Merge pull request #27 from glrs/feature/ss3-dev

Feature/ss3 dev - Safeguarding against aborted sample irregularities

lib/realms/smartseq3/ss3_project.py

@@ -200,6 +200,10 @@ def extract_samples(self):
         samples = []
 
         for sample_id, sample_data in self.doc.get("samples", {}).items():
+            sample_status = sample_data.get("details", {}).get("status_(manual)", "")
+            if sample_status.lower() == "aborted":
+                logging.info(f"Skipping aborted sample '{sample_id}'.")
+                continue  # Skip this sample
             sample = SS3Sample(
                 sample_id, sample_data, self.project_info, self.config, self.ydm
             )

lib/realms/smartseq3/ss3_sample.py

@@ -133,12 +133,18 @@ def get_barcode(self):
         Returns:
             str: The barcode of the sample.
         """
-        barcode = self.sample_data["library_prep"]["A"].get("barcode", None)
-        if barcode:
-            return barcode.split("-")[-1]
-        else:
-            logging.warning(f"No barcode found in StatusDB for sample {self.id}.")
-            return None  # Or handle more appropriately based on your application's requirements
+        try:
+            library_prep = self.sample_data.get("library_prep", {})
+            prep_A = library_prep.get("A", {})
+            barcode = prep_A.get("barcode", None)
+            if barcode:
+                return barcode.split("-")[-1]
+            else:
+                logging.warning(f"No barcode found for sample {self.id}.")
+                return None  # Or handle more appropriately based on your application's requirements
+        except Exception as e:
+            logging.error(f"Error extracting barcode for sample {self.id}: {e}")
+            return None
 
     def _collect_yaml_metadata(self):
         """