Merge pull request #100 from Exabyte-io/update/SOF-7321

chore: add in_memory_entity

Author: timurbazhirov

.babelrc

@@ -15,4 +15,3 @@
         "@babel/plugin-proposal-class-properties"
     ]
 }
-

.eslintrc.json

@@ -1,4 +1,3 @@
 {
     "extends": ["@exabyte-io/eslint-config"]
 }
-

.github/workflows/cicd.yml

@@ -56,7 +56,7 @@ jobs:
           path: actions
 
       - name: Run python unit tests
-        uses: ./actions/py/test
+        uses: ./actions/py/pytest
         with:
           python-version: ${{ matrix.python-version }}
           unit-test-directory: tests/py/unit

.prettierrc

@@ -4,4 +4,3 @@
     "trailingComma": "all",
     "tabWidth": 4
 }
-

README.md

@@ -46,4 +46,3 @@ npm run transpile
 # run tests
 npm run test
 ```
-

pyproject.toml

@@ -16,7 +16,9 @@ classifiers = [
 ]
 dependencies = [
     # add requirements here
-    "numpy"
+    "numpy",
+    "jsonschema>=2.6.0",
+    "mat3ra-utils",
 ]
 
 [project.optional-dependencies]
@@ -27,7 +29,9 @@ tests = [
     "ruff",
     "isort",
     "mypy",
-    "pip-tools"
+    "pip-tools",
+    "pytest",
+    "pytest-cov",
 ]
 all = ["mat3ra-code[tests]"]
 

src/py/mat3ra/code/__init__.py

@@ -1,5 +1,32 @@
-import numpy as np
+from typing import Any, Dict, Optional
 
+from mat3ra.utils import object as object_utils
 
-def get_length(vec: np.ndarray) -> np.float_:
-    return np.linalg.norm(vec)
+
+class BaseUnderscoreJsonPropsHandler(object):
+    def __init__(self, config: Dict[str, Any] = {}) -> None:
+        self._json = object_utils.clone_deep(config)
+
+    def __getattribute__(self, item):
+        try:
+            default_attribute = super().__getattribute__(item)
+            return default_attribute
+        except AttributeError:
+            return self.__getattribute_from_json__(item)
+
+    def __getattribute_from_json__(self, name: str, default_value: Any = None) -> Any:
+        return self._json.get(name, default_value)
+
+    def get_prop(self, name: str, default_value: Any = None) -> Any:
+        return self.__getattribute_from_json__(name, default_value)
+
+    def set_prop(self, name: str, value: Any) -> None:
+        object_utils.set(self._json, name, value)
+
+    def unset_prop(self, name: str) -> None:
+        del self._json[name]
+
+    def set_props(self, json: Dict[str, Any] = {}) -> "BaseUnderscoreJsonPropsHandler":
+        for key, value in json.items():
+            self.set_prop(key, value)
+        return self

src/py/mat3ra/code/constants.py

@@ -0,0 +1,25 @@
+class Coefficients:
+    EV_TO_RY = 0.0734986176
+    BOHR_TO_ANGSTROM = 0.52917721092
+    ANGSTROM_TO_BOHR = 1 / 0.52917721092
+    EV_A_TO_RY_BOHR = 1 / 25.71104309541616
+
+
+class Tolerance:
+    # in crystal coordinates
+    length = 0.01
+    lengthAngstrom = 0.001
+    pointsDistance = 0.001
+
+
+class Units:
+    bohr = "bohr"
+    angstrom = "angstrom"
+    degree = "degree"
+    radian = "radian"
+    alat = "alat"
+
+
+class AtomicCoordinateUnits:
+    crystal = "crystal"
+    cartesian = "cartesian"

src/py/mat3ra/code/entity.py

@@ -0,0 +1,98 @@
+from typing import Any, Dict, List, Optional
+
+import jsonschema
+from mat3ra.utils import object as object_utils
+
+from . import BaseUnderscoreJsonPropsHandler
+from .mixins import DefaultableMixin, HasDescriptionMixin, HasMetadataMixin, NamedMixin
+
+
+class ValidationErrorCode:
+    IN_MEMORY_ENTITY_DATA_INVALID = "IN_MEMORY_ENTITY_DATA_INVALID"
+
+
+class ErrorDetails:
+    def __init__(self, error: Optional[Dict[str, Any]], json: Dict[str, Any], schema: Dict):
+        self.error = error
+        self.json = json
+        self.schema = schema
+
+
+class EntityError(Exception):
+    def __init__(self, code: ValidationErrorCode, details: Optional[ErrorDetails] = None):
+        super().__init__(code)
+        self.code = code
+        self.details = details
+
+
+class InMemoryEntity(BaseUnderscoreJsonPropsHandler):
+    jsonSchema: Optional[Dict] = None
+
+    @classmethod
+    def get_cls(cls) -> str:
+        return cls.__name__
+
+    @property
+    def cls(self) -> str:
+        return self.__class__.__name__
+
+    def get_cls_name(self) -> str:
+        return self.__class__.__name__
+
+    @classmethod
+    def create(cls, config: Dict[str, Any]) -> Any:
+        return cls(config)
+
+    def to_json(self, exclude: List[str] = []) -> Dict[str, Any]:
+        return self.clean(object_utils.clone_deep(object_utils.omit(self._json, exclude)))
+
+    def clone(self, extra_context: Dict[str, Any] = {}) -> Any:
+        return self.__class__.__init__({**self.to_json(), **extra_context})
+
+    @staticmethod
+    def validate_data(data: Dict[str, Any], clean: bool = False):
+        if clean:
+            print("Error: clean is not supported for InMemoryEntity.validateData")
+        if InMemoryEntity.jsonSchema:
+            jsonschema.validate(data, InMemoryEntity.jsonSchema)
+
+    def validate(self) -> None:
+        if self._json:
+            self.__class__.validate_data(self._json)
+
+    def clean(self, config: Dict[str, Any]) -> Dict[str, Any]:
+        # Not implemented, consider the below for the implementation
+        # https://stackoverflow.com/questions/44694835/remove-properties-from-json-object-not-present-in-schema
+        return config
+
+    def is_valid(self) -> bool:
+        try:
+            self.validate()
+            return True
+        except EntityError:
+            return False
+
+    # Properties
+    @property
+    def id(self) -> str:
+        return self.prop("_id", "")
+
+    @id.setter
+    def id(self, id: str) -> None:
+        self.set_prop("_id", id)
+
+    @property
+    def slug(self) -> str:
+        return self.prop("slug", "")
+
+    def get_as_entity_reference(self, by_id_only: bool = False) -> Dict[str, str]:
+        if by_id_only:
+            return {"_id": self.id}
+        else:
+            return {"_id": self.id, "slug": self.slug, "cls": self.get_cls_name()}
+
+
+class HasDescriptionHasMetadataNamedDefaultableInMemoryEntity(
+    InMemoryEntity, DefaultableMixin, NamedMixin, HasMetadataMixin, HasDescriptionMixin
+):
+    pass

src/py/mat3ra/code/mixins/__init__.py

@@ -0,0 +1,57 @@
+from typing import Any, Dict
+
+from .. import BaseUnderscoreJsonPropsHandler
+
+
+class DefaultableMixin(BaseUnderscoreJsonPropsHandler):
+    __default_config__: Dict[str, Any]
+
+    @property
+    def is_default(self) -> bool:
+        return self.get_prop("isDefault", False)
+
+    @is_default.setter
+    def is_default(self, is_default: bool = False) -> None:
+        self.set_prop("isDefault", is_default)
+
+    @classmethod
+    def create_default(cls) -> "DefaultableMixin":
+        return cls(cls.__default_config__)
+
+
+class NamedMixin(BaseUnderscoreJsonPropsHandler):
+    @property
+    def name(self) -> str:
+        return self.get_prop("name", False)
+
+    @name.setter
+    def name(self, name: str = "") -> None:
+        self.set_prop("name", name)
+
+
+class HasMetadataMixin(BaseUnderscoreJsonPropsHandler):
+    @property
+    def metadata(self) -> Dict:
+        return self.get_prop("metadata", False)
+
+    @metadata.setter
+    def metadata(self, metadata: Dict = {}) -> None:
+        self.set_prop("metadata", metadata)
+
+
+class HasDescriptionMixin(BaseUnderscoreJsonPropsHandler):
+    @property
+    def description(self) -> str:
+        return self.get_prop("description", "")
+
+    @description.setter
+    def description(self, description: str = "") -> None:
+        self.set_prop("description", description)
+
+    @property
+    def description_object(self) -> str:
+        return self.get_prop("descriptionObject", "")
+
+    @description_object.setter
+    def description_object(self, description_object: str = "") -> None:
+        self.set_prop("descriptionObject", description_object)