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Add Gen3 Workflow cli and tool. (#244)
* Add cli and tool logic * Add unit tests * Add Documentation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| import click | ||
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| from gen3.tools.wrap import Gen3Wrap | ||
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| @click.command( | ||
| context_settings={"ignore_unknown_options": True, "allow_extra_args": True}, | ||
| help="A wrapper command that forwards COMMAND_ARGS as-is after setting the environment variable GEN3_TOKEN", | ||
| ) | ||
| @click.argument("command_args", nargs=-1, type=click.UNPROCESSED) | ||
| @click.pass_context | ||
| def run(ctx, command_args): | ||
| auth = ctx.obj["auth_factory"].get() | ||
| gen3Wrap_object = Gen3Wrap(auth, command_args) | ||
| gen3Wrap_object.run_command() |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,36 @@ | ||
| import os | ||
| import subprocess | ||
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| from cdislogging import get_logger | ||
| from gen3.auth import Gen3Auth, Gen3AuthError | ||
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| logger = get_logger("__name__") | ||
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| class Gen3Wrap: | ||
| def __init__(self, auth: Gen3Auth, command_args: tuple): | ||
| """ | ||
| auth : Gen3Auth instance | ||
| command_args: A tuple consisting of all the commands sent to the `gen3 run` tool | ||
| """ | ||
| self.auth = auth | ||
| self.command_args = command_args | ||
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| def run_command(self): | ||
| """ | ||
| Take the command args and run a subprocess with appropriate access token in the env var | ||
| """ | ||
| cmd = list(self.command_args) | ||
| try: | ||
| os.environ["GEN3_TOKEN"] = self.auth.get_access_token() | ||
| except Gen3AuthError as e: | ||
| logger.error(f"ERROR getting Gen3 Access Token:", e) | ||
| raise | ||
| logger.info( | ||
| f"Running the command {self.command_args} with gen3 access token in environment variable" | ||
| ) | ||
| try: | ||
| subprocess.run(cmd, stderr=subprocess.STDOUT) | ||
| except Exception as e: | ||
| logger.error(f"ERROR while running '{cmd}':", e) | ||
| raise |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,33 @@ | ||
| import pytest | ||
| from unittest.mock import MagicMock, patch | ||
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| from gen3.tools.wrap import Gen3Wrap, Gen3Auth, Gen3AuthError | ||
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| @patch.object(Gen3Auth, "get_access_token", MagicMock(return_value="1.2.3")) | ||
| def test_gen3_wrap_valid_auth(mock_gen3_auth): | ||
| """ | ||
| Patch subprocess.run and verify that the appropriate arguments are passed to the method when authentication process is valid. | ||
| """ | ||
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| test_command_args = ("echo", "Test1", "Test2") | ||
| with patch("gen3.tools.wrap.subprocess.run") as mock_subprocess_run: | ||
| wrapper_obj = Gen3Wrap(mock_gen3_auth, test_command_args) | ||
| wrapper_obj.run_command() | ||
| mock_subprocess_run.assert_called_once_with(list(test_command_args), stderr=-2) | ||
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| @patch.object(Gen3Auth, "get_access_token", MagicMock(side_effect=Gen3AuthError())) | ||
| def test_gen3_wrap_inavalid_auth(mock_gen3_auth): | ||
| """ | ||
| Break the authentication process to verify the following: | ||
| 1. Ensure a Gen3AuthError is raised. | ||
| 2. Confirm the subprocess is not executed when authentication fails. | ||
| """ | ||
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| test_command_args = ("echo", "Test1", "Test2") | ||
| with pytest.raises(Gen3AuthError): | ||
| with patch("gen3.tools.wrap.subprocess.run") as mock_subprocess_run: | ||
| wrapper_obj = Gen3Wrap(mock_gen3_auth, test_command_args) | ||
| wrapper_obj.run_command() | ||
| mock_subprocess_run.assert_not_called() |