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cmungall / cell-ontology-DO-NOT-USE

Initial attempt to move repo from gcode. USE OBOPHENOTYPE
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Failed to parse cl.obo due to a loop in the term relationships: StackOverflowError #174

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Using same as before software, based on obo:obo:2.0 and obo:bbob:2.0 amd ols 
1.18, etc,,
cannot parse cl.obo 2015-01-29 (http://purl.obolibrary.org/obo/cl.obo), 
but it works ok for the cl.obo 2014-07-08 version.

I suspect, as it has happened with CL OBO not once already, 
there was some change in the ontology that made it not DAG.

This happens for CL:0000560 and CL:0000096 (but you'd better check/test all 
terms). 

 Stack overflow when computing child paths for: CL:0000560 for relationships: [OBO_REL:is_a, isa, DERIVED/DEVELOPS_FROM, is_a, ISA, DEVELOPS_FROM, IS_A, develops_from]
83448 [main] FATAL org.biopax.psidev.ontology_manager.impl.OboLoader  - Parse 
failed: java.lang.StackOverflowError
java.lang.IllegalStateException: java.lang.StackOverflowError
    at org.biopax.ols.impl.OBO2FormatParser.computeChildPaths(OBO2FormatParser.java:171)
    at org.biopax.ols.impl.OBO2FormatParser.computeChildPaths(OBO2FormatParser.java:168)
...

17885 [main] ERROR org.biopax.ols.impl.OBO2FormatParser  - Stack overflow when 
computing child paths for: CL:0000096 for relationships: [OBO_REL:is_a, isa, 
DERIVED/DEVELOPS_FROM, is_a, ISA, DEVELOPS_FROM, IS_A, develops_from]
17888 [main] FATAL org.biopax.psidev.ontology_manager.impl.OboLoader  - Parse 
failed: java.lang.StackOverflowError
...

Original issue reported on code.google.com by rod...@gmail.com on 20 Mar 2015 at 5:16