java.lang.IllegalArgumentException: requirement failed: Given /Users/hickst/Documents/nxml2fries/papers/PMC1234335.csv, but readNXMLPaper only handles .nxml files!

GitHub | hickst | 4 months ago
  1. 0

    AssemblyCLI has lost ability to read CSV files

    GitHub | 4 months ago | hickst
    java.lang.IllegalArgumentException: requirement failed: Given /Users/hickst/Documents/nxml2fries/papers/PMC1234335.csv, but readNXMLPaper only handles .nxml files!
  2. 0

    GitHub comment 1988#201105812

    GitHub | 8 months ago | clockfly
    java.lang.IllegalArgumentException: requirement failed: Cannot push port (responseOut) twice
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    replaceWithContext troubles

    GitHub | 9 months ago | gebner
    java.lang.IllegalArgumentException: requirement failed: Incorrect shallow formula: y = d != c = d
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  5. 0

    Requests with method 'HEAD' must have an empty entity

    GitHub | 8 months ago | jrudnick
    java.lang.IllegalArgumentException: requirement failed: Requests with method 'HEAD' must have an empty entity
  6. 0

    GitHub comment 20209#205896543

    GitHub | 8 months ago | hochgi
    java.lang.IllegalArgumentException: requirement failed: contentLength must be positive (use `HttpEntity.empty(contentType)` for empty entities)

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Root Cause Analysis

  1. java.lang.IllegalArgumentException

    requirement failed: Given /Users/hickst/Documents/nxml2fries/papers/PMC1234335.csv, but readNXMLPaper only handles .nxml files!

    at scala.Predef$.require()
  2. Scala
    Predef$.require
    1. scala.Predef$.require(Predef.scala:224)
    1 frame
  3. org.clulab.reach
    AssemblyCLI$$anonfun$processPapers$1.apply
    1. org.clulab.reach.PaperReader$.readPaper(PaperReader.scala:74)
    2. org.clulab.reach.PaperReader$.getMentionsFromPaper(PaperReader.scala:81)
    3. org.clulab.reach.AssemblyCLI$$anonfun$processPapers$1.apply(AssemblyCLI.scala:51)
    4. org.clulab.reach.AssemblyCLI$$anonfun$processPapers$1.apply(AssemblyCLI.scala:42)
    4 frames
  4. Scala
    ForkJoinWorkerThread.run
    1. scala.collection.parallel.mutable.ParArray$ParArrayIterator.foreach_quick(ParArray.scala:143)
    2. scala.collection.parallel.mutable.ParArray$ParArrayIterator.foreach(ParArray.scala:136)
    3. scala.collection.parallel.ParIterableLike$Foreach.leaf(ParIterableLike.scala:972)
    4. scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
    5. scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
    6. scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
    7. scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
    8. scala.collection.parallel.ParIterableLike$Foreach.tryLeaf(ParIterableLike.scala:969)
    9. scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.internal(Tasks.scala:159)
    10. scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:443)
    11. scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:149)
    12. scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
    13. scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
    14. scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
    15. scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
    16. scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
    17. scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
    17 frames