Alpheios Reader

This repository contains templates, xslt and css for the Alpheios Reader Interface, implemented as a plugin to https://github.com/Capitains/flask-capitains-nemo

Development Environment Setup using Docker

Prerequisites: Docker and Docker-Compose

Without Authentication Support

For Linux

git clone https://github.com/alpheios-project/alpheios_nemo_ui
cd alpheios_nemo_ui
./get_texts.sh
./docker-compose up

For Windows 10 (with WSL)

git clone https://github.com/alpheios-project/alpheios_nemo_ui
cd alpheios_nemo_ui
get_texts.bat
docker-compose up -d

Alpheios Reader flask application will be accessible at http://localhost:5000

With Authentication Support

Prerequisites: alpheios-protected-config repo must be a sibling to the alpheios_nemo_ui clone add dev.alpheios.net mapping for localhost to your /etc/hosts file

For Linux

git clone https://github.com/alpheios-project/alpheios_nemo_ui
cd alpheios_nemo_ui
./get_texts.sh
./setup_env.sh
./docker-compose up

For Windows 10 (with WSL)

git clone https://github.com/alpheios-project/alpheios_nemo_ui
cd alpheios_nemo_ui
get_texts.bat
setup_env.bat
docker-compose up -d

Alpheios Reader flask application will be accessible at http://dev.alpheios.net:5000

Updating Alpheios Embedded library and styles

currently this is a manual process -- needs to be improved upon

copy the distribution build of the alpheios embedded library js files to alpheios_nemo_ui/data/assets/js copy the distribution build of the alpheios embedded library css files to alpheios_nemo_ui/data/assets/css

rebuild the docker image using docker-compose up --build

Updating the CSS for the Reader

The scss source files for the reader are in alpheios_nemo_ui/data/assets/scss

They are a customization of the Bootstrap 4 css library

Build via

cd alpheios_nemo_ui/data/assets
npm install
npm update
npm run build

rebuild the docker image using docker-compose up --build

Updating the JS for the Reader

Production Environment (via Puppet)

The puppet files that are currently used for the production deployment of apheios_nemo_ui can be found at https://github.com/alpheios-project/puppet/tree/master/site-modules/capitains

Important points:

1. the flask application uses a filesystem and redis server to cache some data
2. the flask application itself is served via a gunicorn server behind the firewall
3. an apache server proxies access to the flask application routes and serves the assets (css and javascript) directly

Flask Application Caching

The flask application is configured to use a file system cache for textual data and a redis server to cache html fragments. Relevant lines from the production app.py:

http_cache = Cache(config={'CACHE_TYPE': "redis", "CACHE_REDIS_HOST": "localhost", "CACHE_DEFAULT_TIMEOUT": 0})
nautilus_cache = FileSystemCache("/tmp/ctscache", threshold=10000, default_timeout=28800)

The nautlius_cache caches the "pickled" python objects that represent the internal structures (i.e the MyCapytain data models) created by parsing the XML data files, to speed up retrieval of previously requested structures.

The http_cache contains fragments of specific html templates (used only where the templates specifically retrieve from thethe cache, as in the referenches.html template)

Gunicorn config

the flask application is run by a gunicorn server on port 5000

CONFIG = {
  'mode': 'wsgi',
  'environment': {
    'LANG': 'en_US.UTF-8',
    'LC_ALL': 'en_US.UTF-8',
    'PYTHONPATH': '/usr/local/capitains/venvs'
  },
  'working_dir': '/usr/local/capitains',
  'user': 'www-data',
  'group': 'www-data',
  'python': '/usr/local/capitains/venvs/bin/python',
  'args': (
    '--bind=localhost:5000',
    '--workers=5',
    '--timeout=30',

    '--log-level=error',
    'app:app',
  ),
}

Apache Config

An apache server provides a reverse proxy to the gunicorn server (currently only on port 80 but 443 must be added) apache also intercepts requests for assets.

# ************************************
# Vhost template in module puppetlabs-apache
# Managed by Puppet
# ************************************

<VirtualHost *:80>
  ServerName texts-beta.alpheios.net

  ## Vhost docroot
  DocumentRoot "/tmp/capitains"
  ## Alias declarations for resources outside the DocumentRoot
  Alias /assets/nemo.secondary/static "/usr/local/capitains/alpheios_nemo_ui/data/assets/images"
  Alias /assets/nemo.secondary "/usr/local/capitains/alpheios_nemo_ui/data/assets"

  ## Directories, there should at least be a declaration for /tmp/capitains

  <Directory "/tmp/capitains">
    Options Indexes FollowSymLinks MultiViews
    AllowOverride None
    Require all granted
  </Directory>

  ## Logging
  ErrorLog "/var/log/apache2/texts_error.log"
  ServerSignature Off
  CustomLog "/var/log/apache2/texts_access.log" combined

  ## Header rules
  ## as per http://httpd.apache.org/docs/2.2/mod/mod_headers.html#header
  Header set Access-Control-Allow-Origin '*'
  Header set Access-Control-Allow-Methods 'GET, POST, OPTIONS'

  ## Proxy rules
  ProxyRequests Off
  ProxyPreserveHost Off
  ProxyPass /assets !
  ProxyPassReverse /assets !
  ProxyPass /api/dts http://dts.alpheios.net/api/dts
  ProxyPassReverse /api/dts http://dts.alpheios.net/api/dts
  ProxyPass /api/dts/ http://dts.alpheios.net/api/dts/
  ProxyPassReverse /api/dts/ http://dts.alpheios.net/api/dts/
  ProxyPass / http://localhost:5000/
  ProxyPassReverse / http://localhost:5000/
</VirtualHost>

Other

Updates to the texts can be picked up by a cron job which runs the a script (puppet template for which is at https://github.com/alpheios-project/puppet/blob/master/site-modules/capitains/templates/update_capitains_repos.rb.erb)