Install and use iRODS iCAT server 4.2.0 with docker containers

README.md

The lastet iCAT server on the latest ubuntu LTS, based on the latest Docker engine v1.13 using the latest V3 for YAML format with docker-compose.

Note: there should be an .env file on the root coupled with the docker-compose file which covers the declaration of all the ${VARIABLES} found in YAML format.

To make this work use:

docker-compose up

docker-compose.yml

version: '3'
services:

  # Postgres database server
  sql:
    image: postgres:9.6
    volumes:
      - sqldata:/var/lib/postgresql/data
      - ./pgs_init.sh:/docker-entrypoint-initdb.d/setup-my-schema.sh:ro
    environment:
      POSTGRES_USER: "${ALCHEMY_USER}"
      POSTGRES_PASSWORD: "${ALCHEMY_PASSWORD}"
      POSTGRES_DBS: ${ALCHEMY_DBS}
    networks:
      dbnet:
        aliases:
          - ${ALCHEMY_HOST}

  # iRODS iCAT server for EUDAT B2safe
  icat:
    # B2safe instance on irods
    build: ./icat
    image: myicat
    environment:
      POSTGRES_HOST: "${ALCHEMY_HOST}"
      POSTGRES_USER: "${ALCHEMY_USER}"
      POSTGRES_PASSWORD: "${ALCHEMY_PASSWORD}"
      IRODS_HOST: ${IRODS_HOST}
      IRODS_PORT: ${IRODS_PORT}
      IRODS_ZONE: ${IRODS_ZONE}
      IRODS_DB: "${IRODS_DB}"
      IRODS_USER: ${IRODS_USER}
      IRODS_PASSWORD: ${ALCHEMY_PASSWORD}
    # Open irods port to Outside world
    ports:
      - 1247:1247
    hostname: rodserver
    volumes:
      - etcconf:/etc
      - irodsvar:/var/lib/irods
    networks:
      dbnet
      
volumes:
  sqldata:
    driver: local
  # etc etc..

networks:
  dbnet:
  

docker-entrypoint.sh

#!/bin/bash

# Check postgres at startup
until PGPASSWORD=$POSTGRES_PASSWORD psql -h $POSTGRES_HOST -U $POSTGRES_USER $IRODS_DB -c "\d" 1> /dev/null 2> /dev/null;
do
  >&2 echo "Postgres is unavailable - sleeping"
  sleep 1
done

# Is it init time?
checkirods=$(ls /etc/irods/)
if [ "$checkirods" == "" ]; then

    #############################
    # Install irods&friends     #
    # install irods 4.2 + GSI
    # it automatically create the irods user
    # it automatically fixes permissions
    # it also checks if server is up at the end
    #############################

    MYDATA="/tmp/answers"
    sudo -E /prepare_answers $MYDATA
    # Launch the installation
    sudo python /var/lib/irods/scripts/setup_irods.py < $MYDATA
    # Verify how it went
    if [ "$?" == "0" ]; then
        echo ""
        echo "iRODS INSTALLED!"
    else
        echo "Failed to install irods..."
        exit 1
    fi

else
    # NO: launch irods
    echo "Already installed. Launching..."
    service irods start

fi
## END

echo "iRODS is ready"
sleep infinity
exit 0

Dockerfile

FROM ubuntu:16.04
# LTS
MAINTAINER "Paolo D'Onorio De Meo"

# Preparation
RUN apt-get update -qq && apt-get install -y \
        ## normal base
        wget git vim expect lsof sudo \
        ## fix adding irods to source list
        # lsb-release \
        ## fix the ssl error for apt-key
        gnupg-curl \
        ## fix "The method driver /usr/lib/apt/methods/https could not be found"
        apt-transport-https \
        ## fix the plugin error at irods installation time
        libxml2 \
    # clean
    && apt-get clean autoclean && apt-get autoremove -y && \
    rm -rf /var/lib/cache /var/lib/log /tmp/*

# Add repos, download and install
ENV URL https://packages.irods.org
RUN apt-key adv --fetch-keys $URL/irods-signing-key.asc \
    # && echo "deb $URL/apt/ $(lsb_release -sc) main" \
    && echo "deb $URL/apt/ trusty main" \
        > /etc/apt/sources.list.d/renci-irods.list

ENV IRODS_VERSION 4.2.0
RUN apt-get update && apt-get install -y \
        # iCAT
        irods-server=$IRODS_VERSION \
        # iRODS Plugins (also GSI)
        irods-database-plugin-postgres irods-auth-plugin-gsi \
    # clean
    && apt-get clean autoclean && apt-get autoremove -y && \
    rm -rf /var/lib/cache /var/lib/log /tmp/*

# Note: USER and GROUP are added automatically by irods install scripts

#######################################
## Closing operations

ENV TERM xterm-256color
# VOLUMES
VOLUME /etc
VOLUME /var/lib/irods

COPY ./expect_irods.sh /prepare_answers
COPY ./docker-entrypoint.sh /

EXPOSE 1247
# WORKDIR /tmp
ENTRYPOINT ["/docker-entrypoint.sh"]

expect_irods.sh

#!/bin/bash

# All responses for irods installation script

if [ -z "$1" ]; then
    echo "Usage $0 SCRIPT_NAME"
    exit 1
fi

# Clean
SCRIPT=$1
rm -rf $SCRIPT && touch $SCRIPT

##############################
# Unix account

# account
echo "$IRODS_USER" >> $SCRIPT
# group
echo "$IRODS_USER" >> $SCRIPT
# iRODS server's role
echo "1" >> $SCRIPT
# ODBC driver for postgres
echo "1" >> $SCRIPT

##############################
# DB account

## server host name
echo "$POSTGRES_HOST" >> $SCRIPT
## db port 5432
echo "5432" >> $SCRIPT
# database name
echo "$IRODS_DB" >> $SCRIPT
# database username
echo "$POSTGRES_USER" >> $SCRIPT
# confirmation
echo "yes" >> $SCRIPT
# irods password
echo "$POSTGRES_PASSWORD" >> $SCRIPT
# salt password
echo "$POSTGRES_PASSWORD" >> $SCRIPT

##############################
# IRODS setup

# irods zone
echo "$IRODS_ZONE" >> $SCRIPT
# irods port
echo "$IRODS_PORT" >> $SCRIPT
# range begin
echo "20000" >> $SCRIPT
# range end
echo "20199" >> $SCRIPT
# control plane port
echo "1248" >> $SCRIPT
# schema (default)
echo "" >> $SCRIPT
# irods administrator
echo "$IRODS_USER" >> $SCRIPT
# confirmation
echo "yes" >> $SCRIPT

# zone key
(openssl rand -base64 16 2>/dev/null | sed 's,/,S,g' | sed 's,+,_,g' \
    | cut -c 1-16  | tr -d '\n' ; echo "") >> $SCRIPT
# negotation key
openssl rand -base64 32 2> /dev/null | sed 's,/,S,g' | sed 's,+,_,g' | cut -c 1-32 \
    >> $SCRIPT
# control plane key
openssl rand -base64 32 2> /dev/null | sed 's,/,S,g' | sed 's,+,_,g' | cut -c 1-32 \
    >> $SCRIPT
# admin password
echo "$IRODS_PASSWORD" >> $SCRIPT
# vault
echo "" >> $SCRIPT

echo "created irods expectation"

pgs_init.sh

#!/bin/bash

conf='/var/lib/postgresql/data/pg_hba.conf'
## TO FIX: from an environment variable
net="172.1.0.0/16"
## http://www.postgresql.org/docs/9.1/static/auth-pg-hba-conf.html

echo "Changing access"
echo "" > $conf

# Enable to allow health checks
echo "local   $POSTGRES_USER  $POSTGRES_USER  trust" >> $conf

echo "hostnossl       postgres  $POSTGRES_USER  $net   password" >> $conf

###################
# DBs handling
for obj in $POSTGRES_DBS;
do
    db=$(echo $obj | tr -d "'")
    echo "Enabling DB $db"
# Create it
psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" << EOSQL
    CREATE DATABASE "$db";
EOSQL
    # GRANT ALL PRIVILEGES ON DATABASE "$db" TO $POSTGRES_USER;
# Add privileges
echo "hostnossl       $db  $POSTGRES_USER  $net   password" >> $conf
done

###################
echo "DONE"