Merge pull request #230 from common-workflow-language/stderr-out-types

Stderr out types

Author: mr-c

draft-4/CommandLineTool.yml

@@ -382,7 +382,86 @@ $graph:
       specializeTo: "#CommandOutputArraySchema"
     - specializeFrom: "#OutputBinding"
       specializeTo: "#CommandOutputBinding"
+  fields:
+    - name: type
+      type:
+        - "null"
+        - "#CWLType"
+        - "#stdout"
+        - "#stderr"
+        - "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: stdout
+  type: enum
+  symbols: [ "cwl:stdout" ]
+  docParent: "#CommandOutputParameter"
+  doc: |
+    Only valid as a `type` for an output.
+
+    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 an output.
+
+    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 +515,7 @@ $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 +528,7 @@ $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.

draft-4/Process.yml

@@ -138,7 +138,6 @@ $graph:
     #   type: ["null", long]
     #   doc: Optional directory size.
 
-
 - name: SchemaBase
   type: record
   abstract: true
@@ -209,29 +208,6 @@ $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"
@@ -402,6 +378,29 @@ $graph:
     - specializeFrom: "sld:ArraySchema"
       specializeTo: "#InputArraySchema"
   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: id
       type: string
       jsonldPredicate: "@id"

draft-4/conformance_test_draft-4.yaml

@@ -57,6 +57,43 @@
   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:

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

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

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

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]

draft-4/draft-4/egrep-stderr.cwl

@@ -0,0 +1,15 @@
+#!/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: File
+    outputBinding: {glob: error.txt}
+baseCommand: egrep
+successCodes: [2]
+stderr: error.txt

site/draft4-deps.json

@@ -11,6 +11,10 @@
             "path": "../draft-4/salad/schema_salad/metaschema/metaschema.yml",
             "class": "File"
         },
+        {
+            "path": "../draft-4/salad/schema_salad/metaschema/metaschema_base.yml",
+            "class": "File"
+        },
         {
             "path": "../draft-4/salad/schema_salad/metaschema/salad.md",
             "class": "File"