comparison trinityToolWrapper.py @ 10:a8fa525a2f30 draft

Trying to fix a syntax error.

9:b6152cc26ffd

    # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
    # I just found distutils.spawn.find_executable() which might work, but already implemented the below.
    try:
        pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
    except:
        msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0])
        sys.stderr.write(msg)
        # t, v, tb = sys.exc_info()
        # raise t, v, tb
        # For some reason the above was giving a syntax error. 
        # A simple raise shoudl reraise the existing exception.
        raise
    else:
        TrinityPath, err_info = pipe1.communicate()
        # FIX - probably should be checking err_info for errors...
        # Determine the TRINITY_BASE_DIR from output1.
        # If TrinityPath is a link, we need to dereference the link.
        TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
        # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
        # print os.path.islink(TrinityPath)
        TrinityPath = os.path.abspath(TrinityPath)
        print "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
        # print os.path.islink(TrinityPath)
        while os.path.islink(TrinityPath):
            print "That path is a link."
            TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
            print "The new path is: {:s}".format(TrinityPath)
        # Take off the last part of the path (which is the Trinity command)
        TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
else:
    sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
    sys.exit()

10:a8fa525a2f30

    # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
    # I just found distutils.spawn.find_executable() which might work, but already implemented the below.
    try:
        pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
    except:
        msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0])
        sys.stderr.write(msg)
        # t, v, tb = sys.exc_info()
        # raise t, v, tb
        # For some reason the above was giving a syntax error. 
        # A simple raise should reraise the existing exception.
        raise
    else:
        TrinityPath, err_info = pipe1.communicate()
        # FIX - probably should be checking err_info for errors...
        # Determine the TRINITY_BASE_DIR from output1.
        # If TrinityPath is a link, we need to dereference the link.
        TrinityPath = TrinityPath.rstrip() # Need to strip off a newline.
        # print "Trinity that was found is: {:s}".format(repr(TrinityPath))
        # print os.path.islink(TrinityPath)
        TrinityPath = os.path.abspath(TrinityPath)
        # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath)
        # print msg
        # print os.path.islink(TrinityPath)
        while os.path.islink(TrinityPath):
            # print "That path is a link."
            TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
            # print "The new path is: {:s}".format(TrinityPath)
        # Take off the last part of the path (which is the Trinity command)
        TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
else:
    sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
    sys.exit()