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tom@pisces newstack % ami-plugin/target/appassembler/bin/ami2-species --project ./zika -i scholarly.html --sp.species --context 35 --sp.type binomial genus
java.lang.RuntimeException: invoke runExtractSpecies fails
at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:873)
at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768)
at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749)
at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176)
at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929)
at org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871)
... 5 more
Caused by: java.lang.NullPointerException
at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112)
at org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380)
at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298)
at org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57)
... 10 more
java.lang.RuntimeException: invoke runExtractSpecies fails
at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:873)
at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768)
at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749)
at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176)
at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929)
at org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871)
... 5 more
Caused by: java.lang.NullPointerException
at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112)
at org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380)
at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298)
at org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57)
... 10 more
java.lang.RuntimeException: invoke runExtractSpecies fails
at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:873)
at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768)
at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749)
at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176)
at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929)
at org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871)
... 5 more
Caused by: java.lang.NullPointerException
at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112)
at org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380)
at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298)
at org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57)
... 10 more
This doesn't happen if in ami-plugin. I assume there is some hardcoded path to the/a dictionary somewhere.
The text was updated successfully, but these errors were encountered:
This doesn't happen if in ami-plugin. I assume there is some hardcoded path to the/a dictionary somewhere.
The text was updated successfully, but these errors were encountered: