Upgrading SEEK

If you have an existing SEEK installation, and you haven’t done so already, please take a moment to fill out our very short,optional SEEK Registration Form. Doing so will be very useful to us in the future when we try and raise further funding to develop and support SEEK and the associated tools.

Always backup your SEEK data before starting to upgrade!! - see the Backup Guide.

You should always upgrade between minor (1.X) versions incrementally, i.e:

1.12.x –> 1.13.x –> 1.14.x –> 1.15.x,

rather than jumping directly between versions otherwise some upgrade steps may be missed.

This guide assumes that SEEK has been installed following the Installation Guide. It assumes it is a production server that is being updated, and that commands are run from the root directory of the SEEK application.

Identifying your version

The version of SEEK you are running is shown at the bottom left, within the footer, when viewing pages in SEEK.

You can also tell which version you have installed by looking at the config/version.yml file, so for example version 0.13.2 looks something like:

major: 0
minor: 13
patch: 2

Upgrading between patch versions (e.g. between 1.14.0 and 1.14.1)

When upgrading between patch versions, it should only be necessary to run

bundle install
bundle exec rake seek:upgrade 

Steps to upgrade from 1.14.x to 1.15.x

Set RAILS_ENV

If upgrading a production instance of SEEK, remember to set the RAILS_ENV first

export RAILS_ENV=production

Stopping services before upgrading

bundle exec rake seek:workers:stop 

Getting the upgrade

The steps to fetch the upgrade will be different depending on whether it was originally installed directly from Github or via a downloaded tarball.

Updating from GitHub

If you have an existing installation linked to our GitHub, you can fetch the files with:

git fetch
git checkout v1.15.0

Updating using the tarball

You can download the file from https://github.com/seek4science/seek/archive/v1.15.0.tar.gz You can unpack this file using:

tar zxvf seek-1.15.0.tar.gz
mv seek seek-previous
mv seek-1.15.0 seek
cd seek/

and then copy across your existing filestore and database configuration file from your previous installation and continue with the upgrade steps. The database configuration file you would need to copy is config/database.yml, and the filestore is simply filestore/

Install Python dependencies

First, a specific version of setuptools needs to be installed to avoid an issue when installing dependencies

python3.9 -m pip install setuptools==58

Then the other dependencies can be installed

python3.9 -m pip install -r requirements.txt

Upgrading Ruby

It is necessary to upgrade to Ruby 3.1.4. If you are using RVM (according to the Installation Guide )you should be prompted to install during the standard installation steps that follow. If you are not prompted you can install with the command:

rvm install $(cat .ruby-version)

Doing the upgrade

After updating the files, the following steps will update the database, gems, and other necessary changes. Note that seek:upgrade may take longer than usual if you have data stored that points to remote content.

Please note - during the upgrade the step Updating session store can take a long time and appear that it has frozen, so please be patient.

cd . # this is to allow RVM to set the correct ruby version
gem install bundler
bundle install
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while

Update Cron Services

SEEK requires some cron jobs for periodic background jobs to run. To update these run:

bundle exec whenever --update-crontab

Restarting background job services

bundle exec rake seek:workers:start

Final notes

If you encounter any problems with stringio, particularly when running with Passenger, just manually installing the gem with the explicit version as follows should fix it

 gem install stringio --version 3.0.1.1

Setting PassengerPreloadBundler to on may also fix the problem.


Earlier upgrade notes

For details of how to upgrade between earlier versions please visit Upgrades between earlier versions