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.. code-block:: python
#!/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__)
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