/usr/share/doc/python-mzml/example_scripts/get_example_file.py is in python-mzml 0.7.4-dfsg-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 | #!/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
"""
from __future__ import print_function
import sys
import os.path
import hashlib
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]
gz = False
if filename.split(".")[-1] == "gz":
gz = True
if hashlib.sha256(file.read()).hexdigest() == sha256_sum:
return True
else:
return False
def calc_sha256(file):
gz = False
if file.split(".")[-1] == "gz":
gz = True
sha256 = hashlib.sha256()
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.
"""
download = None
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__)
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