The Specify Collections Consortium is funded by its member institutions. The Consortium web site is: http://wwww.specifysoftware.org
Specify 7 Copyright © 2020 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
- Specify 7
- Installation with Docker
- Ordinary installation
- Deployment to production
- Updating Specify 7
- Updating the database (Specify 6) version
After completing these instructions you will be able to run the test server and interact with the Django based Specify webapp in your browser on your local machine.
Instructions for deployment follow.
Note: If updating from a previous version, some of the python dependencies have changed. It is recommended to place the new version in a separate directory next to the previous version and install all the new dependencies in a Python virtualenv as described below. That will avoid version conflicts and allow the previous version to continue working while the new version is being set up. When the new version is working satisfactorily using the test server, the Apache conf can be changed to point to it (or changed back to the old version, if problems arise).
Installation with Docker
Installing system dependencies
Specify 7 requires Python 3.6. Ubuntu 18.04 LTS is recommended. For other distributions these instructions will have to be adapted.
sudo apt-get -y install --no-install-recommends \ build-essential \ git \ libldap2-dev \ libmariadbclient-dev \ libsasl2-dev \ nodejs \ npm \ openjdk-11-jre-headless \ python3-venv \ python3.6 \ python3.6-dev \ unzip
Installing Specify 6
A copy of the most recent Specify 6 release is required on the server as Specify 7 makes use of resource files. Specify 6 code is also executed by the server for Workbench validation and uploads.
wget http://update.specifysoftware.org/6800/Specify_unix_64.sh sh Specify_unix_64.sh -q -dir ./Specify6.8.0 sudo ln -s $(pwd)/Specify6.8.0 /opt/Specify
Cloning Specify 7 source repository
Clone this repository.
git clone git://github.com/specify/specify7.git
You will now have a specify7 directory containing the source tree.
Setting up Python Virtual Environment
Using a Python virtual environment will avoid version conflicts with other Python libraries on your system. Also, it avoids having to use a superuser account to install the Python dependencies.
python3.6 -m venv specify7/ve specify7/ve/bin/pip install -r specify7/requirements.txt
To build Specify 7 use the default make target.
cd specify7 make
When building the frontend, Webpack will issue the following warnings that can be safely ignored:
Other make targets:
Runs all necessary build steps.
Removes all generated files.
The following targets require the virualenv to be activated:
Install or updates Python dependencies.
Applies Specify schema changes to the database named in the
settings. This step may fail if the master user configured in the
settings does not have DDL privileges. Changing the
MASTER_PASSWORD settings to the MySQL root user will allow the
changes to be applied. Afterward, the master user settings can be
A shortcut for running the Django development server.
Run webpack in watch mode so that changes to the frontend source code will be automatically compiled. Useful during the development process.
Adjusting settings files
In the directory
specify7/specifyweb/settings you will find the
specify_settings.py file. Make a copy of this file as
local_specify_settings.py and edit it. The file contains comments
explaining the various settings.
Turning on debugging
Debugging can be enabled by creating the file
specify7/specifyweb/settings/debug.py with the contents,
DEBUG = True.
The development server
Specify7 can be run using the Django development server.
cd specify7 source ve/bin/activate make runserver
This will start a development server for testing purposes on
When the server starts up, it will issue a warning that some migrations have not been applied:
You have 11 unapplied migration(s). Your project may not work properly until you apply the migrations for app(s): auth, contenttypes, sessions. Run 'python manage.py migrate' to apply them.
Specify 7 makes use of functions from the listed Django apps (auth,
contenttypes, and sessions) but does not need the corresponding tables
to be added to the database. Running
make django_migrations will
apply only those migrations needed for Specify 7 to operate.
Deployment to production
Start by following the development instructions above, but don't enable debugging (or disable it if you enabled it previously).
Installing production requirements
For production environments, Specify7 can be hosted by Apache. The following packages are needed:
- mod-wsgi to connect Python to Apache
sudo apt-get install apache2 libapache2-mod-wsgi-py3
Warning: This will replace the Python 2.7 version of mod-wsgi that was used by Specify 7.4.0 and prior. If executed on a production server running one of those versions, Specify 7 will stop working until the new deployment is configured.
Setting up Apache
specify7 directory you will find the
file. Make a copy of the file as
edit the contents to reflect the location of Specify6 and Specify7 on
your system. There are comments showing what to change.
Then remove the default Apache welcome page and make a link to your
sudo rm /etc/apache2/sites-enabled/000-default.conf sudo ln -s `pwd`/specify7/local_specifyweb_apache.conf /etc/apache2/sites-enabled/
After changing Apache's config files restart the service.
sudo systemctl restart apache2.service
Updating Specify 7
Specify 7.4.0 and prior versions were based on Python 2.7. If updating
from one of these versions, it will be necessary to install Python 3.6
by running the
apt-get commands in the
Install system dependencies and the
Production requirements steps. Then
proceed as follows:
Backup your Specify database using MySQL dump or the Specify backup and restore tool.
Clone or download a new copy of this repository in a directory next to your existing installation.
git clone git://github.com/specify/specify7.git specify7-new-version
Copy the settings from the existing to the new installation.
cp specify7/specifyweb/settings/local* specify7-new-version/specifyweb/settings/
Make sure to update the
local_specify_settings.py, if you are updating the Specify 6 version.
Create a new virtualenv for the new installation by following the Python Virtual Environment section for the new directory.
Build the new version of Specify 7.
Testing it out with the development server.
Deploy the new version by updating your Apache config to replace the old installation paths with the new ones and restarting Apache.
Updating the database (Specify 6) version
The Specify database is updated from one version to the next by the Specify 6 application. To update the database version connect to the database with a new version of Specify 6 and follow the Specify 6 update procedures.
Once the database version is updated, a corresponding copy of Specify 6 must be provided to the Specify 7 server by repeating the Installing Specify 6 section of this guide for the new version of Specify 6.