Update JSON->YAML

common-workflow-lab · Jul 16, 2019 · 178c8b4 · 178c8b4
1 parent 6a2dada
commit 178c8b4
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Showing 25 changed files with 1,172 additions and 1,936 deletions.
diff --git a/cwlex.cwl b/cwlex.cwl
@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+arguments:
+  - cwlex
+  - '$(inputs.inp ? inputs.inp.path : inputs.inpdir.path+''/''+inputs.inpfile)'
+class: CommandLineTool
+cwlVersion: v1.0
+id: '#main'
+inputs:
+  - id: inp
+    type:
+      - 'null'
+      - File
+  - id: inpdir
+    type:
+      - 'null'
+      - Directory
+  - id: inpfile
+    type:
+      - 'null'
+      - string
+  - id: outname
+    type:
+      - 'null'
+      - string
+outputs:
+  - id: converted
+    outputBinding:
+      glob: $(outname(inputs))
+    type: File
+requirements:
+  - class: DockerRequirement
+    dockerPull: commonworkflowlanguage/cwlex
+  - class: InlineJavascriptRequirement
+    expressionLib:
+      - |
+
+        function outname(inputs) {
+          return inputs.outname ? inputs.outname : (inputs.inp ? inputs.inp.nameroot+'.cwl' : inputs.inpfile.replace(/(.*).cwlex/, '$1.cwl'));
+        }
+stdout: $(outname(inputs))
+
diff --git a/src/cwlex-convert.js b/src/cwlex-convert.js
@@ -557,7 +557,7 @@ CwlExListener.prototype.exitCall = function(ctx) {
     if (find !== undefined && ctx.stepinputs().stepinput().length == 1
        && find.id != inkeys[0]) {
         stepin[find.id] = stepin[inkeys[0]];
-        stepin[inkeys[0]] = undefined;
+        delete stepin[inkeys[0]];
     }
 }
 

diff --git a/tests/antlr/antlr.cwl b/tests/antlr/antlr.cwl
@@ -1,39 +1,26 @@
 #!/usr/bin/env cwl-runner
-{
-  "arguments": [
-    "antlr4",
-    "-Dlanguage=JavaScript",
-    "-o",
-    ".",
-    "$(inputs.file)"
-  ],
-  "class": "CommandLineTool",
-  "cwlVersion": "v1.0",
-  "id": "#antlr",
-  "inputs": [
-    {
-      "default": {
-        "class": "File",
-        "location": "cwlex.g4"
-      },
-      "id": "file",
-      "type": "File"
-    }
-  ],
-  "outputs": [
-    {
-      "id": "parser",
-      "outputBinding": {
-        "glob": "*.js"
-      },
-      "type": {
-        "items": "File",
-        "type": "array"
-      }
-    }
-  ],
-  "requirements": {
-    "InlineJavascriptRequirement": {
-    }
-  }
-}
+arguments:
+  - antlr4
+  - '-Dlanguage=JavaScript'
+  - '-o'
+  - .
+  - $(inputs.file)
+class: CommandLineTool
+cwlVersion: v1.0
+id: '#antlr'
+inputs:
+  - default:
+      class: File
+      location: cwlex.g4
+    id: file
+    type: File
+outputs:
+  - id: parser
+    outputBinding:
+      glob: '*.js'
+    type:
+      items: File
+      type: array
+requirements:
+  InlineJavascriptRequirement: {}
+
diff --git a/tests/assign/assign.cwl b/tests/assign/assign.cwl
@@ -1,73 +1,41 @@
 #!/usr/bin/env cwl-runner
-{
-  "$graph": [
-    {
-      "arguments": [
-        "echo",
-        "$(inputs.msg)"
-      ],
-      "class": "CommandLineTool",
-      "id": "#echo",
-      "inputs": [
-        {
-          "id": "msg",
-          "type": "string"
-        }
-      ],
-      "outputs": [
-        {
-          "id": "out",
-          "outputBinding": {
-            "glob": "blub.txt"
-          },
-          "type": "File"
-        }
-      ],
-      "requirements": {
-        "InlineJavascriptRequirement": {
-        }
-      },
-      "stdout": "blub.txt"
-    },
-    {
-      "class": "Workflow",
-      "id": "#main",
-      "inputs": [
-      ],
-      "outputs": [
-        {
-          "id": "e",
-          "outputSource": "echo_1/out",
-          "type": "File"
-        }
-      ],
-      "requirements": {
-        "InlineJavascriptRequirement": {
-        },
-        "MultipleInputFeatureRequirement": {
-        },
-        "ScatterFeatureRequirement": {
-        },
-        "StepInputExpressionRequirement": {
-        },
-        "SubworkflowFeatureRequirement": {
-        }
-      },
-      "steps": [
-        {
-          "id": "echo_1",
-          "in": {
-            "msg": {
-              "default": "hello world"
-            }
-          },
-          "out": [
-            "out"
-          ],
-          "run": "#echo"
-        }
-      ]
-    }
-  ],
-  "cwlVersion": "v1.0"
-}
+$graph:
+  - arguments:
+      - echo
+      - $(inputs.msg)
+    class: CommandLineTool
+    id: '#echo'
+    inputs:
+      - id: msg
+        type: string
+    outputs:
+      - id: out
+        outputBinding:
+          glob: blub.txt
+        type: File
+    requirements:
+      InlineJavascriptRequirement: {}
+    stdout: blub.txt
+  - class: Workflow
+    id: '#main'
+    inputs: []
+    outputs:
+      - id: e
+        outputSource: echo_1/out
+        type: File
+    requirements:
+      InlineJavascriptRequirement: {}
+      MultipleInputFeatureRequirement: {}
+      ScatterFeatureRequirement: {}
+      StepInputExpressionRequirement: {}
+      SubworkflowFeatureRequirement: {}
+    steps:
+      - id: echo_1
+        in:
+          msg:
+            default: hello world
+        out:
+          - out
+        run: '#echo'
+cwlVersion: v1.0
+
diff --git a/tests/const/const_values.cwl b/tests/const/const_values.cwl
@@ -1,85 +1,51 @@
 #!/usr/bin/env cwl-runner
-{
-  "class": "Workflow",
-  "cwlVersion": "v1.0",
-  "id": "#main",
-  "inputs": [
-    {
-      "default": 12,
-      "id": "intval",
-      "type": "int"
-    },
-    {
-      "default": 1.2,
-      "id": "floatval",
-      "type": "float"
-    },
-    {
-      "default": "foobar",
-      "id": "strval",
-      "type": "string"
-    },
-    {
-      "default": {
-        "class": "File",
-        "location": "hello.txt"
-      },
-      "id": "fileval",
-      "type": "File"
-    },
-    {
-      "default": [
-        "a",
-        "b",
-        {
-          "c": [
-            13,
-            "d"
-          ]
-        }
-      ],
-      "id": "listval",
-      "type": "Any"
-    },
-    {
-      "default": {
-        "a": "b",
-        "c": {
-          "d": "e"
-        },
-        "f": [
-          "g",
-          12
-        ]
-      },
-      "id": "structval",
-      "type": "Any"
-    }
-  ],
-  "outputs": [
-    {
-      "id": "iv",
-      "outputSource": "intval",
-      "type": "int"
-    },
-    {
-      "id": "fv",
-      "outputSource": "floatval",
-      "type": "float"
-    }
-  ],
-  "requirements": {
-    "InlineJavascriptRequirement": {
-    },
-    "MultipleInputFeatureRequirement": {
-    },
-    "ScatterFeatureRequirement": {
-    },
-    "StepInputExpressionRequirement": {
-    },
-    "SubworkflowFeatureRequirement": {
-    }
-  },
-  "steps": [
-  ]
-}
+class: Workflow
+cwlVersion: v1.0
+id: '#main'
+inputs:
+  - default: 12
+    id: intval
+    type: int
+  - default: 1.2
+    id: floatval
+    type: float
+  - default: foobar
+    id: strval
+    type: string
+  - default:
+      class: File
+      location: hello.txt
+    id: fileval
+    type: File
+  - default:
+      - a
+      - b
+      - c:
+          - 13
+          - d
+    id: listval
+    type: Any
+  - default:
+      a: b
+      c:
+        d: e
+      f:
+        - g
+        - 12
+    id: structval
+    type: Any
+outputs:
+  - id: iv
+    outputSource: intval
+    type: int
+  - id: fv
+    outputSource: floatval
+    type: float
+requirements:
+  InlineJavascriptRequirement: {}
+  MultipleInputFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  SubworkflowFeatureRequirement: {}
+steps: []
+