Multiple Author Retrieval

jtmiller28 commented 2 years ago

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.

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"}]

jhpoelen commented 2 years ago

@jtmiller28 which version of nomer are you using?

jhpoelen commented 2 years ago

also, what does:

nomer list discoverlife | head

produce for you?

jtmiller28 commented 2 years ago

nomer version 0.2.15

jtmiller28 commented 2 years ago

jhpoelen commented 2 years ago

@jtmiller28 thanks.

I was able to reproduce your issue -

$ nomer list --properties my.properties discoverlife | head 
java.lang.IllegalArgumentException: URI has an authority component
    at java.io.File.<init>(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.<init>(CatalogueOfLifeTaxonService.java:39)
    at org.eol.globi.service.TermMatchEnsembleFactory$2.<init>(TermMatchEnsembleFactory.java:60)
    at org.eol.globi.service.TermMatchEnsembleFactory.getEnrichers(TermMatchEnsembleFactory.java:39)
    at org.globalbioticinteractions.nomer.match.TermMatcherFactoryEnricherFactory$1.<init>(TermMatcherFactoryEnricherFactory.java:23)

jhpoelen commented 2 years ago

@jtmiller28 thanks for sharing the details.

I was able to reproduce the results. The root cause is that Nomer expects the properties file to be a URI

for now, I'd recommend a workaround like, in which you use a file url with absolute path (via $PWD in example below) -

$ echo -e "\tAndrena clypella" | nomer append --properties file://$PWD/my.properties discoverlife
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [discoverlife-taxon]
    Andrena clypella    HAS_ACCEPTED_NAME   https://www.discoverlife.org/mp/20q?search=Andrena+clypella Andrena clypella    Strand, 1921    species

In the future, I am hoping to support local files without having to construct these elaborate absolute file URLs.

Please let me know if this unblocks you for now. If not, please holler and I can expedite a fix.

jtmiller28 commented 2 years ago

That indeed does the trick. I'll use this to reference naming is DiscoverLife & World Flora Online. Thanks!

jhpoelen commented 2 years ago

oops - accidentally closed. Applying "workaround exists" label instead.

jhpoelen commented 2 years ago

@jtmiller28 I've updated the code that loads the properties. Now, you can use relative file paths in addition to URL, and you no longer need the proposed workaround.

For instance:

$ echo -e "\tYucca brevifolia\tL.D.Benson & Darrox" | nomer append wfo --properties my.properties
[main] INFO org.globalbioticinteractions.nomer.match.TermMatcherRegistry - using matcher [wfo]
[main] INFO org.globalbioticinteractions.nomer.match.WorldOfFloraOnlineTaxonService - [WORLD_OF_FLORA_ONLINE] taxonomy already indexed at [/home/jorrit/.cache/nomer/world_of_flora_online/world_of_flora_online], no need to import.
    Yucca brevifolia    L.D.Benson & Darrox HAS_ACCEPTED_NAME   WFO:0000752275  Yucca brevifolia    Engelm. species
    Yucca brevifolia    L.D.Benson & Darrox SYNONYM_OF  WFO:0000753634  Yucca baccata var. brevifolia   L.D.Benson & Darrow variety

globalbioticinteractions / nomer

Multiple Author Retrieval #110