WX-1461 Remove womtool upgrade command (#7382)

Author: aednichols

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## 87 Release Notes
 
+### `upgrade` command removed from Womtool
+
+Womtool previously supported a `womtool upgrade` command for upgrading draft-2 WDLs to 1.0. With WDL 1.1 soon to become the latest supported version, this functionality is retiring.
+
 ### Replacement of `gsutil` with `gcloud storage`
 
 In this release, all **localization** functionality on the GCP backend migrates to use the more modern and performant `gcloud storage`. With sufficiently powerful worker VMs, Cromwell can now localize at up to 1200 MB/s [0][1][2].

centaur/src/it/scala/centaur/AbstractCentaurTestCaseSpec.scala

@@ -76,59 +76,6 @@ abstract class AbstractCentaurTestCaseSpec(cromwellBackends: List[String],
     runOrDont(testCase, tags, isIgnored, retries, runTestAndDeleteZippedImports())
   }
 
-  def executeWdlUpgradeTest(testCase: CentaurTestCase): Unit =
-    executeStandardTest(wdlUpgradeTestWdl(testCase))
-
-  private def wdlUpgradeTestWdl(testCase: CentaurTestCase): CentaurTestCase = {
-    import better.files.File
-    import womtool.WomtoolMain
-
-    // The suffix matters because WomGraphMaker.getBundle() uses it to choose the language factory
-    val rootWorkflowFile = File.newTemporaryFile(suffix = ".wdl").append(testCase.workflow.data.workflowContent.get)
-    val workingDir = File.newTemporaryDirectory()
-    val upgradedImportsDir = File.newTemporaryDirectory()
-    val rootWorkflowFilepath = workingDir / rootWorkflowFile.name
-
-    // Un-upgraded imports go into the working directory
-    testCase.workflow.data.zippedImports match {
-      case Some(importsZip: File) =>
-        importsZip.unzipTo(workingDir)
-      case None => ()
-    }
-
-    // Upgrade the imports and copy to main working dir (precludes transitive imports; no recursion yet)
-    workingDir.list.toList.map { file: File =>
-      val upgradedWdl = WomtoolMain.upgrade(file.pathAsString).stdout.get
-      upgradedImportsDir.createChild(file.name).append(upgradedWdl)
-    }
-
-    // Copy to working directory after we operate on the imports that are in it
-    rootWorkflowFile.copyTo(rootWorkflowFilepath)
-
-    val upgradeResult = WomtoolMain.upgrade(rootWorkflowFilepath.pathAsString)
-
-    upgradeResult.stderr match {
-      case Some(stderr) => println(stderr)
-      case _ => ()
-    }
-
-    val newCase = testCase.copy(
-      workflow = testCase.workflow.copy(
-        testName = testCase.workflow.testName + " (draft-2 to 1.0 upgrade)",
-        data = testCase.workflow.data.copy(
-          workflowContent = Option(upgradeResult.stdout.get), // this '.get' catches an error if upgrade fails
-          zippedImports = Option(upgradedImportsDir.zip())
-        )
-      )
-    )(cromwellTracker) // An empty zip appears to be completely harmless, so no special handling
-
-    rootWorkflowFile.delete(swallowIOExceptions = true)
-    upgradedImportsDir.delete(swallowIOExceptions = true)
-    workingDir.delete(swallowIOExceptions = true)
-
-    newCase
-  }
-
   private def runOrDont(testCase: CentaurTestCase,
                         tags: List[Tag],
                         ignore: Boolean,

centaur/src/it/scala/centaur/CentaurTestSuite.scala

@@ -28,8 +28,6 @@ object CentaurTestSuite extends StrictLogging {
   logger.info(s"Cromwell under test configured with backends ${cromwellBackends.mkString(", ")}")
   logger.info(s"Unless overridden by workflow options file, tests use default backend: $defaultBackend")
 
-  def isWdlUpgradeTest(testCase: CentaurTestCase): Boolean = testCase.containsTag("wdl_upgrade")
-
   def isEngineUpgradeTest(testCase: CentaurTestCase): Boolean = testCase.containsTag("engine_upgrade")
 
   def isPapiUpgradeTest(testCase: CentaurTestCase): Boolean = testCase.containsTag("papi_upgrade")

centaur/src/it/scala/centaur/WdlUpgradeTestCaseSpec.scala

@@ -1,6 +1,5 @@
 name: composedenginefunctions
 testFormat: workflowsuccess
-tags: ["wdl_upgrade"]
 
 files {
   workflow: composedenginefunctions/composedenginefunctions.wdl

centaur/src/main/resources/standardTestCases/composedenginefunctions.test

@@ -1,6 +1,6 @@
 name: ifs_in_scatters
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/ifs_in_scatters/ifs_in_scatters.wdl

centaur/src/main/resources/standardTestCases/conditionals.ifs_in_scatters.test

@@ -1,6 +1,6 @@
 name: nested_lookups
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/nested_lookups/nested_lookups.wdl

centaur/src/main/resources/standardTestCases/conditionals.nested_lookups.test

@@ -1,6 +1,6 @@
 name: scatters_in_ifs
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/scatters_in_ifs/scatters_in_ifs.wdl

centaur/src/main/resources/standardTestCases/conditionals.scatters_in_ifs.test

@@ -1,6 +1,6 @@
 name: simple_if
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/simple_if/simple_if.wdl

centaur/src/main/resources/standardTestCases/conditionals.simple_if.test

@@ -1,6 +1,6 @@
 name: simple_if_workflow_outputs
 testFormat: workflowsuccess
-tags: [ conditionals, "wdl_upgrade" ]
+tags: [ conditionals ]
 
 files {
   workflow: conditionals_tests/simple_if_workflow_outputs/simple_if_workflow_outputs.wdl