[bugfix][hail] Capture error rather than printing it#8150
[bugfix][hail] Capture error rather than printing it#8150danking merged 1 commit intohail-is:masterfrom
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I think we need to at least manually test it. |
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| fatal(s"VEP command '${ cmd.mkString(" ") }' failed with non-zero exit status $rc\n" + | ||
| " VEP Error output:\n" + errorLines) | ||
| " VEP Error output:\n" + err.toString) |
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Can you help me understand why this works when proc.getErrorStream doesn't? I expected we would have an err stream and an out stream and we would include both (separately) in the exception message.
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The output stream is VEP's output, which we parse. The issue here is with the pipe method, changed later in this PR. We set up a thread to read from VEP's stderr pipe. We can only read from that stream once. Previously we were printing it to the JVM's System.err stream, now, we're capturing it in a StringBuilder.
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How do I test this? I don't know how to make vep fail. |
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I just meant we should test that VEP still works on this branch. Like, do we have automated tests for VEP? |
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Oh, that's easy, |
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@johnc1231 |
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This is untested, but probably can't make things worse.
fixes #8146