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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
150 stars 46 forks source link

Error loading case general report #4864

Closed northwestwitch closed 1 week ago

northwestwitch commented 1 week ago 
2024-09-18 07:57:41,266 - [scout.server.app](http://scout.server.app/) - ERROR: Exception on /cust004/18701400006fam/case_report [GET] [in /venv/lib/python3.11/site-packages/flask/app.py:838]
Traceback (most recent call last):
  File "/venv/lib/python3.11/site-packages/flask/app.py", line 1473, in wsgi_app
    response = self.full_dispatch_request()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/flask/app.py", line 882, in full_dispatch_request
    rv = self.handle_user_exception(e)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/flask_cors/extension.py", line 194, in wrapped_function
    return cors_after_request(app.make_response(f(*args, **kwargs)))
                                                ^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/flask/app.py", line 880, in full_dispatch_request
    rv = self.dispatch_request()
         ^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.11/site-packages/flask/app.py", line 865, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/scout/server/utils.py", line 87, in decorated_function
    context = func(*args, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/scout/server/blueprints/cases/views.py", line 265, in case_report
    data = controllers.case_report_content(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/scout/server/blueprints/cases/controllers.py", line 709, in case_report_content
    case_report_variants(store, case_obj, institute_obj, data)
  File "/home/worker/app/scout/server/blueprints/cases/controllers.py", line 630, in case_report_variants
    _append_evaluated_variant_by_type(
  File "/home/worker/app/scout/server/blueprints/cases/controllers.py", line 663, in _append_evaluated_variant_by_type
    _get_decorated_var(var_obj=var_obj, institute_obj=institute_obj, case_obj=case_obj)
  File "/home/worker/app/scout/server/blueprints/cases/controllers.py", line 639, in _get_decorated_var
    return variant_decorator(
           ^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/scout/server/blueprints/variant/controllers.py", line 235, in variant
    add_gene_info(store, variant_obj, gene_panels=panels, genome_build=genome_build)
  File "/home/worker/app/scout/server/blueprints/variant/utils.py", line 264, in add_gene_info
    add_gene_links(variant_gene, genome_build, institute=institute)
  File "/home/worker/app/scout/server/links.py", line 85, in add_gene_links
    gene_obj["alamut_link"] = alamut_gene_link(institute, gene_obj, build)
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/worker/app/scout/server/links.py", line 844, in alamut_gene_link
    return url_template.format(
           ^^^^^^^^^^^^^^^^^^^^
KeyError: 'canonical_transcript'
northwestwitch commented 1 week ago

Looks like the "canonical_transcript" is missing in the variant gene, even if in the list of transcript there is one that is canonical.. weird!