excalibur initdb error on ubuntu

[1rdsk1]

hi, I'm trying to get excalbur to work in ubuntu but get below error. Gemini AI suggests: "The error message you're encountering with excalibur initdb suggests there's a compatibility issue within the excalibur package. It seems the package relies on the MutableMapping class from collections, which has been removed in Python 3.10 and above."

(excalibur) xxx:~$ excalibur initdb
Traceback (most recent call last):
File "/home/rupert/anaconda3/envs/excalibur/bin/excalibur", line 5, in
from excalibur.cli import cli
File "/home/rupert/anaconda3/envs/excalibur/lib/python3.12/site-packages/excalibur/cli.py", line 7, in
from . import version, settings
File "/home/rupert/anaconda3/envs/excalibur/lib/python3.12/site-packages/excalibur/settings.py", line 10, in
from . import configuration as conf
File "/home/rupert/anaconda3/envs/excalibur/lib/python3.12/site-packages/excalibur/configuration.py", line 7, in
from backports.configparser import ConfigParser
File "/home/rupert/anaconda3/envs/excalibur/lib/python3.12/site-packages/backports/configparser/init.py", line 130, in
from collections import MutableMapping
ImportError: cannot import name 'MutableMapping' from 'collections' (/home/rupert/anaconda3/envs/excalibur/lib/python3.12/collections/init.py)

[CHN-STUDENT]

also i get same error using my windows10, python 3.12.4

(venv) D:\python\camelot\excalibur>excalibur initdb
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "D:\python\camelot\venv\Scripts\excalibur.exe\__main__.py", line 4, in <module>
  File "D:\python\camelot\venv\Lib\site-packages\excalibur\cli.py", line 6, in <module>
    from . import settings, __version__
  File "D:\python\camelot\venv\Lib\site-packages\excalibur\settings.py", line 8, in <module>
    from . import configuration as conf
  File "D:\python\camelot\venv\Lib\site-packages\excalibur\configuration.py", line 4, in <module>
    from backports.configparser import ConfigParser
  File "D:\python\camelot\venv\Lib\site-packages\backports\configparser\__init__.py", line 130, in <module>
    from collections import MutableMapping
ImportError: cannot import name 'MutableMapping' from 'collections' (C:\Program Files\Python312\Lib\collections\__init__.py)

[dnlzm]

this might help: https://stackoverflow.com/questions/70870041/cannot-import-name-mutablemapping-from-collections

[fl4p]

>>> from collections import MutableMapping
<stdin>:1: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working

use python<3.10, like your AI prompt already pointed out

[nicolnt]

I initially installed Excalibur without changing python version, so it used python 3.10. Then after getting the same error message as mentioned and seeing this comment:

use python<3.10, like your AI prompt already pointed out

I created a new conda environment "excalibur" with python 3.9 and installed Excalibur here.

python --version
Python 3.9.21

Excalibur installation console log: ERROR

(excalibur) nicolas@computer:~$ pip3 install excalibur-py
Collecting excalibur-py
  Using cached excalibur_py-1.0.1-py3-none-any.whl.metadata (7.9 kB)
Requirement already satisfied: camelot-py>=1.0.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (1.0.0)
Requirement already satisfied: celery>=4.1.1 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (5.4.0)
Requirement already satisfied: click>=8.0.1 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (8.1.8)
Requirement already satisfied: configparser>=7.1.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (7.1.0)
Requirement already satisfied: Flask>=3.1.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (3.1.0)
Requirement already satisfied: SQLAlchemy>=1.2.12 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (2.0.37)
Requirement already satisfied: Werkzeug>=3.1.3 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (3.1.3)
Requirement already satisfied: pypdfium2>=4 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (4.30.1)
Requirement already satisfied: Pillow>=11.1.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from excalibur-py) (11.1.0)
Requirement already satisfied: chardet>=5.1.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (5.2.0)
Requirement already satisfied: numpy>=1.24.4 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (2.0.2)
Requirement already satisfied: openpyxl>=3.1.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (3.1.5)
Requirement already satisfied: pdfminer-six>=20240706 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (20240706)
Requirement already satisfied: pypdf<4.0,>=3.17 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (3.17.4)
Requirement already satisfied: pandas>=1.5.3 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (2.2.3)
Requirement already satisfied: tabulate>=0.9.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (0.9.0)
Requirement already satisfied: typing-extensions>=4.12.2 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (4.12.2)
Requirement already satisfied: opencv-python-headless>=4.7.0.68 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from camelot-py>=1.0.0->excalibur-py) (4.10.0.84)
Requirement already satisfied: billiard<5.0,>=4.2.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (4.2.1)
Requirement already satisfied: kombu<6.0,>=5.3.4 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (5.4.2)
Requirement already satisfied: vine<6.0,>=5.1.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (5.1.0)
Requirement already satisfied: click-didyoumean>=0.3.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (0.3.1)
Requirement already satisfied: click-repl>=0.2.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (0.3.0)
Requirement already satisfied: click-plugins>=1.1.1 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (1.1.1)
Requirement already satisfied: tzdata>=2022.7 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (2024.2)
Requirement already satisfied: python-dateutil>=2.8.2 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from celery>=4.1.1->excalibur-py) (2.9.0.post0)
Requirement already satisfied: Jinja2>=3.1.2 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from Flask>=3.1.0->excalibur-py) (3.1.5)
Requirement already satisfied: itsdangerous>=2.2 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from Flask>=3.1.0->excalibur-py) (2.2.0)
Requirement already satisfied: blinker>=1.9 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from Flask>=3.1.0->excalibur-py) (1.9.0)
Requirement already satisfied: importlib-metadata>=3.6 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from Flask>=3.1.0->excalibur-py) (8.5.0)
Requirement already satisfied: greenlet!=0.4.17 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from SQLAlchemy>=1.2.12->excalibur-py) (3.1.1)
Requirement already satisfied: MarkupSafe>=2.1.1 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from Werkzeug>=3.1.3->excalibur-py) (3.0.2)
Requirement already satisfied: prompt-toolkit>=3.0.36 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from click-repl>=0.2.0->celery>=4.1.1->excalibur-py) (3.0.48)
Requirement already satisfied: zipp>=3.20 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from importlib-metadata>=3.6->Flask>=3.1.0->excalibur-py) (3.21.0)
Requirement already satisfied: amqp<6.0.0,>=5.1.1 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from kombu<6.0,>=5.3.4->celery>=4.1.1->excalibur-py) (5.3.1)
Requirement already satisfied: et-xmlfile in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from openpyxl>=3.1.0->camelot-py>=1.0.0->excalibur-py) (2.0.0)
Requirement already satisfied: pytz>=2020.1 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from pandas>=1.5.3->camelot-py>=1.0.0->excalibur-py) (2024.2)
Requirement already satisfied: charset-normalizer>=2.0.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from pdfminer-six>=20240706->camelot-py>=1.0.0->excalibur-py) (3.4.1)
Requirement already satisfied: cryptography>=36.0.0 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from pdfminer-six>=20240706->camelot-py>=1.0.0->excalibur-py) (44.0.0)
Requirement already satisfied: six>=1.5 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from python-dateutil>=2.8.2->celery>=4.1.1->excalibur-py) (1.17.0)
Requirement already satisfied: cffi>=1.12 in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from cryptography>=36.0.0->pdfminer-six>=20240706->camelot-py>=1.0.0->excalibur-py) (1.17.1)
Requirement already satisfied: wcwidth in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from prompt-toolkit>=3.0.36->click-repl>=0.2.0->celery>=4.1.1->excalibur-py) (0.2.13)
Requirement already satisfied: pycparser in ./miniconda3/envs/excalibur/lib/python3.9/site-packages (from cffi>=1.12->cryptography>=36.0.0->pdfminer-six>=20240706->camelot-py>=1.0.0->excalibur-py) (2.22)
Using cached excalibur_py-1.0.1-py3-none-any.whl (1.5 MB)
Installing collected packages: excalibur-py
Successfully installed excalibur-py-1.0.1

But surprisingly it's still using some library files with python 3.10

Excalibur init console log: OK

(excalibur) nicolas@computer:~$ excalibur initdb
Traceback (most recent call last):
  File "/home/nicolas/.local/bin/excalibur", line 5, in <module>
    from excalibur.cli import cli
  File "/home/nicolas/.local/lib/python3.10/site-packages/excalibur/cli.py", line 7, in <module>
    from . import __version__, settings
  File "/home/nicolas/.local/lib/python3.10/site-packages/excalibur/settings.py", line 10, in <module>
    from . import configuration as conf
  File "/home/nicolas/.local/lib/python3.10/site-packages/excalibur/configuration.py", line 7, in <module>
    from backports.configparser import ConfigParser
  File "/home/nicolas/.local/lib/python3.10/site-packages/backports/configparser/__init__.py", line 130, in <module>
    from collections import MutableMapping

Forcing to use the python version of the environment I managed to start it but still I cannot import a PDF

(excalibur) nicolas@computer:~$ python -m excalibur initdb
/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/pypdf/_crypt_providers/_cryptography.py:32: CryptographyDeprecationWarning: ARC4 has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.ARC4 and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.
  from cryptography.hazmat.primitives.ciphers.algorithms import AES, ARC4

When I upload the file, I get an error both in the console and on the webpage

(excalibur) nicolas@computer:~$ python -m excalibur webserver
/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/pypdf/_crypt_providers/_cryptography.py:32: CryptographyDeprecationWarning: ARC4 has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.ARC4 and will be removed from cryptography.hazmat.primitives.ciphers.algorithms in 48.0.0.
  from cryptography.hazmat.primitives.ciphers.algorithms import AES, ARC4
 * Serving Flask app 'excalibur.www.app'
 * Debug mode: off
WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.
 * Running on http://127.0.0.1:5000
Press CTRL+C to quit
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET / HTTP/1.1" 302 -
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET /files HTTP/1.1" 200 -
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET /static/js/vendor/popper.min.js HTTP/1.1" 200 -
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET /static/js/vendor/bootstrap.min.js HTTP/1.1" 200 -
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET /static/css/base.css HTTP/1.1" 200 -
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET /static/css/vendor/bootstrap.min.css HTTP/1.1" 200 -
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET /static/js/vendor/jquery-3.3.1.min.js HTTP/1.1" 200 -
127.0.0.1 - - [13/Jan/2025 11:24:35] "GET /static/js/files.js HTTP/1.1" 200 -
127.0.0.1 - - [13/Jan/2025 11:33:53] "POST /files HTTP/1.1" 200 -
[2025-01-13 11:33:53,911] ERROR in app: Exception on /workspaces/66e7c8f7-9cd3-4909-b7ef-b63dabc7ee1c [GET]
Traceback (most recent call last):
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/flask/app.py", line 1511, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/flask/app.py", line 919, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/flask/app.py", line 917, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/flask/app.py", line 902, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)  # type: ignore[no-any-return]
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/excalibur/www/views.py", line 106, in workspaces
    return render_template(
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/flask/templating.py", line 150, in render_template
    return _render(app, template, context)
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/flask/templating.py", line 131, in _render
    rv = template.render(context)
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/jinja2/environment.py", line 1295, in render
    self.environment.handle_exception()
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/jinja2/environment.py", line 942, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/excalibur/www/templates/workspace.html", line 1, in top-level template code
    {% extends "base.html" %}
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/excalibur/www/templates/base.html", line 61, in top-level template code
    {% block workspace %}{% endblock %}
  File "/home/nicolas/miniconda3/envs/excalibur/lib/python3.9/site-packages/excalibur/www/templates/workspace.html", line 12, in block 'workspace'
    {% if imagepaths is not none or imagepaths|length == 0 %}
TypeError: object of type 'NoneType' has no len()
127.0.0.1 - - [13/Jan/2025 11:33:53] "GET /workspaces/66e7c8f7-9cd3-4909-b7ef-b63dabc7ee1c HTTP/1.1" 500 -
127.0.0.1 - - [13/Jan/2025 11:33:53] "GET /favicon.ico HTTP/1.1" 404 -
Traceback (most recent call last):
  File "/home/nicolas/.local/bin/excalibur", line 5, in <module>
    from excalibur.cli import cli
  File "/home/nicolas/.local/lib/python3.10/site-packages/excalibur/cli.py", line 7, in <module>
    from . import __version__, settings
  File "/home/nicolas/.local/lib/python3.10/site-packages/excalibur/settings.py", line 10, in <module>
    from . import configuration as conf
  File "/home/nicolas/.local/lib/python3.10/site-packages/excalibur/configuration.py", line 7, in <module>
    from backports.configparser import ConfigParser
  File "/home/nicolas/.local/lib/python3.10/site-packages/backports/configparser/__init__.py", line 130, in <module>
    from collections import MutableMapping
ImportError: cannot import name 'MutableMapping' from 'collections' (/usr/lib/python3.10/collections/__init__.py)