Python package: genome view not loaded

[dmaziec]

I am trying to use the chromoscope package in Jupyter Notebook to load my data and use the genome view. However the view is not loading and the genome is not displayed. Please see my notebook below:

My configuration (public data):

[
    {
        "id": "SRR7890905",
        "cancer": "breast",
        "assembly": "hg38",
        "vcf": "https://somatic-browser-test.s3.amazonaws.com/SNV_test_tumor_normal_with_panel.vcf.gz",
        "vcfIndex": "https://somatic-browser-test.s3.amazonaws.com/SNV_test_tumor_normal_with_panel.vcf.gz.tbi",
        "vcf2": "https://somatic-browser-test.s3.amazonaws.com/INDEL_test_tumor_normal_with_panel.vcf.gz",
        "vcf2Index": "https://somatic-browser-test.s3.amazonaws.com/INDEL_test_tumor_normal_with_panel.vcf.gz.tbi",
        "sv": "https://somatic-browser-test.s3.amazonaws.com/SVTYPE_SV_test_tumor_normal_with_panel.bedpe",
        "cnv": 
"https://gist.githubusercontent.com/sehilyi/6fbceae35756b13472332d6b81b10803/raw/596428a8b0ebc00e7f8cbc52b050db0fbd6e19a5/SRR7890943.ascat.v3.cnv.tsv",
        "bam": "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam",
        "bai": "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam.bai",
        "note": "CNV profile - ASCAT. SVs - Sentieon. Mutations and indels - Sentieon"
    }
]

LINK to the browser with the data loaded. The error I found in the browser console:

To reproduce my environment:

pyenv virtualenv 3.8.12 chromoscope_3812
pyenv activate chromoscope_3812 
pip install ipython==8.12
pip install jupyterlab
pip install chromoscope

Please let me know if you have any ideas what might be wrong. Thank you, Dominika

[sehilyi]

@manzt Are you somehow familiar with this issue or know the potential source of this issue?

[manzt]

I am not able to reproduce this error locally. Could you share more information about your system/environment in which you are running the notebook?

npx envinfo --system --browsers

  System:
    OS: macOS 12.6
    CPU: (16) x64 Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
    Memory: 1000.78 MB / 32.00 GB
    Shell: 5.8.1 - /bin/zsh
  Browsers:
    Brave Browser: 101.1.38.111
    Chrome: 112.0.5615.137
    Chrome Canary: 115.0.5740.0
    Firefox Nightly: 113.0a1
    Safari: 16.0

python --version
# Python 3.8.12

pip freeze
# aiofiles==22.1.0
# aiosqlite==0.19.0
# anyio==3.6.2
# appnope==0.1.3
# argon2-cffi==21.3.0
# argon2-cffi-bindings==21.2.0
# arrow==1.2.3
# asttokens==2.2.1
# attrs==23.1.0
# Babel==2.12.1
# backcall==0.2.0
# beautifulsoup4==4.12.2
# bleach==6.0.0
# certifi==2022.12.7
# cffi==1.15.1
# charset-normalizer==3.1.0
# chromoscope==0.0.1
# click==8.1.3
# comm==0.1.3
# debugpy==1.6.7
# decorator==5.1.1
# defusedxml==0.7.1
# executing==1.2.0
# fastjsonschema==2.16.3
# fqdn==1.5.1
# h11==0.14.0
# idna==3.4
# importlib-metadata==6.6.0
# importlib-resources==5.12.0
# ipykernel==6.22.0
# ipython==8.12.0
# ipython-genutils==0.2.0
# isoduration==20.11.0
# jedi==0.18.2
# Jinja2==3.1.2
# json5==0.9.11
# jsonpointer==2.3
# jsonschema==4.17.3
# jupyter-events==0.6.3
# jupyter-ydoc==0.2.4
# jupyter_client==8.2.0
# jupyter_core==5.3.0
# jupyter_server==2.5.0
# jupyter_server_fileid==0.9.0
# jupyter_server_terminals==0.4.4
# jupyter_server_ydoc==0.8.0
# jupyterlab==3.6.3
# jupyterlab-pygments==0.2.2
# jupyterlab_server==2.22.1
# MarkupSafe==2.1.2
# matplotlib-inline==0.1.6
# mistune==2.0.5
# nbclassic==0.5.6
# nbclient==0.7.4
# nbconvert==7.3.1
# nbformat==5.8.0
# nest-asyncio==1.5.6
# notebook==6.5.4
# notebook_shim==0.2.3
# packaging==23.1
# pandocfilters==1.5.0
# parso==0.8.3
# pexpect==4.8.0
# pickleshare==0.7.5
# pkgutil_resolve_name==1.3.10
# platformdirs==3.5.0
# portpicker==1.5.2
# prometheus-client==0.16.0
# prompt-toolkit==3.0.38
# psutil==5.9.5
# ptyprocess==0.7.0
# pure-eval==0.2.2
# pycparser==2.21
# Pygments==2.15.1
# pyrsistent==0.19.3
# python-dateutil==2.8.2
# python-json-logger==2.0.7
# pytz==2023.3
# PyYAML==6.0
# pyzmq==25.0.2
# requests==2.29.0
# rfc3339-validator==0.1.4
# rfc3986-validator==0.1.1
# Send2Trash==1.8.2
# servir==0.0.6
# six==1.16.0
# sniffio==1.3.0
# soupsieve==2.4.1
# stack-data==0.6.2
# starlette==0.26.1
# terminado==0.17.1
# tinycss2==1.2.1
# tomli==2.0.1
# tornado==6.3.1
# traitlets==5.9.0
# typing_extensions==4.5.0
# uri-template==1.2.0
# urllib3==1.26.15
# uvicorn==0.22.0
# wcwidth==0.2.6
# webcolors==1.13
# webencodings==0.5.1
# websocket-client==1.5.1
# y-py==0.5.9
# ypy-websocket==0.8.2
# zipp==3.15.0

[dmaziec]

Yesterday I tried three different environments:

1. Initially I was using Jupyter Notebook App on HMS O2 (from HMS-RC Applications) . I used the following configuration:

2. Jupyter Notebook installed in Docker (Docker image: jupyterhub/jupyterhub) , and then I used Jupyter in my local browser.

3. Jupyter Notebook installed on an AWS EC2.

The error was the same in these three options; probably HMS O2 is the most straightforward way to reproduce it (if you have an account there).

I also see a warning that might be useful:

But today, I ran it locally on my computer and it loads perfectly fine without any issues!! ☺️ Would that mean it's only for local environments not "remote" ones? I usually keep data on EC2/O2 so I was trying to use it there first, but I can also use it on my computer for now.

[pagnasok]

Hi @dmaziec, would you be able to clarify how you were able to run it locally?

I am also trying to run locally but am just getting the homepage of Chromoscope. It seems like the command is not loading/processing the config variable. I am using VSC with python 3.9.4.

[sehilyi]

@pagnasok Thank you for the question and for finding this issue! This was a bug. We, at some point, changed the URL of the application, but it was not properly reflected on the Python package.

I just updated and released the Python package, so this should be addressed in chromoscope==0.0.3.

[pagnasok]

Thank you! I installed v0.0.3, and it seems to be working now.