dcicutils 8.14.0.1b26__py3-none-any.whl → 8.14.0.1b28__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):
@@ -556,8 +562,11 @@ def _load_data(portal: Portal, load: str, ini_file: str, explicit_schema_name: O
                     else:
                         data = {schema_name: [data]}
                 if not _is_schema_name_list(portal, schema_names := list(data.keys())):
-                    _print(f"Unrecognized types in JSON data file: {inserts_file}")
-                    return False
+                    if not (schema_name := _get_schema_name_from_schema_named_json_file_name(portal, inserts_file)):
+                        _print(f"Unrecognized types in JSON data file: {inserts_file}")
+                    # Assume simple object of type from the JSON file name.
+                    schema_names = [schema_name]
+                    data = {schema_name: [data]}
                 with temporary_directory() as tmpdir:
                     nfiles = 0
                     for schema_name in schema_names:
@@ -571,6 +580,7 @@ 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 +651,19 @@ 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:

{dcicutils-8.14.0.1b26.dist-info → dcicutils-8.14.0.1b28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.14.0.1b26
+Version: 8.14.0.1b28
 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-8.14.0.1b26.dist-info → dcicutils-8.14.0.1b28.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=I7658tq1gQqMRf_iuF51VXwhLZF5Usd6alUazzmCHAA,40237
+dcicutils/scripts/update_portal_object.py,sha256=BwZw1cZx2zhzp1ivn_DXUxfnmUyC5A9fAotjHV0fXf4,41875
 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-8.14.0.1b26.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.14.0.1b26.dist-info/METADATA,sha256=SUWggoccgWGfOmng7IAUTPtQxioG626BNeEYNkWHcoU,3440
-dcicutils-8.14.0.1b26.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.14.0.1b26.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
-dcicutils-8.14.0.1b26.dist-info/RECORD,,
+dcicutils-8.14.0.1b28.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.14.0.1b28.dist-info/METADATA,sha256=_Cl7Wklz95RtMUYcwgxsJk1mox2gnJeshyNHC3imAaA,3440
+dcicutils-8.14.0.1b28.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.14.0.1b28.dist-info/entry_points.txt,sha256=W6kEWdUJk9tQ4myAgpehPdebcwvCAZ7UgB-wyPgDUMg,335
+dcicutils-8.14.0.1b28.dist-info/RECORD,,