nasa-jpl-cord-19 / covid19-knowledge-graph Goto Github PK

@lewismc Continuing from #1

Looks like you fixed the output problem, but introduced a new problem by putting the opening of the destination file within the for loop.

I tried both of patterns to run the program but I got failed the running.
I would like some advice if you know any solution.

What I did is as below:

• From sbt

  • command
    sbt:covid19_knowledge_graph> run /home/taroaso/covid19-knowledge-graph/data/CORD-19_files/comm_use_subset /home/taroaso/covid19-knowledge-graph/data/annie_extraction_files
  • result
    [info] running gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph /home/taroaso/covid19-knowledge-graph/data/CORD-19_files/comm_use_subset /home/taroaso/covid19-knowledge-graph/data/annie_extraction_files
    loading
    [error] (run-main-0) java.util.NoSuchElementException: head of empty array
    [error] java.util.NoSuchElementException: head of empty array
    [error] at scala.collection.ArrayOps$.head$extension(ArrayOps.scala:222)
    [error] at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.loadAFileJSON(covid19_knowledge_graph.scala:76)
    [error] at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.$anonfun$main$3(covid19_knowledge_graph.scala:39)
    [error] at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.$anonfun$main$3$adapted(covid19_knowledge_graph.scala:38)
    [error] at scala.collection.ArrayOps$.foreach$extension(ArrayOps.scala:1323)
    [error] at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.main(covid19_knowledge_graph.scala:38)
    [error] at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.main(covid19_knowledge_graph.scala:16)
    [error] at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph.main(covid19_knowledge_graph.scala)
    [error] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    [error] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    [error] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    [error] at java.lang.reflect.Method.invoke(Method.java:498)
    [error] stack trace is suppressed; run last Compile / bgRun for the full output
    [error] Nonzero exit code: 1
    [error] (Compile / run) Nonzero exit code: 1

• As a standalone JAR

  • command
    java -jar ./target/scala-2.13/covid19_knowledge_graph-assembly-0.1.0-SNAPSHOT.jar '/home/taroaso/covid19-knowledge-graph/data/CORD-19_files/comm_use_subset' '/home/taroaso/covid19-knowledge-graph/data/annie_extraction_files'
  • result
    loading
    Exception in thread "main" java.util.NoSuchElementException: head of empty array
    at scala.collection.ArrayOps$.head$extension(ArrayOps.scala:222)
    at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.loadAFileJSON(covid19_knowledge_graph.scala:76)
    at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.$anonfun$main$3(covid19_knowledge_graph.scala:39)
    at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.$anonfun$main$3$adapted(covid19_knowledge_graph.scala:38)
    at scala.collection.ArrayOps$.foreach$extension(ArrayOps.scala:1323)
    at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.main(covid19_knowledge_graph.scala:38)
    at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph$.main(covid19_knowledge_graph.scala:16)
    at gov.nasa.jpl.covid19_knowledge_graph.covid19_knowledge_graph.main(covid19_knowledge_graph.scala)

In the README.md file you give the following instructions to process the input json files.

## Running

Launch sbt:

    $ sbt

Run the program with an argument indicating the input `data` directory containing the dataset:

    > run path/to/data/containing/Commercial use subset json files

This is not conducive to running in an automated pipeline, is there any way we can get an assembly build task so that processing can be run like

$ java -jar covid19-knowledge-graph.jar path/to/data/containing/commercial_use_subset_json_files