Mercurial > repos > petrn > repeatexplorer

comparison seqclust @ 2:94877d063270 draft

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Uploaded
author petrn
date Fri, 20 Dec 2019 11:14:11 +0000
parents 2d43ed150abe
children 8f7909cf86df
comparison
equal deleted inserted replaced
1:2d43ed150abe 2:94877d063270
25 25
26 LOGGER = logging.getLogger(__name__) 26 LOGGER = logging.getLogger(__name__)
27 27
28 28
29 def get_version(path, tarean_mode): 29 def get_version(path, tarean_mode):
30 # get git version
31 branch = "?"
32 shorthash = "?"
33 revcount = "?"
34 tag = "?"
30 try: 35 try:
31 branch = subprocess.check_output("git rev-parse --abbrev-ref HEAD", 36 branch = subprocess.check_output("git rev-parse --abbrev-ref HEAD",
32 shell=True, 37 shell=True,
33 cwd=path).decode('ascii').strip() 38 cwd=path).decode('ascii').strip()
34 shorthash = subprocess.check_output( 39 shorthash = subprocess.check_output(
36 shell=True, 41 shell=True,
37 cwd=path).decode('ascii').strip() 42 cwd=path).decode('ascii').strip()
38 revcount = len(subprocess.check_output( 43 revcount = len(subprocess.check_output(
39 "git log --oneline", shell=True, 44 "git log --oneline", shell=True,
40 cwd=path).decode('ascii').split()) 45 cwd=path).decode('ascii').split())
41 try: 46 tag = subprocess.check_output("git describe --tags --abbrev=0",
42 tag = subprocess.check_output("git describe --tags --abbrev=0",
43 cwd=path, 47 cwd=path,
44 shell=True).decode('ascii').strip() 48 shell=True).decode('ascii').strip()
45 except subprocess.CalledProcessError: 49 version_info = "{branch}-{tag}-{revcount}({shorthash})".format(
46 tag = " " 50 branch=branch,
47 51 shorthash=shorthash,
48 version_string = ( 52 tag=tag,
49 "-------------------------------------" 53 revcount=revcount
50 "-------------------------------------\n" 54 )
51 "PIPELINE VERSION : " 55 except subprocess.CalledProcessError:
52 "{branch}-{tag}-{revcount}({shorthash})\n\n" 56 # alernativelly - read it from file
53 "PROTEIN DATABASE VERSION : {PD}\n" 57 try:
54 " md5 checksum : {PDmd5}\n\n" 58 with open(path + "/version_info.txt", 'r') as f:
55 "DNA DATABASE VERSION : {DD}\n" 59 version_info = f.read()
56 " md5 checksum : {DDmd5}\n" 60 except FileNotFoundError:
57 "-------------------------------------" 61 version_info = "version of pipeline not available!"
58 "-------------------------------------\n").format( 62
59 branch=branch, 63 ## get database versions:
60 shorthash=shorthash, 64 PD = "?"
61 revcount=revcount, 65 PDmd5 = "?"
62 tag=tag, 66 DD = "?"
63 PD=os.path.basename(config.PROTEIN_DATABASE), 67 DDmd5 = "?"
64 PDmd5=utils.md5checksum(config.PROTEIN_DATABASE + ".psq", fail_if_missing = not tarean_mode), 68 try:
65 DD=os.path.basename(config.DNA_DATABASE), 69 PD = os.path.basename(config.PROTEIN_DATABASE)
66 DDmd5=utils.md5checksum(config.DNA_DATABASE + ".nsq")) 70 PDmd5 = utils.md5checksum(config.PROTEIN_DATABASE + ".psq",
67 71 fail_if_missing=not tarean_mode)
72 DD = os.path.basename(config.DNA_DATABASE)
73 DDmd5 = utils.md5checksum(config.DNA_DATABASE + ".nsq")
68 except: 74 except:
69 version_string = "version of pipeline not available!" 75 ## some problem with databases
76 pass
77 version_string = (
78 "-------------------------------------"
79 "-------------------------------------\n"
80 "PIPELINE VERSION : "
81 "{version_info}\n\n"
82 "PROTEIN DATABASE VERSION : {PD}\n"
83 " md5 checksum : {PDmd5}\n\n"
84 "DNA DATABASE VERSION : {DD}\n"
85 " md5 checksum : {DDmd5}\n"
86 "-------------------------------------"
87 "-------------------------------------\n").format(
88
89 version_info=version_info,
90 PD=PD,
91 PDmd5=PDmd5,
92 DD=DD,
93 DDmd5=DDmd5
94 )
70 95
71 LOGGER.info(version_string) 96 LOGGER.info(version_string)
72 return version_string 97 return version_string
73 98
74 99