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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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DROP TSV header - a few more headings camel case #4800

Closed dnil closed 3 weeks ago

dnil commented 1 month ago

A few more of the DROP column headers have changed names: hgnc_id, gene_name_orig and gene_type have gone camel 🐫!

In addition, we now have: pairedEnd, dnaId, dropGroup, geneCountsFile, geneAnnotation, genome, utrOverlap 🐫🚀

Also nonsplitProportion_99quantile is now nonsplitproportion99quantile. Might be a few more like that - let's see! Compare https://github.com/genomic-medicine-sweden/tomte/pull/132 I suspect!

We still have a few in partial or non-camel e.g. padjustGene, padjust, padjRank, abberrantbysample, aberrantbygene, normcounts, rawcounts, seqnames, nonsplitProportion, nonsplitCounts, but they will stay for now. Stay tuned... 😆

Describe the bug

  File "/home/proj/stage/bin/miniconda3/envs/S_scout/lib/python3.11/site-packages/pydantic/main.py", line 176, in __init__
    self.__pydantic_validator__.validate_python(data, self_instance=self)
pydantic_core._pydantic_core.ValidationError: 3 validation errors for OmicsVariantLoader
hgnc_id
  Field required [type=missing, input_value={'hgncId': '30577', 'gene...ncreasedUsage_clinical'}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.7/v/missing
gene_name_orig
  Field required [type=missing, input_value={'hgncId': '30577', 'gene...ncreasedUsage_clinical'}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.7/v/missing
gene_type
  Field required [type=missing, input_value={'hgncId': '30577', 'gene...ncreasedUsage_clinical'}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.7/v/missing

To Reproduce Steps to reproduce the behavior:

  1. Load a current tomte case, e.g. orientedsheepdog on stage
  2. Note validation errors