Fixed some tests

cg/apps/demultiplex/sample_sheet/sample_models.py

@@ -98,6 +98,8 @@ class FlowCellSampleBCLConvert(FlowCellSample):
     index: str = Field(..., alias=SampleSheetBCLConvertSections.Data.INDEX_1)
     index2: str = Field("", alias=SampleSheetBCLConvertSections.Data.INDEX_2)
     override_cycles: str = Field("", alias=SampleSheetBCLConvertSections.Data.OVERRIDE_CYCLES)
+    adapter_read_1: str = Field("", alias=SampleSheetBCLConvertSections.Data.ADAPTER_READ_1)
+    adapter_read_2: str = Field("", alias=SampleSheetBCLConvertSections.Data.ADAPTER_READ_2)
     barcode_mismatches_1: int = Field(
         1, alias=SampleSheetBCLConvertSections.Data.BARCODE_MISMATCHES_1
     )

cg/apps/demultiplex/sample_sheet/sample_sheet_creator.py

@@ -50,7 +50,7 @@ def __init__(
             FlowCellSampleBCLConvert | FlowCellSampleBcl2Fastq
         ] = flow_cell.sample_type
         self.force: bool = force
-        self.index_settings: IndexSettings = self.run_parameters.index_settings()
+        self.index_settings: IndexSettings = self.run_parameters.index_settings
 
     def _get_index_settings(self) -> IndexSettings:
         # TODO: Remove and move testst to tun parameters

tests/apps/demultiplex/conftest.py

@@ -16,36 +16,33 @@
 
 
 @pytest.fixture
-def bcl_convert_samples_with_updated_indexes() -> list[FlowCellSampleBCLConvert]:
+def bcl_convert_samples_similar_index1() -> list[FlowCellSampleBCLConvert]:
     """Return a list of three FlowCellSampleBCLConvert with updated indexes."""
     sample_1 = FlowCellSampleBCLConvert(
-        lane=1, sample_id="ACC123", index="CAGAAGAT", index2="CAATGTAC"
+        lane=1, sample_id="ACC123", index="CAGAAGAT", index2="GCGCAAGC"
     )
     sample_2 = FlowCellSampleBCLConvert(
         lane=1, sample_id="ACC456", index="CAGAAGAG", index2="CAATGTAT"
     )
     sample_3 = FlowCellSampleBCLConvert(
-        lane=2, sample_id="ACC789", index="AAGCGATAGA", index2="AACCGCAACA"
+        lane=2, sample_id="ACC789", index="AAGCGATA", index2="AACCGCAA"
     )
     return [sample_1, sample_2, sample_3]
 
 
 @pytest.fixture
-def override_cycles_for_samples_with_updated_indexes() -> list[str]:
-    """Return the correspondent Override Cycles values for three samples."""
-    return ["Y151;I8N2;I8N2;Y151", "Y151;I8N2;I8N2;Y151", "Y151;I10;I10;Y151"]
-
-
-@pytest.fixture
-def override_cycles_for_novaseq_x_samples() -> list[str]:
-    """Return the correspondent Override Cycles values for three samples."""
-    return ["Y151;I8N2;N2I8;Y151", "Y151;I8N2;N2I8;Y151", "Y151;I10;I10;Y151"]
-
-
-@pytest.fixture
-def barcode_mismatch_values_for_samples_with_updated_indexes() -> list[tuple[int, int]]:
-    """Return the pairs of barcode mismatch values corresponding to three samples."""
-    return [(0, 0), (0, 0), (1, 1)]
+def bcl_convert_samples_similar_index2() -> list[FlowCellSampleBCLConvert]:
+    """Return a list of three FlowCellSampleBCLConvert with updated indexes."""
+    sample_1 = FlowCellSampleBCLConvert(
+        lane=1, sample_id="ACC123", index="GCGCAAGC", index2="CAATGTAC"
+    )
+    sample_2 = FlowCellSampleBCLConvert(
+        lane=1, sample_id="ACC456", index="CAATGTAT", index2="CAATGTAT"
+    )
+    sample_3 = FlowCellSampleBCLConvert(
+        lane=2, sample_id="ACC789", index="AAGCGATA", index2="AACCGCAA"
+    )
+    return [sample_1, sample_2, sample_3]
 
 
 @pytest.fixture

tests/apps/demultiplex/test_sample_models.py

@@ -1,3 +1,4 @@
+from typing import Type
 from unittest.mock import Mock
 
 import pytest
@@ -197,39 +198,63 @@ def test_update_override_cycles():
     # THEN the override cycles are updated with the expected value
 
 
-def test_update_barcode_mismatches_1():
-    # TODO: Parametrise this test with different sets of samples and expected outputs:
-    #  One that is and one that is 1
-    """."""
+@pytest.mark.parametrize(
+    "sample_list_fixture, expected_barcode_mismatch",
+    [("bcl_convert_samples_similar_index1", 0), ("bcl_convert_samples_similar_index2", 1)],
+    ids=["barcode1_0", "barcode1_1"],
+)
+def test_update_barcode_mismatches_1(
+    sample_list_fixture: str, expected_barcode_mismatch: int, request: pytest.FixtureRequest
+):
+    """Test that index 1 barcode mismatch values are as expected for different sets of samples."""
+    # GIVEN a list of FlowCellSampleBCLConvert
+    sample_list: list[FlowCellSampleBCLConvert] = request.getfixturevalue(sample_list_fixture)
+
     # GIVEN a FlowCellSampleBCLConvert
+    sample_to_update: FlowCellSampleBCLConvert = sample_list[0]
 
     # WHEN updating the barcode mismatches 1
+    sample_to_update.update_barcode_mismatches_1(samples_to_compare=sample_list)
 
     # THEN the barcode mismatches 1 are updated with the expected value
+    assert sample_to_update.barcode_mismatches_1 == expected_barcode_mismatch
 
 
-def test_update_barcode_mismatches_2():
+@pytest.mark.parametrize(
+    "sample_list_fixture, expected_barcode_mismatch",
+    [("bcl_convert_samples_similar_index1", 1), ("bcl_convert_samples_similar_index2", 0)],
+    ids=["barcode2_0", "barcode2_1"],
+)
+def test_update_barcode_mismatches_2(
+    sample_list_fixture: str, expected_barcode_mismatch: int, request: pytest.FixtureRequest
+):
     # TODO: Parametrise this test with different sets of samples and expected outputs:
     #  One that is, one that is 1 and one that is 'na'
-    """."""
+    """Test that index 2 barcode mismatch values are as expected for different sets of samples."""
+    # GIVEN a list of FlowCellSampleBCLConvert
+    sample_list: list[FlowCellSampleBCLConvert] = request.getfixturevalue(sample_list_fixture)
+
     # GIVEN a FlowCellSampleBCLConvert
+    sample_to_update: FlowCellSampleBCLConvert = sample_list[0]
 
     # WHEN updating the barcode mismatches 2
+    sample_to_update.update_barcode_mismatches_2(samples_to_compare=sample_list)
 
-    # THEN the barcode mismatches 2 are updated with the expected value
+    # THEN the barcode mismatches 1 are updated with the expected value
+    assert sample_to_update.barcode_mismatches_2 == expected_barcode_mismatch
 
 
 @pytest.mark.parametrize(
     "run_parameters_fixture, raw_lims_samples_fixture, sample_model",
     [
         ("novaseq_x_run_parameters", "novaseq_x_lims_samples", FlowCellSampleBCLConvert),
         (
-            "novaseq_6000_pre_1_5_kits_run_parameters",
+            "novaseq_6000_run_parameters_pre_1_5_kits",
             "novaseq_6000_pre_1_5_kits_lims_samples",
             FlowCellSampleBCLConvert,
         ),
         (
-            "novaseq_6000_post_1_5_kits_run_parameters",
+            "novaseq_6000_run_parameters_post_1_5_kits",
             "novaseq_6000_post_1_5_kits_lims_samples",
             FlowCellSampleBCLConvert,
         ),
@@ -256,10 +281,12 @@ def test_update_barcode_mismatches_2():
         "HiSeq2500 Bcl2Fastq",
     ],
 )
-def test_process_sample_for_sample_sheet():
+def test_process_sample_for_sample_sheet(
+    run_parameters_fixture: str, raw_lims_samples_fixture: str, sample_model: Type[FlowCellSample]
+):
     # TODO: We need a raw FlowCellSampleBcl2Fastq and a raw FlowCellSampleBCLConvert
     """."""
-    # GIVEN a FlowCellSample
+    # GIVEN a run parameters object and a list of samples from a flow cell
 
     # WHEN processing the sample for a sample sheet
 

tests/apps/demultiplex/test_sample_sheet_creator.py

@@ -2,7 +2,6 @@
 from pathlib import Path
 
 import pytest
-from _pytest.fixtures import FixtureRequest
 
 from cg.apps.demultiplex.sample_sheet.read_sample_sheet import get_validated_sample_sheet
 from cg.apps.demultiplex.sample_sheet.sample_models import (
@@ -15,13 +14,7 @@
     SampleSheetCreatorBCLConvert,
 )
 from cg.apps.demultiplex.sample_sheet.sample_sheet_models import SampleSheet
-from cg.constants.demultiplexing import (
-    NO_REVERSE_COMPLEMENTS,
-    NOVASEQ_6000_POST_1_5_KITS,
-    NOVASEQ_X_INDEX_SETTINGS,
-    BclConverter,
-    IndexSettings,
-)
+from cg.constants.demultiplexing import BclConverter
 from cg.exc import SampleSheetError
 from cg.models.flow_cell.flow_cell import FlowCellDirectoryData
 
@@ -124,55 +117,3 @@ def test_remove_unwanted_samples_no_dual_index(
         f"Removing sample {novaseq6000_flow_cell_sample_no_dual_index} since it does not have dual index"
         in caplog.text
     )
-
-
-def test_add_override_cycles_to_novaseqx_samples(
-    novaseq_x_flow_cell: FlowCellDirectoryData,
-    bcl_convert_samples_with_updated_indexes: list[FlowCellSampleBCLConvert],
-    override_cycles_for_novaseq_x_samples: list[str],
-):
-    """Test that OverrideCycles values are generated correctly for NovaSeqX samples."""
-    # GIVEN a SampleSheetCreator with samples without Override Cycles added
-    sample_sheet_creator = SampleSheetCreatorBCLConvert(
-        flow_cell=novaseq_x_flow_cell, lims_samples=bcl_convert_samples_with_updated_indexes
-    )
-    assert all(sample.override_cycles == "" for sample in sample_sheet_creator.lims_samples)
-
-    # WHEN adding the correct values of override samples
-    sample_sheet_creator.add_override_cycles_to_samples()
-
-    # THEN the Override Cycles attribute is added to all samples
-    assert all(
-        sample.override_cycles == override_cycles_value
-        for sample, override_cycles_value in zip(
-            sample_sheet_creator.lims_samples,
-            override_cycles_for_novaseq_x_samples,
-        )
-    )
-
-
-def test_update_barcode_mismatch_values_for_samples(
-    novaseq_x_flow_cell: FlowCellDirectoryData,
-    bcl_convert_samples_with_updated_indexes: list[FlowCellSampleBCLConvert],
-    barcode_mismatch_values_for_samples_with_updated_indexes: list[tuple[int, int]],
-):
-    """Tests that the barcode mismatch values are updated correctly for NovaSeqX samples."""
-    # GIVEN a sample sheet creator with samples with barcode mismatch values equal to 1
-    sample_sheet_creator = SampleSheetCreatorBCLConvert(
-        flow_cell=novaseq_x_flow_cell, lims_samples=bcl_convert_samples_with_updated_indexes
-    )
-    assert all(
-        sample.barcode_mismatches_1 == 1 and sample.barcode_mismatches_2 == 1
-        for sample in sample_sheet_creator.lims_samples
-    )
-
-    # WHEN updating the barcode mismatch values
-    sample_sheet_creator.update_barcode_mismatch_values_for_samples(
-        sample_sheet_creator.lims_samples
-    )
-
-    # THEN exactly two samples have barcode mismatches equal to zero
-    for sample, barcode_mismatch_tuple in zip(
-        sample_sheet_creator.lims_samples, barcode_mismatch_values_for_samples_with_updated_indexes
-    ):
-        assert (sample.barcode_mismatches_1, sample.barcode_mismatches_2) == barcode_mismatch_tuple

tests/apps/demultiplex/test_sample_sheet_creator_factory.py

@@ -53,4 +53,3 @@ def test_sample_sheet_creator_factory_BCL_convert(
 
     # THEN the sample sheet creator is a BCL Convert sample sheet creator
     assert isinstance(sample_sheet_creator, SampleSheetCreatorBCLConvert)
-nvert)

tests/conftest.py

@@ -1228,7 +1228,7 @@ def demux_results_not_finished_dir(demultiplex_fixtures: Path) -> Path:
 
 
 @pytest.fixture
-def novaseq_6000_post_1_5_kits_flow_cell_dir(tmp_flow_cells_directory: Path) -> Path:
+def novaseq_6000_post_1_5_kits_flow_cell(tmp_flow_cells_directory: Path) -> Path:
     return Path(tmp_flow_cells_directory, "230912_A00187_1009_AHK33MDRX3")
 
 
@@ -1239,16 +1239,16 @@ def novaseq_6000_post_1_5_kits_flow_cell_data(flow_cells_dir: Path) -> FlowCellD
 
 @pytest.fixture
 def novaseq_6000_post_1_5_kits_correct_sample_sheet(
-    novaseq_6000_post_1_5_kits_flow_cell_dir: Path,
+    novaseq_6000_post_1_5_kits_flow_cell: Path,
 ) -> Path:
-    return Path(novaseq_6000_post_1_5_kits_flow_cell_dir, "CorrectSampleSheet.csv")
+    return Path(novaseq_6000_post_1_5_kits_flow_cell, "CorrectSampleSheet.csv")
 
 
 @pytest.fixture
 def novaseq_6000_post_1_5_kits_raw_lims_samples(
-    novaseq_6000_post_1_5_kits_flow_cell_dir: Path,
+    novaseq_6000_post_1_5_kits_flow_cell: Path,
 ) -> Path:
-    return Path(novaseq_6000_post_1_5_kits_flow_cell_dir, "HK33MDRX3_raw.json")
+    return Path(novaseq_6000_post_1_5_kits_flow_cell, "HK33MDRX3_raw.json")
 
 
 @pytest.fixture
@@ -1267,7 +1267,7 @@ def novaseq_6000_pre_1_5_kits_flow_cell_data(flow_cells_dir: Path) -> FlowCellDi
 
 
 @pytest.fixture
-def novaseq_6000_pre_1_5_kits_flow_cell_dir(tmp_flow_cells_directory: Path) -> Path:
+def novaseq_6000_pre_1_5_kits_flow_cell(tmp_flow_cells_directory: Path) -> Path:
     return Path(tmp_flow_cells_directory, "190927_A00689_0069_BHLYWYDSXX")
 
 
@@ -1432,11 +1432,22 @@ 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_dir: Path,
+    novaseq_6000_pre_1_5_kits_flow_cell: Path,
 ) -> Path:
-    """Return the path to a NovaSeq6000 run parameters file."""
+    """Return the path to a NovaSeq6000 pre 1.5 kit run parameters file."""
+    return Path(
+        novaseq_6000_pre_1_5_kits_flow_cell,
+        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,
+) -> Path:
+    """Return the path to a NovaSeq6000 post 1.5 kit run parameters file."""
     return Path(
-        novaseq_6000_pre_1_5_kits_flow_cell_dir,
+        novaseq_6000_post_1_5_kits_flow_cell,
         DemultiplexingDirsAndFiles.RUN_PARAMETERS_PASCAL_CASE,
     )
 
@@ -1502,6 +1513,24 @@ def novaseq_6000_run_parameters(
     return RunParametersNovaSeq6000(run_parameters_path=novaseq_6000_run_parameters_path)
 
 
+@pytest.fixture
+def novaseq_6000_run_parameters_pre_1_5_kits(
+    novaseq_6000_run_parameters_pre_1_5_kits_path: Path,
+) -> RunParametersNovaSeq6000:
+    """Return a NovaSeq6000 run parameters pre 1.5 kit object."""
+    return RunParametersNovaSeq6000(
+        run_parameters_path=novaseq_6000_run_parameters_pre_1_5_kits_path
+    )
+
+
+@pytest.fixture
+def novaseq_6000_run_parameters_post_1_5_kits(novaseq_6000_run_parameters_post_1_5_kits_path: Path):
+    """Return a NovaSeq6000 run parameters post 1.5 kit object."""
+    return RunParametersNovaSeq6000(
+        run_parameters_path=novaseq_6000_run_parameters_post_1_5_kits_path
+    )
+
+
 @pytest.fixture(scope="session")
 def novaseq_x_run_parameters(
     novaseq_x_run_parameters_path: Path,

tests/models/demultiplexing/test_run_parameters.py

@@ -5,7 +5,14 @@
 import pytest
 from _pytest.fixtures import FixtureRequest
 
-from cg.constants.demultiplexing import RunParametersXMLNodes
+from cg.apps.demultiplex.sample_sheet.sample_sheet_creator import SampleSheetCreatorBCLConvert
+from cg.constants.demultiplexing import (
+    NO_REVERSE_COMPLEMENTS,
+    NOVASEQ_6000_POST_1_5_KITS,
+    NOVASEQ_X_INDEX_SETTINGS,
+    IndexSettings,
+    RunParametersXMLNodes,
+)
 from cg.constants.sequencing import Sequencers
 from cg.exc import RunParametersError, XMLError
 from cg.models.demultiplex.run_parameters import (