add dockerfile

.github/workflows/build_and_publish.yaml

@@ -0,0 +1,62 @@
+name: Build and Publish
+
+on:
+  push:
+    branches:
+      - main
+
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: 'Log level'
+        required: true
+        default: 'warning'
+        type: choice
+        options:
+        - info
+        - warning
+        - debug
+      tags:
+        description: 'Manual run'
+        required: false
+        type: boolean
+jobs:
+  publish:
+    name: Publish to ghcr.io
+    runs-on: ubuntu-20.04
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - dockerfile: ./Dockerfile
+            image: ghcr.io/${{ github.repository }}/kg_dashboard
+    permissions:
+      packages: write
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Docker meta
+        uses: docker/metadata-action@v4
+        id: meta
+        with:
+          images: ${{ matrix.image }}
+          tags: |
+            type=raw,value={{date 'YYYYMMDD'}}
+
+      - name: Log in
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: "${{ github.event_name != 'pull_request' }}"
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          file: ${{ matrix.dockerfile }}

Dockerfile

@@ -0,0 +1,34 @@
+# Select base image (can be ubuntu, python, shiny etc)
+FROM python:3.12-slim
+
+# Create user name and home directory variables. 
+# The variables are later used as $USER and $HOME. 
+ENV USER=username
+ENV HOME=/home/$USER
+
+# Add user to system
+RUN useradd -m -u 1000 $USER
+
+# Set working directory (this is where the code should go)
+WORKDIR $HOME/kg
+
+# Update system and install dependencies.
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    build-essential \
+    software-properties-common
+
+# Copy code and start script (this will place the files in home/username/)
+COPY requirements.txt $HOME/kg/requirements.txt
+COPY webapp $HOME/kg/webapp/
+COPY data/ $HOME/kg/data/
+COPY start-script.sh $HOME/kg/start-script.sh
+
+RUN pip install --no-cache-dir -r requirements.txt \
+    && chmod +x start-script.sh \
+    && chown -R $USER:$USER $HOME \
+    && rm -rf /var/lib/apt/lists/*
+
+USER $USER
+EXPOSE 8501
+
+ENTRYPOINT ["./start-script.sh"]

requirements.txt

@@ -16,4 +16,6 @@ openpyxl==3.1.2
 matplotlib_venn==0.11.10
 xgboost
 joblib==1.3.2
-treeinterpreter==0.2.3
+treeinterpreter==0.2.3
+umap-learn==0.5.1
+streamlit==1.36.0

start-script.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+streamlit run webapp/AMR-KG_Database.py --server.port=8501 --server.address=0.0.0.0