diff --git a/.gitignore b/.gitignore index 7172413..e102be8 100644 --- a/.gitignore +++ b/.gitignore @@ -1,211 +1,211 @@ -# postman -.postman -postman - -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[codz] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py.cover -.hypothesis/ -.pytest_cache/ -cover/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -.pybuilder/ -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# UV -# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -#uv.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -#poetry.lock -#poetry.toml - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. -# https://pdm-project.org/en/latest/usage/project/#working-with-version-control -#pdm.lock -#pdm.toml -.pdm-python -.pdm-build/ - -# pixi -# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. -#pixi.lock -# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one -# in the .venv directory. It is recommended not to include this directory in version control. -.pixi - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.envrc -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# pytype static type analyzer -.pytype/ - -# Cython debug symbols -cython_debug/ - -# PyCharm -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore -# and can be added to the global gitignore or merged into this file. For a more nuclear -# option (not recommended) you can uncomment the following to ignore the entire idea folder. -#.idea/ - -# Abstra -# Abstra is an AI-powered process automation framework. -# Ignore directories containing user credentials, local state, and settings. -# Learn more at https://abstra.io/docs -.abstra/ - -# Visual Studio Code -# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore -# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore -# and can be added to the global gitignore or merged into this file. However, if you prefer, -# you could uncomment the following to ignore the entire vscode folder -# .vscode/ - -# Ruff stuff: -.ruff_cache/ - -# PyPI configuration file -.pypirc - -# Cursor -# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to -# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data -# refer to https://docs.cursor.com/context/ignore-files -.cursorignore -.cursorindexingignore - -# Marimo -marimo/_static/ -marimo/_lsp/ -__marimo__/ +# postman +.postman +postman + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[codz] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py.cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# UV +# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +#uv.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock +#poetry.toml + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. +# https://pdm-project.org/en/latest/usage/project/#working-with-version-control +#pdm.lock +#pdm.toml +.pdm-python +.pdm-build/ + +# pixi +# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. +#pixi.lock +# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one +# in the .venv directory. It is recommended not to include this directory in version control. +.pixi + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.envrc +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +# Abstra +# Abstra is an AI-powered process automation framework. +# Ignore directories containing user credentials, local state, and settings. +# Learn more at https://abstra.io/docs +.abstra/ + +# Visual Studio Code +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore +# and can be added to the global gitignore or merged into this file. However, if you prefer, +# you could uncomment the following to ignore the entire vscode folder +# .vscode/ + +# Ruff stuff: +.ruff_cache/ + +# PyPI configuration file +.pypirc + +# Cursor +# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to +# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data +# refer to https://docs.cursor.com/context/ignore-files +.cursorignore +.cursorindexingignore + +# Marimo +marimo/_static/ +marimo/_lsp/ +__marimo__/ diff --git a/dockerfile b/Dockerfile similarity index 95% rename from dockerfile rename to Dockerfile index a3ef7f5..7cb2a92 100644 --- a/dockerfile +++ b/Dockerfile @@ -1,20 +1,20 @@ - -FROM ubuntu:22.04 -# Install openbabel and python -RUN apt-get update \ - && apt-get install --yes --quiet --no-install-recommends \ - openbabel \ - python3 \ - python3-pip \ - && apt-get clean && rm -rf /var/lib/apt/lists/* - -WORKDIR /var/local - -COPY requirements.txt . - -# Install dependencies -RUN /usr/bin/python3 -m pip install --no-cache-dir -r requirements.txt - -COPY src . - -CMD uvicorn app:app --host 0.0.0.0 --port ${PORT} --log-level warning + +FROM ubuntu:22.04 +# Install openbabel and python +RUN apt-get update \ + && apt-get install --yes --quiet --no-install-recommends \ + openbabel \ + python3 \ + python3-pip \ + && apt-get clean && rm -rf /var/lib/apt/lists/* + +WORKDIR /var/local + +COPY requirements.txt . + +# Install dependencies +RUN /usr/bin/python3 -m pip install --no-cache-dir -r requirements.txt + +COPY src . + +CMD uvicorn app:app --host 0.0.0.0 --port ${PORT} --log-level warning diff --git a/requirements.txt b/requirements.txt index 27b1657..b1d3606 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ -openbabel-wheel==3.1.1.22 -fastapi[all]==0.121.3 -fastapi-cache2==0.2.2 -redis==7.1.0 -pyscf==2.11.0 +openbabel-wheel==3.1.1.22 +fastapi[all]==0.121.3 +fastapi-cache2==0.2.2 +redis==7.1.0 +pyscf==2.11.0 diff --git a/src/app.py b/src/app.py index 835f659..1d337be 100644 --- a/src/app.py +++ b/src/app.py @@ -1,104 +1,104 @@ -from collections.abc import AsyncIterator -from contextlib import asynccontextmanager - -from fastapi import FastAPI -from fastapi.exceptions import HTTPException -from fastapi.middleware.cors import CORSMiddleware - -# from fastapi.requests import Request -from fastapi.responses import JSONResponse -from fastapi_cache import FastAPICache -from fastapi_cache.backends.redis import RedisBackend -from fastapi_cache.decorator import cache -from logging_config import logger -from openbabel import pybel -from pyscf import gto # pyright: ignore -from redis import asyncio as aioredis -from request_response_models import BasicError, ConvertRequest, MolFileModel - - -@asynccontextmanager -async def lifespan(_: FastAPI) -> AsyncIterator[None]: - redis = aioredis.from_url("redis://redis:6379") - FastAPICache.init(RedisBackend(redis), prefix="fastapi-cache") - pybel.ob.obErrorLog.SetOutputLevel(0) # NOTE removes logging - yield - - -app = FastAPI(lifespan=lifespan) - - -origins = [ - "http://localhost", - "http://localhost:8001", -] - -app.add_middleware( - CORSMiddleware, - allow_origins=origins, - allow_credentials=True, - allow_methods=["*"], - allow_headers=["*"], -) - - -@app.post( - "/convert", - responses={ - 200: {"description": "Coversion Successful", "model": MolFileModel}, - 400: {"description": "Item created", "model": BasicError}, - }, -) -def convert_molecule(req: ConvertRequest): - try: - # Rad the string and format from request - mol = pybel.readstring(req.format, req.text) - - if req.add_hydrogen: - mol.addh() - if req.convert_3d: - mol.make3D() - if req.optimize_geometry: - mol.localopt() - - logger.info(f"Converting from format {req.format}") - - # To compute the Number of electrons and orbitals - atoms = [(atom.atomicnum, atom.coords) for atom in mol.atoms] - - mol_pyscf = gto.Mole() - mol_pyscf.atom = atoms - mol_pyscf.basis = "sto-3g" # simple basis - mol_pyscf.charge = mol.charge # default net charge - mol_pyscf.spin = mol.spin - 1 # multiplicity - 1 - mol_pyscf.build() - - # Export the resulting molecule - mol.OBMol.SetTitle( - f"Charge={mol.charge} Multiplicity={mol.spin} Electrons={mol_pyscf.nelectron} Orbitals={mol_pyscf.nao_nr()}" - ) - - mol2string = mol.write("xyz") - return JSONResponse({"molfile": mol2string}, 200) - except Exception as e: - raise HTTPException(status_code=400, detail={"error": str(e)}) - - -@app.get("/informats") -@cache() -async def get_informats(): - return pybel.informats - - -@app.get( - "/health", - responses={ - 200: { - "description": "Is the service running?", - "content": {"application/json": {"example": {"status": "healthy"}}}, - }, - }, -) -@cache() -async def health_check(): - return {"status": "healthy"} +from collections.abc import AsyncIterator +from contextlib import asynccontextmanager + +from fastapi import FastAPI +from fastapi.exceptions import HTTPException +from fastapi.middleware.cors import CORSMiddleware + +# from fastapi.requests import Request +from fastapi.responses import JSONResponse +from fastapi_cache import FastAPICache +from fastapi_cache.backends.redis import RedisBackend +from fastapi_cache.decorator import cache +from logging_config import logger +from openbabel import pybel +from pyscf import gto # pyright: ignore +from redis import asyncio as aioredis +from request_response_models import BasicError, ConvertRequest, MolFileModel + + +@asynccontextmanager +async def lifespan(_: FastAPI) -> AsyncIterator[None]: + redis = aioredis.from_url("redis://redis:6379") + FastAPICache.init(RedisBackend(redis), prefix="fastapi-cache") + pybel.ob.obErrorLog.SetOutputLevel(0) # NOTE removes logging + yield + + +app = FastAPI(lifespan=lifespan) + + +origins = [ + "http://localhost", + "http://localhost:8001", +] + +app.add_middleware( + CORSMiddleware, + allow_origins=origins, + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) + + +@app.post( + "/convert", + responses={ + 200: {"description": "Coversion Successful", "model": MolFileModel}, + 400: {"description": "Item created", "model": BasicError}, + }, +) +def convert_molecule(req: ConvertRequest): + try: + # Rad the string and format from request + mol = pybel.readstring(req.format, req.text) + + if req.add_hydrogen: + mol.addh() + if req.convert_3d: + mol.make3D() + if req.optimize_geometry: + mol.localopt() + + logger.info(f"Converting from format {req.format}") + + # To compute the Number of electrons and orbitals + atoms = [(atom.atomicnum, atom.coords) for atom in mol.atoms] + + mol_pyscf = gto.Mole() + mol_pyscf.atom = atoms + mol_pyscf.basis = "sto-3g" # simple basis + mol_pyscf.charge = mol.charge # default net charge + mol_pyscf.spin = mol.spin - 1 # multiplicity - 1 + mol_pyscf.build() + + # Export the resulting molecule + mol.OBMol.SetTitle( + f"Charge={mol.charge} Multiplicity={mol.spin} Electrons={mol_pyscf.nelectron} Orbitals={mol_pyscf.nao_nr()}" + ) + + mol2string = mol.write("xyz") + return JSONResponse({"molfile": mol2string}, 200) + except Exception as e: + raise HTTPException(status_code=400, detail={"error": str(e)}) + + +@app.get("/informats") +@cache() +async def get_informats(): + return pybel.informats + + +@app.get( + "/health", + responses={ + 200: { + "description": "Is the service running?", + "content": {"application/json": {"example": {"status": "healthy"}}}, + }, + }, +) +@cache() +async def health_check(): + return {"status": "healthy"} diff --git a/src/logging_config.py b/src/logging_config.py index 5e8839c..b17a118 100644 --- a/src/logging_config.py +++ b/src/logging_config.py @@ -1,38 +1,38 @@ -import logging -import logging.config -import os - -ROOT_LEVEL = os.environ.get("PROD", "INFO") - -LOGGING_CONFIG = { - "version": 1, - "disable_existing_loggers": True, - "formatters": { - "standard": {"format": "%(asctime)s [%(levelname)s] %(name)s: %(message)s"}, - }, - "handlers": { - "default": { - "formatter": "standard", - "class": "logging.StreamHandler", - "stream": "ext://sys.stdout", # Default is stderr - }, - }, - "loggers": { - "": { # root logger - "level": ROOT_LEVEL, # "INFO", - "handlers": ["default"], - "propagate": False, - }, - "uvicorn.error": { - "level": "WARNING", - "handlers": ["default"], - }, - "uvicorn.access": { - "level": "DEBUG", - "handlers": ["default"], - }, - }, -} - -logging.config.dictConfig(LOGGING_CONFIG) -logger = logging.getLogger(__name__) +import logging +import logging.config +import os + +ROOT_LEVEL = os.environ.get("PROD", "INFO") + +LOGGING_CONFIG = { + "version": 1, + "disable_existing_loggers": True, + "formatters": { + "standard": {"format": "%(asctime)s [%(levelname)s] %(name)s: %(message)s"}, + }, + "handlers": { + "default": { + "formatter": "standard", + "class": "logging.StreamHandler", + "stream": "ext://sys.stdout", # Default is stderr + }, + }, + "loggers": { + "": { # root logger + "level": ROOT_LEVEL, # "INFO", + "handlers": ["default"], + "propagate": False, + }, + "uvicorn.error": { + "level": "WARNING", + "handlers": ["default"], + }, + "uvicorn.access": { + "level": "DEBUG", + "handlers": ["default"], + }, + }, +} + +logging.config.dictConfig(LOGGING_CONFIG) +logger = logging.getLogger(__name__) diff --git a/src/request_response_models.py b/src/request_response_models.py index 357f621..c8eec84 100644 --- a/src/request_response_models.py +++ b/src/request_response_models.py @@ -1,17 +1,17 @@ -from pydantic import BaseModel - - -class ConvertRequest(BaseModel): - text: str - format: str # e.g. "mol", "smi", "sdf", "inchi", etc. - add_hydrogen: bool = False - convert_3d: bool = False - optimize_geometry: bool = False - - -class MolFileModel(BaseModel): - molfile: str - - -class BasicError(BaseModel): - error: str +from pydantic import BaseModel + + +class ConvertRequest(BaseModel): + text: str + format: str # e.g. "mol", "smi", "sdf", "inchi", etc. + add_hydrogen: bool = False + convert_3d: bool = False + optimize_geometry: bool = False + + +class MolFileModel(BaseModel): + molfile: str + + +class BasicError(BaseModel): + error: str