Merge commit '467faabb0b209ca4d71c80eab3cb35cea8b410ce' into cwl-v1.1.0-dev1

Author: mr-c

cwltool/schemas/doc/add-new-draft.md

@@ -11,8 +11,8 @@ How to make a new draft version of the CWL spec
 
 4. In the reference implementation (cwltool): make a new branch, and update the
    subtree checkout of the spec:
-   
-     git subtree merge -P cwltool/schemas/ cwl_repo/v1.1.0-dev1
+  
+     git subtree merge --squash -P cwltool/schemas/ cwl_repo/v1.1.0-dev1
 
    Where `cwl_repo` is the remote repository for the CWL specifications.
 4. In the reference implementation, teach it about the new draft version:

cwltool/schemas/run_test.sh

@@ -17,6 +17,7 @@ JUNIT_XML=""
 RUNNER=cwl-runner
 PLATFORM=$(uname -s)
 COVERAGE="python"
+EXTRA=""
 
 while [[ -n "$1" ]]
 do
@@ -70,7 +71,7 @@ runtest() {
     (cd $DRAFT
      cwltest --tool "$1" \
 	     --test=conformance_test_${DRAFT}.yaml ${TEST_N} \
-	     ${TEST_L} ${ONLY_TOOLS} ${JUNIT_XML} --basedir ${DRAFT}
+	     ${TEST_L} ${ONLY_TOOLS} ${JUNIT_XML} --basedir ${DRAFT} -- ${EXTRA}
     )
     checkexit
 }

cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml

@@ -42,7 +42,7 @@ $graph:
       maintenance release of the CWL CommandLineTool specification.
       Version 1.1 introduces the followings additions:
 
-      *
+        * Addition of `stdin` type shortcut for `CommandInputParamater`s.
 
       ## Introduction to v1.0
 
@@ -375,6 +375,30 @@ $graph:
       specializeTo: CommandInputArraySchema
     - specializeFrom: InputBinding
       specializeTo: CommandLineBinding
+  fields:
+    - name: type
+      type:
+        - "null"
+        - CWLType
+        - stdin
+        - 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.
 
 - type: record
   name: CommandOutputParameter
@@ -409,6 +433,31 @@ $graph:
       doc: |
         Specify valid types of data that may be assigned to this parameter.
 
+- name: stdin
+  type: enum
+  symbols: [ "cwl:stdin" ]
+  docParent: "#CommandInputParameter"
+  doc: |
+    Only valid as a `type` for a `CommandLineTool` input with no
+    `inputBinding` set. `stdin` must not be specified at the `CommandLineTool`
+    level.
+
+    The following
+    ```
+    inputs:
+       an_input_name:
+       type: stdin
+    ```
+    is equivalent to
+    ```
+    inputs:
+      an_input_name:
+        type: File
+        streamable: true
+
+    stdin: ${inputs.an_input_name.path}
+    ```
+
 - name: stdout
   type: enum
   symbols: [ "cwl:stdout" ]
@@ -558,6 +607,7 @@ $graph:
         "_container": "@list"
     - name: stdin
       type: ["null", string, Expression]
+      jsonldPredicate: "https://w3id.org/cwl/cwl#stdin"
       doc: |
         A path to a file whose contents must be piped into the command's
         standard input stream.

cwltool/schemas/v1.1.0-dev1/Process.yml

@@ -568,28 +568,6 @@ $graph:
         The default value for this parameter if not provided in the input
         object.
 
-    - name: type
-      type:
-        - "null"
-        - 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: OutputParameter
   type: record

cwltool/schemas/v1.1.0-dev1/Workflow.yml

@@ -107,10 +107,39 @@ $graph:
       doc: |
         Specify valid types of data that may be assigned to this parameter.
 
+- name: RegularInputParameter
+  type: record
+  extends: InputParameter
+  fields:
+    - name: type
+      type:
+        - "null"
+        - 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.
+
 - type: record
   name: ExpressionTool
   extends: Process
   specialize:
+    - specializeFrom: "#InputParameter"
+      specializeTo: "#RegularInputParameter"
     - specializeFrom: "#OutputParameter"
       specializeTo: "#ExpressionToolOutputParameter"
   documentRoot: true
@@ -462,6 +491,8 @@ $graph:
   extends: "#Process"
   documentRoot: true
   specialize:
+    - specializeFrom: "#InputParameter"
+      specializeTo: "#RegularInputParameter"
     - specializeFrom: "#OutputParameter"
       specializeTo: "#WorkflowOutputParameter"
   doc: |

cwltool/schemas/v1.1.0-dev1/conformance_test_v1.1.0-dev1.yaml

@@ -117,6 +117,17 @@
   tool: v1.1.0-dev1/cat4-tool.cwl
   doc: Test command execution in Docker with stdin and stdout redirection
 
+- job: v1.1.0-dev1/cat-job.json
+  output:
+    output_txt:
+      class: File
+      checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
+      location: output.txt
+      size: 13
+  tool: v1.1.0-dev1/cat4b-tool.cwl
+  doc: Test command execution in Docker with stdin and stdout redirection
+          with stdin shortcut
+
 - job: v1.1.0-dev1/empty.json
   tool: v1.1.0-dev1/null-expression1-tool.cwl
   output: