Use file content literals for InitialWorkDir.

Author: Peter Amstutz

draft-4/CommandLineTool.yml

@@ -630,6 +630,23 @@ $graph:
         IRI such as an [RRID](http://www.identifiers.org/rrid/SCR_001156).
         Example: `http://identifiers.org/rrid/RRID:SCR_001156`
 
+- name: FileExt
+  type: record
+  extends: File
+  fields:
+    writable:
+      type: boolean?
+      doc: If true, the File must be writable.
+
+- name: DirectoryExt
+  type: record
+  extends: Directory
+  fields:
+    writable:
+      type: boolean?
+      doc: If true, the Directory must be writable.
+
+
 - name: InitialWorkDirRequirement
   type: record
   extends: ProcessRequirement
@@ -641,13 +658,11 @@ $graph:
     - name: listing
       type:
         - type: array
-          items: [File, Directory]
+          items: [FileExt, DirectoryExt, string, Expression]
         - string
         - Expression
       jsonldPredicate:
         _id: "cwl:listing"
-        mapSubject: entryname
-        mapPredicate: entry
       doc: |
         The list of files or subdirectories that must be placed in the
         designated output directory prior to executing the command line tool.

draft-4/Process.yml

@@ -65,7 +65,7 @@ $graph:
         _type: "@vocab"
       doc: Must be `File` to indicate this object describes a file.
     - name: location
-      type: string
+      type: [string, Expression]
       doc: |
         A URI that identifies the file resource.  This may be a relative
         reference, in which case it must be resolved using the base URI of the
@@ -82,6 +82,8 @@ $graph:
         If the `path` field is provided but the `location` field is not, an
         implementation may assign the value of the `path` field to `location`,
         then follow the rules above.
+
+        Must be evaluated as an expression only when appearing in InitialWorkDirRequirement.
       jsonldPredicate:
         _id: "@id"
         _type: "@id"
@@ -102,7 +104,7 @@ $graph:
         "_id": "cwl:path"
         "_type": "@id"
     - name: basename
-      type: string
+      type: [string, Expression]
       doc: |
         The base name of the file, that is, the name of the file without any
         leading directory path.  The base name must not contain a slash `/`.
@@ -115,6 +117,8 @@ $graph:
         When this file is made available to a CommandLineTool, it must be named
         with `basename`, i.e. the final component of the `path` field must match
         `basename`.
+
+        Must be evaluated as an expression only when appearing in InitialWorkDirRequirement.
     - name: dirname
       type: string?
       doc: |
@@ -189,9 +193,19 @@ $graph:
         root of the document.  If no ontologies are specified in `$schema`, the
         runtime may perform exact file format matches.
     - name: contents
-      type: string?
+      type: ["null", string, Expression]
       doc: |
-        content
+        File contents literal.  Maximum of 64 KiB.
+
+        If neither `location` nor `path` is provided, `contents` must be
+        non-null.  The implementation must assign a unique identifier for the
+        `location` field.  When the file is staged as input to CommandLineTool,
+        the value of `contents` must be written to a file.
+
+        If `loadContents` of `Binding` is true and `location` is valid, the
+        implementation must read up to the first 64 KiB of text from the file
+        and place it in the "contents" field.
+
 
 - name: Directory
   type: record
@@ -247,6 +261,8 @@ $graph:
         - "null"
         - type: array
           items: [File, Directory]
+        - string
+        - Expression
       doc: |
         List of files or subdirectories contained in this directory.  The name
         of each file or subdirectory is determined by the `basename` field of
@@ -255,6 +271,8 @@ $graph:
         `Directory` object share the same `basename`, this must be treated as
         equivalent to a single subdirectory with the listings recursively
         merged.
+
+        Must be evaluated as an expression only when appearing in InitialWorkDirRequirement.
       jsonldPredicate:
         _id: "cwl:listing"
         mapSubject: entryname

draft-4/draft-4/dir4-job.yml

@@ -4,7 +4,6 @@ inf:
   secondaryFiles:
     - class: File
       location: index.py
-    - entryname: xtestdir
-      entry:
-        class: Directory
-        location: testdir
+    - class: Directory
+      basename: xtestdir
+      location: testdir

draft-4/draft-4/rename.cwl

@@ -4,8 +4,9 @@ baseCommand: "true"
 requirements:
   InitialWorkDirRequirement:
     listing:
-      - entryname: $(inputs.newname)
-        entry: $(inputs.srcfile)
+      - class: File
+        basename: $(inputs.newname)
+        location: $(inputs.srcfile.location)
 inputs:
   srcfile: File
   newname: string

draft-4/draft-4/search.cwl

@@ -9,7 +9,7 @@ $graph:
   requirements:
     - class: InitialWorkDirRequirement
       listing:
-        input.txt: $(inputs.file)
+        - $(inputs.file)
     - class: InlineJavascriptRequirement
 
   inputs:

draft-4/draft-4/stagefile.cwl

@@ -3,8 +3,8 @@ cwlVersion: draft-4.dev3
 requirements:
   InitialWorkDirRequirement:
     listing:
-      - entryname: $(inputs.infile.basename)
-        entry: $(inputs.infile)
+      - class: File
+        location: $(inputs.infile.location)
         writable: true
 inputs:
   infile: File

draft-4/draft-4/template-tool.cwl

@@ -10,8 +10,9 @@ requirements:
       - "var t = function(s) { return _.template(s)({'inputs': inputs}); };"
   - class: InitialWorkDirRequirement
     listing:
-      foo.txt: >
-          $(t("The file is <%= inputs.file1.path.split('/').slice(-1)[0] %>\n"))
+      - class: File
+        basename: foo.txt
+        contents: $(t("The file is <%= inputs.file1.path.split('/').slice(-1)[0] %>\n"))
 inputs:
   - id: file1
     type: File