fix: added spectra router

Dockerfile

@@ -43,4 +43,10 @@ RUN python3 -m pip install uvicorn[standard]
 
 COPY ./app /code/app
 
+RUN curl -sL https://deb.nodesource.com/setup_current.x | bash -
+RUN apt-get install -y nodejs
+RUN npm install -g npm@latest
+
+RUN npm install -g /code/app/scripts/nmr-cli
+
 CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "80", "--workers", "4", "--reload"]

README.md

@@ -49,5 +49,5 @@ NMRKit is developed and maintained by the [NFDI4Chem partners](https://www.nfdi4
 The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT).
 
 
-<p align="left"><a href="https://nfdi4chem.de/" target="_blank"><img src="https://www.nfdi4chem.de/wp-content/themes/wptheme/assets/img/logo.svg" width="50%" alt="NFDI4Chem Logo"></a></p>
+<p align="left"><a href="https://nfdi4chem.de/" target="_blank"><img src="https://www.nfdi4chem.de/wp-content/themes/wptheme/assets/img/logo.svg" width="30%" alt="NFDI4Chem Logo"></a></p>
 <p align="left"><a href="https://cheminf.uni-jena.de/" target="_blank"><img src="/public/img/fsu-jena.jpg" width="30%" alt="NFDI4Chem Logo"></a></p>

app/main.py

@@ -5,6 +5,7 @@
 
 from .routers import registration
 from .routers import chem
+from .routers import spectra
 from fastapi.middleware.cors import CORSMiddleware
 
 from app.core import config, tasks
@@ -29,6 +30,7 @@
 
 app.include_router(registration.router)
 app.include_router(chem.router)
+app.include_router(spectra.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/chem.py

@@ -38,7 +38,7 @@ def get_health() -> HealthCheck:
 
 @router.get(
     "/hosecode",
-    tags=["registration"],
+    tags=["chem"],
     summary="Generates HOSE codes of molecule",
     response_model=list[str],
     response_description="Returns an array of hose codes generated",

app/routers/spectra.py

@@ -0,0 +1,70 @@
+from typing import Annotated
+from fastapi import APIRouter, HTTPException, status, FastAPI, File, UploadFile
+from fastapi.responses import Response
+from app.schemas import HealthCheck
+import subprocess
+import json
+
+router = APIRouter(
+    prefix="/spectra",
+    tags=["spectra"],
+    dependencies=[],
+    responses={404: {"description": "Not found"}},
+)
+
+@router.get("/", include_in_schema=False)
+@router.get(
+    "/health",
+    tags=["healthcheck"],
+    summary="Perform a Health Check on Chem 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 Docker
+    to ensure a robust container orchestration and management is in place. Other
+    services which rely on 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(
+    "/parse",
+    tags=["spectra"],
+    summary="Parse the input spectra format and extract metadata",
+    response_description="",
+    status_code=status.HTTP_200_OK,
+    
+)
+async def parse_spectra(file: UploadFile):
+    """
+    ## Parse the spectra file and extract meta-data
+    Endpoint to uses nmr-load-save to read the input spectra file (.jdx,.nmredata,.dx) and extracts metadata
+
+    Returns:
+        data: spectra data in json format
+    """
+    try:
+        contents = file.file.read()
+        file_path = "/tmp/" + file.filename
+        with open(file_path, 'wb') as f:
+            f.write(contents)
+        p = subprocess.Popen("npx nmr-cli -p " + file_path, stdout=subprocess.PIPE, shell=True)
+        (output, err) = p.communicate()
+        p_status = p.wait()
+        return output
+    except Exception as e:
+        raise HTTPException(
+            status_code=422,
+            detail="Error paring the structure " + e.message + ". Error: " + err + ". Status:" + p_status,
+            headers={"X-Error": "RDKit molecule input parse error"},
+        )
+    finally:
+        file.file.close()

app/scripts/nmr-cli/bin/index.js

@@ -0,0 +1,69 @@
+#!/usr/bin/env node
+const {join,isAbsolute}= require("path");
+const yargs = require("yargs");
+const loader = require("nmr-load-save");
+const fileUtils = require("filelist-utils");
+
+const usageMessage ="Usage: nmr-cli -u <url> or -p <path>" 
+
+const options = yargs
+ .usage(usageMessage)
+ .option("u", { alias: "url", describe: "File URL", type: "string",nargs:1})
+ .option("p", { alias: "path", describe: "Directory path", type: "string",nargs:1}).showHelpOnFail();
+
+  async function loadSpectrumFromURL(url) {
+    const {pathname:relativePath,origin:baseURL} = new URL(url);
+    const source = {
+        entries: [
+          {
+            relativePath,
+          }
+        ],
+        baseURL
+      };
+    const fileCollection = await fileUtils.fileCollectionFromWebSource(source,{});
+
+    const {
+      nmriumState: { data },
+    } = await loader.read(fileCollection);
+    return data;
+  }
+
+
+  async function loadSpectrumFromFilePath(path) {
+    const dirPath = isAbsolute(path)?path:join(process.cwd(),path)
+
+    const fileCollection = await fileUtils.fileCollectionFromPath(dirPath,{});
+
+    const {
+      nmriumState: { data },
+    } = await loader.read(fileCollection);
+    return data;
+  }
+
+
+  const parameters = options.argv;
+
+if(parameters.u && parameters.p){
+  options.showHelp();
+}else{
+
+  if(parameters.u){
+    loadSpectrumFromURL(parameters.u).then((result)=>{
+    console.log(JSON.stringify(result))
+ })
+
+  }
+
+  if(parameters.p){
+    loadSpectrumFromFilePath(parameters.p).then((result)=>{
+      console.log(JSON.stringify(result))
+   })
+  }
+
+}
+
+
+
+
+

requirements.txt

@@ -10,4 +10,5 @@ prometheus-fastapi-instrumentator
 databases[postgresql]==0.4.2
 SQLAlchemy==2.0.19
 alembic==1.11.1
-psycopg2-binary
+psycopg2-binary
+python-multipart