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NCI-Thesaurus / thesaurus-obo-edition

OBO Library edition of NCIt
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Setting up docker build #81

Closed matentzn closed 1 year ago

matentzn commented 1 year ago

When running the pipeline I get:

2022.08.19 10:57:19:714 main INFO org.renci.blazegraph.Load.runUsingConnection:43
    Loading reactome.ttl
org.openrdf.rio.RDFParseException: Not a valid (absolute) URI: /html [line 1]
        at org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:486)
        at org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:718)
        at org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1377)
        at org.openrdf.rio.helpers.RDFParserBase.createURI(RDFParserBase.java:414)
        at org.openrdf.rio.helpers.RDFParserBase.resolveURI(RDFParserBase.java:401)
        at org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:982)
        at org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
        at org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
        at org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
        at org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
        at org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
        at org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)
        at org.renci.blazegraph.Load$.findOntologyURI(Load.scala:65)
        at org.renci.blazegraph.Load$.$anonfun$runUsingConnection$3(Load.scala:44)
        at org.renci.blazegraph.Load$.$anonfun$runUsingConnection$3$adapted(Load.scala:42)
        at scala.collection.immutable.List.foreach(List.scala:333)
        at org.renci.blazegraph.Load$.runUsingConnection(Load.scala:42)
        at org.renci.blazegraph.Common.run(Common.scala:30)
        at org.renci.blazegraph.Common.run$(Common.scala:18)
        at org.renci.blazegraph.Load$.run(Load.scala:16)
        at org.renci.blazegraph.Main$.$anonfun$new$1(Main.scala:8)
        at org.renci.blazegraph.Main$.$anonfun$new$1$adapted(Main.scala:8)
        at scala.Option.foreach(Option.scala:437)
        at org.renci.blazegraph.Main$.delayedEndpoint$org$renci$blazegraph$Main$1(Main.scala:8)
        at org.renci.blazegraph.Main$delayedInit$body.apply(Main.scala:5)
        at scala.Function0.apply$mcV$sp(Function0.scala:39)
        at scala.Function0.apply$mcV$sp$(Function0.scala:39)
        at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
        at scala.App.$anonfun$main$1(App.scala:76)
        at scala.App.$anonfun$main$1$adapted(App.scala:76)
        at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:563)
        at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561)
        at scala.collection.AbstractIterable.foreach(Iterable.scala:926)
        at scala.App.main(App.scala:76)
        at scala.App.main$(App.scala:74)
        at org.renci.blazegraph.Main$.main(Main.scala:5)
        at org.renci.blazegraph.Main.main(Main.scala)
Caused by: java.lang.IllegalArgumentException: Not a valid (absolute) URI: /html
        at org.openrdf.model.impl.URIImpl.setURIString(URIImpl.java:79)
        at org.openrdf.model.impl.URIImpl.<init>(URIImpl.java:68)
        at org.openrdf.model.impl.ValueFactoryImpl.createURI(ValueFactoryImpl.java:51)
        at org.openrdf.rio.helpers.RDFParserBase.createURI(RDFParserBase.java:411)
        ... 33 more
make: *** [Makefile:67: ncit-graph.jnl] Error 1

This is far out my area of expertise - @balhoff do you have any idea what this is?

matentzn commented 1 year ago

Ready for review, thanks! Release already out, PURL config in PR.