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
|
.. code-block:: python
#!/usr/bin/env python
import os
import re
import shutil
import subprocess
import sys
import tempfile
from argparse import ArgumentParser
"""Download all versions of the psidev OBO for mzML files"""
CVS_SERVER = ":pserver:anonymous:" "@psidev.cvs.sourceforge.net:/cvsroot/psidev"
class CVSClient(object):
def __init__(self, root, client_dir=None, verbose=False):
self.root = root
self.client_dir = client_dir
self.cleanup = False
self.verbose = verbose
def __enter__(self):
if not self.client_dir or not os.path.isdir(self.client_dir):
self.client_dir = tempfile.mkdtemp(prefix="cvs")
self.cleanup = True
return self
def __exit__(self, exc_type, exc_value, traceback):
if self.cleanup:
shutil.rmtree(self.client_dir, ignore_errors=True)
def __call__(self, *args, **kwargs):
command = ["cvs", "-d" + self.root] + list(args)
# Default args for subprocess
processkwargs = dict(cwd=self.client_dir)
if not self.verbose:
command.insert(1, "-Q")
processkwargs["stderr"] = open(os.devnull, "w")
# Override defaults with provided args
processkwargs.update(kwargs)
if self.verbose:
print(">>> " + " ".join(command), file=sys.stderr)
return subprocess.check_output(command, **processkwargs)
def get_version_map(cvs):
filename = "psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
# Download the OBO file and get its revision log
cvs("-z3", "co", filename)
revisions = parse_revisions(cvs("-z3", "log").split("\n"))
version_map = {}
for revision in revisions:
file_at_revision = cvs("-z3", "co", "-p", "-r", revision, filename)
version = parse_version(file_at_revision)
# Revisions go from newest to oldest, so if a version exists in the
# dictionary, it's already the newest revision of that version
if version and version not in version_map:
version_map[version] = file_at_revision
return version_map
def parse_revisions(revision_log):
revisions = []
revision_regexp = re.compile(r"revision (\d+\.\d+)")
for line in revision_log:
match = revision_regexp.match(line)
if match:
revisions.append(match.group(1))
return revisions
def parse_version(file_string):
version_regexp = re.compile(r"remark:\s+version: (\d+\.\d+\.\d+\S*)")
version = None
for line in file_string.split("\n"):
match = version_regexp.match(line)
if match:
version = match.group(1)
return version
def save_versions(version_map, destination):
for version, file_at_version in version_map.iteritems():
destination_path = os.path.join(destination, "psi-ms-{0}.obo".format(version))
with open(destination_path, "w+") as destination_file:
destination_file.write(file_at_version)
if __name__ == "__main__":
parser = ArgumentParser(description=__doc__)
parser.add_argument("destination", help="directory into which the OBO files go")
parser.add_argument(
"-v", "--verbose", action="store_true", help="show extra logging information"
)
args = parser.parse_args()
# Sanity checking
assert os.path.isdir(args.destination), "destination must be a valid directory"
with CVSClient(CVS_SERVER, verbose=args.verbose) as cvs:
cvs("login")
revision_map = get_version_map(cvs)
save_versions(revision_map, args.destination)
# vim: ts=4:sw=4:sts=4
|
