vincent review

cg/services/deliver_files/deliver_files_service/deliver_files_service.py

@@ -75,7 +75,7 @@ def deliver_files_for_case(
         formatted_files: FormattedFiles = self.file_formatter.format_files(
             delivery_files=moved_files
         )
-     
+
         folders_to_deliver: set[Path] = set(
             [formatted_file.formatted_path.parent for formatted_file in formatted_files.files]
         )

cg/services/deliver_files/factory.py

@@ -25,14 +25,14 @@
 from cg.services.deliver_files.file_formatter.destination.base_service import (
     BaseDeliveryFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.case_service import CaseFileFormatter
-from cg.services.deliver_files.file_formatter.component_files.mutant_service import (
+from cg.services.deliver_files.file_formatter.files.case_service import CaseFileFormatter
+from cg.services.deliver_files.file_formatter.files.mutant_service import (
     MutantFileFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.concatenation_service import (
+from cg.services.deliver_files.file_formatter.files.concatenation_service import (
     SampleFileConcatenationFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.sample_service import (
+from cg.services.deliver_files.file_formatter.files.sample_service import (
     SampleFileFormatter,
     FileManager,
 )

cg/services/deliver_files/file_formatter/destination/base_service.py

@@ -9,14 +9,14 @@
     FormattedFile,
     FormattedFiles,
 )
-from cg.services.deliver_files.file_formatter.component_files.case_service import CaseFileFormatter
-from cg.services.deliver_files.file_formatter.component_files.mutant_service import (
+from cg.services.deliver_files.file_formatter.files.case_service import CaseFileFormatter
+from cg.services.deliver_files.file_formatter.files.mutant_service import (
     MutantFileFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.concatenation_service import (
+from cg.services.deliver_files.file_formatter.files.concatenation_service import (
     SampleFileConcatenationFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.sample_service import (
+from cg.services.deliver_files.file_formatter.files.sample_service import (
     SampleFileFormatter,
 )
 

cg/services/deliver_files/file_formatter/component_files/abstract.py → cg/services/deliver_files/file_formatter/files/abstract.py

@@ -5,8 +5,8 @@
 from cg.services.deliver_files.file_formatter.destination.models import FormattedFile
 
 
-class ComponentFormatter(ABC):
-
+class FileFormatter(ABC):
+    # rename to file formatter
     @abstractmethod
     def format_files(
         self, moved_files: list[CaseFile | SampleFile], delivery_path: Path

cg/services/deliver_files/file_formatter/component_files/case_service.py → cg/services/deliver_files/file_formatter/files/case_service.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 from cg.services.deliver_files.file_fetcher.models import CaseFile
-from cg.services.deliver_files.file_formatter.component_files.abstract import ComponentFormatter
+from cg.services.deliver_files.file_formatter.files.abstract import FileFormatter
 from cg.services.deliver_files.file_formatter.destination.models import FormattedFile
 from cg.services.deliver_files.file_formatter.path_name.abstract import PathNameFormatter
 from cg.services.deliver_files.file_formatter.path_name.nested_structure import (
@@ -13,7 +13,7 @@
 LOG = logging.getLogger(__name__)
 
 
-class CaseFileFormatter(ComponentFormatter):
+class CaseFileFormatter(FileFormatter):
     """
     Format the case files to deliver and return the formatted files.
     args:

cg/services/deliver_files/file_formatter/component_files/concatenation_service.py → cg/services/deliver_files/file_formatter/files/concatenation_service.py

@@ -3,8 +3,8 @@
 import re
 
 from cg.constants.constants import ReadDirection, FileFormat, FileExtensions
-from cg.services.deliver_files.file_formatter.component_files.abstract import ComponentFormatter
-from cg.services.deliver_files.file_formatter.component_files.models import FastqFile
+from cg.services.deliver_files.file_formatter.files.abstract import FileFormatter
+from cg.services.deliver_files.file_formatter.files.models import FastqFile
 from cg.services.deliver_files.file_formatter.path_name.abstract import PathNameFormatter
 
 from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
@@ -13,7 +13,7 @@
 from cg.services.fastq_concatenation_service.utils import generate_concatenated_fastq_delivery_path
 from cg.services.deliver_files.file_fetcher.models import SampleFile
 from cg.services.deliver_files.file_formatter.destination.models import FormattedFile
-from cg.services.deliver_files.file_formatter.component_files.sample_service import (
+from cg.services.deliver_files.file_formatter.files.sample_service import (
     FileManager,
 )
 from cg.services.deliver_files.file_formatter.path_name.nested_structure import (
@@ -24,7 +24,7 @@
 LOG = logging.getLogger(__name__)
 
 
-class SampleFileConcatenationFormatter(ComponentFormatter):
+class SampleFileConcatenationFormatter(FileFormatter):
     """
     Format the sample files to deliver, concatenate fastq files and return the formatted files.
     Used for workflows: Microsalt.

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

@@ -3,17 +3,17 @@
 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
+from cg.services.deliver_files.file_formatter.files.abstract import FileFormatter
 from cg.services.deliver_files.file_formatter.destination.models import FormattedFile
-from cg.services.deliver_files.file_formatter.component_files.concatenation_service import (
+from cg.services.deliver_files.file_formatter.files.concatenation_service import (
     SampleFileConcatenationFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.sample_service import FileManager
+from cg.services.deliver_files.file_formatter.files.sample_service import FileManager
 
 LOG = logging.getLogger(__name__)
 
 
-class MutantFileFormatter(ComponentFormatter):
+class MutantFileFormatter(FileFormatter):
     """
     Formatter for file to deliver or upload for the Mutant workflow.
     Args:
@@ -127,7 +127,7 @@ def _filter_unique_path_combinations(
         Filter out duplicates from the formatted files list.
 
         note:
-            During fastq concatenation Sample_R1 and Sample_R2 files are concatenated
+            During fastq concatenation Sample_L1_R1 and Sample_L2_R1 files are concatenated
             and moved to the same file Concat_Sample. This mean that there can be multiple entries
             for the same concatenated file in the formatted_files list
             coming from the SampleFileConcatenationService.

cg/services/deliver_files/file_formatter/component_files/sample_service.py → cg/services/deliver_files/file_formatter/files/sample_service.py

@@ -2,15 +2,15 @@
 from pathlib import Path
 
 from cg.services.deliver_files.file_fetcher.models import SampleFile
-from cg.services.deliver_files.file_formatter.component_files.abstract import ComponentFormatter
+from cg.services.deliver_files.file_formatter.files.abstract import FileFormatter
 from cg.services.deliver_files.file_formatter.destination.models import FormattedFile
 from cg.services.deliver_files.file_formatter.path_name.abstract import PathNameFormatter
 from cg.services.deliver_files.utils import FileManager
 
 LOG = logging.getLogger(__name__)
 
 
-class SampleFileFormatter(ComponentFormatter):
+class SampleFileFormatter(FileFormatter):
     """
     Format the sample files to deliver.
     Used for all workflows except Microsalt and Mutant.

cg/services/deliver_files/file_formatter/path_name/flat_structure.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from cg.services.deliver_files.file_formatter.component_files.sample_service import LOG
+from cg.services.deliver_files.file_formatter.files.sample_service import LOG
 from cg.services.deliver_files.file_formatter.path_name.abstract import PathNameFormatter
 
 

cg/services/deliver_files/file_formatter/path_name/nested_structure.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from cg.services.deliver_files.file_formatter.component_files.sample_service import LOG
+from cg.services.deliver_files.file_formatter.files.sample_service import LOG
 from cg.services.deliver_files.file_formatter.path_name.abstract import PathNameFormatter
 
 

tests/fixture_plugins/delivery_fixtures/delivery_services_fixtures.py

@@ -18,10 +18,10 @@
 from cg.services.deliver_files.file_fetcher.raw_data_service import (
     RawDataDeliveryFileFetcher,
 )
-from cg.services.deliver_files.file_formatter.component_files.case_service import (
+from cg.services.deliver_files.file_formatter.files.case_service import (
     CaseFileFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.sample_service import (
+from cg.services.deliver_files.file_formatter.files.sample_service import (
     SampleFileFormatter,
     FileManager,
 )

tests/services/file_delivery/delivery_file_service/test_service_builder.py

@@ -18,13 +18,13 @@
 )
 from cg.services.deliver_files.file_fetcher.analysis_service import AnalysisDeliveryFileFetcher
 from cg.services.deliver_files.file_fetcher.raw_data_service import RawDataDeliveryFileFetcher
-from cg.services.deliver_files.file_formatter.component_files.mutant_service import (
+from cg.services.deliver_files.file_formatter.files.mutant_service import (
     MutantFileFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.concatenation_service import (
+from cg.services.deliver_files.file_formatter.files.concatenation_service import (
     SampleFileConcatenationFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.sample_service import (
+from cg.services.deliver_files.file_formatter.files.sample_service import (
     SampleFileFormatter,
 )
 from cg.services.deliver_files.file_formatter.path_name.abstract import PathNameFormatter

tests/services/file_delivery/file_formatter/destination/test_formatting_service.py

@@ -70,10 +70,10 @@ def test_reformat_files(
 
     expected_formatted_files = FormattedFiles(files=files)
     with mock.patch(
-        "cg.services.deliver_files.file_formatter.component_files.sample_service.SampleFileFormatter.format_files",
+        "cg.services.deliver_files.file_formatter.files.sample_service.SampleFileFormatter.format_files",
         return_value=formatted_sample_files,
     ), mock.patch(
-        "cg.services.deliver_files.file_formatter.component_files.case_service.CaseFileFormatter.format_files",
+        "cg.services.deliver_files.file_formatter.files.case_service.CaseFileFormatter.format_files",
         return_value=formatted_case_files,
     ):
         # WHEN reformatting the delivery files

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

@@ -3,8 +3,8 @@
 import pytest
 from pathlib import Path
 
-from cg.services.deliver_files.file_formatter.component_files.abstract import ComponentFormatter
-from cg.services.deliver_files.file_formatter.component_files.mutant_service import (
+from cg.services.deliver_files.file_formatter.files.abstract import FileFormatter
+from cg.services.deliver_files.file_formatter.files.mutant_service import (
     MutantFileFormatter,
 )
 from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
@@ -15,13 +15,13 @@
     SampleFile,
 )
 from cg.services.deliver_files.file_formatter.destination.models import FormattedFile
-from cg.services.deliver_files.file_formatter.component_files.case_service import (
+from cg.services.deliver_files.file_formatter.files.case_service import (
     CaseFileFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.concatenation_service import (
+from cg.services.deliver_files.file_formatter.files.concatenation_service import (
     SampleFileConcatenationFormatter,
 )
-from cg.services.deliver_files.file_formatter.component_files.sample_service import (
+from cg.services.deliver_files.file_formatter.files.sample_service import (
     SampleFileFormatter,
     FileManager,
 )
@@ -73,7 +73,7 @@
 def test_component_formatters(
     moved_files: list[CaseFile | SampleFile],
     expected_formatted_files: list[FormattedFile],
-    file_formatter: ComponentFormatter,
+    file_formatter: FileFormatter,
     request,
 ):
     # GIVEN existing case files, a case file formatter and a ticket directory path and a customer inbox