Fixing tests

tests/apps/demultiplex/conftest.py

@@ -2,7 +2,6 @@
 
 import pytest
 
-from cg.apps.demultiplex.sample_sheet.index import Index
 from cg.apps.demultiplex.sample_sheet.sample_models import (
     FlowCellSampleBcl2Fastq,
     FlowCellSampleBCLConvert,
@@ -45,12 +44,6 @@ def bcl_convert_samples_similar_index2() -> list[FlowCellSampleBCLConvert]:
     return [sample_1, sample_2, sample_3]
 
 
-@pytest.fixture
-def valid_index() -> Index:
-    """Return a valid index."""
-    return Index(name="C07 - UDI0051", sequence="AACAGGTT-ATACCAAG")
-
-
 @pytest.fixture
 def bcl2fastq_sample_sheet_creator(
     novaseq_flow_cell_demultiplexed_with_bcl2fastq: FlowCellDirectoryData,

tests/apps/demultiplex/test_sample_models.py

@@ -174,7 +174,7 @@ def test_get_index1_override_cycles(
 def test_get_index2_override_cycles(
     raw_index: str, index2_cycles: int, reverse_cycle: bool, expected_parsed_cycles: str
 ):
-    """Test that the returned index 2 cycles is teh expected for different index configurations."""
+    """Test that the returned index 2 cycles is the expected for different index configurations."""
     # GIVEN a FlowCellSampleBCLConvert with separated indexes
     sample = FlowCellSampleBCLConvert(lane=1, index=raw_index, sample_id="ACC123")
     sample.separate_indexes()
@@ -191,6 +191,8 @@ def test_get_index2_override_cycles(
 def test_update_override_cycles():
     # TODO: Parametrise this test with different run parameter files and samples
     """."""
+    # GIVEN a run parameters object
+
     # GIVEN a FlowCellSampleBCLConvert
 
     # WHEN updating the override cycles
@@ -245,49 +247,40 @@ def test_update_barcode_mismatches_2(
 
 
 @pytest.mark.parametrize(
-    "run_parameters_fixture, raw_lims_samples_fixture, sample_model",
+    "run_parameters_fixture, raw_lims_samples_fixture",
     [
-        ("novaseq_x_run_parameters", "novaseq_x_lims_samples", FlowCellSampleBCLConvert),
-        (
-            "novaseq_6000_run_parameters_pre_1_5_kits",
-            "novaseq_6000_pre_1_5_kits_lims_samples",
-            FlowCellSampleBCLConvert,
-        ),
-        (
-            "novaseq_6000_run_parameters_post_1_5_kits",
-            "novaseq_6000_post_1_5_kits_lims_samples",
-            FlowCellSampleBCLConvert,
-        ),
-        ("hiseq_x_run_parameters_single_index", "hiseq_x_lims_samples", FlowCellSampleBCLConvert),
-        ("hiseq_x_run_parameters_single_index", "hiseq_x_lims_samples", FlowCellSampleBcl2Fastq),
-        (
-            "hiseq_2500_run_parameters_double_index",
-            "hiseq_2500_lims_samples",
-            FlowCellSampleBCLConvert,
-        ),
-        (
-            "hiseq_2500_run_parameters_double_index",
-            "hiseq_2500_lims_samples",
-            FlowCellSampleBcl2Fastq,
-        ),
+        ("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"),
+        ("hiseq_x_run_parameters_single_index", "hiseq_x_lims_samples"),
+        ("hiseq_2500_run_parameters_double_index", "hiseq_2500_lims_samples"),
     ],
     ids=[
         "NovaSeqX",
         "NovaSeq6000 pre1.5",
         "NovaSeq6000 post1.5",
-        "HiSeqX BclConvert",
-        "HiSeqX Bcl2Fastq",
-        "HiSeq2500 BCLConvert",
-        "HiSeq2500 Bcl2Fastq",
+        "HiSeqX",
+        "HiSeq2500",
     ],
 )
-def test_process_sample_for_sample_sheet(
-    run_parameters_fixture: str, raw_lims_samples_fixture: str, sample_model: Type[FlowCellSample]
+def test_process_sample_for_sample_sheet_bcl_convert(
+    run_parameters_fixture: str, raw_lims_samples_fixture: str, request: pytest.FixtureRequest
 ):
-    # TODO: We need a raw FlowCellSampleBcl2Fastq and a raw FlowCellSampleBCLConvert
+    # TODO: We need a raw FlowCellSampleBCLConvert
     """."""
-    # GIVEN a run parameters object and a list of samples from a flow cell
+    # GIVEN a run parameters object and a list of BCLConvert samples from a flow cell
+    run_parameters: RunParameters = request.getfixturevalue(run_parameters_fixture)
+    raw_lims_samples: list[FlowCellSampleBCLConvert] = request.getfixturevalue(
+        raw_lims_samples_fixture
+    )
+
+    # GIVEN a FlowCellSampleBCLConvert
+    sample: FlowCellSampleBCLConvert = raw_lims_samples[0]
 
     # WHEN processing the sample for a sample sheet
+    sample.process_sample_for_sample_sheet(run_parameters=run_parameters)
 
     # THEN the sample is processed
+    assert sample.barcode_mismatches_1
+    assert sample.barcode_mismatches_2
+    assert sample.override_cycles

tests/conftest.py

@@ -1396,12 +1396,6 @@ def novaseq_bcl_convert_sample_sheet_path(bcl_convert_flow_cell_dir: Path) -> Pa
     return Path(bcl_convert_flow_cell_dir, DemultiplexingDirsAndFiles.SAMPLE_SHEET_FILE_NAME)
 
 
-@pytest.fixture(scope="session")
-def run_parameters_missing_versions_path(run_parameters_dir: Path) -> Path:
-    """Return a NovaSeq6000 run parameters file path without software and reagent kit versions."""
-    return Path(run_parameters_dir, "RunParameters_novaseq_no_software_nor_reagent_version.xml")
-
-
 @pytest.fixture(scope="session")
 def run_parameters_wrong_instrument(run_parameters_dir: Path) -> Path:
     """Return a NovaSeqX run parameters file path with a wrong instrument value."""
@@ -1483,10 +1477,11 @@ def run_parameters_novaseq_x_different_index(run_parameters_dir: Path) -> RunPar
 
 @pytest.fixture(scope="module")
 def run_parameters_missing_versions(
-    run_parameters_missing_versions_path: Path,
+    run_parameters_dir: Path,
 ) -> RunParametersNovaSeq6000:
     """Return a NovaSeq6000 run parameters object without software and reagent kit versions."""
-    return RunParametersNovaSeq6000(run_parameters_path=run_parameters_missing_versions_path)
+    path = Path(run_parameters_dir, "RunParameters_novaseq_no_software_nor_reagent_version.xml")
+    return RunParametersNovaSeq6000(run_parameters_path=path)
 
 
 @pytest.fixture(scope="session")

tests/fixtures/apps/demultiplexing/flow_cells/180509_D00450_0598_BHGYFNBCX2/README.txt

@@ -1,4 +1,5 @@
 Sequencer: HiSeq2500
+Workflow: CUSTOM
 Indexes: 17,8
 BCL converter: BCLConvert
 

tests/models/demultiplexing/test_run_parameters.py

@@ -4,6 +4,7 @@
 
 import pytest
 from _pytest.fixtures import FixtureRequest
+from pydantic import BaseModel
 
 from cg.apps.demultiplex.sample_sheet.sample_sheet_creator import SampleSheetCreatorBCLConvert
 from cg.constants.demultiplexing import (
@@ -75,41 +76,67 @@ def test_run_parameters_init(
     assert run_parameters.sequencer == sequencer
 
 
+class RunParametersScenario(BaseModel):
+    wrong_run_parameters_path_fixture: str
+    constructor: Type[RunParameters]
+    error_msg: str
+
+
 @pytest.mark.parametrize(
-    "wrong_run_parameters_path_fixture, constructor, node_name",
+    "scenario",
     [
-        (
-            "novaseq_6000_run_parameters_path",
-            RunParametersHiSeq,
-            RunParametersXMLNodes.APPLICATION_NAME,
+        RunParametersScenario(
+            wrong_run_parameters_path_fixture="novaseq_6000_run_parameters_path",
+            constructor=RunParametersHiSeq,
+            error_msg=f"Could not find node {RunParametersXMLNodes.APPLICATION_NAME} in the run parameters file.",
+        ),
+        RunParametersScenario(
+            wrong_run_parameters_path_fixture="novaseq_x_run_parameters_path",
+            constructor=RunParametersHiSeq,
+            error_msg=f"Could not find node {RunParametersXMLNodes.APPLICATION_NAME} in the run parameters file.",
+        ),
+        RunParametersScenario(
+            wrong_run_parameters_path_fixture="novaseq_x_run_parameters_path",
+            constructor=RunParametersNovaSeq6000,
+            error_msg=f"The file parsed does not correspond to {RunParametersXMLNodes.NOVASEQ_6000_APPLICATION}",
+        ),
+        RunParametersScenario(
+            wrong_run_parameters_path_fixture="hiseq_x_single_index_run_parameters_path",
+            constructor=RunParametersNovaSeq6000,
+            error_msg=f"Could not find node {RunParametersXMLNodes.APPLICATION} in the run parameters file.",
         ),
-        (
-            "novaseq_x_run_parameters_path",
-            RunParametersNovaSeq6000,
-            RunParametersXMLNodes.APPLICATION,
+        RunParametersScenario(
+            wrong_run_parameters_path_fixture="hiseq_x_single_index_run_parameters_path",
+            constructor=RunParametersNovaSeqX,
+            error_msg=f"Could not find node {RunParametersXMLNodes.INSTRUMENT_TYPE} in the run parameters file.",
         ),
-        (
-            "hiseq_x_single_index_run_parameters_path",
-            RunParametersNovaSeqX,
-            RunParametersXMLNodes.INSTRUMENT_TYPE,
+        RunParametersScenario(
+            wrong_run_parameters_path_fixture="novaseq_6000_run_parameters_path",
+            constructor=RunParametersNovaSeqX,
+            error_msg=f"Could not find node {RunParametersXMLNodes.INSTRUMENT_TYPE} in the run parameters file.",
         ),
     ],
+    ids=[
+        "NovaSeq 6000 file, HiSeq constructor",
+        "NovaSeq X file, HiSeq constructor",
+        "NovaSeq X file, NovaSeq6000 constructor",
+        "HiSeq X file, NovaSeq600 constructor",
+        "HiSeq X file, NovaSeqX constructor",
+        "NovaSeq6000 constructor, NovaSeqX constructor",
+    ],
 )
-def test_run_parameters_wrong_file(
-    wrong_run_parameters_path_fixture: str,
-    constructor: Type[RunParameters],
-    node_name: str,
-    request: FixtureRequest,
-):
+def test_run_parameters_wrong_file(scenario: RunParametersScenario, request: FixtureRequest):
     """Test that creating a RunParameters object with a wrong file fails."""
     # GIVEN a run parameters path from an instrument different from the expected
-    wrong_run_parameters_path: Path = request.getfixturevalue(wrong_run_parameters_path_fixture)
+    wrong_run_parameters_path: Path = request.getfixturevalue(
+        scenario.wrong_run_parameters_path_fixture
+    )
 
     # WHEN trying to create a RunParameters object with the file
     with pytest.raises(RunParametersError) as exc_info:
         # THEN a RunParametersError is raised
-        constructor(run_parameters_path=wrong_run_parameters_path)
-    assert f"Could not find node {node_name} in the run parameters file" in str(exc_info.value)
+        scenario.constructor(run_parameters_path=wrong_run_parameters_path)
+    assert scenario.error_msg in str(exc_info.value)
 
 
 def test_run_parameters_hiseq_wrong_file(novaseq_6000_run_parameters_path: Path):