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Add error output to VEP exceptions #5224

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merged 2 commits into from Feb 14, 2019
Merged

Add error output to VEP exceptions #5224

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579bf3d
Add error output to VEP exceptions
tpoterba Jan 31, 2019
727e25c
Address
tpoterba Feb 13, 2019
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26 changes: 18 additions & 8 deletions hail/src/main/scala/is/hail/methods/VEP.scala
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@@ -1,5 +1,7 @@
package is.hail.methods

import java.io.BufferedInputStream

import com.fasterxml.jackson.core.JsonParseException
import is.hail.annotations._
import is.hail.expr._
Expand All @@ -11,13 +13,13 @@ import is.hail.sparkextras.ContextRDD
import is.hail.table.Table
import is.hail.utils._
import is.hail.variant.{Locus, RegionValueVariant, VariantMethods}
import org.apache.hadoop
import org.apache.spark.sql.Row
import org.apache.spark.storage.StorageLevel
import org.json4s.jackson.JsonMethods
import org.apache.hadoop

import scala.collection.JavaConverters._
import scala.util.{Failure, Success, Try}
import scala.io.Source

case class VEPConfiguration(
command: Array[String],
Expand Down Expand Up @@ -62,6 +64,18 @@ object VEP {
}
}

def waitFor(proc: Process, cmd: Array[String]): Unit = {
val rc = proc.waitFor()

if (rc != 0) {
val errorLines = Source.fromInputStream(new BufferedInputStream(proc.getErrorStream)).getLines().mkString("\n")

fatal(s"VEP command '${ cmd.mkString(" ") }' failed with non-zero exit status $rc\n" +
" VEP Error output:\n" +
Source.fromInputStream(new BufferedInputStream(proc.getErrorStream)).getLines().mkString("\n"))
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this should just be errorLines, no?

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yeah, oops.

}
}

def getCSQHeaderDefinition(cmd: Array[String], confEnv: Map[String, String]): Option[String] = {
val csqHeaderRegex = "ID=CSQ[^>]+Description=\"([^\"]+)".r
val pb = new ProcessBuilder(cmd.toList.asJava)
Expand All @@ -74,9 +88,7 @@ object VEP {
_ => ())

val csqHeader = jt.flatMap(s => csqHeaderRegex.findFirstMatchIn(s).map(m => m.group(1)))
val rc = proc.waitFor()
if (rc != 0)
fatal(s"VEP command failed with non-zero exit status $rc")
waitFor(proc, cmd)

if (csqHeader.hasNext)
Some(csqHeader.next())
Expand Down Expand Up @@ -183,9 +195,7 @@ object VEP {
val r = kt.toArray
.sortBy(_._1)(rowKeyOrd.toOrdering)

val rc = proc.waitFor()
if (rc != 0)
fatal(s"vep command '${ cmd.mkString(" ") }' failed with non-zero exit status $rc")
waitFor(proc, cmd)

r
}
Expand Down