Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/cwltool/tests/test_load_tool.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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from pathlib import Path import pytest from cwltool.context import LoadingContext, RuntimeContext from cwltool.errors import WorkflowException from cwltool.load_tool import load_tool from cwltool.process import use_custom_schema, use_standard_schema from cwltool.update import INTERNAL_VERSION from cwltool.utils import CWLObjectType from .test_fetch import norm from .util import get_data, windows_needs_docker @windows_needs_docker def test_check_version() -> None: """ It is permitted to load without updating, but not execute. Attempting to execute without updating to the internal version should raise an error. """ joborder = {"inp": "abc"} # type: CWLObjectType loadingContext = LoadingContext({"do_update": True}) tool = load_tool(get_data("tests/echo.cwl"), loadingContext) for _ in tool.job(joborder, None, RuntimeContext()): pass loadingContext = LoadingContext({"do_update": False}) tool = load_tool(get_data("tests/echo.cwl"), loadingContext) with pytest.raises(WorkflowException): for _ in tool.job(joborder, None, RuntimeContext()): pass def test_use_metadata() -> None: """Use the version from loadingContext.metadata if cwlVersion isn't present in the document.""" loadingContext = LoadingContext({"do_update": False}) tool = load_tool(get_data("tests/echo.cwl"), loadingContext) loadingContext = LoadingContext() loadingContext.metadata = tool.metadata tooldata = tool.tool.copy() del tooldata["cwlVersion"] load_tool(tooldata, loadingContext) def test_checklink_outputSource() -> None: """Is outputSource resolved correctly independent of value of do_validate.""" outsrc = ( norm(Path(get_data("tests/wf/1st-workflow.cwl")).as_uri()) + "#argument/classfile" ) loadingContext = LoadingContext({"do_validate": True}) tool = load_tool(get_data("tests/wf/1st-workflow.cwl"), loadingContext) assert norm(tool.tool["outputs"][0]["outputSource"]) == outsrc loadingContext = LoadingContext({"do_validate": False}) tool = load_tool(get_data("tests/wf/1st-workflow.cwl"), loadingContext) assert norm(tool.tool["outputs"][0]["outputSource"]) == outsrc def test_load_graph_fragment() -> None: """Reloading from a dictionary without a cwlVersion.""" loadingContext = LoadingContext() uri = Path(get_data("tests/wf/scatter-wf4.cwl")).as_uri() + "#main" tool = load_tool(uri, loadingContext) loader = tool.doc_loader assert loader rs, metadata = loader.resolve_ref(uri) # Reload from a dict (in 'rs'), not a URI. The dict is a fragment # of original document and doesn't have cwlVersion set, so test # that it correctly looks up the root document to get the # cwlVersion. assert isinstance(rs, str) or isinstance(rs, dict) tool = load_tool(rs, loadingContext) assert tool.metadata["cwlVersion"] == INTERNAL_VERSION def test_load_graph_fragment_from_packed() -> None: """Loading a fragment from packed with update.""" loadingContext = LoadingContext() uri = Path(get_data("tests/wf/packed-with-loadlisting.cwl")).as_uri() + "#main" try: with open(get_data("cwltool/extensions.yml")) as res: use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read()) # The updater transforms LoadListingRequirement from an # extension (in v1.0) to a core feature (in v1.1) but there # was a bug when loading a packed workflow and loading a # specific fragment it would get the un-updated document. # This recreates that case and asserts that we are using the # updated document like we should. tool = load_tool(uri, loadingContext) assert tool.tool["requirements"] == [ {"class": "LoadListingRequirement", "loadListing": "no_listing"} ] finally: use_standard_schema("v1.0")