ogc-ap-validator

This repository contains files for testing, building and publishing the validation tool for checking OGC compliance of CWL files for application packages.

The tool checks an input CWL against the CWL-related defined in the OGC Best Practice for Earth Observation Application Package

Development and debugging

It is recommended to use Visual Studio Code with the provided devcontainer environment.

Install the package locally with:

python setup.py install

Run streamlit demo:

streamlit run demo/app.py

Container

The Dockerfile targets exposing the Application Package streamlit demo via JupyterHub.

PyPI package

If necessary, change the version in setup.cfg and build the PyPI package with the following command:

python -m build

Upload the package to a PyPI repository (make sure the dist directory contains only files of the latest version). In this example, test.pypi.org is used.

twine upload --verbose -r testpypi dist/*

Install the package on any other machine

Command line tool

After the installation, use the command line tool ap-validator

Usage: ap-validator [OPTIONS] CWL_URL

  Checks whether the given CWL file (URL or local file path) is compliant with
  the OGC application package best practices

Options:
  --entry-point TEXT              Name of entry point (Workflow or
                                  CommandLineTool)
  --detail [none|errors|hints|all]
                                  Output detail (none|errors|hints|all;
                                  default: hints
  --format [text|json]            Output format (text|json; default: text)
  --help                          Show this message and exit.

The validator shows issues and returns an exit code according to the conformance of the CWL file:

• 0 if the CWL file is a valid application package,
• 1 if there are missing elements or other clearly identifyable issues,
• 2 if there is a more fundamental problem with the CWL file.

Using the library

Install the library with pip (from PyPI):

pip install ogc_ap_validator

Write a quick program using the library (make sure you have the test CWL file at the correct location):

from ap_validator.app_package import AppPackage
import json

ap = AppPackage.from_url("tests/data/req_8_no_clt_basecommand.cwl", entry_point="water_bodies")
result = ap.check_all(include=["error", "hint"])

print(f"VALID:   {result['valid']}")
print(f"CONTENT: {json.dumps(result, indent=2)}")

The method AppPackage.check_all() returns a dictionary with three entries:

• valid: a bool telling the overall validation result, i.e. whether the CWL file is compliant with the OGC application package best practices,
• issues: a list of issues (each a dictionary with type, message and req entries). Only issues that match the type in the method's include argument are listed (the types are: error, hint and note). The req value refers to an OGC requirement (if there is no explicit requirement, the value is None), see next point,
• requirements: a dictionary where the values are the specifications of all relevant OGC requirements.

Run the program like this:

python3 quick-test.py

The output will look like this:

VALID:   False
CONTENT: {
  "valid": false,
  "issues": [
    {
      "type": "error",
      "message": "Missing element for CommandLineTool 'crop': baseCommand",
      "req": "req-8"
    },
    {
      "type": "hint",
      "message": "No input of type 'Directory'/'Directory[]' for CommandLineTool 'crop'; make sure inputs referencing GeoJSON features of EO products that need to be staged in are of type 'Directory'",
      "req": "req-12"
    },
    {
      "type": "hint",
      "message": "No input of type 'Directory'/'Directory[]' for CommandLineTool 'norm_diff'; make sure inputs referencing GeoJSON features of EO products that need to be staged in are of type 'Directory'",
      "req": "req-12"
    },
    {
      "type": "hint",
      "message": "No input of type 'Directory'/'Directory[]' for CommandLineTool 'otsu'; make sure inputs referencing GeoJSON features of EO products that need to be staged in are of type 'Directory'",
      "req": "req-12"
    },
    {
      "type": "hint",
      "message": "No input of type 'Directory'/'Directory[]' for CommandLineTool 'stac'; make sure inputs referencing GeoJSON features of EO products that need to be staged in are of type 'Directory'",
      "req": "req-12"
    },
    {
      "type": "hint",
      "message": "No input of type 'Directory'/'Directory[]' for Workflow 'water_bodies'; make sure inputs referencing GeoJSON features of EO products that need to be staged in are of type 'Directory'",
      "req": "req-13"
    },
    {
      "type": "hint",
      "message": "No output of type 'Directory'/'Directory[]' for CommandLineTool 'crop'; make sure CommandLineTool outputs that need to be staged are of type 'Directory'",
      "req": "req-14"
    },
    {
      "type": "hint",
      "message": "No output of type 'Directory'/'Directory[]' for CommandLineTool 'norm_diff'; make sure CommandLineTool outputs that need to be staged are of type 'Directory'",
      "req": "req-14"
    },
    {
      "type": "hint",
      "message": "No output of type 'Directory'/'Directory[]' for CommandLineTool 'otsu'; make sure CommandLineTool outputs that need to be staged are of type 'Directory'",
      "req": "req-14"
    }
  ],
  "requirements": {
    "req-14": "The outputs field of the CommandLineTool that requires the stage-out of EO products SHALL retrieve all the files produced in the working directory.",
    "req-8": "The Application Package CWL CommandLineTool classes SHALL contain the following elements: Identifier ('id'); Command line name ('baseCommand'); Input parameters ('inputs'); Environment requirements ('requirements'); Docker information ('DockerRequirement').",
    "req-12": "All input parameters of the CWL CommandLineTool that require the staging of EO products SHALL be of type 'Directory'.",
    "req-13": "Input parameters of the CWL Workflow that require the staging of EO products SHALL be of type 'Directory'."
  }
}