docker switching to docker compose

The initial docker configuration wasn't working correctly, so this was
an opportunity to switch to a docker-compose to manage individual
services.
This allowed to also better fit the docker philosophy of lightweight
containers that manage only a single services and/or process

docker/Dockerfile

+FROM ubuntu:16.04
+
+
+
+COPY entrypoint.sh /usr/local/bin/entrypoint.sh
+
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]

docker/docker-compose.yml

+version: '2'
+services:
+    mysql:
+        image: mysql:5.7
+        environment:
+            - MYSQL_ROOT_PASSWORD=MySRPimSRP
+        volumes:
+            - ./mysql/:/docker-entrypoint-initdb.d/
+            - /var/lib/mysql:/var/lib/mysql
+    postfix:
+        image: catatnight/postfix
+        environment:
+            - maildomain=mail.example.com
+            - smtp_user=user:pwd
+        ports:
+                - "25:25"
+    uwsgi:
+        build: ./vidjil
+        image: vidjil:test
+        command: bash /entrypoints/uwsgi-entrypoint.sh
+        volumes:
+            - /opt/vidjil/databases:/usr/share/vidjil/server/web2py/applications/vidjil/databases
+            - /opt/vidjil/result/results:/mnt/result/results
+            - /opt/vidjil/result/tmp:/mnt/result/tmp
+            - /opt/vidjil/upload/uploads:/mnt/upload/uploads
+            - /var/vidjil:/var/vidjil
+            - /home/ryan/vidjil:/usr/share/vidjil
+        depends_on:
+            - mysql
+            - postfix
+            - fuse
+        links:
+            - mysql:mysql
+            - postfix:postfix
+            - fuse:fuse
+    fuse:
+        image: vidjil:test
+        volumes:
+            - /home/user/vidjil:/usr/share/vidjil
+    nginx:
+        image: vidjil:test
+        volumes:
+            - /home/user/vidjil:/usr/share/vidjil
+            #- /home/user/ssl:/etc/nginx/ssl
+        depends_on:
+            - uwsgi
+        links:
+                - uwsgi:uwsgi
+        ports:
+            - "80:80"
+            - "443:443"
+        #command: bash /entrypoints/nginx-entrypoint.sh
+        command: nginx -g 'daemon off;'
+
+    workers:
+        image: vidjil:test
+        command: /usr/local/bin/gosu www-data python /usr/share/vidjil/server/web2py/web2py.py -K vidjil,vidjil,vidjil
+        volumes:
+            - /opt/vidjil/databases:/usr/share/vidjil/server/web2py/applications/vidjil/databases
+            - /opt/vidjil/result:/mnt/result
+            - /opt/vidjil/result/tmp:/mnt/result/tmp
+            - /opt/vidjil/upload:/mnt/upload
+            - /var/vidjil:/var/vidjil
+            - /home/ryan/vidjil:/usr/share/vidjil
+        depends_on:
+            - uwsgi
+            - mysql
+        links:
+            - mysql
+    reporter:
+        build: ./reporter
+        image: reporter:test
+        volumes:
+            - /opt/vidjil/databases:/usr/share/vidjil/server/web2py/applications/vidjil/databases
+            - /opt/vidjil/result/results:/mnt/result/results
+            - /opt/vidjil/result/tmp:/mnt/result/tmp
+            - /opt/vidjil/upload/uploads:/mnt/upload/uploads
+            - /var/vidjil:/var/vidjil
+            - /home/ryan/vidjil:/usr/share/vidjil
+            - ./reporter/code:/opt/reporter
+        depends_on:
+            - uwsgi
+        links:
+            - postfix:postfix
+            - uwsgi:uwsgi

docker/mysql/create_db.sql

+CREATE USER vidjil_user;
+SET PASSWORD FOR USER vidjil_user = PASSWORD('rootpass');
+CREATE DATABASE vidjil;
+GRANT ALL ON vidjil.* TO 'vidjil_user'@'%'; 

docker/postfix/Dockerfile

+from ubuntu:16.04
+
+label version="1.0"
+label description="An Ubuntu based docker image which postfix"
+
+# Install Postfix. Shamelessly stolen from https://github.com/noteed/docker-postfix/blob/master/Dockerfile
+run echo "postfix postfix/main_mailer_type string Internet site" > preseed.txt
+run echo "postfix postfix/mailname string mail.example.com" >> preseed.txt
+# Use Mailbox format.
+run debconf-set-selections preseed.txt
+run apt-get update
+run DEBIAN_FRONTEND=noninteractive apt-get install -q -y postfix
+
+run postconf -e myhostname=mail.example.com
+run postconf -e mydestination="mail.example.com, example.com, localhost.localdomain, localhost"
+run postconf -e mail_spool_directory="/var/spool/mail/"
+run postconf -e mailbox_command=""

docker/reporter/Dockerfile

+from vidjil:test
+
+run apt-get update && apt-get install -y cron python python-pip iputils-ping
+
+run pip install crontab requests
+
+add crontab /etc/cron.d/reporter
+
+run chmod 0644 /etc/cron.d/reporter
+
+run touch /var/log/cron.log
+
+cmd cron && tail -f /var/log/cron.log

docker/reporter/code/README.org

+*Reporter
+ The reporter is designed to connect to a machine on the same network (or remotely when possible) via ssh and execute a list of scripts on the target system. The results are then posted via HTTP to a monitorserv instance.
+
+**Configuration
+
+***Basic
+   The reporter script is has a series of parameters that can be configured that range from the setting of a cron task for repeat execution to the configuration of users that should be executing the scripts.
+   The script takes the following parameters:
+	     --init       Set following arguments as default and start cron
+	     --delete     Unset all cron jobs created by this script
+	     --set        Set values in config file without setting a cron
+	     --reset      Reset config file to default values
+	     --start      Launch Cron with current settings
+	-tgt --host       Host name
+	-c   --cron       Cron expression
+	-u   --username   SSH Username
+	-p   --path       Path to Vidjil installation
+	-py  --python     Path to the python installation
+	-m   --monitor    host of the monitor that will receive the report
+	-s   --servername ID of the server entry in the monitor database
+	     --cron-user  User that will be executing the cron task on this machine
+
+	Using the set or init parameters will write the parameters to the =config= file with the following format:
+	<param_name> <param_value>
+	The config file is read at each execution of the monitoring process.
+
+***Scripts
+   Upon starting the reporter process reads thre =script_map= file in order to determine what will be executed on the remote machine.
+   A =key= =value= pair is used to in this file where the =key= is the name of the field that will be sent to the monitorserv instance and the =value= is the path to the script (relative to the scripts folder)
+   The order in which scripts are added represents the order in which the fields will be placed and numbered in the form that will be sent. This can be an important detail when using the reporter in conjunction with monitorserv because it will define the order in which the fields are displayed in the webapp.
+
+***Dependencies
+  On the local system: ssh, crontab and python are necessary. Bash or shell are highly recommended for script testing.
+  On the remote system: Bash or shell and ssh are necessary
+
+***SSH Authentication
+   Given that the Reporter uses ssh tunneling to execute scripts on the remote system, it is important that the username parameter be set to a user that has the correct permissions on the remote system.
+   It is also necessary to have the a public key on the remote system in order to connect automatically or the deamonized execution during the crontab task will fail as the ssh connection will require a manually entered password.
+   For one-time execution the password prompt will be displayed in the terminal.
+
+**Usage
+  For single execution, one can simply run the script with of without parameters. In the absence of a parameter the value included in the =config= file will be applied to the execution.
+  For repeat execution it is necessary to use the =--init= parameter which will not only set any given parameter as default in the config file but also start a crontab task with the cron expression in the =config= file (giving a cron expression as parameter will also work since it will be set in the =config= file before initialising the crontab task).

docker/reporter/code/configs/default.cfg

+username ryan
+key /home/ryan/.ssh/id_rsa
+monitor http://monitor.vidjil.org/server
+python /usr/bin/python
+servername vidjil-ryan
+cron_user www-data
+cron 0 5 * * * *
+host 127.0.0.1
+path /home/www-data/vidjil

docker/reporter/code/reporter.py

+#!/usr/bin/python
+from subprocess import Popen, PIPE, check_output
+from crontab import CronTab
+from collections import OrderedDict
+import argparse
+import os
+from datetime import datetime
+parser = argparse.ArgumentParser()
+
+#-db DATABSE -u USERNAME -p PASSWORD -size 20
+parser.add_argument("--init", help="Set following arguments as default and start cron", action="store_true")
+parser.add_argument("--delete", help="Unset all cron jobs created by this script", action="store_true")
+parser.add_argument("--set", help="Set values in config file without setting a cron", action="store_true")
+parser.add_argument("--reset", help="Reset config file to default values", action="store_true")
+parser.add_argument("--start", help="Launch Cron with current settings", action="store_true")
+parser.add_argument("-tgt", "--host", help="Host name")
+parser.add_argument("-c", "--cron", help="Cron expression")
+parser.add_argument("-u", "--username", help="SSH Username")
+parser.add_argument("-p", "--path", help="Path to Vidjil installation")
+parser.add_argument("-py", "--python", help="Path to the python installation")
+parser.add_argument("-m", "--monitor", help="host of the monitor that will receive the report")
+parser.add_argument("-s", "--servername", help="ID of the server entry in the monitor database")
+parser.add_argument("-k", "--key", help="Path to ssh key to use")
+parser.add_argument("-l", "--local", help="Execute scripts on local machine")
+parser.add_argument("--cron-user", help="user that will be executing the cron task on this machine")
+parser.add_argument("--config", help="location of the config file that should be used")
+
+CUR_DIR = os.path.dirname(os.path.realpath(__file__)) + '/'
+SCRIPT_DIR = CUR_DIR + 'scripts/'
+SCRIPT_MAP = CUR_DIR + 'script_map'
+CONFIG_DIR = CUR_DIR + 'configs/'
+CMD = os.path.realpath(__file__)
+
+DEFAULT_CRON_USER = 'www-data'
+DEFAULT_MONITOR_HOST = 'http://127.0.0.1:5000/monitor'
+DEFAULT_SERVER_NAME = 'banana'
+DEFAULT_HOST = '127.0.0.1'
+DEFAULT_CRON = '* * * * * *'
+DEFAULT_USERNAME = 'www-data'
+DEFAULT_KEY = '/home/www-data/.ssh/id_rsa'
+DEFAULT_PATH = '/home/www-data/vidjil'
+DEFAULT_PYTHON = '/usr/bin/python'
+DEFAULT_CONFIG = CONFIG_DIR + 'default.cfg'
+DEFAULT_LOCAL = 'false'
+
+def init(config, host=None, cron=None, username=None, local=None, key=None, path=None, python=None, monitor=None, servername=None, cron_user=None):
+    params = set_args(config, host, cron, username, local, key, path, python, monitor, servername, cron_user)
+    set_cron(params['python'] + ' ' + CMD + ' --config ' + config, params['cron_user'], params['cron'])
+
+def start(config):
+    params = load(config)
+    set_cron(params['python'] + ' ' + CMD + ' --config ' + config, params['cron_user'], params['cron'])
+
+def set_args(config, host=None, cron=None, username=None, local=None, key=None, path=None, python=None, monitor=None, servername=None, cron_user=None):
+    params = load(DEFAULT_CONFIG)
+
+    params['host'] = params['host'] if host is None else host
+    params['cron'] = params['cron'] if cron is None else cron
+    params['username'] = params['username'] if username is None else username
+    params['local'] = params['local'] if local is None else local
+    params['key'] = params['key'] if key is None else key
+    params['path'] = params['path'] if path is None else path
+    params['python'] =  params['python'] if python is None else python
+    params['monitor'] = params['monitor'] if monitor is None else monitor
+    params['servername'] = params['servername'] if servername is None else servername
+    params['cron_user'] = params['cron_user'] if cron_user is None else cron_user
+    print "Initialising monitor for host " + params['host'] + " with cron expression " + params['cron'] + " username " + params['username'] + " path " + params['path'] + " in config file " + config
+    
+    write_config(params, config)
+    return params
+
+def reset(config=None):
+    p = {} 
+    p['host'] = DEFAULT_HOST
+    p['cron'] = DEFAULT_CRON
+    p['username'] = DEFAULT_USERNAME
+    p['local'] = DEFAULT_LOCAL
+    p['key'] = DEFAULT_KEY
+    p['path'] = DEFAULT_PATH
+    p['python'] = DEFAULT_PYTHON
+    p['monitor'] = DEFAULT_MONITOR_HOST
+    p['servername'] = DEFAULT_SERVER_NAME
+    p['cron_user'] = DEFAULT_CRON_USER
+
+    write_config(p, config)
+
+def write_config(params, cfg_file):
+    config_file = open(cfg_file, 'w+')
+    for key in params:
+        config_file.write(key + ' ' + params[key] + '\n')
+
+    
+def delete(cmd, user):
+    tab = CronTab(user=user)
+    tab.remove_all(command=cmd) 
+    tab.write()
+
+def load(file):
+    conf = open(file, 'r')
+    params = OrderedDict()
+    for line in conf.readlines():
+        if (line[0] != '#' and not line.isspace()):
+            l = line.split(' ')
+            params[l[0]] = ' '.join(l[1:len(l)]).rstrip()
+    print "Loaded params: " + str(params)
+    return params
+
+def set_cron(cmd, user, cron_exp):
+    my_cron = CronTab(user=user)
+    job = my_cron.new(command=cmd)
+    cron_arr = cron_exp.split(' ')
+    job.setall(cron_arr[0], cron_arr[1], cron_arr[2], cron_arr[3], cron_arr[4], cron_arr[5])
+    my_cron.write()
+
+def ping(host):
+    p = Popen("ping -c 1 " + host, shell=True, stdout=PIPE)
+    return p.stdout.read()
+
+def tunnel(host, username, key, path, script):
+    cat = Popen("cat " + SCRIPT_DIR + script, shell=True, close_fds=True, stdout=PIPE)
+    cmd = "ssh -i " + key + " " + username + "@" + host + " \"cd " + path + " ; exec \$SHELL\""
+    ssh = Popen(cmd, shell=True, stdin=cat.stdout, stdout=PIPE, stderr=PIPE)
+    out, err = ssh.communicate()
+    return out + err
+
+def execute(path, script):
+    cmd = "cd " + path + " ; exec " + SCRIPT_DIR + script
+    proc = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE)
+    out, err = proc.communicate()
+    return out + err
+
+def run_scripts(params):
+    scripts = load(SCRIPT_MAP)
+    results = OrderedDict()
+    for key in scripts:
+        #remove file extensions
+        new_key = key.split('.')[0]
+        if params['local'] != 'False':
+            results[new_key] = tunnel(params['host'], params['username'], params['key'], params['path'], scripts[key])
+        else:
+            results[new_key] = execute(params['path'], scripts[key])
+    return results
+
+def post_results(server_addr, servername, is_up, results):
+    import requests
+    session = requests.Session()
+    payload = {}
+    payload['up'] = is_up
+    for key in results:
+        payload[key] = results[key]
+    addr = server_addr + '/' + servername
+
+    print addr
+    for key in payload:
+        print "  %-15s %s" % (key, str(payload[key]).replace('\n', '\\n')[:80])
+
+    session.post(addr, data=payload)
+
+def main():
+    args = parser.parse_args()
+    config_file = ''
+    if args.config is None:
+        config_file = DEFAULT_CONFIG
+    else:
+        if args.config[0] != '/':
+            config_file += CUR_DIR
+        config_file += args.config
+    if args.init:
+        init(config_file, args.host, args.cron, args.username, args.key, args.path, args.python, args.monitor, args.servername, args.cron_user)
+    elif args.set:
+        set_args(config_file, args.host, args.cron, args.username, args.key, args.path, args.python, args.monitor, args.servername, args.cron_user)
+    elif args.delete:
+        params = load(config_file)
+        delete(params['python'] + ' ' + CMD, params['cron_user'])
+    elif args.reset:
+        reset(config_file)
+    elif args.start:
+        start(config_file)
+    else :
+        params = load(config_file)
+        results = ''
+        response = os.system("ping -c 1 " + params['host'])
+        up = 0
+        if (response == 0):
+            up = 1
+
+            results = run_scripts(params)
+            results['ping'] = ping(params['host'])
+
+        post_results(params['monitor'], params['servername'], up, results)
+
+if __name__ == "__main__":
+    main()

docker/reporter/code/script_map

+revision git_rev.sh
+patients count-patients.sh
+samples count-samples.sh
+uptime uptime.sh
+workers workers.sh
+#stats bash_stats.sh
+algo vidjil-algo-version.sh
+

docker/reporter/code/scripts/bash_stats.sh

+#!/bin/bash
+cd server/web2py/applications/vidjil/scripts
+bash stats.sh

docker/reporter/code/scripts/count-patients.sh

+#!/bin/sh
+python server/web2py/web2py.py -S vidjil -M -R applications/vidjil/scripts/count-patients.py

docker/reporter/code/scripts/count-samples.sh

+#!/bin/sh
+python server/web2py/web2py.py -S vidjil -M -R applications/vidjil/scripts/count-samples.py

docker/reporter/code/scripts/git_rev.sh

+#!/bin/bash
+git rev-parse HEAD

docker/reporter/code/scripts/uptime.sh

+#!/bin/bash
+uptime

docker/reporter/code/scripts/vidjil-algo-version.sh

+#!/bin/sh
+python server/web2py/web2py.py -S vidjil -M -R applications/vidjil/scripts/vidjil-algo-version.py | grep -E "(# version|# git)"
+
+

docker/reporter/code/scripts/workers.sh

+#!/bin/sh
+python server/web2py/web2py.py -S vidjil -M -R applications/vidjil/scripts/worker-status.py

docker/reporter/crontab

+* * * * * root /usr/bin/python /opt/reporter/reporter.py >> /var/log/cron.log 2>&1
+

docker/ubuntu_systemd/Dockerfile

-FROM ubuntu:16.04
-ENV container docker
-ENV LC_ALL C
-ENV DEBIAN_FRONTEND noninteractive
-RUN echo 'APT::Install-Recommends "0"; \n\
-APT::Get::Assume-Yes "true"; \n\
-APT::Get::force-yes "true"; \n\
-APT::Install-Suggests "0";' > /etc/apt/apt.conf.d/01buildconfig
-RUN mkdir -p  /etc/apt/sources.d/
-RUN echo "deb mirror://mirrors.ubuntu.com/mirrors.txt vivid main restricted universe multiverse \n\
-deb mirror://mirrors.ubuntu.com/mirrors.txt vivid-updates main restricted universe multiverse \n\
-deb mirror://mirrors.ubuntu.com/mirrors.txt vivid-backports main restricted universe multiverse \n\
-deb mirror://mirrors.ubuntu.com/mirrors.txt vivid-security main restricted universe multiverse" > /etc/apt/sources.d/ubuntu-mirrors.list
-RUN apt-get update && apt-get install systemd
-RUN (cd /lib/systemd/system/sysinit.target.wants/; for i in *; do [ $i == systemd-tmpfiles-setup.service  ] || rm -f $i; done); \
-rm -f /lib/systemd/system/multi-user.target.wants/*;\
-rm -f /etc/systemd/system/*.wants/*;\
-rm -f /lib/systemd/system/local-fs.target.wants/*; \
-rm -f /lib/systemd/system/sockets.target.wants/*udev*; \
-rm -f /lib/systemd/system/sockets.target.wants/*initctl*; \
-rm -f /lib/systemd/system/basic.target.wants/*;\
-rm -f /lib/systemd/system/anaconda.target.wants/*; \
-rm -f /lib/systemd/system/plymouth*; \
-rm -f /lib/systemd/system/systemd-update-utmp*;
-RUN systemctl set-default multi-user.target
-ENV init /lib/systemd/systemd
-VOLUME [ "/sys/fs/cgroup"  ]
-# docker run -it --privileged=true -v /sys/fs/cgroup:/sys/fs/cgroup:ro 444c127c995b /lib/systemd/systemd systemd.unit=emergency.service
-ENTRYPOINT ["/lib/systemd/systemd"]
-CMD ["systemd.unit=emergency.service"]

docker/vidjil_ubuntu/Dockerfile → docker/vidjil/Dockerfile

-from ubuntu_systemd
+from ubuntu:16.04
 
 label version="1.0"
 label description="An Ubuntu based docker image which comes \
 with a full installation of the Vidjil algoright and browser/server."
 
-run apt-get update
-run apt-get -y -q install apt-utils sudo curl nginx-full
-
-run echo deb http://apt.vidjil.org:8080/archive sid/all/ >> /etc/apt/sources.list
-run echo deb http://apt.vidjil.org:8080/archive sid/amd64/ >> /etc/apt/sources.list
-run echo deb http://apt.vidjil.org:8080/archive wheezy/all/ >> /etc/apt/sources.list
-run echo deb http://apt.vidjil.org:8080/archive wheezy/amd64/ >> /etc/apt/sources.list
-
-# Install Postfix. Shamelessly stolen from https://github.com/noteed/docker-postfix/blob/master/Dockerfile
-run echo "postfix postfix/main_mailer_type string Internet site" > preseed.txt
-run echo "postfix postfix/mailname string mail.example.com" >> preseed.txt
-# Use Mailbox format.
-run debconf-set-selections preseed.txt
-run DEBIAN_FRONTEND=noninteractive apt-get install -q -y postfix
-
-run postconf -e myhostname=mail.example.com
-run postconf -e mydestination="mail.example.com, example.com, localhost.localdomain, localhost"
-run postconf -e mail_spool_directory="/var/spool/mail/"
-run postconf -e mailbox_command=""
+env GOSU_VERSION 1.7
+run set -x \
+	&& apt-get update && apt-get install -y --no-install-recommends ca-certificates wget && rm -rf /var/lib/apt/lists/* \
+	&& wget -O /usr/local/bin/gosu "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture)" \
+	&& wget -O /usr/local/bin/gosu.asc "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$(dpkg --print-architecture).asc" \
+	&& export GNUPGHOME="$(mktemp -d)" \
+	&& gpg --keyserver ha.pool.sks-keyservers.net --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4 \
+	&& gpg --batch --verify /usr/local/bin/gosu.asc /usr/local/bin/gosu \
+	&& rm -r "$GNUPGHOME" /usr/local/bin/gosu.asc \
+	&& chmod +x /usr/local/bin/gosu \
+	&& apt-get purge -y --auto-remove ca-certificates wget
+
+run echo deb http://rby.vidjil.org:8080/archive sid/all/ >> /etc/apt/sources.list
+run echo deb http://rby.vidjil.org:8080/archive sid/amd64/ >> /etc/apt/sources.list
+run echo deb http://rby.vidjil.org:8080/archive wheezy/all/ >> /etc/apt/sources.list
+run echo deb http://rby.vidjil.org:8080/archive wheezy/amd64/ >> /etc/apt/sources.list
 
 run echo "vidjil-server vidjil/reconfigure-webserver string nginx" > preseed.txt
-run echo "vidjil-server vidjil/restart-webserver boolean true" >> preseed.txt
-run echo "vidjil-server vidjil/configure-startup string systemd" >> preseed.txt
+run echo "vidjil-server vidjil/restart-webserver boolean false" >> preseed.txt
+run echo "vidjil-server vidjil/configure-startup string none" >> preseed.txt
 run echo "vidjil-server vidjil/start-services boolean false" >> preseed.txt
 run echo "vidjil-server vidjil/web2py-password string VidjilAdm1n" >> preseed.txt
 run echo "vidjil-server vidjil/ssl-country string AU" >> preseed.txt
@@ -38,21 +35,26 @@ run echo "vidjil-server vidjil/ssl-name string VidjilTeam" >> preseed.txt
 run echo "vidjil-server vidjil/ssl-email string team@vidjil.org" >> preseed.txt
 
 run debconf-set-selections preseed.txt
-run echo 91.121.76.104 apt.vidjil.org >> /etc/hosts ;\
- gpg --recv-key --keyserver apt.vidjil.org 9187987418E1A625 ;\
- apt-get update ;\
- DEBIAN_FRONTEND=noninteractive apt-get -y -q --allow-unauthenticated install vidjil-archive-keyring ;\
- apt-get update ;\
- DEBIAN_FRONTEND=noninteractive apt-get install -y -q --allow-unauthenticated vidjil-server
+run gpg --recv-keys --keyserver rby.vidjil.org 9187987418E1A625
+run apt-get update ; apt-get install --no-install-recommends --no-install-suggests -y -q sudo curl apt-utils uwsgi-plugin-python nginx-full
+run apt-get update ; DEBIAN_FRONTEND=noninteractive apt-get -y -q --allow-unauthenticated install vidjil-archive-keyring
+run apt-get update ; DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends --no-install-suggests -y -q --allow-unauthenticated vidjil-server
 
 run cd /usr/share/vidjil/germline && make
 run cd /usr/share/web2py && chown -R www-data:www-data .
 
-run systemctl enable web2py.scheduler.service fuse.server.service
-
-cmd ["/bin/systemctl", "start", "nginx.service"]
-cmd ["/bin/systemctl", "start", "uwsgi.service"]
-
-expose 80
-expose 443
-cmd ["/usr/sbin/init"]
+run ln -sf /dev/stdout /var/log/nginx/access.log \
+	&& ln -sf /dev/stderr /var/log/nginx/error.log
+
+copy ./conf/gzip_static.conf /etc/nginx/conf.d/web2py/gzip_static.conf
+copy ./conf/gzip.conf /etc/nginx/conf.d/web2py/gzip.conf
+copy ./sites/nginx_conf /etc/nginx/sites-enabled/web2py
+copy ./sites/nginx_conf /etc/nginx/sites-available/web2py
+
+copy ./conf/uwsgi.ini /etc/uwsgi/apps-enabled/web2py.ini
+copy ./conf/defs.py /etc/vidjil/defs.py
+copy ./conf/conf.js /etc/vidjil/conf.js
+copy ./scripts/nginx-entrypoint.sh /entrypoints/nginx-entrypoint.sh
+copy ./scripts/uwsgi-entrypoint.sh /entrypoints/uwsgi-entrypoint.sh
+run mkdir /usr/share/vidjil/server/web2py/applications/vidjil/databases && touch /usr/share/vidjil/server/web2py/applications/vidjil/databases/sql.log
+run adduser vidjil && usermod -aG sudo vidjil

docker/vidjil/conf/conf.js

+/* 
+ * Vidjil browser, main configuration file
+ * This file must be named 'js/conf.js' to be taken into account
+ * */
+
+var config = {
+
+    /* Used for the 'align' script 
+     * If this is not defined, the 'align' button is not available
+     */    
+    "cgi_address" : "http://localhost/cgi/", // Public test server
+    // "cgi_address" : "http://127.0.1.1/cgi-bin/",
+
+    /* The following options control how the user may have access to .vidjil files.
+     * Any combination of 1), 2) and 3) should work
+     */
+
+    /* 1) Patient database */
+    "use_database" : true,
+    "db_address" : "https://localhost/vidjil/", // Public test server
+    "login" : "",
+    "password" : "",
+
+    /* 2) and 3) Static files
+    /* - relative paths if Vidjil browser is online on the same server
+     * - absolute paths to a CORS active server only if browser is offline or on another server 
+     */
+
+    /* 2) Menu with a list of static files */
+    "file_menu" : {
+        "path" : "/browser/data/",
+        "file" : [
+            "Stanford-S22.vidjil",
+            "L2-LIL-2.vidjil"
+        ]
+    },
+    
+    /* 3) Static file autoload, possibly with an .analysis file */
+    "autoload" : "data/Stanford-S22.vidjil",
+    // "autoload_analysis" : "data/Stanford-S22.analysis"
+
+    // Proxy config for IMGT querying
+    "proxy": "http://localhost/proxy"
+}

docker/vidjil/conf/defs.py

+###
+### Vidjil server, main configuration file
+### This file must be named 'modules/defs.py' to be taken into account
+###