Sequencescape

Sequencescape is a cloud based and highly extensible LIMS system for use in labs with large numbers of samples.

• Work order tracking
• Sample and study management
• Capacity management for pipelines
• Accounting
• Accessioning for samples and studies at the EBI ENA/EGA
• Dynamically defined workflows for labs with support for custom processes
• Labware and freezer tracking
• API support for 3rd party applications

Current installation supports over 5 million samples and 1.8 million pieces of labware and is used in a organisation of 900 people.

Contents

• Sequencescape
  • Contents
  • Documentation
    • Linting
  • Requirements
  • Getting started (using Docker)
  • Getting started (using native installation)
    • Installing ruby
      • rbenv
    • Automatic Sequencescape setup
    • Manual Sequencescape setup
      • Installing gems
      • Adjusting config
      • Default setup
    • Starting rails
      • Delayed job
    • Message broker
  • Testing
  • Linting and formatting
  • Rake tasks
  • Supporting applications
    • Barcode printing
    • Plate barcode service
    • Data warehousing
  • Miscellaneous
    • Lefthook
    • Ruby warnings and rake 11
    • NPG - Illumina tracking software
    • Troubleshooting
      • MySQL errors when installing
      • Installing on Apple Silicon (M1)
    • API V2 Authentication
    • Publishing AMQP Messages
    • Updating the table of contents
    • CI
    • ERD

Documentation

The Yard documentation is also hosted at GitHub Pages under https://sanger.github.io/sequencescape/. The documentation is automatically updated via a CI workflow when a merge to master occurs, but you can also trigger it manually against any branch (the branch can be selected using the "Run Workflow" button in the corresponding action).

To preview this documentation, you can spin up a yard server locally using the following command:

yard server --reload sequencescape .

You can then access the Sequencescape documentation through: http://localhost:8808/docs

If the server complains that the stack depth is too deep, this only appears to be a problem when you try to view the documentation without pre-compiling it. Precompiling is the simple solution and can be achieved with the following.

yard doc

This will pre-fill the cache and allow the server command above to display the documentation without complaining about stack depths.

Linting

Yard-Junk is used to check for missing or incorrect documentation. To run the checks:

bundle exec yard-junk --sanity

Requirements

The following tools are required for development:

• ruby (version defined in the .ruby-version)
• yarn (brew install yarn)
• node (brew install node@<version> version defined in the .nvmrc, ensure node is in your PATH)
• mysql client libraries - if you do not want to install mysql server on your machine, consider using mysql-client: brew install mysql-client. Alternatively, to install the MySQL required by Sequencescape (currently 8.0)

Getting started (using Docker)

To set up a local development environment in Docker, you have to build a new Docker image for Sequencescape. start a stack of services that include a mysql database, and reset this database contents. You can do all together by running the commands:

docker compose build
RESET_DATABASE=true docker compose up

Or if you are using an Apple M1 Chip:

docker compose build --build-arg CHIPSET=m1
USE_POLLING_FILE_WATCHER=true RESET_DATABASE=true docker compose up

Optionally, if this is not the first time you start the app, you may not want to reset the database, and you can run this command instead:

docker compose up

With this we should have started Sequencescape server and all required services. You should be able to access Sequencescape by going to http://localhost:3000 and log in with username and password admin/admin.

The envvar PRECOMPILE_ASSETS is also available as PRECOMPILE_ASSETS=false docker compose up which will avoid precompiling the assets as Sequencescape is started.

If you are using Apple silicon and encounter any issues, please see Troubleshooting below.

ABOUT LOCAL DEVELOPMENT SETUP You may want to start only the required services for Sequencescape (server and jobs worker) and use your local version of Mysql instead of the Docker version, in that case you can start this setup with the command:

docker compose -f docker compose-dev.yml up

ABOUT RECREATE DOCKER IMAGE If you ever need to recreate the image built on first start (because you made modifications to the Dockerfile file) you can run the building process again with:

docker compose build

Getting started (using native installation)

This section only applies if you don't have Docker installed or if you prefer a native installation of Sequencescape.

Installing ruby

It is strongly recommended that you use a ruby version manager such as RVM or rbenv to manage the Ruby version you are using. The ruby version required should be found in .ruby-version.

rbenv

If you have the rbenv ruby-build plugin it is as simple as:

rbenv install

It will pick up the version from the .ruby-version file automatically

Automatic Sequencescape setup

To automatically install the required gems, set-up default configuration files, and set up your database run:

bin/setup

Manual Sequencescape setup

In the event you have trouble with the automatic process, you may wish to step through the various steps manually.

Installing gems

Bundler is used to install the required gems:

gem install bundler
bundle install

Adjusting config

The config/database.yml file saves the list of databases.

Default setup

1. Create the database tables

   bundle exec rake db:setup

2. Install webpacker and the required JS libraries

   yarn

Starting rails

bundle exec rails s

Once setup, the default user/password is admin/admin.

Vite

Ensure Node is installed, and in your PATH. You might need to run bin/vite build --clear --mode=development

Delayed job

For background processing Sequencescape uses delayed_job to ensure that the server is running. It is strongly recommended to start one for Sequencescape to behave as expected.

bundle exec rake jobs:work

OR

bundle exec ./script/delayed_job start

Message broker

Sequencescape has its own message broker and consumer. To develop this or run it locally, you must have RabbitMQ installed. It may be easiest to use the docker image https://hub.docker.com/_/rabbitmq.

docker run -d --hostname my-rabbit --name some-rabbit -p 8080:15672 -p 5672:5672 rabbitmq:3-management

It can be useful to follow the rabbitmq logs, to look for broken connections or other problems. To do this using the docker image, get the container id using docker ps, and then:

docker logs -f <container id>

To start the consumer off listening for messages:

bundle exec warren consumer start

The consumer will run in the foreground, logging to the console. You can stop it with Ctrl-C.

For more warren actions, either use bundle exec warren help or see the warren documentation

You will also have to change the config in config/warren.yml from type: log to type: broadcast to get it to actually send messages in development mode.

Testing

Testing is done in one of three ways; using rspec, via rails tests or with cucumber.

1. To run the rspec tests (found in rspec/ dir.):

   bundle exec rspec --fail-fast [<path_to_spec>]

2. To run the rails tests (found in tests/ dir.):

   bundle exec rake test -f

   For a single file:

   bundle exec ruby -Itest test/lib/label_printer/print_job_test.rb

3. To run cucumber tests (found in features/ dir.) first ensure you have a sequencescape_test_cuke database configured by running:

   RAILS_ENV=cucumber bundle exec rake db:setup

   then run cucumber itself:

   bundle exec cucumber

For a single file:

bundle exec cucumber features/create_plates.feature

Linting and formatting

Rubocop is used for linting.

bundle exec rubocop

Note that permanent Excludes should be defined in .rubocop.yml, with 'temporary' ones (automatically) listed in .rubocop_todo.yml.

To update .rubocop_todo.yml, execute

rubocop --auto-gen-config --no-exclude-limit

Prettier is used for formatting.

yarn prettier --check .
yarn prettier --write .

(If prettier is not yet installed, run yarn. This should have ben run in bin/setup)

• Prettier rules are configured in .prettierrc.json
• Whole files can be ignored in .prettierignore
• Sections of files can be disabled using #prettier-ignore

Rake tasks

Rake tasks are available for specialised tasks as well as support tasks. Support tasks allow ease of running standalone scripts multiple times.

A breakdown of the the available tasks and how to run them can be found here

Supporting applications

There are a number of services that are needed in certain parts of Sequencescape these are listed below.

Barcode printing

Barcode printing is carried out by a separate REST service, PrintMyBarcode. The source for this is also available on GitHub sanger/print_my_barcode

Plate barcode service

Due to DNA plate barcode series being stored in a legacy system in Sanger you are required to use a webservice for supplying numbers for plates with a simple service.

Data warehousing

There is a client application for building a data warehouse based on the information in Sequencescape. This is driven asynchronously via RabbitMQ.

See our various clients on GitHub:

sanger/unified_warehouse

sanger/event_warehouse

Miscellaneous

Lefthook

Lefthook is a git-hook manager that will ensure staged files are linted before committing.

You can install it either via homebrew brew install Arkweid/lefthook/lefthook or rubygems gem install lefthook

You'll then need to initialize it for each repository you wish to track lefthook install

Hooks will run automatically on commit, but you can test them with: lefthook run pre-commit

In addition you can also run lefthook run fix to run the auto-fixers on staged files only. Note that after doing this you will still need to stage the fixes before committing. I'd love to be able to automate this, but haven't discovered a solution that maintains the ability to partially stage a file, and doesn't involve running the linters directly on files in the .git folder.

Ruby warnings and rake 11

Rake 11 enables ruby warnings by default when running the test suite. These can be disabled with RUBYOPT='-W0', (eg. RUBYOPT='-W0' bundle exec rake test).

Currently these warnings are excessive, covering both our own code and external dependencies. As it stands it makes the output of the test suite unusable in travis, as it fills the buffer. These warnings will need to be fixed, especially in our own code.

NPG - Illumina tracking software

For tracking illumina instruments you need the NPG systems. NPG is linked to Sequencescape via a cluster formation batch which represents a flowcell.

NPG Software

Troubleshooting

MySQL errors when installing

• If you are using homebrew with rbenv and run into errors relating to SSL, have a look here

• If you are upgrading a homebrew MySQL locally and have an error about a missing libmysqlclient dylib file, you may need to redownload the mysql2 gem to fix it i.e. bundle install --redownload This is because the mysql2 gem is simlinked to the homebrew mysql.

• If bundle install is failing to install the mysql2 gem, try the below (updating the paths as required):

gem install mysql2 -v '0.5.6' -- \
--with-mysql-lib=/opt/homebrew/Cellar/mysql/ \
--with-mysql-dir=/opt/homebrew/Cellar/mysql/9.0.1_1 \
--with-mysql-config=/opt/homebrew/Cellar/mysql/9.0.1_1/bin/mysql_config \
--with-mysql-include=/opt/homebrew/Cellar/mysql/9.0.1_1/include

Installing on Apple Silicon (M1)

If installation issues are encountered with Docker on M1 processors, try the fixes below:

• The docker compose build command fails with any mentions to a processor architecture ('amd64', 'x86') or the message below:

  ...
  #0 1.528 The following packages have unmet dependencies:
  #0 1.568  google-chrome-stable:amd64 : Depends: libasound2:amd64 (>= 1.0.17) but it is not installable
  #0 1.568                               Depends: libatk-bridge2.0-0:amd64 (>= 2.5.3) but it is not installable
  ...
  #0 1.568                               Depends: libxkbcommon0:amd64 (>= 0.5.0) but it is not installable
  #0 1.568                               Depends: libxrandr2:amd64 but it is not installable
  #0 1.581 E: Unable to correct problems, you have held broken packages.
  ------
  failed to solve: process "/bin/bash --login -c apt install -y ./google-chrome-stable_current_amd64.deb" did not complete successfully: exit code: 100

  Force docker to use the an AMD image as the base by setting --build-arg CHIPSET=m1 during the build. It is also recommended to install and enable Rosetta 2.

• The sequencescape_server container terminates with the error:

  Function not implemented - Failed to initialize inotify (Errno::ENOSYS)

  Use a polling instead of event file update checker by setting USE_POLLING_FILE_WATCHER=true during the compose up.

  [GitHub issue]

API V2 Authentication

The V2 API has had authentication checks added to it so that other applications calling the API should provide a valid key. The key is passed by the client application via the X-Sequencescape-Client-Id header. Keys can be generated via the Rail Console by creating new ApiApplication records and observing the key attribute on them. As of the time of writing, there are three outcomes to a request made, with respect to API key submission:

• The client calls an API V2 endpoint with a valid API key in the header of the request.
  • The response given has a valid status code and the body contains the requested information/confirmation.
• The client calls an API V2 endpoint with an invalid API key in the header of the request.
  • The response given has status code 401 Unauthorized and contains a JSON body explaining that a valid API key must be provided for the header.
  • The request is logged with the prefix "Request made with invalid API key" including information about the client and the API key used.
• The client calls an API V2 endpoint without the API key header in the request.
  • The response is given as if a valid API key was provided.
  • The request is logged with the prefix "Request made without an API key" including information about the client.
  • The client application should be updated to use a valid API key in future.

Publishing AMQP Messages

Some API endpoints (such as /api/v2/bioscan/export_pool_xp_to_traction) trigger background jobs which are responsible for publishing data to another instance of RabbitMQ. In the case of the Bioscan Export Pool XP to Traction job, the message goes to the ISG managed RabbitMQ instance. In order to publish a message, the job must get a schema from a registry. Under development conditions, you may not have a registry running, hence the default config directs to the UAT instance of PSD's supported RedPanda. This means, the first time you publish a message with this schema, you need to be connected to the Sanger network directly or via VPN. After the first use, a cached file will be created in data/avro_schema_cache so that the registry does not need to be reachable to continue generating messages.

Because this is the first and only job doing this pubishing / RedPanda caching / Avro encoding, etc, there are parts which could be extracted in future if further jobs of this type are created. This isn't necessary at this stage, but it seems wise to note the intended pattern of usage here for future work.

Updating the table of contents

To update the table of contents after adding things to this README you can use the markdown-toc node module. To install it, make sure you have installed the dev dependencies from yarn. To update the table of contents, run:

npx markdown-toc -i README.md --bullets "-"

CI

The GH actions builds use the Knapsack-pro gem to reduce build time by parallelizing the RSpec and Cucumber tests. There is no need to regenerate the knapsack_rspec_report.json file, Knapsack Pro will dynamically allocate tests to ensure tests finish as close together as possible.

Copyright (c) 2007, 2010-2021 Genome Research Ltd.

ERD

You can create a database entity relationship diagram, by specifying the title and attributes optionally, and view the output:

bundle exec rake erd title='Sequencescape Entity Relationship Diagram' attributes='primary_keys,foreign_keys,inheritance' orientation=horizontal polymorphism=true notation=bachman indirect=false inheritance=true only='Sample,Study,AliquotIndex,Aliquot,Project,Order,Submission,Labware,Receptacle,Request,Request::Metadata,Batch,BatchRequest,LabEvent,RequestType,Pipeline,SampleManifest,Sample::Metadata,Study::Metadata,Item,BaitLibrary,RequestEvent,Project::Metadata,Barcode,Purpose,QCResult,QCAssay,User,Plate,Tube,Well' exclude='Target,Commentable,Failable,Eventful,Eventable,Resource,Attributable,Owner,Authorizable,Documentable'

open erd.pdf

The command uses the rails-erd gem.