Refrain from patching known-invalid fields (will fix source database …

…instead)

This commit also includes a minor simplification to the `remove_id_pattern_constraints` function.

demo/metadata_migration/notebooks/migrate_10_0_0_to_10_1_4.ipynb

@@ -278,7 +278,7 @@
     "    Note: This algorithm was copied from the `without_id_patterns` function in `nmdc_runtime/util.py`.\n",
     "    \"\"\"\n",
     "    custom_schema = deepcopy(nmdc_schema)\n",
-    "    for _, spec in custom_schema[\"$defs\"].items():\n",
+    "    for spec in custom_schema[\"$defs\"].values():\n",
     "        if \"properties\" in spec and \"id\" in spec[\"properties\"] and \"pattern\" in spec[\"properties\"][\"id\"]:\n",
     "            del spec[\"properties\"][\"id\"][\"pattern\"]\n",
     "    return custom_schema\n",
@@ -437,12 +437,6 @@
     "        #       Reference: https://docs.python.org/3/library/stdtypes.html#dict (see the \"type constructor\" section)\n",
     "        #\n",
     "        document_without_underscore_id_key = {key: value for key, value in document.items() if key != \"_id\"}\n",
-    "        \n",
-    "        # Patch documents that contain invalid data, while the team is figuring out how we'll handle these long term.\n",
-    "        for field_name in [\"compression_type\", \"was_generated_by\"]:\n",
-    "            if field_name in document_without_underscore_id_key and document_without_underscore_id_key[field_name] is None:\n",
-    "                document_without_underscore_id_key[field_name] = \"\"\n",
-    "\n",
     "        root_to_validate = dict([(collection_name, [document_without_underscore_id_key])])\n",
     "        try:\n",
     "            nmdc_jsonschema_validator.validate(root_to_validate)  # raises exception if invalid\n",