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comparison tools/mira4_9/mirabait/mira_check_version.py @ 1:33bfaf5865c5 draft default tip

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit cd0ab853082e608d5646638b2d46489480616436
author peterjc
date Tue, 13 Oct 2015 10:01:25 -0400
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0:5979f13c2dc5 1:33bfaf5865c5
1 #!/usr/bin/env python
2 """A simple wrapper script to call a MIRA binary to check/report its version.
3
4 Syntax: mira_check_version.py binary [expected pattern]
5
6 The binary can be a full path, otherwise ``$PATH`` is searched as normal.
7
8 Example output from MIRA V3.4 suite installed on the ``$PATH``::
9
10 $ python mira_check_version.py mira
11 This is MIRA V3.4.1.1 (production version).
12 $ python mira_check_version.py mirabait
13 V3.4.1.1
14
15 Example output from MIRA v4.0.2::
16
17 $ python mira_check_version.py ~/downloads/mira_4.0.2_linux-gnu_x86_64_static/bin/mira
18 4.0.2
19 $ python mira_check_version.py ~/downloads/mira_4.0.2_linux-gnu_x86_64_static/bin/mirabait
20 4.0.2
21 $ python mira_check_version.py ~/downloads/mira_4.0.2_linux-gnu_x86_64_static/bin/miraconvert
22 4.0.2
23
24 Example output from MIRA v4.9.5::
25
26 $ python mira_check_version.py ~/downloads/mira_4.9.5_2_linux-gnu_x86_64_static/bin/mira
27 4.9.5_2
28 $ python mira_check_version.py ~/downloads/mira_4.9.5_2_linux-gnu_x86_64_static/bin/mirabait
29 4.9.5_2
30 $ python mira_check_version.py ~/downloads/mira_4.9.5_2_linux-gnu_x86_64_static/bin/miraconvert
31 4.9.5_2
32
33 The optional version checking is simple substring approach (beware of potential
34 issues if MIRA versions ever use double digits for minor version), and returns
35 zero if this matched::
36
37 $ python mira_check_version.py mirabait 4.9 && echo "Return value $?"
38 4.9.5_2
39 Return value 0
40
41 If the expected version did not match, the return value is one (error)::
42
43 $ python mira_check_version.py mirabait 4.9 && echo "Return value $?"
44 Expected MIRA v4.9, but mirabait reports: V3.4.1.1
45 Return value 1
46
47 This script is intended to be used as part of my Galaxy wrappers for MIRA,
48 where it will capture and record the version used - and give a clear error
49 message if there is a version mismatch (otherwise due to API changes the
50 MIRA error messages tend to be very long and somewhare confusing).
51 """
52 import os
53 import sys
54 import subprocess
55 import shutil
56 import time
57
58 WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
59
60 def sys_exit(msg, err=1):
61 sys.stderr.write(msg+"\n")
62 sys.exit(err)
63
64
65 def get_version(mira_binary):
66 """Run MIRA to find its version number"""
67 # At the commend line I would use: mira -v | head -n 1
68 # however there is some pipe error when doing that here.
69 cmd = [mira_binary, "-v"]
70 try:
71 child = subprocess.Popen(cmd,
72 stdout=subprocess.PIPE,
73 stderr=subprocess.STDOUT)
74 except Exception, err:
75 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
76 sys.exit(1)
77 ver, tmp = child.communicate()
78 del child
79 #Workaround for -v not working in mirabait 4.0RC4
80 if "invalid option" in ver.split("\n", 1)[0]:
81 for line in ver.split("\n", 1):
82 if " version " in line:
83 line = line.split()
84 return line[line.index("version")+1].rstrip(")")
85 sys_exit("Could not determine MIRA version:\n%s" % ver)
86 return ver.split("\n", 1)[0]
87
88
89 if "-v" in sys.argv or "--version" in sys.argv:
90 print("mira_check_version.py version %s" % WRAPPER_VER)
91 sys.exit(0)
92
93 if len(sys.argv) == 2:
94 mira_binary = sys.argv[1]
95 expected = None
96 elif len(sys.argv) == 3:
97 mira_binary = sys.argv[1]
98 expected = sys.argv[2]
99 else:
100 sys_exit("Usage: mira_check_version.py mira_binary [expected version]")
101
102 mira_ver = get_version(mira_binary)
103 if expected and not mira_ver.strip().startswith(expected):
104 sys_exit("Expected MIRA v%s, but %s reports: %s" % (expected, mira_binary, mira_ver))
105 print(mira_ver)