Merge pull request #34 from bento-platform/features/dockerize

v0.7.0 rc-1

.github/workflows/build.yml

@@ -0,0 +1,33 @@
+name: Build and push bento_drs
+
+on:
+  release:
+    types: [ published ]
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+
+jobs:
+  build-push:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Run Bento build action
+        uses: bento-platform/bento_build_action@v0.6
+        with:
+          registry: ghcr.io
+          registry-username: ${{ github.actor }}
+          registry-password: ${{ secrets.GITHUB_TOKEN }}
+          image-name: ghcr.io/bento-platform/bento_drs
+          development-dockerfile: dev.Dockerfile
+          dockerfile: Dockerfile

Dockerfile

@@ -0,0 +1,20 @@
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2022.10.11
+
+# TODO: change USER
+USER root
+
+RUN apt install gcc libffi-dev -y
+
+RUN echo "Building DRS in Production Mode";
+WORKDIR /drs/bento_drs
+RUN mkdir /wes && \
+    mkdir -p /drs/bento_drs/data/obj && \
+    mkdir -p /drs/bento_drs/data/db;
+COPY requirements.txt requirements.txt
+RUN ["pip", "install", "-r", "requirements.txt"]
+COPY . .
+
+# Run
+WORKDIR /drs/bento_drs/chord_drs
+COPY startup.sh ./startup.sh
+CMD ["sh", "startup.sh"]

chord_drs/package.cfg

@@ -1,5 +1,5 @@
 [package]
 name = chord_drs
-version = 0.6.0
+version = 0.7.0
 authors = Simon Chénard, David Lougheed
 author_emails = simon.chenard2@mcgill.ca, david.lougheed@mail.mcgill.ca

dev.Dockerfile

@@ -0,0 +1,18 @@
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2022.10.11
+
+# TODO: change USER
+USER root
+
+RUN apt install libffi-dev -y
+
+RUN echo "Building DRS in Development Mode";
+WORKDIR /drs/bento_drs
+RUN mkdir /wes && \
+    mkdir -p /drs/bento_drs/data/obj && \
+    mkdir -p /drs/bento_drs/data/db;
+COPY ./requirements.txt .
+RUN ["pip", "install", "debugpy", "-r", "requirements.txt"]
+
+# Run
+WORKDIR /drs/bento_drs/chord_drs
+COPY startup.sh ./startup.sh

requirements.txt

@@ -20,7 +20,7 @@ flake8-polyfill==1.0.2
 Flask==2.0.1
 Flask-Migrate==3.1.0
 Flask-SQLAlchemy==2.5.1
-greenlet==1.0.0
+greenlet==2.0.1
 idna==2.10
 iniconfig==1.1.1
 itsdangerous==2.0.1

startup.sh

@@ -0,0 +1,13 @@
+cd ../data;
+mkdir -p db;
+mkdir -p obj;
+
+cd ../chord_drs;
+flask db upgrade;
+
+# call variant endpoint to trigger init
+cd ..;
+
+# using 1 worker, multiple threads
+# see https://stackoverflow.com/questions/38425620/gunicorn-workers-and-threads
+gunicorn chord_drs.app:application -w 1 --threads $(expr 2 \* $(nproc --all) + 1) -b 0.0.0.0:5000