dcicutils 8.13.3.1b9__tar.gz → 8.13.3.1b11__tar.gz

{dcicutils-8.13.3.1b9 → dcicutils-8.13.3.1b11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.13.3.1b9
+Version: 8.13.3.1b11
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.13.3.1b9 → dcicutils-8.13.3.1b11}/dcicutils/misc_utils.py

@@ -984,14 +984,15 @@ def str_to_bool(x: Optional[str]) -> Optional[bool]:
         raise ValueError(f"An argument to str_or_bool must be a string or None: {x!r}")
 
 
-def to_integer(value: str, fallback: Optional[Any] = None) -> Optional[Any]:
+def to_integer(value: str, fallback: Optional[Any] = None, strict: bool = False) -> Optional[Any]:
     try:
         return int(value)
     except Exception:
-        try:
-            return int(float(value))
-        except Exception:
-            pass
+        if strict is not True:
+            try:
+                return int(float(value))
+            except Exception:
+                pass
     return fallback
 
 

{dcicutils-8.13.3.1b9 → dcicutils-8.13.3.1b11}/dcicutils/scripts/update_portal_object.py

@@ -165,6 +165,7 @@ def main():
                                  update_action_name="PATCH",
                                  patch_delete_fields=args.delete,
                                  confirm=args.confirm, verbose=args.verbose, quiet=args.quiet, debug=args.debug)
+        args.delete = None
     if args.upsert:
         _post_or_patch_or_upsert(portal=portal,
                                  file_or_directory=args.upsert,
@@ -173,6 +174,7 @@ def main():
                                  update_action_name="UPSERT",
                                  patch_delete_fields=args.delete,
                                  confirm=args.confirm, verbose=args.verbose, quiet=args.quiet, debug=args.debug)
+        args.delete = None
 
     if args.delete:
         if not portal.get_metadata(args.delete, raise_exception=False):
@@ -256,14 +258,17 @@ def _post_or_patch_or_upsert(portal: Portal, file_or_directory: str,
                     _print(f"ERROR: Schema cannot be inferred from file name and --schema not specified: {file}")
                     continue
                 post_or_patch_or_upsert(portal, file_and_schema[0], schema_name=schema_name,
+                                        patch_delete_fields=patch_delete_fields,
                                         confirm=confirm, quiet=quiet, verbose=verbose, debug=debug)
     elif os.path.isfile(file := file_or_directory):
         if ((schema_name := _get_schema_name_from_schema_named_json_file_name(portal, file)) or
             (schema_name := explicit_schema_name)):  # noqa
             post_or_patch_or_upsert(portal, file, schema_name=schema_name,
+                                    patch_delete_fields=patch_delete_fields,
                                     confirm=confirm, quiet=quiet, verbose=verbose, debug=debug)
         else:
             post_or_patch_or_upsert(portal, file, schema_name=schema_name,
+                                    patch_delete_fields=patch_delete_fields,
                                     confirm=confirm, quiet=quiet, verbose=verbose, debug=debug)
             # _print(f"ERROR: Schema cannot be inferred from file name and --schema not specified: {file}")
             # return

{dcicutils-8.13.3.1b9 → dcicutils-8.13.3.1b11}/dcicutils/structured_data.py

@@ -706,7 +706,7 @@ class Schema(SchemaBase):
 
     def _map_function_integer(self, typeinfo: dict) -> Callable:
         def map_integer(value: str, src: Optional[str]) -> Any:
-            return to_integer(value, value)
+            return to_integer(value, value, strict=True)
         return map_integer
 
     def _map_function_number(self, typeinfo: dict) -> Callable:

{dcicutils-8.13.3.1b9 → dcicutils-8.13.3.1b11}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.13.3.1b9"  # TODO: To become 8.13.4
+version = "8.13.3.1b11"  # TODO: To become 8.13.4
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"