Unit Ontology (UO) cant be loaded

[SmartMonkey-git]

Good day @ielis ,

I just tried loading the Unit Ontology using ontolius. I go the ontology from this link: https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/uo.owl

There error that I see is:

called `Result::unwrap()` on an `Err` value: OntologyFactoryError(CantBuild { source: Reading graph document

Caused by:
    0: Reading JSON
    1: expected value at line 1 column 1

Stack backtrace:
   0: std::backtrace_rs::backtrace::libunwind::trace
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9
   1: std::backtrace_rs::backtrace::trace_unsynchronized
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14
   2: std::backtrace::Backtrace::create
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/backtrace.rs:331:13
   3: <E as anyhow::context::ext::StdError>::ext_context
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.100/src/backtrace.rs:27:14
   4: anyhow::context::<impl anyhow::Context<T,E> for core::result::Result<T,E>>::context
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.100/src/context.rs:54:37
   5: obographs_dev::io::<impl obographs_dev::model::GraphDocument>::from_reader
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/obographs-dev-0.2.2/src/io.rs:23:42
   6: <ontolius::io::obographs::ObographsParser<TF,CU> as ontolius::io::OntologyDataParser<I,T>>::load_from_buf_read
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/obographs.rs:356:13
   7: ontolius::io::OntologyLoader<P>::load_from_buf_read
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/mod.rs:144:32
   8: ontolius::io::OntologyLoader<P>::load_from_read
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/mod.rs:134:14
   9: ontolius::io::OntologyLoader<P>::load_from_path
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/mod.rs:124:14
  10: phenoxtract::ontology::ontology_factory::CachedOntologyFactory::init_ontolius
             at ./src/ontology/ontology_factory.rs:291:31
  11: phenoxtract::ontology::ontology_factory::CachedOntologyFactory::build_ontology
             at ./src/ontology/ontology_factory.rs:125:13
  12: phenoxtract::ontology::ontology_factory::CachedOntologyFactory::build_bidict
             at ./src/ontology/ontology_factory.rs:169:14
  13: <phenoxtract::pipeline::Pipeline as core::convert::TryFrom<phenoxtract::config::pipeline_config::PipelineConfig>>::try_from
             at ./src/pipeline.rs:122:55
  14: <phenoxtract::pipeline::Pipeline as core::convert::TryFrom<phenoxtract::config::phenoxtracter_config::PhenoXtractorConfig>>::try_from
             at ./src/pipeline.rs:166:9
  15: phenoxtract::pipeline::tests::test_try_from_pipeline_config::test_try_from_pipeline_config
             at ./src/pipeline.rs:206:13
  16: phenoxtract::pipeline::tests::test_try_from_pipeline_config
             at ./src/pipeline.rs:198:5
  17: phenoxtract::pipeline::tests::test_try_from_pipeline_config::{{closure}}
             at ./src/pipeline.rs:198:14
  18: core::ops::function::FnOnce::call_once
             at /Users/rouvenreuter/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/src/rust/library/core/src/ops/function.rs:250:5
  19: core::ops::function::FnOnce::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/ops/function.rs:250:5
  20: test::__rust_begin_short_backtrace
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:648:18
  21: test::run_test_in_process::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:671:74
  22: <core::panic::unwind_safe::AssertUnwindSafe<F> as core::ops::function::FnOnce<()>>::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/panic/unwind_safe.rs:272:9
  23: std::panicking::catch_unwind::do_call
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:589:40
  24: std::panicking::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:552:19
  25: std::panic::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panic.rs:359:14
  26: test::run_test_in_process
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:671:27
  27: test::run_test::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:592:43
  28: test::run_test::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:622:41
  29: std::sys::backtrace::__rust_begin_short_backtrace
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/sys/backtrace.rs:152:18
  30: std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/thread/mod.rs:559:17
  31: <core::panic::unwind_safe::AssertUnwindSafe<F> as core::ops::function::FnOnce<()>>::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/panic/unwind_safe.rs:272:9
  32: std::panicking::catch_unwind::do_call
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:589:40
  33: std::panicking::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:552:19
  34: std::panic::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panic.rs:359:14
  35: std::thread::Builder::spawn_unchecked_::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/thread/mod.rs:557:30
  36: core::ops::function::FnOnce::call_once{{vtable.shim}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/ops/function.rs:250:5
  37: <alloc::boxed::Box<F,A> as core::ops::function::FnOnce<Args>>::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/alloc/src/boxed.rs:1966:9
  38: std::sys::pal::unix::thread::Thread::new::thread_start
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/sys/pal/unix/thread.rs:107:17
  39: __pthread_cond_wait, ontology: OntologyRef(ResourceRef { version: "latest", prefix_id: "UO" }) })
thread 'pipeline::tests::test_try_from_pipeline_config' panicked at src/pipeline.rs:206:48:
called `Result::unwrap()` on an `Err` value: OntologyFactoryError(CantBuild { source: Reading graph document

Caused by:
    0: Reading JSON
    1: expected value at line 1 column 1

Stack backtrace:
   0: std::backtrace_rs::backtrace::libunwind::trace
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9
   1: std::backtrace_rs::backtrace::trace_unsynchronized
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14
   2: std::backtrace::Backtrace::create
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/backtrace.rs:331:13
   3: <E as anyhow::context::ext::StdError>::ext_context
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.100/src/backtrace.rs:27:14
   4: anyhow::context::<impl anyhow::Context<T,E> for core::result::Result<T,E>>::context
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/anyhow-1.0.100/src/context.rs:54:37
   5: obographs_dev::io::<impl obographs_dev::model::GraphDocument>::from_reader
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/obographs-dev-0.2.2/src/io.rs:23:42
   6: <ontolius::io::obographs::ObographsParser<TF,CU> as ontolius::io::OntologyDataParser<I,T>>::load_from_buf_read
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/obographs.rs:356:13
   7: ontolius::io::OntologyLoader<P>::load_from_buf_read
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/mod.rs:144:32
   8: ontolius::io::OntologyLoader<P>::load_from_read
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/mod.rs:134:14
   9: ontolius::io::OntologyLoader<P>::load_from_path
             at /Users/rouvenreuter/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/ontolius-0.6.0/src/io/mod.rs:124:14
  10: phenoxtract::ontology::ontology_factory::CachedOntologyFactory::init_ontolius
             at ./src/ontology/ontology_factory.rs:291:31
  11: phenoxtract::ontology::ontology_factory::CachedOntologyFactory::build_ontology
             at ./src/ontology/ontology_factory.rs:125:13
  12: phenoxtract::ontology::ontology_factory::CachedOntologyFactory::build_bidict
             at ./src/ontology/ontology_factory.rs:169:14
  13: <phenoxtract::pipeline::Pipeline as core::convert::TryFrom<phenoxtract::config::pipeline_config::PipelineConfig>>::try_from
             at ./src/pipeline.rs:122:55
  14: <phenoxtract::pipeline::Pipeline as core::convert::TryFrom<phenoxtract::config::phenoxtracter_config::PhenoXtractorConfig>>::try_from
             at ./src/pipeline.rs:166:9
  15: phenoxtract::pipeline::tests::test_try_from_pipeline_config::test_try_from_pipeline_config
             at ./src/pipeline.rs:206:13
  16: phenoxtract::pipeline::tests::test_try_from_pipeline_config
             at ./src/pipeline.rs:198:5
  17: phenoxtract::pipeline::tests::test_try_from_pipeline_config::{{closure}}
             at ./src/pipeline.rs:198:14
  18: core::ops::function::FnOnce::call_once
             at /Users/rouvenreuter/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/src/rust/library/core/src/ops/function.rs:250:5
  19: core::ops::function::FnOnce::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/ops/function.rs:250:5
  20: test::__rust_begin_short_backtrace
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:648:18
  21: test::run_test_in_process::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:671:74
  22: <core::panic::unwind_safe::AssertUnwindSafe<F> as core::ops::function::FnOnce<()>>::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/panic/unwind_safe.rs:272:9
  23: std::panicking::catch_unwind::do_call
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:589:40
  24: std::panicking::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:552:19
  25: std::panic::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panic.rs:359:14
  26: test::run_test_in_process
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:671:27
  27: test::run_test::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:592:43
  28: test::run_test::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/test/src/lib.rs:622:41
  29: std::sys::backtrace::__rust_begin_short_backtrace
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/sys/backtrace.rs:152:18
  30: std::thread::Builder::spawn_unchecked_::{{closure}}::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/thread/mod.rs:559:17
  31: <core::panic::unwind_safe::AssertUnwindSafe<F> as core::ops::function::FnOnce<()>>::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/panic/unwind_safe.rs:272:9
  32: std::panicking::catch_unwind::do_call
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:589:40
  33: std::panicking::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:552:19
  34: std::panic::catch_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panic.rs:359:14
  35: std::thread::Builder::spawn_unchecked_::{{closure}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/thread/mod.rs:557:30
  36: core::ops::function::FnOnce::call_once{{vtable.shim}}
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/ops/function.rs:250:5
  37: <alloc::boxed::Box<F,A> as core::ops::function::FnOnce<Args>>::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/alloc/src/boxed.rs:1966:9
  38: std::sys::pal::unix::thread::Thread::new::thread_start
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/sys/pal/unix/thread.rs:107:17
  39: __pthread_cond_wait, ontology: OntologyRef(ResourceRef { version: "latest", prefix_id: "UO" }) })
stack backtrace:
   0: __rustc::rust_begin_unwind
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/std/src/panicking.rs:697:5
   1: core::panicking::panic_fmt
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/panicking.rs:75:14
   2: core::result::unwrap_failed
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/result.rs:1761:5
   3: core::result::Result<T,E>::unwrap
             at /Users/rouvenreuter/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/src/rust/library/core/src/result.rs:1167:23
   4: phenoxtract::pipeline::tests::test_try_from_pipeline_config::test_try_from_pipeline_config
             at ./src/pipeline.rs:206:48
   5: phenoxtract::pipeline::tests::test_try_from_pipeline_config
             at ./src/pipeline.rs:198:5
   6: phenoxtract::pipeline::tests::test_try_from_pipeline_config::{{closure}}
             at ./src/pipeline.rs:198:14
   7: core::ops::function::FnOnce::call_once
             at /Users/rouvenreuter/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/src/rust/library/core/src/ops/function.rs:250:5
   8: core::ops::function::FnOnce::call_once
             at /rustc/29483883eed69d5fb4db01964cdf2af4d86e9cb2/library/core/src/ops/function.rs:250:5
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.

Let me know if you need further information.

[ielis]

Hey, you seem to be loading an OWL file but Ontolius only supports loading Obograph JSON documents.

The UO provides a JSON file that looks OK on the first look (see /uo.json in the repo). However, chances are you will need to tweak Ontolius code a bit to make work, or that it will not work at all, and further work would be needed.

[iimpulse]

The other thing is that some ontologies dont follow "the standard". In which case, working with an expert to get it on par with what ontolius expects as a normal ontology.

[ielis]

Ontolius works with Obograph format and UO is available as an Obograph document. So, there was not too much work needed to make it work (work done in #64 ).