uta schema overhaul

[reece]

This epic is an umbrella for UTA schema overhaul plans

Goals:

Admin changes

• enable schema migrations. This amounts to choosing between keeping SA and using Alembic, or ditching SA (and using direct SQL) with yoyo migrations (presumably).
• use py models?

Updated schema elements

• create index exon_set_alt_ac_method_idx on exon_set(alt_ac, alt_aln_method);
• exon sets defined on sequence digests (rather than accessions)
• sequence aliases (wholesale import from seqrepo?)
• exon-set-relationships view: exon-exon relationships based on digests
• store multiple alignments (currently, only 1 aln per <tx_ac, alt_ac, alt_aln_method>

New schema and content

• cds se on all coding exon sets
• digest table (linked to exon set, I think)
• assembly data
• LRG data
• exon set digests as PK
• alignment digests as PK
• gene-tx table

[github-actions]

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

[github-actions]

This issue was closed because it has been stalled for 7 days with no activity.

[reece]

This issue was closed by stalebot. It has been reopened to give more time for community review. See biocommons coding guidelines for stale issue and pull request policies. This resurrection is expected to be a one-time event.

[github-actions]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.