Pipeline broken at blazegraph-runner stage

Knowledge-Graph-Hub / kg-covid-19

An instance of KG Hub to produce a knowledge graph for COVID-19 response.

https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki

BSD 3-Clause "New" or "Revised" License

79 stars 26 forks source link

Pipeline broken at blazegraph-runner stage #346

Closed justaddcoffee closed 3 years ago

justaddcoffee commented 3 years ago

Describe the bug

Failing currently at this stage: export JAVA_OPTS=-Xmx128G && ./target/universal/stage/bin/blazegraph-runner load --informat=ntriples --journal=../merged-kg.jnl --use-ontology-graph=true ../data/merged/merged-kg.nt (self time 19s)

To Reproduce

run full pipeline on this commit 9fd270e1b141487ee422d138cd74add87118f669

Expected behavior

blazegraph-runner stage should complete

Version

9fd270e1b141487ee422d138cd74add87118f669

justaddcoffee commented 3 years ago

I'm going to try and fix this here then merge into add_versioning branch/PR

justaddcoffee commented 3 years ago

Looking at this error message org.openrdf.rio.RDFParseException: Not a valid (absolute) URI: xrefs [line 4]

It looks like this step is failing because there is some URI(s) in our nt that is not absolute and needs the default namespace to be defined, similar to this SO issue: https://stackoverflow.com/questions/7248931/openrdf-turtleparser-not-handling-prefixes-properly

justaddcoffee commented 3 years ago

@deepakunni3 do you recall if KGX defines a default namespace when converting KGX TSV to RDF? i.e. something up top in the NT file like: @prefix : <http://default.org/> .

justaddcoffee commented 3 years ago

Probably fixed now, testing this here