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comparison trinityToolWrapper.py @ 5:98d99fed9d35 draft

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Strip eol off of TrinityPath, so os.path.islink() works correctly.
author trinity_ctat
date Tue, 26 Sep 2017 13:33:20 -0400
parents cb71c6b0bf66
children 12bc09b4a26d
comparison
equal deleted inserted replaced
4:cb71c6b0bf66 5:98d99fed9d35
14 assert sys.version_info[:2] >= ( 2, 4 ) 14 assert sys.version_info[:2] >= ( 2, 4 )
15 15
16 TRINITY_BASE_DIR = "" 16 TRINITY_BASE_DIR = ""
17 if os.environ.has_key('TRINITY_HOME'): 17 if os.environ.has_key('TRINITY_HOME'):
18 TRINITY_BASE_DIR = os.environ['TRINITY_HOME']; 18 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
19 else: 19 elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions.
20 # 2017-09-26 20 # 2017-09-26
21 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility. 21 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
22 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that. 22 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
23 # I just found distutils.spawn.find_executable() which might work, but already implemented the below. 23 # I just found distutils.spawn.find_executable() which might work, but already implemented the below.
24 try: 24 try:
30 else: 30 else:
31 TrinityPath, err_info = pipe1.communicate() 31 TrinityPath, err_info = pipe1.communicate()
32 # FIX - probably should be checking err_info for errors... 32 # FIX - probably should be checking err_info for errors...
33 # Determine the TRINITY_BASE_DIR from output1. 33 # Determine the TRINITY_BASE_DIR from output1.
34 # If TrinityPath is a link, we need to dereference the link. 34 # If TrinityPath is a link, we need to dereference the link.
35 TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
36 # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
37 # print os.path.islink(TrinityPath)
38 TrinityPath = os.path.abspath(TrinityPath)
39 print "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
40 # print os.path.islink(TrinityPath)
35 while os.path.islink(TrinityPath): 41 while os.path.islink(TrinityPath):
42 print "That path is a link."
36 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) 43 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
44 print "The new path is: {:s}".format(TrinityPath)
37 # Take off the last part of the path (which is the Trinity command) 45 # Take off the last part of the path (which is the Trinity command)
38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) 46 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
39 47
40 # get bindir 48 # get bindir
41 bindir = sys.argv[0] 49 bindir = sys.argv[0]
68 return 76 return
69 77
70 # If one needs to silence stdout 78 # If one needs to silence stdout
71 #args.append( ">" ) 79 #args.append( ">" )
72 #args.append( "/dev/null" ) 80 #args.append( "/dev/null" )
81 print "The TRINITY_BASE_DIR is:\n\t{:s}".format(TRINITY_BASE_DIR)
73 82
74 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); 83 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
75 84
76 cmdline = " ".join(args) 85 cmdline = " ".join(args)
77 86
87 print "The command being invoked is:\n\t{:s}".format(cmdline)
78 88
79 89
80 try: 90 try:
81 # Run program 91 # Run program
82 err_capture = open("stderr.txt", 'w') 92 err_capture = open("stderr.txt", 'w')