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INCATools / ontology-development-kit

Bootstrap an OBO Library ontology
http://incatools.github.io/ontology-development-kit/
BSD 3-Clause "New" or "Revised" License
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barfing on example #34

Closed mateolan closed 5 years ago

mateolan commented 6 years ago

I was trying to set-up a new ontology and got errors pulling-in import ontologies. It looks like OSK pulls in ontologies as '.txt' files but then searches for .owl files to import and barfs on not finding them. What am I missing? Relevant snips from command and error message below:

campus-108-115:ontology-starter-kit matthewlange$ ./seed-my-ontology-repo.pl -d po -d ro -d pato -d mmo -u mateolan -t "Food Phenotype Ontology" -c foodphen WRITING: target/food-phenotype-ontology/src/ontology/imports/po_terms.txt WRITING: target/food-phenotype-ontology/src/ontology/imports/ro_terms.txt WRITING: target/food-phenotype-ontology/src/ontology/imports/pato_terms.txt WRITING: target/food-phenotype-ontology/src/ontology/imports/mmo_terms.txt WRITING: target/food-phenotype-ontology/src/ontology/reports/README.md **

** EXECUTING: git init Initialized empty Git repository in /Users/matthewlange/ontology-starter-kit/target/food-phenotype-ontology/.git/ EXECUTING: git add -A . EXECUTING: git commit -m 'initial commit of ontology sources of foodphen using ontology-starter-kit' -a [master (root-commit) 58f0349] initial commit of ontology sources of foodphen using ontology-starter-kit 34 files changed, 735 insertions(+) create mode 100644 src/ontology/foodphen-edit.owl create mode 100644 src/ontology/foodphen-idranges.owl create mode 100644 src/ontology/imports/mmo_terms.txt create mode 100644 src/ontology/imports/pato_terms.txt create mode 100644 src/ontology/imports/po_terms.txt create mode 100644 src/ontology/imports/ro_terms.txt ** ** Preparing initial release, may take a few minutes, or longer if you depend on large ontologies like chebi EXECUTING: cd src/ontology && make prepare_release && echo SUCCESS || echo FAILURE robot verify -i foodphen-edit.owl --queries ../sparql/equivalent-classes-violation.sparql ../sparql/trailing-whitespace-violation.sparql ../sparql/owldef-self-reference-violation.sparql ../sparql/xref-syntax-violation.sparql ../sparql/nolabels-violation.sparql -O reports/ org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: Cause: /Users/matthewlange/ontology-starter-kit/target/food-phenotype-ontology/src/ontology/imports/po_import.owl (No such file or directory) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1690) ** ** Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: /Users/matthewlange/ontology-starter-kit/target/food-phenotype-ontology/src/ontology/imports/po_import.owl (No such file or directory) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) ** ** Caused by: java.io.FileNotFoundException: /Users/matthewlange/ontology-starter-kit/target/food-phenotype-ontology/src/ontology/imports/po_import.owl (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.(FileInputStream.java:138) at java.io.FileInputStream.(FileInputStream.java:93) at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90) at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188) ** ** matthewlange$ ls /Users/matthewlange/ontology-starter-kit/target/food-phenotype-ontology/src/ontology/imports mmo_terms.txt pato_terms.txt po_terms.txt ro_terms.txt ****
matentzn commented 5 years ago

Hey, closing this issue due to long inactivity. Please re-open if necessary.