dcicutils 8.7.1.1b5__tar.gz → 8.7.1.1b6__tar.gz

{dcicutils-8.7.1.1b5 → dcicutils-8.7.1.1b6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.7.1.1b5
+Version: 8.7.1.1b6
 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-8.7.1.1b5 → dcicutils-8.7.1.1b6}/dcicutils/misc_utils.py

@@ -2,6 +2,7 @@
 This file contains functions that might be generally useful.
 """
 
+from collections import namedtuple
 import contextlib
 import datetime
 import functools
@@ -17,6 +18,7 @@ import re
 import rfc3986.validators
 import rfc3986.exceptions
 import time
+import uuid
 import warnings
 import webtest  # importing the library makes it easier to mock testing
 
@@ -1525,6 +1527,17 @@ def create_dict(**kwargs) -> dict:
     return result
 
 
+def create_readonly_object(**kwargs):
+    """
+    Returns a new/unique object instance with readonly properties equal to the give kwargs.
+    """
+    readonly_class_name = "readonlyclass_" + str(uuid.uuid4()).replace("-", "")
+    readonly_class_args = " ".join(kwargs.keys())
+    readonly_class = namedtuple(readonly_class_name, readonly_class_args)
+    readonly_object = readonly_class(**kwargs)
+    return readonly_object
+
+
 def is_c4_arn(arn: str) -> bool:
     """
     Returns True iff the given (presumed) AWS ARN string value looks like it

{dcicutils-8.7.1.1b5 → dcicutils-8.7.1.1b6}/dcicutils/portal_object_utils.py

@@ -3,6 +3,7 @@ from functools import lru_cache
 import re
 from typing import Any, List, Optional, Tuple, Type, Union
 from dcicutils.data_readers import RowReader
+from dcicutils.misc_utils import create_readonly_object
 from dcicutils.portal_utils import Portal
 from dcicutils.schema_utils import Schema
 
@@ -136,21 +137,33 @@ class PortalObject:
             comparing_data = value
         else:
             return {}
-        return PortalObject._compare(this_data, comparing_data)
+        return PortalObject._compare(this_data, comparing_data, self.type)
 
     _ARRAY_KEY_REGULAR_EXPRESSION = re.compile(rf"^({Schema._ARRAY_NAME_SUFFIX_CHAR}\d+)$")
 
     @staticmethod
-    def _compare(a: Any, b: Any, _path: Optional[str] = None) -> dict:
+    def _compare(a: Any, b: Any, value_type: str, _path: Optional[str] = None) -> dict:
+        def diff_creating(value: Any) -> object:  # noqa
+            nonlocal value_type
+            return create_readonly_object(value=value, type=value_type,
+                                          creating_value=True, updating_value=None, deleting_value=False)
+        def diff_updating(value: Any, updating_value: Any) -> object:  # noqa
+            nonlocal value_type
+            return create_readonly_object(value=value, type=value_type,
+                                          creating_value=False, updating_value=updating_value, deleting_value=False)
+        def diff_deleting(value: Any) -> object:  # noqa
+            nonlocal value_type
+            return create_readonly_object(value=value, type=value_type,
+                                          creating_value=False, updating_value=None, deleting_value=True)
         diffs = {}
         if isinstance(a, dict) and isinstance(b, dict):
             for key in a:
                 path = f"{_path}.{key}" if _path else key
                 if key not in b:
                     if a[key] != PortalObject._PROPERTY_DELETION_SENTINEL:
-                        diffs[path] = {"value": a[key], "creating_value": True}
+                        diffs[path] = diff_creating(a[key])
                 else:
-                    diffs.update(PortalObject._compare(a[key], b[key], _path=path))
+                    diffs.update(PortalObject._compare(a[key], b[key], type, _path=path))
         elif isinstance(a, list) and isinstance(b, list):
             # Ignore order of array elements; not absolutely technically correct but suits our purpose.
             for index in range(len(a)):
@@ -159,21 +172,21 @@ class PortalObject:
                     if a[index] not in b:
                         if a[index] != PortalObject._PROPERTY_DELETION_SENTINEL:
                             if index < len(b):
-                                diffs[path] = {"value": a[index], "updating_value": b[index]}
+                                diffs[path] = diff_updating(a[index], b[index])
                             else:
-                                diffs[path] = {"value": a[index], "creating_value": True}
+                                diffs[path] = diff_creating(a[index])
                         else:
                             if index < len(b):
-                                diffs[path] = {"value": b[index], "deleting_value": True}
+                                diffs[path] = diff_deleting(b[index])
                 elif len(b) < index:
-                    diffs.update(PortalObject._compare(a[index], b[index], _path=path))
+                    diffs.update(PortalObject._compare(a[index], b[index], value_type, _path=path))
                 else:
-                    diffs[path] = {"value": a[index], "creating_value": True}
+                    diffs[path] = diff_creating(a[index])
         elif a != b:
             if a == PortalObject._PROPERTY_DELETION_SENTINEL:
-                diffs[_path] = {"value": b, "deleting_value": True}
+                diffs[_path] = diff_deleting(b)
             else:
-                diffs[_path] = {"value": a, "updating_value": b}
+                diffs[_path] = diff_updating(a, b)
         return diffs
 
     def normalize_refs(self, refs: List[dict]) -> None:
@@ -183,8 +196,9 @@ class PortalObject:
         based on the given "refs" list which is assumed to be a list of dictionaries, where each
         contains a "path" and a "uuid" property; this list is typically (for our first usage of
         this function) the value of structured_data.StructuredDataSet.resolved_refs_with_uuid.
-        Change is made to this Portal object in place; use normalized_refs function to make a copy.
-        If there are no "refs" (None or empty) then the references will be looked up via Portal calls.
+        Changes are made to this Portal object in place; use normalized_refs function to make a copy.
+        If there are no "refs" (None or empty) or if the speicified reference is not found in this
+        list then the references will be looked up via Portal calls (via Portal.get_metadata).
         """
         PortalObject._normalize_refs(self.data, refs=refs, schema=self.schema, portal=self.portal)
 

{dcicutils-8.7.1.1b5 → dcicutils-8.7.1.1b6}/dcicutils/structured_data.py

@@ -369,7 +369,7 @@ class Schema:
     def validate(self, data: dict) -> List[str]:
         errors = []
         for error in SchemaValidator(self.data, format_checker=SchemaValidator.FORMAT_CHECKER).iter_errors(data):
-            errors.append(error.message)
+            errors.append(f"Validation error at '{error.json_path}': {error.message}")
         return errors
 
     def get_typeinfo(self, column_name: str) -> Optional[dict]:

{dcicutils-8.7.1.1b5 → dcicutils-8.7.1.1b6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.7.1.1b5"  # TODO: To become 8.7.2
+version = "8.7.1.1b6"  # TODO: To become 8.7.2
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"