Add metadata and permission management for Illumina ancillary files

src/npg_irods/cli/repair_common_metadata.py

@@ -137,7 +137,3 @@ def main():
         num_repaired=num_repaired,
         num_errors=num_errors,
     )
-
-
-if __name__ == "__main__":
-    main()

src/npg_irods/cli/update_secondary_metadata.py

@@ -47,82 +47,84 @@
 error message summarising the results will be sent to STDERR.
 """
 
-parser = argparse.ArgumentParser(
-    description=description, formatter_class=argparse.RawDescriptionHelpFormatter
-)
-add_logging_arguments(parser)
-
-parser.add_argument(
-    "--database-config",
-    "--database_config",
-    "--db-config",
-    "--db_config",
-    help="Configuration file for database connection.",
-    type=argparse.FileType("r"),
-    required=True,
-)
-parser.add_argument(
-    "-i",
-    "--input",
-    help="Input filename.",
-    type=argparse.FileType("r"),
-    default=sys.stdin,
-)
-parser.add_argument(
-    "-o",
-    "--output",
-    help="Output filename.",
-    type=argparse.FileType("w"),
-    default=sys.stdout,
-)
-parser.add_argument(
-    "--print-update",
-    help="Print to output those paths that were updated. Defaults to True.",
-    action="store_true",
-)
-parser.add_argument(
-    "--print-fail",
-    help="Print to output those paths that require updating, where the update failed. "
-    "Defaults to False.",
-    action="store_true",
-)
-parser.add_argument(
-    "-c",
-    "--clients",
-    help="Number of baton clients to use. Defaults to 4.",
-    type=int,
-    default=4,
-)
-parser.add_argument(
-    "-t",
-    "--threads",
-    help="Number of threads to use. Defaults to 4.",
-    type=int,
-    default=4,
-)
-parser.add_argument(
-    "--version", help="Print the version and exit.", action="store_true"
-)
-parser.add_argument(
-    "--zone",
-    help="Specify a federated iRODS zone in which to find data objects and/or "
-    "collections to update. This is not required if the target paths "
-    "are on the local zone.",
-    type=str,
-)
-
-args = parser.parse_args()
-configure_logging(
-    config_file=args.log_config,
-    debug=args.debug,
-    verbose=args.verbose,
-    colour=args.colour,
-    json=args.json,
-)
+
 log = structlog.get_logger("main")
 
 
 def main():
+    parser = argparse.ArgumentParser(
+        description=description, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+    add_logging_arguments(parser)
+
+    parser.add_argument(
+        "--database-config",
+        "--database_config",
+        "--db-config",
+        "--db_config",
+        help="Configuration file for database connection.",
+        type=argparse.FileType("r"),
+        required=True,
+    )
+    parser.add_argument(
+        "-i",
+        "--input",
+        help="Input filename.",
+        type=argparse.FileType("r"),
+        default=sys.stdin,
+    )
+    parser.add_argument(
+        "-o",
+        "--output",
+        help="Output filename.",
+        type=argparse.FileType("w"),
+        default=sys.stdout,
+    )
+    parser.add_argument(
+        "--print-update",
+        help="Print to output those paths that were updated. Defaults to True.",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--print-fail",
+        help="Print to output those paths that require updating, where the update failed. "
+        "Defaults to False.",
+        action="store_true",
+    )
+    parser.add_argument(
+        "-c",
+        "--clients",
+        help="Number of baton clients to use. Defaults to 4.",
+        type=int,
+        default=4,
+    )
+    parser.add_argument(
+        "-t",
+        "--threads",
+        help="Number of threads to use. Defaults to 4.",
+        type=int,
+        default=4,
+    )
+    parser.add_argument(
+        "--version", help="Print the version and exit.", action="store_true"
+    )
+    parser.add_argument(
+        "--zone",
+        help="Specify a federated iRODS zone in which to find data objects and/or "
+        "collections to update. This is not required if the target paths "
+        "are on the local zone.",
+        type=str,
+    )
+
+    args = parser.parse_args()
+    configure_logging(
+        config_file=args.log_config,
+        debug=args.debug,
+        verbose=args.verbose,
+        colour=args.colour,
+        json=args.json,
+    )
+
     if args.version:
         print(version())
         exit(0)

src/npg_irods/exception.py

@@ -50,13 +50,44 @@ def __init__(
         self.observed = observed
 
 
+class NonUniqueError(DataManagementError):
+    """Exception raised when a unique constraint is violated.
+
+    Args:
+        args: Optional positional arguments, the first of which should be a message
+        string.
+        observed: The observed non-unique objects, if any.
+    """
+
+    def __init__(self, *args, path: Any = None, observed: Any = None):
+        super().__init__(*args)
+        self.message = args[0] if len(args) > 0 else ""
+        self.observed = observed
+
+
 class CollectionNotFound(DataManagementError):
     """Exception raised when an iRODS collection is expected to exist, but is not found.
 
     Args:
        args: Optional positional arguments, the first of which should be a message
        string.
-       path: The path of the affected collection in iRODS.
+       path: The path of the missing collection in iRODS.
+    """
+
+    def __init__(self, *args, path: Any = None):
+        super().__init__(*args)
+        self.message = args[0] if len(args) > 0 else ""
+        self.path = path
+
+
+class DataObjectNotFound(DataManagementError):
+    """Exception raised when an iRODS data object is expected to exist, but is not
+    found.
+
+    Args:
+       args: Optional positional arguments, the first of which should be a message
+       string.
+       path: The path of the missing data object in iRODS.
     """
 
     def __init__(self, *args, path: Any = None):