expr refactor: improve test coverage

Author: mr-c

testdata/scatter-valuefrom-inputs-wf1_v10.cwl

@@ -0,0 +1,62 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: Workflow
+inputs:
+  inp:
+    type:
+      type: array
+      items:
+        type: record
+        name: instr
+        fields:
+          - name: instr
+            type: string
+outputs:
+  out:
+    type:
+      type: array
+      items: string
+    outputSource: step1/echo_out
+
+requirements:
+  - class: ScatterFeatureRequirement
+  - class: StepInputExpressionRequirement
+
+steps:
+  step1:
+    in:
+      echo_unused: inp
+      echo_in:
+        valueFrom: $(inputs.echo_unused.instr)
+      first:
+        source: inp
+        valueFrom: "$(self[0].instr)"
+    out: [echo_out]
+    scatter: echo_unused
+    run:
+      class: CommandLineTool
+      hints:
+        ResourceRequirement:
+          ramMin: 8
+      inputs:
+        first:
+          type: string
+          inputBinding:
+            position: 1
+        echo_in:
+          type: string
+          inputBinding:
+            position: 2
+        echo_unused: Any
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      arguments:
+        - "-n"
+        - "foo"
+      stdout: "step1_out"

testdata/step-valuefrom2-wf_v10.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.0
+requirements:
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+  - class: MultipleInputFeatureRequirement
+
+inputs:
+  a: int
+  b: int
+
+outputs:
+  val:
+    type: string
+    outputSource: step1/echo_out
+
+steps:
+  step1:
+    run:
+      id: echo
+      class: CommandLineTool
+      inputs:
+        c:
+          type: int
+          inputBinding: {}
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      stdout: step1_out
+
+    in:
+      c:
+        source: [a, b]
+        valueFrom: "$(self[0] + self[1])"
+    out: [echo_out]

testdata/step-valuefrom2-wf_v11.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.1
+requirements:
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+  - class: MultipleInputFeatureRequirement
+
+inputs:
+  a: int
+  b: int
+
+outputs:
+  val:
+    type: string
+    outputSource: step1/echo_out
+
+steps:
+  step1:
+    run:
+      id: echo
+      class: CommandLineTool
+      inputs:
+        c:
+          type: int
+          inputBinding: {}
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      stdout: step1_out
+
+    in:
+      c:
+        source: [a, b]
+        valueFrom: "$(self[0] + self[1])"
+    out: [echo_out]

testdata/step-valuefrom2-wf_v12.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.2
+requirements:
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+  - class: MultipleInputFeatureRequirement
+
+inputs:
+  a: int
+  b: int
+
+outputs:
+  val:
+    type: string
+    outputSource: step1/echo_out
+
+steps:
+  step1:
+    run:
+      id: echo
+      class: CommandLineTool
+      inputs:
+        c:
+          type: int
+          inputBinding: {}
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      stdout: step1_out
+
+    in:
+      c:
+        source: [a, b]
+        valueFrom: "$(self[0] + self[1])"
+    out: [echo_out]

testdata/step-valuefrom3-wf_v10.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.0
+requirements:
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+
+inputs:
+  a: int
+  b: int
+
+outputs:
+  val:
+    type: string
+    outputSource: step1/echo_out
+
+steps:
+  step1:
+    run:
+      id: echo
+      class: CommandLineTool
+      inputs:
+        c:
+          type: int
+          inputBinding: {}
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      stdout: step1_out
+
+    in:
+      a: a
+      b: b
+      c:
+        valueFrom: "$(inputs.a + inputs.b)"
+    out: [echo_out]

testdata/step-valuefrom3-wf_v11.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.1
+requirements:
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+
+inputs:
+  a: int
+  b: int
+
+outputs:
+  val:
+    type: string
+    outputSource: step1/echo_out
+
+steps:
+  step1:
+    run:
+      id: echo
+      class: CommandLineTool
+      inputs:
+        c:
+          type: int
+          inputBinding: {}
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      stdout: step1_out
+
+    in:
+      a: a
+      b: b
+      c:
+        valueFrom: "$(inputs.a + inputs.b)"
+    out: [echo_out]

testdata/step-valuefrom3-wf_v12.cwl

@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.2
+requirements:
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement
+
+inputs:
+  a: int
+  b: int
+
+outputs:
+  val:
+    type: string
+    outputSource: step1/echo_out
+
+steps:
+  step1:
+    run:
+      id: echo
+      class: CommandLineTool
+      inputs:
+        c:
+          type: int
+          inputBinding: {}
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      stdout: step1_out
+
+    in:
+      a: a
+      b: b
+      c:
+        valueFrom: "$(inputs.a + inputs.b)"
+    out: [echo_out]

tests/test_etools_to_clt.py

@@ -146,6 +146,72 @@ def test_v1_2_workflow_top_level_sf_expr_array() -> None:
         )
 
 
+def test_v1_0_step_valuefrom_expr_multisource() -> None:
+    """Convert a valueFrom expression that has multiple sources."""
+    result, modified = traverse0(
+        parser.load_document(str(HERE / "../testdata/step-valuefrom2-wf_v10.cwl")),
+        False,
+        False,
+        False,
+        False,
+    )
+
+
+def test_v1_1_step_valuefrom_expr_multisource() -> None:
+    """Convert a valueFrom expression that has multiple sources."""
+    result, modified = traverse1(
+        parser1.load_document(str(HERE / "../testdata/step-valuefrom2-wf_v11.cwl")),
+        False,
+        False,
+        False,
+        False,
+    )
+
+
+def test_v1_2_step_valuefrom_expr_multisource() -> None:
+    """Convert a valueFrom expression that has multiple sources."""
+    result, modified = traverse2(
+        parser2.load_document(str(HERE / "../testdata/step-valuefrom2-wf_v12.cwl")),
+        False,
+        False,
+        False,
+        False,
+    )
+
+
+def test_v1_0_step_valuefrom_expr_sibling_inputs() -> None:
+    """Convert a valueFrom expression from a step input that has uninvolved sibling inputs."""
+    result, modified = traverse0(
+        parser.load_document(str(HERE / "../testdata/step-valuefrom3-wf_v10.cwl")),
+        False,
+        False,
+        False,
+        False,
+    )
+
+
+def test_v1_1_step_valuefrom_expr_sibling_inputs() -> None:
+    """Convert a valueFrom expression from a step input that has uninvolved sibling inputs."""
+    result, modified = traverse1(
+        parser1.load_document(str(HERE / "../testdata/step-valuefrom3-wf_v11.cwl")),
+        False,
+        False,
+        False,
+        False,
+    )
+
+
+def test_v1_2_step_valuefrom_expr_sibling_inputs() -> None:
+    """Convert a valueFrom expression from a step input that has uninvolved sibling inputs."""
+    result, modified = traverse2(
+        parser2.load_document(str(HERE / "../testdata/step-valuefrom3-wf_v12.cwl")),
+        False,
+        False,
+        False,
+        False,
+    )
+
+
 @pytest.fixture(scope="session")
 def cwl_v1_0_dir(
     tmp_path_factory: TempPathFactory,