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ClickHouse within GitLab

This document gives a high-level overview of how to develop features using ClickHouse in the GitLab Rails application.

NOTE: Most of the tooling and APIs are considered unstable.

GDK setup

Setup ClickHouse server

  1. Install ClickHouse locally as described in ClickHouse installation documentation. If you use QuickInstall it will be installed in current directory, if you use homebrew it will be installed to /opt/homebrew/bin/clickhouse

  2. Enable experimental services with gdk config set gdk.experimental.ruby_services true

  3. Add clickhouse section to your gdk.yml. See gdk.example.yml

  4. Adjust gdk.yml clickhouse config to point to your local clickhouse installation and local data storage. E.g.

    clickhouse:
  bin: "/opt/homebrew/bin/clickhouse"
  enabled: true
  # these are optional if we have more then one GDK:
  # http_port: 8123
  # interserver_http_port: 9009
  # tcp_port: 9001

  5. Run gdk reconfigure

  6. Start clickhouse with gdk start clickhouse

Configure your Rails application

  1. Copy the example file and configure the credentials:

    cp config/click_house.yml.example
config/click_house.yml

  2. Create the database using the clickhouse-client CLI tool:

    clickhouse client --port 9001
    create database gitlab_clickhouse_development;

Validate your setup

Run the Rails console and invoke a simple query:

ClickHouse::Client.select('SELECT 1', :main)
# => [{"1"=>1}]

Database schema and migrations

To run database migrations, execute:

bundle exec rake gitlab:clickhouse:migrate

To rollback last N migrations, execute:

bundle exec rake gitlab:clickhouse:rollback:main STEP=N

Or use the following command to rollback all migrations:

bundle exec rake gitlab:clickhouse:rollback:main VERSION=0

You can create a migration by creating a Ruby migration file in db/click_house/migrate folder. It should be prefixed with a timestamp in the format YYYYMMDDHHMMSS_description_of_migration.rb

# 20230811124511_create_issues.rb
# frozen_string_literal: true

class CreateIssues < ClickHouse::Migration
  def up
    execute <<~SQL
      CREATE TABLE issues
      (
        id UInt64 DEFAULT 0,
        title String DEFAULT ''
      )
      ENGINE = MergeTree
      PRIMARY KEY (id)
    SQL
  end

  def down
    execute <<~SQL
      DROP TABLE sync_cursors
    SQL
  end
end

Writing database queries

For the ClickHouse database we don't use ORM (Object Relational Mapping). The main reason is that the GitLab application has many customizations for the ActiveRecord PostgresSQL adapter and the application generally assumes that all databases are using PostgreSQL. Since ClickHouse-related features are still in a very early stage of development, we decided to implement a simple HTTP client to avoid hard to discover bugs and long debugging time when dealing with multiple ActiveRecord adapters.

Additionally, ClickHouse might not be used the same way as other adapters for ActiveRecord. The access patterns differ from traditional transactional databases, in that ClickHouse:

  • Uses nested aggregation SELECT queries with GROUP BY clauses.
  • Doesn't use single INSERT statements. Data is inserted in batches via background jobs.
  • Has different consistency characteristics, no transactions.
  • Has very little database-level validations.

Database queries are written and executed with the help of the ClickHouse::Client gem.

A simple query from the events table:

rows = ClickHouse::Client.select('SELECT * FROM events', :main)

When working with queries with placeholders you can use the ClickHouse::Query object where you need to specify the placeholder name and its data type. The actual variable replacement, quoting and escaping will be done by the ClickHouse server.

raw_query = 'SELECT * FROM events WHERE id > {min_id:UInt64}'
placeholders = { min_id: Integer(100) }
query = ClickHouse::Client::Query.new(raw_query: raw_query, placeholders: placeholders)

rows = ClickHouse::Client.select(query, :main)

When using placeholders the client can provide the query with redacted placeholder values which can be ingested by our logging system. You can see the redacted version of your query by calling the to_redacted_sql method:

puts query.to_redacted_sql

ClickHouse allows only one statement per request. This means that the common SQL injection vulnerability where the statement is closed with a ; character and then another query is "injected" cannot be exploited:

ClickHouse::Client.select('SELECT 1; SELECT 2', :main)

# ClickHouse::Client::DatabaseError: Code: 62. DB::Exception: Syntax error (Multi-statements are not allowed): failed at position 9 (end of query): ; SELECT 2. . (SYNTAX_ERROR) (version 23.4.2.11 (official build))

Subqueries

You can compose complex queries with the ClickHouse::Client::Query class by specifying the query placeholder with the special Subquery type. The library will make sure to correctly merge the queries and the placeholders:

subquery = ClickHouse::Client::Query.new(raw_query: 'SELECT id FROM events WHERE id = {id:UInt64}', placeholders: { id: Integer(10) })

raw_query = 'SELECT * FROM events WHERE id > {id:UInt64} AND id IN ({q:Subquery})'
placeholders = { id: Integer(10), q: subquery }

query = ClickHouse::Client::Query.new(raw_query: raw_query, placeholders: placeholders)
rows = ClickHouse::Client.select(query, :main)

# ClickHouse will replace the placeholders
puts query.to_sql # SELECT * FROM events WHERE id > {id:UInt64} AND id IN (SELECT id FROM events WHERE id = {id:UInt64})

puts query.to_redacted_sql # SELECT * FROM events WHERE id > $1 AND id IN (SELECT id FROM events WHERE id = $2)

puts query.placeholders # { id: 10 }

In case there are placeholders with the same name but different values the query will raise an error.

Writing query conditions

When working with complex forms where multiple filter conditions are present, building queries by concatenating query fragments as string can get out of hands very quickly. For queries with several conditions you may use the ClickHouse::QueryBuilder class. The class uses the Arel gem to generate queries and provides a similar query interface like ActiveRecord.

builder = ClickHouse::QueryBuilder.new('events')

query = builder
  .where(builder.table[:created_at].lteq(Date.today))
  .where(id: [1,2,3])

rows = ClickHouse::Client.select(query, :main)

Inserting data

The ClickHouse client supports inserting data through the standard query interface:

raw_query = 'INSERT INTO events (id, target_type) VALUES ({id:UInt64}, {target_type:String})'
placeholders = { id: 1, target_type: 'Issue' }

query = ClickHouse::Client::Query.new(raw_query: raw_query, placeholders: placeholders)
rows = ClickHouse::Client.execute(query, :main)

Inserting data this way is acceptable if:

  • The table contains settings or configuration data where we need to add one row.
  • For testing, test data has to be prepared in the database.

When inserting data, we should always try to use batch processing where multiple rows are inserted at once. Building large INSERT queries in memory is discouraged because of the increased memory usage. Additionally, values specified within such queries cannot be redacted automatically by the client.

To compress data and reduce memory usage, insert CSV data. You can do this with the internal CsvBuilder gem:

iterator = Event.find_each

# insert from events table using only the id and the target_type columns
column_mapping = {
  id: :id,
  target_type: :target_type
}

CsvBuilder::Gzip.new(iterator, column_mapping).render do |tempfile|
  query = 'INSERT INTO events (id, target_type) FORMAT CSV'
  ClickHouse::Client.insert_csv(query, File.open(tempfile.path), :main)
end

NOTE: It's important to test and verify efficient batching of database records from PostgreSQL. Consider using the techniques described in the Iterating tables in batches.

Iterating over tables

You can use the ClickHouse::Iterator class for batching over large volumes of data in ClickHouse. The iterator works a bit differently than existing tooling for the PostgreSQL database (see iterating tables in batches docs), as the tool does not rely on database indexes and uses fixed size numeric ranges.

Prerequisites:

  • Single integer column.
  • No huge gaps between the column values, the ideal columns would be auto-incrementing PostgreSQL primary keys.
  • Duplicated values are not a problem if the data duplication is minimal.

Usage:

connection = ClickHouse::Connection.new(:main)
builder = ClickHouse::QueryBuilder.new('events')

iterator = ClickHouse::Iterator.new(query_builder: builder, connection: connection)
iterator.each_batch(column: :id, of: 100_000) do |scope|
  records = connection.select(scope.to_sql)
end

In case you want to iterate over specific rows, you could add filters to the query builder object. Be advised that efficient filtering and iteration might require a different database table schema optimized for the use case. When introducing such iteration, always ensure that the database queries are not scanning the whole database table.

connection = ClickHouse::Connection.new(:main)
builder = ClickHouse::QueryBuilder.new('events')

# filtering by target type and stringified traversal ids/path
builder = builder.where(target_type: 'Issue')
builder = builder.where(path: '96/97/') # points to a specific project

iterator = ClickHouse::Iterator.new(query_builder: builder, connection: connection)
iterator.each_batch(column: :id, of: 10) do |scope, min, max|
  puts "processing range: #{min} - #{max}"
  puts scope.to_sql
  records = connection.select(scope.to_sql)
end

Min-max strategies

As the first step, the iterator determines the data range which will be used as condition in the iteration database queries. The data range is determined using MIN(column) and MAX(column) aggregations. For some database tables this strategy causes inefficient database queries (full table scan). One example would be partitioned database tables.

Example query:

SELECT MIN(id) AS min, MAX(id) AS max FROM events;

Alternatively a different min-max strategy can be used which uses ORDER BY + LIMIT for determining the data range.

iterator = ClickHouse::Iterator.new(query_builder: builder, connection: connection, min_max_strategy: :order_limit)

Example query:

SELECT (SELECT id FROM events ORDER BY id ASC LIMIT 1) AS min, (SELECT id FROM events ORDER BY id DESC LIMIT 1) AS max;

Implementing Sidekiq workers

Sidekiq workers leveraging ClickHouse databases should include the ClickHouseWorker module. This ensures that the worker is paused while database migrations are running, and that migrations do not run while the worker is active.

# events_sync_worker.rb
# frozen_string_literal: true

module ClickHouse
  class EventsSyncWorker
    include ApplicationWorker
    include ClickHouseWorker

    ...
  end
end

Testing

ClickHouse is enabled on CI/CD but to avoid significantly affecting the pipeline runtime we've decided to run the ClickHouse server for test cases tagged with :click_house only.

The :click_house tag ensures that the database schema is properly set up before every test case.

RSpec.describe MyClickHouseFeature, :click_house do
  it 'returns rows' do
    rows = ClickHouse::Client.select('SELECT 1', :main)
    expect(rows.size).to eq(1)
  end
end

Multiple databases

By design, the ClickHouse::Client library supports configuring multiple databases. Because we're still at a very early stage of development, we only have one database called main.

Multi database configuration example:

development:
  main:
    database: gitlab_clickhouse_main_development
    url: 'http://localhost:8123'
    username: clickhouse
    password: clickhouse

  user_analytics: # made up database
    database: gitlab_clickhouse_user_analytics_development
    url: 'http://localhost:8123'
    username: clickhouse
    password: clickhouse

Observability

All queries executed via the ClickHouse::Client library expose the query with performance metrics (timings, read bytes) via ActiveSupport::Notifications.

ActiveSupport::Notifications.subscribe('sql.click_house') do |_, _, _, _, data|
  puts data.inspect
end

Additionally, to view the executed ClickHouse queries in web interactions, on the performance bar, next to the ch label select the count.

Getting help

For additional information or specific questions, please reach out to the ClickHouse Datastore working group in the #f_clickhouse Slack channel, or mention @gitlab-org/maintainers/clickhouse in a comment on GitLab.com.