Improved logging and error handling.

Based on PR review feedback adding additional details to response for
failed barcode validation, additional logging for debugging purposes,
and respone with 500 status code for unidentified errors.

lib/id3c/api/datastore.py

@@ -411,15 +411,16 @@ def store_sample(session: DatabaseSession, sample: dict) -> Any:
             result["details"] = f"sample barcode «{sample_barcode}» not found"
         elif sample_identifier and sample_identifier.set_use != 'sample':
             result["status"] = "validation_failed"
-            result["details"] = f"barcode «{sample_barcode}» has use type «{sample_identifier.set_use}»"
+            result["details"] = f"barcode «{sample_barcode}» has use type «{sample_identifier.set_use}» instead of expected use type «sample»"
         elif collection_barcode and not collection_identifier:
             result["status"] = "validation_failed"
             result["details"] = f"collection barcode «{collection_barcode}» not found"
         elif collection_identifier and collection_identifier.set_use != 'collection':
             result["status"] = "validation_failed"
-            result["details"] = f"barcode «{collection_barcode}» has use type «{collection_identifier.set_use}»"
+            result["details"] = f"barcode «{collection_barcode}» has use type «{collection_identifier.set_use}» instead of expected use type «collection»"
 
         if result.get("status", None) == "validation_failed":
+            LOG.debug(f"Validation failed for {sample} with details: {result.get('details')}")
             return result
 
         collected_date = sample.get("collection_date", None)
@@ -428,16 +429,22 @@ def store_sample(session: DatabaseSession, sample: dict) -> Any:
         # the 'sample_barcode' and 'collection_barcode' keys
         should_update_identifiers = True if (sample_identifier and collection_identifier) else False
 
-        sample, status = upsert_sample(session,
-                update_identifiers          = should_update_identifiers,
-                identifier                  = sample_identifier.uuid if sample_identifier else None,
-                collection_identifier       = collection_identifier.uuid if collection_identifier else None,
-                collection_date             = collected_date,
-                encounter_id                = None,
-                additional_details          = sample)
+        try:
+            sample, status = upsert_sample(session,
+                    update_identifiers          = should_update_identifiers,
+                    identifier                  = sample_identifier.uuid if sample_identifier else None,
+                    collection_identifier       = collection_identifier.uuid if collection_identifier else None,
+                    collection_date             = collected_date,
+                    encounter_id                = None,
+                    additional_details          = sample)
+
+            result["sample"] = sample
+            result["status"] = status
+        except Exception as e:
+            result["status"] = "upsert_error"
+            result["details"] = f"error upserting sample record: {str(e)}"
+            LOG.debug(f"Error on upsert_sample: {str(e)}")
 
-        result["sample"] = sample
-        result["status"] = status
         return result
 
 @export

lib/id3c/api/routes.py

@@ -329,7 +329,13 @@ def post_sample(*, session):
 
     result = datastore.store_sample(session, sample)
 
-    return (jsonify(result), 200) if "sample" in result else (jsonify(result), 400)
+    status_code = 500
+    if "sample" in result:
+        status_code = 200
+    elif result.get("status") == "validation_failed":
+        status_code = 400
+
+    return (jsonify(result), status_code)
 
 # Load all extra API routes from extensions
 # Needs to be at the end of route declarations to allow customization of