fixed dockerfile, added fastapi

app.py

@@ -1,15 +0,0 @@
-from openbabel import openbabel
-
-mol = openbabel.OBMol()
-print(mol.NumAtoms()) #Should print 0 (atoms)
-
-a = mol.NewAtom()
-a.SetAtomicNum(6)   # carbon atom
-a.SetVector(0.0, 1.0, 2.0) # coordinates
-
-b = mol.NewAtom()
-mol.AddBond(1, 2, 1)   # atoms indexed from 1
-print(mol.NumAtoms()) #Should print 2 (atoms)
-print(mol.NumBonds()) 
-
-mol.Clear();

docker-compose.yaml

@@ -0,0 +1,9 @@
+services:
+  openbabel-app:
+    build:
+      context: .
+    environment:
+      PORT: 1654
+    ports:
+      - 1654:1654
+    tty: true

dockerfile

@@ -1,75 +1,20 @@
-FROM ubuntu:18.04
-
-ARG DEBIAN_FRONTEND=noninteractive
 
+FROM ubuntu:22.04
 # Install openbabel dependencies
 RUN apt-get update \
   && apt-get install --yes --quiet --no-install-recommends \
-    libboost-filesystem1.65.1 \
-    libboost-iostreams1.65.1 \
-    libboost-program-options1.65.1 \
-    libboost-regex1.65.1 \
-    libboost-system1.65.1 \
-    libboost-test1.65.1 \
-    libpython3.6 \
-    libxml2 \
+  openbabel \
   python3 \
-    python3-cairo \
-    swig \
+  python3-pip \
   && apt-get clean && rm -rf /var/lib/apt/lists/*
 
-ARG OPENBABEL_VERSION=3.1.1
-ARG OPENBABEL_HOME=/usr/local/openbabel/$OPENBABEL_VERSION
-SHELL ["/bin/bash", "-c"]
-
-# Install openbabel
-RUN build_deps="\
-    build-essential \
-    cmake \
-    libboost-filesystem1.65-dev \
-    libboost-iostreams1.65-dev \
-    libboost-program-options1.65-dev \
-    libboost-regex1.65-dev \
-    libboost-system1.65-dev \
-    libboost-test1.65-dev \
-    libboost1.65-dev \
-    libcairo2-dev \
-    libeigen3-dev \
-    libxml2-dev \
-    python3-dev \
-    rapidjson-dev \
-    wget \
-    zlib1g-dev" \
-  && apt-get update \
-  && apt-get install --yes --quiet $build_deps \
-  && wget --quiet --no-hsts --output-document=- https://github.com/openbabel/openbabel/archive/openbabel-${OPENBABEL_VERSION//./-}.tar.gz | tar -zxvf - -C /tmp \
-  && mkdir -p /tmp/openbabel-openbabel-${OPENBABEL_VERSION//./-}/build \
-  && cd /tmp/openbabel-openbabel-${OPENBABEL_VERSION//./-}/build \
-  && cmake .. \
-    -Wno-dev \
-    -DRUN_SWIG=ON \
-    -DPYTHON_BINDINGS=ON \
-    -DPYTHON_EXECUTABLE=/usr/bin/python3.6 \
-    -DCMAKE_INSTALL_PREFIX=$OPENBABEL_HOME \
-    -DCMAKE_BUILD_TYPE=Release \
-  && make -j $(nproc) && make install \
-  # This is a heck to pass Test #218, which fails
-  # because \N in a string is interpreted for unicode
-  # but in our case \N has nothing to do with unicode.
-  # So we make the string as a raw string.
-  && sed -i -e "45s|'C|r'C|" -e "50s|'C|r'C|" /tmp/openbabel-openbabel-${OPENBABEL_VERSION//./-}/test/testdistgeom.py \
-  && make test \
-  && ln -s $OPENBABEL_HOME/lib/python3.6/site-packages/openbabel /usr/local/lib/python3.6/dist-packages/openbabel \
-  && cd / && rm -rf /tmp/* \
-  && apt-get purge --yes --auto-remove $build_deps \
-  && apt-get clean && rm -rf /var/lib/apt/lists/*
-
-# Set environment variables
-ENV LD_LIBRARY_PATH=$OPENBABEL_HOME/lib:$LD_LIBRARY_PATH
-ENV PATH=$OPENBABEL_HOME/bin:$PATH
-
 WORKDIR /var/local
 
-COPY . .
+COPY requirements.txt .
 
-CMD ["/usr/bin/python3", "app.py"]
+# Install dependencies
+RUN /usr/bin/python3 -m pip install --no-cache-dir -r requirements.txt
+
+COPY src .
+
+CMD fastapi run app.py --port ${PORT}

requirements.txt

@@ -0,0 +1,4 @@
+openbabel-wheel==3.1.1.22
+fastapi[all]==0.121.3
+fastapi-cache2==0.2.2
+redis==7.1.0

src/app.py

@@ -0,0 +1,40 @@
+from collections.abc import AsyncIterator
+from contextlib import asynccontextmanager
+
+from fastapi import FastAPI
+from starlette.requests import Request
+from starlette.responses import Response
+
+from fastapi_cache import FastAPICache
+from fastapi_cache.backends.redis import RedisBackend
+from fastapi_cache.decorator import cache
+
+from redis import asyncio as aioredis
+from openbabel import pybel
+
+
+@asynccontextmanager
+async def lifespan(_: FastAPI) -> AsyncIterator[None]:
+    redis = aioredis.from_url("redis://localhost")
+    FastAPICache.init(RedisBackend(redis), prefix="fastapi-cache")
+    yield
+
+
+app = FastAPI(lifespan=lifespan)
+
+
+@app.get("/informats")
+async def get_informats():
+    return pybel.informats
+
+
+@app.get("/")
+@cache(expire=60)
+async def index():
+    return dict(hello="world")
+
+
+
+
+
+