Merge branch 'development' into improve-predictions

Author: hamed-musallam

.github/workflows/dev-build.yml

@@ -23,15 +23,15 @@ env:
 
 jobs:
   test_and_lint:
-    uses: NFDI4Chem/nmrkit/.github/workflows/test.yml@main
+    uses: ./.github/workflows/test.yml
 
   push_to_registry:
     name: Push Docker image to Docker Hub
     runs-on: ubuntu-latest
-    #needs: test_and_lint
+    needs: test_and_lint
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Log in to Docker Hub
         uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a

.github/workflows/doc-deploy.yml

@@ -29,23 +29,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Not needed if lastUpdated is not enabled
       # - uses: pnpm/action-setup@v2 # Uncomment this if you're using pnpm
       - name: Setup Node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
           node-version: 18
           cache: npm # or pnpm / yarn
       - name: Setup Pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v4
       - name: Install dependencies
         run: npm ci # or pnpm install / yarn install
       - name: Build with VitePress
         run: npm run docs:build # or pnpm docs:build / yarn docs:build
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: docs/.vitepress/dist
 
@@ -60,4 +60,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

.github/workflows/prod-build.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       #Fetch Latest release
       - name: Fetch latest release

.github/workflows/test.yml

@@ -31,9 +31,9 @@ jobs:
         python-version: ["3.10"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: 'Create env file'
@@ -62,4 +62,4 @@ jobs:
         flake8 --per-file-ignores="__init__.py:F401" --ignore E402,E501,W503 $(git ls-files 'app/*.py') .
     - name: Run test
       run: |
-        python3 -m pytest -p no:warnings --ignore=lwreg/lwreg/test-cli.py --ignore=lwreg/lwreg/test_lwreg.py
+        python3 -m pytest -p no:warnings --ignore=lwreg/lwreg/test-cli.py --ignore=lwreg/lwreg/test_lwreg.py --ignore=lwreg/lwreg/test_dbutils.py

Dockerfile

@@ -1,17 +1,24 @@
-FROM continuumio/miniconda3 AS nmrkit-ms
+FROM continuumio/miniconda3:24.1.2-0 AS nmrkit-ms
 
 ENV PYTHON_VERSION=3.10
 ENV OPENBABEL_VERSION=v3.1
 
 ARG RELEASE_VERSION
 ENV RELEASE_VERSION=${RELEASE_VERSION}
 
-# Install runtime dependencies
+# Install runtime and build dependencies
 RUN apt-get update && \
-    apt-get install -y software-properties-common && \
-    apt-get update -y && \
-    apt-get install -y openjdk-11-jre && \
-    apt-get install -y curl && \
+    apt-get install -y --no-install-recommends \
+    software-properties-common \
+    openjdk-17-jre \
+    curl \
+    build-essential \
+    gcc \
+    g++ \
+    git \
+    wget && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* && \
     conda update -n base -c defaults conda
 
 RUN apt-get update && apt-get -y install docker.io
@@ -23,7 +30,7 @@ RUN pip3 install rdkit
 
 RUN python3 -m pip install -U pip
 
-ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
+ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64/
 RUN export JAVA_HOME
 
 RUN git clone "https://github.com/rinikerlab/lightweight-registration.git" lwreg
@@ -34,8 +41,7 @@ WORKDIR /code
 COPY ./requirements.txt /code/requirements.txt
 COPY ./alembic.ini /code/alembic.ini
 
-RUN pip3 install --upgrade setuptools pip && \
-    apt-get update && apt-get install -y git
+RUN pip3 install --upgrade setuptools pip
 
 RUN pip3 install --no-cache-dir -r /code/requirements.txt
 

app/routers/chem.py

@@ -99,10 +99,11 @@ async def label_atoms(data: Annotated[str, Body(embed=False, media_type="text/pl
         url = "http://alatis.nmrfam.wisc.edu/upload"
         payload = {"input_text": data, "format": "format_", "response_type": "json"}
         response = requests.request("POST", url, data=payload)
+        response.raise_for_status()  # Raise an error for bad status codes
         return response.json()
     except Exception as e:
         raise HTTPException(
             status_code=422,
-            detail="Error parsing the structure " + e.message,
+            detail=f"Error parsing the structure: {str(e)}",
             headers={"X-Error": "RDKit molecule input parse error"},
         )

app/scripts/nmr-cli/Dockerfile

@@ -12,6 +12,12 @@ WORKDIR /app
 ENV BASE_NMRIUM_URL=https://nmriumdev.nmrxiv.org/
 ENV NMR_PREDICTION_URL=https://nmrshiftdb.nmr.uni-koeln.de/NmrshiftdbServlet/nmrshiftdbaction/quickcheck
 
+# Install Java (OpenJDK 17 for Ubuntu Noble)
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends openjdk-17-jre && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
 COPY package.json ./
 
 RUN npm install
@@ -20,8 +26,8 @@ COPY . ./
 
 RUN npm run build
 
-#install the nmr-cli as a global package 
-# for example, nmr-cli parse-spectra -u https://cheminfo.github.io/bruker-data-test/data/zipped/aspirin-1h.zip
+# Install the nmr-cli as a global package 
+# For example, nmr-cli parse-spectra -u https://cheminfo.github.io/bruker-data-test/data/zipped/aspirin-1h.zip
 # nmr-cli predict -n "1H" --id 1 --type "nmr;1H;1d" --shifts "1" --solvent "Dimethylsulphoxide-D6 (DMSO-D6, C2D6SO)" -m $"\n Ketcher  6122516162D 1   1.00000     0.00000     0\n\n 16 17  0  0  0  0  0  0  0  0999 V2000\n    1.1954   -4.6484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -4.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0622   -4.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -5.6488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1954   -5.6533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0644   -6.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7902   -4.1495    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6574   -4.6498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7964   -6.1512    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6596   -5.6458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5228   -4.1488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5277   -6.1421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    6.3895   -4.6477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5216   -3.1488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    7.2548   -4.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.1215   -4.6455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  3  1  2  0  0  0  0\n  1  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  4  1  0  0  0  0\n  4  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  4  9  1  0  0  0  0\n  9 10  2  0  0  0  0\n 10  8  1  0  0  0  0\n  8  7  2  0  0  0  0\n  7  2  1  0  0  0  0\n  8 11  1  0  0  0  0\n 10 12  1  0  0  0  0\n 11 13  1  0  0  0  0\n 11 14  2  0  0  0  0\n 13 15  1  0  0  0  0\n 15 16  1  0  0  0  0\nM  END"
 RUN npm install . -g
 

app/scripts/nmr-respredict/Dockerfile

@@ -1,12 +1,14 @@
-FROM continuumio/miniconda3 AS nmr-respredict-ms
+FROM continuumio/miniconda3:24.1.2-0 AS nmr-respredict-ms
 
 ENV PYTHON_VERSION=3.10
 
 # Install runtime dependencies
 RUN apt-get update && \
-    apt-get install -y software-properties-common && \
-    apt-get update -y && \
-    apt-get install -y curl && \
+    apt-get install -y --no-install-recommends \
+    software-properties-common \
+    curl && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* && \
     conda update -n base -c defaults conda
 
 RUN conda install -c conda-forge python>=PYTHON_VERSION

docker-compose.yml

@@ -12,7 +12,7 @@ services:
       - "/var/run/docker.sock:/var/run/docker.sock"
       - shared-data:/shared
     ports:
-      - "80:80"
+      - "8080:80"
     healthcheck:
       test:
         [
@@ -62,7 +62,7 @@ services:
   redis:
     image: "redis:alpine"
     ports:
-      - "${FORWARD_REDIS_PORT:-6379}:6379"
+      - "${FORWARD_REDIS_PORT:-6380}:6379"
     volumes:
       - "redis:/data"
     networks:
@@ -74,7 +74,7 @@ services:
   pgsql:
     image: "informaticsmatters/rdkit-cartridge-debian"
     ports:
-      - "${FORWARD_DB_PORT:-5432}:5432"
+      - "${FORWARD_DB_PORT:-5433}:5432"
     env_file:
       - ./.env
     volumes:
@@ -97,8 +97,8 @@ services:
   minio:
     image: 'minio/minio:latest'
     ports:
-      - '${FORWARD_MINIO_PORT:-9001}:9001'
-      - '${FORWARD_MINIO_CONSOLE_PORT:-8900}:8900'
+      - '${FORWARD_MINIO_PORT:-9002}:9001'
+      - '${FORWARD_MINIO_CONSOLE_PORT:-8901}:8900'
     environment:
       MINIO_ROOT_USER: 'sail'
       MINIO_ROOT_PASSWORD: 'password'

ops/docker-compose-dev.yml

@@ -32,6 +32,21 @@ services:
     env_file:
       - ./.env
 
+  nmr-load-save:
+    image: nfdi4chem/nmr-cli:dev-latest
+    entrypoint: /bin/sh
+    stdin_open: true
+    tty: true
+    container_name: nmr-converter
+  nmr-respredict:
+    image: nfdi4chem/nmr-respredict:dev-latest
+    entrypoint: /bin/sh
+    stdin_open: true
+    tty: true
+    container_name: nmr-respredict
+    volumes:
+      - shared-data:/shared
+
   prometheus:
     image: prom/prometheus
     container_name: nmrkit_prometheus