Code Monkey home page Code Monkey logo

Comments (2)

kunalchandan avatar kunalchandan commented on August 19, 2024

This probably arose as a result of my account being removed, I believe that it was some .bed files that it may have been pointing to.
I'm not sure where it crashed, but I believe one place to help catch this could be:

cbioportal_tools/src/lib/support/helper.py

Lines 132 to 143 in ca7df1d

if input_file.endswith(".tar.gz"):
call_shell("tar -xzf {} -C {}".format(input_file, temp), verb)
mutate_config.data_frame['FILE_NAME'][i] = mutate_config.data_frame['FILE_NAME'][i].strip('.tar.gz')
elif input_file.endswith('.gz'):
call_shell("zcat {} > {}".format(input_file, output_file.strip('.gz')), verb)
mutate_config.data_frame['FILE_NAME'][i] = mutate_config.data_frame['FILE_NAME'][i].strip('.gz')
else:
call_shell("cp {} {}".format(input_file, output_file), verb)

Get the exit code for each call_shell, then:

if any(exit_codes)
    print('there is a missing file')
    exit(1)

from cbioportal_tools.

iainrb avatar iainrb commented on August 19, 2024

This issue is a subset of #87

from cbioportal_tools.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.