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Test AssertionError #213

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jamdodot opened this issue Oct 7, 2022 · 2 comments
Open

Test AssertionError #213

jamdodot opened this issue Oct 7, 2022 · 2 comments

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@jamdodot
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jamdodot commented Oct 7, 2022

Subject of the issue

I get a lot of this kind of test errors
for example pubmeddump

test01 (Lindenbaum CloneIt)
java.lang.AssertionError: expected [0] but found [-1]
	at com.github.lindenb.jvarkit.tools.pubmed.PubmedDumpTest.dumpAsXml(PubmedDumpTest.java:29)
	at com.github.lindenb.jvarkit.tools.pubmed.PubmedDumpTest.test01(PubmedDumpTest.java:40)
	at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
	at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
... Removed 28 stack frames

call stack is:

dumpAsXml()
PubmedDump().instanceMain(new String[] {
		"-o",out.toString(),
		query
		}),0);
-->

src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java
public int instanceMain(final String args[]) 

-->
src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java
parseArgs
getJCommander().parse
return Status.EXIT_FAILURE;  

-->
src/main/java/com/github/lindenb/jvarkit/util/jcommander/Launcher.java
instanceMain()
case EXIT_FAILURE: return -1;

It looks like getJCommander().parse has some problem.

there is a problem with the input parameters of instanceMain? How can I pass the test case here?

Your environment

  • version of jvarkit : latest
  • version of java : jdk-11
@lindenb
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lindenb commented Oct 7, 2022

it's because I've not updated the tests while I changed the tool (my bad).

@jamdodot
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jamdodot commented Oct 7, 2022

okkk , what do I need to change to make the test pass?

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