If upgrading from a version earlier than v0.11.x please contact us.

Also if upgrading from a Mercurial based SEEK to our Git one, please contact us. Mercurial versions of SEEK are only available up to v0.21.

You can find details on how to contact us at the Contact Page

When upgrading between versions greater than v0.11.x you need to upgrade to each released minor version in order incrementally (i.e. 0.13.x -> 0.14.x -> 0.15.x -> 0.16.x, you can skip patch versions such as 0.13.3).

Each version has a tag, which has the format of v prefix followed by the version - e.g. v0.11.1, v0.13.2, v0.17.1

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 v1.15.2

Updating using the tarball

You can download the file from https://github.com/seek4science/seek/archive/v1.15.2.tar.gz You can unpack this file using:

tar zxvf seek-1.15.2.tar.gz
mv seek seek-previous
mv seek-1.15.2 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 loading gems (likely stringio or strscan) when running with Passenger, add the following to your Apache configuration:

 PassengerPreloadBundler on

more details at PassengerPreloadBundler

If using Nginx, the setting is

 passenger_preload_bundler on;

more details at passenger_preload_bundler

Steps to upgrade from 1.13.x to 1.14.x

Dependencies

You will need to update Python to version 3.9

sudo apt install python3.9-dev python3.9-distutils

you may remove 3.7 unless it is used for other applications. If unsure there is no harm leaving it installed

sudo apt remove python3.7-dev python3.7-distutils

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 pull
git checkout v1.14.2

Updating using the tarball

You can download the file from https://github.com/seek4science/seek/archive/v1.14.2.tar.gz You can unpack this file using:

tar zxvf seek-1.14.2.tar.gz
mv seek seek-previous
mv seek-1.14.2 seek
cd seek/

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

rvm install $(cat .ruby-version)

Doing the upgrade

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 pick up the ruby and gemset changes
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

Steps to upgrade from 1.12.x to 1.13.x

Dependencies

Graphviz, and Python 3.7 are new required dependencies

First add a repo which contains python versions that may not be available in the default repositories

sudo apt update
sudo apt install software-properties-common
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt update

and now install the packages:

sudo apt install graphviz python3.7-dev python3.7-distutils python3-pip

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

Updating from GitHub

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

git pull
git checkout v1.13.4

Updating using the tarball

You can download the file from https://github.com/seek4science/seek/archive/v1.13.4.tar.gz You can unpack this file using:

tar zxvf seek-1.13.4.tar.gz
mv seek seek-previous
mv seek-1.13.4 seek
cd seek/

Install Python dependencies

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

python3.7 -m pip install setuptools==58

Then the other dependencies can be installed

python3.7 -m pip install -r requirements.txt

Upgrading Ruby

You are recommended to upgrade to Ruby 2.7.8 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

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 pick up the ruby and gemset changes
gem install bundler
bundle install --deployment --without development test
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

Steps to upgrade from 1.11.x to 1.12.x

Note the requirement to setup Apache Solr, which is no longer bundled together with FAIRDOM-SEEK.

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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.12.3

Updating using the tarball

You can download the file from https://github.com/seek4science/seek/archive/v1.12.3.tar.gz You can unpack this file using:

tar zxvf seek-1.12.3.tar.gz
mv seek seek-previous
mv seek-1.12.3 seek
cd seek/

Upgrading Ruby

You are recommended to upgrade to Ruby 2.7. 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

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 pick up the ruby and gemset changes
gem install bundler
bundle install --deployment --without development test
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

Setting up Apache Solr

The Apache Solr Search Engine now needs to be set up separately. It is relatively straightforward and there are instructions on how to do this in Setting Up Solr.

Restarting background job services

bundle exec rake seek:workers:start

Stopping soffice

From version 1.12.0 it is no longer necessary to run soffice as a service. If you had previously set up the /etc/init.d/soffice service, you now stop and remove this (the soffice executable from LibreOffice is still required though).

Steps to upgrade from 1.10.x to 1.11.x

Upgrading Ruby

You will need to upgrade Ruby to Ruby 2.6.6. 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 ruby-2.6.6

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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.11.3

Updating using the tarball

You can download the file from https://github.com/seek4science/seek/archive/v1.11.3.tar.gz You can unpack this file using:

tar zxvf seek-1.11.3.tar.gz
mv seek seek-previous
mv seek-1.11.3 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Doing the upgrade

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 pick up the ruby and gemset changes
gem install bundler
bundle install --deployment --without development test
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while       

Setup Cron Services

This version includes an update to ActiveJob and requires some cron jobs for periodic background jobs to run. To set these up run:

bundle exec whenever --update-crontab

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start                

bundle exec rake tmp:clear  

Steps to upgrade from 1.9.x to 1.10.x

Upgrading Ruby

You will need to upgrade Ruby to Ruby 2.4.10. 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 ruby-2.4.10

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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.10.3

Updating using the tarball

You can download the file from https://github.com/seek4science/seek/archive/v1.10.3.tar.gz You can unpack this file using:

tar zxvf seek-1.10.3.tar.gz
mv seek seek-previous
mv seek-1.10.3 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Doing the upgrade

cd . #this is to allow RVM to pick up the ruby and gemset changes
gem install bundler
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while       

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start                

bundle exec rake tmp:clear         

Steps to upgrade from 1.8.x to 1.9.x

Upgrading Ruby

You will need to upgrade Ruby to Ruby 2.4.9. 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 ruby-2.4.9

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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.9.1

Updating using the tarball

You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.9.1.tar.gz You can unpack this file using:

tar zxvf seek-1.9.1.tar.gz
mv seek seek-previous
mv seek-1.9.1 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Doing the upgrade

cd . #this is to allow RVM to pick up the ruby and gemset changes
gem install bundler
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while       

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start                

bundle exec rake tmp:clear

Steps to upgrade from 1.7.x to 1.8.x

Upgrading Ruby

You will need to upgrade Ruby to Ruby 2.4.5. 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 ruby-2.4.5

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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.8.3

Updating using the tarball

You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.8.3.tar.gz You can unpack this file using:

tar zxvf seek-1.8.3.tar.gz
mv seek seek-previous
mv seek-1.8.3 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Doing the upgrade

cd . #this is to allow RVM to pick up the ruby and gemset changes
gem install bundler
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while       

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start                

bundle exec rake tmp:clear

Steps to upgrade from 1.6.x to 1.7.x

Upgrading Ruby

You will need to upgrade Ruby to Ruby 2.4.4. 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 ruby-2.4.4

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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.7.1

Updating using the tarball

You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.7.1.tar.gz You can unpack this file using:

tar zxvf seek-1.7.1.tar.gz
mv seek seek-previous
mv seek-1.7.1 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Doing the upgrade

cd . #this is to allow RVM to pick up the ruby and gemset changes
gem install bundler
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while       

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start                

touch tmp/restart.txt
bundle exec rake tmp:clear

Steps to upgrade from 1.5.x to 1.6.x

Updating Java

This version requires at least Java 8. Please make sure this is installed by trying:

java --version

which should report java version 1.8.0 or greater. If not, install with:

sudo apt install openjdk-8-jdk
java --version

if this still doesn’t report the correct version you may need to do:

sudo update-alternatives --config java

.. and select the java-8 version

You can also use the Oracle version of Java 8. This can be easily installed with Apt, through the Oracle PPA

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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.6.3

Updating using the tarball

You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.6.3.tar.gz You can unpack this file using:

tar zxvf seek-1.6.3.tar.gz
mv seek seek-previous
mv seek-1.6.3 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Doing the upgrade

cd . #this is to allow RVM to pick up the ruby and gemset changes
gem install bundler
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while       

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start

Steps to upgrade from 1.4.x to 1.5.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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.5.2

Updating using the tarball

You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.5.2.tar.gz You can unpack this file using:

tar zxvf seek-1.5.2.tar.gz
mv seek seek-previous
mv seek-1.5.2 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Update RVM and Ruby

rvm get stable
rvm install $(cat .ruby-version) 

Doing the upgrade

cd . #this is to allow RVM to pick up the ruby and gemset changes
gem install bundler
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while

Note: During the upgrade, and items that previously were shared with All registered users have had their permissions updated, and this permission has been transferred to its associated projects. An audit CSV file is created, tmp/all-users-policy-update-audit-.csv . This file contains a list of all the items affected, along with the contributor and project ids.

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start  

Steps to upgrade from 1.3.x to 1.4.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

For this version, it really is critical to stop these services at this stage. You will be unable to later.

bundle exec rake seek:workers:stop
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull
git checkout v1.4.1

Updating using the tarball

You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.4.1.tar.gz You can unpack this file using:

tar zxvf seek-1.4.1.tar.gz
mv seek seek-previous
mv seek-1.4.1 seek
cd seek/

If you have a modified config/sunspot.yml you will also need to copy that across.

Update RVM and Ruby

rvm get stable
rvm install $(cat .ruby-version) 

Doing the upgrade

cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
gem install bundler
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while

Updating the Sunspot configuration

If you moved away from the default Sunspot/SOLR config, by making your own copy of config/sunspot.yml, this will need updating.

If you don’t have a config/sunspot.yml you don’t need to do anything.

Update your sunspot.yml based on the new format in config/sunspot.default.yml

Restarting services

bundle exec rake sunspot:solr:start
bundle exec rake seek:workers:start            

If you are running a production SEEK behing Apache, then move onto the next part. Otherwise, or you want to do a quick test, you can simply start SEEK again with:

bundle exec rails s

Upgrading Passenger Phusion

If you are running SEEK with Passenger, it is likely you will need to upgrade Passenger and your Apache or Ngninx configuration.

Please read Serving SEEK through Apache for a reminder on how to install the new version, and update your virtual host configuration accordingly.

Note on Search results

Initially you won’t get any search results, due to the upgrade of Sunspot/SOLR. The upgrade steps will have triggered some jobs to rebuild the search index. How long this takes depends upon the number of items in the database and the speed of your machine. You can track the progress by going to the Admin page of SEEK, and looking at Job Queue under Statistics.

Steps to upgrade from 1.2.x to 1.3.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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull https://github.com/seek4science/seek.git
git checkout v1.3.3

Updating using the tarball

You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.3.3.tar.gz You can unpack this file using:

tar zxvf seek-1.3.3.tar.gz

Doing the upgrade

cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while

Restarting services

bundle exec rake seek:workers:start
bundle exec rake sunspot:solr:start
touch tmp/restart.txt
bundle exec rake tmp:clear

Steps to upgrade from 1.1.x to 1.2.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
bundle exec rake sunspot:solr:stop

Updating from GitHub

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

git pull https://github.com/seek4science/seek.git
git checkout v1.2.3

Updating using the tarball

Starting with version 0.22, we’ve started making SEEK available as a download. You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.2.3.tar.gz You can unpack this file using:

tar zxvf seek-1.2.3.tar.gz

Doing the upgrade

cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while

Restarting services

bundle exec rake seek:workers:start
bundle exec rake sunspot:solr:start
touch tmp/restart.txt
bundle exec rake tmp:clear

Steps to upgrade from 1.0.x to 1.1.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
bundle exec rake sunspot:solr:stop

Update Ruby with RVM

Although not critical, we recommend updating Ruby to 2.1.9. If you are using RVM, as recommended in the installation, you can do this with:

rvm get stable
rvm upgrade 2.1.7 2.1.9

The above upgrade command will copy across all previous gemsets (see:https://rvm.io/rubies/upgrading). If you have gemsets for other applications and copying them all isn’t desirable, then you may want to start afresh:

rvm install ruby-2.1.9

Make sure bundler is installed

gem install bundler

Updating from GitHub

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

git pull https://github.com/seek4science/seek.git
git checkout v1.1.2

Updating using the tarball

Starting with version 0.22, we’ve started making SEEK available as a download. You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.1.2.tar.gz You can unpack this file using:

tar zxvf seek-1.1.2.tar.gz

Doing the upgrade

cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while

Restarting services

bundle exec rake seek:workers:start
bundle exec rake sunspot:solr:start
touch tmp/restart.txt
bundle exec rake tmp:clear

Extra steps for a production server

If the upgrade has involved an upgrade of Ruby, and you are running a production service with Apache and Passenger Phusion, you will need to update the Apache config. You will need to point to the correct ruby wrapper script according to your version. The full path may differ, but for example

PassengerDefaultRuby /home/www-data/.rvm/gems/ruby-2.1.7/wrappers/ruby

would need changing to

PassengerDefaultRuby /home/www-data/.rvm/gems/ruby-2.1.9/wrappers/ruby

after upgrading from ruby 2.1.7 to ruby 2.1.9

If you have problems, you may need to upgrade and reinstall the Passenger Phusion modules (if unsure there no harm in doing so).

Please read Installing SEEK in a production environment for more details about setting up Apache and installing the module.

Steps to upgrade from 0.23.x to 1.0.x

Dependencies

libgmp-dev is needed for RedCloth with ruby 2.1.7

sudo apt-get update
sudo apt-get install libgmp-dev

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
bundle exec rake sunspot:solr:stop

Update Ruby with RVM

Although not critical, we recommend updating Ruby to 2.1.7. If you are using RVM, as recommended in the installation, you can do this with:

rvm get stable
rvm upgrade 2.1.6 2.1.7

rvm install ruby-2.1.7

Make sure bundler is installed

gem install bundler

Updating from GitHub

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

git pull https://github.com/seek4science/seek.git
git checkout v1.0.2

Updating using the tarball

Starting with version 0.22, we’ve started making SEEK available as a download. You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-1.0.3.tar.gz You can unpack this file using:

tar zxvf seek-1.0.3.tar.gz

Doing the upgrade

cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while

Restarting services

bundle exec rake seek:workers:start
bundle exec rake sunspot:solr:start
touch tmp/restart.txt
bundle exec rake tmp:clear

Extra steps for a production server

PassengerDefaultRuby /home/www-data/.rvm/gems/ruby-2.1.6/wrappers/ruby

would need changing to

PassengerDefaultRuby /home/www-data/.rvm/gems/ruby-2.1.7/wrappers/ruby

after upgrading from ruby 2.1.6 to ruby 2.1.7

If you have problems, you may need to upgrade and reinstall the Passenger Phusion modules (if unsure there no harm in doing so).

Please read Installing SEEK in a production environment for more details about setting up Apache and installing the module.

Steps to upgrade from 0.22.x to 0.23.x

Dependencies

You will need to install nodejs. First install this using

sudo apt-get install nodejs

Stopping services before upgrading

export RAILS_ENV=production # if upgrading a production server - remember to set this again if closing and reopening the shell
bundle exec rake seek:workers:stop
bundle exec rake sunspot:solr:stop

Update Ruby with RVM

Although not critical, we recommend updating Ruby to 2.1.6. If you are using RVM, as recommended in the installation, you can do this with:

rvm get stable
rvm install ruby-2.1.6
gem install bundler

Updating from GitHub

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

git pull https://github.com/seek4science/seek.git
git checkout v0.23.0

Updating using the tarball

Starting with version 0.22, we’ve started making SEEK available as a download. You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-0.23.0.tgz You can unpack this file using:

tar zxvf seek-0.23.0.tgz

Doing the upgrade

After updating the files, the following steps will update the database, gems, and other necessary changes:

cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while
bundle exec rake seek:workers:start
bundle exec rake sunspot:solr:start
touch tmp/restart.txt
bundle exec rake tmp:clear

Steps to upgrade from 0.21.x to 0.22.x

If you need to upgrade from v0.21 based on Mercurial rather than Git or the downloaded tarball, please contact us on our mailing lists.

Stopping services before upgrading

export RAILS_ENV=production # if upgrading a production server - remember to set this again if closing and reopening the shell
bundle exec rake seek:workers:stop
bundle exec rake sunspot:solr:stop

Update Ruby with RVM

Although not critical, we recommend updating Ruby to 2.1.5. If you are using RVM, as recommended in the installation, you can do this with:

rvm get stable
rvm install ruby-2.1.5
gem install bundler

Updating from GitHub

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

git pull https://github.com/seek4science/seek.git
git checkout v0.22.0

Updating using the tarball

Starting with version 0.22, we’ve started making SEEK available as a download. You can download the file from https://bitbucket.org/fairdom/seek/downloads/seek-0.22.0.tgz You can unpack this file using:

tar zxvf seek-0.22.0.tgz

Doing the upgrade

After updating the files, the following steps will update the database, gems, and other necessary changes:

cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
bundle install --deployment
bundle exec rake seek:upgrade
bundle exec rake assets:precompile # this task will take a while
bundle exec rake seek:workers:start
bundle exec rake sunspot:solr:start
touch tmp/restart.txt
bundle exec rake tmp:clear

Upgrades to 0.21.x and earlier

Steps to upgrade from 0.20.x to 0.21.x

export RAILS_ENV=production # if upgrading a production server - remember to set this again if closing and reopening the shell

bundle exec ./script/delayed_job stop
bundle exec rake sunspot:solr:stop

#if using rvm do: rvm get stable rvm install ruby-2.1.3 gem install bundler

#then:

hg pull https://bitbucket.org/fairdom/seek -r v0.21.0
hg update # only if no other changes have been made to your local version, if you get an error ignore it and do merge
hg merge # only required if you've made changes since installing. If you have, you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
cd .. && cd seek #this is to allow RVM to pick up the ruby and gemset changes
bundle install --deployment
bundle exec rake seek:upgrade

The mechanism to start, stop and restart the delayed-job process has now changed you you should use the rake task seek:workers:<start|stop|restart|status>, e.g

bundle exec rake seek:workers:start

there is a new init.d script for this described at https://gist.github.com/e4219ec7cb161129f1c7

Steps to upgrade from 0.19.x to 0.20.x

Start the upgrade following the standard steps:

#if using rvm do:
rvm get stable
rvm install ruby-1.9.3-p545
gem install bundler

export RAILS_ENV=production # if upgrading a production server - remember to set this again if closing and reopening the shell

./script/delayed_job stop
bundle exec rake sunspot:solr:stop
hg pull https://bitbucket.org/fairdom/seek -r v0.20.0
hg update # only if no other changes have been made to your local version, if you get an error ignore it and do merge
hg merge # only required if you've made changes since installing. If you have, you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
bundle install --deployment
bundle exec rake seek:upgrade

If you are upgrading a production server, you also need to run the following task. Be patient, as this can take a few minutes

bundle exec rake assets:precompile

Now proceed with the rest of the usual tasks:

bundle exec rake sunspot:solr:start # to restart the search server
./script/delayed_job start

touch tmp/restart.txt
bundle exec rake tmp:clear

If you are running through Apache, you should also add the following block to your Apache configuration, after the Directory block:

<LocationMatch "^/assets/.*$">
         Header unset ETag
         FileETag None
         # RFC says only cache for 1 year
         ExpiresActive On
         ExpiresDefault "access plus 1 year"
</LocationMatch>

so it will look something like:

<VirtualHost *:80>
     ServerName www.yourhost.com
     DocumentRoot /srv/rails/seek/public
        <Directory /srv/rails/seek/public>
         AllowOverride all
         Options -MultiViews
      </Directory>
      <LocationMatch "^/assets/.*$">
         Header unset ETag
         FileETag None
         # RFC says only cache for 1 year
         ExpiresActive On
         ExpiresDefault "access plus 1 year"
      </LocationMatch>
</VirtualHost>

You may also need to enable a couple of Apache modules, so run:

sudo a2enmod headers
sudo a2enmod expires

You will then need to restart Apache

sudo service apache2 restart

Steps to upgrade from 0.18.x to 0.19.x

Upgrading follows the standard steps:

RAILS_ENV=production ./script/delayed_job stop
bundle exec rake sunspot:solr:stop RAILS_ENV=production
hg pull https://bitbucket.org/fairdom/seek -r v0.19.1
hg update
hg merge # only required if you've made changes since installing. If you have you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
bundle install --deployment
bundle exec rake seek:upgrade RAILS_ENV=production

bundle exec rake sunspot:solr:start RAILS_ENV=production # to restart the search server
RAILS_ENV=production ./script/delayed_job start

touch tmp/restart.txt
bundle exec rake tmp:assets:clear RAILS_ENV=production
bundle exec rake tmp:clear RAILS_ENV=production

Steps to upgrade from 0.17.x to 0.18.x

The changes for Version 0.18 included upgrading Ruby to version 1.9.3 and Rails to version 3.2 - this means the upgrade process is a little bit more involved that usual. For this reason we have a seperate page detailing this upgrade.

Please visit Upgrading to 0.18 for details of how to do this upgrade.

Steps to upgrade from 0.16.x to 0.17.x

Upgrading follows the standard steps:

RAILS_ENV=production ./script/delayed_job stop
bundle exec rake sunspot:solr:stop RAILS_ENV=production
hg pull https://bitbucket.org/fairdom/seek -r v0.17.1
hg update
hg merge # only required if you've made changes since installing. If you have you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
bundle install --deployment
bundle exec rake seek:upgrade RAILS_ENV=production

bundle exec rake sunspot:solr:start RAILS_ENV=production # to restart the search server
RAILS_ENV=production ./script/delayed_job start

touch tmp/restart.txt
bundle exec rake tmp:assets:clear RAILS_ENV=production
bundle exec rake tmp:clear RAILS_ENV=production

Steps to upgrade from 0.15.x to 0.16.x

First there are additional dependencies you will need, which on Ubuntu 12.04 can be installed with:

sudo apt-get install poppler-utils libreoffice

On Ubuntu 10.04:

sudo apt-get install poppler-utils openoffice.org openoffice.org-java-common

Libre Office is a background service which is called by convert_office plugin, to convert some document types (ms office documents, open office documents, etc.) into pdf document.

The command to start libre office in headless mode and as the background process:

nohup soffice --headless --accept="socket,host=127.0.0.1,port=8100;urp;" --nofirststartwizard > /dev/null 2>&1

If you run on production server, using apache and phusion passenger, you will need to run the Libre Office service under www-data user. To do this it will need to create a working directory in /var/www. The name of the directory changes between versions, but will be called something similar to libreoffice or .openoffice.org2. The easiest way to create this directory is to make a note of the permissions for /var/www, then make it writable to www-data, start the service, and then put the permissions on /var/www back to what they were originally.

sudo chown www-data:www-data /var/www

Then to start the service manually you use:

nohup sudo -H -u www-data soffice --headless --accept="socket,host=127.0.0.1,port=8100;urp;" --nofirststartwizard > /dev/null 2>&1

The 8100 port is used by default, if you’d like to run on another port, you need also to synchronize the changed port with the default soffice_port setting for convert_office plugin in config/environment.rb

We recommend the Libre Office service is setup using an init.d script, following the same procedures for delayed job using the script found at: https://gist.github.com/3787679

If you have problem with converting speed, you should upgrade OS to Ubuntu 12.04 to use Libre Office. Or you can install libre office 3.5 from PPA, but there could be problems later on when upgrading OS. Here are the command to install libre office from PPA:

sudo apt-get purge openoffice* libreoffice*
sudo apt-get install python-software-properties
sudo add-apt-repository ppa:libreoffice/libreoffice-3-5
sudo apt-get update
sudo apt-get install libreoffice

Other than this, the remaining steps are the same standard steps are previous versions:

RAILS_ENV=production ./script/delayed_job stop
bundle exec rake sunspot:solr:stop RAILS_ENV=production
hg pull https://bitbucket.org/fairdom/seek -r v0.16.3
hg update
hg merge # only required if you've made changes since installing. If you have you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
bundle install --deployment
bundle exec rake seek:upgrade RAILS_ENV=production
bundle exec rake tmp:assets:clear RAILS_ENV=production
bundle exec rake tmp:clear RAILS_ENV=production

bundle exec rake sunspot:solr:start RAILS_ENV=production # to restart the search server
RAILS_ENV=production ./script/delayed_job start
touch tmp/restart.txt ---

Steps to upgrade from 0.14.x to 0.15.x

SEEK 0.15 upgraded Rails to the latest 2 version,2.3.14. This requires an update of Rubygems to 1.6.2. You can update rubygems directly by running

gem update --system 1.6.2

or install from scratch by reading the INSTALL guide. You can also use RVM. SEEK 0.15 also runs fine on the latest Rubygems (currently 1.8.24) but you will get some deprecation warnings. You can check you have the correct version of rubygems by running

gem -v

Then you will need to install additional dependency:

sudo apt-get install git

Once Rubygems has been updated and additional dependency has been installed, the upgrade is the typical:

RAILS_ENV=production ./script/delayed_job stop
bundle exec rake sunspot:solr:stop RAILS_ENV=production
hg pull https://bitbucket.org/fairdom/seek -r v0.15.4
hg update
hg merge # only required if you've made changes since installing. If you have you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
bundle install --deployment
bundle exec rake seek:upgrade RAILS_ENV=production
bundle exec rake tmp:assets:clear RAILS_ENV=production
bundle exec rake tmp:clear RAILS_ENV=production

bundle exec rake sunspot:solr:start RAILS_ENV=production # to restart the search server
RAILS_ENV=production ./script/delayed_job start
touch tmp/restart.txt

Steps to upgrade from 0.13.x to 0.14.x

These are the fairly standard steps when upgrading between minor versions. Note, the seek:upgrade task can take a while if there are many people and assets in your SEEK, as it needs to populate some tables for the default subscriptions (for email notifications).

RAILS_ENV=production ./script/delayed_job stop
bundle exec rake sunspot:solr:stop RAILS_ENV=production
hg pull https://bitbucket.org/fairdom/seek -r v0.14.1
hg update
hg merge # only required if you've made changes since installing. If you have you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
bundle install --deployment
bundle exec rake seek:upgrade RAILS_ENV=production
bundle exec rake tmp:assets:clear RAILS_ENV=production
bundle exec rake tmp:clear RAILS_ENV=production

bundle exec rake sunspot:solr:start RAILS_ENV=production # to restart the search server
RAILS_ENV=production ./script/delayed_job start
touch tmp/restart.txt ---

Steps to upgrade from 0.11.x to 0.13.x

There follows the commands required to upgrade. Anything after # are notes and do not need to be included in the command run. There are a few additional steps for this upgrade due to the switch from Solr to Sunspot as the search system, and the introduction of Delayed Job for background processing.

First there is an additional dependency you will need, which on Ubuntu 10.04 or Debian can be installed with:

sudo apt-get install libxslt-dev

on Ubuntu 12.04 this will be:

sudo apt-get install libxslt1-dev

then the following steps will update the SEEK server:

bundle exec rake solr:stop RAILS_ENV=production # this is specific to this upgrade, since the command to stop and start the search has changed.
hg pull https://bitbucket.org/fairdom/seek -r v0.13.3
hg update
hg merge # only required if you've made changes since installing. If you have you may need to deal with conflicts.
hg commit -m "merged" # likewise - only required if you made changes since installing
bundle install --deployment
bundle exec rake seek:upgrade RAILS_ENV=production
bundle exec rake sunspot:solr:start RAILS_ENV=production # to restart the search server
bundle exec rake sunspot:solr:reindex RAILS_ENV=production  # to reindex
bundle exec rake tmp:assets:clear RAILS_ENV=production
bundle exec rake tmp:clear RAILS_ENV=production

SEEK v0.13.x now uses a Ruby tool called Delayed Job to handle background processing which now needs to be started using:

RAILS_ENV=production ./script/delayed_job start

And now SEEK should be ready to restart. If running together with Passenger Phusion as described in the install guide this is simply a case of:

touch tmp/restart.txt

If you auto start solr with an init.d/ script - this will need updating to reflect the change to sunspot:solr:start. The updated script should look something like: https://gist.github.com/3143434