Mercurial > repos > shellac > sam_consensus_v3
annotate 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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1 from pathlib import Path |
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2 |
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3 import pytest |
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4 |
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5 from cwltool.context import LoadingContext, RuntimeContext |
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6 from cwltool.errors import WorkflowException |
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7 from cwltool.load_tool import load_tool |
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8 from cwltool.process import use_custom_schema, use_standard_schema |
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9 from cwltool.update import INTERNAL_VERSION |
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10 from cwltool.utils import CWLObjectType |
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11 |
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12 from .test_fetch import norm |
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13 from .util import get_data, windows_needs_docker |
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14 |
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15 |
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16 @windows_needs_docker |
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17 def test_check_version() -> None: |
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18 """ |
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19 It is permitted to load without updating, but not execute. |
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20 |
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21 Attempting to execute without updating to the internal version should raise an error. |
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22 """ |
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23 joborder = {"inp": "abc"} # type: CWLObjectType |
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24 loadingContext = LoadingContext({"do_update": True}) |
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25 tool = load_tool(get_data("tests/echo.cwl"), loadingContext) |
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26 for _ in tool.job(joborder, None, RuntimeContext()): |
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27 pass |
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28 |
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29 loadingContext = LoadingContext({"do_update": False}) |
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30 tool = load_tool(get_data("tests/echo.cwl"), loadingContext) |
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31 with pytest.raises(WorkflowException): |
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32 for _ in tool.job(joborder, None, RuntimeContext()): |
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33 pass |
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34 |
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35 |
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36 def test_use_metadata() -> None: |
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37 """Use the version from loadingContext.metadata if cwlVersion isn't present in the document.""" |
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38 loadingContext = LoadingContext({"do_update": False}) |
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39 tool = load_tool(get_data("tests/echo.cwl"), loadingContext) |
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40 |
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41 loadingContext = LoadingContext() |
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42 loadingContext.metadata = tool.metadata |
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43 tooldata = tool.tool.copy() |
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44 del tooldata["cwlVersion"] |
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45 load_tool(tooldata, loadingContext) |
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46 |
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47 |
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48 def test_checklink_outputSource() -> None: |
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49 """Is outputSource resolved correctly independent of value of do_validate.""" |
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50 outsrc = ( |
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51 norm(Path(get_data("tests/wf/1st-workflow.cwl")).as_uri()) |
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52 + "#argument/classfile" |
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53 ) |
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54 |
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55 loadingContext = LoadingContext({"do_validate": True}) |
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56 tool = load_tool(get_data("tests/wf/1st-workflow.cwl"), loadingContext) |
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57 assert norm(tool.tool["outputs"][0]["outputSource"]) == outsrc |
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58 |
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59 loadingContext = LoadingContext({"do_validate": False}) |
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60 tool = load_tool(get_data("tests/wf/1st-workflow.cwl"), loadingContext) |
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61 assert norm(tool.tool["outputs"][0]["outputSource"]) == outsrc |
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62 |
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63 |
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64 def test_load_graph_fragment() -> None: |
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65 """Reloading from a dictionary without a cwlVersion.""" |
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66 loadingContext = LoadingContext() |
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67 uri = Path(get_data("tests/wf/scatter-wf4.cwl")).as_uri() + "#main" |
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68 tool = load_tool(uri, loadingContext) |
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69 |
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70 loader = tool.doc_loader |
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71 assert loader |
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72 rs, metadata = loader.resolve_ref(uri) |
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73 # Reload from a dict (in 'rs'), not a URI. The dict is a fragment |
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74 # of original document and doesn't have cwlVersion set, so test |
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75 # that it correctly looks up the root document to get the |
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76 # cwlVersion. |
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77 assert isinstance(rs, str) or isinstance(rs, dict) |
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78 tool = load_tool(rs, loadingContext) |
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79 assert tool.metadata["cwlVersion"] == INTERNAL_VERSION |
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80 |
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81 |
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82 def test_load_graph_fragment_from_packed() -> None: |
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83 """Loading a fragment from packed with update.""" |
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84 loadingContext = LoadingContext() |
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85 uri = Path(get_data("tests/wf/packed-with-loadlisting.cwl")).as_uri() + "#main" |
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86 try: |
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87 with open(get_data("cwltool/extensions.yml")) as res: |
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88 use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read()) |
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89 |
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90 # The updater transforms LoadListingRequirement from an |
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91 # extension (in v1.0) to a core feature (in v1.1) but there |
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92 # was a bug when loading a packed workflow and loading a |
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93 # specific fragment it would get the un-updated document. |
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94 # This recreates that case and asserts that we are using the |
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95 # updated document like we should. |
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96 |
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97 tool = load_tool(uri, loadingContext) |
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98 |
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99 assert tool.tool["requirements"] == [ |
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100 {"class": "LoadListingRequirement", "loadListing": "no_listing"} |
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101 ] |
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102 finally: |
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103 use_standard_schema("v1.0") |