dice-group / dice-group/LD2NL

RDF/XML format error running owl2nl.sh

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Dominant language
Java
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Description

Execitng the following example command
./owl2nl.sh -a ./home/demir/Desktop/Softwares/Ontolearn/examples/best_pred.owl -u false -o ./home/demir/Desktop/Softwares/Ontolearn/KGs/Family/family.owl -t json -s test_out.json -m rule
leads to the following RDF parsing error

(onto) demir@demir:~/Desktop/Softwares/Ontolearn/LD2NL/owl2nl$ ./owl2nl.sh -a ./home/demir/Desktop/Softwares/Ontolearn/examples/best_pred.owl -u false -o ./home/demir/Desktop/Softwares/Ontolearn/KGs/Family/family.owl -t json -s test_out.json -m rule
15/Jan/202409:49:33  INFO (RAKICommandLineInterface.java:main:27) - 
==============================
Parsing arguments ...
15/Jan/202409:49:33  INFO (RAKICommandLineInterface.java:main:61) - ==============================Checking arguments...
15/Jan/202409:49:33  INFO (RAKICommandLineInterface.java:main:83) - 
==============================
Running Pipeline ...
15/Jan/202409:49:33 DEBUG (RakiIO.java:readRDFXML:23) - ./home/demir/Desktop/Softwares/Ontolearn/examples/best_pred.owl
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.aksw.jena_sparql_api.mapper.proxy.MapperProxyUtils (file:/home/demir/.m2/repository/org/aksw/jena-sparql-api/jena-sparql-api-mapper-proxy/3.14.0-1/jena-sparql-api-mapper-proxy-3.14.0-1.jar) to constructor java.lang.invoke.MethodHandles$Lookup(java.lang.Class)
WARNING: Please consider reporting this to the maintainers of org.aksw.jena_sparql_api.mapper.proxy.MapperProxyUtils
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
15/Jan/202409:49:34 ERROR (RakiIO.java:readRDFXML:28) - Could not read: ./home/demir/Desktop/Softwares/Ontolearn/examples/best_pred.owl
15/Jan/202409:49:34 ERROR (RakiIO.java:readRDFXML:29) - Not found: ./home/demir/Desktop/Softwares/Ontolearn/examples/best_pred.owl
org.apache.jena.riot.RiotNotFoundException: Not found: ./home/demir/Desktop/Softwares/Ontolearn/examples/best_pred.owl
        at org.apache.jena.riot.RDFParser.openTypedInputStream(RDFParser.java:394) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFParser.parseURI(RDFParser.java:301) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFParser.parse(RDFParser.java:295) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFParserBuilder.parse(RDFParserBuilder.java:506) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFDataMgr.parseFromURI(RDFDataMgr.java:890) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:221) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:190) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:120) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:111) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.riot.adapters.RDFReaderRIOT.read(RDFReaderRIOT.java:76) ~[jena-arq-3.12.0.jar:3.12.0]
        at org.apache.jena.rdf.model.impl.ModelCom.read(ModelCom.java:263) ~[jena-core-3.12.0.jar:3.12.0]
        at org.aksw.owl2nl.pipeline.io.RakiIO.readRDFXML(RakiIO.java:24) ~[classes/:?]
        at org.aksw.owl2nl.pipeline.data.input.RAKIInput.init(RAKIInput.java:86) ~[classes/:?]
        at org.aksw.owl2nl.pipeline.data.input.RAKIInput.setAxioms(RAKIInput.java:122) ~[classes/:?]
        at org.aksw.owl2nl.pipeline.ui.RAKICommandLineInterface.main(RAKICommandLineInterface.java:88) ~[classes/:?]
        at org.codehaus.mojo.exec.ExecJavaMojo.lambda$execute$0(ExecJavaMojo.java:283) ~[?:?]
        at java.lang.Thread.run(Thread.java:829) [?:?]
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:3.1.1:java (default-cli) on project owl2nl: An exception occurred while executing the Java class. 
[ERROR] 
[ERROR] -> !! The given input seem to be not in RDF/XML format!!
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

Files are here Prediction_and_kb.zip

The two files can be ready without a problem with rdflib see below

>>> import rdflib
>>> rdflib.Graph().parse("best_pred.owl")
<Graph identifier=N2f70772cfc4741f7bf78bfdef644c864 (<class 'rdflib.graph.Graph'>)>

Any suggestion to solve this problem ?

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the command in the issue and trace its input handling through RAKICommandLineInterface.main, RAKIInput.init, and RakiIO.readRDFXML. Compare the supplied OWL input and its paths with what the Java/Jena pipeline receives; done means the example command reads the file successfully instead of reporting it as missing or invalid RDF/XML.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
cli
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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