Nextflow runner: throw error when using a non-existent argument in a …

…map passed to fromState (#793)

CHANGELOG.md

@@ -1,6 +1,8 @@
 # Viash 0.x.x (yyyy-MM-dd): TODO Add title
 
-TODO add summary
+## NEW FEATURES
+
+* `Nextflow` runner: specifying a non-existent argument as a hashmap key for `fromState` and `toState` now raises an error (PR #793). 
 
 # Viash 0.9.1 (2024-12-16): Enhanced nextflow support and Scala 3 update
 

src/main/resources/io/viash/runners/nextflow/workflowFactory/processWorkflowArgs.nf

@@ -117,12 +117,16 @@ def _processFromState(fromState, key_, config_) {
     assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings"
     assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings"
     def fromStateMap = fromState.clone()
-    def requiredInputNames = meta.config.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName}
+    def allArgumentNames = config_.allArguments.collect{it.plainName}
+    def requiredInputNames = config_.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName}
     // turn the map into a closure to be used later on
     fromState = { it ->
       def state = it[1]
       assert state instanceof Map : "Error in module '$key_': the state is not a Map"
       def data = fromStateMap.collectMany{newkey, origkey ->
+        if (!allArgumentNames.contains(newkey)) {
+          throw new Exception("Error processing fromState for '$key_': invalid argument '$newkey'")
+        }
         // check whether newkey corresponds to a required argument
         if (state.containsKey(origkey)) {
           [[newkey, state[origkey]]]
@@ -161,6 +165,7 @@ def _processToState(toState, key_, config_) {
     assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings"
     assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings"
     def toStateMap = toState.clone()
+    def allArgumentNames = config_.allArguments.collect{it.plainName}
     def requiredOutputNames = config_.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName}
     // turn the map into a closure to be used later on
     toState = { it ->
@@ -169,6 +174,9 @@ def _processToState(toState, key_, config_) {
       assert output instanceof Map : "Error in module '$key_': the output is not a Map"
       assert state instanceof Map : "Error in module '$key_': the state is not a Map"
       def extraEntries = toStateMap.collectMany{newkey, origkey ->
+        if (!allArgumentNames.contains(origkey)) {
+          throw new Exception("Error processing toState for '$key_': invalid argument '$origkey'")
+        }
         // check whether newkey corresponds to a required argument
         if (output.containsKey(origkey)) {
           [[newkey, output[origkey]]]

src/test/resources/testnextflowvdsl3/src/test_wfs/invalid_fromstate_argument/config.vsh.yaml

@@ -0,0 +1,12 @@
+name: invalid_fromstate_argument
+namespace: test_wfs
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: base
+  # TODO: make absolute when the ns build uses the right CWD
+  - path: ../../../resources
+dependencies:
+  - name: sub_workflow
+platforms:
+  - type: nextflow

src/test/resources/testnextflowvdsl3/src/test_wfs/invalid_fromstate_argument/main.nf

@@ -0,0 +1,33 @@
+workflow base {
+  take: input_ch
+  main:
+
+  // generate list from 0 to 1000
+  ch = Channel.fromList(0..1000)
+    | map { num ->
+      // create temporary file
+      def file = tempFile()
+      file.write("num: $num")
+
+      ["num$num", [ file: file ], ["num": num]]
+    }
+    | sub_workflow.run(
+      fromState: [
+        "file": "file",
+        "thisargumentdoesnotexist": "file", // this should raise
+      ],
+      toState: {id, output, state -> 
+        def newState = [
+          "step1_output": output.output, 
+          "num": state.num,
+          "file": state.file,
+          "thisargumentdoesnotexist": "foo" 
+        ]
+        return newState
+      }
+    )
+
+
+  emit:
+  input_ch
+}

src/test/resources/testnextflowvdsl3/src/test_wfs/invalid_tostate_argument/config.vsh.yaml

@@ -0,0 +1,12 @@
+name: invalid_tostate_argument
+namespace: test_wfs
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: base
+  # TODO: make absolute when the ns build uses the right CWD
+  - path: ../../../resources
+dependencies:
+  - name: sub_workflow
+platforms:
+  - type: nextflow

src/test/resources/testnextflowvdsl3/src/test_wfs/invalid_tostate_argument/main.nf

@@ -0,0 +1,28 @@
+workflow base {
+  take: input_ch
+  main:
+
+  // generate list from 0 to 1000
+  ch = Channel.fromList(0..1000)
+    | map { num ->
+      // create temporary file
+      def file = tempFile()
+      file.write("num: $num")
+
+      ["num$num", [ file: file ], ["num": num]]
+    }
+    | sub_workflow.run(
+      fromState: [
+        "file": "file",
+      ],
+      toState: [
+        "step1_output": "output",
+        "file": "file",
+        "newkey": "thisargumentdoesnotexist" // This should raise
+      ]
+    )
+
+
+  emit:
+  input_ch
+}

src/test/scala/io/viash/runners/nextflow/NextflowScriptTest.scala

@@ -201,6 +201,33 @@ class NextflowScriptTest extends AnyFunSuite with BeforeAndAfterAll {
   } 
 
 
+  test("Test invalid argument in fromState map", DockerTest, NextflowTest) {
+    val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
+      mainScript = "target/nextflow/test_wfs/invalid_fromstate_argument/main.nf",
+      args = List(
+        "--publish_dir", "output"
+      ),
+      cwd = tempFolFile
+    )
+
+    assert(exitCode == 1, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
+    assert(stdOut.contains("Error processing fromState for 'sub_workflow': invalid argument 'thisargumentdoesnotexist'"))
+  } 
+
+  test("Test invalid argument in toState map", DockerTest, NextflowTest) {
+    val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
+      mainScript = "target/nextflow/test_wfs/invalid_tostate_argument/main.nf",
+      args = List(
+        "--publish_dir", "output"
+      ),
+      cwd = tempFolFile
+    )
+
+    assert(exitCode == 1, s"\nexit code was $exitCode\nStd output:\n$stdOut\nStd error:\n$stdErr")
+    assert(stdOut.contains("Error processing toState for 'sub_workflow': invalid argument 'thisargumentdoesnotexist'"))
+  }
+
+
   test("Run multiple output channels standalone", NextflowTest) {
     val (exitCode, stdOut, stdErr) = NextflowTestHelper.run(
       mainScript = "target/nextflow/multiple_emit_channels/main.nf",