Re: Pellet error - AttributeError: 'CompletedProcess' object has no attribute 'decode'
Posted by
stelios on
URL: http://owlready.306.s1.nabble.com/Pellet-error-AttributeError-CompletedProcess-object-has-no-attribute-decode-tp2701p2703.html
Hi Carsten, thanks for your quick response.
I added your fix to my setup but another error is thrown.
Specifically:
* Owlready2 * Warning: optimized Cython parser module 'owlready2_optimized' is not available, defaulting to slower Python implementation
* Owlready2 * Running Pellet...
java -Xmx2000M -cp /home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/slf4j-api-1.6.4.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jgrapht-jdk1.5.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/slf4j-log4j12-1.6.4.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/aterm-java-1.6.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/pellet-2.3.1.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/log4j-1.2.16.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-tdb-0.10.0.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/xml-apis-1.4.01.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/antlr-runtime-3.2.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/xercesImpl-2.10.0.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/httpcore-4.2.2.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-iri-0.9.5.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/antlr-3.2.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/httpclient-4.2.3.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/owlapi-distribution-3.4.3-bin.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-arq-2.10.0.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/commons-codec-1.6.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jcl-over-slf4j-1.6.4.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-core-2.10.0.jar pellet.Pellet realize --loader Jena --input-format N-Triples --ignore-imports /tmp/tmpt9he5926
Traceback (most recent call last):
File "/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/reasoning.py", line 271, in sync_reasoner_pellet
output = subprocess.run(command, stdout = subprocess.PIPE, stderr = subprocess.PIPE, check = True, **_subprocess_kargs).stdout
File "/usr/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['java', '-Xmx2000M', '-cp', '/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/slf4j-api-1.6.4.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jgrapht-jdk1.5.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/slf4j-log4j12-1.6.4.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/aterm-java-1.6.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/pellet-2.3.1.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/log4j-1.2.16.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-tdb-0.10.0.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/xml-apis-1.4.01.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/antlr-runtime-3.2.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/xercesImpl-2.10.0.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/httpcore-4.2.2.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-iri-0.9.5.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/antlr-3.2.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/httpclient-4.2.3.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/owlapi-distribution-3.4.3-bin.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-arq-2.10.0.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/commons-codec-1.6.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jcl-over-slf4j-1.6.4.jar:/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/pellet/jena-core-2.10.0.jar', 'pellet.Pellet', 'realize', '--loader', 'Jena', '--input-format', 'N-Triples', '--ignore-imports', '/tmp/tmpt9he5926']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/stelios/VirtualPythonEnvironments/ProverPlayground/lib/python3.9/site-packages/owlready2/reasoning.py", line 281, in sync_reasoner_pellet
raise OwlReadyInconsistentOntologyError("Java error message is: %s" % msg)
owlready2.base.OwlReadyInconsistentOntologyError: Java error message is: log4j:WARN No appenders could be found for logger (com.hp.hpl.jena.sparql.mgt.ARQMgt).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
ERROR: Ontology is inconsistent, run "pellet explain" to get the reason
This is the output of `pellet explain`:
log4j:WARN No appenders could be found for logger (com.hp.hpl.jena.sparql.mgt.ARQMgt).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Exception in thread "main" org.semanticweb.owlapi.model.OWLRuntimeException: No explanation computed
at com.clarkparsia.owlapi.explanation.GlassBoxExplanation.convertExplanation(GlassBoxExplanation.java:258)
at com.clarkparsia.owlapi.explanation.GlassBoxExplanation.getPelletExplanation(GlassBoxExplanation.java:228)
at com.clarkparsia.owlapi.explanation.GlassBoxExplanation.getExplanation(GlassBoxExplanation.java:191)
at com.clarkparsia.owlapi.explanation.HSTExplanationGenerator.getExplanation(HSTExplanationGenerator.java:113)
at com.clarkparsia.owlapi.explanation.HSTExplanationGenerator.getExplanations(HSTExplanationGenerator.java:137)
at pellet.PelletExplain.explainAxiom(PelletExplain.java:269)
at pellet.PelletExplain.explainSubClass(PelletExplain.java:371)
at pellet.PelletExplain.explainUnsatisfiableClass(PelletExplain.java:385)
at pellet.PelletExplain.run(PelletExplain.java:233)
at pellet.Pellet.run(Pellet.java:105)
at pellet.Pellet.main(Pellet.java:59)
Since it works for you, there should be something wrong with my java setup?
Stelios