Mercurial > repos > guerler > springsuite
view planemo/lib/python3.7/site-packages/cwltool/tests/test_load_tool.py @ 0:d30785e31577 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author | guerler |
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date | Fri, 31 Jul 2020 00:18:57 -0400 |
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from cwltool.load_tool import load_tool from cwltool.context import LoadingContext, RuntimeContext from cwltool.errors import WorkflowException from cwltool.update import INTERNAL_VERSION import pytest from .util import (get_data, get_main_output, get_windows_safe_factory, needs_docker, working_directory, needs_singularity, temp_dir, windows_needs_docker) from cwltool.resolver import Path, resolve_local from .test_fetch import norm @windows_needs_docker def test_check_version(): """ 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"} loadingContext = LoadingContext({"do_update": True}) tool = load_tool(get_data("tests/echo.cwl"), loadingContext) for j 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 j in tool.job(joborder, None, RuntimeContext()): pass def test_use_metadata(): """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"] tool2 = load_tool(tooldata, loadingContext) def test_checklink_outputSource(): """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(): """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) rs, metadata = tool.doc_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. tool = load_tool(tool.tool, loadingContext) assert tool.metadata["cwlVersion"] == INTERNAL_VERSION