more vdsl3 testing wip

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

@@ -0,0 +1,15 @@
+functionality:
+  name: concurrency
+  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: step1
+    - name: step2
+    - name: step3
+platforms:
+  - type: nextflow

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

@@ -0,0 +1,104 @@
+workflow base {
+  take: input_ch
+  main:
+
+  // generate list from 0 to 1000
+  ch = Channel.fromList(0..1000)
+    | map { num ->
+      // create temporary file
+      file = tempFile()
+      file.write("num: $num")
+
+      ["num$num", [ num: num, file: file ]]
+    }
+
+    // test fromstate and tostate with list[string]
+    | step1.run(
+      fromState: ["input": "file"],
+      toState: ["step1_output": "output"]
+    )
+
+    | view{ id, state ->
+      def num = state.num
+
+      // check id
+      assert id == "num$num": "id should be 'num$num'. Found: '$id'"
+
+      // check file text
+      def file_text = state.file.toFile().readLines()[0]
+      assert file_text == "num: $num": "file text should be 'num: $num'. Found: '$file_text'"
+
+      // check step1_output text
+      def step1_output_text = state.step1_output.toFile().readLines()[0]
+      assert step1_output_text == "num: $num": "step1_output text should be 'num: $num'. Found: '$step1_output_text'"
+
+      if (num == 0) {
+        "after step1: id: $id, state: $state"
+      } else {
+        null
+      }
+    }
+
+    | step1.run(
+      key: "step1bis",
+      // TODO: renameKeys, map, mapId, mapData will be deprecated
+      // TODO: test filter, runIf
+      map: { id, state -> 
+        def new_state = state + [
+          "oid": id,
+          "extra_key": "foo"
+        ]
+        [id, new_state]
+      },
+      mapId: { id ->
+        "${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]
+      }
+    )
+
+    | view { id, state ->
+      def num = state.num
+
+      // check id
+      assert id == "num${num}_modified": "id should be 'num${num}_modified'. Found: '$id'"
+
+      // check orig id
+      assert state.original_id == "num$num": "original_id should be 'num$num'. Found: '${state.original_id}'"
+
+      // check file text
+      def file_text = state.file.toFile().readLines()[0]
+      assert file_text == "num: $num": "file text should be 'num: $num'. Found: '$file_text'"
+
+      // check step1_output text
+      def step1_output_text = state.step1_output.toFile().readLines()[0]
+      assert step1_output_text == "num: $num": "step1_output text should be 'num: $num'. Found: '$step1_output_text'"
+
+      // check step1bis_output text
+      def step1bis_output_text = state.step1bis_output.toFile().readLines()[0]
+      assert step1bis_output_text == "num: $num": "step1bis_output text should be 'num: $num'. Found: '$step1bis_output_text'"
+
+      // check extra_key
+      assert state.extra_key == "foo": "extra_key should be 'foo'. Found: '${state.extra_key}'"
+
+      // check another_key
+      assert state.another_key == "bar": "another_key should be 'bar'. Found: '${state.another_key}'"
+
+      if (num == 0) {
+        "after step1bis: id: $id, state: $state"
+      } else {
+        null
+      }
+    }
+
+  emit:
+  input_ch
+}

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

@@ -0,0 +1,15 @@
+functionality:
+  name: runeach
+  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: step1
+    - name: step2
+    - name: step3
+platforms:
+  - type: nextflow

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

@@ -0,0 +1,124 @@
+workflow base {
+  take: input_ch
+  main:
+
+  comps = [
+    "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m",
+    "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z"
+  ]
+    .collect{ let ->
+      step1.run(key: "step1" + let)
+    }
+
+  // generate list from 0 to 1000
+  ch = Channel.fromList(0..100)
+
+    | map { num ->
+      // create temporary file
+      file = tempFile()
+      file.write("num: $num")
+
+      ["num$num", [ num: num, file: file ]]
+    }
+
+    | step1.run(
+      fromState: ["input": "file"],
+      toState: ["step1_output": "output"]
+    )
+
+
+    | step1.run(
+      key: "step1bis",
+      fromState: { id, state ->
+        ["input": state.step1_output]
+      },
+      toState: { id, output, state ->
+        state + ["step1bis_output": output.output]
+      }
+    )
+
+    | runEach(
+      components: comps,
+      filter: { id, state, comp ->
+        id != "num0" || comp.name != "step1a"
+      },
+      id: { id, state, comp ->
+        "${id}_${comp.name}".toString()
+      },
+      fromState: { id, state, comp ->
+        ["input": state.step1bis_output]
+      },
+      toState: { id, output, state, comp ->
+        state + [
+          "runEach_output": output.output,
+          "runEach_key": comp.name,
+          "extra_key": "foo"
+        ]
+      }
+      // todo: test filter
+      // todo: test fromState and toState as maps or arrays
+    )
+
+    | view { id, state ->
+      def num = state.num
+
+      // check id
+      assert id ==~ /num${num}_step1[a-z]/: "id should match 'num${num}_step1[a-z]'. Found: '$id'"
+
+      // check file text
+      def file_text = state.file.toFile().readLines()[0]
+      assert file_text == "num: $num": "file text should be 'num: $num'. Found: '$file_text'"
+
+      // check runEach_output text
+      def runEach_output_text = state.runEach_output.toFile().readLines()[0]
+      assert runEach_output_text == "num: $num": "runEach_output text should be 'num: $num'. Found: '$runEach_output_text'"
+
+      // check extra_key
+      assert state.extra_key == "foo": "extra_key should be 'foo'. Found: '${state.extra_key}'"
+
+      // check runEach_key
+      assert state.runEach_key ==~ /step1[a-z]/: "runEach_key should match 'step1[a-z]'. Found: '${state.runEach_key}'"
+
+      if (num == 0) {
+        "after runEach: id: $id, state: $state"
+      } else {
+        null
+      }
+    }
+
+    | toSortedList{ a, b -> a[0] <=> b[0] }
+    | view { list ->
+      assert list.size() == 100 * 26 + 1: "list size should be 100 * 25 + 1. Found: ${list.size()}"
+
+      def ids = list.collect{it[0]}
+      def expectedIds = (0..100).collectMany{ num ->
+        if (num == 0) {
+          ["num0_step1a"]
+        } else {
+          comps.collect{ comp ->
+            "num${num}_${comp.name}".toString()
+          }
+        }
+      }
+      def unexpectedIds = ids - expectedIds
+      def missingIds = expectedIds - ids
+
+      // println()
+      // println()
+      // println("ids: $ids")
+      // println()
+      // println("expectedIds: $expectedIds")
+      // println()
+      // println("unexpectedIds: $unexpectedIds")
+      // println()
+      // println("missingIds: $missingIds")
+      // println()
+      // println()
+      assert unexpectedIds.size() == 0: "unexpected ids: $unexpectedIds"
+      assert missingIds.size() == 0: "missing ids: $missingIds"
+
+      null
+    }
+  emit:
+  input_ch
+}