get_example_file.py

#!/usr/bin/env python

"""

Check for presence of example files and download them.
Just call the function open_example()

For using the correct output directory just state get_example_file.OUTPUT_DIR

"""
import hashlib
import os.path
import sys


SHA256_DICT = {
    "deconvolution.mzML.gz": (
        "19399e4f87d8937cf7be32bab7fd8889700e119cbc2ede215270cbfc9913b394",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
    "dta_example.mzML": (
        "2cd7207d5106ee5fb3ab7867961a6c1ad02f0ef72da19532e7ebb41c8d010b1a",
        "http://dev.thep.lu.se/fp6-prodac/export/80/trunk/mzML/",
    ),
    "neutral_loss_example_1.1.0.mzML": (
        "5911fa5d91a435aedd7be5a2ea09272f437d44f350948179a96146705a177a16",
        "http://dev.thep.lu.se/fp6-prodac/export/80/trunk/mzML/scans/",
    ),
    "precursor_spectrum_example_1.1.0.mzML": (
        "783187ec7eb2ee2713aecd9f6032508caad3439afa0b4a20232480b33472c17b",
        "http://dev.thep.lu.se/fp6-prodac/export/80/trunk/mzML/scans/",
    ),
    "profile-mass-spectrum.mzml": (
        "2e952de2a25db421f3e30d8c659acc6c3f5e862e4d0fd32ec24c7c606c9a62fd",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
    "small-1.0.0.mzml": (
        "9e15d6d2eba26932e4d5c61f92df7771da0bbb8589b7237d05bd915017dbf82f",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
    "BSA1.mzML": (
        "d4bde93c77ec9e948cc62f4c022b8d54591073fd1170e264b69a79dc8d259830",
        "http://open-ms.svn.sourceforge.net/viewvc/open-ms/OpenMS/share/OpenMS/examples/BSA/",
    ),
    "proteomeDiscoverer.mzML.gz": (
        "7fdd45bfcb6d82b2a75abd63fdc0d8cc1f14c1bd717ba2f3d4eec87ec201f3be",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
    "32-bit.mzML.gz": (
        "199d2611c9894f2a07fb734fbe4db2226cd2a43e806d4e9662b66b979f7df264",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
    "32-bit-compressed.mzML.gz": (
        "30fdde9ebf3bb145a60ea589f466cb0db8b3b2c451646156db3e56ffe1bf0e59",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
    "64-bit.mzML.gz": (
        "0d56a2295096e7499a8a90509661d22d4a6a097ad58f3c03310804c9698113aa",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
    "small.pwiz.1.1.mzML": (
        "87ddde776c9933857edb22f404116f23e85ca8bddadc84d10308eb8853a58768",
        "http://proteowizard.sourceforge.net/example_data/",
    ),
    "MRM_example_1.1.0.mzML": (
        "8140d77921be6fe49e73d71536b211ad39ae48f0272d4a465da2dd202185bdd9",
        "http://dev.thep.lu.se/fp6-prodac/export/80/trunk/mzML/scans/",
    ),
    "emptyScan.mzML.gz": (
        "4d82ea02c1f938e8fbe97b907371aad0eceee074bbee37f7513374a1bb7c3f3b",
        "http://www.uni-muenster.de/hippler/pymzml/example_mzML_files/",
    ),
}

EXAMPLE_DIR = os.path.join(os.path.dirname(__file__), "mzML_example_files")
OUTPUT_DIR = os.path.join(os.path.dirname(__file__), "output")

try:
    os.makedirs(EXAMPLE_DIR)
except OSError:
    pass
try:
    os.makedirs(OUTPUT_DIR)
except OSError:
    pass


def open_example(filename):
    """
    filename = filename of a file in the example directory
    If the file "filename" is not present in the example directory, the file is downloaded.
    Path with filename is returned.
    """
    try:
        SHA256_DICT[filename]
    except KeyError:
        print('File "{0}" not available.'.format(filename), file=sys.stderr)
        exit(1)

    filename_with_path = os.path.join(EXAMPLE_DIR, filename)
    # check file presence
    checked_file = check_file(filename_with_path, filename)
    if checked_file:
        return filename_with_path

    # file is not present or corrupt
    server_url = SHA256_DICT[filename][1]
    url = server_url + filename
    if download(filename_with_path, url):
        checked_file = check_file(filename_with_path, filename)
        if checked_file:
            return filename_with_path
        else:
            os.remove(filename_with_path)
            print("Downloaded file is corrupt. Please try again.", file=sys.stderr)
            exit(1)

        exit(1)


def check_file(filename_with_path, filename):
    # check file presence
    if os.path.isfile(filename_with_path):
        # file exists, check SHA224 sum
        file = open(filename_with_path, "rb")
        if check_sha256(file, filename):
            return True


def check_sha256(file, filename):
    sha256_sum = SHA256_DICT[filename][0]

    if hashlib.sha256(file.read()).hexdigest() == sha256_sum:
        return True
    else:
        return False


def calc_sha256(file):
    file = open(file, "rb")
    return hashlib.sha256(file.read()).hexdigest()


def download(filename_with_path, url):
    """
    filename_with_path = path and filename, where to save downloaded file
    url = url to download
    Path with filename is returned.
    """

    if sys.version_info[0] < 3:
        from urllib2 import Request, urlopen, URLError, HTTPError
    else:
        from urllib.request import Request, urlopen, URLError, HTTPError

    print("Downloading file ...", end="\r", file=sys.stderr)
    req = Request(url)
    print("Downloading file completed.", file=sys.stderr)
    try:
        response = urlopen(req)
        with open(filename_with_path, "wb") as f:
            f.write(response.read())
        return filename_with_path
    except HTTPError:
        print(
            "HTTP Error: The server could not fulfill the request.",
            "Possibly, the file is not found on the server.",
            file=sys.stderr,
        )
        exit(1)
    except URLError:
        print(
            "URL Error: Server not available. Please check your internet connection.",
            file=sys.stderr,
        )
        exit(1)


if __name__ == "__main__":
    print(__doc__)