Input json does not support symlink file while input_parameters works fine with it

[yuankunzhu]

Recently noticed this. Only tested on v1.0.2 as I have the same issue in #380 with v1.0.3.

Basically before running rabix, I have

ln -s /path/to/file.txt data/

and got input_1.json as

{ "input_file": {"class": "File", "path":"data/file.txt"} }

input_2.json

{ "input_file": {"class": "File", "path":"/path/to/file.txt"} }

Then, when execute rabix, I will get

• [ERROR] Job failed with exit code 1. if I do rabix tool.cwl input_1.json
• [INFO] Job root has completed if I do rabix tool.cwl input_2.json
• [INFO] Job root has completed if I do rabix tool.cwl -- --input_file data/file.txt

[milos-ljubinkovic]

Yes it seems that we have 2 different methods for path resolution, one that follows links used in resolving "--file" syntax and one that doesn't which is used everywhere else.

Not really sure that this should be changed so that every method follows links as there might be some complications with staging input files that uses links (this system should be changed soon as well).