Protocol of experiments 06.06.2017

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exec(open('../tooldog/analyse/container.py').read())


    

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import urllib.request


    

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import urllib.parse


    

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import os


    

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import tarfile


    

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def write_to_file(filename, data = '', mode='w'):
    f = open(filename, mode)
    f.write(data)
    f.close()


    

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REPO_URL = "https://github.com/gem-pasteur/Integron_Finder/"


    

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ZIP_URL = urllib.parse.urljoin(REPO_URL, "archive/master.zip") # unstable


    

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WORKDIR = "/" + REPO_URL.split('/')[4] + "-master" # dir path after unzip at root, like "/Integron_Finder-master"


    

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response = urllib.request.urlopen(ZIP_URL)


    

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data = response.read()


    

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write_to_file('tool.zip', data, 'wb')


    

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CURRENT_PATH = os.path.realpath(os.getcwd())


    

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ZIP_PATH = os.path.join(CURRENT_PATH, 'tool.zip')


    

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TAR_PATH = os.path.join(CURRENT_PATH, 'tool.tar')


    

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with tarfile.open('tool.tar', mode='w') as archive:
    archive.add(ZIP_PATH, arcname="tool.zip")


    

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PYTHON_VERSION = 2 # version of python tool


    

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TOOL_NAME = 'integron_finder' # name of the tool


    

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OUTPUT_FORMAT = 'cwl' # output: cwl / xml


    

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OUTPUT_FILENAME = TOOL_NAME + "." + OUTPUT_FORMAT # output filename


    

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PYTHON_PATH = "/usr/local/lib/python3.5/dist-packages/" if PYTHON_VERSION == 3 else \
"/usr/local/lib/python2.7/dist-packages/" # PYTHONPATH, required for argparse2tool


    

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c = Container("inkuzm/tooldog-analyser-sandbox",
              "tail -f /dev/null",  # run until we will stop the container
              environment={'PYTHONPATH': PYTHON_PATH})


    

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c.put(TAR_PATH, "/")


    

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def cd(path, cmd):
    return "bash -c 'cd " + path + " && " + cmd + "'"


    

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def pip(v, cmd):
    return "pip" + str(v) + " " + cmd


    

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GEN_CMD = TOOL_NAME + " " + "--generate_cwl_tool" if OUTPUT_FORMAT == 'cwl' else \
"--generate_galaxy_xml"


    

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def execute(ctx, cmd, verbose=True):
    result = ''
    exe = ctx.exec(cmd)
    for line in exe:
        if verbose: print(line)
        result += line.decode("utf-8")[:-1]
    return result


    

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cwl_tool = '' 
with c:
    exe_stack = [
        "unzip /tool.zip",
        cd(WORKDIR, pip(PYTHON_VERSION, "install .")),
        cd(WORKDIR, pip(PYTHON_VERSION, "install argparse2tool")),
        cd(WORKDIR, GEN_CMD),
    ]
    for cmd in exe_stack:
        cwl_tool = execute(c, cmd)


    

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write_to_file(OUTPUT_FILENAME, cwl_tool)


    

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os.remove(TAR_PATH)


    

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os.remove(ZIP_PATH)


    

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print("Success!")