Help with errors running Whistle

[David Drubin]

Hi OpenBEL Folks!

Hope all are well!

I was attempting to bring the BEL Framework 3.0 online with Whistle.  I was able to compile KAMs from both the large and small corpus, but have been unable to get the example datasets from the Whistle RCR dataset to run successfully.  Any insight is greatly appreciated.  

Thank you all in advance.  (Error is described below)

-David

The main problem I believe is that the measurements in the data file are not being matched in the KAM as I get this main announcement:  "Mapped 0 measurements to Mechanisms", which I think then leads to the errors:

Error running Whistle: Invalid terms for kam node 72.

java.lang.RuntimeException: Invalid terms for kam node 72.

at com.selventa.whistle.cli.Rcr$RcrDialect.getLabel(Rcr.java:1029)

at org.openbel.framework.api.KamDialect$KamDialectNode.getLabel(KamDialect.java:509)

at com.selventa.whistle.score.service.Scorer.getScore(Scorer.java:213)

at com.selventa.whistle.score.service.Scorer.score(Scorer.java:73)

at com.selventa.whistle.cli.Rcr.run(Rcr.java:522)

at com.selventa.whistle.cli.Rcr$1.onAcceptance(Rcr.java:193)

at com.selventa.whistle.cli.license.LicenseAgreement.promptLicense(LicenseAgreement.java:190)

at com.selventa.whistle.cli.Rcr.main(Rcr.java:225)

Caused by: org.openbel.framework.common.InvalidArgument: function enum is null

at org.openbel.framework.common.model.Term.<init>(Term.java:100)

at org.openbel.framework.common.bel.parser.BELStatementParser.outer_term(BELStatementParser.java:390)

at org.openbel.framework.common.bel.parser.BELParser.parseTerm(BELParser.java:121)

at com.selventa.whistle.cli.Rcr$RcrDialect.getLabel(Rcr.java:1024)

... 7 more

[Christian Ebeling]

Dear David,

we have developed at the German research institute Fraunhofer SCAI a BEL parser in python published as an open source on pypi and github: https://pypi.python.org/pypi/PyBEL , https://github.com/pybel/pybel . This parser handles also BEL 2.0. Next version 0.4., we plan to publish in the next days, have also graph manager (relational database options MySQL, PostgreSQL, MsSQL, Oracle). Because our software library uses networkx you can use all of the great graph algorithms the networkx team have implemented ( http://networkx.readthedocs.io/en/stable/reference/algorithms.html ) . Perhaps this could be an alternative for you. Happy to help, if you need support or wants to collaborate in a Cologne/Berkley research project ;-) .

Best regards
Christian Ebeling

[David Drubin]

Thank you Christian!  I will take a look!

D

[Natalie Catlett]

Hi All,

An update - with help from Tony Bargnesi, we determined that the build of the BEL Framework used was likely causing this error. The most recent release (https://github.com/OpenBEL/openbel-framework/releases/tag/3.0.0_build20150728) appears to work.

Best,
Natalie