Update sample_public_name for RVI Program - Bait Capture study #4586
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| # frozen_string_literal: true | ||
| namespace :samples do | ||
| desc 'Update sample_public_name for RVI Program - Bait Capture study' | ||
| task update_public_name: :environment do | ||
| ActiveRecord::Base.connection.execute('SET autocommit = 0') | ||
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There was a problem hiding this comment. Could you explain the benefit of having autocommit turned off, please? I was reading the docs - https://dev.mysql.com/doc/refman/8.4/en/innodb-autocommit-commit-rollback.html - and it looks like the benefit would come if there were multiple SQL statements - but we only have one here? There was a problem hiding this comment. You are right; it is only one SQL statement, but it runs on all the samples of the RVI studies (quite a lot). Turning off auto-commit ensures the atomicity of the operation. |
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| ActiveRecord::Base.connection.execute(<<~SQLQUERY) | ||
| UPDATE sample_metadata | ||
| JOIN samples ON sample_metadata.sample_id = samples.id | ||
| JOIN study_samples ON sample_metadata.sample_id = study_samples.sample_id | ||
| JOIN studies ON study_samples.study_id = studies.id | ||
| SET sample_metadata.sample_public_name = samples.sanger_sample_id | ||
| WHERE studies.name = 'RVI Program - Bait Capture' AND sanger_sample_id LIKE 'RVI%'; | ||
| SQLQUERY | ||
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There was a problem hiding this comment. Did you consider whether to check if |
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| ActiveRecord::Base.connection.execute('COMMIT') | ||
| ActiveRecord::Base.connection.execute('SET autocommit = 1') | ||
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| puts 'Sample public names updated successfully for RVI Program - Bait Capture study.' | ||
| end | ||
| end | ||
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Using SQL directly means not using the ORM... which I think might mean you're bypassing some useful functionality. When a sample (and hopefully sample metadata) is updated, Sequencescape automatically updates the corresponding value in the MLWH (via the RabbitMQ queue). If you directly use SQL, I don't think this will happen.
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Good point!