Specify 7

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
  • Table of Contents
• Installation
  • Installation with Docker
  • Ordinary installation
    • Installing system dependencies
    • Installing Specify 6
    • Cloning Specify 7 source repository
    • Setting up Python Virtual Environment
    • Building
    • Adjusting settings files
    • Turning on debugging
    • The development server
  • Deployment to production
    • Installing production requirements
    • Setting up Apache
    • Restarting Apache
• Updating Specify 7
• Updating the database (Specify 6) version

Installation

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

If you would like to deploy Specify 7 in a Docker container checkout the instructions in this repository: https://github.com/specify/specify7-docker

Ordinary installation

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

Building

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:

WARNING in ./bower_components/handsontable/dist/handsontable.full.js
Critical dependencies:
41:48-74 This seems to be a pre-built javascript file. Though this is
possible, it's not recommended. Try to require the original source to
get better results.
 @ ./bower_components/handsontable/dist/handsontable.full.js 41:48-74

WARNING in ./bower_components/handsontable/dist/handsontable.full.js
Critical dependencies:
47:38-65 This seems to be a pre-built javascript file. Though this is
possible, it's not recommended. Try to require the original source to
get better results.
 @ ./bower_components/handsontable/dist/handsontable.full.js 47:38-65

Other make targets:

make build

Runs all necessary build steps.

make frontend

Installs or updates Javascript dependencies and builds the Javascript modules only.

make clean

Removes all generated files.

The following targets require the virualenv to be activated:

make pip_requirements

Install or updates Python dependencies.

make django_migrations

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_NAME and MASTER_PASSWORD settings to the MySQL root user will allow the changes to be applied. Afterward, the master user settings can be restored.

make runserver

A shortcut for running the Django development server.

make webpack_watch

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

For development purposes, Django debugging should be turned on. It will enable stack traces in responses that encounter exceptions, and allow operation with the unoptimized Javascript files.

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 localhost:8000.

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:

• Apache
• 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

In the specify7 directory you will find the specifyweb_apache.conf file. Make a copy of the file as local_specifyweb_apache.conf and 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 local_specifyweb_apache.conf file.

sudo rm /etc/apache2/sites-enabled/000-default.conf
sudo ln -s `pwd`/specify7/local_specifyweb_apache.conf /etc/apache2/sites-enabled/

Restarting Apache

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:

0. Backup your Specify database using MySQL dump or the Specify backup and restore tool.

1. 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

2. Copy the settings from the existing to the new installation.

   cp specify7/specifyweb/settings/local* specify7-new-version/specifyweb/settings/

3. Make sure to update the THICK_CLIENT_LOCATION setting in local_specify_settings.py, if you are updating the Specify 6 version.

4. Create a new virtualenv for the new installation by following the Python Virtual Environment section for the new directory.

5. Build the new version of Specify 7.

6. Testing it out with the development server.

7. 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.