Comments (10)
andres-holvi
commented on July 28, 2024
2
It seems like [email protected] uses [email protected]. However, [email protected] has been released, and [email protected] breaks because of this libxml2 version mismatch (?)
Not sure who should be in charge of fixing this, but I suppose using [email protected] could work.
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eliasmazur
commented on July 28, 2024
1
I'm getting this same error on a container that I just re-compiled and it was working fine. I use python3-saml and that's breaking with this error when I run the container.
Here is the log:
[2024-05-20 02:54:20 +0000] [11] [ERROR] Exception in worker process
2024-05-19 22:54:20 Traceback (most recent call last):
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/arbiter.py", line 583, in spawn_worker
2024-05-19 22:54:20 worker.init_process()
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/workers/ggevent.py", line 203, in init_process
2024-05-19 22:54:20 super(GeventWorker, self).init_process()
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/workers/base.py", line 129, in init_process
2024-05-19 22:54:20 self.load_wsgi()
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/workers/base.py", line 138, in load_wsgi
2024-05-19 22:54:20 self.wsgi = self.app.wsgi()
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/app/base.py", line 67, in wsgi
2024-05-19 22:54:20 self.callable = self.load()
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/app/wsgiapp.py", line 52, in load
2024-05-19 22:54:20 return self.load_wsgiapp()
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/app/wsgiapp.py", line 41, in load_wsgiapp
2024-05-19 22:54:20 return util.import_app(self.app_uri)
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/gunicorn/util.py", line 350, in import_app
2024-05-19 22:54:20 __import__(module)
2024-05-19 22:54:20 File "/opt/app/tinyflask/__init__.py", line 11, in <module>
2024-05-19 22:54:20 import tinyflask.views
2024-05-19 22:54:20 File "/opt/app/tinyflask/views.py", line 24, in <module>
2024-05-19 22:54:20 from onelogin.saml2.auth import OneLogin_Saml2_Auth
2024-05-19 22:54:20 File "/usr/local/lib/python3.6/dist-packages/onelogin/saml2/auth.py", line 12, in <module>
2024-05-19 22:54:20 import xmlsec
2024-05-19 22:54:20 xmlsec.InternalError: (-1, 'lxml & xmlsec libxml2 library version mismatch')
2024-05-19 22:54:20 [2024-05-20 02:54:20 +0000] [11] [INFO] Worker exiting (pid: 11)
Here is my Dockerfile:
FROM ubuntu:bionic
RUN apt update
RUN apt-get update
RUN apt-get -y upgrade
RUN apt-get install -y pkg-config
RUN apt-get install -y software-properties-common apt-utils
RUN add-apt-repository -y ppa:deadsnakes/ppa
RUN apt-get install -y vim
RUN apt-get install -y python3.7
RUN apt-get install -y python3-pip
RUN apt-get install -y libxml2-dev libxmlsec1-dev
RUN mkdir -p /opt/app
WORKDIR /opt/app/
COPY . .
RUN pip3 install --upgrade pip
RUN pip3 install --no-cache-dir -r requirements.txt
RUN pip3 install python3-saml
RUN touch /var/log/cron.log
RUN echo "35 6 * * * root /usr/bin/python3 /opt/app/last_login.py >> /opt/app/audit.log" >> /etc/crontab
CMD (cron) && exec gunicorn tinyflask:app -b 0.0.0.0:80 --workers 3 -k gevent
And this is the requirements.txt:
Click==7.0
Flask==1.1.1
Flask-Cors==3.0.8
gevent==1.4.0
greenlet==0.4.15
gunicorn==19.9.0
itsdangerous==1.1.0
Jinja2==2.10.1
MarkupSafe==1.1.1
Werkzeug==0.15.5
flask-compress==1.4.0
requests==2.24.0
python-dateutil==2.8.0
pytz==2021.1
pickleshare==0.7.5
xmltodict
I'm stuck. Any help is appreciated.
Thanks
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gregbrant2
commented on July 28, 2024
1
@eliasmazur I have the same use case as you with python3-saml. Based on what @andersk said, I've restricted the package version of LXML like so
lxml >= 4.6.5, !=4.7.0, <=5.2.1
My build is working again now.
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andersk
commented on July 28, 2024
Some debugging information:
>>> import ctypes, lxml, xmlsec
>>> libxml2 = ctypes.CDLL("libxml2.so.2")
>>> ctypes.c_char_p.in_dll(libxml2, "xmlParserVersion").value
b'20913'
>>> lxml.etree.LIBXML_VERSION
(2, 12, 6)
>>> lxml.etree.LIBXML_COMPILED_VERSION
(2, 12, 6)
>>> xmlsec.get_libxml_version()
(2, 12, 6)
>>> xmlsec.get_libxml_compiled_version()
(2, 12, 6)xmlParserVersion, LIBXML_VERSION, and LIBXML_COMPILED_VERSION are the same inside and outside uWSGI.
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eliasmazur
commented on July 28, 2024
Thanks for the help. I realized I was restricting all packages except xmlsec. I restricted to an earlier version and it now works. Looks like python3-saml was installing the latest xmlsec and that was causing the mismatch.
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mstuttgart
commented on July 28, 2024
In my work, we use sigxml and xmlsec. Both install lxml with binaries, causing the same error.
xmlsec.InternalError: (-1, 'lxml & xmlsec libxml2 library version mismatch')
To resolve this, I install using the --no-binary pip flag. (work on Ubuntu 22.04, Python 3.10 and Pip 22.0.2)
pip install --no-binary lxml==4.6.3 lxml==4.6.3 --force-reinstall
pip install --no-binary xmlsec==1.3.13 xmlsec==1.3.13
pip install --no-binary signxml==3.2.2 signxml==3.2.2
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buddhi-vamsi13
commented on July 28, 2024
Thanks for the help. I realized I was restricting all packages except xmlsec. I restricted to an earlier version and it now works. Looks like python3-saml was installing the latest xmlsec and that was causing the mismatch.
Hi,
we have the similiar issue can you provide us the version which u have mentioned
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