Wrong input when using directory type in tests

[lvarin]

This is similar than issue #26, but I am openong a new issue in case.

We are running some tests on TESK (https://github.com/EMBL-EBI-TSI/TESK), this one fails:

/usr/local/bin/cwl-tes --tes $TESKURL --remote-storage-url $FTPURL --outdir=/tmp/tmpjx8uh9wv --quiet v1.0/cat-from-dir.cwl v1.0/cat-from-dir-job.yaml

The test fails because the input is:

  "inputs": [
    {
      "name": "dir1",
      "description": "cwl_input:dir1",
      "url": "_:5cb672c1-2c9b-4659-a5eb-24289b3a83ad",
      "path": "/tmp/tmpkwk6af3w/stg1a4045b0-0eaa-4c90-b584-2443d8984ee7/cwl",
      "type": "DIRECTORY"
    }
  ],

As you can see the directory was not uploaded and translated to a FTP URL, as I think in #26 was suggested it will happen.

Regards

[aniewielska]

The problem is likely not (only) FTP related, as it behaves exactly the same way for shared filesystem and produces inputs like this in a TES request with an invalid URL.

"inputs": [{"name": "dir1", "description": "cwl_input:dir1", "url": "_:bab083c3-4c54-4dcc-95bb-1532f0e89d3c",
        "path": "/tmp/tmp_2rxk35r/stge3538b61-6f3c-4c48-ac09-565e95ca81da/cwl", "type":
        "DIRECTORY"}]