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Web Asset Server

This is a sample attachment server implementation for Specify. This implementation is targetted at Ubuntu flavors, but will work with minor modifications on other Linux systems. It is not expected to work without extensive adaptation on Windows systems.

The Specify Collections Consortium is funded by its member institutions. The Consortium web site is: http://www.specifysoftware.org

Web Asset Server Copyright © 2021 Specify Collections Consortium. Specify comes with ABSOLUTELY NO WARRANTY. This is free software licensed under GNU General Public License 2 (GPL2).

Specify Collections Consortium
Biodiversity Institute
University of Kansas
1345 Jayhawk Blvd.
Lawrence, KS 66045 USA

Table of Contents

Installation

Docker

Docker in the preferred installation method for Web Asset Server.

Example docker-compose.yml is provided:

version: '3.7'
services:

  asset-server:
    restart: unless-stopped
    image: specifyconsortium/specify-asset-service
    init: true
    volumes:
      # Store all attachments outside the container, in a separate
      # volume
      - "attachments:/home/specify/attachments"
    environment:
      # Replace this with the URL at which asset server would be
      # publicly available
      - SERVER_NAME=host.docker.internal
      - SERVER_PORT=80
      - ATTACHMENT_KEY=your asset server access key
      - DEBUG_MODE=false

volumes:
  attachments: # the asset-servers attachment files

For production use, it's recommended to also add an nginx web server between the web asset server and the outside world. Example nginx.conf and docker-compose.yml.

For development/evaluation, web asset server can be exposed directly. To do so, add the following lines to your docker-compose.yml right after the asset-server: line:

    ports:
      - "8080:3306"

Installing system dependencies

The dependencies are:

  1. Python 3.6 is known to work. (2.6 and 2.7 is available with modifications).
  2. ExifRead for EXIF metadata.
  3. sh the Python shell command utility.
  4. bottlepy the Python web micro-framework.
  5. ImageMagick for thumbnailing.
  6. Ghostscript for PDF thumbnailing.
  7. Paste Python web server.

To install dependencies the following commands work on Ubuntu:

sudo apt-get -y install --no-install-recommends \
  python-pip \
  imagemagick \
  ghostscript
sudo pip install -r requirements.txt

Cloning Web Asset Server source repository

Clone this repository.

git clone git://github.com/specify/web-asset-server.git

Deployment

Adjust the settings in the settings.py in your working directory. Then run the server with the following command:

python server.py

In my experience, it has been easiest to deploy using the Python Paste server.

In settings.py set the value SERVER = 'paste'.

To run the server on a privileged port, e.g. 80, the utility authbind is recommended.

sudo apt-get install authbind

Assuming you are logged in as the user that will be used to run the server process, the following commands will tell authbind to allow port 80 to be used:

touch 80
chmod u+x 80
sudo mv 80 /etc/authbind/byport

An upstart script or systemd unit file can be created to make sure the web asset server is started automatically.

It is important that the working directory is set to the path containing server.py so that bottle.py can find the template files. See “TEMPLATE NOT FOUND” IN MOD_WSGI/MOD_PYTHON.

Note: Some users have reported that authbind must be provided with the --deep option. If the asset server is failing to start due to permission problems, this may be a solution.

Upstart

Create the file /etc/init/web-asset-server.conf with the following contents, adjusting the setuid user and directories as appropriate:

description "Specify Web Asset Server"
author "Ben Anhalt <anhalt@ku.edu>"

start on runlevel [234]
stop on runlevel [0156]

setuid anhalt

chdir /home/anhalt/web-asset-server
exec /usr/bin/authbind /usr/bin/python /home/anhalt/web-asset-server/server.py
respawn

Then reload the init config files and start the server:

sudo initctl reload-configuration
sudo start web-asset-server

By default, the server's logs go to standard output which upstart will redirect to /var/log/upstart/web-asset-server.log

Systemd

Create the file /etc/systemd/system/web-asset-server.conf with the following contents, adjusting the usernames and paths as appropriate:

[Unit]
Description=Specify Web Asset Server
Wants=network.target

[Service]
User=specify
WorkingDirectory=/home/specify/web-asset-server
ExecStart=/usr/bin/authbind /usr/bin/python /home/specify/web-asset-server/server.py

Tell Systemd to reload its config with

sudo systemctl daemon-reload

HTTPS

The easiest way to add HTTPS support, which is necessary to use the asset server with a Specify 7 server that is using HTTPS, is to place the asset server behind a reverse proxy such as Nginx. This also makes it possible to forego authbind and run the asset server on an unprivileged port. The proxy must be configured to rewrite the web_asset_store.xml resource to adjust the links therein. An example configuration can be found in this gist.

Specify 6 Settings

You will generally want to add the asset server settings to the global Specify preferences so that all of the Specify clients obtain the same configuration.

The easiest way to do this is to open the database in Specify and navigate to the About option in the help menu.

About Specify

In the resulting dialog double-click on the division name under System Information on the right hand side. This will open a properties editor for the global preferences.

You will need to set four properties to configure access to the asset server:

  • USE_GLOBAL_PREFS - true
  • attachment.key – ##
    • Replace ## with the key from the following location:
      • obtain from asset server settings.py file if you have a local installation of 7
      • obtain from docker-compose.yml file if you use a Docker deployment
  • attachment.url http://[YOUR_SERVER]/web_asset_store.xml
  • attachment.use_path false

If these properties do not already exist, they can be added using the Add Property button.

Specify 7 Settings

If you are using the Docker deployment method, you need to make sure that the attachment.key and attachment.url match the configuration in Specify 6.

For both the specify7 and specify7-worker sections, you need to make sure that:

  • attachment.key = ASSET_SERVER_KEY
  • attachment.url = ASSET_SERVER_URL
  specify7:
    restart: unless-stopped
    image: specifyconsortium/specify7-service:v7
    init: true
    volumes:
      - "specify6:/opt/Specify:ro"
      - "static-files:/volumes/static-files"
    environment:
      - DATABASE_HOST=mariadb
      - DATABASE_PORT=3306
      - DATABASE_NAME=specify
      - MASTER_NAME=master
      - MASTER_PASSWORD=master
      - SECRET_KEY=change this to some unique random string
      - ASSET_SERVER_URL=http://host.docker.internal/web_asset_store.xml
      - ASSET_SERVER_KEY=your asset server access key
      - REPORT_RUNNER_HOST=report-runner
      - REPORT_RUNNER_PORT=8080
      - CELERY_BROKER_URL=redis://redis/0
      - CELERY_RESULT_BACKEND=redis://redis/1
      - LOG_LEVEL=WARNING
      - SP7_DEBUG=false

If you are using a local installation, in the settings.py file, you need to make sure that:

  • attachment.key = WEB_ATTACHMENT_KEY
  • attachment.url = WEB_ATTACHMENT_URL
# The Specify web attachment server URL.
WEB_ATTACHMENT_URL = None

# The Specify web attachment server key.
WEB_ATTACHMENT_KEY = None

Compatibility with older versions of Python