.. _linux-install:

=======================
 Installation on Linux
=======================

This chapter describes how to install the CBGM application on a linux server.
If you want to run the application on a desktop machine an
:ref:`installation with Docker <docker-install>` might be the easier way to go.


Install Prerequisites
=====================

The application should run as a user that has no special privileges.

.. warning::

   Do not run the application as a user with administrative rights.

As a user with admin privileges do:

1. Create user *ntg*

   .. code-block:: shell

      sudo useradd -m -d /home/ntg -s /bin/bash -U ntg
      sudo passwd ntg

2. Install the software:

   .. code-block:: shell

      sudo apt-get update
      sudo apt-get install git make
      sudo -u ntg bash

      mkdir -p ~/prj/ntg
      cd !!$
      git clone https://github.com/cceh/ntg
      cd ntg
      exit

      sudo bash
      cd ~ntg/prj/ntg/ntg/
      make install-prerequisites


.. _database-access:

Database Access
===============


MySQL database
--------------

1. Edit (or create) your :file:`~/.my.cnf` and add this section:

   .. code-block:: ini

       [mysql]
       host="localhost"
       user="<username>"
       password="<password>"
       default-character-set="utf8"

   Replace *<username>* and *<password>* with your own MySQL username and password.

   .. warning::

      Make sure :file:`~/.my.cnf` is readable only by yourself!

2. Create databases for ECM, Leitzeile and VarGenAtt:

   .. code-block:: shell

      sudo mysql -e "CREATE DATABASE ECM_ActsPh4"
      sudo mysql -e "CREATE DATABASE Nestle29"
      sudo mysql -e "CREATE DATABASE VarGenAtt_ActPh4"



Postgres database
-----------------

0. Make sure you have the following lines in :file:`pg_hba.conf` so you can
   connect to postgres using password identification.

   .. code-block:: none

      # IPv4 local connections:
      host    all             all             127.0.0.1/32            md5
      # IPv6 local connections:
      host    all             all             ::1/128                 md5


1. Create a postgres user and a foreign data wrapper for MySQL.  The FDW allows
   Postgres to access the MySQL databases.

   Login as administrative user and say:

   .. code-block:: shell

      sudo -u postgres psql

   .. code-block:: psql

      CREATE USER ntg CREATEDB PASSWORD '<password>';
      CREATE DATABASE ntg_user OWNER ntg;
      \q

   Replace <password> with a real password.

   .. code-block:: bash

      sudo -u postgres ~ntg/prj/ntg/ntg/scripts/cceh/create_database.sh acts_ph4

   Logout.

2. Edit (or create) your :file:`~/.pgpass` and add this line:

   Login as user *ntg* and say:

   .. code-block:: none

      localhost:5432:*:ntg:<password>

   .. warning::

      Make sure :file:`~/.pgpass` is readable only by yourself!

   .. note::

      You can now login to the Postgres database as user ntg without having
      to enter your password:

      .. code-block:: bash

         psql acts_ph4

   Logout.


Application server
==================

1. Configure the global settings for the application server.  This configures
   the user management database that holds user credentials and the sending of
   confirmation mails.

   Login as user *ntg* and edit (or create) your :file:`server/instance/_global.conf`

   .. code-block:: ini

      APPLICATION_NAME    = "Root"
      APPLICATION_ROOT    = "/"
      SESSION_COOKIE_PATH = "/"
      SECRET_KEY          = "<a long random string>"

      PGHOST="localhost"
      PGPORT="5432"
      PGDATABASE="ntg_user"
      PGUSER="ntg"

      USER_PASSWORD_HASH="pbkdf2_sha512"
      USER_PASSWORD_SALT="<a random string>"

      MAIL_SERVER  = "smtp.domain.tld"
      MAIL_PORT    = 25
      MAIL_USE_TLS = True
      MAIL_DEFAULT_SENDER = "ntg appserver <noreply@domain.tld>"


2. Configure the CBGM database or databases.  Create one .conf file per
   database, the name of the file may be chosen at will but should not start
   with an underscore.

   The APPLICATION_ROOT is the root of the url.  It must have two segments and
   must be different for each database.

   Edit (or create) your :file:`server/instance/acts_ph4.conf`

   .. code-block:: ini

      APPLICATION_NAME="Acts Phase 4"
      APPLICATION_ROOT="/acts/ph4"
      BOOK="Acts"

      PGHOST="localhost"
      PGPORT="5432"
      PGDATABASE="acts_ph4"
      PGUSER="ntg"

      MYSQL_CONF="~/.my.cnf"
      MYSQL_GROUP="mysql"

      MYSQL_ECM_DB="ECM_ActsPh4"
      MYSQL_ATT_TABLES="Acts{n}GVZ"
      MYSQL_LAC_TABLES="Acts{n}GVZlac"

      MYSQL_VG_DB="VarGenAtt_ActPh4"
      MYSQL_LOCSTEM_TABLES="LocStemEdAct{n}"
      MYSQL_RDG_TABLES="RdgAct{n}"
      MYSQL_VAR_TABLES="VarGenAttAct{n}"
      MYSQL_MEMO_TABLE="Memo"

      MYSQL_NESTLE_DB="Nestle29"


3. Initialize the user management database and add an administrator user for the
   application server.  You'll need this user to login in the browser.

   .. note::

      This should not be the same username (and password) as the database user
      above!

   .. code-block:: shell

      python3 -m scripts.cceh.mk_users -e <email> -u <username> -p <password> server/instance/_globals.conf


CBGM
====

1. Get the mysql database dumps from Münster (exercise left to the reader) and
   import them into mysql:

   .. code-block:: shell

      mysql -D "ECM_ActsPh4"      < ECM_ActsPh4.dump
      mysql -D "VarGenAtt_ActPh4" < VarGenAtt_ActPh4.dump
      mysql -D "Nestle29"         < Nestle29.dump

2. Import the databases into postgres:

   .. code-block:: shell

      python3 -m scripts.cceh.import -vvv server/instance/acts_ph4.conf
      python3 -m scripts.cceh.prepare -vvv server/instance/acts_ph4.conf

3. Run the CBGM process once.

   .. code-block:: shell

      python3 -m scripts.cceh.cbgm -vvv server/instance/acts_ph4.conf

4. Setup cron to run the CBGM nightly:

   This step is optional.  You may also run the cbgm script manually whenever
   you need it.

   Edit your user crontab

   .. code-block:: shell

      crontab -e

   and put these lines into it:

   .. code-block:: shell

      MAILTO=user@example.com

      13 02 * * * cd /home/ntg/prj/ntg/ntg && scripts/cceh/update_cbgm



Run Server
==========

1. Run the application server:

   .. code-block:: shell

      make server


Build and run client
====================

1. Build and run the client

   .. code-block:: shell

      cd client
      npm install
      cd ..
      make dev-server

Point your browser to http://localhost:5000/acts/ph4/