Get rid of Dirent. Update spec for basename. Add contents field to File spec.

Author: Peter Amstutz

draft-4/CommandLineTool.yml

@@ -630,48 +630,6 @@ $graph:
         IRI such as an [RRID](http://www.identifiers.org/rrid/SCR_001156).
         Example: `http://identifiers.org/rrid/RRID:SCR_001156`
 
-- name: DirentExt
-  type: record
-  doc: |
-    Define a file or subdirectory that must be placed in the designated output
-    directory prior to executing the command line tool.  May be the result of
-    executing an expression, such as building a configuration file from a
-    template.
-  fields:
-    - name: entryname
-      type: [string, Expression]
-      jsonldPredicate:
-        _id: cwl:entryname
-      doc: |
-        The name of the file or subdirectory to create in the output directory.
-    - name: entry
-      type: [string, Expression]
-      jsonldPredicate:
-        _id: cwl:entry
-      doc: |
-        If the value is a string literal or an expression which evaluates to a
-        string, a new file must be created with the string as the file contents.
-
-        If the value is an expression that evaluates to a `File` object, this
-        indicates the referenced file should be added to the designated output
-        directory prior to executing the tool.
-
-        If the value is an expression that evaluates to a `Dirent` object, this
-        indicates that the File or Directory in `entry` should be added to the
-        designated output directory with the name in `entryname`.
-
-        If `writable` is false, the file may be made available using a bind
-        mount or file system link to avoid unnecessary copying of the input
-        file.
-    - name: writable
-      type: boolean?
-      doc: |
-        If true, the file or directory must be writable by the tool.  Changes
-        to the file or directory must be isolated and not visible by any other
-        CommandLineTool process.  This may be implemented by making a copy of
-        the original file or directory.  Default false (files and directories
-        read-only by default).
-
 - name: InitialWorkDirRequirement
   type: record
   extends: ProcessRequirement
@@ -683,7 +641,7 @@ $graph:
     - name: listing
       type:
         - type: array
-          items: [File, DirentExt]
+          items: [File, Directory]
         - string
         - Expression
       jsonldPredicate:
@@ -695,7 +653,7 @@ $graph:
         designated output directory prior to executing the command line tool.
 
         May be an expression.  If so, the expression return value must validate
-        as `{type: array, items: [File, Dirent]}`.
+        as `{type: array, items: [File, Directory]}`.
 
 - name: EnvVarRequirement
   type: record

draft-4/Process.yml

@@ -75,6 +75,10 @@ $graph:
         remote resource (due to unsupported protocol, access denied, or other
         issue) it must signal an error.
 
+        If the `location' field is not provided, the `contents` field must be
+        provided.  The implementation must assign a unique identifier for
+        the `location` field.
+
         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.
@@ -84,24 +88,33 @@ $graph:
     - name: path
       type: string?
       doc: |
-        The local path where the File is made available prior to executing a
-        CommandLineTool.  This must be set by the implementation.  This field
+        The local host path where the File is available when a CommandLineTool is
+        executed.  This field must be set by the implementation.  The final
+        path component must match the value of `basename`.  This field
         must not be used in any other context.  The command line tool being
         executed must be able to to access the file at `path` using the POSIX
         `open(2)` syscall.
+
+        As a special case, if the `path` field is provided but the `location`
+        field is not, an implementation may assign the value of the `path`
+        field to `location`, and remove the `path` field.
       jsonldPredicate:
         "_id": "cwl:path"
         "_type": "@id"
     - name: basename
-      type: string?
+      type: string
       doc: |
-        The base name of the file, that is, the path component following the
-        final slash in the path.
+        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 `/`.
 
-        The implementation must set this field based on the value of `path`
-        prior to evaluating parameter references or expressions in a
-        CommandLineTool document.  This field must not be used in any other
-        context.
+        If not provided, the implementation must set this field based on the
+        `location` field by taking the final path component after parsing
+        `location` as an IRI.  If `basename` is provided, it is not required to
+        match the value from `location`.
+
+        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`.
     - name: dirname
       type: string?
       doc: |
@@ -121,10 +134,8 @@ $graph:
         period.  Leading periods on the basename are ignored; a basename of
         `.cshrc` will have a nameroot of `.cshrc`.
 
-        The implementation must set this field based on the value of `path`
-        prior to evaluating parameter references or expressions in a
-        CommandLineTool document.  This field must not be used in any other
-        context.
+        The implementation must set this field automatically based on the value
+        of `basename` prior to evaluating parameter references or expressions.
     - name: nameext
       type: string?
       doc: |
@@ -133,10 +144,8 @@ $graph:
         period.  Leading periods on the basename are ignored; a basename of
         `.cshrc` will have an empty `nameext`.
 
-        The implementation must set this field based on the value of `path`
-        prior to evaluating parameter references or expressions in a
-        CommandLineTool document.  This field must not be used in any other
-        context.
+        The implementation must set this field automatically based on the value
+        of `basename` prior to evaluating parameter references or expressions.
     - name: checksum
       type: ["null", string]
       doc: |
@@ -149,7 +158,7 @@ $graph:
       type:
         - "null"
         - type: array
-          items: [File, Dirent]
+          items: [File, Directory]
       jsonldPredicate: "cwl:secondaryFiles"
       doc: |
         A list of additional files that are associated with the primary file
@@ -179,26 +188,16 @@ $graph:
         File format ontologies may be provided in the "$schema" metadata at the
         root of the document.  If no ontologies are specified in `$schema`, the
         runtime may perform exact file format matches.
-
-
-- name: Dirent
-  type: record
-  fields:
-    - name: entryname
-      type: string
-      jsonldPredicate:
-        "_id": cwl:entryname
-    - name: entry
-      type: [File, Directory]
-      jsonldPredicate:
-        "_id": cwl:entry
+    - name: contents
+      type: string?
+      doc: |
+        content
 
 - name: Directory
   type: record
   docParent: "#CWLType"
   doc: |
-    Represents a directory to present to a command line tool. This could be a virtual
-    directory, made of files assembled from multiple locations.
+    Represents a directory to present to a command line tool.
   fields:
     - name: class
       type:
@@ -223,7 +222,7 @@ $graph:
         error.
 
         If the `location' field is not provided, the `listing` field must be
-        provided.  The implementation must generate an internal identifier for
+        provided.  The implementation must assign a unique identifier for
         the `location` field.
 
         If the `path` field is provided but the `location` field is not, an
@@ -247,8 +246,15 @@ $graph:
       type:
         - "null"
         - type: array
-          items: [File, Dirent]
-      doc: List of files or subdirectories contained in this directory
+          items: [File, Directory]
+      doc: |
+        List of files or subdirectories contained in this directory.  The name
+        of each file or subdirectory is determined by the `basename` field of
+        each `File` or `Directory` object.  It is an error if a `File` shares a
+        `basename` with any other entry in `listing`.  If two or more
+        `Directory` object share the same `basename`, this must be treated as
+        equivalent to a single subdirectory with the listings recursively
+        merged.
       jsonldPredicate:
         _id: "cwl:listing"
         mapSubject: entryname