try using opensource dockerfiles

appserver/Dockerfile

@@ -1,44 +1,133 @@
-FROM fedora:33 as base
-LABEL app=kg-prototypes
+# ========================================
+# Base image
+# ========================================
+FROM python:3.10-slim as base
+
+ENV LANG C.UTF-8
+ENV LC_ALL C.UTF-8
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONFAULTHANDLER 1
 
-# Install dependencies
-RUN dnf install htop postgresql graphviz python-pip python3-devel vim net-tools which -y \
-    && dnf groupinstall 'Development Tools' -y \
-    && dnf clean packages
 RUN pip install pipenv
 
-ENV N4J_USER n4j
-ENV N4J_HOME /home/$N4J_USER
-ENV UID 1000
-ENV GID 1000
 
-# User and group creation
-RUN groupadd -g $GID $N4J_USER && \
-    useradd -u $UID -g $GID -G wheel --create-home --home-dir $N4J_HOME --shell /bin/bash $N4J_USER
+# ========================================
+# Build dependencies stage
+# ========================================
+FROM base as build-deps
+
+# Install build dependencies
+RUN apt-get update \
+    && apt-get install -y liblmdb-dev python3-dev libxml2-dev libxslt-dev build-essential \
+    && apt-get clean
+
+# Copy Pipfiles
+COPY Pipfile Pipfile.lock ./
+
+# Install Python dependencies
+ARG DEV
+RUN PIPENV_VENV_IN_PROJECT=1 pipenv install --deploy $(if [ "$DEV" ]; then echo --dev; fi)
+
+
+# ========================================
+# Runtime stage
+# ========================================
+FROM base
+LABEL org.opencontainers.image.source https://github.com/SBRG/lifelike
+
+# Install runtime system dependencies
+RUN apt-get update \
+    && apt-get install -y libmagic-dev graphviz libgraphviz-dev curl \
+    && apt-get clean
+
+# Copy Python virtual environment
+COPY --from=build-deps /.venv /.venv
+ENV PATH="/.venv/bin:$PATH"
+
+# Set user and workdir
+WORKDIR /app
+RUN useradd -m -d /app app
+USER app
+
+# Copy application code
+COPY --chown=app . .
+
+# Set to 1 to automatically apply any pending DB migrations at startup
+ENV MIGRATE_DB=
+
+# Create an initial admin user
+ENV INITIAL_ADMIN_EMAIL=
+
+# LMDB database volume
+ENV LMDB_DATA_DIR=/lmdb
+VOLUME /lmdb
+
+# LMDB download cloud storage
+# ENV AZURE_ACCOUNT_STORAGE_NAME=
+# ENV AZURE_ACCOUNT_STORAGE_KEY=
+
+# JWT Authendication
+ENV JWT_SECRET=secret
+
+# Base URL of this app, reachable by external services
+ENV APPSERVER_URL=http://localhost:5000
+
+# Base URL of the frontend app, for link generation
+ENV FRONTEND_URL=http://localhost:4242
+
+# PostgreSQL configuration
+ENV POSTGRES_HOST=postgres
+ENV POSTGRES_PORT=5432
+ENV POSTGRES_USER=postgres
+ENV POSTGRES_PASSWORD=postgres
+ENV POSTGRES_DB=postgres
+
+# Neo4j configuration
+ENV NEO4J_HOST=neo4j
+ENV NEO4J_PORT=7687
+ENV NEO4J_AUTH=neo4j/password
+ENV NEO4J_DATABASE=neo4j
+ENV NEO4J_SCHEME=bolt
+
+# Elasticsearch configuration
+ENV ELASTICSEARCH_URL=http://elasticsearch:9200
+ENV ELASTICSEARCH_FILE_INDEX=file
+
+# Statistical enrichment service
+ENV STATISTICAL_ENRICHMENT_URL=http://statistical-enrichment:5000
+
+# PDFParser service
+ENV PDFPARSER_URL=http://pdfparser:7600
 
-WORKDIR $N4J_HOME
+# NLP Processing service
+ENV NLP_URL=https://nlp-api.lifelike.bio/v1/predict
+ENV NLP_SECRET=secret
 
-# Copy Pipfiles and install dependencies FIRST to better apply Docker layer cache
-COPY --chown=1000:1000 Pipfile .
-COPY --chown=1000:1000 Pipfile.lock .
-RUN pipenv install --dev --deploy --system
+# Mailserver configuration
+ENV [email protected]
 
-# ...then copy everything else
-COPY --chown=1000:1000 . .
+# Sendgrid integration
+ENV SENDGRID_API_KEY=
 
-# TODO: We should consider breaking this apart into dev and prod
-# builds, so we don't build unnecessary packages
+# Optional Sentry logging configuration
+ENV SENTRY_DSN=
 
-# Don't lose stdin, stdout and stderr output due to buffering
-ENV PYTHONUNBUFFERED 1
-ENV PYTHONPATH $N4J_HOME
+# Optional Elastic APM configuration.
+# To enable, at least ELASTIC_APM_SERVER_URL must be set
+# Other available variables: https://www.elastic.co/guide/en/apm/agent/python/master/configuration.html
+ENV ELASTIC_APM_SERVER_URL=
+ENV ELASTIC_APM_SERVICE_NAME=appserver
 
-# Set Python3 as the default when running "python"
-RUN echo 'alias python=python3' >> ~/.bashrc && source ~/.bashrc
+# Flask env (development, testing, production)
+ENV FLASK_ENV=production
 
-USER $N4J_USER
+# Listen port
+ENV PORT=5000
+EXPOSE $PORT
 
-# Setup flask application environment vars
-ENV MAX_ALLOWED_LOGIN_FAILURES 6
+# Health check by requesting system info to /meta endpoint
+HEALTHCHECK --start-period=30s \
+    CMD curl -f localhost:$PORT/meta || exit 1
 
-CMD [ "bin/startup.sh" ]
+RUN chmod +x bin/docker-entrypoint.sh
+ENTRYPOINT ["bin/docker-entrypoint.sh"]

cache-invalidator/Dockerfile

@@ -1,33 +1,64 @@
+# ========================================
+# Base image
+# ========================================
 FROM python:3.10-slim as base
-LABEL app=kg-prototypes
 
-# Install dependencies
-RUN apt-get update && apt-get install -y curl && apt-get clean
+ENV LANG C.UTF-8
+ENV LC_ALL C.UTF-8
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONFAULTHANDLER 1
+
 RUN pip install pipenv
 
-ENV APP_USER lifelike
-ENV APP_HOME /home/$APP_USER
-ENV UID 1000
-ENV GID 1000
 
-# User and group creation
-RUN groupadd -g $GID $APP_USER && \
-    useradd -u $UID -g $GID -G sudo --create-home --home-dir $APP_HOME --shell /bin/bash $APP_USER
+# ========================================
+# Build dependencies stage
+# ========================================
+FROM base as build-deps
+
+# Copy Pipfiles
+COPY Pipfile Pipfile.lock ./
+
+# Install Python dependencies
+ARG DEV
+RUN PIPENV_VENV_IN_PROJECT=1 pipenv install --deploy $(if [ "$DEV" ]; then echo --dev; fi)
+
+
+# ========================================
+# Runtime stage
+# ========================================
+FROM base
+LABEL org.opencontainers.image.source https://github.com/SBRG/lifelike
+
+# Copy Python virtual environment
+COPY --from=build-deps /.venv /.venv
+ENV PATH="/.venv/bin:$PATH"
+
+# Set user and working directory
+WORKDIR /app
+RUN useradd -m -d /app app
+USER app
 
-WORKDIR $APP_HOME
+# Copy application code
+COPY --chown=app main.py ./
 
-# Copy Pipfiles and install dependencies FIRST to better apply Docker layer cache
-COPY --chown=1000:1000 Pipfile .
-COPY --chown=1000:1000 Pipfile.lock .
-RUN pipenv install --deploy --dev --system
+# Neo4j configuration
+ENV NEO4J_HOST=neo4j
+ENV NEO4J_PORT=7687
+ENV NEO4J_AUTH=neo4j/password
+ENV NEO4J_SCHEME=bolt
+ENV NEO4J_DATABASE=neo4j
 
-# ...then copy everything else
-COPY --chown=1000:1000 . .
+# Redis cache configuration
+ENV REDIS_HOST=redis
+ENV REDIS_PORT=6379
+ENV REDIS_PASSWORD=password
+ENV REDIS_DB=0
 
-# Don't lose stdin, stdout and stderr output due to buffering
-ENV PYTHONUNBUFFERED 1
-ENV PYTHONPATH $APP_HOME
+# Default TTL for cache
+ENV CACHE_TTL=86400
 
-USER $APP_USER
+# Logging level
+ENV LOG_LEVEL=INFO
 
-CMD [ "bin/startup.sh" ]
+CMD ["python", "main.py"]

client/Dockerfile

@@ -1,20 +1,5 @@
 ARG NODE_IMAGE_TAG=node:14
 
-# ========================================
-# Landing page
-# ========================================
-FROM $NODE_IMAGE_TAG as landing-build
-WORKDIR /app
-
-# Install dependencies
-COPY landing/package.json landing/yarn.lock ./
-RUN yarn install
-
-# Build landing page
-COPY landing ./
-RUN yarn build
-
-
 # ==================================================================
 # Angular app dependencies by default used for local development
 # ==================================================================
@@ -23,71 +8,58 @@ WORKDIR /app
 
 # Install dependencies
 COPY package.json yarn.lock ./
-RUN yarn install
+ARG YARN_INSTALL_OPTS
+RUN yarn install ${YARN_INSTALL_OPTS}
+
+ENV ENVIRONMENT_CONFIG development
 
-# build time arguments for Angular environment
-ARG ANGULAR_CONFIG=development
-ARG CLIENT_VERSION=undefined
-# default enviroment presets
-ENV ENVIRONMENT_CONFIG $ANGULAR_CONFIG
 
 # ========================================
 # Angular app bundle build
 # ========================================
 FROM angular-deps as angular-build
 
-# build time arguments for Angular environment
-ARG ANGULAR_CONFIG=production
-ARG CLIENT_VERSION=undefined
-
 # Copy the code and build the app bundle
 COPY src ./src
 COPY tslint ./tslint
 COPY e2e ./e2e
 COPY *.json browserslist ./
-RUN sed -i "s/__VERSION__/${CLIENT_VERSION}/" src/environments/environment.ts
-RUN yarn build --configuration=$ANGULAR_CONFIG --aot --output-path=dist
+
+ARG ANGULAR_CONFIG=production
+ENV NODE_OPTIONS=--max-old-space-size=4096
+RUN yarn build --configuration=$ANGULAR_CONFIG --output-path=dist
+
+# When targeting this image stage, run angulat dev server
+EXPOSE 4200
+HEALTHCHECK --interval=5m --timeout=10s \
+  CMD curl -f localhost:4200 || exit 1
+CMD yarn dev-start
+
 
 # ========================================
 # Runtime stage - NGINX
 # ========================================
-FROM nginx:1.25.1
-LABEL app=kg-prototypes
-WORKDIR /usr/share/nginx/html
+FROM nginx:1.21
+LABEL org.opencontainers.image.source https://github.com/SBRG/lifelike
 
-# URL to proxy requests to /api
-ENV APPSERVER_UPSTREAM http://appserver:5000
-
-# Whether to run the app in prod mode
-ENV PRODUCTION_MODE true
-
-# Whether we are running with valid KEGG license
-ENV KEGG_ENABLED false
+WORKDIR /usr/share/nginx/html
 
-# Whether to run the app with oauth login
-ENV OAUTH_ENABLED false
+# Copy built assets
+COPY --from=angular-build /app/dist ./
 
-# OAuth issuer discovert URL
-ENV OAUTH_ISSUER ""
+# Copy nginx configuraiton template
+COPY nginx.conf /etc/nginx/templates/default.conf.template
 
-# Client ID of the OAuth application
-ENV OAUTH_CLIENT_ID ""
+# appserver URL to proxy /api requests
+ENV APPSERVER_URL http://appserver:5000
 
 # List of space delimited list of non-stantdard MIME types
 # which are known to benefit from gzip compression (text based content)
 ENV GZIP_EXTRA_TYPES text/tsv vnd.lifelike.document/bioc vnd.lifelike.document/enrichment-table vnd.lifelike.document/graph vnd.lifelike.document/map
 
-# build time argument for Angular environment
-ARG ANGULAR_CONFIG=production
-
-# default enviroment presets
-ENV ENVIRONMENT_CONFIG $ANGULAR_CONFIG
-
-# Copy nginx configuraiton template
-COPY nginx.conf /etc/nginx/templates/default.conf.template
-
-# Copy built assets
-COPY --from=landing-build /app/dist ./
-COPY --from=angular-build /app/dist ./
+# Runtime environment configuration preset
+ENV ENVIRONMENT_CONFIG production
 
-EXPOSE 80
+# Listen port
+ENV PORT 80
+EXPOSE $PORT