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ontodev / rdftab.rs

RDF Tables in Rust
BSD 3-Clause "New" or "Revised" License
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Can't load micro.owl with rdftab #21

Open turbomam opened 3 years ago

turbomam commented 3 years ago

I assume the problem is in the micro.owl content, not in the rdftab logic. I can robot convert micro.owl to Turtle, but I get a Content is not allowed in prolog error message when trying to convert the Turtle back to RDF/XML

With export RUST_BACKTRACE=full:

./rdftab multi_obo.db < micro.owl

thread 'main' panicked at 'called Result::unwrap() on an Err value: RdfXmlError { kind: Xml(EscapeError(UnrecognizedSymbol(1..4, Ok("obo")))) }', src/main.rs:57:5 stack backtrace: 0: 0x10fa1de45 - ::fmt::h30b85a1761190f28 1: 0x10fa3c44e - core::fmt::write::h5b0722e6ee659e34 2: 0x10fa1c269 - std::io::Write::write_fmt::hf468289e762fa2f9 3: 0x10fa20a9a - std::panicking::default_hook::{{closure}}::h836d46ca6b872224 4: 0x10fa207bf - std::panicking::default_hook::h2afcf1998cd93f8c 5: 0x10fa210ed - std::panicking::rust_panic_with_hook::he4f5d8b43533efd5 6: 0x10fa20c82 - rust_begin_unwind 7: 0x10fa3eacf - core::panicking::panic_fmt::h3559129da805eab4 8: 0x10fa3eb45 - core::result::unwrap_failed::h170de03e7ee26a1a 9: 0x10fa083a5 - rdftab::main::h1bc34813cbf130e1 10: 0x10f9f76a6 - std::rt::lang_start::{{closure}}::h63a82885a43041b4 11: 0x10fa20b58 - std::panicking::try::do_call::h29bd6a8b4eb65398 12: 0x10fa2918b - __rust_maybe_catch_panic 13: 0x10fa24389 - std::rt::lang_start_internal::h1cbb853ed77189ce 14: 0x10fa08559 - main

jamesaoverton commented 3 years ago

I think this is the same problem as https://github.com/ontodev/rdftab.rs/issues/17. It's been fixed upstream and we just need to roll that out.

jamesaoverton commented 3 years ago

Hmm. Rolling out that change is a bit tricky, and will have to wait until I'm back from vacation.

As a workaround, can you run robot convert -i micro.owl -o micro2.owl and then see if RDFTab works on micro2.owl?

turbomam commented 3 years ago

sure will do

cmungall commented 2 years ago

Yes, there is a problem with the OWL file from micro, reported in 2019: https://github.com/carrineblank/MicrO/issues/22

Same problem with http://www.biopax.org/release/biopax-level3.owl -- but in this case I'm not sure there is anthing wrong with the OWL? In any case the problem is easily fixed with the roundtrip via robot