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annotate planemo/lib/python3.7/site-packages/cwltool/tests/test_dependencies.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 pytest
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2
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3 import pytest
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4
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5 from cwltool.utils import onWindows
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6
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7 from .util import get_data, get_main_output, needs_docker
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8
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9
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10 try:
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11 from galaxy.tools import deps
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12 except ImportError:
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13 deps = None
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14
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15 @needs_docker
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16 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
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17 def test_biocontainers():
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18 wflow = get_data("tests/seqtk_seq.cwl")
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19 job = get_data("tests/seqtk_seq_job.json")
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20 error_code, _, _ = get_main_output(
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21 ["--beta-use-biocontainers", wflow, job])
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22
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23 assert error_code == 0
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24
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25 @pytest.mark.skipif(onWindows(), reason="bioconda currently not working on MS Windows")
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26 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
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27 def test_bioconda():
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28 wflow = get_data("tests/seqtk_seq.cwl")
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29 job = get_data("tests/seqtk_seq_job.json")
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30 error_code, _, stderr = get_main_output(
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31 ["--beta-conda-dependencies", "--debug", wflow, job])
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32
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33 assert error_code == 0, stderr
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34
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35 import os
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36 from distutils import spawn
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37 @pytest.mark.skipif(not spawn.find_executable("modulecmd"), reason="modulecmd not installed")
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38 def test_modules():
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39 wflow = get_data("tests/random_lines.cwl")
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40 job = get_data("tests/random_lines_job.json")
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41 os.environ["MODULEPATH"] = os.path.join(os.getcwd(), 'tests/test_deps_env/modulefiles')
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42 error_code, _, stderr = get_main_output(
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43 ["--beta-dependency-resolvers-configuration",
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44 "tests/test_deps_env_modules_resolvers_conf.yml", "--debug", wflow, job])
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45
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46 assert error_code == 0, stderr