Specify 7

The Specify Collections Consortium is pleased to offer Specify 7, the web implementation of our biological collections data management platform.

We encourage members to use our Dockerized compositions of Specify 7. You can choose a version, make the necessary adjustments and then run a single command to get everything working. It is very simple and can be easily updated when new versions are released. Members can contact us at [email protected] to gain access to this repository.

The new generation of Specify combines the interface design components and data management foundation of Specify 6 with the efficiency and ease-of-use of web-based data access and cloud computing. Specify 7 uses the same interface layout language as Specify 6, so any user interface customization made in one platform is mirrored in the other. Also Specify 6 and Specify 7 use the same data model and can work from the same Specify MySQL or MariaDB database, which means 6 and 7 can be run simultaneously with any Specify collection. Specify 7 helps transition Specify 6 collections to cloud computing. It is also a great starting platform for institutions that prefer zero workstation software installation and ubiquitous web browser access.

Specify 7’s architecture supports collaborative digitization projects and remote hosting of specimen databases. Without the need for a local area or campus network to connect to the MySQL data server, Specify 7 gives you and your collaborators access to a shared specimen database through any web browser. Finding it challenging to obtain IT support to maintain a local secure database server? With the Specify 7 server software supported on generic Linux servers, museums can utilize a server hosting service to provide support for the technical complexities of systems administration, security management, and backing-up. Want to create a joint database for a collaborative digitizing effort? No problem! Host, hire a hosting service or use our Specify Cloud service for your Specify database, set up accounts and go. We provide the same efficient user interface, report and labels customization and help desk support for Specify 7 as we do for Specify 6.

Secure. Support for Single Sign-On (SSO) integrates Specify 7 with a campus or institutional identity providers. It supports all identity providers (IdPs) that have an OpenID endpoints.

The Security and Accounts tool allows administrators to give access based on roles and policies. Create, edit, and copy roles among collections and databases. Administrators can give users as many or few permissions as desired, from guest accounts to collection managers.

Accessible. It is important that web applications work for people with disabilities. Specify 7 is developed with this top of mind, not only meeting international accessibility standards but also providing a better experience for everyone.

Specify 7 is largely compliant with the main WWW accessibility standard – WCAG 2.1 (AA). It supports screen readers and allows each user to customize their color scheme and appearance as well as reduce motion and resize all elements.

This accessible design respects system and web browser preferences for date formats, language, theme, and animations.

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

Specify 7 Copyright © 2024 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
  • Changelog
• Installation
  • Docker Installation (Recommended)
    • Specify Collections Consortium (SCC) Members:
    • Non-Members:
  • Local Installation
    • Installing system dependencies
    • Installing Specify 6
    • Cloning Specify 7 source repository
    • Adjusting settings files
    • Setting up Python Virtual Environment
    • Building
      • make build
      • make frontend
      • make clean
      • make pip_requirements
      • make django_migrations
      • make runserver
      • make webpack_watch
    • Turning on debugging
    • The development server
    • The Specify 7 Worker
    • Installing production requirements
    • Setting up Apache
    • Restarting Apache
    • Nginx configuration
  • Updating Specify 7
  • Updating the database (Specify 6) version
  • Localizing Specify 7

Changelog

Changelog is available in CHANGELOG.md

Installation

We encourage all users to read our documentation on the Community Forum regarding installing and deploying Specify – Specify 7 Installation Instructions.

If you are an existing Specify 6 user who is looking to evaluate Specify 7, you can contact [email protected] along with a copy of your database and we can configure a temporary deployment for evaluation purposes.

Docker Installation (Recommended)

Specify Collections Consortium (SCC) Members:

We encourage members to use our Dockerized compositions of Specify 7. You can choose your desired version, make the necessary adjustments and then run a single command to get everything working. It is very simple and can be easily updated when new versions are released. Documentation for deploying Specify using Docker is available within the repository.

📨 Click here to request access or email [email protected] with your GitHub username, member institution or collection, and any additional questions you have for us.

Non-Members:

If your institution is not a member of the Specify Collections Consortium, you can follow the local installation instructions below or contact [email protected] to learn more about joining the SCC to receiving configuration assistance, support, and hosting services if you are interested.

Local 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).

Installing system dependencies

Specify 7 requires Python 3.8. Ubuntu 20.04 LTS is recommended. For other distributions these instructions will have to be adapted.

Ubuntu 20.04 LTS:

sudo apt install -y curl
curl -fsSL https://deb.nodesource.com/setup_20.x | sudo -E bash -
sudo apt-get -y install --no-install-recommends \
  build-essential \
  git \
  libldap2-dev \
  libmariadbclient-dev \
  libsasl2-dev \
  nodejs \
  python3-venv \
  python3.8 \
  python3.8-dev \
  redis \
  unzip

CentOS 7 / Red Hat 7:

yum install -y epel-release sudo wget
yum install -y \
  gcc make \
  git \
  openldap-devel \
  mariadb-devel \
  nodejs \
  npm \
  java-11-openjdk-headless \
  python36-virtualenv \
  python36 \
  python36u-devel \
  redis \
  unzip

Afterward, please make sure you have Node.js 20 installed:

node -v

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. A Java runtime is required to execute the Specify 6 installer, but is not needed to run Specify 7. It is possible to copy the Specify 6 install from another Linux system to avoid the need to install Java on the server.

wget https://update.specifysoftware.org/Specify_unix_64.sh
sh Specify_unix_64.sh -q -dir ./Specify6.8.03
sudo ln -s $(pwd)/Specify6.8.03 /opt/Specify

Cloning Specify 7 source repository

Clone this repository.

git clone https://github.com/specify/specify7.git

You will now have a specify7 directory containing the source tree.

Note, by default, git clone checks out the production branch of Specify 7. That branch contains the latest tested features and bug fixes. If you prefer a more stable release, you can switch to one of our tagged released.

cd specify7
git checkout tags/v7.8.6

Tagged releases are coming out every other week and undergo more testing.

See the list of tags to check what's the latest stable release.

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.

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.

python3.8 -m venv specify7/ve
specify7/ve/bin/pip install wheel
specify7/ve/bin/pip install --upgrade -r specify7/requirements.txt

Building

To build Specify 7 use the default make target.

cd specify7
source ve/bin/activate
make

Note, if source command is not available on your system, try running . ve/bin/activate instead

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.

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

NOTE: development server should only be run in debug mode. See previous section for instructions on how to turn on debugging.

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.

The Specify 7 Worker

Starting from version v7.6.0, the Specify WorkBench utilizes this dedicated worker process to handle the upload and validation operations.

Starting from version v7.9.0, the record merging functionality employs the worker to handle all record merging activities.

This worker process utilizes Celery, a job queue management system, with Redis serving as the broker.

The worker process can be started from the commandline by executing:

cd specify7
celery -A specifyweb worker -l INFO --concurrency=1

For deployment purposes it is recommended to configure a systemd unit to automatically start the Specify 7 worker process on system start up by executing the above command within the installation directory. It is possible to run Redis and worker process on a separate server and to provision multiple worker processes for high volume scenarios. Contact the Specify team about these use cases.

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

Ubuntu:

sudo apt-get install apache2 libapache2-mod-wsgi-py3

CentOS / Red Hat:

yum install httpd python3-mod_wsgi

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.

Ubuntu:

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

CentOS / Red Hat:

sudo ln -s $(pwd)/specify7/local_specifyweb_apache.conf /etc/httpd/conf.d/

Restarting Apache

After changing Apache's config files restart the service.

Ubuntu:

sudo systemctl restart apache2.service

CentOS / Red Hat:

sudo systemctl restart httpd.service

Nginx configuration

Specify 7 is web-server agnostic. Example nginx.conf (note, you would have to adjust the host names and enable HTTPs).

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 3.8 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 https://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. Update the system level dependencies by executing the apt-get command in the Installing system dependencies section.

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

6. Build the new version of Specify 7.

7. Test it out with the development server.

8. Deploy the new version by updating your Apache config to replace the old installation paths with the new ones and restarting Apache.

9. Configure the Specify 7 worker process to execute at system start up as described in The Specify 7 worker section.

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.

Localizing Specify 7

Specify 7 interface is localized to a few languages out of the box. We welcome contributions of new translations. We are using Weblate continuous localization platform. Instructions on how you can contribute