Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/cwltool/tests/test_trs.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/cwltool/tests/test_trs.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,114 @@ +from typing import Any, Optional +from unittest import mock +from unittest.mock import MagicMock + +from cwltool.main import main + +from .util import get_data + + +class MockResponse1: + def __init__( + self, json_data: Any, status_code: int, raise_for_status: Optional[bool] = None + ) -> None: + """Create a fake return object for requests.Session.head.""" + self.json_data = json_data + self.status_code = status_code + self.raise_for_status = mock.Mock() + self.raise_for_status.side_effect = raise_for_status + + def json(self) -> Any: + return self.json_data + + +def mocked_requests_head(*args: Any) -> MockResponse1: + + return MockResponse1(None, 200) + + +class MockResponse2: + def __init__( + self, json_data: Any, status_code: int, raise_for_status: Optional[bool] = None + ) -> None: + """Create a fake return object for requests.Session.get.""" + self.json_data = json_data + self.text = json_data + self.status_code = status_code + self.raise_for_status = mock.Mock() + self.raise_for_status.side_effect = raise_for_status + + def json(self) -> Any: + return self.json_data + + headers = {"content-type": "text/plain"} + + +def mocked_requests_get(*args: Any, **kwargs: Any) -> MockResponse2: + if ( + args[0] + == "https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/CWL/files" + ): + return MockResponse2( + [ + {"file_type": "CONTAINERFILE", "path": "Dockerfile"}, + {"file_type": "PRIMARY_DESCRIPTOR", "path": "Dockstore.cwl"}, + {"file_type": "TEST_FILE", "path": "test.json"}, + ], + 200, + ) + elif ( + args[0] + == "https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl" + ): + string = open(get_data("tests/trs/Dockstore.cwl")).read() + return MockResponse2(string, 200) + elif ( + args[0] + == "https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-tool.cwl" + ): + string = open(get_data("tests/trs/md5sum-tool.cwl")).read() + return MockResponse2(string, 200) + elif ( + args[0] + == "https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl" + ): + string = open(get_data("tests/trs/md5sum-workflow.cwl")).read() + return MockResponse2(string, 200) + elif ( + args[0] + == "https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/CWL/files" + ): + return MockResponse2( + [ + {"file_type": "TEST_FILE", "path": "md5sum-input-cwl.json"}, + {"file_type": "SECONDARY_DESCRIPTOR", "path": "md5sum-tool.cwl"}, + {"file_type": "PRIMARY_DESCRIPTOR", "path": "md5sum-workflow.cwl"}, + ], + 200, + ) + + print("A mocked call to TRS missed, target was %s", args[0]) + return MockResponse2(None, 404) + + +@mock.patch("requests.Session.head", side_effect=mocked_requests_head) +@mock.patch("requests.Session.get", side_effect=mocked_requests_get) +def test_tool_trs_template(mock_head: MagicMock, mock_get: MagicMock) -> None: + params = ["--make-template", r"quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4"] + return_value = main(params) + mock_head.assert_called() + mock_get.assert_called() + assert return_value == 0 + + +@mock.patch("requests.Session.head", side_effect=mocked_requests_head) +@mock.patch("requests.Session.get", side_effect=mocked_requests_get) +def test_workflow_trs_template(mock_head: MagicMock, mock_get: MagicMock) -> None: + params = [ + "--make-template", + r"#workflow/github.com/dockstore-testing/md5sum-checker:develop", + ] + return_value = main(params) + mock_head.assert_called() + mock_get.assert_called() + assert return_value == 0