loadContents does not load contents for an array of files

[Zymergen-phaverty]

Expected Behavior

loadContents for type: File[] should load the contents into the file object.

Actual Behavior

Loading only happens for type: File. For File[] the contents field is empty

Workflow Code

Broken case, input yaml:
my_json:

• {class: File, location: /Users/phaverty/my_json.json}
  Broken case, cwl:
  #!/usr/bin/env cwl-runner
  cwlVersion: v1.0
  class: ExpressionTool
  expression: |-
  ${
  return JSON.parse(inputs.my_json.contents);
  }
  inputs:
  • id: my_json
    type: File[]
    inputBinding:
    loadContents: true
    outputs:
  • id: out
    type: string
    outputBinding:
    glob: out.txt
    requirements:
  • class: InlineJavascriptRequirement

Working case, input yaml:
my_json: {class: File, location: /Users/phaverty/my_json.json}

Working case, input cwl:
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: ExpressionTool
expression: |-
${
return JSON.parse(inputs.my_json.contents);
}
inputs:

• id: my_json
  type: File
  inputBinding:
  loadContents: true
  outputs:
• id: out
  type: string
  outputBinding:
  glob: out.txt
  requirements:
• class: InlineJavascriptRequirement

Full Traceback

INFO /Users/phaverty/miniconda3/bin/cwltool 2.0.20200122124526
INFO Resolved '/Users/phaverty/echo.cwl' to 'file:///Users/phaverty/echo.cwl'
WARNING Failed to evaluate expression:
Expression evaluation error:
Expecting value: line 1 column 1 (char 0)
script was:
01 "use strict";
02 var inputs = {
03     "my_json": [
04         {
05             "class": "File",
06             "location": "file:///Users/phaverty/my_json.json",
07             "size": 777,
08             "basename": "my_json.json",
09             "nameroot": "my_json",
10             "nameext": ".json"
11         }
12     ]
13 };
14 var self = null;
15 var runtime = {
16     "cores": 1,
17     "ram": 1024,
18     "tmpdirSize": 1024,
19     "outdirSize": 1024,
20     "tmpdir": "/private/var/folders/9y/tk505d9x5g39g72jjxts0d4c0000gn/T/tmpgwy4d1zt",
21     "outdir": "/private/tmp/docker_tmpyk5cb1yn"
22 };
23 (function(){
24   return JSON.parse(inputs.my_json.contents);
25  })()
stdout was: ''
stderr was: 'undefined:1
undefined
^

SyntaxError: Unexpected token u in JSON at position 0
    at JSON.parse (<anonymous>)
    at evalmachine.<anonymous>:24:15
    at evalmachine.<anonymous>:25:4
    at Script.runInContext (vm.js:107:20)
    at Script.runInNewContext (vm.js:113:17)
    at Object.runInNewContext (vm.js:296:38)
    at Socket.<anonymous> ([eval]:11:57)
    at Socket.emit (events.js:182:13)
    at addChunk (_stream_readable.js:283:12)
    at readableAddChunk (_stream_readable.js:260:13)'

{}
WARNING Final process status is permanentFail

Note how the my_json object does not have a contents field. Using the single file case and using a javascript syntax error to generate error output, one can see that the contents field contains the JSON from the JSON file.

Your Environment

• cwltool version:
  Check using cwltool --version
  2.0.20200122124526