GeneGrid issues - GenCC for non-HGNC
- Dominant language
- Python
- Stars
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- 9h 28m
- Merged PRs (30d)
- 42
Description
1) Add "GenCC columsn, then add "T" gene - because it doesn't have HGNC get issue:
View details in Rollbar: [https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/4815](https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/4815)
```
Traceback (most recent call last):
File "/opt/variantgrid/env/lib/python3.11/site-packages/django/core/handlers/base.py", line 197, in _get_response
response = wrapped_callback(request, *callback_args, **callback_kwargs)
File "/opt/variantgrid/env/lib/python3.11/site-packages/django/views/decorators/csrf.py", line 56, in wrapper_view
return view_func(*args, **kwargs)
File "/opt/variantgrid/env/lib/python3.11/site-packages/django/views/generic/base.py", line 104, in view
return self.dispatch(request, *args, **kwargs)
File "/opt/variantgrid/env/lib/python3.11/site-packages/rest_framework/views.py", line 509, in dispatch
response = self.handle_exception(exc)
File "/opt/variantgrid/env/lib/python3.11/site-packages/rest_framework/views.py", line 469, in handle_exception
self.raise_uncaught_exception(exc)
File "/opt/variantgrid/env/lib/python3.11/site-packages/rest_framework/views.py", line 480, in raise_uncaught_exception
raise exc
File "/opt/variantgrid/env/lib/python3.11/site-packages/rest_framework/views.py", line 506, in dispatch
response = handler(request, *args, **kwargs)
File "/opt/variantgrid/env/lib/python3.11/site-packages/django/utils/decorators.py", line 46, in _wrapper
return bound_method(*args, **kwargs)
File "/opt/variantgrid/env/lib/python3.11/site-packages/django/utils/decorators.py", line 134, in _wrapper_view
response = view_func(request, *args, **kwargs)
File "/opt/variantgrid/ontology/views_rest.py", line 62, in get
for otr in ontology_version.gene_disease_relations(self.kwargs['gene_symbol'],
File "/opt/variantgrid/ontology/models/models_ontology.py", line 799, in gene_disease_relations
snake = self.terms_for_gene_symbol(gene_symbol, OntologyService.MONDO,
File "/opt/variantgrid/ontology/models/models_ontology.py", line 794, in terms_for_gene_symbol
return OntologySnake.terms_for_gene_symbol(gene_symbol, desired_ontology, max_depth=max_depth,
File "/opt/variantgrid/ontology/models/models_ontology.py", line 1089, in terms_for_gene_symbol
gene_ontology = OntologyTerm.get_gene_symbol(gene_symbol)
File "/opt/variantgrid/ontology/models/models_ontology.py", line 447, in get_gene_symbol
raise ValueError(f"Cannot find HGNC for {gene_symbol}")
ValueError: Cannot find HGNC for T
```
2) It appears that the "classification count" doesn't work
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