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:
Load a current tomte case, e.g. orientedsheepdog on stage
A few more of the DROP column headers have changed names:
hgnc_id
,gene_name_orig
andgene_type
have gone camel 🐫!In addition, we now have:
pairedEnd, dnaId, dropGroup, geneCountsFile, geneAnnotation, genome, utrOverlap
🐫🚀Also
nonsplitProportion_99quantile
is nownonsplitproportion99quantile
. 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
To Reproduce Steps to reproduce the behavior:
orientedsheepdog
on stage