Remove map, mapId, mapData, mapPassthrough

docs/reference/nextflow_vdsl3/import_module.qmd

@@ -74,14 +74,6 @@ workflow {
 
 - `auto.transcript`: If `true`, the module's transcript will be published to the `params.transcriptDir` folder. Default: `false` (inherited from Viash config).
 
-- `map` (`Function`): Apply a map over the incoming tuple. Example: `{ tup -> [ tup[0], [input: tup[1].output] ] + tup.drop(2) }`. Default: `null`.
-
-- `mapId` (`Function`): Apply a map over the ID element of a tuple (i.e. the first element). Example: `{ id -> id + "_foo" }`. Default: `null`.
-
-- `mapData` (`Function`): Apply a map over the data element of a tuple (i.e. the second element). Example: `{ data -> [ input: data.output ] }`. Default: `null`.
-
-- `mapPassthrough` (`Function`): Apply a map over the passthrough elements of a tuple (i.e. the tuple excl. the first two elements). Example: `{ pt -> pt.drop(1) }`. Default: `null`.
-
 - `filter` (`Function`): Filter the channel. Example: `{ tup -> tup[0] == "foo" }`. Default: `null`.
 
 - `fromState`: Fetch data from the state and pass it to the module without altering the current state. `fromState` should be `null`, `List[String]`, `Map[String, String]` or a function. 

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

@@ -14,7 +14,7 @@ def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) {
   assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}"
 
   // check for any unexpected keys
-  def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"]
+  def expectedKeys = ["key", "directives", "auto" "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"]
   def unexpectedKeys = workflowArgs.keySet() - expectedKeys
   assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'"
 
@@ -74,19 +74,12 @@ def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) {
     workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"])
   }
 
-  for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter", "runIf"]) {
+  for (nam in ["filter", "runIf"]) {
     if (workflowArgs.containsKey(nam) && workflowArgs[nam]) {
       assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}"
     }
   }
 
-  // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well?
-  for (nam in ["map", "mapData", "mapPassthrough", "renameKeys"]) {
-    if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) {
-      log.warn "module '$key': workflow argument '$nam' is deprecated and will be removed in Viash 0.9.0. Please use 'fromState' and 'toState' instead."
-    }
-  }
-
   // check fromState
   workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, meta.config)
 

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

@@ -109,22 +109,6 @@ object NextflowHelper {
       |  // auto settings
       |  auto: readJsonBlob('''${jsonPrinter.print(autoJson)}'''),
       |
-      |  // Apply a map over the incoming tuple
-      |  // Example: `{ tup -> [ tup[0], [input: tup[1].output] ] + tup.drop(2) }`
-      |  map: null,
-      |
-      |  // Apply a map over the ID element of a tuple (i.e. the first element)
-      |  // Example: `{ id -> id + "_foo" }`
-      |  mapId: null,
-      |
-      |  // Apply a map over the data element of a tuple (i.e. the second element)
-      |  // Example: `{ data -> [ input: data.output ] }`
-      |  mapData: null,
-      |
-      |  // Apply a map over the passthrough elements of a tuple (i.e. the tuple excl. the first two elements)
-      |  // Example: `{ pt -> pt.drop(1) }`
-      |  mapPassthrough: null,
-      |
       |  // Filter the channel
       |  // Example: `{ tup -> tup[0] == "foo" }`
       |  filter: null,

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

@@ -41,7 +41,6 @@ workflow base {
 
     | step1.run(
       key: "step1bis",
-      // TODO: renameKeys, map, mapId, mapData will be deprecated
       // TODO: test filter, runIf
       map: { id, state -> 
         def new_state = state + [
@@ -50,18 +49,18 @@ workflow base {
         ]
         [id, new_state]
       },
-      mapId: { id ->
-        "${id}_modified"
-      },
-      mapData: { state -> 
-        state + [another_key: "bar"]
-      },
-      renameKeys: ["original_id": "oid"],
       fromState: { id, state ->
         ["input": state.file]
       },
       toState: { id, output, state ->
-        state + ["step1bis_output": output.output]
+        def original_id = state.original_id
+        def new_state = state.findAll{k, v -> k != "original_id"}
+
+        ["${id}_modified", state + 
+          ["step1bis_output": output.output] + 
+          ["another_key": "bar"] + 
+          ["oid": original_id]
+        ]
       }
     )