ISA-tools / ISA-tools/isa-api

ImportError: cannot import name 'soft_unicode' from 'markupsafe'

Open
#476 5 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
48
Forks
42
PR merge metrics
No merged PRs in 30d

Description

FYI: seen at BioHackathon with @proccaserra

erwan@computer:~/Code/plant-brapi-to-isa$ sudo docker run -it -v /home/erwan/Code/plant-brapi-to-isa/outputdir:/outputdir brapi2isa -t aHR0cHM6Ly9kb2kub3JnLzEwLjE1NDU0L0lBU1NUTg%3D%3D -e https://urgi.versailles.inra.fr/faidare/brapi/v1/
[sudo] password for erwan: 
Traceback (most recent call last):
  File "/brapi_to_isa.py", line 12, in <module>
    from isatools.convert import isatab2json
  File "/usr/local/lib/python3.7/site-packages/isatools/__init__.py", line 20, in <module>
    from isatools.convert import (
  File "/usr/local/lib/python3.7/site-packages/isatools/convert/isatab2sra.py", line 9, in <module>
    from isatools.convert import isatab2json, json2sra
  File "/usr/local/lib/python3.7/site-packages/isatools/convert/json2sra.py", line 5, in <module>
    from isatools import isajson, sra
  File "/usr/local/lib/python3.7/site-packages/isatools/sra.py", line 17, in <module>
    import jinja2
  File "/usr/local/lib/python3.7/site-packages/jinja2/__init__.py", line 12, in <module>
    from .environment import Environment
  File "/usr/local/lib/python3.7/site-packages/jinja2/environment.py", line 25, in <module>
    from .defaults import BLOCK_END_STRING
  File "/usr/local/lib/python3.7/site-packages/jinja2/defaults.py", line 3, in <module>
    from .filters import FILTERS as DEFAULT_FILTERS  # noqa: F401
  File "/usr/local/lib/python3.7/site-packages/jinja2/filters.py", line 13, in <module>
    from markupsafe import soft_unicode
ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/usr/local/lib/python3.7/site-packages/markupsafe/__init__.py)

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

The traceback starts in brapi_to_isa.py, reaches isatools/sra.py, and fails while importing Jinja2 and MarkupSafe. Reproduce it with the shown Docker command and inspect the image's Python dependency metadata. Done means the container starts without this ImportError and the invocation proceeds further.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.