fix; update docker installation

Dockerfile

@@ -1,7 +1,6 @@
 FROM continuumio/miniconda3 AS nmrkit-ms
 
 ENV PYTHON_VERSION=3.10
-ENV RDKIT_VERSION=2023.03.1
 ENV OPENBABEL_VERSION=v3.1
 
 ARG RELEASE_VERSION
@@ -15,10 +14,13 @@ RUN apt-get update && \
     apt-get install -y curl && \
     conda update -n base -c defaults conda
 
+RUN apt-get update && apt-get -y install docker.io
+
 RUN conda install -c conda-forge python>=PYTHON_VERSION
-RUN conda install -c conda-forge rdkit>=RDKIT_VERSION
 RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
 
+RUN pip3 install rdkit
+
 RUN python3 -m pip install -U pip
 
 ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/

app/main.py

@@ -5,7 +5,7 @@
 
 from .routers import registration
 from .routers import chem
-from .routers import spectra
+from .routers import spectra, converter
 from fastapi.middleware.cors import CORSMiddleware
 
 from app.core import config, tasks
@@ -31,6 +31,7 @@
 app.include_router(registration.router)
 app.include_router(chem.router)
 app.include_router(spectra.router)
+app.include_router(converter.router)
 
 app.add_event_handler("startup", tasks.create_start_app_handler(app))
 app.add_event_handler("shutdown", tasks.create_stop_app_handler(app))

app/routers/converter.py

@@ -0,0 +1,63 @@
+import subprocess
+from fastapi import APIRouter, HTTPException, status, Response
+from app.schemas import HealthCheck
+from urllib.parse import unquote
+import json
+
+router = APIRouter(
+    prefix="/convert",
+    tags=["converter"],
+    dependencies=[],
+    responses={404: {"description": "Not Found"}},
+)
+
+
+@router.get("/", include_in_schema=False)
+@router.get(
+    "/health",
+    tags=["healthcheck"],
+    summary="Perform a Health Check on Converter Module",
+    response_description="Return HTTP Status Code 200 (OK)",
+    status_code=status.HTTP_200_OK,
+    include_in_schema=False,
+    response_model=HealthCheck,
+)
+def get_health() -> HealthCheck:
+    """
+    ## Perform a Health Check
+    Endpoint to perform a healthcheck on. This endpoint can primarily be used by Docker
+    to ensure a robust container orchestration and management are in place. Other
+    services that rely on the proper functioning of the API service will not deploy if this
+    endpoint returns any other HTTP status code except 200 (OK).
+    Returns:
+        HealthCheck: Returns a JSON response with the health status
+    """
+    return HealthCheck(status="OK")
+
+
+@router.get(
+    "/spectra",
+    tags=["converter"],
+    summary="Load and convert NMR raw data",
+    #response_model=List[int],
+    response_description="Load and convert NMR raw data",
+    status_code=status.HTTP_200_OK,
+)
+async def nmr_load_save(url: str):
+    """
+    ## Return nmrium json
+
+    Returns:
+        Return nmrium json
+    """
+    process = subprocess.Popen(
+        ["docker exec nmr-converter nmr-cli -u " + url],
+        stdout=subprocess.PIPE,
+        shell=True,
+    )
+    (output, err) = process.communicate()
+    process.wait()
+    if err:
+        raise HTTPException(status_code=500, detail=err)
+    else:
+        return Response(content=output, media_type="application/json")

app/scripts/nmr-cli/Dockerfile

@@ -12,8 +12,6 @@ COPY package.json ./
 COPY package-lock.json ./
 RUN npm install
 
-RUN apk add docker
-
 COPY . ./
 
 #install the nmr-cli as a global package 

app/scripts/nmr-respredict/Dockerfile

@@ -1,7 +1,6 @@
 FROM continuumio/miniconda3 AS nmr-respredict-ms
 
 ENV PYTHON_VERSION=3.10
-ENV RDKIT_VERSION=2023.09.1
 
 # Install runtime dependencies
 RUN apt-get update && \
@@ -11,7 +10,6 @@ RUN apt-get update && \
     conda update -n base -c defaults conda
 
 RUN conda install -c conda-forge python>=PYTHON_VERSION
-# RUN conda install -c conda-forge rdkit>=RDKIT_VERSION
 RUN python3 -m pip install -U pip
 
 RUN pip3 install rdkit

docker-compose.yml

@@ -5,9 +5,11 @@ services:
     build:
       context: ./
       dockerfile: Dockerfile
+    # image: nfdi4chem/nmrkit:dev-latest
     container_name: nmrkit-api
     volumes:
       - ./app:/code/app
+      - "/var/run/docker.sock:/var/run/docker.sock"
     ports:
       - "80:80"
     healthcheck:
@@ -29,15 +31,12 @@ services:
     entrypoint: /bin/sh
     stdin_open: true
     tty: true
-    volumes:
-      - "/var/run/docker.sock:/var/run/docker.sock"
+    container_name: nmr-converter
   nmr-respredict:
     build: ./app/scripts/nmr-respredict
     entrypoint: /bin/sh
     stdin_open: true
     tty: true
-    volumes:
-      - "/var/run/docker.sock:/var/run/docker.sock"
   prometheus:
     image: prom/prometheus
     container_name: nmrkit_prometheus