Merge pull request #3354 from PecanProject/docker-gha

start new docker build

CHANGELOG.md

@@ -10,6 +10,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 ### Added
 
 ### Fixed
+- updated github action to build docker images
 
 ### Changed
 

apps/api/Dockerfile

@@ -6,7 +6,6 @@ ARG IMAGE_VERSION="latest"
 # PECAN FOR MODEL BASE IMAGE
 # --------------------------------------------------------------------------
 FROM pecan/base:${IMAGE_VERSION} 
-LABEL maintainer="Tezan Sahu <[email protected]>"
 
 EXPOSE 8000
 
@@ -15,9 +14,7 @@ EXPOSE 8000
 # --------------------------------------------------------------------------
 
 # COMMAND TO RUN
-RUN  --mount=type=secret,id=github_token \
-  export GITHUB_PAT=`cat /run/secrets/github_token` \
-  &&  apt-get update \
+RUN apt-get update \
   &&  apt-get install libsodium-dev -y \
   &&  rm -rf /var/lib/apt/lists/* \
   &&  Rscript -e "devtools::install_version('promises', '1.1.0')" \
@@ -35,7 +32,6 @@ ENV AUTH_REQ="TRUE" \
     SECRET_KEY_BASE="thisisnotasecret"
 
 WORKDIR /api/R
-
-CMD Rscript entrypoint.R
-
 COPY ./ /api
+
+CMD ["Rscript", "entrypoint.R"]

docker-compose.yml

@@ -52,6 +52,11 @@ services:
       - "traefik.http.routers.rabbitmq.rule=Host(`rabbitmq.pecan.localhost`)"
     volumes:
       - rabbitmq:/var/lib/rabbitmq
+    healthcheck:
+      test: rabbitmqctl ping
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
   # ----------------------------------------------------------------------
   # Database to hold the data from PEcAn and BETY.
@@ -65,6 +70,11 @@ services:
       - pecan
     volumes:
       - postgres:/var/lib/postgresql/data
+    healthcheck:
+      test: pg_isready -U postgres
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
   # ----------------------------------------------------------------------
   # BETY rails frontend to the database
@@ -82,11 +92,17 @@ services:
     volumes:
       - bety:/home/bety/log
     depends_on:
-      - postgres
+      postgres:
+        condition: service_healthy
     labels:
       - "traefik.enable=true"
       - "traefik.http.services.bety.loadbalancer.server.port=8000"
       - "traefik.http.routers.bety.rule=Host(`${TRAEFIK_HOST:-pecan.localhost}`) && PathPrefix(`/bety/`)"
+    healthcheck:
+      test: "curl --silent --fail http://localhost:8000/${RAILS_RELATIVE_URL_ROOT} > /dev/null || exit 1"
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
   # ----------------------------------------------------------------------
   # RStudio
@@ -98,8 +114,10 @@ services:
     networks:
       - pecan
     depends_on:
-      - rabbitmq
-      - postgres
+      postgres:
+        condition: service_healthy
+      rabbitmq:
+        condition: service_healthy
     environment:
       - KEEP_ENV=RABBITMQ_URI RABBITMQ_PREFIX RABBITMQ_PORT FQDN NAME
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
@@ -141,6 +159,11 @@ services:
       - "traefik.enable=true"
       - "traefik.http.services.docs.loadbalancer.server.port=80"
       - "traefik.http.routers.docs.rule=Host(`${TRAEFIK_HOST:-pecan.localhost}`) && PathPrefix(`/`)"
+    healthcheck:
+      test: "curl --silent --fail http://localhost/ > /dev/null || exit 1"
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
   # PEcAn web front end, this is just the PHP code
   pecan:
@@ -155,15 +178,22 @@ services:
       - NAME=${PECAN_NAME:-docker}
       - SECRET_KEY_BASE=${BETY_SECRET_KEY:-thisisnotasecret}
     depends_on:
-       - postgres
-       - rabbitmq
+      postgres:
+        condition: service_healthy
+      rabbitmq:
+        condition: service_healthy
     labels:
       - "traefik.enable=true"
       - "traefik.http.services.pecan.loadbalancer.server.port=8080"
       - "traefik.http.routers.pecan.rule=Host(`${TRAEFIK_HOST:-pecan.localhost}`) && PathPrefix(`/pecan/`)"
     volumes:
       - pecan:/data
       - pecan:/var/www/html/pecan/data
+    healthcheck:
+      test: "curl --silent --fail http://localhost/pecan/ > /dev/null || exit 1"
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
   # PEcAn model monitor
   monitor:
@@ -176,14 +206,22 @@ services:
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
       - FQDN=${PECAN_FQDN:-docker}
     depends_on:
-       - rabbitmq
+      postgres:
+        condition: service_healthy
+      rabbitmq:
+        condition: service_healthy
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.monitor.rule=Host(`${TRAEFIK_HOST:-pecan.localhost}`) && PathPrefix(`/monitor/`)"
       - "traefik.http.routers.monitor.middlewares=monitor-stripprefix"
       - "traefik.http.middlewares.monitor-stripprefix.stripprefix.prefixes=/monitor"
     volumes:
       - pecan:/data
+    healthcheck:
+      test: "curl --silent --fail http://localhost:9999/monitor/ > /dev/null || exit 1"
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
   # PEcAn executor, executes jobs. Does not the actual models
   executor:
@@ -198,8 +236,10 @@ services:
       - RABBITMQ_PORT=15672
       - FQDN=${PECAN_FQDN:-docker}
     depends_on:
-       - postgres
-       - rabbitmq
+      postgres:
+        condition: service_healthy
+      rabbitmq:
+        condition: service_healthy
     volumes:
       - pecan:/data
 
@@ -216,7 +256,8 @@ services:
     environment:
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
     depends_on:
-       - rabbitmq
+      rabbitmq:
+        condition: service_healthy
     volumes:
       - pecan:/data
 
@@ -230,7 +271,8 @@ services:
     environment:
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
     depends_on:
-       - rabbitmq
+      rabbitmq:
+        condition: service_healthy
     volumes:
       - pecan:/data
 
@@ -244,7 +286,8 @@ services:
     environment:
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
     depends_on:
-       - rabbitmq
+      rabbitmq:
+        condition: service_healthy
     volumes:
       - pecan:/data
 
@@ -258,7 +301,8 @@ services:
     environment:
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
     depends_on:
-       - rabbitmq
+      rabbitmq:
+        condition: service_healthy
     volumes:
       - pecan:/data
 
@@ -272,7 +316,8 @@ services:
     environment:
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
     depends_on:
-       - rabbitmq
+      rabbitmq:
+        condition: service_healthy
     volumes:
       - pecan:/data
 
@@ -286,7 +331,8 @@ services:
     environment:
       - RABBITMQ_URI=${RABBITMQ_URI:-amqp://guest:guest@rabbitmq/%2F}
     depends_on:
-       - rabbitmq
+      rabbitmq:
+        condition: service_healthy
     volumes:
       - pecan:/data
 
@@ -300,12 +346,18 @@ services:
     networks:
       - pecan
     depends_on:
-       - postgres
+      postgres:
+        condition: service_healthy
     labels:
       - "traefik.enable=true"
       - "traefik.http.routers.dbsync.rule=Host(`${TRAEFIK_HOST:-pecan.localhost}`) && PathPrefix(`/dbsync/`)"
       - "traefik.http.routers.dbsync.middlewares=dbsync-stripprefix"
       - "traefik.http.middlewares.dbsync-stripprefix.stripprefix.prefixes=/monitor"
+    healthcheck:
+      test: "curl --silent --fail http://localhost/dbsync/ > /dev/null || exit 1"
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
   # ----------------------------------------------------------------------
   # PEcAn API
@@ -329,9 +381,15 @@ services:
       - "traefik.http.routers.api.rule=Host(`${TRAEFIK_HOST:-pecan.localhost}`) && PathPrefix(`/api/`)"
       - "traefik.http.services.api.loadbalancer.server.port=8000"
     depends_on:
-      - postgres
+      postgres:
+        condition: service_healthy
     volumes:
       - pecan:/data/
+    healthcheck:
+      test: "curl --silent --fail http://localhost/api/ping > /dev/null || exit 1"
+      interval: 10s
+      timeout: 5s
+      retries: 5
 
 # ----------------------------------------------------------------------
 # Name of network to be used by all containers

docker/base/Dockerfile

@@ -2,7 +2,6 @@
 ARG IMAGE_VERSION="latest"
 ARG FROM_IMAGE="depends"
 FROM pecan/${FROM_IMAGE}:${IMAGE_VERSION}
-MAINTAINER Rob Kooper <[email protected]>
 
 # ----------------------------------------------------------------------
 # PEcAn version information
@@ -26,9 +25,7 @@ COPY models   /pecan/models/
 # install all PEcAn packages
 # `make clean` is to remove artifacts copied in from host system
 #   (e.g. basgra.so)
-RUN --mount=type=secret,id=github_token \
-    export GITHUB_PAT=`cat /run/secrets/github_token` \
-    && cd /pecan \
+RUN cd /pecan \
     && make clean \
     && make \
     && rm -rf /tmp/downloaded_packages
@@ -38,7 +35,7 @@ WORKDIR /work
 COPY web/workflow.R docker/base/rstudio.sh /work/
 
 # COMMAND TO RUN
-CMD Rscript --vanilla workflow.R | tee workflow.Rout
+CMD ["bash", "-c", "Rscript --vanilla workflow.R | tee workflow.Rout"]
 
 # variables to store in docker image
 ENV PECAN_VERSION=${PECAN_VERSION} \

docker/data/Dockerfile

@@ -1,5 +1,4 @@
 FROM alpine
-MAINTAINER Rob Kooper <[email protected]>
 
 # name to use in the machines table FQDN when registering the data files
 ENV FQDN="" \
@@ -19,4 +18,4 @@ RUN apk --no-cache add bash curl rsync postgresql-client unzip \
     && curl -s -o create_met_driver.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/create_met_driver.tar.gz
 
 COPY add-data.sh add.util.sh /work/
-CMD bash /work/add-data.sh
+CMD ["bash", "-c", "/work/add-data.sh"]

docker/depends/Dockerfile

@@ -5,8 +5,6 @@ ARG FROM_IMAGE="rocker/tidyverse"
 # PECAN FOR MODEL BASE IMAGE
 # ----------------------------------------------------------------------
 FROM ${FROM_IMAGE}:${R_VERSION}
-MAINTAINER Rob Kooper <[email protected]>
-
 
 # ----------------------------------------------------------------------
 # INSTALL BINARY/LIBRARY DEPENDENCIES
@@ -33,9 +31,7 @@ RUN apt-get update \
 # INSTALL DEPENDENCIES
 # ----------------------------------------------------------------------
 COPY pecan.depends.R pecan_package_dependencies.csv pecan_deps_from_github.txt /
-RUN  --mount=type=secret,id=github_token \
-  export GITHUB_PAT=`cat /run/secrets/github_token` \
-  && Rscript -e "install.packages(c('desc', 'remotes'))" \
+RUN Rscript -e "install.packages(c('desc', 'remotes'))" \
   && R_LIBS_USER='/usr/local/lib/R/site-library' Rscript /pecan.depends.R \
   && rm -rf /tmp/*
 

docker/docs/Dockerfile

@@ -5,7 +5,6 @@ ARG IMAGE_VERSION="latest"
 # compile bookdown to html
 # ----------------------------------------------------------------------
 FROM pecan/base:${IMAGE_VERSION} AS pecandocs
-MAINTAINER Rob Kooper <[email protected]>
 
 RUN apt-get update \
     && apt-get install -y --no-install-recommends pandoc \
@@ -28,7 +27,6 @@ RUN make build
 # copy html pages to container
 # ----------------------------------------------------------------------
 FROM httpd
-MAINTAINER Rob Kooper <[email protected]>
 
 COPY docker/docs/index.html /usr/local/apache2/htdocs/
 COPY --from=pecandocs /src/book_source/_book/ /usr/local/apache2/htdocs/docs/pecan/

docker/executor/Dockerfile

@@ -5,7 +5,6 @@ ARG IMAGE_VERSION="latest"
 # PECAN FOR MODEL BASE IMAGE
 # ----------------------------------------------------------------------
 FROM pecan/base:${IMAGE_VERSION}
-MAINTAINER Rob Kooper <[email protected]>
 
 # ----------------------------------------------------------------------
 # SETUP FOR PYTHON CODE
@@ -24,4 +23,4 @@ ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq/%2F" \
 
 # actual application that will be executed
 COPY executor.py /work/
-CMD python3 /work/executor.py
+CMD ["python3", "/work/executor.py"]

docker/models/Dockerfile

@@ -5,7 +5,6 @@ ARG IMAGE_VERSION="latest"
 # PECAN FOR MODEL BASE IMAGE
 # ----------------------------------------------------------------------
 FROM pecan/base:${IMAGE_VERSION}
-MAINTAINER Rob Kooper <[email protected]>
 
 # ----------------------------------------------------------------------
 # SETUP FOR PYTHON CODE
@@ -23,4 +22,4 @@ ENV RABBITMQ_URI="amqp://guest:guest@rabbitmq/%2F" \
 
 # actual application that will be executed
 COPY model.py /work/
-CMD python3 /work/model.py
+CMD ["python3", "/work/model.py"]

docker/monitor/Dockerfile

@@ -17,4 +17,4 @@ COPY requirements.txt /src/
 RUN pip3 install -r /src/requirements.txt
 
 COPY . /src/
-CMD python3 monitor.py
+CMD ["python3", "./monitor.py"]

docker/rstudio-nginx/Dockerfile

@@ -1,4 +1,3 @@
 FROM nginx:alpine
-MAINTAINER Rob Kooper <[email protected]>
 
 COPY nginx.conf /etc/nginx/conf.d/default.conf

docker/web/Dockerfile

@@ -1,5 +1,4 @@
 FROM php:8-apache
-MAINTAINER Rob Kooper <[email protected]>
 
 # ----------------------------------------------------------------------
 # install rabbitmq and postgresql extentions