SACGF / SACGF/variantgrid

T2T allele liftover issues

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#1,220 0 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
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Python
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30
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9h 28m
Merged PRs (30d)
42

Description

* When you create a new genome build, it leaves a heap of alleles that need liftover. Should add something to deployment warnings saying to go to liftover page and click button for that build.
* If you click "liftover" on t2t on liftover page - it tries ClinGenAllele registry (which can't possibly work)
* I also ran into this problem:

```
File "/mnt/variantgrid/analysis/management/commands/fix_liftover_existing_variant_tags.py", line 23, in handle
create_liftover_pipelines(admin_bot(), alleles, ImportSource.COMMAND_LINE, genome_build)
File "/mnt/variantgrid/snpdb/liftover.py", line 86, in create_liftover_pipelines
AlleleLiftover.objects.bulk_create(allele_liftover_records, batch_size=2000)

psycopg2.errors.UniqueViolation: duplicate key value violates unique constraint "snpdb_liftovererror_liftover_id_allele_id_ac62c5c6_uniq"
DETAIL: Key (liftover_id, allele_id)=(4916, 72775) already exists.
```

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