feat(deposition): use foreign key constraints and use ORM with transactions and joins in more places

[anna-parker]

1. add proper foreign key annotations for all tables!
2. Reduce number of database calls:

• do status updates in batches where possible
• use transactions for syncing state across databases (no more splitting up updates SubmissionTable.StatusAll=SUBMITTED_SAMPLE and SampleTable.Status=SUBMITTED into 2 db calls)
• use table joins for getting sequence metadata from the SubmissionTable for submissions

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by appropriate, automated tests.
• Any manual testing that has been done is documented (i.e. what exactly was tested?)

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