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petermr / openVirus

aggregation of scholarly publications and extracted knowledge on viruses and epidemics.
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NullPointerException in AMIGetpapersTool #43

Closed richardofsussex closed 4 years ago

richardofsussex commented 4 years ago

Trying a 'Hello World!' test of getpapers, on a Linux Mint laptop from the command line. Just trying to run the query found in the documentation:

richard@richard-SATELLITE-Z830:~/ami3/target/appassembler/bin/test1$ ../ami getpapers -q "((social distance) AND (epidemic))"

Generic values (AMIGetpapersTool)

-v to see generic values

Specific values (AMIGetpapersTool)

java.lang.NullPointerException at org.contentmine.ami.tools.AMIGetpapersTool.runGetpapers(AMIGetpapersTool.java:88) at org.contentmine.ami.tools.AMIGetpapersTool.runSpecifics(AMIGetpapersTool.java:79) at org.contentmine.ami.tools.AbstractAMITool.runCommands(AbstractAMITool.java:203) at org.contentmine.ami.tools.AbstractAMITool.call(AbstractAMITool.java:183) at org.contentmine.ami.tools.AbstractAMITool.call(AbstractAMITool.java:33) at picocli.CommandLine.executeUserObject(CommandLine.java:1783) at picocli.CommandLine.access$900(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2150) at picocli.CommandLine$RunLast.handle(CommandLine.java:2144) at picocli.CommandLine$RunLast.handle(CommandLine.java:2108) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:1975) at picocli.CommandLine.execute(CommandLine.java:1904) at org.contentmine.ami.tools.AMI.main(AMI.java:102)

richardofsussex commented 4 years ago

This error is caused by trying to use getpapers from within the AMI code. It needs to be downloaded as a separate resource. See the FAQ: https://github.com/petermr/openVirus/wiki/FAQ