ImportError: cannot import name 'soft_unicode' from 'markupsafe'
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- Dominant language
- Python
- Stars
- 48
- Forks
- 42
- PR merge metrics
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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)
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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