Merge pull request #228 from common-workflow-language/scoped-ref-and-typedsl

Scoped ref and typedsl

Author: mr-c

draft-4/Process.yml

@@ -10,7 +10,7 @@ $graph:
   type: documentation
   doc: {$include: concepts.md}
 
-- $import: "salad/schema_salad/metaschema/metaschema.yml"
+- $import: "salad/schema_salad/metaschema/metaschema_base.yml"
 
 - name: BaseTypesDoc
   type: documentation
@@ -32,6 +32,7 @@ $graph:
     - cwl:draft-3.dev5
     - cwl:draft-3
     - cwl:draft-4.dev1
+    - cwl:draft-4.dev2
 
 - name: CWLType
   type: enum
@@ -226,6 +227,8 @@ $graph:
       jsonldPredicate:
         "_id": "sld:type"
         "_type": "@vocab"
+        refScope: 2
+        typeDSL: True
       doc: |
         Specify valid types of data that may be assigned to this parameter.
 

draft-4/Workflow.yml

@@ -53,7 +53,7 @@ $graph:
 
 - type: record
   name: ExpressionTool
-  extends: "#Process"
+  extends: Process
   documentRoot: true
   doc: |
     Execute an expression as a process step.
@@ -64,7 +64,7 @@ $graph:
         "_type": "@vocab"
       type: string
     - name: expression
-      type: [string, "#Expression"]
+      type: [string, Expression]
       doc: |
         The expression to execute.  The expression must return a JSON object which
         matches the output parameters of the ExpressionTool.
@@ -80,12 +80,30 @@ $graph:
 
 - name: WorkflowOutputParameter
   type: record
-  extends: ["#OutputParameter", "#Sink"]
+  extends: OutputParameter
   docParent: "#Workflow"
   doc: |
     Describe an output parameter of a workflow.  The parameter must be
     connected to one or more parameters defined in the workflow that will
     provide the value of the output parameter.
+  fields:
+    - name: outputSource
+      doc: |
+        Specifies one or more workflow parameters that supply the value of to
+        the output parameter.
+      jsonldPredicate:
+        "_id": "cwl:outputSource"
+        "_type": "@id"
+        refScope: 0
+      type:
+        - string?
+        - string[]?
+    - name: linkMerge
+      type: ["null", "#LinkMergeMethod"]
+      jsonldPredicate: "cwl:linkMerge"
+      doc: |
+        The method to use to merge multiple sources into a single array.
+        If not specified, the default method is "merge_nested".
 
 
 - name: Sink
@@ -99,21 +117,21 @@ $graph:
       jsonldPredicate:
         "_id": "cwl:source"
         "_type": "@id"
+        refScope: 2
       type:
-        - "null"
-        - string
-        - type: array
-          items: string
+        - string?
+        - string[]?
     - name: linkMerge
-      type: ["null", "#LinkMergeMethod"]
+      type: LinkMergeMethod?
+      jsonldPredicate: "cwl:linkMerge"
       doc: |
         The method to use to merge multiple inbound links into a single array.
         If not specified, the default method is "merge_nested".
 
 
 - type: record
   name: WorkflowStepInput
-  extends: "#Sink"
+  extends: Sink
   docParent: "#WorkflowStep"
   doc: |
     The input of a workflow step connects an upstream parameter (from the
@@ -278,9 +296,7 @@ $graph:
       jsonldPredicate: "@id"
       doc: "The unique identifier for this workflow step."
     - name: in
-      type:
-        type: array
-        items: "#WorkflowStepInput"
+      type: WorkflowStepInput[]
       jsonldPredicate:
         _id: "cwl:in"
         mapSubject: id
@@ -294,7 +310,7 @@ $graph:
     - name: out
       type:
         - type: array
-          items: [string, "#WorkflowStepOutput"]
+          items: [string, WorkflowStepOutput]
       jsonldPredicate:
         _id: "cwl:out"
         _type: "@id"
@@ -303,10 +319,7 @@ $graph:
         Defines the parameters representing the output of the process.  May be
         used to generate and/or validate the output object.
     - name: requirements
-      type:
-        - "null"
-        - type: array
-          items: "#ProcessRequirement"
+      type: ProcessRequirement[]?
       jsonldPredicate:
         _id: "cwl:requirements"
         mapSubject: class
@@ -318,10 +331,7 @@ $graph:
         error and the implementation must not attempt to run the process,
         unless overridden at user option.
     - name: hints
-      type:
-        - "null"
-        - type: array
-          items: "Any"
+      type: Any[]?
       jsonldPredicate:
         _id: "cwl:hints"
         noLinkCheck: true
@@ -332,40 +342,33 @@ $graph:
         not an error if an implementation cannot satisfy all hints, however
         the implementation may report a warning.
     - name: label
-      type:
-        - "null"
-        - string
+      type: string?
       jsonldPredicate: "rdfs:label"
       doc: "A short, human-readable label of this process object."
     - name: description
-      type:
-        - "null"
-        - string
+      type: string?
       jsonldPredicate: "rdfs:comment"
       doc: "A long, human-readable description of this process object."
     - name: run
-      type: [string, "#Process"]
+      type: [string, Process]
       jsonldPredicate:
         "_id": "cwl:run"
         "_type": "@id"
       doc: |
         Specifies the process to run.
     - name: scatter
       type:
-        - "null"
-        - string
-        - type: array
-          items: string
+        - string?
+        - string[]?
       jsonldPredicate:
         "_id": "cwl:scatter"
         "_type": "@id"
         "_container": "@list"
+        refScope: 0
     - name: scatterMethod
       doc: |
         Required if `scatter` is an array of more than one element.
-      type:
-        - "null"
-        - "#ScatterMethod"
+      type: ScatterMethod?
       jsonldPredicate:
         "_id": "cwl:scatterMethod"
         "_type": "@vocab"
@@ -445,28 +448,28 @@ $graph:
 
 - type: record
   name: SubworkflowFeatureRequirement
-  extends: "#ProcessRequirement"
+  extends: ProcessRequirement
   doc: |
     Indicates that the workflow platform must support nested workflows in
     the `run` field of (WorkflowStep)(#WorkflowStep).
 
 - name: ScatterFeatureRequirement
   type: record
-  extends: "#ProcessRequirement"
+  extends: ProcessRequirement
   doc: |
     Indicates that the workflow platform must support the `scatter` and
     `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
 
 - name: MultipleInputFeatureRequirement
   type: record
-  extends: "#ProcessRequirement"
+  extends: ProcessRequirement
   doc: |
     Indicates that the workflow platform must support multiple inbound data links
     listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
 
 - type: record
   name: StepInputExpressionRequirement
-  extends: "#ProcessRequirement"
+  extends: ProcessRequirement
   doc: |
     Indicate that the workflow platform must support the `valueFrom` field
     of [WorkflowStepInput](#WorkflowStepInput).

draft-4/draft-4/binding-test.cwl

@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 
 inputs:
   reference:

draft-4/draft-4/bwa-mem-tool.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 
 class: CommandLineTool
 

draft-4/draft-4/cat1-tool.cwl

@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
@@ -10,7 +10,7 @@ inputs:
     type: File
     inputBinding: {position: 1}
   numbering:
-    type: ["null", boolean]
+    type: boolean?
     inputBinding:
       position: 0
       prefix: -n

draft-4/draft-4/cat2-tool.cwl

@@ -1,13 +1,12 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  file1:
-    type: File
+  file1: File
 outputs: []
 baseCommand: cat
 stdin: $(inputs.file1.path)

draft-4/draft-4/cat3-tool.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:

draft-4/draft-4/cat4-tool.cwl

@@ -1,13 +1,12 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  file1:
-    type: File
+  file1: File
 outputs:
   output_txt:
     type: File

draft-4/draft-4/cat5-tool.cwl

@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:

draft-4/draft-4/conflict-wf.cwl

@@ -1,4 +1,4 @@
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 $graph:
 - id: echo
   class: CommandLineTool
@@ -41,35 +41,32 @@ $graph:
   id: collision
 
   inputs:
-    input_1:
-      type: string
-
-    input_2:
-      type: string
+    input_1: string
+    input_2: string
 
   outputs:
     fileout:
       type: File
-      source: "#collision/cat_step/fileout"
+      outputSource: cat_step/fileout
 
   steps:
     echo_1:
       run: "#echo"
       in:
-        text: "#collision/input_1"
+        text: input_1
       out: [fileout]
 
     echo_2:
       run: "#echo"
       in:
-        text: "#collision/input_2"
+        text: input_2
       out: [fileout]
 
     cat_step:
       run: "#cat"
       in:
         file1:
-          source: "#collision/echo_1/fileout"
+          source: echo_1/fileout
         file2:
-          source: "#collision/echo_2/fileout"
+          source: echo_2/fileout
       out: [fileout]

draft-4/draft-4/count-lines1-wf.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 
 inputs:
   file1:
@@ -9,17 +9,17 @@ inputs:
 outputs:
   count_output:
     type: int
-    source: "#step2/output"
+    outputSource: step2/output
 
 steps:
   step1:
     run: wc-tool.cwl
     in:
-      file1: "#file1"
+      file1: file1
     out: [output]
 
   step2:
     run: parseInt-tool.cwl
     in:
-      file1: "#step1/output"
+      file1: step1/output
     out: [output]