diff env/lib/python3.9/site-packages/cwltool/tests/test_load_tool.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/cwltool/tests/test_load_tool.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,103 @@
+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")