adjust fastq file check

cg/services/deliver_files/file_formatter/component_files/mutant_service.py

@@ -1,6 +1,6 @@
 import logging
 from pathlib import Path
-
+import re
 from cg.apps.lims import LimsAPI
 from cg.services.deliver_files.file_fetcher.models import SampleFile
 from cg.services.deliver_files.file_formatter.component_files.abstract import ComponentFormatter
@@ -59,6 +59,20 @@ def format_files(
             )
         return unique_formatted_files
 
+    @staticmethod
+    def _is_concatenated_file(file_path: Path) -> bool:
+        """Check if the file is a concatenated file.
+        Returns True if the file is a concatenated file, otherwise False.
+        regex pattern: *._R[1,2]_[0-9]+.fastq.gz
+        *. is the sample id
+        _R[1,2] is the read direction
+        .fastq.gz is the file extension
+        args:
+            file_path: The file path to check
+        """
+        pattern = ".*_[1,2].fastq.gz"
+        return re.fullmatch(pattern, file_path.name) is not None
+
     def _add_lims_metadata_to_file_name(
         self, formatted_files: list[FormattedFile], sample_files: list[SampleFile]
     ) -> list[FormattedFile]:
@@ -73,7 +87,7 @@ def _add_lims_metadata_to_file_name(
         """
         appended_formatted_files: list[FormattedFile] = []
         for formatted_file in formatted_files:
-            if self.file_formatter._is_lane_fastq_file(formatted_file.formatted_path):
+            if self._is_concatenated_file(formatted_file.formatted_path):
                 sample_id: str = self._get_sample_id_by_original_path(
                     original_path=formatted_file.original_path, sample_files=sample_files
                 )

tests/fixture_plugins/delivery_fixtures/delivery_files_models_fixtures.py

@@ -1,3 +1,4 @@
+import os
 from pathlib import Path
 
 import pytest
@@ -361,20 +362,20 @@ def swap_file_paths_with_inbox_paths(
 
 
 @pytest.fixture
-def lims_naming_matadata() -> str:
+def lims_naming_metadata() -> str:
     return "01_SE100_"
 
 
 @pytest.fixture
 def expected_mutant_formatted_files(
-    expected_concatenated_fastq_formatted_files, lims_naming_matadata
+    expected_concatenated_fastq_formatted_files, lims_naming_metadata
 ) -> list[FormattedFile]:
     unique_combinations = []
     for formatted_file in expected_concatenated_fastq_formatted_files:
         formatted_file.original_path = formatted_file.formatted_path
         formatted_file.formatted_path = Path(
             formatted_file.formatted_path.parent,
-            f"{lims_naming_matadata}{formatted_file.formatted_path.name}",
+            f"{lims_naming_metadata}{formatted_file.formatted_path.name}",
         )
         if formatted_file not in unique_combinations:
             unique_combinations.append(formatted_file)

tests/fixture_plugins/delivery_fixtures/path_fixtures.py

@@ -9,7 +9,7 @@
 
 @pytest.fixture
 def delivery_fastq_file(tmp_path: Path, sample_id: str) -> Path:
-    file = Path(tmp_path, f"{sample_id}_R1_001{FileExtensions.FASTQ_GZ}")
+    file = Path(tmp_path, f"{sample_id}_L001_R1_001{FileExtensions.FASTQ_GZ}")
     file.touch()
     return file
 
@@ -34,7 +34,7 @@ def delivery_bam_file(tmp_path: Path, sample_id: str) -> Path:
 
 @pytest.fixture
 def delivery_another_fastq_file(tmp_path: Path, another_sample_id: str) -> Path:
-    file = Path(tmp_path, f"{another_sample_id}_R1_001{FileExtensions.FASTQ_GZ}")
+    file = Path(tmp_path, f"{another_sample_id}L001_R1_001{FileExtensions.FASTQ_GZ}")
     file.touch()
     return file
 

tests/services/file_delivery/file_formatter/component_files/test_formatter_utils.py

@@ -104,7 +104,7 @@ def test_component_formatters(
 def test_mutant_file_formatter(
     mutant_moved_files: list[SampleFile],
     expected_mutant_formatted_files: list[FormattedFile],
-    lims_naming_matadata: str,
+    lims_naming_metadata: str,
 ):
     # GIVEN existing ticket directory path and a customer inbox
     ticket_dir_path: Path = mutant_moved_files[0].file_path.parent
@@ -115,7 +115,7 @@ def test_mutant_file_formatter(
         moved_file.file_path.touch()
 
     lims_mock = Mock()
-    lims_mock.get_sample_region_and_lab_code.return_value = lims_naming_matadata
+    lims_mock.get_sample_region_and_lab_code.return_value = lims_naming_metadata
     file_formatter = MutantFileFormatter(
         file_manager=FileManager(),
         file_formatter=SampleFileConcatenationFormatter(