Sample attachment server implementation for Specify.
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README.md

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.

Dependencies

The dependencies are:

  1. Python 2.7 is known to work. (see below for Python 2.6)
  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

Bottle is included in the distribution. To install the other dependencies the following commands work on Ubuntu:

sudo apt-get install python-pip imagemagick ghostscript
sudo pip install -r requirements.txt

Installing

It is easiest just to clone this repository.

Running the development server

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

python server.py

Deploying

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 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. 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 obtain from asset server settings.py file
  • 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.

Python 2.6 compatibility

The following information is courtesy of David Konrad of The Natural History Museum of Denmark:

It is possible to install the Attachment Server on a SuSe Enterprise 11 SP3 with python 2.6.8.

  • python-pip should be installed manually from RPM, v1.2.1 only version that works without conflict / break
  • python-exif should be installed manually from PRM
  • OrderedDict needs a "backport" -> https://pypi.python.org/pypi/ordereddict

changes in server.py :

try:
    from collections import OrderedDict
except ImportError:
    # python 2.6 or earlier, use backport
    from ordereddict import OrderedDict

changes in settings.py :

#CAN_THUMBNAIL = {'image/jpeg', 'image/gif', 'image/png', 'image/tiff', 'application/pdf'}
CAN_THUMBNAIL = ['image/jpeg', 'image/gif', 'image/png', 'image/tiff', 'application/pdf']