Removing symbolic test resource links, read from test classpath instead

bigdatagenomics · Jan 25, 2016 · aa446d2 · aa446d2
1 parent cd6ef41
commit aa446d2
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Showing 6 changed files with 17 additions and 12 deletions.
diff --git a/adam-apis/src/test/resources/small.sam b/adam-apis/src/test/resources/small.sam
diff --git a/adam-apis/src/test/scala/org/bdgenomics/adam/apis/java/JavaADAMContextSuite.scala b/adam-apis/src/test/scala/org/bdgenomics/adam/apis/java/JavaADAMContextSuite.scala
@@ -27,14 +27,14 @@ import org.bdgenomics.formats.avro.AlignmentRecord
 class JavaADAMContextSuite extends ADAMFunSuite {
 
   sparkTest("can read a small .SAM file") {
-    val path = resourcePath("small.sam")
+    val path = copyResource("small.sam")
     val ctx = new JavaADAMContext(sc)
     val reads = ctx.adamRecordLoad(path)
     assert(reads.jrdd.count() === 20)
   }
 
-  ignore("can read a small .SAM file inside of java") {
-    val path = resourcePath("small.sam")
+  sparkTest("can read a small .SAM file inside of java") {
+    val path = copyResource("small.sam")
     val aRdd = sc.loadAlignments(path)
 
     val newReads = JavaADAMConduit.conduit(aRdd.rdd, aRdd.sequences, aRdd.recordGroups)

diff --git a/adam-cli/src/test/resources/ordered.sam b/adam-cli/src/test/resources/ordered.sam
diff --git a/adam-cli/src/test/resources/unordered.sam b/adam-cli/src/test/resources/unordered.sam
diff --git a/adam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformSuite.scala b/adam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformSuite.scala
@@ -23,23 +23,23 @@ import org.bdgenomics.adam.util.ADAMFunSuite
 
 class TransformSuite extends ADAMFunSuite {
   sparkTest("unordered sam to unordered sam") {
-    val inputPath = resourcePath("unordered.sam")
+    val inputPath = copyResource("unordered.sam")
     val actualPath = tmpFile("unordered.sam")
     val expectedPath = inputPath
     Transform(Array("-single", inputPath, actualPath)).run(sc)
     checkFiles(expectedPath, actualPath)
   }
 
   sparkTest("unordered sam to ordered sam") {
-    val inputPath = resourcePath("unordered.sam")
+    val inputPath = copyResource("unordered.sam")
     val actualPath = tmpFile("ordered.sam")
-    val expectedPath = resourcePath("ordered.sam")
+    val expectedPath = copyResource("ordered.sam")
     Transform(Array("-single", "-sort_reads", inputPath, actualPath)).run(sc)
     checkFiles(expectedPath, actualPath)
   }
 
   sparkTest("unordered sam, to adam, to sam") {
-    val inputPath = resourcePath("unordered.sam")
+    val inputPath = copyResource("unordered.sam")
     val intermediateAdamPath = tmpFile("unordered.adam")
     val actualPath = tmpFile("unordered.sam")
     val expectedPath = inputPath
@@ -49,10 +49,10 @@ class TransformSuite extends ADAMFunSuite {
   }
 
   sparkTest("unordered sam, to adam, to ordered sam") {
-    val inputPath = resourcePath("unordered.sam")
+    val inputPath = copyResource("unordered.sam")
     val intermediateAdamPath = tmpFile("unordered.adam")
     val actualPath = tmpFile("ordered.sam")
-    val expectedPath = resourcePath("ordered.sam")
+    val expectedPath = copyResource("ordered.sam")
     Transform(Array(inputPath, intermediateAdamPath)).run(sc)
     Transform(Array("-single", "-sort_reads", intermediateAdamPath, actualPath)).run(sc)
     checkFiles(expectedPath, actualPath)

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/util/ADAMFunSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/util/ADAMFunSuite.scala
@@ -19,6 +19,8 @@ package org.bdgenomics.adam.util
 
 import java.nio.file.Files
 
+import com.google.common.io.Resources
+
 import org.bdgenomics.utils.misc.SparkFunSuite
 
 import scala.io.Source
@@ -50,5 +52,11 @@ trait ADAMFunSuite extends SparkFunSuite {
         )
     }
   }
+
+  def copyResource(name: String): String = {
+    val tempFile = Files.createTempFile(name, "." + name.split('.').last)
+    Files.write(tempFile, Resources.toByteArray(getClass().getResource("/" + name)))
+    tempFile.toString
+  }
 }