address comments by CO and SA

Clinical-Genomics · Jul 26, 2024 · f73d6b8 · f73d6b8
1 parent c173235
commit f73d6b8
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Showing 2 changed files with 13 additions and 5 deletions.
diff --git a/cg/services/post_processing/abstract_classes.py b/cg/services/post_processing/abstract_classes.py
@@ -36,9 +36,10 @@ def get_files_to_store(self, run_data: RunData) -> list[Path]:
 
 class PostProcessingMetricsParser(ABC):
 
-    @staticmethod
-    @abstractmethod
-    def parse_metrics(metrics_files: list[Path]) -> RunMetrics:
+    def __init__(self, file_manager: RunFileManager):
+        self.file_manager: RunFileManager = file_manager
+
+    def parse_metrics(self, run_data: RunData) -> RunMetrics:
         pass
 
 

diff --git a/cg/services/post_processing/pacbio/metrics_parser/metrics_parser.py b/cg/services/post_processing/pacbio/metrics_parser/metrics_parser.py
@@ -13,14 +13,21 @@
 from cg.services.post_processing.pacbio.metrics_parser.utils import (
     get_parsed_metrics_from_file_name,
 )
+from cg.services.post_processing.pacbio.run_data_generator.run_data import PacBioRunData
+from cg.services.post_processing.pacbio.run_file_manager.run_file_manager import (
+    PacBioRunFileManager,
+)
 
 
 class PacBioMetricsParser(PostProcessingMetricsParser):
     """Class for parsing PacBio sequencing metrics."""
 
-    @staticmethod
-    def parse_metrics(metrics_files: list[Path]) -> PacBioMetrics:
+    def __init__(self, file_manager: PacBioRunFileManager):
+        super().__init__(file_manager=file_manager)
+
+    def parse_metrics(self, run_data: PacBioRunData) -> PacBioMetrics:
         """Return all the relevant PacBio metrics parsed in a single Pydantic object."""
+        metrics_files: list[Path] = self.file_manager.get_files_to_parse(run_data)
         hifi_metrics: HiFiMetrics = get_parsed_metrics_from_file_name(
             metrics_files=metrics_files, file_name=PacBioDirsAndFiles.BASECALLING_REPORT
         )