Fix/nextflow executable build info (#720)

* Decide whether the executable filename is the component name or 'main.nf' based on runner type and not mainScript type

* Test build_info output

Need to set workingDir, create a _viash.yaml file and need to remain in the same folder with the output folder to avoid anonymizing

* Add changelog entry

CHANGELOG.md

@@ -6,6 +6,10 @@ TODO add summary
 
 * `resources_test`: This field is removed again from the `_viash.yaml` as it was decided to impliment this temporary functionality using the `info` field (PR #711).
 
+## BUG FIXES
+
+* `build_info`: Correctly set the `.build_info.executable` to `main.nf` when building a component with a Nextflow runner (PR #720).
+
 * `vsh organization`: ViashHub repositories now use `vsh` as the default organization (PR #718).
   Instead of having to specify `repo: vsh/repo_name`, you can now just specify `repo: repo_name`, which is now also the prefered way.
 

src/main/scala/io/viash/ViashBuild.scala

@@ -42,7 +42,7 @@ object ViashBuild extends Logging {
     val exec_path = resources.mainScript.map(scr => Paths.get(output, scr.resourcePath).toString)
 
     // convert config to a yaml wrapped inside a PlainFile
-    val configYaml = ConfigMeta.toMetaFile(appliedConfig.config, Some(dir))
+    val configYaml = ConfigMeta.toMetaFile(appliedConfig, Some(dir))
 
     // write resources to output directory
     IO.writeResources(configYaml :: resources.resources, dir)

src/main/scala/io/viash/ViashRun.scala

@@ -42,7 +42,7 @@ object ViashRun extends Logging {
     var code = -1
     try {
       // convert config to a yaml wrapped inside a PlainFile
-      val configYaml = ConfigMeta.toMetaFile(appliedConfig.config, Some(dir))
+      val configYaml = ConfigMeta.toMetaFile(appliedConfig, Some(dir))
 
       // write executable and resources to temporary directory
       IO.writeResources(configYaml :: resources.resources, dir)

src/main/scala/io/viash/ViashTest.scala

@@ -280,7 +280,7 @@ object ViashTest extends Logging {
           dest = Some("test_executable"),
           text = resourcesOnlyTest.resources.head.text
         )
-        val configYaml = ConfigMeta.toMetaFile(appliedConfig.config, Some(dir))
+        val configYaml = ConfigMeta.toMetaFile(appliedConfig, Some(dir))
 
         // assemble full resources list for test
         val confFinal = resourcesLens.set(

src/main/scala/io/viash/config/ConfigMeta.scala

@@ -27,6 +27,7 @@ import io.circe.Json
 import io.circe.JsonObject
 import io.viash.config.resources.NextflowScript
 import io.viash.helpers.IO
+import io.viash.runners.NextflowRunner
 
 object ConfigMeta {
   // create a yaml printer for writing the viash.yaml file
@@ -71,14 +72,16 @@ object ConfigMeta {
     })
   }
 
-  def toMetaFile(config: Config, buildDir: Option[Path]): PlainFile = {
+  def toMetaFile(appliedConfig: AppliedConfig, buildDir: Option[Path]): PlainFile = {
+    val config = appliedConfig.config
+
     // get resources
     val placeholderMap = config.resources.filter(_.text.isDefined).map{ res =>
       (res, "VIASH_PLACEHOLDER~" + res.filename + "~")
     }.toMap
 
-    val executableName = config.mainScript match {
-      case Some(n: NextflowScript) => "main.nf"
+    val executableName = appliedConfig.runner match {
+      case Some(_: NextflowRunner) => "main.nf"
       case _ => config.name
     }
 

src/test/scala/io/viash/e2e/build/NativeSuite.scala

@@ -11,6 +11,7 @@ import io.viash.config.Config
 import scala.io.Source
 import io.viash.helpers.{IO, Exec, Logger}
 import io.viash.exceptions.ConfigParserException
+import java.nio.file.Files
 
 class NativeSuite extends AnyFunSuite with BeforeAndAfterAll {
   Logger.UseColorOverride.value = Some(false)
@@ -261,6 +262,68 @@ class NativeSuite extends AnyFunSuite with BeforeAndAfterAll {
     assert(testOutput.stderr.contains("Warning: no resources specified!"))
   }
 
+  test("Check data in build_info for executable runners") {
+    val newConfigFilePath = configDeriver.derive(Nil, "build_info_native")
+    Files.write(temporaryConfigFolder.resolve("_viash.yaml"), Array.emptyByteArray)
+
+    val outputFolder = temporaryConfigFolder.resolve("output_build_info_native")
+
+    val testOutput = TestHelper.testMain(
+      workingDir = Some(temporaryConfigFolder),
+      "build",
+      "-o", outputFolder.toString,
+      "--runner", "executable",
+      newConfigFilePath
+    )
+
+    val executable = outputFolder.resolve("testbash").toFile
+    val buildConfig = outputFolder.resolve(".config.vsh.yaml").toFile
+
+    assert(executable.exists())
+    assert(buildConfig.exists())
+
+    val buildConfigFile = Source.fromFile(buildConfig)
+    try {
+      val buildOutput = buildConfigFile.mkString
+      assert(buildOutput.contains("runner: \"executable\""))
+      assert(buildOutput.contains("engine: \"native|docker|throwawayimage\""))
+      assert(buildOutput.contains("executable: \"output_build_info_native/testbash\""))
+    } finally {
+      buildConfigFile.close()
+    }
+  }
+
+  test("Check data in build_info for nextflow runners") {
+    val newConfigFilePath = configDeriver.derive(Nil, "build_info_nextflow")
+    Files.write(temporaryConfigFolder.resolve("_viash.yaml"), Array.emptyByteArray)
+
+    val outputFolder = temporaryConfigFolder.resolve("output_build_info_nextflow")
+
+    val testOutput = TestHelper.testMain(
+      workingDir = Some(temporaryConfigFolder),
+      "build",
+      "-o", outputFolder.toString,
+      "--runner", "nextflow",
+      newConfigFilePath
+    )
+
+    val executable = outputFolder.resolve("main.nf").toFile
+    val buildConfig = outputFolder.resolve(".config.vsh.yaml").toFile
+
+    assert(executable.exists())
+    assert(buildConfig.exists())
+
+    val buildConfigFile = Source.fromFile(buildConfig)
+    try {
+      val buildOutput = buildConfigFile.mkString
+      assert(buildOutput.contains("runner: \"nextflow\""))
+      assert(buildOutput.contains("engine: \"native|docker|throwawayimage\""))
+      assert(buildOutput.contains("executable: \"output_build_info_nextflow/main.nf\""))
+    } finally {
+      buildConfigFile.close()
+    }
+  }
+
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
     IO.deleteRecursively(temporaryConfigFolder)