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comparison planemo/lib/python3.7/site-packages/cwltool/tests/test_load_tool.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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-1:000000000000 0:d30785e31577
1 from cwltool.load_tool import load_tool
2 from cwltool.context import LoadingContext, RuntimeContext
3 from cwltool.errors import WorkflowException
4 from cwltool.update import INTERNAL_VERSION
5 import pytest
6 from .util import (get_data, get_main_output,
7 get_windows_safe_factory,
8 needs_docker, working_directory,
9 needs_singularity, temp_dir,
10 windows_needs_docker)
11 from cwltool.resolver import Path, resolve_local
12 from .test_fetch import norm
13
14 @windows_needs_docker
15 def test_check_version():
16 """
17 It is permitted to load without updating, but not execute.
18
19 Attempting to execute without updating to the internal version should raise an error.
20 """
21 joborder = {"inp": "abc"}
22 loadingContext = LoadingContext({"do_update": True})
23 tool = load_tool(get_data("tests/echo.cwl"), loadingContext)
24 for j in tool.job(joborder, None, RuntimeContext()):
25 pass
26
27 loadingContext = LoadingContext({"do_update": False})
28 tool = load_tool(get_data("tests/echo.cwl"), loadingContext)
29 with pytest.raises(WorkflowException):
30 for j in tool.job(joborder, None, RuntimeContext()):
31 pass
32
33 def test_use_metadata():
34 """Use the version from loadingContext.metadata if cwlVersion isn't present in the document."""
35 loadingContext = LoadingContext({"do_update": False})
36 tool = load_tool(get_data("tests/echo.cwl"), loadingContext)
37
38 loadingContext = LoadingContext()
39 loadingContext.metadata = tool.metadata
40 tooldata = tool.tool.copy()
41 del tooldata["cwlVersion"]
42 tool2 = load_tool(tooldata, loadingContext)
43
44 def test_checklink_outputSource():
45 """Is outputSource resolved correctly independent of value of do_validate."""
46 outsrc = norm(Path(get_data("tests/wf/1st-workflow.cwl")).as_uri())+"#argument/classfile"
47
48 loadingContext = LoadingContext({"do_validate": True})
49 tool = load_tool(get_data("tests/wf/1st-workflow.cwl"), loadingContext)
50 assert norm(tool.tool["outputs"][0]["outputSource"]) == outsrc
51
52 loadingContext = LoadingContext({"do_validate": False})
53 tool = load_tool(get_data("tests/wf/1st-workflow.cwl"), loadingContext)
54 assert norm(tool.tool["outputs"][0]["outputSource"]) == outsrc
55
56 def test_load_graph_fragment():
57 """Reloading from a dictionary without a cwlVersion."""
58 loadingContext = LoadingContext()
59 uri = Path(get_data("tests/wf/scatter-wf4.cwl")).as_uri()+"#main"
60 tool = load_tool(uri, loadingContext)
61
62 rs, metadata = tool.doc_loader.resolve_ref(uri)
63 # Reload from a dict (in 'rs'), not a URI. The dict is a fragment
64 # of original document and doesn't have cwlVersion set, so test
65 # that it correctly looks up the root document to get the
66 # cwlVersion.
67 tool = load_tool(tool.tool, loadingContext)
68 assert tool.metadata["cwlVersion"] == INTERNAL_VERSION