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Simplify HGVS errors in search #1113

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davmlaw opened this issue Jul 12, 2024 · 1 comment
Open

Simplify HGVS errors in search #1113

davmlaw opened this issue Jul 12, 2024 · 1 comment
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@davmlaw
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davmlaw commented Jul 12, 2024

Some HGVS errors are due to user input, some are due to implementation issues

For implementation details, that the user can do nothing about, we should just give a simplified error like "Cannot resolve HGVS"

We can separate this for admin/non admin

For non-admin examples of well formed HGVS that fail and they can do nothing about, eg:

NM_001145022.1:c.731C>T - This transcript exists, but we don't have it, or any versions for it - so will just sent to ClinGen and get back

Could not convert "NM_001145022:c.731C>T" - tried:
CLINGEN_ALLELE_REGISTRY as "NM_001145022.1:c.731C>T"

Some examples of bad HGVS that should be reported are:

  • NM_001145022.4:c.731C>T - we know this is a bad transcript
  • NM_004183.4:c.10889G>A - coordinate out of range
  • NM_004183.4:c.10880_10889delins9 - no sequence supplied
  • NM_004183.4:c.10880_10889 - bad HGVS

See examples from #830

@davmlaw davmlaw added bug Something isn't working search HGVS and removed bug Something isn't working labels Jul 12, 2024
@davmlaw davmlaw self-assigned this Jul 19, 2024
davmlaw added a commit that referenced this issue Aug 13, 2024
…ng in other. Make the error simpler for non-admin
davmlaw added a commit that referenced this issue Aug 14, 2024
davmlaw added a commit that referenced this issue Aug 14, 2024
@davmlaw
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davmlaw commented Aug 14, 2024

Have tried to go through and make all user errors appear, but I have probably missed some, happy to fix any examples you find

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