Testing run

How to perform this step?

Specifying the inputs in a yaml file.

The inputs of a model component is a list of input parameters/files that control its execution. Each input has an id for the name, and type describing what types of values are valid for that input.

Available primitive types are string, int, and null; complex types are array and; in addition there are special type File.

To direct its execution, the inputs must be specified in a .yml file.

Using our simple line fitting model, we create a file called simpleModelAnnotatedValues.yml, containing the following text, representative of the input file, parameters, and output files in our Notebook:

a: 1
b: 20
c: 30
input_file:
  class: File
  path: https://raw.githubusercontent.com/mosoriob/simpleModel-1/master/x.csv

Notice that input_file, as a File type, must be provided as an object with the fields class: File and path.

Info

If the input file is hosted on GitHub, remember to copy the sharable download URL. GitHub: how to find the sharable download URL for files on GitHub

Run and test your component

Warning

Make sure that cwltool is installed on your system before proceeding.

The command line execution looks something like:

$ cwltool simpleModelAnnotated.cwl simpleModelAnnotatedValues.yml

where simplemodelAnnotated.cwl was automatically created in the previous step and simpleModelAnnotatedValues.yml is the file generated above.

Expected results

$ cwltool simpleModelAnnotated.cwl simpleModelAnnotatedValues.yml
INFO [job simpleModelAnnotated.cwl] completed success
{
    "output_file": {
        "location": "file:///home/mosorio/tmp/demo/y.csv",
        "basename": "y.csv",
        "class": "File",
        "checksum": "sha1$b70550bfaf3178152371dada56c7aaa826c85127",
        "size": 24950,
        "path": "/home/mosorio/tmp/demo/y.csv"
    }
}
INFO Final process status is success

The output file y.csv is generated in this step.