Merge pull request #69 from NFDI4Chem/development

Development

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+exclude =
+    ./app/scripts/nmr-respredict/*.py

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, predict
 from fastapi.middleware.cors import CORSMiddleware
 
 from app.core import config, tasks
@@ -31,6 +31,8 @@
 app.include_router(registration.router)
 app.include_router(chem.router)
 app.include_router(spectra.router)
+app.include_router(converter.router)
+app.include_router(predict.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 +1,61 @@
+import subprocess
+from fastapi import APIRouter, HTTPException, status, Response
+from app.schemas import HealthCheck
+
+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/routers/predict.py

@@ -0,0 +1,145 @@
+import subprocess
+from fastapi import APIRouter, HTTPException, status, Response, Body
+from app.schemas import HealthCheck
+from app.schemas.respredict_response_schema import ResPredictModel
+from app.schemas.error import ErrorResponse, BadRequestModel, NotFoundModel
+import uuid
+from typing import Annotated
+import os
+
+router = APIRouter(
+    prefix="/predict",
+    tags=["predict"],
+    dependencies=[],
+    responses={404: {"description": "Not Found"}},
+)
+
+
+@router.get("/", include_in_schema=False)
+@router.get(
+    "/health",
+    tags=["healthcheck"],
+    summary="Perform a Health Check on Predict 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.post(
+    "/respredict",
+    summary="",
+    responses={
+        200: {
+            "description": "Successful response",
+            "model": ResPredictModel,
+        },
+        400: {"description": "Bad Request", "model": BadRequestModel},
+        404: {"description": "Not Found", "model": NotFoundModel},
+        422: {"description": "Unprocessable Entity", "model": ErrorResponse},
+    },
+)
+async def predict_mol(
+    data: Annotated[
+        str,
+        Body(
+            embed=False,
+            media_type="text/plain",
+            openapi_examples={
+                "example1": {
+                    "summary": "Example: C",
+                    "value": """
+  CDK     09012310592D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END""",
+                },
+            },
+        ),
+    ]
+):
+    """
+    Standardize molblock using the ChEMBL curation pipeline
+    and return the standardized molecule, SMILES, InChI, and InCHI-Key.
+
+    Parameters:
+    - **molblock**: The request body containing the "molblock" string representing the molecule to be standardized.
+
+    Returns:
+    - dict: A dictionary containing the following keys:
+        - "standardized_mol" (str): The standardized molblock of the molecule.
+        - "canonical_smiles" (str): The canonical SMILES representation of the molecule.
+        - "inchi" (str): The InChI representation of the molecule.
+        - "inchikey" (str): The InChI-Key of the molecule.
+
+    Raises:
+    - ValueError: If the SMILES string is not provided or is invalid.
+
+    """
+    try:
+        if data:
+            file_name = "/shared/" + str(uuid.uuid4()) + ".mol"
+            f = open(file_name, "a")
+            f.write(data)
+            f.close()
+            process = subprocess.Popen(
+                [
+                    "docker exec nmr-respredict python3 predict_standalone.py --filename "
+                    + file_name
+                ],
+                stdout=subprocess.PIPE,
+                shell=True,
+            )
+            (output, err) = process.communicate()
+            process.wait()
+            if err:
+                raise HTTPException(status_code=500, detail=err)
+            else:
+                if os.path.exists(file_name):
+                    os.remove(file_name)
+                return Response(content=output, media_type="application/json")
+    except Exception as e:
+        raise HTTPException(status_code=422, detail=str(e))
+
+
+# @router.get(
+#     "/predict",
+#     tags=["predict"],
+#     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_respredict(url: str):
+#     """
+#     ## Return nmrium json
+
+#     Returns:
+#         Return nmrium json
+#     """
+#     file = "/shared" + str(uuid.uuid4()) + ".mol"
+
+#     process = subprocess.Popen(
+#         ["docker exec nmr-respredict python3 ./predict_standalone.py --filename " + file],
+#         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")