upd: models.py added (pydantic) and PEP 518

iemap/functions.py

@@ -3,12 +3,15 @@
 import time
 from functools import wraps
 from requests_toolbelt import MultipartEncoder
+from requests.exceptions import ConnectionError
 import requests
-from os.path import dirname, isfile
+from os.path import dirname
+from os import getcwd
 import mimetypes
 import json
 from bson import ObjectId
 from iemap.helpers import get_file_size, endpoints
+from iemap.models import newProject
 
 
 

iemap/models.py

@@ -0,0 +1,153 @@
+from __future__ import annotations
+from datetime import  datetime
+from bson.objectid import ObjectId as BsonObjectId
+from typing import Annotated, List, Union, Optional
+import json
+from pydantic import BaseModel, Field, validator
+from re import findall
+
+
+class ObjectIdStr(str):
+    @classmethod
+    def __get_validators__(cls):
+        yield cls.validate
+
+    @classmethod
+    def validate(cls, v):
+        try:
+            return BsonObjectId(v)
+        except Exception:
+            raise ValueError(f"{v} is not a valid ObjectId")
+        return str(v)
+
+
+class PydanticObjectId(BsonObjectId):
+    @classmethod
+    def __get_validators__(cls):
+        yield cls.validate
+
+    @classmethod
+    def validate(cls, v):
+        if not isinstance(v, BsonObjectId):
+            raise TypeError("ObjectId required")
+        return str(v)
+
+
+class Provenance(BaseModel):
+    email: Optional[str]  # email retrieved from JWT
+    affiliation: Optional[str]  # affiliation retrieved from JWT
+    createdAt: Annotated[
+        datetime, Field(default_factory=lambda: datetime.now().utcnow())
+    ]
+    updatedAt: Annotated[
+        datetime, Field(default_factory=lambda: datetime.now().utcnow())
+    ]
+
+
+class Project(BaseModel):
+    name: str
+    label: str
+    description: Optional[str]
+
+
+class Parameter(BaseModel):
+    name: str
+    value: Union[float, str]
+
+
+class Agent(BaseModel):
+    name: str
+    version: str
+
+
+class ChemicalCompositionItem(BaseModel):
+    element: str
+    percentage: str
+
+
+class Lattice(BaseModel):
+    a: str
+    b: str
+    c: str
+    alpha: str
+    beta: str
+    gamma: str
+
+
+class InputMaterial(BaseModel):
+    lattice: Optional[Lattice]
+    sites: List[List[float]]
+    species: List[str]
+    cell: List[List[float]]
+
+
+class OutputMaterial(BaseModel):
+    lattice: Optional[Lattice]
+    sites: List[List[float]]
+    species: List[str]
+    cell: List[List[float]]
+
+
+class Material(BaseModel):
+    formula: str
+    elements: Optional[List[str]]  # List[Union[str, str]]
+    input: Optional[InputMaterial]
+    output: Optional[OutputMaterial]
+
+    @validator("elements", always=True)
+    def composite_name(cls, v, values, **kwargs):
+        elements = [
+            x
+            for x in findall("[A-Z][a-z]?|[0-9]+", values["formula"])
+            if not x.isnumeric()
+        ]
+        return elements
+
+
+class PropertyFile(BaseModel):
+    fullpath: str
+
+
+class Property(BaseModel):
+    name: str
+    value: Union[float, str]
+    file: Optional[PropertyFile]
+
+
+class Process(BaseModel):
+    isExperiment: bool
+    method: str
+    agent: Optional[Agent]
+
+
+class FileProject(BaseModel):
+    hash: Optional[str]
+    name: str
+    extention: str
+    size: Optional[str]
+    createdAt: Annotated[
+        datetime, Field(default_factory=lambda: datetime.now().utcnow())
+    ]
+    updatedAt: Annotated[
+        datetime, Field(default_factory=lambda: datetime.now().utcnow())
+    ]
+
+    class Config:
+        use_enum_values = True
+
+
+def validate_datetime(cls, values):
+    """
+    Reusable validator for pydantic models
+    """
+    return values or datetime.now().utcnow()
+
+
+class newProject(BaseModel):
+    identifier: Optional[str]
+    provenance: Optional[Provenance]
+    project: Project
+    process: Process
+    material: Material
+    parameters: List[Parameter]
+    properties: List[Property]

pyproject.toml

@@ -0,0 +1,38 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "iemap"
+version = "0.3.1"
+authors = [
+    { name="Sergio Ferlito", email="sergio.ferlito@enea.it" },
+    { name="marco.puccini", email="marco.puccini@enea.it" }
+]
+maintainers = [
+    { name = "Marco Puccini", email = "marco.puccini@enea.it" }
+]
+description = "Tools to use IEMAP Rest API"
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "License :: OSI Approved :: GNU General Public License (GPL)",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Utilities"
+]
+dependencies = [
+    "requests==2.28.1",
+    "requests_toolbelt==0.9.1",
+    "bson==0.5.10",
+    "pydantic==1.10.2"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/ai4mat/iemap-module"
+"Bug Tracker" = "https://github.com/ai4mat/iemap-module/issues"