lightrdf.Error: error while parsing IRI '': No scheme found in an absolute IRI

[vadyushkins]

Hi @ozekik!

Thank you for the awesome library! :clap:

Unfortunately, while using your library, I got the error :bug: mentioned in the title. :disappointed: But using rdflib I was not getting a similar error. :thinking:

Environment

• OS: Ubuntu 20.04
• Python: 3.8.5
• LightRDF: 0.2.1

Steps to reproduce.

1. Download pathways archive.

wget -q https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/pathways.rdf.xz

2. Unzip it using xz package.

sudo apt install xz-utils
unxz pathways.rdf.xz 

3. Run count_triples_lightrdf_parser.py.

python3 count_triples_lightrdf_parser.py pathways.rdf

4. Error log.

Traceback (most recent call last):
  File "count_triples_lightrdf_parser.py", line 8, in <module>
    for triple in parser.parse(sys.argv[1]):
lightrdf.Error: error while parsing IRI '': No scheme found in an absolute IRI

Please tell me where I am wrong. Thank you :pray:

[ozekik]

I'm sorry for the late reply. Thank you for the very clear report!

A quick solution is to specify base_iri of parse() to some absolute URI (like https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/pathways.rdf.xz):

import lightrdf
import sys

parser = lightrdf.Parser()

cnt = 0

for triple in parser.parse(sys.argv[1], base_iri="https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/pathways.rdf.xz"):
    cnt += 1

print(cnt)

More specifically, the problem is <owl:Ontology rdf:about=""> in pathways.rdf, for rdf:about="" means "the URI of the document containing the ontology" (as stated in OWL1/2 specs and in general), but there is no definitive URI/IRI for downloaded local files.

RDFLib avoids this problem by using the local IRI of the file (file:///.../pathways.rdf) for base IRI by default. We may make lightrdf do the same thing, but before that I'd like to investigate if it is reasonable.

[vadyushkins]

Thanks for your reply @ozekik!

I think the best solution would be to put your example in the README, as the base IRI default setting might be more confusing in other situations.