Update sample_public_name for RVI Program - Bait Capture study #4586
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Particularly when it comes to creating new Orders from a SubmissionTemplate
There are more to add, but this is WIP
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Additional details and impacted files@@ Coverage Diff @@
## develop #4586 +/- ##
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- Coverage 89.30% 89.21% -0.09%
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Files 1406 1407 +1
Lines 30010 30018 +8
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- Hits 26799 26780 -19
- Misses 3211 3238 +27 ☔ View full report in Codecov by Sentry. |
sabrine33
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dasunpubudumal and
stevieing
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| 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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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?
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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.
| 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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Did you consider whether to check if sample_public_name already has a value, to avoid overwriting it if it has been intentionally set already?
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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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Oh and finally - What's your plan for testing? You could add some unit tests, or just test it in training (should definitely do this anyway). If just manual tests in training, you could put a couple of SQL queries here that you intend to run to check the data? Thanks! |
…ent updates if needed
Populate the sample_public_name field with sanger_sample_id values for samples associated with the 'RVI Program - Bait Capture' study, and where the sanger_sample_id starts with "RVI".