Update metadata assignment logic in add_metadata_to_scan.py

Refactored the script to handle metadata assignment more robustly, ensuring owners and project associations are properly set.
Added user creation and authentication for database interactions.
Improved handling of existing metadata while maintaining flexibility for updates.

scripts/add_metadata_to_scan.py

@@ -4,7 +4,7 @@
 """
 Metadata Management for Database Scans
 
-This module provides functionality for adding metadata to scans in a database.
+This script provides functionality for adding metadata to scans in a database.
 
 Key Features:
 - Connects to a database using the `FSDB` module.
@@ -13,19 +13,41 @@
 - Provides an easy-to-use method for specifying metadata, such as ownership and project details, in bulk or customized workflows.
 """
 
-import os
-
 from plantdb.fsdb import FSDB
 from plantdb.fsdb_tools import add_metadata_to_scan
 
-path = os.environ.get('ROMI_DB', None)
+#path = "/data/ROMI/Romi_Alexis/analyse/Arabidopsis/ahp6_E1"
+#path = "/data/ROMI/Romi_Alexis/analyse/Arabidopsis/ahp6_E2"
+#path = "/data/ROMI/Romi_GG/analysis/Phyllotaxis_afb1_mutant"
+path = "/data/ROMI/test_owner"
 
-if path is None:
-    raise ValueError('Environment variable ROMI_DB not set.')
+owner_id = "geraldine"
+project_id = "afb1_mutant"
 
 db = FSDB(path)
-db.connect("anonymous")
+db.create_user('alexis', 'Alexis LACROIX')
+db.create_user('geraldine', 'Géraldine BRUNOUD')
+db.create_user('fabfab', 'Fabrice Besnard')
+db.connect(owner_id)
+
+db.list_scans()  # list scans owned by current user
+
+for scan in db.get_scans(owner_only=False):
+    new_md = {}
+    # Process the dataset owner
+    owner = scan.get_metadata("owner", None)
+    if owner is None:
+        new_md["owner"] = db.user
+    else:
+        print(f"Scan '{scan.id}' already has an owner: '{owner}'!")
+    # Process the project the dataset belongs to
+    project = scan.get_metadata("project", None)
+    if project is None:
+        project = [project_id]
+    else:
+        if project_id not in project:
+            project.append(project_id)
+    new_md["project"] = project
+    # Update the scan metadata
+    add_metadata_to_scan(db, scan.id, metadata=new_md)
 
-for scan in db.get_scans():
-    new_md = {"owner": "test", "project": "test"}
-    add_metadata_to_scan(db, scan, metadata=new_md)