.. _server:
.. highlight:: bash

=======================
Setting up a web-server
=======================

The CMR web-pages
=================

Use the ``python3 -m cmr.cli build-web-page`` command.

This will create a new compressed tar-file ``cmr-web-page.tar.gz``.
The tar-file contains static HTML
and can be copied to a web-server and unpacked there.


The CMR database server
=======================

The following should be done as the ``cmr`` user on the machine running the
PostgreSQL server (``fysik-cmr01``).

Get the code::

    $ cd
    $ git clone https://gitlab.com/ase/ase.git
    $ git clone https://gitlab.com/asr-dev/asr.git
    $ git clone https://gitlab.com/camd/cmr.git

and install it::

    $ python3 -m pip install -e ase/ --user
    $ python3 -m pip install -e asr/ --user
    $ python3 -m pip install -e cmr/ --user

Create these folders::

    $ mkdir data uwsgi

Install ``psycopg2`` and ``uwsgi``::

    $ python3 -m pip install --user psycopg2-binary uwsgi

Create a secret password and add the following to ``~/.bash_profile``::

    export CMR_URL=postgresql://ase:password@localhost:5432
    export CMR_TMPDIR=~/uwsgi/static/
    export PATH=$PATH:~/.local/bin

Log in as the ``postgres`` user and run the ``psql`` command
(or do ``sudo -u postgres psql``).  Create the ``ase`` user and the
databases::

    $ psql
    postgres=# create user ase login password 'password';
    postgres=# create database c2db;
    postgres=# create database oqmd12;
    ...
    ...

See the ``~/cmr/cmrconf.py`` script for how to do this for all the databases.

.. note::

   You may also need to edit ``/var/lib/pgsql/data/pg_hba.conf``::

     host    all     all     127.0.0.1/32       password
     host    all     all     ::1/128            password

   and restart postgres.

From Niflheim, copy all the SQLite database files and static files
(stored in ``/home/camd/jensj/CMR-backup/``) to the PostgreSQL server::

    $ scp *.db *.tar.gz cmr@fysik-cmr01:data/

On the PostgreSQL server, insert the SQLite databases into the PostgreSQL
database::

    $ cd data
    $ ase -T db c2db.db -i postgresql://ase:password@localhost:5432/c2db
    ...
    ...

Again, see the ``~/cmr/cmrconf.py`` script for how to automate this.

Start creating the static files::

    $ python3 -m cmr.robot
    ...
    ...

Install the ``jsmol`` code::

    $ cd
    $ tar -xf data/jsmol.tar.gz
    $ cd ase/ase/db/static
    $ ln -s ~/jsmol

Add this line to ``crontab``::

  PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/cmr/.local/bin
  CMR_URL=postgresql://ase:cmr3000@localhost:5432
  CMR_TMPDIR=/home/cmr/uwsgi/static/
  MPLBACKEND=agg

  UWSGI="uwsgi /home/cmr/cmr/uwsgi.ini
   --daemonize=/home/cmr/uwsgi/uwsgi.log
   --buffer-size=32768"
  @reboot . ~/.bashrc && $UWSGI && wget localhost:8000

and reboot.


Checking that things are OK
---------------------------

Check that things are OK with something like this in a crontab::

    def check_cmr_db():
        print('checking CMR database')
        with urlopen('https://cmrdb.fysik.dtu.dk/catapp/json/6') as fd:
            json = fd.read().decode()
        atoms = ase.db.connect(io.StringIO(json), 'json').get_atoms()
        formula = atoms.get_chemical_formula()
        assert formula == 'Ag3Hg'


Updating the databases
----------------------

As the ``postgres`` user, drop and create the database::

    $ psql
    postgres=# drop database c2db;
    postgres=# create database c2db;

Insert new data::

    $ cd ~/data
    $ ase -T db c2db.db -i postgresql://ase:password@localhost:5432/c2db

and create new static files::

    $ cd ~/uwsgi
    $ rm static/c2db/*
    $ python3 -m cmr.robot

Update ASE and CMR code::

    $ cd ~/ase
    $ git pull
    $ cd ~/asr
    $ git pull
    $ cd ~/cmr
    $ git pull

Then restart::

    $ killall uwsgi
    $ uwsgi ~/cmr/uwsgi.ini --daemonize=$HOME/uwsgi/uwsgi.log
    $ wget localhost:8000


More information
----------------

https://intra4.fysik.dtu.dk/it/PostgreSQL-databases