Merge pull request #19 from glrs/feature/10x-dev

Improve status tracking and logging

lib/realms/tenx/run_sample.py

@@ -127,7 +127,7 @@ def collect_reference_genomes(self) -> Optional[Dict[str, str]]:
                     )
                     logging.error(
                         f"Conflicting reference genomes found for reference key '{ref_key}' "
-                        f"in sample '{self.run_sample_id}'"
+                        f"in sample '{self.id}'"
                     )
                     self.status = "failed"
                     return None
@@ -220,6 +220,7 @@ async def pre_process(self):
 
         # If all pre-processing steps succeeded
         self.status = "pre_processed"
+        logging.info(f"[{self.id}] Pre-processing completed successfully.")
 
     async def process(self):
         """Process the sample."""
@@ -277,12 +278,12 @@ def assemble_cellranger_command(self) -> str:
 
         command_parts = [f"{pipeline_exec} {pipeline}"]
 
-        logging.debug(f"[{self.run_sample_id}] Pipeline: {pipeline}")
-        logging.debug(f"[{self.run_sample_id}] Pipeline executable: {pipeline_exec}")
+        logging.debug(f"[{self.id}] Pipeline: {pipeline}")
+        logging.debug(f"[{self.id}] Pipeline executable: {pipeline_exec}")
 
         # Mapping of argument names to their values
         arg_values: Dict[str, Any] = {
-            "--id": self.run_sample_id,
+            "--id": self.id,
             "--csv": str(self.file_handler.get_multi_csv_path()),
             "--transcriptome": self.reference_genomes["gex"],
             "--fastqs": ",".join(
@@ -312,9 +313,7 @@ def assemble_cellranger_command(self) -> str:
             if value:
                 command_parts.append(f"{arg}={value}")
             else:
-                logging.error(
-                    f"[{self.run_sample_id}] Missing value for required argument {arg}"
-                )
+                logging.error(f"[{self.id}] Missing value for required argument {arg}")
 
         # Include additional arguments
         command_parts.extend(additional_args)
@@ -333,7 +332,7 @@ def collect_libraries_data(self) -> List[Dict[str, str]]:
             feature_type = self.feature_to_library_type.get(lab_sample.feature)
             if not feature_type:
                 logging.error(
-                    f"[{self.run_sample_id}] Feature type not found for feature "
+                    f"[{self.id}] Feature type not found for feature "
                     f"'{lab_sample.feature}' in sample '{lab_sample.sample_id}'"
                 )
                 continue
@@ -351,7 +350,7 @@ def collect_libraries_data(self) -> List[Dict[str, str]]:
 
     def generate_libraries_csv(self) -> None:
         """Generate the libraries CSV file required for processing."""
-        logging.info(f"[{self.run_sample_id}] Generating library CSV")
+        logging.info(f"[{self.id}] Generating library CSV")
         library_csv_path = self.file_handler.get_libraries_csv_path()
 
         # Ensure the directory exists
@@ -367,19 +366,17 @@ def generate_libraries_csv(self) -> None:
             for lib in libraries_data:
                 writer.writerow(lib)
 
-        logging.info(
-            f"[{self.run_sample_id}] Libraries CSV generated at {library_csv_path}"
-        )
+        logging.info(f"[{self.id}] Libraries CSV generated at {library_csv_path}")
 
     def generate_feature_reference_csv(self) -> None:
         """Generate the feature reference CSV file required for processing."""
-        logging.info(f"[{self.run_sample_id}] Generating feature reference CSV")
+        logging.info(f"[{self.id}] Generating feature reference CSV")
         # feature_ref_csv_path = self.file_handler.get_feature_reference_csv_path()
         pass
 
     def generate_multi_sample_csv(self) -> None:
         """Generate the multi-sample CSV file required for processing."""
-        logging.info(f"[{self.run_sample_id}] Generating multi-sample CSV")
+        logging.info(f"[{self.id}] Generating multi-sample CSV")
         multi_csv_path = self.file_handler.get_multi_csv_path()
 
         # Ensure the directory exists
@@ -417,23 +414,24 @@ def generate_multi_sample_csv(self) -> None:
                     f"{lib['sample']},{lib['fastqs']},{lib['library_type']}\n"
                 )
 
-        logging.info(
-            f"[{self.run_sample_id}] Multi-sample CSV generated at {multi_csv_path}"
-        )
+        logging.info(f"[{self.id}] Multi-sample CSV generated at {multi_csv_path}")
 
     def post_process(self) -> None:
         """Perform post-processing steps after job completion."""
         logging.info("\n")
-        logging.info(f"[{self.run_sample_id}] Post-processing...")
+        logging.info(f"[{self.id}] Post-processing...")
+        self.status = "post_processing"
 
         # Check if the run was successful
         if not self.file_handler.check_run_success():
-            self.status = "failed"
+            logging.error(f"[{self.id}] CellRanger run was not successful.")
+            self.status = "post_processing_failed"
             return
 
         # Extract the report path
         if not self.file_handler.extract_report_path():
-            self.status = "failed"
+            logging.error(f"[{self.id}] Failed to extract report path.")
+            self.status = "post_processing_failed"
             return
 
         # Transfer the report
@@ -442,6 +440,12 @@ def post_process(self) -> None:
             project_id=self.project_info.get("project_id", ""),
             sample_id=self.id,
         ):
-            logging.info(f"Report for sample {self.id} transferred successfully.")
+            logging.info(f"[{self.id}] Report transferred successfully.")
         else:
-            logging.error(f"Failed to transfer report for sample {self.id}.")
+            logging.error(f"[{self.id}] Failed to transfer report.")
+            self.status = "post_processing_failed"
+            return
+
+        # If all post-processing steps succeeded
+        self.status = "completed"
+        logging.info(f"[{self.id}] Post-processing completed successfully.")