SACGF / SACGF/variantgrid

Classification recalc_c_hgvs c.HGVS generation errors not captured

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#1,364 1 comment 0 reactions 1 assignee Claimed by @TheMadBug View on GitHub
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Python
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Description

Found while testing #1115 - to recreate:

* Import classification using c.HGVS field: NC_012920.1:m.11037_11038insT

This fails:

```
c_hgvs_resolution = self.recalc_c_hgvs()
^^^^^^^^^^^^^^^^^^^^
[2025-10-07 15:31:01,734: WARNING/ForkPoolWorker-2] File "/home/dlawrence/localwork/variantgrid/classification/models/classification_variant_info_models.py", line 193, in recalc_c_hgvs
hgvs_variant, used_converter_type, method = hgvs_matcher.variant_to_hgvs_variant_used_converter_type_and_method(variant, imported_transcript)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[2025-10-07 15:31:01,734: WARNING/ForkPoolWorker-2] File "/home/dlawrence/localwork/variantgrid/genes/hgvs/hgvs_matcher.py", line 569, in variant_to_hgvs_variant_used_converter_type_and_method
return self.variant_coordinate_to_hgvs_used_converter_type_and_method(variant.coordinate, transcript_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[2025-10-07 15:31:01,734: WARNING/ForkPoolWorker-2] File "/home/dlawrence/localwork/variantgrid/genes/hgvs/hgvs_matcher.py", line 507, in variant_coordinate_to_hgvs_used_converter_type_and_method
for transcript_version, potential_converter_type in self.filter_best_transcripts_and_converter_type_by_accession(transcript_accession):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[2025-10-07 15:31:01,734: WARNING/ForkPoolWorker-2] File "/home/dlawrence/localwork/variantgrid/genes/hgvs/hgvs_matcher.py", line 329, in filter_best_transcripts_and_converter_type_by_accession
TranscriptVersion.raise_bad_or_missing_transcript(transcript_accession)
[2025-10-07 15:31:01,734: WARNING/ForkPoolWorker-2] File "/home/dlawrence/localwork/variantgrid/genes/models.py", line 967, in raise_bad_or_missing_transcript
annotation_consortium = AnnotationConsortium.get_from_transcript_accession(transcript_accession).label
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[2025-10-07 15:31:01,734: WARNING/ForkPoolWorker-2] File "/home/dlawrence/localwork/variantgrid/genes/models_enums.py", line 19, in get_from_transcript_accession
raise ValueError(f"Couldn't determine annotation consortium for \"{transcript_accession}\"")
[2025-10-07 15:31:01,734: WARNING/ForkPoolWorker-2] ValueError: Couldn't determine annotation consortium for "NC_012920.1"
```

But it isn't captured and you can't see it here:

https://test.shariant.org.au/classification/imported_allele_info/67127?on_allele_page=false

We should capture it, and report it loudly so you can work out what's wrong

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