update logging warnings

medema-group · Nov 18, 2024 · a098509 · a098509
1 parent 5e5fc0a
commit a098509
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Showing 2 changed files with 23 additions and 1 deletion.
diff --git a/big_scape/file_input/load_files.py b/big_scape/file_input/load_files.py
@@ -197,7 +197,7 @@ def remove_duplicate_gbk(gbks: list[GBK]) -> list[GBK]:
     unique_gbks = set()
     for gbk in gbks:
         if gbk in unique_gbks:
-            logging.info("Skipping duplicate %s", gbk)
+            logging.info("Skipping duplicate %s", gbk.path)
             continue
         unique_gbks.add(gbk)
 

diff --git a/big_scape/genbank/bgc_record.py b/big_scape/genbank/bgc_record.py
@@ -403,13 +403,20 @@ def get_sub_records(
     Returns:
         list[BGCRecord]: list of records of the specified type
     """
+    err_path = region.parent_gbk.path if region.parent_gbk else ""
+
     if region is None:
         return []
 
     if record_type == bs_enums.genbank.RECORD_TYPE.REGION:
         return [region]
 
     if region.cand_clusters is None:
+        logging.warning(
+            "%s: No %s records found, using region instead.",
+            err_path,
+            record_type.value,
+        )
         return [region]
 
     cand_clusters = [
@@ -419,6 +426,11 @@ def get_sub_records(
     ]
 
     if len(cand_clusters) == 0:
+        logging.warning(
+            "%s: No %s records found, using region instead.",
+            err_path,
+            record_type.value,
+        )
         return [region]
 
     # TODO: check if properly implemented, or at all
@@ -445,6 +457,11 @@ def get_sub_records(
                 proto_cluster_numbers.append(proto_cluster.number)
 
     if len(proto_clusters) == 0:
+        logging.warning(
+            "%s: No %s records found, using cand_cluster instead.",
+            err_path,
+            record_type.value,
+        )
         return cand_clusters
 
     if record_type == bs_enums.genbank.RECORD_TYPE.PROTO_CLUSTER:
@@ -461,6 +478,11 @@ def get_sub_records(
                 proto_core_numbers.append(proto_core.number)
 
     if len(proto_cores) == 0:
+        logging.warning(
+            "%s: No %s records found, using protocluster instead.",
+            err_path,
+            record_type.value,
+        )
         return proto_clusters
 
     return proto_cores