Merge branch 'develop_0_8' into develop

CHANGELOG.md

@@ -110,6 +110,8 @@ Additionally changes are made to sanitize the built config output and include ad
 
 * `viash test` and `viash ns test`: Add a hidden `--deterministic_working directory` argument to use a fixed directory path (PR #683).
 
+* `component names`: Verify that component namespace and name combinations are unique (PR #685).
+
 ## BUG FIXES
 
 * `NextflowPlatform`: Fix publishing state for output arguments with `multiple: true` (#638, PR #639). 

src/main/scala/io/viash/Main.scala

@@ -412,8 +412,7 @@ object Main extends Logging {
         Some(ViashNamespace.targetOutputPath(
           targetDir = td,
           runnerId = ex.id,
-          namespace = appliedConfig.config.namespace,
-          name = appliedConfig.config.name
+          config = appliedConfig.config
         ))
       case _ => None
     }

src/main/scala/io/viash/ViashNamespace.scala

@@ -52,6 +52,9 @@ object ViashNamespace extends Logging {
         list.foreach(f)
   }
 
+  def targetOutputPath(targetDir: String, runnerId: String, config: Config): String =
+    targetOutputPath(targetDir, runnerId, config.namespace, config.name)
+
   def targetOutputPath(
     targetDir: String,
     runnerId: String,
@@ -88,7 +91,7 @@ object ViashNamespace extends Logging {
             if (flatten) {
               target
             } else {
-              targetOutputPath(target, runnerId, ns, funName)
+              targetOutputPath(target, runnerId, ac.config)
             }
           val nsStr = ns.map(" (" + _ + ")").getOrElse("")
           infoOut(s"Exporting $funName$nsStr =$runnerId=> $out")

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

@@ -27,6 +27,7 @@ import io.viash.helpers.{Git, GitInfo, IO, Logging}
 import io.viash.helpers.circe._
 import io.viash.helpers.{status => BuildStatus};
 import io.viash.helpers.Yaml
+import io.viash.ViashNamespace.targetOutputPath
 
 import java.net.URI
 
@@ -747,7 +748,7 @@ object Config extends Logging {
         attrs.isRegularFile
     })
 
-    scriptFiles.map { file =>
+    val allConfigs = scriptFiles.map { file =>
       try {
         val rmos = new ReplayableMultiOutputStream()
 
@@ -799,6 +800,19 @@ object Config extends Logging {
           AppliedConfig(Config("failed"), None, Nil, Some(BuildStatus.ParseError))
       }
     }
+
+    // Verify that all configs except the disabled ones are unique
+    // Even configs disabled by the query should be unique as they might be picked up as a dependency
+    // Only allowed exception are configs where the status is set to disabled
+    val allEnabledConfigs = allConfigs.collect{ case ac if ac.config.isEnabled => ac.config }
+    val uniqueConfigs = allEnabledConfigs.groupBy(c => targetOutputPath("", "", c))
+    val duplicateConfigs = uniqueConfigs.filter(_._2.size > 1)
+    if (duplicateConfigs.nonEmpty) {
+      val duplicateNames = duplicateConfigs.keys.map(_.dropWhile(_ == '/')).toSeq.sorted.mkString(", ")
+      throw new RuntimeException(s"Duplicate component name${ if (duplicateConfigs.size == 1) "" else "s" } found: $duplicateNames")
+    }
+
+    allConfigs
   }
 
 val reservedParameters = List("-h", "--help", "--version", "---v", "---verbose", "---verbosity")

src/main/scala/io/viash/helpers/DependencyResolver.scala

@@ -161,7 +161,7 @@ object DependencyResolver extends Logging {
             case "nextflow" => "main.nf"
             case _ => c.name
           }
-          Paths.get(ViashNamespace.targetOutputPath("", rid, c.namespace, c.name), executableName).toString()
+          Paths.get(ViashNamespace.targetOutputPath("", rid, c), executableName).toString()
       }
       val info = c.build_info.get.copy(
         executable = executable

src/main/scala/io/viash/runners/nextflow/NextflowHelper.scala

@@ -222,7 +222,7 @@ object NextflowHelper {
   def renderDependencies(config: Config): String = {
     // TODO ideally we'd already have 'thisPath' precalculated but until that day, calculate it here
     // The name of the runner doesn't really matter here as it is just used to generate the relative location, and we don't have access to it anyway.
-    val thisPath = Paths.get(ViashNamespace.targetOutputPath("", "invalid_runner_name", config.namespace, config.name))
+    val thisPath = Paths.get(ViashNamespace.targetOutputPath("", "invalid_runner_name", config))
 
     val depStrs = config.dependencies.map{ dep =>
       NextflowHelper.renderInclude(dep, thisPath)

src/main/scala/io/viash/wrapper/BashWrapper.scala

@@ -235,7 +235,7 @@ object BashWrapper {
     val localDependenciesStrings = localDependencies.map{ d =>
       // relativize the path of the main component to the local dependency
       // TODO ideally we'd already have 'thisPath' precalculated but until that day, calculate it here
-      val thisPath = ViashNamespace.targetOutputPath("", "invalid_runner_name", config.namespace, config.name)
+      val thisPath = ViashNamespace.targetOutputPath("", "invalid_runner_name", config)
       val relativePath = Paths.get(thisPath).relativize(Paths.get(d.configInfo.getOrElse("executable", "")))
       s"${d.VIASH_DEP}=\"$$VIASH_META_RESOURCES_DIR/$relativePath\""
     }

src/test/scala/io/viash/e2e/ns_build/MainNSBuildNativeSuite.scala

@@ -115,6 +115,96 @@ class MainNSBuildNativeSuite extends AnyFunSuite with BeforeAndAfterAll{
     }
   }
 
+  test("Check uniqueness of component names, same name, different namespace") {
+    val compStr =
+      """functionality:
+        |  name: comp
+        |  namespace: %s
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("ns1"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("ns2"), tempSrcDir.resolve("config2.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val testOutput = TestHelper.testMain(
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(testOutput.exitCode == Some(0))
+    assert(testOutput.stderr.contains("All 2 configs built successfully"))
+  }
+
+  test("Check uniqueness of component names, different name, same namespace") {
+    val compStr =
+      """functionality:
+        |  name: %s
+        |  namespace: ns
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("comp1"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("comp2"), tempSrcDir.resolve("config2.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val testOutput = TestHelper.testMain(
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(testOutput.exitCode == Some(0))
+    assert(testOutput.stderr.contains("All 2 configs built successfully"))
+  }
+
+  test("Check uniqueness of component names, same name, same namespace") {
+    val compStr =
+      """functionality:
+        |  name: %s
+        |  namespace: ns
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("comp"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("comp"), tempSrcDir.resolve("config2.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val testOutput = TestHelper.testMainException[RuntimeException](
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(!testOutput.stderr.contains("All 2 configs built successfully"))
+    assert(testOutput.exceptionText.contains("Duplicate component name found: ns/comp"))
+  }
+
+  test("Check uniqueness of component names, same name, same namespace - multiple duplicates") {
+    val compStr =
+      """functionality:
+        |  name: %s
+        |  namespace: ns
+        |""".stripMargin
+    val tempSrcDir = IO.makeTemp("viash_ns_build_check_uniqueness_src")
+    IO.write(compStr.format("comp1"), tempSrcDir.resolve("config1.vsh.yaml"))
+    IO.write(compStr.format("comp1"), tempSrcDir.resolve("config2.vsh.yaml"))
+    IO.write(compStr.format("comp2"), tempSrcDir.resolve("config3.vsh.yaml"))
+    IO.write(compStr.format("comp2"), tempSrcDir.resolve("config4.vsh.yaml"))
+
+    val tempTargetDir = IO.makeTemp("viash_ns_build_check_uniqueness_target")
+
+    val testOutput = TestHelper.testMainException[RuntimeException](
+      "ns", "build",
+        "-s", tempSrcDir.toString(),
+        "-t", tempTargetDir.toString()
+      )
+
+    assert(!testOutput.stderr.contains("All 2 configs built successfully"))
+    assert(testOutput.exceptionText.contains("Duplicate component names found: ns/comp1, ns/comp2"))
+  }
+
   override def afterAll(): Unit = {
     IO.deleteRecursively(temporaryFolder)
   }