Comments (3)
trungdong
commented on August 25, 2024
Hello, could you provide an example where it failed? I'm not sure what issue you are having at the moment.
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NathanCummings
commented on August 25, 2024
I'm filling a ProvDocument programmatically by reading the metadata. In the event that someone hasn't filled a field, I am trying to define a namespace with an empty string. When this happens, I don't get an exception thrown until I come to serialise the document. Now of course, I have encountered the problem and built a check into my code, but in a more complex pipeline, the error I received and the point in the code that it was thrown did not make it clear where the problem was. An earlier check on the call to add_namespace() would have told me which namespace was invalid.
Traceback (most recent call last):
File "/afs/eufus.eu/g2itmdev/user/g2ncummi/fusionprov/venv/bin/imasprov", line 11, in <module>
load_entry_point('fusionprov==0.1.4', 'console_scripts', 'imasprov')()
File "/afs/eufus.eu/g2itmdev/user/g2ncummi/fusionprov/venv/lib/python3.6/site-packages/fusionprov/imasprov.py", line 225, in main
ids_prov.prov_from_data_ids(graph=args.graph)
File "/afs/eufus.eu/g2itmdev/user/g2ncummi/fusionprov/venv/lib/python3.6/site-packages/fusionprov/imasprov.py", line 197, in prov_from_data_ids
self.serialize_provenance(graph=graph)
File "/afs/eufus.eu/g2itmdev/user/g2ncummi/fusionprov/venv/lib/python3.6/site-packages/fusionprov/imasprov.py", line 139, in serialize_provenance
self.prov_doc.serialize(xml_path, format="xml")
File "/afs/eufus.eu/g2itmdev/user/g2ncummi/fusionprov/venv/lib/python3.6/site-packages/prov/model.py", line 2494, in serialize
serializer.serialize(stream, **args)
File "/afs/eufus.eu/g2itmdev/user/g2ncummi/fusionprov/venv/lib/python3.6/site-packages/prov/serializers/provxml.py", line 52, in serialize
xml_root = self.serialize_bundle(bundle=self.document, force_types=force_types)
File "/afs/eufus.eu/g2itmdev/user/g2ncummi/fusionprov/venv/lib/python3.6/site-packages/prov/serializers/provxml.py", line 110, in serialize_bundle
xml_bundle_root = etree.Element(_ns_prov("document"), nsmap=nsmap)
File "src/lxml/etree.pyx", line 3022, in lxml.etree.Element
File "src/lxml/apihelpers.pxi", line 131, in lxml.etree._makeElement
File "src/lxml/apihelpers.pxi", line 118, in lxml.etree._makeElement
File "src/lxml/apihelpers.pxi", line 219, in lxml.etree._setNodeNamespaces
File "src/lxml/apihelpers.pxi", line 1749, in lxml.etree._prefixValidOrRaise
ValueError: Invalid namespace prefix ''
In a script with multiple namespaces defined, the above traceback does not indicate where the problem occurred, as the error isn't caught until much later.
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trungdong
commented on August 25, 2024
Thanks for the information, Nathan. I'll pop this test in the code next time.
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Related Issues (20)
- Sphinx docs don't contain prov_to_graph HOT 1
- missing label property in ProvBundle class HOT 3
- More example usages HOT 2
- prefixes from external context HOT 1
- pydot would not work until I installed graphviz on macOS HOT 2
- No type hints for ProvDocument.agent etc. HOT 1
- ProvDocument.set_default_namespace doesn't add to namespaces list HOT 1
- JSON deserialisation/serialisation: objects are duplicated HOT 2
- New ProvRecord objects aren't added to bundles HOT 2
- RecursionError when using .serialize
- Newbie question on how to work with thematic ontologies HOT 3
- Add prov_doc to jena datastore? HOT 1
- serialization takes a long time HOT 3
- failing test when building HOT 1
- Adding a rdfs:label or description to Prov:Activity HOT 3
- ProvRecord.get_attribute behaviour differs from its doc string
- Add convenient assertion methods for revision, quotation, primary source, mention & influence records
- XML deserialization with prov as default namespace
- Numerous tests fail with `_pytest.outcomes.XFailed` and other issues HOT 4
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