Mercurial > repos > peterjc > mira4_9_mirabait

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