Abstract operation

Operation.yml

@@ -0,0 +1,87 @@
+saladVersion: v1.1
+$base: "https://w3id.org/cwl/cwl#"
+
+$namespaces:
+  cwl: "https://w3id.org/cwl/cwl#"
+
+$graph:
+
+- name: OperationInputParameter
+  type: record
+  extends: InputParameter
+  docParent: "#Operation"
+  doc: |
+    Describe an input parameter of an operation.
+  fields:
+    - name: type
+      type:
+        - CWLType
+        - InputRecordSchema
+        - InputEnumSchema
+        - InputArraySchema
+        - string
+        - type: array
+          items:
+            - CWLType
+            - InputRecordSchema
+            - InputEnumSchema
+            - InputArraySchema
+            - string
+      jsonldPredicate:
+        "_id": "sld:type"
+        "_type": "@vocab"
+        refScope: 2
+        typeDSL: True
+      doc: |
+        Specify valid types of data that may be assigned to this parameter.
+
+- name: OperationOutputParameter
+  type: record
+  extends: OutputParameter
+  docParent: "#Operation"
+  doc: |
+    Describe an output parameter of an operation.
+  fields:
+    - name: type
+      type:
+        - CWLType
+        - OutputRecordSchema
+        - OutputEnumSchema
+        - OutputArraySchema
+        - string
+        - type: array
+          items:
+            - CWLType
+            - OutputRecordSchema
+            - OutputEnumSchema
+            - OutputArraySchema
+            - string
+      jsonldPredicate:
+        "_id": "sld:type"
+        "_type": "@vocab"
+        refScope: 2
+        typeDSL: True
+      doc: |
+        Specify valid types of data that may be assigned to this parameter.
+
+- type: record
+  name: Operation
+  extends: Process
+  documentRoot: true
+  specialize:
+    - specializeFrom: InputParameter
+      specializeTo: OperationInputParameter
+    - specializeFrom: OutputParameter
+      specializeTo: OperationOutputParameter
+  doc: |
+    This record describes an abstract operation.  It is a potential
+    step of a workflow that has not yet been bound to a concrete
+    implementation.  It specifies an input and output signature, but
+    cannot be executed.
+
+  fields:
+    - name: class
+      jsonldPredicate:
+        "_id": "@type"
+        "_type": "@vocab"
+      type: string

Workflow.yml

@@ -24,12 +24,12 @@ $graph:
     - |
       # Abstract
 
-      One way to define a workflow is: an analysis task represented by a
-      directed graph describing a sequence of operations that transform an
-      input data set to output. This specification defines the Common Workflow
-      Language (CWL) Workflow description, a vendor-neutral standard for
-      representing workflows intended to be portable across a variety of
-      computing platforms.
+      This specification defines the Common Workflow Language (CWL)
+      Workflow description, a vendor-neutral standard for representing
+      analysis tasks where a sequence of operations are described
+      using a directed graph of operations to transform input to
+      output.  CWL is portable across a variety of computing
+      platforms.
 
     - {$include: intro.md}
 
@@ -734,3 +734,5 @@ $graph:
       jsonldPredicate:
         "_id": "@type"
         "_type": "@vocab"
+
+- {$import: Operation.yml}

tests/operation.cwl

@@ -0,0 +1,25 @@
+#
+# Example of an operation that has not yet been implemented
+#
+class: Operation
+cwlVersion: v1.2.0-dev1
+
+# an Operation is a placeholder for a CommandLineTool or
+# Workflow to be added later, therefore its documentation
+# are very important.
+id: reverse
+doc: "Reverse each line"
+
+# The "inputs" array work the same as in CommandLineTool, but do
+# not have any inputBinding
+inputs:
+  input:
+    type: File
+
+# The "outputs" array defines the structure of the output object, just like
+# in CommandLineTool, but without outputBinding
+outputs:
+  output:
+    type: File
+
+# There are no "run" or "steps" command (FIXME: Should they be allowed?)

tests/revsort-abstract.cwl

@@ -0,0 +1,52 @@
+#
+# This is a variant of revsort.cwl where the "sorted"
+# step has not yet been implemented, but has a placeholder
+# Operation.
+#
+class: Workflow
+doc: "Reverse the lines in a document, then sort those lines."
+cwlVersion: v1.2.0-dev1
+
+inputs:
+  input:
+    type: File
+    doc: "The input file to be processed."
+  reverse_sort:
+    type: boolean
+    default: true
+    doc: "If true, reverse (decending) sort"
+
+outputs:
+  output:
+    type: File
+    outputSource: sort/sorted
+    doc: "The output with the lines reversed and sorted."
+
+steps:
+  rev:
+    in:
+      input: input
+    out: [output]
+    run: revtool.cwl
+
+  sort:
+    in:
+      input: rev/output
+      reverse: reverse_sort
+    out: [sorted]
+    run:
+      class: Operation
+      id: "sort"
+      doc: "Sort the lines of the file"
+      inputs:
+        input:
+          type: File
+          doc: "The input file to be sorted."
+        reverse:
+          type: boolean
+          default: true
+          doc: "If true, reverse (decending) sort"
+      outputs:
+        sorted:
+          type: File
+          doc: "The sorted file"