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annotate planemo/lib/python3.7/site-packages/cwltool/tests/test_http_input.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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d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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1 import os
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2 import tempfile
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3
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4 from cwltool.pathmapper import PathMapper
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7 def test_http_path_mapping():
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8 class SubPathMapper(PathMapper):
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9 def __init__(self, referenced_files, basedir, stagedir):
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10 super(SubPathMapper, self).__init__(referenced_files, basedir, stagedir)
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11 input_file_path = "https://raw.githubusercontent.com/common-workflow-language/cwltool/master/tests/2.fasta"
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12 tempdir = tempfile.mkdtemp()
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13 base_file = [{
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14 "class": "File",
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15 "location": "https://raw.githubusercontent.com/common-workflow-language/cwltool/master/tests/2.fasta",
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16 "basename": "chr20.fa"
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17 }]
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18 pathmap = SubPathMapper(base_file, os.getcwd(), tempdir)._pathmap
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19
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20 assert input_file_path in pathmap
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21 assert os.path.exists(pathmap[input_file_path].resolved)
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23 with open(pathmap[input_file_path].resolved) as file:
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24 contents = file.read()
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25
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26 assert ">Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;" in contents