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Setting to reject symbolic variants #1114

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davmlaw opened this issue Jul 12, 2024 · 2 comments
Open

Setting to reject symbolic variants #1114

davmlaw opened this issue Jul 12, 2024 · 2 comments
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@davmlaw
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Shariant June 202...

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@davmlaw
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davmlaw commented Jul 12, 2024

Can reject in vcf_clean_and_filter
@davmlaw davmlaw self-assigned this Jul 12, 2024
@davmlaw davmlaw added this to the Shariant June 2024 Release milestone Jul 12, 2024
davmlaw added a commit that referenced this issue Jul 12, 2024
@davmlaw
issue #1114 - setting to reject symbolic variants
3510193
@davmlaw
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davmlaw commented Jul 12, 2024

@TheMadBug - 3510193 needs to be patched into shariant prod branch

This should just break everything really loudly if symbolics are ever used

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davmlaw commented Jul 12, 2024

@TheMadBug I made it throw an exception if a symbolic VariantCoordinate is ever instantiated

This may be too much and break migrations etc, so can just remove pedantic validation there

Reason was it left some imports hanging if you strip everything out if VCF will fix that monday

@davmlaw davmlaw mentioned this issue Jul 12, 2024
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TheMadBug pushed a commit that referenced this issue Jul 13, 2024
@davmlaw @TheMadBug
issue #1114 - setting to reject symbolic variants
0c460bd
TheMadBug added a commit that referenced this issue Jul 15, 2024
@TheMadBug
Squashed commit of the following:
a8419be 
commit 5a13047
Author: TheMadBug <[email protected]>
Date:   Sun Jul 14 00:50:04 2024 +1000

    Put more progress debug in one_off_fix_symbolic_variants

commit 7e3090d
Author: TheMadBug <[email protected]>
Date:   Sat Jul 13 23:54:08 2024 +1000

    Revert change that upgrade upgrade script to use sha before sha was in use

commit 9c54168
Author: TheMadBug <[email protected]>
Date:   Sat Jul 13 23:51:14 2024 +1000

    Update dependency of migrations (requires sha to be in place)

commit f75e9a4
Author: TheMadBug <[email protected]>
Date:   Sat Jul 13 20:13:01 2024 +1000

    Update deploy check to handle if Symbolic variants are disbaled

commit 1499a26
Author: TheMadBug <[email protected]>
Date:   Sat Jul 13 20:07:51 2024 +1000

    Fix error report on deploy check

commit aaac12f
Author: TheMadBug <[email protected]>
Date:   Sat Jul 13 20:05:08 2024 +1000

    Include error message for hgvs test

commit 0c460bd
Author: Dave Lawrence <[email protected]>
Date:   Fri Jul 12 17:20:31 2024 +0930

    issue #1114 - setting to reject symbolic variants
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