(CWL 1.x) WIP Feature/add metadata

CommandLineTool.yml

@@ -223,6 +223,7 @@ $graph:
       - loadContents
       - outputEval
       - secondaryFiles
+      - addMetadata
   fields:
     - name: glob
       type:
@@ -251,6 +252,23 @@ $graph:
         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.
+    - name: addMetadata
+      type:
+        - "null"
+        - string
+        - Expression
+        - string[]
+      doc: |
+        If the value is an expression, expression should return a key-value map. 
+        Returned map should be set as the `metadata` property of the output file 
+        or files. The same map should be set as the `metadata` property of all 
+        secondary files. 
+
+        If the value is a string or an array of strings, these must be input 
+        parameter references. The `metadata` fields for the referenced inputs are
+        intersected and the resulting key-value map is set as the `metadata` 
+        property of the output file or files. The same map should be set as the 
+        `metadata` property of all secondary files. 
 
 - name: CommandLineBindable
   type: record

Process.yml

@@ -279,6 +279,14 @@ $graph:
         If `loadContents` of `inputBinding` or `outputBinding` 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: metadata
+      type: Any?
+      doc: |
+       Metadata should be a key-value map further describing a `File`.
+       Metadata can be propagated from inputs to outputs of a tool using
+       `addMetadata` option in the `CommandOutputBinding`. It is up to the
+       implementation to make use of the `metadata` property of final outputs
+       of the execution.
 
 
 - name: Directory

conformance_tests.yaml

@@ -1768,3 +1768,61 @@
   tool: tests/networkaccess2.cwl
   doc: Test networkaccess is disabled by default
   tags: [ networkaccess ]
+
+
+
+- job: tests/inherit-metadata-job.yml
+  output: {
+      "out": {
+          "basename": "out",
+          "checksum": "sha1$4a7edca069beb3fbdcc3ce9d8626025d262c046a",
+          "class": "File",
+          "location": "out",
+          "metadata": {
+              "foo": 1,
+              "hello": "world"
+          },
+          "secondaryFiles": [
+              {
+                  "basename": "out",
+                  "checksum": "sha1$4a7edca069beb3fbdcc3ce9d8626025d262c046a",
+                  "class": "File",
+                  "location": "out",
+                  "metadata": {
+                      "foo": 1,
+                      "hello": "world"
+                  },
+                  "size": 23
+              }
+          ],
+          "size": 23
+      },
+      "out_intersected": [
+          {
+              "basename": "out",
+              "checksum": "sha1$4a7edca069beb3fbdcc3ce9d8626025d262c046a",
+              "class": "File",
+              "location": "out",
+              "metadata": {
+                  "hello": "world"
+              },
+              "secondaryFiles": [
+                  {
+                      "basename": "out",
+                      "checksum": "sha1$4a7edca069beb3fbdcc3ce9d8626025d262c046a",
+                      "class": "File",
+                      "location": "out",
+                      "metadata": {
+                          "hello": "world"
+                      },
+                      "size": 23
+                  }
+              ],
+              "size": 23
+          }
+      ]
+  }
+  tool: tests/inherit-metadata.cwl
+  doc: Test addmetadata via expression or input id
+  tags: [ addmetadata ]
+

tests/inherit-metadata-job.yml

@@ -0,0 +1,12 @@
+input_file:
+  class: File
+  path: hello.txt
+  metadata:
+    hello: world
+    foo: 1
+input_list:
+  - class: File
+    path: whale.txt
+    metadata:
+      hello: world
+      foo: 2

tests/inherit-metadata.cwl

@@ -0,0 +1,37 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.1.0-dev1
+baseCommand:
+  - echo
+  - this
+  - file
+  - has
+  - metadata
+inputs:
+  - id: input_file
+    type: File
+  - id: input_list
+    type: File[]
+outputs:
+  - id: out
+    type: File
+    secondaryFiles:
+      - $(self.basename)
+    outputBinding:
+      glob: out
+      addMetadata: $(inputs.input_file.metadata)
+  - id: out_intersected
+    type: File[]
+    secondaryFiles:
+      - $(self.basename)
+    outputBinding:
+      glob: out
+      addMetadata: 
+      - input_file
+      - input_list
+requirements:
+  - class: DockerRequirement
+    dockerPull: 'debian:stretch-slim'
+  - class: InlineJavascriptRequirement
+stdout: out