java.lang.RuntimeException: invoke runExtractSpecies fails

GitHub | tarrow | 1 year ago
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    Dictionary based search fails if not in code dir

    GitHub | 1 year ago | tarrow
    java.lang.RuntimeException: invoke runExtractSpecies fails

    Root Cause Analysis

    1. java.lang.NullPointerException

      No message provided

      at org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains()
    2. org.xmlcml.ami2
      SpeciesArgProcessor.runExtractSpecies
      1. org.xmlcml.ami2.dictionary.DefaultAMIDictionary.contains(DefaultAMIDictionary.java:112)
      2. org.xmlcml.ami2.plugins.AMISearcher.markFalsePositives(AMISearcher.java:380)
      3. org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
      4. org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:298)
      5. org.xmlcml.ami2.plugins.species.SpeciesArgProcessor.runExtractSpecies(SpeciesArgProcessor.java:57)
      5 frames
    3. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:497)
      4 frames
    4. org.xmlcml.cmine
      DefaultArgProcessor.runRunMethodsOnChosenArgOptions
      1. org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:871)
      2. org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:768)
      3. org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:749)
      3 frames
    5. org.xmlcml.ami2
      AMIArgProcessor.runRunMethodsOnChosenArgOptions
      1. org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:176)
      1 frame
    6. org.xmlcml.cmine
      DefaultArgProcessor.runAndOutput
      1. org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:929)
      1 frame
    7. org.xmlcml.ami2
      SpeciesPlugin.main
      1. org.xmlcml.ami2.plugins.species.SpeciesPlugin.main(SpeciesPlugin.java:36)
      1 frame