jhpoelen
commented
2 years ago @jtmiller28 thanks for sharing your issue
As far as I can see, your nomer properties -
nomer.append.schema.output.example.taxon.rank.order=[{"column":0,"type":"path.order.id"},{"column": 1,"type":"path.order.name"},{"column": 2,"type":"path.order"}]
nomer.append.schema.output=[{"column":0,"type":"externalId"},{"column": 1,"type":"name"},{"column": 2,"type":"authorship"},{"column":3,"type":"rank"}]
nomer.schema.input=[{"column":0,"type":"externalId"},{"column": 1,"type":"name"},{"column": 2,"type":"authorship"},{"column": 3, "type":"rank"}]
jtmiller28
Currently I am trying to create example code to process plant names through Nomer creating a table output with each name and their current taxonomic status with listed authorship. This goal is accurately represented by the second comment in issue #58 , where the authorship, and taxonomic status is matched per name.
While trying to recreate that issue's table I ran into the following java exception when running:
nomer list --properties my.properties discoverlife | head
java.lang.IllegalArgumentException: URI has an authority component at java.base/java.io.File.(File.java:425)
at org.eol.globi.util.ResourceServiceLocalFile.retrieve(ResourceServiceLocalFile.java:21)
at org.globalbioticinteractions.nomer.cmd.CmdDefaultParams$1$1.retrieve(CmdDefaultParams.java:65)
at org.eol.globi.util.ResourceServiceGzipAware.retrieve(ResourceServiceGzipAware.java:20)
at org.globalbioticinteractions.nomer.cmd.CmdDefaultParams.initProperties(CmdDefaultParams.java:84)
at org.globalbioticinteractions.nomer.cmd.CmdDefaultParams.getProperties(CmdDefaultParams.java:38)
at org.globalbioticinteractions.nomer.cmd.CmdDefaultParams.getProperty(CmdDefaultParams.java:33)
at org.globalbioticinteractions.nomer.match.CatalogueOfLifeTaxonService.(CatalogueOfLifeTaxonService.java:39)
at org.eol.globi.service.TermMatchEnsembleFactory$2.(TermMatchEnsembleFactory.java:60)
at org.eol.globi.service.TermMatchEnsembleFactory.getEnrichers(TermMatchEnsembleFactory.java:39)
at org.globalbioticinteractions.nomer.match.TermMatcherFactoryEnricherFactory$1.(TermMatcherFactoryEnricherFactory.java:23)
at org.globalbioticinteractions.nomer.match.TermMatcherFactoryEnricherFactory.createTermMatchFactories(TermMatcherFactoryEnricherFactory.java:22)
at org.globalbioticinteractions.nomer.match.TermMatcherRegistry.getRegistry(TermMatcherRegistry.java:135)
at org.globalbioticinteractions.nomer.match.TermMatcherRegistry.termMatcherFor(TermMatcherRegistry.java:152)
at org.globalbioticinteractions.nomer.match.MatchUtil.lambda$resolveMatcher$0(MatchUtil.java:54)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.ArrayList$ArrayListSpliterator.tryAdvance(ArrayList.java:1632)
at java.base/java.util.stream.ReferencePipeline.forEachWithCancel(ReferencePipeline.java:127)
at java.base/java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:502)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:488)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.FindOps$FindOp.evaluateSequential(FindOps.java:150)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.findFirst(ReferencePipeline.java:543)
at org.globalbioticinteractions.nomer.match.MatchUtil.resolveMatcher(MatchUtil.java:59)
at org.globalbioticinteractions.nomer.match.MatchUtil.getTermMatcher(MatchUtil.java:46)
at org.globalbioticinteractions.nomer.match.MatchUtil.getAppendingRowHandler(MatchUtil.java:91)
at org.globalbioticinteractions.nomer.match.MatchUtil.getAppendingRowHandlers(MatchUtil.java:115)
at org.globalbioticinteractions.nomer.cmd.CmdDump.run(CmdDump.java:19)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078)
at org.globalbioticinteractions.nomer.Nomer.run(Nomer.java:57)
at org.globalbioticinteractions.nomer.Nomer.main(Nomer.java:46)
my.properties were downloaded from the issue: my.properties.gz
java -version openjdk version "11.0.16" 2022-07-19 OpenJDK Runtime Environment (build 11.0.16+8-post-Ubuntu-0ubuntu122.04) OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Ubuntu-0ubuntu122.04, mixed mode, sharing)
Also a bit of a follow up, can --properties be used with append? Currently I plan to construct this list to identify possible multiple accepted name mappings dependent on just authorship rather than the name itself, but if possible letting the user submit a name list to nomer and returning all possible name designations based upon authorship might be ideal. This may be important since some large lists (vascular plants) may comprise different accepted names based upon the authors species concept.