Added new loop test (#2188)

Author: LanderOtto

tests/loop-ext/value-from-loop-2.cwl

@@ -0,0 +1,56 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+
+inputs: 
+  limit: 
+    type: int 
+    default: 5
+
+outputs:
+  - id: result
+    type: string[]
+    outputSource: step1/result
+
+steps:
+  step1:
+    run: 
+      class: CommandLineTool
+      inputs:
+        lfile: 
+          type: File
+          inputBinding:
+            position: 1
+      stdout: "out.txt"
+      outputs:
+        result: 
+          type: string
+          outputBinding:
+            glob: "out.txt"
+            loadContents: true
+            outputEval: $(self[0].contents)-$(self[0].checksum)
+      baseCommand: ["cat"]
+    in:
+      counter: 
+        default: 0
+      limit: limit
+      lfile:
+        valueFrom: "${return {'class': 'File', 'basename': 'init-value-from.' + inputs.counter, 'contents': 'first,' + inputs.counter  }}"
+    out:
+      - id: result
+    requirements:
+      cwltool:Loop:
+        loopWhen: $(inputs.counter < inputs.limit)
+        loop:
+          counter:
+            valueFrom: $(inputs.counter + 1)
+          lfile:
+            valueFrom: "${return {'class': 'File', 'basename': 'iter-value-from.' + (inputs.counter + 1), 'contents': 'first,' + (inputs.counter + 1)}}"
+        outputMethod: all

tests/loop-ext/value-from-loop-3.cwl

@@ -0,0 +1,54 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+$namespaces:
+  cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+
+inputs: 
+  limit: 
+    type: int 
+    default: 5
+
+outputs:
+  - id: result
+    type: string[]
+    outputSource: step1/result
+
+steps:
+  step1:
+    run: 
+      class: CommandLineTool
+      inputs:
+        lfile: 
+          type: File
+          inputBinding:
+            position: 1
+      stdout: "out.txt"
+      outputs:
+        result: 
+          type: string
+          outputBinding:
+            glob: "out.txt"
+            loadContents: true
+            outputEval: $(self[0].contents)-$(self[0].checksum)
+      baseCommand: ["cat"]
+    in:
+      counter: 
+        default: 0
+      limit: limit
+      lfile:
+        valueFrom: "${return {'class': 'File', 'basename': 'init-value-from.' + inputs.counter, 'contents': 'first,' + inputs.counter  }}"
+    out:
+      - id: result
+    requirements:
+      cwltool:Loop:
+        loopWhen: $(inputs.counter < inputs.limit)
+        loop:
+          counter:
+            valueFrom: $(inputs.counter + 1)
+        outputMethod: all

tests/loop/value-from-loop-2.cwl

@@ -0,0 +1,49 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.3.0-dev1
+class: Workflow
+requirements:
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+inputs:
+  limit: 
+    type: int 
+    default: 5
+
+outputs:
+  - id: result
+    type: string[]
+    outputSource: step1/result
+
+steps:
+  step1:
+    run: 
+      class: CommandLineTool
+      inputs:
+        lfile: 
+          type: File
+          inputBinding:
+            position: 1
+      stdout: "out.txt"
+      outputs:
+        result: 
+          type: string
+          outputBinding:
+            glob: "out.txt"
+            loadContents: true
+            outputEval: $(self[0].contents)-$(self[0].checksum)
+      baseCommand: ["cat"]
+    in:
+      counter: 
+        default: 0
+      limit: limit
+      lfile:
+        valueFrom: "${return {'class': 'File', 'basename': 'init-value-from.' + inputs.counter, 'contents': 'first,' + inputs.counter  }}"
+    out:
+      - id: result
+    when: $(inputs.counter < inputs.limit)
+    loop:
+      counter:
+        valueFrom: $(inputs.counter + 1)
+      lfile:
+        valueFrom: "${return {'class': 'File', 'basename': 'iter-value-from.' + (inputs.counter + 1), 'contents': 'first,' + (inputs.counter + 1)}}"
+    outputMethod: all_iterations

tests/loop/value-from-loop-3.cwl

@@ -0,0 +1,47 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.3.0-dev1
+class: Workflow
+requirements:
+  InlineJavascriptRequirement: {}
+  StepInputExpressionRequirement: {}
+inputs:
+  limit: 
+    type: int 
+    default: 5
+
+outputs:
+  - id: result
+    type: string[]
+    outputSource: step1/result
+
+steps:
+  step1:
+    run: 
+      class: CommandLineTool
+      inputs:
+        lfile: 
+          type: File
+          inputBinding:
+            position: 1
+      stdout: "out.txt"
+      outputs:
+        result: 
+          type: string
+          outputBinding:
+            glob: "out.txt"
+            loadContents: true
+            outputEval: $(self[0].contents)-$(self[0].checksum)
+      baseCommand: ["cat"]
+    in:
+      counter: 
+        default: 0
+      limit: limit
+      lfile:
+        valueFrom: "${return {'class': 'File', 'basename': 'init-value-from.' + inputs.counter, 'contents': 'first,' + inputs.counter  }}"
+    out:
+      - id: result
+    when: $(inputs.counter < inputs.limit)
+    loop:
+      counter:
+        valueFrom: $(inputs.counter + 1)
+    outputMethod: all_iterations

tests/test_loop.py

@@ -191,6 +191,46 @@ def test_loop_value_from_fail_no_requirement() -> None:
     assert main(params) == 1
 
 
+def test_loop_value_from_literal_file() -> None:
+    """Test a loop case with a literal file generated by a valueFrom directive inside the loop."""
+    stream = StringIO()
+    params = [
+        "--enable-dev",
+        get_data("tests/loop/value-from-loop-2.cwl"),
+    ]
+    main(params, stdout=stream)
+    expected = {
+        "result": [
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,1-sha1$c2ee1cb0abf988529ae1d67c5a6798a9db9e133a",
+            "first,2-sha1$7663c0076cdf1dbe14373237e8c2eea8735b04f2",
+            "first,3-sha1$83b77de68c3c6cce92a381adc9159d6e59332545",
+            "first,4-sha1$eb74efd51e4399144f465534f4077f515d996d57",
+        ]
+    }
+    assert json.loads(stream.getvalue()) == expected
+
+
+def test_loop_and_value_from_literal_file() -> None:
+    """Test a loop case with a literal file generated by a valueFrom directive outside the loop."""
+    stream = StringIO()
+    params = [
+        "--enable-dev",
+        get_data("tests/loop/value-from-loop-3.cwl"),
+    ]
+    main(params, stdout=stream)
+    expected = {
+        "result": [
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+        ]
+    }
+    assert json.loads(stream.getvalue()) == expected
+
+
 def test_loop_inside_scatter() -> None:
     """Test a loop subworkflow inside a scatter step."""
     stream = StringIO()

tests/test_loop_ext.py

@@ -220,6 +220,46 @@ def test_loop_value_from() -> None:
     assert json.loads(stream.getvalue()) == expected
 
 
+def test_loop_value_from_literal_file() -> None:
+    """Test a loop case with a literal file generated by a valueFrom directive inside the loop."""
+    stream = StringIO()
+    params = [
+        "--enable-ext",
+        get_data("tests/loop-ext/value-from-loop-2.cwl"),
+    ]
+    main(params, stdout=stream)
+    expected = {
+        "result": [
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,1-sha1$c2ee1cb0abf988529ae1d67c5a6798a9db9e133a",
+            "first,2-sha1$7663c0076cdf1dbe14373237e8c2eea8735b04f2",
+            "first,3-sha1$83b77de68c3c6cce92a381adc9159d6e59332545",
+            "first,4-sha1$eb74efd51e4399144f465534f4077f515d996d57",
+        ]
+    }
+    assert json.loads(stream.getvalue()) == expected
+
+
+def test_loop_and_value_from_literal_file() -> None:
+    """Test a loop case with a literal file generated by a valueFrom directive outside the loop."""
+    stream = StringIO()
+    params = [
+        "--enable-ext",
+        get_data("tests/loop-ext/value-from-loop-3.cwl"),
+    ]
+    main(params, stdout=stream)
+    expected = {
+        "result": [
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+            "first,0-sha1$e445e7ebf0b1e19e5eb7f3e8e4d86f5424c4b103",
+        ]
+    }
+    assert json.loads(stream.getvalue()) == expected
+
+
 def test_loop_value_from_fail_no_requirement() -> None:
     """Test workflow loop fails for valueFrom without StepInputExpressionRequirement."""
     params = [