="session")
+def hiseq_x_single_index_flow_cell_name() -> str:
+    """Return the full name of a HiSeqX flow cell with only one index."""
+    return "170517_ST-E00266_0210_BHJCFFALXX"
+
+
+@pytest.fixture(scope="session")
+def hiseq_x_dual_index_flow_cell_name() -> str:
+    """Return the full name of a HiSeqX flow cell with two indexes."""
+    return "180508_ST-E00269_0269_AHL32LCCXY"
+
+
+@pytest.fixture(scope="session")
+def hiseq_2500_dual_index_flow_cell_name() -> str:
+    """Return the full name of a HiSeq2500 flow cell with double indexes."""
+    return "181005_D00410_0735_BHM2LNBCX2"
+
+
+@pytest.fixture(scope="session")
+def hiseq_2500_custom_index_flow_cell_name() -> str:
+    """Return the full name of a HiSeq2500 flow cell with double indexes."""
+    return "180509_D00450_0598_BHGYFNBCX2"
+
+
+@pytest.fixture(scope="session")
+def bcl2fastq_flow_cell_full_name() -> str:
+    """Return full flow cell name."""
+    return "201203_D00483_0200_AHVKJCDRXX"
+
+
+@pytest.fixture(scope="session")
+def bcl_convert_flow_cell_full_name() -> str:
+    """Return the full name of a bcl_convert flow cell."""
+    return "211101_A00187_0615_AHLG5GDRZZ"
+
+
+@pytest.fixture(scope="session")
+def novaseq_x_flow_cell_full_name() -> str:
+    """Return the full name of a NovaSeqX flow cell."""
+    return "20230508_LH00188_0003_A22522YLT3"
+
+
+# Lists
+
+
+@pytest.fixture(scope="session")
+def bcl_convert_demultiplexed_flow_cell_sample_internal_ids() -> list[str]:
+    """
+    Sample id:s present in sample sheet for dummy flow cell demultiplexed with BCL Convert in
+    cg/tests/fixtures/apps/demultiplexing/demultiplexed-runs/230504_A00689_0804_BHY7FFDRX2.
+    """
+    return ["ACC11927A2", "ACC11927A5"]
+
+
+@pytest.fixture(scope="session")
+def bcl2fastq_demultiplexed_flow_cell_sample_internal_ids() -> list[str]:
+    """
+    Sample id:s present in sample sheet for dummy flow cell demultiplexed with BCL Convert in
+    cg/tests/fixtures/apps/demultiplexing/demultiplexed-runs/170407_A00689_0209_BHHKVCALXX.
+    """
+    return ["SVE2528A1"]