diff save_to_db.py @ 4:c7a7520afb4b draft

planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae

--- a/save_to_db.py	Fri May 23 08:51:50 2025 +0000
+++ b/save_to_db.py	Mon Jun 02 09:48:14 2025 +0000
@@ -5,11 +5,22 @@
 import os
 import re
 import pandas as pd
+import json
 from sqlalchemy import create_engine, inspect
 from sqlalchemy.sql import text
 from sqlalchemy.engine.url import make_url
 from sqlalchemy.exc import OperationalError
 
+def resolve_parameters(user_params: dict, json_params: dict, keys: list):
+    resolved = {}
+    for key in keys:
+        # Prefer user parameter if it's provided (not None or empty string)
+        if key in user_params and user_params[key]:
+            resolved[key] = user_params[key]
+        else:
+            resolved[key] = json_params.get(f"JSON_{key}")
+    return resolved
+
 def fix_db_uri(uri):
     """Replace __at__ with @ in the URI if needed."""
     return uri.replace("__at__", "@")
@@ -177,19 +188,53 @@
     parser.add_argument("--fragment_column", required=True, help="Fragment column name in the database")
     parser.add_argument("--output", required=True, help="Text report")
     parser.add_argument("--file_name_mapping", required=True, help="real fragments names")
+    parser.add_argument("--json_conf", required=False, help="JSON config file with DB parameters")
     args = parser.parse_args()
 
-    # Start the Docker container (if not already running)
+    # Load JSON config if provided
+    json_config = {}
+    if args.json_conf != 'None' or '':
+        with open(args.json_conf, "r") as f:
+            json_config = json.load(f)
+
+    # Prefer user input; fallback to JSON_ values if not provided
+    user_params = {
+        "table": args.table,
+        "sequence_column": args.sequence_column,
+        "annotation_column": args.annotation_column,
+        "fragment_column": args.fragment_column,
+        "db_uri": args.db_uri
+    }
+
+    keys = ["table", "sequence_column", "annotation_column", "fragment_column", "db_uri"]
+    resolved = resolve_parameters(user_params, json_config, keys)
+
+    # Unpack resolved parameters
+    table = resolved["table"]
+    sequence_column = resolved["sequence_column"]
+    annotation_column = resolved["annotation_column"]
+    fragment_column = resolved["fragment_column"]
+    db_uri = fix_db_uri(resolved["db_uri"])
+
+    # Prepare gb files
     gb_file_list = [f.strip() for f in args.input.split(",") if f.strip()]
-    db_uri = fix_db_uri(args.db_uri)
+
+    # Start and wait for DB
     db_name = extract_db_name(db_uri)
     start_postgres_container(db_name)
-
-    # Wait until the database is ready
     wait_for_db(db_uri)
 
-    # Fetch annotations from the database and save as gb
-    push_gb_annotations(gb_file_list, args.sequence_column, args.annotation_column, db_uri, args.table, args.fragment_column, args.output, args.file_name_mapping)
+    # Push annotations
+    push_gb_annotations(
+        gb_file_list,
+        sequence_column,
+        annotation_column,
+        db_uri,
+        table,
+        fragment_column,
+        args.output,
+        args.file_name_mapping
+    )
 
 if __name__ == "__main__":
     main()