Merge branch 'master' into directory

Peter Amstutz · Peter Amstutz · commit 8798dc8435f5 · 2016-06-23T09:31:58.000-04:00
diff --git a/draft-4/CommandLineTool.yml b/draft-4/CommandLineTool.yml
@@ -368,21 +368,95 @@ $graph:
     - specializeFrom: "#InputBinding"
       specializeTo: "#CommandLineBinding"
 
-
 - type: record
   name: CommandOutputParameter
   extends: "#OutputParameter"
   doc: An output parameter for a CommandLineTool.
   specialize:
-    - specializeFrom: "#OutputRecordSchema"
-      specializeTo: "#CommandOutputRecordSchema"
-    - specializeFrom: "#OutputEnumSchema"
-      specializeTo: "#CommandOutputEnumSchema"
-    - specializeFrom: "#OutputArraySchema"
-      specializeTo: "#CommandOutputArraySchema"
     - specializeFrom: "#OutputBinding"
       specializeTo: "#CommandOutputBinding"
+  fields:
+    - name: type
+      type:
+        - "null"
+        - "#CWLType"
+        - "#stdout"
+        - "#stderr"
+        - "#CommandOutputRecordSchema"
+        - "#CommandOutputEnumSchema"
+        - "#CommandOutputArraySchema"
+        - string
+        - type: array
+          items:
+            - "#CWLType"
+            - "#CommandOutputRecordSchema"
+            - "#CommandOutputEnumSchema"
+            - "#CommandOutputArraySchema"
+            - 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: stdout
+  type: enum
+  symbols: [ "cwl:stdout" ]
+  docParent: "#CommandOutputParameter"
+  doc: |
+    Only valid as a `type` for a `CommandLineTool` output with no
+    `outputBinding` set.
+
+    The following
+    ```
+    outputs:
+       an_output_name:
+       type: stdout
+
+    stdout: a_stdout_file
+    ```
+    is equivalent to
+    ```
+    outputs:
+       an_output_name:
+         type: File
+         outputBinding:
+           glob: a_stdout_file
+
+    stdout: a_stdout_file
+    ```
+
+    If there is no `stdout` name provided, a random filename will be created.
+
+
+- name: stderr
+  type: enum
+  symbols: [ "cwl:stderr" ]
+  docParent: "#CommandOutputParameter"
+  doc: |
+    Only valid as a `type` for a `CommandLineTool` output with no
+    `outputBinding` set.
+
+    The following
+    ```
+    outputs:
+       an_output_name:
+       type: stderr
+
+    stderr: a_stderr_file
+    ```
+    is equivalent to
+    ```
+    outputs:
+       an_output_name:
+         type: File
+         outputBinding:
+           glob: a_stderr_file
+    ```
+
+    If there is no `stderr` name provided, a random filename will be created.
 
 - type: record
   name: CommandLineTool
@@ -436,6 +510,7 @@ $graph:
         standard input stream.
     - name: stderr
       type: ["null", string, "#Expression"]
+      jsonldPredicate: "https://w3id.org/cwl/cwl#stderr"
       doc: |
         Capture the command's standard error stream to a file written to
         the designated output directory.
@@ -448,6 +523,7 @@ $graph:
         characters (such as the path separator `/`) it is an error.
     - name: stdout
       type: ["null", string, "#Expression"]
+      jsonldPredicate: "https://w3id.org/cwl/cwl#stdout"
       doc: |
         Capture the command's standard output stream to a file written to
         the designated output directory.
diff --git a/draft-4/Process.yml b/draft-4/Process.yml
@@ -230,7 +230,6 @@ $graph:
         mapSubject: basename
         mapPredicate: entry
 
-
 - name: SchemaBase
   type: record
   abstract: true
@@ -301,29 +300,6 @@ $graph:
     Define an input or output parameter to a process.
 
   fields:
-    - name: type
-      type:
-        - "null"
-        - "#CWLType"
-        - "sld:RecordSchema"
-        - "sld:EnumSchema"
-        - "sld:ArraySchema"
-        - string
-        - type: array
-          items:
-            - "#CWLType"
-            - "sld:RecordSchema"
-            - "sld:EnumSchema"
-            - "sld:ArraySchema"
-            - 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: label
       type:
         - "null"
@@ -486,13 +462,6 @@ $graph:
 - name: InputParameter
   type: record
   extends: "#Parameter"
-  specialize:
-    - specializeFrom: "sld:RecordSchema"
-      specializeTo: "#InputRecordSchema"
-    - specializeFrom: "sld:EnumSchema"
-      specializeTo: "#InputEnumSchema"
-    - specializeFrom: "sld:ArraySchema"
-      specializeTo: "#InputArraySchema"
   fields:
     - name: id
       type: string
@@ -513,6 +482,28 @@ $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
diff --git a/draft-4/Workflow.yml b/draft-4/Workflow.yml
@@ -50,10 +50,39 @@ $graph:
 
     - {$include: concepts.md}
 
+- name: ExpressionToolOutputParameter
+  type: record
+  extends: Parameter
+  fields:
+    - name: type
+      type:
+        - "null"
+        - "#CWLType"
+        - "sld:RecordSchema"
+        - "sld:EnumSchema"
+        - "sld:ArraySchema"
+        - string
+        - type: array
+          items:
+            - "#CWLType"
+            - "sld:RecordSchema"
+            - "sld:EnumSchema"
+            - "sld:ArraySchema"
+            - 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: "#OutputParameter"
+      specializeTo: "#ExpressionToolOutputParameter"
   documentRoot: true
   doc: |
     Execute an expression as a process step.
@@ -104,6 +133,28 @@ $graph:
       doc: |
         The method to use to merge multiple sources into a single array.
         If not specified, the default method is "merge_nested".
+    - name: type
+      type:
+        - "null"
+        - "#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.
 
 
 - name: Sink
diff --git a/draft-4/conformance_test_draft-4.yaml b/draft-4/conformance_test_draft-4.yaml
@@ -63,6 +63,43 @@
   tool: draft-4/cat3-tool.cwl
   doc: Test command execution in Docker with stdout redirection
 
+- job: draft-4/cat-job.json
+  tool: draft-4/cat3-tool-shortcut.cwl
+  doc: Test command execution in Docker with stdout redirection
+
+- job: draft-4/cat-job.json
+  output:
+    output_file:
+      class: File
+      checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
+      path: cat-out
+      size: 13
+  tool: draft-4/cat3-tool-mediumcut.cwl
+  doc: Test command execution in Docker with stdout redirection
+
+- args: [egrep]
+  stderr: error.txt
+  job:
+  tool: draft-4/egrep-stderr.cwl
+  doc: Test command line with stderr redirection
+
+- args: [egrep]
+  job:
+  tool: draft-4/egrep-stderr-shortcut.cwl
+  doc: Test command line with stderr redirection, brief syntax
+
+- args: [egrep]
+  stderr: std.err
+  output:
+    output_file:
+      class: File
+      size: 84
+      checksum: sha1$cec7b8746a78c42060c96505887449bca0142976
+      path: std.err
+  job:
+  tool: draft-4/egrep-stderr-mediumcut.cwl
+  doc: Test command line with stderr redirection, named brief syntax
+
 - job: draft-4/cat-job.json
   output:
     output_txt:
diff --git a/draft-4/draft-4/cat3-tool-mediumcut.cwl b/draft-4/draft-4/cat3-tool-mediumcut.cwl
@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+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
+    label: Input File
+    description: "The file that will be copied using 'cat'"
+    inputBinding: {position: 1}
+outputs:
+  output_file:
+    type: stdout
+baseCommand: cat
+stdout: cat-out
diff --git a/draft-4/draft-4/cat3-tool-shortcut.cwl b/draft-4/draft-4/cat3-tool-shortcut.cwl
@@ -0,0 +1,17 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+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
+    label: Input File
+    description: "The file that will be copied using 'cat'"
+    inputBinding: {position: 1}
+outputs:
+  output_file:
+    type: stdout
+baseCommand: cat
diff --git a/draft-4/draft-4/egrep-stderr-mediumcut.cwl b/draft-4/draft-4/egrep-stderr-mediumcut.cwl
@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: cwl:draft-4.dev2
+description: "Test of capturing stderr output in a docker container."
+hints:
+  DockerRequirement:
+    dockerPull: debian:wheezy
+
+inputs: []
+
+outputs:
+  output_file:
+    type: stderr
+
+baseCommand: egrep
+successCodes: [2]
+
+stderr: std.err
diff --git a/draft-4/draft-4/egrep-stderr-shortcut.cwl b/draft-4/draft-4/egrep-stderr-shortcut.cwl
@@ -0,0 +1,16 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: cwl:draft-4.dev2
+description: "Test of capturing stderr output in a docker container."
+hints:
+  DockerRequirement:
+    dockerPull: debian:wheezy
+
+inputs: []
+
+outputs:
+  output_file:
+    type: stderr
+
+baseCommand: egrep
+successCodes: [2]
diff --git a/draft-4/draft-4/egrep-stderr.cwl b/draft-4/draft-4/egrep-stderr.cwl
diff --git a/site/draft4-deps.json b/site/draft4-deps.json
