Owlready2's Hermit Vs Protege's Hermit or Pellet

[Jos Lehmann 2]

UPDATE (12/06/2025):


- As per first version of this post (below) Hermit was not working in owlready but both Hermit and Pellet worked in Protege;

- Then I tried Pellet in owlready and it did work;

- After some changes to the code, now in owlready Pellet returns the error below while Hermit seems to do nothing (the code completes but the inferred ontology is not written), while in Protege both Hermit and Pellet work.

KR, Jos

provenance-collection-v1  | * Owlready2 * Running Pellet...
provenance-collection-v1  |     java -Xmx2000M -cp /usr/local/lib/python3.11/site-packages/owlready2/pellet/log4j-api-2.19.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jgrapht-jdk1.5.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/xercesImpl-2.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/log4j-1.2-api-2.19.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/httpclient-4.2.3.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-tdb-0.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-iri-0.9.5.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/antlr-runtime-3.2.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/xml-apis-1.4.01.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/antlr-3.2.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jcl-over-slf4j-1.6.4.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/slf4j-log4j12-1.6.4.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/httpcore-4.2.2.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/log4j-core-2.19.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/commons-codec-1.6.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/slf4j-api-1.6.4.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/pellet-2.3.1.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-arq-2.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/aterm-java-1.6.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-core-2.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/owlapi-distribution-3.4.3-bin.jar pellet.Pellet realize --loader Jena --input-format N-Triples --ignore-imports /tmp/tmpestkd8q4
provenance-collection-v1  | Traceback (most recent call last):
-v1  |   File "/usr/local/lib/python3.11/site-packages/owlready2/reasoning.py", line 261, in sync_reasoner_pellet
-v1  |
-v1  |     output = subprocess.run(command, stdout = subprocess.PIPE, stderr = subprocess.PIPE, check = True, **_subprocess_kargs).stdout
-v1  |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-v1  |   File "/usr/local/lib/python3.11/subprocess.py", line 569, in run
-v1  |     raise CalledProcessError(retcode, process.args,
-v1  | subprocess.CalledProcessError: Command '['java', '-Xmx2000M', '-cp', '/usr/local/lib/python3.11/site-packages/owlready2/pellet/log4j-api-2.19.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jgrapht-jdk1.5.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/xercesImpl-2.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/log4j-1.2-api-2.19.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/httpclient-4.2.3.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-tdb-0.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-iri-0.9.5.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/antlr-runtime-3.2.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/xml-apis-1.4.01.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/antlr-3.2.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jcl-over-slf4j-1.6.4.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/slf4j-log4j12-1.6.4.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/httpcore-4.2.2.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/log4j-core-2.19.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/commons-codec-1.6.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/slf4j-api-1.6.4.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/pellet-2.3.1.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-arq-2.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/aterm-java-1.6.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/jena-core-2.10.0.jar:/usr/local/lib/python3.11/site-packages/owlready2/pellet/owlapi-distribution-3.4.3-bin.jar', 'pellet.Pellet', 'realize', '--loader', 'Jena', '--input-format', 'N-Triples', '--ignore-imports', '/tmp/tmpestkd8q4']' returned non-zero exit status 1.
-v1  |
-v1  | During handling of the above exception, another exception occurred:
-v1  |
-v1  | Traceback (most recent call last):
-v1  |   File "/home/ubuntu/git/DigECAT/ _v10b.py", line 906, in <module>
-v1  |     sync_reasoner_pellet()
-v1  |   File "/usr/local/lib/python3.11/site-packages/owlready2/reasoning.py", line 274, in sync_reasoner_pellet
-v1  |     raise OwlReadyJavaError("Java error message is:\n%s" % _decode((e.stderr or e.output or b"")))
-v1  | owlready2.base.OwlReadyJavaError: Java error message is:
-v1  | [line: 55149, col: 197] Triple not terminated by DOT: [INTEGER:3]
-v1  | Use -v for detail.



ORIGINAL (27/05/2025):


Hi there

Hermit gets stuck when reasoning on an ontology from owlready2 (lauched by sync()), while it does not get stuck (nor does Pellet) when reasoning on the same ontology from Protege.

In owlready it seems to complain about time (see bold bit of trace below).

Any idea why?

Please note: it is all running in wsl in a docker container...
Not sure that may be creating issues, at face value that does not seem to be the problem though.

KR, Jos



* Owlready2 * Running HermiT...
-v1  |     java -Xmx2000M -cp /usr/local/lib/python3.11/site-packages/owlready2/hermit:/usr/local/lib/python3.11/site-packages/owlready2/hermit/HermiT.jar org.semanticweb.HermiT.cli.CommandLine -c -O -D -I file:////tmp/tmpg0kb7cnz
-v1  | Traceback (most recent call last):
-v1  |   File "/usr/local/lib/python3.11/site-packages/owlready2/reasoning.py", line 149, in sync_reasoner_hermit
-v1  |     output = subprocess.check_output(command, stderr = subprocess.STDOUT, **_subprocess_kargs)
-v1  |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-v1  |   File "/usr/local/lib/python3.11/subprocess.py", line 465, in check_output
-v1  |     return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
-v1  |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-v1  |   File "/usr/local/lib/python3.11/subprocess.py", line 569, in run
-v1  |     raise CalledProcessError(retcode, process.args,
-v1  | subprocess.CalledProcessError: Command '['java', '-Xmx2000M', '-cp', '/usr/local/lib/python3.11/site-packages/owlready2/hermit:/usr/local/lib/python3.11/site-packages/owlready2/hermit/HermiT.jar', 'org.semanticweb.HermiT.cli.CommandLine', '-c', '-O', '-D', '-I', 'file:////tmp/tmpg0kb7cnz']' returned non-zero exit status 1.
-v1  |
-v1  | During handling of the above exception, another exception occurred:
-v1  |
-v1  | Traceback (most recent call last):
-v1  |   File "v10.py", line 41, in <module>
-v1  |     sync_reasoner()
-v1  |   File "/usr/local/lib/python3.11/site-packages/owlready2/reasoning.py", line 154, in sync_reasoner_hermit
-v1  |     raise OwlReadyJavaError("Java error message is:\n%s" % _decode(e.stderr or e.output or b""))
-v1  | owlready2.base.OwlReadyJavaError: Java error message is:
-v1  | Exception in thread "main" org.semanticweb.HermiT.datatypes.UnsupportedDatatypeException: HermiT supports all and only the datatypes of the OWL 2 datatype map, see
-v1  | http://www.w3.org/TR/owl2-syntax/#Datatype_Maps.
-v1  | The datatype 'http://www.w3.org/2001/XMLSchema#time' is not part of the OWL 2 datatype map and
-v1  | no custom datatype definition is given;
-v1  | therefore, HermiT cannot handle this datatype.
-v1  |     at org.semanticweb.HermiT.datatypes.DatatypeRegistry.getDatatypeHandlerFor(Unknown Source)