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bridgedb / create-bridgedb-metabolites

Create BridgeDb identity mapping files from HMDB, ChEBI, and Wikidata
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(Jenkins) build failure for Bridgedb 2.3.8 (secondary IDs). #26

Closed DeniseSl22 closed 3 years ago

DeniseSl22 commented 3 years ago

When I updated the code with the latest BridgeDb libraries https://github.com/bridgedb/create-bridgedb-metabolites/commit/0162ff1197ac4eb73207409ba5a8b6e2ae8bfd07, I got the following build failure in Jenkins:

+ CLASSPATH=derby.jar:org.bridgedb.bio.jar:org.bridgedb.jar:org.bridgedb.rdb.construct.jar:org.bridgedb.rdb.jar:. groovy createDerby.groovy
Caught: groovy.lang.GroovyRuntimeException: Could not find matching constructor for: org.bridgedb.Xref(java.lang.String, org.bridgedb.DataSource, java.lang.Boolean)
groovy.lang.GroovyRuntimeException: Could not find matching constructor for: org.bridgedb.Xref(java.lang.String, org.bridgedb.DataSource, java.lang.Boolean)
    at createDerby$_run_closure2.doCall(createDerby.groovy:167)
    at createDerby.run(createDerby.groovy:140)
Build step 'Execute shell' marked build as failure
Archiving artifacts
Recording test results
Finished: FAILURE

Apparently this happened before, see https://github.com/bridgedb/create-bridgedb-metabolites/commit/70b24a37a1f5df1228527a5035d6c51a343409f6 . What should be done, to get the Xref class compatible with the secondary IDs additions?

egonw commented 3 years ago

Turns out we're already using master for this tool. I forgot about that. But it was because of secondary ID support. But the tool is currently still set to create BridgeDb 2.3 (schema 3) version Derby databaes.