dcicutils 8.13.3.1b9__py3-none-any.whl → 8.13.3.1b11__py3-none-any.whl

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/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/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.dist-info → dcicutils-8.13.3.1b11.dist-info}/METADATA

@@ -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.dist-info → dcicutils-8.13.3.1b11.dist-info}/RECORD

@@ -45,7 +45,7 @@ dcicutils/license_policies/park-lab-gpl-pipeline.jsonc,sha256=vLZkwm3Js-kjV44nug
 dcicutils/license_policies/park-lab-pipeline.jsonc,sha256=9qlY0ASy3iUMQlr3gorVcXrSfRHnVGbLhkS427UaRy4,283
 dcicutils/license_utils.py,sha256=2Yxnh1T1iuMe6wluwbvpFO_zYSGPxB4-STAMc-vz-YM,47202
 dcicutils/log_utils.py,sha256=7pWMc6vyrorUZQf-V-M3YC6zrPgNhuV_fzm9xqTPph0,10883
-dcicutils/misc_utils.py,sha256=-syqTAj8DESiiP_KHoyBv9VvfboFYB03QbBlmXnBZXw,109423
+dcicutils/misc_utils.py,sha256=YRUjQ4Yg7GapOGxN_KWB96hcl1XJVGr24ktHZvD9g6A,109492
 dcicutils/obfuscation_utils.py,sha256=fo2jOmDRC6xWpYX49u80bVNisqRRoPskFNX3ymFAmjw,5963
 dcicutils/opensearch_utils.py,sha256=V2exmFYW8Xl2_pGFixF4I2Cc549Opwe4PhFi5twC0M8,1017
 dcicutils/portal_object_utils.py,sha256=Az3n1aL-PQkN5gOFE6ZqC2XkYsqiwKlq7-tZggs1QN4,11062
@@ -60,13 +60,13 @@ dcicutils/s3_utils.py,sha256=h2B9ftOo-kxqfiKth5ZDC_cAUFy1Pbu7BrVanFnE5Iw,28839
 dcicutils/schema_utils.py,sha256=GmRm-XqZKJ6qine16SQF1txcby9WougDav_sYmKNs9E,12400
 dcicutils/scripts/publish_to_pypi.py,sha256=sMd4WASQGlxlh7uLrt2eGkFRXYgONVmvIg8mClMS5RQ,13903
 dcicutils/scripts/run_license_checker.py,sha256=z2keYnRDZsHQbTeo1XORAXSXNJK5axVzL5LjiNqZ7jE,4184
-dcicutils/scripts/update_portal_object.py,sha256=UbvDMtBtZirTAk5JZ7IGZqGn-QiNS1S7v0gn5rtIlUg,20084
+dcicutils/scripts/update_portal_object.py,sha256=Lrgj01JuxmQSoWikukYgwm5LKi9CgSzjAogoMIBsQC4,20373
 dcicutils/scripts/view_portal_object.py,sha256=h8COy0lcLNWF9b5spjrlQ28wfqyTTMqAeC_xpFXutus,32262
 dcicutils/secrets_utils.py,sha256=8dppXAsiHhJzI6NmOcvJV5ldvKkQZzh3Fl-cb8Wm7MI,19745
 dcicutils/sheet_utils.py,sha256=VlmzteONW5VF_Q4vo0yA5vesz1ViUah1MZ_yA1rwZ0M,33629
 dcicutils/snapshot_utils.py,sha256=YDeI3vD-MhAtHwKDzfEm2q-n3l-da2yRpRR3xp0Ah1M,23021
 dcicutils/ssl_certificate_utils.py,sha256=F0ifz_wnRRN9dfrfsz7aCp4UDLgHEY8LaK7PjnNvrAQ,9707
-dcicutils/structured_data.py,sha256=TA7kJ-utVj_xa5XnVs7VaG_XQicl5MUWmrVkDm0N8qE,64471
+dcicutils/structured_data.py,sha256=0M80TxxXltPi_jX66ryBwwYGE7PyC4z29HVQBcA4amg,64484
 dcicutils/submitr/progress_constants.py,sha256=5bxyX77ql8qEJearfHEvsvXl7D0GuUODW0T65mbRmnE,2895
 dcicutils/submitr/ref_lookup_strategy.py,sha256=VJN-Oo0LLna6Vo2cu47eC-eU-yUC9NFlQP29xajejVU,4741
 dcicutils/task_utils.py,sha256=MF8ujmTD6-O2AC2gRGPHyGdUrVKgtr8epT5XU8WtNjk,8082
@@ -75,8 +75,8 @@ dcicutils/trace_utils.py,sha256=g8kwV4ebEy5kXW6oOrEAUsurBcCROvwtZqz9fczsGRE,1769
 dcicutils/validation_utils.py,sha256=cMZIU2cY98FYtzK52z5WUYck7urH6JcqOuz9jkXpqzg,14797
 dcicutils/variant_utils.py,sha256=2H9azNx3xAj-MySg-uZ2SFqbWs4kZvf61JnK6b-h4Qw,4343
 dcicutils/zip_utils.py,sha256=_Y9EmL3D2dUZhxucxHvrtmmlbZmK4FpSsHEb7rGSJLU,3265
-dcicutils-8.13.3.1b9.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.13.3.1b9.dist-info/METADATA,sha256=Rw87lqJzYwFrz2nivFVNRXlvqZ8AM2hfi3Ae6nidGKk,3439
-dcicutils-8.13.3.1b9.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.13.3.1b9.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
-dcicutils-8.13.3.1b9.dist-info/RECORD,,
+dcicutils-8.13.3.1b11.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.13.3.1b11.dist-info/METADATA,sha256=rsngEd_b8J_mQqyeUHqk1_yiCBInGYi7GHHcr6cPUmg,3440
+dcicutils-8.13.3.1b11.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.13.3.1b11.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
+dcicutils-8.13.3.1b11.dist-info/RECORD,,