Merge pull request #40 from bento-platform/image-perms

Image permissions

.github/workflows/build.yml

@@ -23,7 +23,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Run Bento build action
-        uses: bento-platform/bento_build_action@v0.10.1
+        uses: bento-platform/bento_build_action@v0.11.0
         with:
           registry: ghcr.io
           registry-username: ${{ github.actor }}

Dockerfile

@@ -1,22 +1,20 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.09
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.27
 
-# TODO: change USER
-USER root
+RUN apt-get update -y && \
+    apt-get install gcc libffi-dev -y && \
+    rm -rf /var/lib/apt/lists/*
 
-RUN apt install gcc libffi-dev -y
-
-RUN echo "Building DRS in Production Mode";
 WORKDIR /drs
-RUN mkdir /wes && \
-    mkdir -p /drs/data/obj && \
-    mkdir -p /drs/data/db
+RUN mkdir /wes
 
 # Install dependencies
-COPY requirements.txt requirements.txt
-RUN ["pip", "install", "-r", "requirements.txt"]
+COPY requirements.txt .
+RUN pip install --no-cache-dir gunicorn==20.1.0 -r requirements.txt
 
 # Copy only what's required for a production instance
 COPY chord_drs chord_drs
 COPY entrypoint.bash .
+COPY run.bash .
 
 ENTRYPOINT ["/bin/bash", "./entrypoint.bash"]
+CMD ["/bin/bash", "./run.bash"]

chord_drs/app.py

@@ -1,5 +1,4 @@
 import os
-import subprocess
 
 from bento_lib.responses import flask_errors
 from flask import Flask
@@ -46,9 +45,6 @@
     if not application.config["CHORD_URL"]:
         metrics.init_app(application)
 
-    if application.config["BENTO_DEBUG"]:
-        subprocess.run(["git", "config", "--global", "--add", "safe.directory", str(APP_DIR)])
-
 # # debugger section
 # Ensure 'debugpy' is installed (via requirements.txt or manually)
 DEBUG = os.environ.get("FLASK_DEBUG", "false").strip().lower() in ("true", "1")

chord_drs/package.cfg

@@ -1,5 +1,5 @@
 [package]
 name = chord_drs
-version = 0.9.0
+version = 0.9.1
 authors = Simon Chénard, David Lougheed
 author_emails = [email protected], [email protected]

dev.Dockerfile

@@ -1,20 +1,21 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.09
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.02.27
 
-# TODO: change USER
-USER root
+RUN apt-get update -y && \
+    apt-get install libffi-dev -y && \
+    rm -rf /var/lib/apt/lists/*
 
-RUN apt install libffi-dev -y
-
-RUN echo "Building DRS in Development Mode";
 WORKDIR /drs
-RUN mkdir /wes && \
-    mkdir -p /drs/data/obj && \
-    mkdir -p /drs/data/db;
+RUN mkdir /wes
 
-# Install requirements
+# Install dependencies
 COPY requirements.txt .
-RUN pip install debugpy -r requirements.txt
+RUN pip install --no-cache-dir debugpy -r requirements.txt
+
+# Copy in just the entrypoint + runner so we have somewhere to start
+COPY entrypoint.bash .
+COPY run.dev.bash .
 
-# Don't copy anything in - the dev compose file will mount the repo
+# Don't copy any code in - the dev compose file will mount the repo
 
-ENTRYPOINT ["/bin/bash", "./entrypoint.dev.bash"]
+ENTRYPOINT ["/bin/bash", "./entrypoint.bash"]
+CMD ["/bin/bash", "./run.dev.bash"]

entrypoint.bash

@@ -1,18 +1,17 @@
 #!/bin/bash
 
-# CWD: /drs
+cd /drs || exit
 
+# Create bento_user + home
+source /create_service_user.bash
+
+# Make data directories if needed
+# TODO: Don't hardcode these; this should be determined by an environment variable
 mkdir -p /drs/data/db
 mkdir -p /drs/data/obj
 
-export FLASK_APP="chord_drs.app:application"
-if [ -z "${INTERNAL_PORT}" ]; then
-  # Set default internal port to 5000
-  export INTERNAL_PORT=5000
-fi
-
-flask db upgrade
+# Fix permissions on /drs
+chown -R bento_user:bento_user /drs
 
-# using 1 worker, multiple threads
-# see https://stackoverflow.com/questions/38425620/gunicorn-workers-and-threads
-gunicorn "${FLASK_APP}" -w 1 --threads $(expr 2 \* $(nproc --all) + 1) -b "0.0.0.0:${INTERNAL_PORT}"
+# Drop into bento_user from root and execute the CMD specified for the image
+exec gosu bento_user "$@"

run.bash

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# CWD: /drs
+
+export FLASK_APP="chord_drs.app:application"
+if [[ -z "${INTERNAL_PORT}" ]]; then
+  # Set default internal port to 5000
+  export INTERNAL_PORT=5000
+fi
+
+flask db upgrade
+
+# using 1 worker, multiple threads
+# see https://stackoverflow.com/questions/38425620/gunicorn-workers-and-threads
+gunicorn "${FLASK_APP}" \
+  -w 1 \
+  --threads $(( 2 * $(nproc --all) + 1)) \
+  -b "0.0.0.0:${INTERNAL_PORT}"

entrypoint.dev.bash → run.dev.bash

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+# CWD: /drs
+
 # Set .gitconfig for development
 /set_gitconfig.bash
 
@@ -11,7 +13,7 @@ if [ -z "${INTERNAL_PORT}" ]; then
   export INTERNAL_PORT=5000
 fi
 
-python -m pip install -r requirements.txt
+python -m pip install --user -r requirements.txt
 
 flask db upgrade