Add test cases for CLI. (broadinstitute#101)

* Add test cases for CLI.

* Update setup.py file.

* Try a different approach.

* I'm going nuts ... Github Actions does not care scm_version

Author: rexwangcc

cromwell_tools/__init__.py

@@ -10,7 +10,7 @@
     __version__ = get_distribution(__name__).version
 except DistributionNotFound:
     # package is not installed
-    pass
+    __version__ = "Unknown Ver."
 
 # By using the below import statement when you call import cromwell_tools you get:
 # cromwell_tools.api.status

cromwell_tools/cli.py

@@ -3,7 +3,7 @@
 from cromwell_tools.cromwell_api import CromwellAPI
 from cromwell_tools.cromwell_auth import CromwellAuth
 from cromwell_tools.diag import task_runtime
-from cromwell_tools import __version__
+from cromwell_tools import __version__ as cromwell_tools_version
 import sys
 
 
@@ -24,7 +24,10 @@ def parser(arguments=None):
 
     # Check the installed version of Cromwell-tools
     main_parser.add_argument(
-        '-V', '--version', action='version', version=f'%(prog)s {__version__}'
+        '-V',
+        '--version',
+        action='version',
+        version=f'%(prog)s {cromwell_tools_version}',
     )
 
     subparsers = main_parser.add_subparsers(help='sub-command help', dest='command')

cromwell_tools/tests/test_cli.py

@@ -0,0 +1,225 @@
+import pytest
+from cromwell_tools.cli import parser as cli_parser
+import tempfile
+import os
+import six
+import json
+from cromwell_tools.cromwell_auth import CromwellAuth
+
+
+six.add_move(six.MovedModule('mock', 'mock', 'unittest.mock'))
+from six.moves import mock  # noqa
+
+
+@pytest.fixture(scope="module")
+def username_password_auth():
+    return [
+        "--username",
+        "fake-user",
+        "--password",
+        "fake-pwd",
+        "--url",
+        "https://fake-cromwell",
+    ]
+
+
+@pytest.fixture(scope="module")
+def no_auth():
+    return ["--url", "https://fake-cromwell"]
+
+
+@pytest.fixture(scope="module")
+def service_account_auth():
+    temp_dir = tempfile.mkdtemp()
+    service_account_key = os.path.join(temp_dir, 'fake_key.json')
+    fake_svc_info = {"token_uri": "foo", "client_email": "bar", "private_key": "baz"}
+    with open(service_account_key, 'w') as f:
+        json.dump(fake_svc_info, f)
+    return [
+        "--service-account-key",
+        service_account_key,
+        "--url",
+        "https://fake-cromwell",
+    ]
+
+
+@pytest.fixture(scope="module")
+def secret_file_auth():
+    temp_dir = tempfile.mkdtemp()
+    secrets_file = os.path.join(temp_dir, 'fake_secrets.json')
+    auth_params = {
+        "url": "https://fake-cromwell",
+        "username": "fake-user",
+        "password": "fake-pwd",
+    }
+    with open(secrets_file, 'w') as f:
+        json.dump(auth_params, f)
+    return ["--secrets-file", secrets_file]
+
+
+def test_cli_print_version_info():
+    """Make sure the CLI prints version info properly"""
+    user_inputs = ["-V"]
+    with pytest.raises(SystemExit) as pytest_wrapped_exit:
+        cli_parser(user_inputs)
+    assert pytest_wrapped_exit.type == SystemExit
+    assert pytest_wrapped_exit.value.code == 0
+
+
+def test_cli_command_raise_value_error_when_no_creds_provided():
+    """Make sure the CLI raise exception about the auth when no creds provided."""
+    user_inputs = ["submit", "--wdl-file", "fake.wdl", "--inputs-files", "fake.json"]
+    with pytest.raises(ValueError):
+        command, args = cli_parser(user_inputs)
+
+
+def test_cli_command_works_with_username_password_auth(username_password_auth):
+    """Use the submit command as an example to prove CLI works with u/p auth."""
+    user_inputs = [
+        "submit",
+        "--wdl-file",
+        "fake.wdl",
+        "--inputs-files",
+        "fake.json",
+    ] + username_password_auth
+    command, args = cli_parser(user_inputs)
+
+
+def test_cli_command_works_with_no_auth(no_auth):
+    """Use the submit command as an example to prove CLI works with u/p auth."""
+    user_inputs = [
+        "submit",
+        "--wdl-file",
+        "fake.wdl",
+        "--inputs-files",
+        "fake.json",
+    ] + no_auth
+    command, args = cli_parser(user_inputs)
+
+
+@mock.patch('cromwell_tools.cromwell_auth.CromwellAuth.from_service_account_key_file')
+def test_cli_command_works_with_service_account_auth(mock_header, service_account_auth):
+    """Use the submit command as an example to prove CLI works with u/p auth."""
+    expected_auth = CromwellAuth(
+        url="https://fake-cromwell",
+        header={"Authorization": "bearer fake_token"},
+        auth=None,
+    )
+    mock_header.return_value = expected_auth
+    user_inputs = [
+        "submit",
+        "--wdl-file",
+        "fake.wdl",
+        "--inputs-files",
+        "fake.json",
+    ] + service_account_auth
+    command, args = cli_parser(user_inputs)
+
+
+def test_cli_command_works_with_secrets_file_auth(secret_file_auth):
+    """Use the submit command as an example to prove CLI works with u/p auth."""
+    user_inputs = [
+        "submit",
+        "--wdl-file",
+        "fake.wdl",
+        "--inputs-files",
+        "fake.json",
+    ] + secret_file_auth
+    command, args = cli_parser(user_inputs)
+
+
+def test_cli_submit_command(no_auth):
+    """Test the submit command (with no-auth for simplicity)."""
+    user_inputs = [
+        "submit",
+        "--wdl-file",
+        "fake.wdl",
+        "--inputs-files",
+        "fake.json",
+    ] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "submit"
+    assert args['wdl_file'] == "fake.wdl"
+    assert "fake.json" in args['inputs_files']
+
+
+def test_cli_wait_command(no_auth):
+    """Test the wait command (with no-auth for simplicity)."""
+    user_inputs = [
+        "wait",
+        "--poll-interval-seconds",
+        "10",
+        "00000000-0000-0000-0000-000000000000",
+        "00000000-0000-0000-0000-000000000000",
+    ] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "wait"
+    assert "00000000-0000-0000-0000-000000000000" in args["workflow_ids"]
+
+
+def test_cli_status_command(no_auth):
+    """Test the status command (with no-auth for simplicity)."""
+    user_inputs = ["status", "--uuid", "00000000-0000-0000-0000-000000000000"] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "status"
+    assert args["uuid"] == "00000000-0000-0000-0000-000000000000"
+
+
+def test_cli_abort_command(no_auth):
+    """Test the abort command (with no-auth for simplicity)."""
+    user_inputs = ["abort", "--uuid", "00000000-0000-0000-0000-000000000000"] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "abort"
+    assert args["uuid"] == "00000000-0000-0000-0000-000000000000"
+
+
+def test_cli_release_hold_command(no_auth):
+    """Test the release hold command (with no-auth for simplicity)."""
+    user_inputs = [
+        "release_hold",
+        "--uuid",
+        "00000000-0000-0000-0000-000000000000",
+    ] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "release_hold"
+    assert args["uuid"] == "00000000-0000-0000-0000-000000000000"
+
+
+def test_cli_metadata_command(no_auth):
+    """Test the metadata command (with no-auth for simplicity)."""
+    user_inputs = [
+        "metadata",
+        "--uuid",
+        "00000000-0000-0000-0000-000000000000",
+        "--includeKey",
+        "jobId",
+    ] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "metadata"
+    assert args["uuid"] == "00000000-0000-0000-0000-000000000000"
+    assert "jobId" in args["includeKey"]
+
+
+def test_cli_query_command(no_auth):
+    """Test the query command (with no-auth for simplicity)."""
+    # Not Implemented yet
+    assert True
+
+
+def test_cli_health_command(no_auth):
+    """Test the health command (with no-auth for simplicity)."""
+    user_inputs = ["health"] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "health"
+
+
+def test_cli_task_runtime_command(no_auth):
+    """Test the task_runtime command (with no-auth for simplicity)."""
+    user_inputs = [
+        "task_runtime",
+        "--uuid",
+        "00000000-0000-0000-0000-000000000000",
+    ] + no_auth
+    command, args = cli_parser(user_inputs)
+    assert command.__name__ == "run"  # task_runtime's entrypoint is run()
+    assert args["uuid"] == "00000000-0000-0000-0000-000000000000"

setup.py

@@ -16,6 +16,8 @@
     'six>=1.11.0',
     'google-auth>=1.6.1,<2',
     'setuptools_scm>=3.1.0,<4',
+    'google-api-python-client>=1.7,<2',
+    'python-dateutil>=2.8,<3',
 ]
 
 extras_require = {