feat: vendor jsonasobj2

Makefile

@@ -8,6 +8,7 @@ MODEL_DIR = ../linkml-model/linkml_model/
 
 update_model:
 	cp -pr $(MODEL_DIR)/* linkml_runtime/linkml_model
+	sed -i 's/from jsonasobj2/from linkml_runtime.utils.jsonasobj2/g' linkml_runtime/linkml_model/*.py
 
 test:
 	poetry run pytest
@@ -16,3 +17,4 @@ test:
 # temporary measure until linkml-model is synced
 linkml_runtime/processing/validation_datamodel.py: linkml_runtime/processing/validation_datamodel.yaml
 	gen-python $< > $@.tmp && mv $@.tmp $@
+	sed -i 's/from jsonasobj2/from linkml_runtime.utils.jsonasobj2/g' linkml_runtime/processing/validation_datamodel.py

README.md

@@ -29,3 +29,13 @@ It also includes the [SchemaView](https://linkml.io/linkml/developers/manipulati
 ## Notebooks
 
 See the [notebooks](https://github.com/linkml/linkml-runtime/tree/main/notebooks) folder for examples
+
+## Development
+
+### Measure tests code coverage
+
+```shell
+poetry add pytest-coverage
+poetry run coverage run -m pytest # run the existing tests, measuring coverage
+poetry run coverage html # to generate an HTML, browsable report
+```

linkml_runtime/dumpers/json_dumper.py

@@ -10,7 +10,7 @@
 from linkml_runtime.utils.context_utils import CONTEXTS_PARAM_TYPE
 from linkml_runtime.utils.formatutils import remove_empty_items
 from linkml_runtime.utils.yamlutils import YAMLRoot, as_json_object
-from jsonasobj2 import JsonObj
+from linkml_runtime.utils.jsonasobj2 import JsonObj
 
 
 class JSONDumper(Dumper):

linkml_runtime/linkml_model/annotations.py

@@ -8,7 +8,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/linkml_model/datasets.py

@@ -8,7 +8,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/linkml_model/extensions.py

@@ -8,7 +8,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/linkml_model/mappings.py

@@ -8,7 +8,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/linkml_model/meta.py

@@ -32,7 +32,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/linkml_model/types.py

@@ -8,7 +8,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/linkml_model/units.py

@@ -8,7 +8,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/linkml_model/validation.py

@@ -8,7 +8,7 @@
 
 import dataclasses
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 

linkml_runtime/loaders/loader_root.py

@@ -4,7 +4,7 @@
 
 from pydantic import BaseModel
 from hbreader import FileInfo, hbread
-from jsonasobj2 import as_dict, JsonObj
+from linkml_runtime.utils.jsonasobj2 import as_dict, JsonObj
 
 from linkml_runtime.utils.yamlutils import YAMLRoot
 from linkml_runtime import URI_TO_LOCAL
@@ -168,4 +168,4 @@ def _read_source(self,
         else:
             data = source
 
-        return data
+        return data

linkml_runtime/processing/validation_datamodel.py

@@ -9,7 +9,7 @@
 import dataclasses
 import sys
 import re
-from jsonasobj2 import JsonObj, as_dict
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict
 from typing import Optional, List, Union, Dict, ClassVar, Any
 from dataclasses import dataclass
 from linkml_runtime.linkml_model.meta import (

linkml_runtime/utils/context_utils.py

@@ -4,7 +4,7 @@
 from typing import Optional, Union, List, Any, Dict, Callable
 
 import yaml
-from jsonasobj2 import JsonObj, loads
+from linkml_runtime.utils.jsonasobj2 import JsonObj, loads
 
 CONTEXT_TYPE = Union[str, dict, JsonObj]
 CONTEXTS_PARAM_TYPE = Optional[Union[CONTEXT_TYPE, List[CONTEXT_TYPE]]]

linkml_runtime/utils/formatutils.py

@@ -3,7 +3,7 @@
 from numbers import Number
 from typing import List, Any, Union
 
-from jsonasobj2 import JsonObj, as_dict, is_list, is_dict, items, as_json_obj
+from linkml_runtime.utils.jsonasobj2 import JsonObj, as_dict, is_list, is_dict, items, as_json_obj
 
 ws_pattern = re.compile(r'\s+')
 us_pattern = re.compile(r'_+')

linkml_runtime/utils/inference_utils.py

@@ -2,7 +2,7 @@
 from dataclasses import field, dataclass
 from enum import Enum
 from typing import Union, Optional, Any, Dict, Callable
-from jsonasobj2 import JsonObj, items
+from linkml_runtime.utils.jsonasobj2 import JsonObj, items
 
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import SlotDefinitionName, PermissibleValue, ClassDefinitionName

linkml_runtime/utils/jsonasobj2/__init__.py

@@ -0,0 +1,6 @@
+from ._jsonobj import JsonObj, as_dict, as_json, as_json_obj, get, items, loads, load, setdefault, \
+    keys, items, values, JsonTypes, JsonObjTypes, is_dict, is_list
+from .extendednamespace import ExtendedNamespace
+
+__all__ = ['JsonObj', 'ExtendedNamespace', 'is_dict', 'is_list', 'as_dict', 'as_json', 'as_json_obj', 'get', 'items',
+           'load', 'loads', 'setdefault', 'keys', 'values', 'JsonTypes', 'JsonObjTypes']