Topic/multiple compose files

.gitignore

@@ -1,3 +1,4 @@
+.env
 sgn_local.conf
 repos
 sgn

Dockerfile

@@ -1,7 +1,5 @@
 FROM debian:stretch
 
-LABEL maintainer="lam87@cornell.edu"
-
 ENV CPANMIRROR=http://cpan.cpantesters.org
 # based on the vagrant provision.sh script by Nick Morales <nm529@cornell.edu>
 
@@ -39,9 +37,9 @@ RUN echo "deb http://apt.postgresql.org/pub/repos/apt/ stretch-pgdg main" | tee
 # install system dependencies
 #
 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
-RUN apt-get update -y --allow-unauthenticated 
+RUN apt-get update -y --allow-unauthenticated
 RUN apt-get upgrade -y
-RUN apt-get install build-essential pkg-config apt-utils gnupg2 curl wget -y 
+RUN apt-get install build-essential pkg-config apt-utils gnupg2 curl wget -y
 # key for cran-backports (not working though)
 #
 RUN bash -c "apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF' 1>/key.out   2> /key.err"
@@ -51,8 +49,8 @@ RUN wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc |  apt-
 #RUN apt-get update --fix-missing -y
 RUN apt-get update -y
 
-RUN apt-get install -y aptitude 
-RUN aptitude install -y libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-4.9.0-11-amd64 perl-doc ack-grep make xutils-dev nfs-common lynx xvfb ncbi-blast+ libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 blast2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron
+RUN apt-get install -y aptitude
+RUN aptitude install -y libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-4.9.0-14-amd64 perl-doc ack-grep make xutils-dev nfs-common lynx xvfb ncbi-blast+ libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 blast2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron
 
 # Set the locale correclty to UTF-8
 RUN locale-gen en_US.UTF-8
@@ -136,14 +134,30 @@ ENV R_LIBS_USER=/home/production/cxgn/R_libs
 
 #INSTALL OPENCV IMAGING LIBRARY
 RUN apt-get install -y python3-dev python-pip python3-pip python-numpy libgtk2.0-dev libgtk-3-0 libgtk-3-dev libavcodec-dev libavformat-dev libswscale-dev libhdf5-serial-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libxvidcore-dev libatlas-base-dev gfortran libgdal-dev exiftool libzbar-dev cmake
-
+RUN pip3 install --upgrade pip
 RUN pip3 install imutils numpy matplotlib pillow statistics PyExifTool pytz pysolar scikit-image packaging pyzbar pandas opencv-python \
     && pip3 install -U keras-tuner
 
 RUN bash /home/production/cxgn/sgn/js/install_node.sh
 
 COPY entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
 RUN ln -s /home/production/cxgn/starmachine/bin/starmachine_init.d /etc/init.d/sgn
 
+ARG CREATED
+ARG REVISION
+ARG BUILD_VERSION
+
+LABEL maintainer="lam87@cornell.edu"
+LABEL org.opencontainers.image.created=$CREATED
+LABEL org.opencontainers.image.url="https://breedbase.org/"
+LABEL org.opencontainers.image.source="https://github.com/solgenomics/breedbase_dockerfile"
+LABEL org.opencontainers.image.version=$BUILD_VERSION
+LABEL org.opencontainers.image.revision=$REVISION
+LABEL org.opencontainers.image.vendor="Boyce Thompson Institute"
+LABEL org.opencontainers.image.title="breedbase/breedbase"
+LABEL org.opencontainers.image.description="Breedbase web server"
+LABEL org.opencontainers.image.documentation="https://solgenomics.github.io/sgn/"
+
 # start services when running container...
 ENTRYPOINT /bin/bash /entrypoint.sh

docker-compose.override.yml

@@ -0,0 +1,10 @@
+version: "3.7"
+
+services:
+  breedbase:
+    volumes:
+      - type: bind
+        source: ./repos
+        target: /home/production/cxgn
+    environment:
+      MODE: 'DEVELOPMENT'

docker-compose.yml

@@ -2,50 +2,36 @@ version: "3.7"
 
 services:
   breedbase:
-    image: breedbase/breedbase:v0.17
-    depends_on:
-      - breedbase_db
-    container_name: breedbase_web
-    ports:
-      - 7080:8080
-      - 25:25
+    environment:
+      PGDATABASE: ${PGDATABASE:?}
+      PGHOST: ${PGHOST:?}
+      PGPASSWORD: ${PGPASSWORD:?}
+      PGUSER: ${PGUSER:?}
     volumes:
       - type: bind
-        source: ${HOME}/sgn_local.conf
+        source: ./sgn_local.conf
         target: /home/production/cxgn/sgn/sgn_local.conf
-    #  - type: bind
-    #    source: ${HOME}/empty_dump_20200313.sql
-    #    target: /home/production/empty_dump_20200313.sql
-    #   - type: bind
-    #     source: ${HOME}/archive
-    #     target: /home/production/archive
-    #   - type: bind
-    #     source: ${HOME}/tmp
-    #     target: /home/production/tmp
-    #   - type: bind
-    #     source: ${HOME}/cache
-    #     target: /home/production/cache
-    #   - type: bind
-    #     source: ${HOME}/cluster
-    #     target: /home/production/cluster
-    #   - type: bind
-    #     source: ${HOME}/blast
-    #     target: /home/production/blast
-    #   - type: bind
-    #     source: ${HOME}/images
-    #     target: /home/production/images
-      - breedbase_volume:/home/production/breedbase_volume
+      - webdata:/home/production/volume
+    ports:
+      - 7080:8080
+      - 25:25
+    image: breedbase/breedbase:v0.21
+    depends_on:
+      - breedbase_db
+    container_name: breedbase_web
+
   breedbase_db:
-    image: breedbase/breedbase_pg12.4:v0.5
-    container_name: breedbase_db
-#    ports:
-#      - 5431:5432
     volumes:
-      # - type: bind
-      #   source: /home/production/pgdata
-      #   target: /var/lib/postgresql/data
-      - db_volume:/home/production/breedbase_volume
+      - dbdata:/var/lib/postgresql/data
+    image: postgres:12.6
+    container_name: breedbase_db
+    environment:
+      POSTGRES_DB: ${PGDATABASE:?}
+      POSTGRES_PASSWORD: ${PGPASSWORD:?}
+    healthcheck:
+      test: "pg_isready -U postgres -d $${POSTGRES_DB} || exit 1"
+      interval: 10s
 
 volumes:
-  breedbase_volume:
-  db_volume:
+  webdata:
+  dbdata:

entrypoint.sh

@@ -7,11 +7,80 @@ sed -i s/localhost/$HOSTNAME/g /etc/slurm-llnl/slurm.conf
 /etc/init.d/slurmd start
 #/etc/init.d/postgres start
 
+# load empty fixture and run any missing patches
+
+if [ $(psql -Atc 'select count(distinct table_schema) from information_schema.tables;') -eq 2 ]; then
+    psql -c "CREATE USER web_usr PASSWORD 'postgres';"
+    psql -f t/data/fixture/empty_fixture.sql
+    ( cd db && ./run_all_patches.pl -u ${PGUSER} -p "${PGPASSWORD}" -h ${PGHOST} -d ${PGDATABASE} -e janedoe )
+fi
+
+# create necessary dirs/permissions if we have a docker volume dir
+# at /home/production/volume
+
+if [[ -e /home/production/volume ]]
+then
+    if [[ ! -e /home/production/volume/archive ]]
+    then
+        mkdir /home/production/volume/archive
+        chown www-data /home/production/volume/archive
+    fi
+
+    if [[ ! -e /home/production/volume/logs ]]
+    then
+        mkdir /home/production/volume/logs
+        chown www-data /home/production/volume/logs
+    fi
+
+    if [[ ! -e /home/production/volume/blast ]]
+    then
+        mkdir /home/production/volume/blast
+    fi
+
+    if [[ ! -e /home/production/volume/public ]]
+    then
+        mkdir /home/production/volume/public
+    fi
+
+    if [[ ! -e /home/production/volume/public/images ]]
+    then
+        mkdir /home/production/volume/public/images
+        chown www-data /home/production/volume/public/images
+    fi
+
+    if [[ ! -e /home/production/volume/tmp ]]
+    then
+        mkdir /home/production/volume/tmp
+        chown www-data /home/production/volume/tmp
+    fi
+
+    if [[ ! -e /home/production/volume/cache ]]
+    then
+        mkdir /home/production/volume/cache
+        chown www-data /home/production/volume/cache
+    fi
+
+    if [[ ! -e /home/production/volume/cluster ]]
+    then
+        mkdir /home/production/volume/cluster
+        chown www-data /home/production/volume/cluster
+    fi
+
+    if [[ ! -e /home/production/volume/pgdata ]]
+    then
+        mkdir /home/production/volume/pgdata
+        chown postgres /home/production/pgdata
+    fi
+else
+    echo "/home/production/volume does not exist... not creating dirs";
+fi
+
+
+
 if [ "$MODE" == "DEVELOPMENT" ]; then
-	/home/production/cxgn/sgn/bin/sgn_server.pl --fork -r -d -p 8080
+        /home/production/cxgn/sgn/bin/sgn_server.pl --fork -r -d -p 8080
 else
   /etc/init.d/sgn start
   chmod 777 /var/log/sgn/error.log
   tail -f /var/log/sgn/error.log
 fi
-

prepare.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+# create local conf file and dir for code repos
+cp sgn_local.conf.template  sgn_local.conf
 mkdir repos
 
 # main code

production.yml

@@ -0,0 +1,10 @@
+version: "3.7"
+
+services:
+  breedbase:
+    restart: always
+    environment:
+      MODE: 'PRODUCTION'
+
+  breedbase_db:
+    restart: always

sgn_local.conf.template

@@ -1,7 +1,7 @@
-dbhost <dbhost>
-dbname <dbname>
+dbhost breedbase_db
+dbname breedbase
 dbuser web_usr
-dbpass <password>
+dbpass postgres
 
 rootpath /home/production/cxgn
 basepath /home/production/cxgn/sgn