dcicutils 8.14.0.1b25__py3-none-any.whl → 8.14.0.1b27__py3-none-any.whl

dcicutils/scripts/update_portal_object.py

@@ -139,6 +139,8 @@ def main():
     parser.add_argument("--noignore", action="store_true", required=False, default=False,
                         help="Do not ignore standard fields on update(s).")
     parser.add_argument("--ignore", nargs="+", help="Ignore these additional fields.")
+    parser.add_argument("--unresolved-output", "--unresolved", type=str,
+                        help="Output file to write unresolved references to for --load only.")
     parser.add_argument("--confirm", action="store_true", required=False, default=False, help="Confirm before action.")
     parser.add_argument("--verbose", action="store_true", required=False, default=False, help="Verbose output.")
     parser.add_argument("--quiet", action="store_true", required=False, default=False, help="Quiet output.")
@@ -162,6 +164,7 @@ def main():
 
     if args.load:
         _load_data(portal=portal, load=args.load, ini_file=args.ini, explicit_schema_name=args.schema,
+                   unresolved_output=args.unresolved_output,
                    verbose=args.verbose, debug=args.debug, noprogress=args.noprogress)
 
     if explicit_schema_name := args.schema:
@@ -397,6 +400,7 @@ def _upsert_data(portal: Portal, data: dict, schema_name: str,
 
 
 def _load_data(portal: Portal, load: str, ini_file: str, explicit_schema_name: Optional[str] = None,
+               unresolved_output: Optional[str] = False,
                verbose: bool = False, debug: bool = False, noprogress: bool = False,
                _single_insert_file: Optional[str] = None) -> bool:
 
@@ -515,6 +519,7 @@ def _load_data(portal: Portal, load: str, ini_file: str, explicit_schema_name: O
     if not os.path.isabs(load := os.path.normpath(os.path.expanduser(load))):
         load = os.path.normpath(os.path.join(os.getcwd(), load))
     if not os.path.exists(load):
+        _print(f"Specified JSON data file not found: {load}")
         return False
 
     if os.path.isdir(load):
@@ -544,6 +549,7 @@ def _load_data(portal: Portal, load: str, ini_file: str, explicit_schema_name: O
                     with io.open(file_name, "w") as f:
                         json.dump(data, f)
                     return _load_data(portal=portal, load=tmpdir, ini_file=ini_file, explicit_schema_name=schema_name,
+                                      unresolved_output=unresolved_output,
                                       verbose=verbose, debug=debug, noprogress=noprogress,
                                       _single_insert_file=inserts_file)
             elif isinstance(data, dict):
@@ -571,6 +577,7 @@ def _load_data(portal: Portal, load: str, ini_file: str, explicit_schema_name: O
                         nfiles += 1
                     if nfiles > 0:
                         return _load_data(portal=portal, load=tmpdir, ini_file=ini_file,
+                                          unresolved_output=unresolved_output,
                                           verbose=verbose, debug=debug, noprogress=noprogress,
                                           _single_insert_file=inserts_file)
                 return True
@@ -641,6 +648,19 @@ def _load_data(portal: Portal, load: str, ini_file: str, explicit_schema_name: O
             _print(f"  ✗ {item}: {len(loadxl_unresolved[item])}")
             for subitem in loadxl_unresolved[item]:
                 _print(f"     ▶ {subitem}")
+        if unresolved_output:
+            if unresolved_output:
+                if not os.path.isabs(unresolved_output := os.path.normpath(os.path.expanduser(unresolved_output))):
+                    unresolved_output = os.path.normpath(os.path.join(os.getcwd(), unresolved_output))
+                if os.path.exists(unresolved_output):
+                    if os.path.isdir(unresolved_output):
+                        _print("Unresolved output file exists as a directory: {unresolved_output}")
+                        return False
+                    _print(f"Unresolved output file already exists: {unresolved_output}")
+                    if yes_or_no(f"Do you want to overwrite this file?"):
+                        with io.open(unresolved_output, "w") as f:
+                            for item in loadxl_unresolved:
+                                f.write(f"{item}\n")
     if debug and loadxl_output:
         _print("✗ Output from loadxl:")
         for item in loadxl_output:
@@ -707,9 +727,10 @@ def _create_portal(env: Optional[str] = None, ini: Optional[str] = None, app: Op
             if (not load) and (app == APP_SMAHT) and (env := os.environ.get(_SMAHT_ENV_ENVIRON_NAME)):
                 env_from_environ = True
         if not env:
-            if os.path.exists(ini_file := os.path.normpath(os.path.join(os.getcwd(), _DEFAULT_INI_FILE_FOR_LOAD))):
-                return _create_portal(ini=ini_file, app=app, verbose=verbose, debug=debug)
-            return None
+            if not os.path.exists(ini_file := os.path.normpath(os.path.join(os.getcwd(), _DEFAULT_INI_FILE_FOR_LOAD))):
+                _print("Must specify --ini or --env option in order to create a Portal object.")
+                return None
+            return _create_portal(ini=ini_file, app=app, verbose=verbose, debug=debug)
         if not (portal := Portal(env, app=app) if env or app else None):
             _print(f"Cannot create access-key based Portal object: {env}{f' ({app})' if app else ''}")
             return None

{dcicutils-8.14.0.1b25.dist-info → dcicutils-8.14.0.1b27.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.14.0.1b25
+Version: 8.14.0.1b27
 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-8.14.0.1b25.dist-info → dcicutils-8.14.0.1b27.dist-info}/RECORD

@@ -60,7 +60,7 @@ 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=S9ev5KTXtEg0SAxWm0dEuPi1O11fa_EIoqpZqD3QABE,40136
+dcicutils/scripts/update_portal_object.py,sha256=c4-nQ_QkmVA6pnAM-08TjhdISseLPh0rg_OX3_V2ugU,41613
 dcicutils/scripts/view_portal_object.py,sha256=vsJzS985JFEW6-xOe_ExkuE4Dk21G6d8xfC9RBUNwUg,38655
 dcicutils/secrets_utils.py,sha256=8dppXAsiHhJzI6NmOcvJV5ldvKkQZzh3Fl-cb8Wm7MI,19745
 dcicutils/sheet_utils.py,sha256=VlmzteONW5VF_Q4vo0yA5vesz1ViUah1MZ_yA1rwZ0M,33629
@@ -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-8.14.0.1b25.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.14.0.1b25.dist-info/METADATA,sha256=MHTo5d_M_ABEZo9vONtd3bpR7Df4BmxSTwpkVOp7DyU,3440
-dcicutils-8.14.0.1b25.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.14.0.1b25.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
-dcicutils-8.14.0.1b25.dist-info/RECORD,,
+dcicutils-8.14.0.1b27.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.14.0.1b27.dist-info/METADATA,sha256=eTXjvupOrwP4AJOFmh9XvYc91x12alWq6dGPFKakDq8,3440
+dcicutils-8.14.0.1b27.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.14.0.1b27.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
+dcicutils-8.14.0.1b27.dist-info/RECORD,,