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globalbioticinteractions / nomer

maps identifiers and names to other identifiers and names
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ITIS appender crashes when matching for echo -e "\tDufourea glaboabdominalis_sic" #59

Closed seltmann closed 2 years ago

seltmann commented 2 years ago

nomer dump discoverlife | cut -f 1,2 | nomer append itis

nomer dump discoverlife | grep "_sic" | head | cut -f 1,2

echo -e "\tDufourea glaboabdominalis_sic" | nomer append itis | cut -f 1,2

Output is below, expected NONE to be returned instead as _sic is not in ITIS

using matcher [itis-taxon-id]

java.lang.NullPointerException at org.globalbioticinteractions.nomer.match.CommonTaxonService.match(CommonTaxonService.java:61) at org.eol.globi.service.TermMatcherHierarchical.match(TermMatcherHierarchical.java:57) at org.globalbioticinteractions.nomer.util.AppendingRowHandler.onRow(AppendingRowHandler.java:34) at org.globalbioticinteractions.nomer.match.MatchUtil.apply(MatchUtil.java:76) at org.globalbioticinteractions.nomer.match.MatchUtil.match(MatchUtil.java:29) at org.globalbioticinteractions.nomer.cmd.CmdAppend.run(CmdAppend.java:11) at org.globalbioticinteractions.nomer.cmd.CmdLine.run(CmdLine.java:18) at org.globalbioticinteractions.nomer.cmd.CmdLine.run(CmdLine.java:27) at org.globalbioticinteractions.nomer.Nomer.main(Nomer.java:15)

jhpoelen commented 2 years ago

Fixed in v0.2.6 . Please re-open / comment if the issue remains.