def get_kmdi_version(self, path, verb=1):
"""for the given program, run: mdls -name kMDItemVersion
return found version string, or an empty one on failure
"""
cmd = 'mdls -name kMDItemVersion %s' % path
s, soe = UTIL.exec_tcsh_command(cmd, lines=1)
# return on failure
if len(soe) == 0: return ''
rstr = soe[0]
rposn = rstr.find('kMDItemVersion')
if rposn < 0: return ''
rlist = rstr[rposn:].split()
if verb > 1: print("-- kmdi_v: list is %s" % rlist)
if len(rlist) < 3: return ''
if rlist[0] != 'kMDItemVersion' or rlist[1] != '=':
return ''
# found something, remove any quotes, tabs and spaces, and return
rstr = rlist[2].strip('\'" \t')
return rstr
def check_output(cmd, showerr=1):
"""return text output from the given command, executed via 'tcsh -c cmd'
if showerr and there is a command error, show it
"""
status, output = afni_util.exec_tcsh_command(cmd)
if status and showerr:
print(cmd)
print(output)
return output
def exec_or_error(cmd_str, error_msg="ERROR!!!"):
"""Execute subprocess.Popen(cmd_str,stdout=subprocess.PIPE,shell=True)
Return status and shell output.
On non 0 status print error_msg and exit.
"""
print("")
print(cmd_str)
sys.stdout.flush()
# use local library, which returns strings instead of bytes
retcode, cmd_output = afni_util.exec_tcsh_command(cmd_str)
if retcode != 0:
print("\n%s\n\n%s" % (error_msg, cmd_output))
sys.exit(1)
return retcode, cmd_output
def show_general_afni_info(self, header=1):
print(UTIL.section_divider('AFNI and related program tests', hchar='-'))
self.afni_dir = self.get_afni_dir()
check_list = ['afni', 'afni label', 'AFNI_version.txt',
'python', 'R', 'tcsh']
nfound = self.check_for_progs(check_list, show_missing=1)
if nfound < len(check_list):
self.comments.append('failure under initial ' \
'"AFNI and related program tests"')
# make generic but pretty
print("instances of various programs found in PATH:")
proglist = ['afni', 'R', 'python', 'python2', 'python3']
ml = UTIL.max_len_in_list(proglist)
for prog in proglist:
rv, files = UTIL.search_path_dirs(prog, mtype=1)
if not rv:
if len(files) > 1: fstr = '\n '+'\n '.join(files)
elif len(files) > 0: fstr = ' (%s)' % files[0]
else: fstr = ''
print(' %-*s : %d %s' % (ml, prog, len(files), fstr))
if prog == 'afni':
if len(files) > 1:
self.comments.append("have multiple versions of AFNI in PATH")
if len(files) > 0:
if os.stat(files[0]).st_uid == 0:
self.comments.append("'afni' executable is owned by root")
print('')
# explicit python2 vs python3 check 7 Dec 2016
n2 = UTIL.num_found_in_path('python2', mtype=1)
n3 = UTIL.num_found_in_path('python3', mtype=1)
if n3 > 0 and n2 <= 0:
print("** have python3 but not python2")
print('')
# try select AFNI programs
print('testing ability to start various programs...')
ind = '%8s' % ' '
indn = '\n%8s' % ' '
proglist = ['afni', 'suma', '3dSkullStrip', 'uber_subject.py',
'3dAllineate', '3dRSFC', 'SurfMesh', '3dClustSim', '3dMVM']
fcount = 0
for prog in proglist:
st, so, se = BASE.shell_exec2('%s -help'%prog, capture=1)
# if 3dMVM, status will be 0 on failed library load (fix that, too)
if prog == '3dMVM' and not st:
mesg = ''.join(se)
if mesg.find('Error in dyn.load') >= 0:
st = 1
if st:
print(' %-20s : FAILURE' % prog)
print(ind + indn.join(se))
fcount += 1
else:
print(' %-20s : success' % prog)
# no OpenMP problem
if prog == '3dAllineate': self.ok_openmp = 1
print('')
pfailure = fcount == len(proglist)
if fcount > 0:
self.afni_fails = fcount
self.comments.append('AFNI programs show FAILURE')
# if complete failure, retry from exec dir
ascdir = UTIL.executable_dir()
if pfailure and self.afni_dir != ascdir:
fcount = 0
print('none working, testing programs under implied %s...' % ascdir)
for prog in proglist:
st, so, se = BASE.shell_exec2('%s/%s -help'%(ascdir,prog),capture=1)
if st:
print(' %-20s : FAILURE' % prog)
print(ind + indn.join(se))
fcount += 1
else: print(' %-20s : success' % prog)
print('')
if fcount < len(proglist):
self.comments.append('consider adding %s to your PATH' % ascdir)
# if afni_dir is not set, use ascdir
if self.afni_dir == '': self.afni_dir = ascdir
print('checking for R packages...')
cmd = 'rPkgsInstall -pkgs ALL -check'
st, so, se = BASE.shell_exec2(cmd, capture=1)
if st or len(se) < 2: okay = 0
else:
if se[1].startswith('++ Note:'): se = se[2:]
okay = 1
# do not require "verified", but fail on "not installed"
# (to avoid failing on 'unknown timezone' warnings)
for estr in se:
if estr != '' and estr.find('not installed') >= 0:
okay = 0 # any failure is terminal
break
if okay:
print(' %-20s : success' % cmd)
else:
print(' %-20s : FAILURE' % cmd)
print(ind + indn.join(se))
self.comments.append('missing R packages (see rPkgsInstall)')
print('')
status, cout = UTIL.exec_tcsh_command("R RHOME")
print('R RHOME : %s' % cout.strip())
print('')
print('checking for $HOME files...')
flist = ['.afnirc', '.sumarc', '.afni/help/all_progs.COMP']
for ff in flist:
if os.path.isfile('%s/%s'%(self.home_dir, ff)): fstr = 'found'
else: fstr = 'missing'
print(' %-25s : %s' % (ff, fstr))
# add to comments
if self.afni_dir:
ccc = 'run: cp %s/AFNI.afnirc ~/.afnirc' % self.afni_dir
else:
ccc = 'copy AFNI.afnirc to ~/.afnirc'
self.add_file_comment(None, '.afnirc', 'please %s' % ccc)
self.add_file_comment(None, '.sumarc',
'please run: "suma -update_env" for .sumarc')
self.add_file_comment(None, '.afni/help/all_progs.COMP',
'please run: apsearch -update_all_afni_help')
print('')