NPE in AMI.execute without subcommand

[petermr]

No description provided.

[petermr]

`AMI.execute(class, cmd) is used to extract the abstractTool and read the options summary.

successful example

org.contentmine.ami.tools.AMIFilterTest.testFallback(), creates a testable Options value output:

	@Test
	public void testFallback() {
		AMIFilterTool filterTool = AMI.execute(AMIFilterTool.class, "-vv filter --duplicate --monochrome");
		Assert.assertEquals("options value", "" +
				"--duplicate         : m duplicate\n" + 
				"--maxheight         : d      1000\n" + 
				"--maxwidth          : d      1000\n" + 
				"--minheight         : d       100\n" + 
				"--minwidth          : d       100\n" + 
				"--monochrome        : m monochrome\n" + 
				"--small             : d      null\n" + 
				"--help              : d     false\n" + 
				"--version           : d     false\n" + 
				"", filterTool.getOptionsValue());
	}

## unsuccessful example

org.contentmine.ami.tools.AMIFilterTest.testGenericHelp()
with the subcommand omitted,

		AbstractAMITool abstractTool;
		abstractTool = AMI.execute(AMIFilterTool.class, "ami --help");
		Assert.assertEquals(""
				+ "  assert               Makes assertions about objects created by AMI.\n" +
... 
				"  transform            Runs XSLT transformation on XML (NYFI).\n" + 
				"  words                Analyzes word frequencies.\n" + 
				"  help                 Displays help information about the specified command\n" + 
				"  generate-completion  Generate bash/zsh completion script for ami.",
				abstractTool.getOptionsValue());

fails with

	@Test
	public void testGenericHelp() {
		/** fails 
		 * java.lang.NullPointerException
	at org.contentmine.ami.tools.AMI.execute(AMI.java:138)
	at org.contentmine.ami.tools.AMI.execute(AMI.java:133)
	at org.contentmine.ami.tools.AMIFilterTest.testGenericHelp(AMIFilterTest.java:57)

	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
...
	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:209)

		abstractTool = AMI.execute(AbstractAMITool.class, " --help");

[remkop]

Fixed in ami3 master.

FYI: You may be interested in https://stefanbirkner.github.io/system-rules/#SystemErrAndOutRule
for asserting on tool's output to system.out/system.err

[petermr]

On Mon, May 25, 2020 at 11:59 AM Remko Popma ***@***.***> wrote: Fixed in ami3 master. FYI: You may be interested in https://stefanbirkner.github.io/system-rules/#SystemErrAndOutRule for asserting on tool's output to system.out/system.err

Thanks - useful. Probably cleaner than what I did...

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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[remkop]

I don't have privileges to close this ticket, but is there any work still outstanding?