Merge pull request #111 from Integrative-Transcriptomics/update-repo

Updates repo
Creates a docker image that has a complete functional version of Evidente.

Author: mwittep

.babelrc

@@ -1,4 +1,3 @@
 {
   "presets": ["es2015", "react"],
-  "plugins": ["transform-decorators-legacy", "transform-class-properties"]
 }

.github/workflows/docker_release.yml

@@ -0,0 +1,35 @@
+name: Build and Push Docker Image
+
+# when to run the workflow
+on:
+  push:
+    branches: [master]
+
+# the jobs to run
+jobs:
+  build:
+    # the os to run the job on
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      # build the image now
+      - name: Build Docker image
+
+        run: |
+          docker build -t evidente:latest .
+
+      - name: save images
+        run: |
+          docker save evidente:latest | gzip > image_evidente.tar.gz
+
+      - name: Release WebImage to Repo
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: image_evidente.tar.gz
+          asset_name: Evidente
+          tag: ${{ github.ref }}
+          overwrite: true
+          body: "The image for the web app of Evidente"

Dockerfile

@@ -0,0 +1,46 @@
+# Use an official Node.js runtime as a parent image
+# Using a specific version like '20-bullseye-slim' is reliable
+FROM node:20-bullseye-slim
+
+# Set the working directory in the container
+WORKDIR /app
+
+# Prevent apt-get from asking for user input
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install Python and pip, then clean up
+# 1. Update package lists
+# 2. Install python3, python3-pip, and a helper to link 'python' to 'python3'
+# 3. Clean up apt cache to reduce image size
+RUN apt-get update && \
+    apt-get install -y python3 python3-pip python-is-python3 && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install git
+RUN apt-get update && \
+    apt-get install -y git && \
+    rm -rf /var/lib/apt/lists/*
+
+    # install java 17
+RUN apt-get update && \
+    apt-get install -y openjdk-17-jre && \
+    rm -rf /var/lib/apt/lists/*
+
+COPY src src
+COPY public public
+COPY package.json package.json
+COPY server server
+COPY requirements.txt requirements.txt
+COPY setup.py setup.py
+
+RUN pip install --no-cache-dir -r requirements.txt
+RUN pip install --no-cache-dir .
+RUN npm install 
+RUN npm run build
+
+# expose the port the app runs on
+EXPOSE 3000
+
+
+# Define the command to run the app
+CMD ["gunicorn", "--bind", "0.0.0.0:3000", "server.wsgi:app"]

package.json

@@ -9,7 +9,6 @@
     "@testing-library/jest-dom": "^4.2.4",
     "@testing-library/react": "^9.5.0",
     "@testing-library/user-event": "^7.2.1",
-    "popper.js": "^1.16.1",
     "array-move": "^2.2.1",
     "bootstrap": "^4.5.0",
     "browserify": "^17.0.0",
@@ -20,16 +19,17 @@
     "evergreen-ui": "^2.0.1",
     "html2canvas": "^1.3.2",
     "jquery": "^3.5.1",
-    "lodash": "^4.17.21",
     "jspdf": "^2.3.1",
-    "phylotree": "github:mwittep/phylotree.js",
+    "lodash": "^4.17.21",
+    "phylotree": "github:Integrative-Transcriptomics/phylotree.js",
+    "popper.js": "^1.16.1",
     "react": "^16.13.1",
     "react-bootstrap": "^1.0.1",
     "react-color": "^2.18.1",
     "react-dom": "^16.13.1",
     "react-draggable": "^4.4.3",
     "react-loading-overlay": "^1.0.1",
-    "react-scripts": "^4.*.*",
+    "react-scripts": "^5.0.1",
     "react-select": "^2.4.4",
     "react-sortable-hoc": "^1.11.0",
     "react-virtualized": "^9.21.2",
@@ -38,8 +38,8 @@
   "scripts": {
     "server": "cd server && flask run --no-debugger",
     "evidente": "run-p server start",
-    "start": "react-scripts start",
-    "build": "react-scripts build",
+    "start": "react-scripts --openssl-legacy-provider  start",
+    "build": "react-scripts --openssl-legacy-provider  build",
     "test": "react-scripts test",
     "eject": "react-scripts eject"
   },

requirements.txt

@@ -4,13 +4,13 @@ charset-normalizer==2.0.8
 click==8.0.3
 docopt==0.6.2
 Flask==2.0.2
-goatools==1.1.6
+goatools==1.4.12
 idna==3.3
 importlib-metadata==4.8.2
 itsdangerous==2.0.1
 Jinja2==3.0.3
 MarkupSafe==2.0.1
-numpy==1.21.4
+numpy==1.22.0
 ordered-set==4.0.2
 packaging==21.3
 pandas==1.3.4
@@ -32,3 +32,4 @@ wget==3.2
 xlrd==1.2.0
 XlsxWriter==3.0.2
 zipp==3.6.0
+gunicorn==23.0.0

server/__init__.py

@@ -238,4 +238,4 @@ def index():
 if __name__ == "__main__":
     mp.set_start_method('spawn')
 
-    app.run(debug=True, port=int("3001"))
+    app.run(port=int("3001"))

server/wsgi.py

@@ -0,0 +1,4 @@
+from server import app
+
+if __name__ == "__main__":
+    app.run()