Scout: Error when creating general report

[northwestwitch]

Traceback (most recent call last):
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 2446, in wsgi_app
response = self.full_dispatch_request()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1951, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1820, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/_compat.py", line 39, in reraise
raise value
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1949, in full_dispatch_request
rv = self.dispatch_request()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/app.py", line 1935, in dispatch_request
return self.view_functionsrule.endpoint
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/utils.py", line 28, in decorated_function
return render_template(template_name, *context)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/templating.py", line 140, in render_template
ctx.app,
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/flask/templating.py", line 120, in _render
rv = template.render(context)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/jinja2/environment.py", line 1090, in render
self.environment.handle_exception()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/jinja2/environment.py", line 832, in handle_exception
reraise(rewrite_traceback_stack(source=source))
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/jinja2/_compat.py", line 28, in reraise
raise value.with_traceback(tb)
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/cases/templates/cases/case_report.html", line 1110, in top-level template code
{% for comment in variant.comments %}
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/templates/report_base.html", line 14, in top-level template code
{% block body %}
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/cases/templates/cases/case_report.html", line 58, in block "body"
{{ pinned_panel() }}
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/jinja2/runtime.py", line 679, in _invoke
rv = self._func(arguments)
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/cases/templates/cases/case_report.html", line 300, in template
{{ sv_variant_content(pinned, loop.index) }}
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/jinja2/runtime.py", line 679, in _invoke
rv = self._func(arguments)
File "/home/hiseq.clinical/SERVER/apps/scout/git/scout/scout/server/blueprints/cases/templates/cases/case_report.html", line 986, in template

ValueError: too many values to unpack (expected 2)

[hassanfa]

To Chiara: https://i.imgur.com/XleZ71U.gifv :-)

[northwestwitch]

I can't reproduce the error with the default demo sample, must something related to the specific case(s)

[dnil]

And perhaps with a macro that is shared through "utils"? Renaming those into more object like hierarchies at some point will shed some light on many things.

[northwestwitch]

But in theory general report should not be importing stuff from other files. All the used macros are there in the file already

[dnil]

Oooh, interesting!

[northwestwitch]

Ok it has to do with SVs, reproduced by marking a SV as causative

[dnil]

😊

[dnil]

I can't see your picture, but SVs and unexpectedly many values to unpack does hint at an array of gene names..

[northwestwitch]

Sorry, this loop here:

Apparently we are unpacking just 2 items for each element of the list

But each tuple has 3.

[('GnomAD', 'NA', None), ('1000G(left)', 0.000998400035314262, None), ('1000G(right)', 0.000998400035314262, None)]

[northwestwitch]

What's this None that appears now?

[dnil]

Sorry, was over at paper resubmission. Something brand new it seems! Will check!

[dnil]

from .utils import (
    add_gene_info,
    callers,
    clinsig_human,
    default_panels,
    end_position,
    evaluation,
**frequency,**
    is_affected,
    predictions,
**frequencies,**
)

...

variant_obj.update(get_variant_links(variant_obj, int(genome_build)))
    variant_obj["frequencies"] = **frequencies**(variant_obj)
    if variant_type in ["snv", "cancer"]:
        # This is to convert a summary of frequencies to a string
        variant_obj["frequency"] = **frequency**(variant_obj)

There is no way this could go wrong. ⛑

[northwestwitch]

The code was actually changed some days ago:

In here: https://github.com/Clinical-Genomics/scout/commit/e5468f439ee9c89fe68280ebb3cffe76611a53d7#diff-d9cb1085635fe83b6a8e3b4b9677c9d2

[northwestwitch]

@moonso shall we have this link item in the frequencies or we can remove it? In this case the report will work if we leave it unchanged.

[northwestwitch]

from .utils import (
    add_gene_info,
    callers,
    clinsig_human,
    default_panels,
    end_position,
    evaluation,
**frequency,**
    is_affected,
    predictions,
**frequencies,**
)

...

variant_obj.update(get_variant_links(variant_obj, int(genome_build)))
    variant_obj["frequencies"] = **frequencies**(variant_obj)
    if variant_type in ["snv", "cancer"]:
        # This is to convert a summary of frequencies to a string
        variant_obj["frequency"] = **frequency**(variant_obj)

There is no way this could go wrong. ⛑

Where is this?

[dnil]

in utils ofcourse, where else? 😜

[dnil]

server.blueprints.variant.utils

[dnil]

Note to self and others: there are other variant types that cancer, snv and sv now..

[northwestwitch]

I'm very tired at the moment and I feel like whatever I touch has the potential to go wrong. I'll continue tomorrow!

[dnil]

Which is ofcourse the same as you linked. I am also quite tired - that adrenaline is wearing off.. 😅

[northwestwitch]

Tomorrow then!

[dnil]

I'll just test your PR, then call it a day. After reading this it seems it should cover most of what worked before.