Initial commit

.gitignore

@@ -0,0 +1,10 @@
+.*
+!.gitignore
+settings.local.*
+data
+portainer
+postgres
+mesos-master
+mesos-slave
+woken/application.conf
+woken/validation.conf

docker-compose.yml

@@ -0,0 +1,260 @@
+#                    Copyright (c) 2018-2018
+#   Data Intensive Applications and Systems Labaratory (DIAS)
+#            Ecole Polytechnique Federale de Lausanne
+#
+#                      All Rights Reserved.
+#
+# Permission to use, copy, modify and distribute this software and its
+# documentation is hereby granted, provided that both the copyright notice
+# and this permission notice appear in all copies of the software, derivative
+# works or modified versions, and any portions thereof, and that both notices
+# appear in supporting documentation.
+#
+# This code is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. THE AUTHORS AND ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
+# DISCLAIM ANY LIABILITY OF ANY KIND FOR ANY DAMAGES WHATSOEVER RESULTING FROM THE
+# USE OF THIS SOFTWARE.
+
+version: '3'
+
+networks:
+  local:
+
+services:
+  zookeeper:
+    image: ${ZOOKEEPER_IMAGE}${ZOOKEEPER_VERSION}
+    environment:
+      ZOO_MY_ID: 1
+      ZOO_SERVERS: server.1=zookeeper:2888:3888
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    networks:
+      - local
+#    ports:
+#      - "${ZOOKEEPER_PORT1}:2181"
+#      - "${ZOOKEEPER_PORT2}:2888"
+#      - "${ZOOKEEPER_PORT3}:3888"
+
+  mesos-master:
+    image: ${MESOS_MASTER_IMAGE}${MESOS_MASTER_VERSION}
+    environment:
+      MESOS_PORT: 5050
+      MESOS_ZK: zk://zookeeper:${ZOOKEEPER_PORT1}/mesos
+      MESOS_QUORUM: 1
+      MESOS_REGISTRY: in_memory
+      MESOS_CLUSTER: local
+      MESOS_HOSTNAME: mesos-master
+      MESOS_LOG_DIR: /var/log/mesos
+      MESOS_WORK_DIR: /tmp/mesos
+    volumes:
+      - ${MESOS_MASTER_LOGS}:/var/log/mesos:rw
+      - ${MESOS_MASTER_TMP}:/tmp/mesos:rw
+    depends_on:
+      - zookeeper
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    networks:
+      - local
+#    ports:
+#      - "${MESOS_MASTER_PORT}:5050"
+
+  mesos-slave:
+    image: ${MESOS_SLAVE_IMAGE}${MESOS_SLAVE_VERSION}
+    environment:
+      MESOS_MASTER: zk://zookeeper:${ZOOKEEPER_PORT1}/mesos
+      MESOS_PORT: 5051
+      MESOS_LOG_DIR: /var/log/mesos
+      MESOS_WORK_DIR: /tmp/mesos
+      MESOS_CONTAINERIZERS: docker,mesos
+      MESOS_EXECUTOR_REGISTRATION_TIMEOUT: 5mins
+      MESOS_EXECUTOR_SHUTDOWN_GRACE_PERIOD: 90secs
+      MESOS_DOCKER_STOP_TIMEOUT: 60secs
+      MESOS_HOSTNAME: mesos-slave
+      MESOS_SWITCH_USER: 0
+      # see bug resolution for "Failed to determine the hierarchy where the subsystem freezer is attached" at https://github.com/eBayClassifiedsGroup/PanteraS/issues/142
+      MESOS_LAUNCHER: "posix"
+#    privileged: true
+    depends_on:
+      - zookeeper
+      - mesos-master
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    volumes:
+      - /sys:/sys:ro
+      - /var/run/docker.sock:/var/run/docker.sock:rw
+      - ${MESOS_SLAVE_LOGS}:/var/log/mesos:rw
+      - ${MESOS_SLAVE_TMP}:/tmp/mesos:rw
+    networks:
+      - local
+#    ports:
+#      - "${MESOS_SLAVE_PORT}:5051"
+
+  chronos:
+    image: ${CHRONOS_IMAGE}${CHRONOS_VERSION}
+    command: "--zk_hosts zookeeper:${ZOOKEEPER_PORT1} --master zk://zookeeper:${ZOOKEEPER_PORT1}/mesos --zk_timeout 30000"
+    environment:
+      PORT0: 4400
+      PORT1: 4401
+    depends_on:
+      - zookeeper
+      - mesos-slave
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    networks:
+      - local
+#    ports:
+#      - "${CHRONOS_PORT1}:4400"
+#      - "${CHRONOS_PORT2}:4401"
+
+  db:
+    image: ${DB_IMAGE}${DB_VERSION}
+    environment:
+      POSTGRES_USER: ${DB_USER_ADMIN}
+      POSTGRES_PASSWORD: ${DB_PASSWORD_ADMIN}
+      PGDATA: "/data/pgdata"
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    volumes:
+      - ${DB_DATA}:/data:rw
+      - ${DB_DATASETS}:/datasets:ro
+    networks:
+      - local
+#    ports:
+#      - "${DB_PORT}:5432"
+
+  woken:
+    image: ${WOKEN_IMAGE}${WOKEN_VERSION}
+    depends_on:
+      - chronos
+#      - db
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    volumes:
+      - ${WOKEN_CONF}:/opt/woken/config/application.conf:ro
+    networks:
+      - local
+#    ports:
+#      - "${WOKEN_PORT2}:${WOKEN_PORT2}"
+#      - "${WOKEN_PORT1}:${WOKEN_PORT1}"
+
+  woken-validation:
+    image: ${WOKEN_VALIDATION_IMAGE}${WOKEN_VALIDATION_VERSION}
+    depends_on:
+      - woken
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    volumes:
+      - ${WOKEN_VALIDATION_CONF}:/opt/woken-validation/config/application.conf:ro
+    networks:
+      - local
+#    ports:
+#      - "${WOKEN_VALIDATION_PORT}:${WOKEN_VALIDATION_PORT}"
+
+  backend:
+    image: ${PORTAL_BACKEND_IMAGE}${PORTAL_BACKEND_VERSION}
+    environment:
+      PORTAL_DB_URL: jdbc:postgresql://${DB_HOST}:${DB_PORT}/${DB_NAME4}
+      PORTAL_DB_SERVER: ${DB_HOST}:${DB_PORT}
+      PORTAL_DB_USER: ${DB_USER4}
+      PORTAL_DB_PASSWORD: ${DB_PASSWORD4}
+      META_DB_URL: jdbc:postgresql://${DB_HOST}:${DB_PORT}/${DB_NAME1}
+      META_DB_SERVER: ${DB_HOST}:${DB_PORT}
+      META_DB_USER: ${DB_USER1}
+      META_DB_PASSWORD: ${DB_PASSWORD1}
+      FEATURES_DB_URL: jdbc:postgresql://${DB_HOST}:${DB_PORT}/${DB_NAME2}
+      FEATURES_DB_SERVER: ${DB_HOST}:${DB_PORT}
+      FEATURES_DB_USER: ${DB_USER2}
+      FEATURES_DB_PASSWORD: ${DB_PASSWORD2}
+      FEATURES_DB_MAIN_TABLE: cde_features_a
+      CONTEXT_PATH: /services
+      AUTHENTICATION: ${PORTAL_BACKEND_AUTHENTICATION}
+      CLIENT_ID: ${PORTAL_BACKEND_CLIENT_ID}
+      CLIENT_SECRET: ${PORTAL_BACKEND_CLIENT_SECRET}
+      TOKEN_URI: https://services.humanbrainproject.eu/oidc/token
+      AUTH_URI: https://services.humanbrainproject.eu/oidc/authorize
+      USER_INFO_URI: https://services.humanbrainproject.eu/oidc/userinfo
+      FRONTEND_LOGIN_URL: ${PORTAL_FRONTEND_URL}/services/login/hbp
+      FRONTEND_AFTER_LOGIN_URL: ${PORTAL_FRONTEND_URL}/home
+      FRONTEND_AFTER_LOGOUT_URL: ${PORTAL_FRONTEND_URL}/services/login/hbp
+      WOKEN_HOST: ${WOKEN_HOST}
+      WOKEN_PORT: ${WOKEN_PORT1}
+      WOKEN_AKKA_PATH: /user/entrypoint
+      EXAREME_URL: ${WOKEN_EXAREME_URL}
+      LOGGING_LEVEL_WEB: DEBUG
+      LOGGING_LEVEL_HIBERNATE: WARN
+      SESSION_TIMEOUT: 2592000
+      VIRTUAL_HOST: backend
+      VIRTUAL_PORT: 8080
+    depends_on:
+#      - db
+      - woken
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    networks:
+      - local
+#    ports:
+#      - "8080:8080"
+#      - "8089:8089"
+
+  frontend:
+    image: ${PORTAL_FRONTEND_IMAGE}${PORTAL_FRONTEND_VERSION}
+    environment:
+      WORKER_PROCESSES: 1
+      ERROR_LOG_LEVEL: warn
+      PORTAL_VIRTUAL_HOST: frontend
+      PORTAL_BACKEND_SERVER: backend:8080
+      PORTAL_BACKEND_CONTEXT: services
+    depends_on:
+      - backend
+    restart: unless-stopped # Used only by docker-compose
+    deploy:                 # Used only by docker stack
+      restart_policy:
+        condition: on-failure
+        delay: 5s
+        max_attempts: 3
+        window: 120s
+    networks:
+      - local
+    ports:
+      - "${PORTAL_FRONTEND_PORT}:80"

load_data.sh

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+#!/bin/sh
+#                    Copyright (c) 2018-2018
+#   Data Intensive Applications and Systems Labaratory (DIAS)
+#            Ecole Polytechnique Federale de Lausanne
+#
+#                      All Rights Reserved.
+#
+# Permission to use, copy, modify and distribute this software and its
+# documentation is hereby granted, provided that both the copyright notice
+# and this permission notice appear in all copies of the software, derivative
+# works or modified versions, and any portions thereof, and that both notices
+# appear in supporting documentation.
+#
+# This code is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. THE AUTHORS AND ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
+# DISCLAIM ANY LIABILITY OF ANY KIND FOR ANY DAMAGES WHATSOEVER RESULTING FROM THE
+# USE OF THIS SOFTWARE.
+
+# Import settings
+. ./settings.sh
+
+# 1. Create all the DB at once
+echo "Create databases..."
+db_id=$(docker run --rm -d \
+	-e POSTGRES_USER="${DB_USER_ADMIN}" \
+	-e POSTGRES_PASSWORD="${DB_PASSWORD_ADMIN}" \
+	-e PGDATA="/data/pgdata" \
+	-v ${DB_DATA}:/data:rw \
+	-v ${DB_DATASETS}:/datasets:ro \
+	--network=${MIP_PRIVATE_NETWORK} \
+	--name ${DB_HOST} \
+	${DB_IMAGE}${DB_VERSION}
+	)
+
+db_list=""
+for f in ${DB_CREATE_LIST}
+do
+	eval "t=\"\
+-e DB${f}=\${DB_NAME${f}} \
+-e USER${f}=\${DB_USER${f}} \
+-e PASSWORD${f}=\${DB_PASSWORD${f}}\""
+	db_list="$db_list $t"
+done
+
+sleep 5
+
+docker run --rm \
+	-e DB_HOST="${DB_HOST}" \
+	-e DB_PORT="${DB_PORT}" \
+	-e DB_ADMIN_USER="${DB_USER_ADMIN}" \
+	-e DB_ADMIN_PASSWORD="${DB_PASSWORD_ADMIN}" \
+	${db_list} \
+	--network=${MIP_PRIVATE_NETWORK} \
+	${DB_CREATE_IMAGE}${DB_CREATE_VERSION}
+
+# 2. Pre-populate the DBs which needs it
+for f in ${DB_SETUP_LIST}
+do
+	eval "img=\${${f}_IMAGE}"
+	eval "version=\${${f}_VERSION}"
+	eval "db=\${${f}_DB}"
+
+	echo
+	echo "Executing ${img}${version}"
+
+	docker run --rm \
+		-e FLYWAY_HOST="${DB_HOST}" \
+		-e FLYWAY_PORT="${DB_PORT}" \
+		-e FLYWAY_USER="${DB_USER_ADMIN}" \
+		-e FLYWAY_PASSWORD="${DB_PASSWORD_ADMIN}" \
+		-e FLYWAY_DATABASE_NAME="${db}" \
+		--network=${MIP_PRIVATE_NETWORK} \
+		${img}${version}
+done
+
+docker stop ${db_id}

run.sh

@@ -0,0 +1,33 @@
+#!/bin/sh
+#                    Copyright (c) 2018-2018
+#   Data Intensive Applications and Systems Labaratory (DIAS)
+#            Ecole Polytechnique Federale de Lausanne
+#
+#                      All Rights Reserved.
+#
+# Permission to use, copy, modify and distribute this software and its
+# documentation is hereby granted, provided that both the copyright notice
+# and this permission notice appear in all copies of the software, derivative
+# works or modified versions, and any portions thereof, and that both notices
+# appear in supporting documentation.
+#
+# This code is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. THE AUTHORS AND ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
+# DISCLAIM ANY LIABILITY OF ANY KIND FOR ANY DAMAGES WHATSOEVER RESULTING FROM THE
+# USE OF THIS SOFTWARE.
+
+# Import settings
+. ./settings.sh
+
+for f in ${WOKEN_CONF} ${WOKEN_VALIDATION_CONF}
+do
+	for v in $(grep '^:' settings.default.sh|cut -c 5- |cut -d: -f1)
+	do
+		eval "t=\"s#${v}#\${${v}}#g\""
+		script="${script}${t};"
+		sed -e "${script}" $f.in > $f
+	done
+done
+
+docker-compose $@

settings.default.sh

@@ -0,0 +1,115 @@
+: ${SHOW_SETTINGS:=false}
+
+#############################################################################
+# DATABASES
+# Service Parameters
+: ${DB_IMAGE:="postgres"}
+: ${DB_VERSION:=":9.6.5-alpine"}
+: ${DB_HOST:="db"}
+: ${DB_PORT:="5432"}
+: ${DB_DATA:="${PWD}/postgres"}
+: ${DB_DATASETS:="${PWD}/datasets"}
+: ${DB_USER_ADMIN:="postgres"}
+: ${DB_PASSWORD_ADMIN:="test"}
+
+# Databases Definitions:
+#  1. To add a new DB, copy the last 3 lines below and increment the id
+#  2. Add the new number in DB_CREATE_LIST
+: ${DB_NAME1:="meta"}
+: ${DB_USER1:="meta"}
+: ${DB_PASSWORD1:="metapwd"}
+
+: ${DB_NAME2:="features"}
+: ${DB_USER2:="features"}
+: ${DB_PASSWORD2:="featurespwd"}
+
+: ${DB_NAME3:="woken"}
+: ${DB_USER3:="woken"}
+: ${DB_PASSWORD3:="wokenpwd"}
+
+: ${DB_NAME4:="portal"}
+: ${DB_USER4:="portal"}
+: ${DB_PASSWORD4:="portalpwd"}
+
+# Database setup tools
+: ${DB_CREATE_IMAGE:="hbpmip/create-databases"}
+: ${DB_CREATE_VERSION:=":1.0.0"}
+# List of databases to create
+: ${DB_CREATE_LIST:="1 2 3 4"}
+
+: ${WOKEN_SETUP_IMAGE:="hbpmip/woken-db-setup"}
+: ${WOKEN_SETUP_VERSION:=":1.0.2"}
+: ${WOKEN_SETUP_DB:=${DB_NAME3}}
+
+: ${METADATA_SETUP_IMAGE:="hbpmip/sample-meta-db-setup"}
+: ${METADATA_SETUP_VERSION:=":0.4.0"}
+: ${METADATA_SETUP_DB:=${DB_NAME1}}
+
+: ${DATA_SETUP_IMAGE:="hbpmip/sample-data-db-setup"}
+: ${DATA_SETUP_VERSION:=":0.5.0"}
+: ${DATA_SETUP_DB:=${DB_NAME2}}
+
+# List of databases to populate
+: ${DB_SETUP_LIST:="WOKEN_SETUP METADATA_SETUP DATA_SETUP"}
+
+#############################################################################
+: ${MIP_PRIVATE_NETWORK:="mip_local"}
+: ${COMPOSE_PROJECT_NAME:="mip"}
+
+: ${PORTAINER_IMAGE:="portainer/portainer"}
+: ${PORTAINER_VERSION:=":latest"}
+: ${PORTAINER_HOST:="portainer"}
+: ${PORTAINER_PORT:="9000"}
+: ${PORTAINER_DATA:="${PWD}/portainer"}
+: ${PORTAINER_ENABLED:="true"}
+
+#############################################################################
+# Services
+: ${ZOOKEEPER_IMAGE:="zookeeper"}
+: ${ZOOKEEPER_VERSION:=":3.4.11"}
+: ${ZOOKEEPER_PORT1:="2181"}
+: ${ZOOKEEPER_PORT2:="2888"}
+: ${ZOOKEEPER_PORT3:="3888"}
+
+: ${MESOS_MASTER_IMAGE:="mesosphere/mesos-master"}
+: ${MESOS_MASTER_VERSION:=":1.3.0"}
+: ${MESOS_MASTER_PORT:="5050"}
+: ${MESOS_MASTER_LOGS:="${PWD}/mesos-master/logs"}
+: ${MESOS_MASTER_TMP:="${PWD}/mesos-master/tmp"}
+
+: ${MESOS_SLAVE_IMAGE:="mesosphere/mesos-slave"}
+: ${MESOS_SLAVE_VERSION:=":1.3.0"}
+: ${MESOS_SLAVE_PORT:="5051"}
+: ${MESOS_SLAVE_LOGS:="${PWD}/mesos-slave/logs"}
+: ${MESOS_SLAVE_TMP:="${PWD}/mesos-slave/tmp"}
+
+: ${CHRONOS_IMAGE:="mesosphere/chronos"}
+: ${CHRONOS_VERSION:=":v3.0.2"}
+: ${CHRONOS_HOST:="chronos"}
+: ${CHRONOS_PORT1:="4400"}
+: ${CHRONOS_PORT2:="4401"}
+
+: ${WOKEN_IMAGE:="hbpmip/woken"}
+: ${WOKEN_VERSION:=":2.1.4"}
+: ${WOKEN_HOST:="woken"}
+: ${WOKEN_CONF:="${PWD}/woken/application.conf"}
+: ${WOKEN_PORT1:="8088"}
+: ${WOKEN_PORT2:="8087"}
+: ${WOKEN_EXAREME_URL:="http://prozac.madgik.di.uoa.gr:9090/mining/query"}
+
+: ${WOKEN_VALIDATION_IMAGE:="hbpmip/woken-validation"}
+: ${WOKEN_VALIDATION_VERSION:=":2.1.0"}
+: ${WOKEN_VALIDATION_HOST:="woken-validation"}
+: ${WOKEN_VALIDATION_PORT:="8082"}
+: ${WOKEN_VALIDATION_CONF:="${PWD}/woken/validation.conf"}
+
+: ${PORTAL_BACKEND_IMAGE:="hbpmip/portal-backend"}
+: ${PORTAL_BACKEND_VERSION:=":2.5.4"}
+: ${PORTAL_BACKEND_AUTHENTICATION:="0"}
+: ${PORTAL_BACKEND_CLIENT_ID:="none"}
+: ${PORTAL_BACKEND_CLIENT_SECRET:="none"}
+
+: ${PORTAL_FRONTEND_IMAGE:="hbpmip/portal-frontend"}
+: ${PORTAL_FRONTEND_VERSION:=":2.6.0"}
+: ${PORTAL_FRONTEND_PORT:="80"}
+: ${PORTAL_FRONTEND_URL:="http://172.16.22.176:80"}

settings.sh

@@ -0,0 +1,39 @@
+#Settings are taken in the following order of precedence:
+#  1. Shell Environment, or on the command line
+
+#  2. Node-specific settings `settings.local.<Alias>.sh`
+if test ! -z "$1" && test -f ./settings.local.$1.sh;
+then
+	. ./settings.local.$1.sh;
+fi
+
+#  3. Federation-specific `settings.local.sh`
+if test -f ./settings.local.sh;
+then
+	. ./settings.local.sh;
+fi
+
+#  4. Default settings `settings.default.sh`
+if test -f ./settings.default.sh;
+then
+	. ./settings.default.sh;
+fi
+
+if ${SHOW_SETTINGS};
+then
+	echo "Current settings:"
+fi
+
+for v in $(grep '^:' settings.default.sh|cut -c 5- |cut -d: -f1)
+do
+	eval "export $v=\"\$$v\""
+	if ${SHOW_SETTINGS};
+	then
+		eval "echo $v=\$$v"
+	fi
+done
+
+if ${SHOW_SETTINGS};
+then
+	echo
+fi

setup.sh

@@ -0,0 +1,49 @@
+#!/bin/sh
+#                    Copyright (c) 2018-2018
+#   Data Intensive Applications and Systems Labaratory (DIAS)
+#            Ecole Polytechnique Federale de Lausanne
+#
+#                      All Rights Reserved.
+#
+# Permission to use, copy, modify and distribute this software and its
+# documentation is hereby granted, provided that both the copyright notice
+# and this permission notice appear in all copies of the software, derivative
+# works or modified versions, and any portions thereof, and that both notices
+# appear in supporting documentation.
+#
+# This code is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. THE AUTHORS AND ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
+# DISCLAIM ANY LIABILITY OF ANY KIND FOR ANY DAMAGES WHATSOEVER RESULTING FROM THE
+# USE OF THIS SOFTWARE.
+
+# Import settings
+. ./settings.sh
+
+# If requested, setup portainer:
+if ${PORTAINER_ENABLED}
+then
+	# Permanent storage for Portainer
+	mkdir -p ${PORTAINER_DATA}
+
+	docker run -d -p ${PORTAINER_PORT}:9000 \
+		--restart unless-stopped \
+		-v /var/run/docker.sock:/var/run/docker.sock:rw \
+		-v ${PORTAINER_DATA}:/data:rw \
+		--name ${COMPOSE_PROJECT_NAME}_${PORTAINER_HOST} \
+		${PORTAINER_IMAGE}${PORTAINER_VERSION}
+fi
+
+# Permanent storage for the Databases
+mkdir -p ${DB_DATA}
+mkdir -p ${DB_DATASETS}
+sudo chown -R 999:999 ${DB_DATA} ${DB_DATASETS}
+
+# Permanent storage for Mesos
+mkdir -p ${MESOS_MASTER_LOGS}
+mkdir -p ${MESOS_MASTER_TMP}
+mkdir -p ${MESOS_SLAVE_LOGS}
+mkdir -p ${MESOS_SLAVE_TMP}
+
+# Preload the databases
+./load_data.sh

woken/application.conf.in

@@ -0,0 +1,172 @@
+
+# Sample configuration for local execution of the woken
+
+akka {
+  log-dead-letters = 1
+  log-dead-letters-during-shutdown = off
+  loglevel = INFO
+
+  actor {
+    provider = "akka.cluster.ClusterActorRefProvider"
+    debug {
+      receive = on
+      autoreceive = off
+      lifecycle = on
+      fsm = on
+      unhandled = on
+      event-stream = off
+    }
+  }
+
+  remote {
+    log-sent-messages = off
+    log-received-messages = off
+    log-remote-lifecycle-events = off
+
+    maximum-payload-bytes = 10000000 bytes
+    enabled-transports = [ "akka.remote.netty.tcp" ]
+
+    netty.tcp {
+
+      hostname = WOKEN_HOST        # external (logical) hostname
+      port = WOKEN_PORT1           # external (logical) port
+
+      bind-hostname = localhost    # internal (bind) hostname
+      bind-port = WOKEN_PORT1      # internal (bind) port
+
+      message-frame-size = 10000000b
+      send-buffer-size = 10000000b
+      receive-buffer-size = 10000000b
+      maximum-frame-size = 10000000b
+    }
+  }
+
+  cluster {
+    seed-nodes = [ "akka.tcp://woken@WOKEN_HOST:WOKEN_PORT1" ]
+
+    roles = [ "woken" ]
+  }
+}
+
+spray.can.server {
+  idle-timeout = 300s
+  request-timeout = 180s
+  ssl-encryption = off
+  ssl-tracing = on
+}
+
+spray.can.client {
+  request-timeout = 20s
+  chunkless-streaming = off
+  connecting-timeout = 10s
+}
+
+spray.can.host-connector {
+  max-connections = 5
+  host-connector.max-retries = 2
+  pipelining = on
+}
+
+app {
+  clusterSystemName = "woken"
+  jobServiceName = "job-service"
+  dockerBridgeNetwork = "MIP_PRIVATE_NETWORK"
+  networkInterface = "0.0.0.0"
+  webServicesPort = WOKEN_PORT2
+
+  master.router {
+    actors {
+      mining.limit = 5
+      experiment.limit = 5
+    }
+  }
+
+  basicAuth {
+    username = "admin"
+    password = "WoKeN"
+  }
+}
+
+jobs {
+  node = "federation"
+  owner = "admin@mip.chuv.ch"
+  chronosServerUrl = "http://CHRONOS_HOST:CHRONOS_PORT1"
+  featuresDb = "DB_NAME2"
+  featuresTable = "cde_features_a"
+  resultDb = "DB_NAME3"
+  metaDb = "DB_NAME1"
+}
+
+db {
+  woken {
+    jdbc_driver = "org.postgresql.Driver"
+    jdbc_url = "jdbc:postgresql://DB_HOST:DB_PORT/DB_NAME3"
+    host = "DB_HOST"
+    port = DB_PORT
+    user = "DB_USER3"
+    password = "DB_PASSWORD3"
+  }
+
+  features {
+    jdbc_driver = "org.postgresql.Driver"
+    jdbc_url = "jdbc:postgresql://DB_HOST:DB_PORT/DB_NAME2"
+    host = "DB_HOST"
+    port = DB_PORT
+    user = "DB_USER2"
+    password = "DB_PASSWORD2"
+  }
+
+  metadata {
+    jdbc_driver = "org.postgresql.Driver"
+    jdbc_url = "jdbc:postgresql://DB_HOST:DB_PORT/DB_NAME1"
+    host = "DB_HOST"
+    port = DB_PORT
+    user = "DB_USER1"
+    password = "DB_PASSWORD1"
+  }
+}
+
+# The actual Algorithm Library
+algorithms {
+  histograms = {
+    dockerImage = "hbpmip/python-histograms:0.3.6"
+    predictive = false
+  }
+
+  statisticsSummary = {
+    dockerImage = "hbpmip/r-summary-stats:2afe249"
+    predictive = false
+  }
+
+  anova = {
+    dockerImage = "hbpmip/python-anova:0.3.6"
+    predictive = false
+  }
+
+  linearRegression = {
+    dockerImage = "hbpmip/python-linear-regression:0.0.7"
+    predictive = false
+  }
+
+  knn = {
+    dockerImage = "hbpmip/java-rapidminer-knn:0.2.1"
+    predictive = true
+  }
+
+  naiveBayes = {
+    dockerImage = "hbpmip/java-rapidminer-naivebayes:0.2.0"
+    predictive = true
+  }
+
+  tSNE = {
+    dockerImage = "hbpmip/python-tsne:0.3.3"
+    predictive = true
+    maturity = "experimental"
+  }
+
+  ggparci = {
+    dockerImage = "hbpmip/r-ggparci:0.2.0"
+    predictive = false
+    maturity = "experimental"
+  }
+}

woken/validation.conf.in

@@ -0,0 +1,42 @@
+akka {
+  loglevel = INFO
+
+  actor {
+    provider = "akka.cluster.ClusterActorRefProvider"
+    debug {
+      receive = on
+      autoreceive = on
+      lifecycle = on
+      fsm = on
+    }
+  }
+
+  remote {
+    maximum-payload-bytes = 10000000 bytes
+    enabled-transports = [ "akka.remote.netty.tcp" ]
+    netty.tcp {
+
+      hostname = WOKEN_VALIDATION_HOST  # external (logical) hostname
+      port = WOKEN_VALIDATION_PORT      # external (logical) port
+
+      bind-hostname = localhost         # internal (bind) hostname
+      bind-port = WOKEN_VALIDATION_PORT # internal (bind) port
+
+      message-frame-size = 10000000b
+      send-buffer-size = 10000000b
+      receive-buffer-size = 10000000b
+      maximum-frame-size = 10000000b
+    }
+  }
+
+  cluster {
+    seed-nodes = [ "akka.tcp://woken@WOKEN_HOST:WOKEN_PORT1" ]
+
+    roles = [ "validation" ]
+
+    #role {
+    #  woken.min-nr-of-members = 1
+    #  validation.min-nr-of-members = 1
+    #}
+  }
+}