Merge branch 'master' into map_syntax

Author: mr-c

CommandLineTool-standalone.yml

@@ -1,2 +1,3 @@
+saladVersion: v1.1
 - $import: Process.yml
-- $import: CommandLineTool.yml
+- $import: CommandLineTool.yml

CommandLineTool.yml

@@ -1,3 +1,4 @@
+saladVersion: v1.1
 $base: "https://w3id.org/cwl/cwl#"
 
 $namespaces:
@@ -56,8 +57,8 @@ $graph:
         * When defining record types with `CommandInputRecordSchema`, fields of
           type `File` may now include `format`, `loadContents`,
           `secondaryFiles` and `streamable`.
-        * `CommandInputRecordSchema`, `CommandOutputRecordSchema`, 
-          `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional 
+        * `CommandInputRecordSchema`, `CommandOutputRecordSchema`,
+          `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional
           `doc` field.
         * `inputBinding` has been added as an optional field for
           `CommandInputRecordSchema` (was previously in CWL `draft-3` but
@@ -100,6 +101,10 @@ $graph:
         * [Added](#LoadListingRequirement) `LoadListingRequirement`
           and [loadListing](#LoadContents) to control whether and how
           `Directory` listings should be loaded for use in expressions.
+        * The position field of the [CommandLineBinding](#CommandLineBinding) can
+          now be calculated from a CWL Expression.
+        * The exit code of a CommandLineTool invocation is now
+          available to expressions in `outputEval` as `runtime.exitCode`
         * [Better explain](#map) the `map<…>` notation that has existed since v1.0.
         * Fixed schema error where the `type` field inside the `inputs` and
           `outputs` field was incorrectly listed as optional.
@@ -200,8 +205,14 @@ $graph:
 
   fields:
     - name: position
-      type: int?
-      doc: "The sorting key.  Default position is 0."
+      type: [ int, Expression, string, "null" ]
+      doc: |
+        The sorting key.  Default position is 0. If the inputBinding is
+        associated with an input parameter, then the value of `self` in the
+        expression will be the value of the input parameter.  Input parameter
+        defaults (as specified by the `InputParameter.default` field) must be
+        applied before evaluating the expression. Expressions must return a
+        single value of type int or a null.
     - name: prefix
       type: string?
       doc: "Command line prefix to add before the value."
@@ -319,13 +330,15 @@ $graph:
         - string
         - Expression
       doc: |
-        Evaluate an expression to generate the output value.  If `glob` was
-        specified, the value of `self` must be an array containing file objects
-        that were matched.  If no files were matched, `self` must be a zero
-        length array; if a single file was matched, the value of `self` is an
-        array of a single element.  Additionally, if `loadContents` is `true`,
-        the File objects must include up to the first 64 KiB of file contents
-        in the `contents` field.
+        Evaluate an expression to generate the output value.  If
+        `glob` was specified, the value of `self` must be an array
+        containing file objects that were matched.  If no files were
+        matched, `self` must be a zero length array; if a single file
+        was matched, the value of `self` is an array of a single
+        element.  Additionally, if `loadContents` is `true`, the File
+        objects must include up to the first 64 KiB of file contents
+        in the `contents` field.  The exit code of the process is
+        available in the expression as `runtime.exitCode`.
 
 - name: CommandLineBindable
   type: record

CommonWorkflowLanguage.yml

@@ -1,3 +1,4 @@
+saladVersion: v1.1
 $base: "https://w3id.org/cwl/cwl#"
 
 $namespaces:

Process.yml

@@ -1,3 +1,4 @@
+saladVersion: v1.1
 $base: "https://w3id.org/cwl/cwl#"
 
 $namespaces:

Workflow.yml

@@ -1,3 +1,4 @@
+saladVersion: v1.1
 $base: "https://w3id.org/cwl/cwl#"
 
 $namespaces:

conformance_tests.yaml

@@ -3184,3 +3184,19 @@
     subdirectory objects when input parameter loadListing is
     'deep_listing'
   tags: [ command_line_tool ]
+
+- job: tests/echo-position-expr-job.yml
+  tool: tests/echo-position-expr.cwl
+  label: inputBinding_position_expr
+  output:
+    out: "🕺 1 singular sensation!\n"
+  doc: TBD
+  tags: [ command_line_tool, required ]
+
+- job: tests/empty.json
+  tool: tests/exitcode.cwl
+  label: outputEval_exitCode
+  output:
+    code: 7
+  doc: Can access exit code in outputEval
+  tags: [ command_line_tool, required ]

invocation.md

@@ -146,6 +146,9 @@ providing the fields `successCodes`, `temporaryFailCodes`, and
 `permanentFailCodes`.  An implementation may choose to default unspecified
 non-zero exit codes to either `temporaryFailure` or `permanentFailure`.
 
+The exit code of the process is available to expressions in
+`outputEval` as `runtime.exitCode`.
+
 ## Output binding
 
 If the output directory contains a file named "cwl.output.json", that file

tests/echo-position-expr-job.yml

@@ -0,0 +1,2 @@
+one: 1
+two: 2

tests/echo-position-expr.cwl

@@ -0,0 +1,30 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.1.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+  one:
+    type: int
+    inputBinding:
+      position: $(self)
+  two:
+    type: int
+    inputBinding:
+      valueFrom: sensation!
+      position: ${return self+1;}
+arguments:
+  - position: ${return 2;}
+    valueFrom: singular
+  - position: ${return null;}
+    valueFrom: 🕺
+outputs:
+  out:
+    type: string
+    outputBinding:
+      glob: out.txt
+      loadContents: true
+      outputEval: $(self[0].contents)
+baseCommand: echo
+stdout: out.txt

tests/exitcode.cwl

@@ -0,0 +1,12 @@
+cwlVersion: v1.1.0-dev1
+class: CommandLineTool
+requirements:
+  ShellCommandRequirement: {}
+inputs: []
+outputs:
+  code:
+    type: int
+    outputBinding:
+      outputEval: $(runtime.exitCode)
+successCodes: [7]
+arguments: ["exit", "7"]