Arvados CWL Tester

Framework for testing Common Workflow Language on Arvados

Arvados CWL Tester is an open-source testing framework that allows you to write and manage reproducible e2e CWL tests and execute them on Arvados (more information about Arvados can be find here). It supports parallel execution of multiple tests.

Introduction

Arvados CWL Tester API allows you to write tests in Python and organize them in Python scripts. It uses pytest library for tests execution.

Additionally Arvados CWL Tester allows to keep testing space well organized. Execution of the test creates separate Project on Arvados per day and per Arvados user. All tests executed in the same day and by the same user starts a process inside this Project. Projects are then automatically removed after one week which helps to keep your testing space clean and tidy.

Installation

git clone [email protected]:arvados/arvados_cwl_tester.git
cd arvados_cwl_tester
pip install .

Write your first test

You can define all your tests in single test_<your_name>.py file. Here you can see an example of how this file can look like:

from arvados_cwl_tester import *

# Set global variable with project uuid where all your tests will be executed:
arvados_project_uuid("pirca-*******************82")

# Define your first test for a single CWL step (CommanLineTool)
def test_single_step():
    result = arvados_run(
        "./components/single_step/single_step.cwl",
        {
            "name": "example"
        },
    )
    assert "example.txt" in result.files
    assert result.files["example.txt"]["size"] == 0
    assert result.command == ["touch", "example.txt"]

Execute the test

Run following command in Command Line:

$ pytest -k single_step

Run multiple tests in parallel - it will execute your tests as separated processes on Arvados:

$ pytest --workers 10 --tests-per-worker auto

CWL inputs imported as variables

There is an optional feature implemented in this framework that helps to organize definitions of CWL inputs, defining them in single place. You can create ./test/variables.json file which will be used by arvados_cwl_tester to create global variables with matching names. You are free to name and organize your variables in any way you like. It solves problem with repetition of names if you have more testing scripts in your repository and all of them use some common variables. Content of variables.json can be imported as dictionary named 'VARIABLES' and uppercase names of main keys. For example you can store project uuids, files, and directories handles, as so:

{
  "pirca": "pirca-*******************82",
  "dirs": {
    "fastq_collection": {
      "type": "Directory",
      "path": "keep:********************************6185"
    }
  },
  "reference_genome": {
    "class": "File",
    "path": "keep:********************************6184/Homo_sapiens_assembly38.fasta",
    "secondaryFiles": [
      {
        "class": "File",
        "path": "keep:********************************6183/Homo_sapiens_assembly38.fasta.fai"
      }
    ]
    }
}

Then you can access them in following way:

from arvados_cwl_tester import *

arvados_project_uuid(VARIABLES["akau"])

# using "VARIABLES" that is a dictionary
def test_single_step_variables():
    out = arvados_run(
      "./my_cwl.cwl",
      {
          "fastq_collection": VARIABLES["dirs"]["fastq_collection"],
          "reference_genome": VARIABLES["reference_genome"],
      }
    )

# or uppercase key names from VARIABLES like:
def test_single_step_key_names():
    out = arvados_run(
      "./my_cwl.cwl",
      {
          "fastq_collection": DIRS["fastq_collection"],
          "reference_genome": REFERENCE_GENOME,
          "gene_panel": GENE_PANEL
      }
    )

Playground - try it for yourself

Arvados CWL Tester Playground is a sample project to help you learn how to use Arvados CWL Tester. You can use this project as a starting point to create your own tests for your own CWL Workflows.

Contributing

We welcome contributions to the Arvados CWL Tester project! If you find any issues or have suggestions for improvements please create a new issue or pull request.

To activate development environment run following command in Command Line:

$ bash setup.sh
$ source venv/bin/activate

Authors

Monika Krzyzanowska @monigenomi e-mail: [email protected]

Joana Butkiewicz @joanna-butkiewicz

Licensing

This project is licensed under Apache 2.0