fix(submission): Auto-transform ProtectedDonor workbooks during validate/submit

envs.toml

@@ -0,0 +1,3 @@
+[smaht-submitr-pEqN3rsm]
+minor = "3.11"
+patch = "3.11.5"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "smaht-submitr"
-version = "1.16.0"
+version = "1.16.0.1b2"
 description = "Support for uploading file submissions to SMAHT."
 # TODO: Update this email address when a more specific one is available for SMaHT.
 authors = ["SMaHT DAC <smhelp@hms-dbmi.atlassian.net >"]
@@ -47,7 +47,8 @@ include = [
 
 python = ">=3.10,<3.13"
 boto3 = "^1.43.58"
-dcicutils = "^8.19.0"
+# dcicutils = "^8.19.0"
+dcicutils = { git = "https://github.com/4dn-dcic/utils.git", branch = "fm/protected-donor-dcicutils" }
 PyYAML = "^6.0.1"
 requests = "^2.31.0"
 googleapi = "^0.1.0"

submitr/scripts/submit_metadata_bundle.py

@@ -233,6 +233,10 @@ def main(simulated_args_for_testing=None):
     parser.add_argument('--timeout', help="Wait timeout for server validation/submission.")
     parser.add_argument('--debug', action="store_true", help="Debug output.", default=False)
     parser.add_argument('--debug-sleep', help="Sleep on each row read for troubleshooting/testing.", default=False)
+    # Retained as a hidden compatibility switch for internal workflows/tests.
+    parser.add_argument('--no-transform-protected-donor', action="store_true",
+                        help=argparse.SUPPRESS, default=False)
+    parser.add_argument('--save-transformed-workbook', help=argparse.SUPPRESS, default=None)
     parser.add_argument('--skip-validator', action='append', dest='skip_validators',
                         help=argparse.SUPPRESS, default=None)
     parser.add_argument('--ping', action="store_true", help="Ping server.", default=False)
@@ -336,6 +340,10 @@ def main(simulated_args_for_testing=None):
         else:
             args.timeout = int(args.timeout)
 
+    if args.no_transform_protected_donor and args.save_transformed_workbook:
+        PRINT("May not specify both --no-transform-protected-donor and --save-transformed-workbook.")
+        sys.exit(2)
+
     if args.info:
         if not os.path.exists(args.bundle_filename):
             PRINT(f"File does not exist: {args.bundle_filename}")
@@ -392,7 +400,9 @@ def main(simulated_args_for_testing=None):
                              timeout=args.timeout,
                              debug=args.debug,
                              debug_sleep=args.debug_sleep,
-                             skip_validators=args.skip_validators)
+                             skip_validators=args.skip_validators,
+                             transform_protected_donor=not args.no_transform_protected_donor,
+                             transformed_workbook_path=args.save_transformed_workbook)
 
 
 def _sanity_check_submitted_file(file_name: str) -> bool: