Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/tests/test_fetch.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 import os
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2
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3 from six.moves import urllib
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4
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5 import pytest
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6
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7 import schema_salad.main
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8 import schema_salad.ref_resolver
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9 import schema_salad.schema
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10
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11 from cwltool.context import LoadingContext
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12 from cwltool.load_tool import load_tool
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13 from cwltool.main import main
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14 from cwltool.resolver import Path, resolve_local
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15 from cwltool.utils import onWindows
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16 from cwltool.workflow import default_make_tool
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17
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18 from .util import get_data, working_directory
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19
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20 def test_fetcher():
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21 class TestFetcher(schema_salad.ref_resolver.Fetcher):
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22 def __init__(self, a, b):
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23 pass
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24
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25 def fetch_text(self, url): # type: (unicode) -> unicode
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26 if url == "baz:bar/foo.cwl":
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27 return """
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28 cwlVersion: v1.0
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29 class: CommandLineTool
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30 baseCommand: echo
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31 inputs: []
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32 outputs: []
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33 """
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34 raise RuntimeError("Not foo.cwl, was %s" % url)
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35
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36 def check_exists(self, url): # type: (unicode) -> bool
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37 return url == "baz:bar/foo.cwl"
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38
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39 def urljoin(self, base, url):
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40 urlsp = urllib.parse.urlsplit(url)
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41 if urlsp.scheme:
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42 return url
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43 basesp = urllib.parse.urlsplit(base)
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44
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45 if basesp.scheme == "keep":
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46 return base + "/" + url
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47 return urllib.parse.urljoin(base, url)
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48
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49 def test_resolver(d, a):
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50 if a.startswith("baz:bar/"):
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51 return a
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52 return "baz:bar/" + a
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53
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54 loadingContext = LoadingContext({"construct_tool_object": default_make_tool,
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55 "resolver": test_resolver,
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56 "fetcher_constructor": TestFetcher})
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57
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58 load_tool("foo.cwl", loadingContext)
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59
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60 assert main(["--print-pre", "--debug", "foo.cwl"], loadingContext=loadingContext) == 0
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61
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62 root = Path(os.path.join(get_data("")))
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63
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64 path_fragments = [
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65 (os.path.join("tests", "echo.cwl"), "/tests/echo.cwl"),
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66 (os.path.join("tests", "echo.cwl") + "#main", "/tests/echo.cwl#main"),
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67 (str(root / "tests" / "echo.cwl"), "/tests/echo.cwl"),
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68 (str(root / "tests" / "echo.cwl") + "#main", "/tests/echo.cwl#main")
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69 ]
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70
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71 def norm(uri):
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72 if onWindows():
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73 return uri.lower()
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74 return uri
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75
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76 @pytest.mark.parametrize('path,expected_path', path_fragments)
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77 def test_resolve_local(path, expected_path):
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78 with working_directory(root):
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79 expected = norm(root.as_uri() + expected_path)
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80 assert norm(resolve_local(None, path)) == expected