Squashed 'cwltool/schemas/' changes from 5239b16..a5976f3

a5976f3 Unify Directory listing, InitialWorkDir and secondaryFiles to accept equivalent type.
eb9449f Adding directory feature tests.
9dfbb8e Update tests to use InitialWorkDirRequirement

git-subtree-dir: cwltool/schemas
git-subtree-split: a5976f3

Author: Peter Amstutz

draft-4/CommandLineTool.yml

@@ -646,7 +646,7 @@ $graph:
     - name: listing
       type:
         - type: array
-          items: DirentExt
+          items: [File, DirentExt]
         - string
         - Expression
       jsonldPredicate:

draft-4/Process.yml

@@ -225,7 +225,10 @@ $graph:
         _id: "cwl:path"
         _type: "@id"
     - name: listing
-      type: Dirent[]?
+      type:
+        - "null"
+        - type: array
+          items: [File, Dirent]
       doc: List of files or subdirectories contained in this directory
       jsonldPredicate:
         _id: "cwl:listing"

draft-4/conformance_test_draft-4.yaml

@@ -735,4 +735,28 @@
         ],
     }
   tool: draft-4/dir3.cwl
-  doc: Test directory input in Docker
+  doc: Test directory input in Docker
+
+- job: draft-4/dir4-job.yml
+  output:
+    "outlist": {
+        "size": 20,
+        "location": "output.txt",
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592",
+        "class": "File"
+    }
+  tool: draft-4/dir4.cwl
+  doc: Test directories in secondaryFiles
+
+- job: draft-4/dir-job.yml
+  output: {
+    "outlist": {
+        "checksum": "sha1$907a866a3e0b7f1fc5a2222531c5fb9063704438",
+        "path": "/home/peter/work/common-workflow-language/draft-4/draft-4/output.txt",
+        "size": 33,
+        "location": "file:///home/peter/work/common-workflow-language/draft-4/draft-4/output.txt",
+        "class": "File"
+    }
+  }
+  tool: draft-4/dir5.cwl
+  doc: Test dynamic initial work dir

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

@@ -0,0 +1,10 @@
+inf:
+  class: File
+  location: hello.tar
+  secondaryFiles:
+    - class: File
+      location: index.py
+    - entryname: testdir
+      entry:
+        class: Directory
+        location: testdir

draft-4/draft-4/dir4.cwl

@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: draft-4.dev3
+requirements:
+  - class: ShellCommandRequirement
+inputs:
+  inf: File
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+baseCommand: []
+arguments: ["cd", "$(inputs.inf.dirname)",
+  {shellQuote: false, valueFrom: "&&"},
+  "find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt

draft-4/draft-4/dir5.cwl

@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: draft-4.dev3
+requirements:
+  - class: ShellCommandRequirement
+  - class: InitialWorkDirRequirement
+    listing: $(inputs.indir.listing)
+inputs:
+  indir: Directory
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+baseCommand: []
+arguments: ["find", ".",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt

draft-4/draft-4/rename.cwl

@@ -2,7 +2,7 @@ class: CommandLineTool
 cwlVersion: cwl:draft-4.dev3
 baseCommand: "true"
 requirements:
-  CreateFileRequirement:
+  InitialWorkDirRequirement:
     listing:
       - entryname: $(inputs.newname)
         entry: $(inputs.srcfile)

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

@@ -8,7 +8,7 @@ requirements:
     expressionLib:
       - { $include: underscore.js }
       - "var t = function(s) { return _.template(s)({'inputs': inputs}); };"
-  - class: CreateFileRequirement
+  - class: InitialWorkDirRequirement
     listing:
       foo.txt: >
           $(t("The file is <%= inputs.file1.path.split('/').slice(-1)[0] %>\n"))