renku graph export failed after importing DS from Zenodo

[jachro]

Describe the bug
I'm not sure if that's very specific to my project (https://dev.renku.ch/projects/jakub.chrobasik/create-test-1) but when I imported a DS from Zenodo (in fact it was there was only a single PDF) https://dev.renku.ch/projects/jakub.chrobasik/create-test-1/datasets/biodiversity_and_healthy/ TG failed during renku graph export with the following error:

caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
caught a TypeError, retrying call to <class 'pyshacl.monkey.memory2.Memory2'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info; 
Traceback (most recent call last):; 
File \"/home/tguser/.local/lib/python3.11/site-packages/rdflib/namespace/__init__.py\", line 636, in _store_bind; 
return self.store.bind(prefix, namespace, override=override); 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^; 
TypeError: Memory2.bind() got an unexpected keyword argument 'override'; 
Error: Validation Report; 
Conforms: False; 
Results (1):; 
Constraint Violation in PatternConstraintComponent (http://www.w3.org/ns/shacl#PatternConstraintComponent):; 
Severity: sh:Violation; 
Source Shape: [ sh:class schema1:ImageObject ; 
sh:path schema1:image ; 
sh:pattern Literal(\"http(s)?://[^/]+/datasets/[0-9a-f]+/images/[0-9]+\") ]; 
Focus Node: <https://renku-kg-dev.dev.renku.ch/datasets/7eea74351bd743858b794e67012bc51f>; 
Value Node: <https://renku-kg-dev.dev.renku.ch/static/img/logos/zenodo-gradient-round.svg>; 
Result Path: schema1:image; 
Message: Value does not match pattern 'http(s)?://[^/]+/datasets/[0-9a-f]+/images/[0-9]+'; 
; 
Couldn't export: Invalid Knowledge Graph data

By the way
It looks like importing from Dataverse works (the way the acceptance tests do)
renku dataset import --name flight-data https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/WTZS4K

Link to project
https://dev.renku.ch/projects/jakub.chrobasik/create-test-1
DS
https://dev.renku.ch/projects/jakub.chrobasik/create-test-1/datasets/biodiversity_and_healthy/

To Reproduce
Steps to reproduce the behavior:

1. Create a project
2. start a session
3. do renku dataset import 10.5281/zenodo.7822477
4. processing in TG fails

Expected behavior
I expected the renku graph export to work :)

Run environment (please complete the following information):

• renku-python: 2.6.1
• Python version: 3.10.11
• in-browser session