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'
]
fcount = 0
for prog in proglist:
st, so, se = BASE.shell_exec2('%s -help' % prog, capture=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
# require every subsequent string to say verified
for estr in se:
if estr != '' and estr.find('has been verified') < 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('')
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 = 'running: cp %s/AFNI.afnirc ~/.afnirc' % self.afni_dir
else:
ccc = 'copying AFNI.afnirc to ~/.afnirc'
self.add_file_comment(None, '.afnirc', 'consider %s' % ccc)
self.add_file_comment(
None, '.sumarc', 'consider running "suma -update_env" for .sumarc')
self.add_file_comment(
None, '.afni/help/all_progs.COMP',
'consider running: apsearch -update_all_afni_help')
print('')
class SysInfo:
"""system info class"""
def __init__(self, data_root='', verb=1):
self.system = platform.system()
self.home_dir = os.environ['HOME']
self.data_root = data_root
self.verb = verb
self.afni_ver = ''
self.os_dist = ''
self.comments = [] # comments to print at the end
def get_afni_dir(self):
s, so, se = BASE.simple_shell_exec('which afni', capture=1)
if s: return ''
return so.strip()
def show_general_sys_info(self, header=1):
if header: print UTIL.section_divider('general', hchar='-')
def tostr(some_tuple):
if type(some_tuple) == str: return some_tuple
tlist = [t for t in list(some_tuple) if type(t) == str]
return ' '.join(tlist)
print 'architecture: %s' % tostr(platform.architecture())
print 'system: %s' % platform.system()
print 'release: %s' % platform.release()
print 'version: %s' % platform.version()
# check distributions by type
checkdist = 0
dstr = ''
if self.system == 'Linux':
try:
dstr = tostr(platform.linux_distribution())
except:
checkdist = 1
elif self.system == 'Darwin':
try:
dstr = tostr(platform.mac_ver())
except:
checkdist = 1
else:
checkdist = 1
if checkdist: dstr = tostr(platform.dist())
self.os_dist = dstr # save result
print 'distribution: %s' % dstr
print 'number of CPUs: %s' % self.get_cpu_count()
# note shell, and if we are not in login shell
logshell = UTIL.get_login_shell()
curshell = UTIL.get_current_shell()
if logshell == curshell: note = ''
else: note = ' (current shell is %s)' % curshell
print 'apparent login shell: %s%s' % (logshell, note)
print
def show_top_line(self, fname, prefix=''):
htxt = UTIL.read_top_lines(fname, nlines=1, strip=1, verb=0)
if len(htxt) == 0: htxt = 'NONE FOUND'
else: htxt = htxt[0]
print '%s%s' % (prefix, htxt)
def show_data_dir_info(self, ddir, histfile=''):
"""try to locate and display the given data directory
if histfile, display the top line
"""
status, droot = self.find_data_root(ddir, hvar=0)
if status:
print 'data dir : missing %s' % ddir
return
# have a directory, show it
dhome = droot.replace(self.home_dir, '$HOME')
print 'data dir : found %-12s under %s' % (ddir, dhome)
# possibly show histfile
if histfile == '': return
prefix = ' top history: '
hname = '%s/%s/%s' % (droot, ddir, histfile)
self.show_top_line(hname, prefix=prefix)
def show_data_info(self, header=1):
"""checks that are specific to data
- class data existence and tree root
- assume $HOME if not found
- disk space under data root
- maybe check for mounted file system
- atlases (maybe just @Find TT_N27+tlrc?)
"""
if header: print UTIL.section_divider('data checks', hchar='-')
# locate various data trees, and possibly show recent history
self.show_data_dir_info('AFNI_data6', 'history.txt')
self.show_data_dir_info('suma_demo', 'README.archive_creation')
evar = 'AFNI_ATLAS_DIR'
tryenv = 0 # might suggest setting evar
haveenv = os.environ.has_key(evar)
if haveenv: edir = os.environ[evar]
else: edir = ''
# look for atlases in multiple directories
atlas = 'TT_N27+tlrc'
if os.path.isfile('%s/%s.HEAD' % (edir, atlas)): glist = [edir]
else: glist = []
cmd = '@FindAfniDsetPath %s' % atlas
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: tryenv = 1 # failed
else: glist.append(so[0])
for ddir in ['/usr/share/afni/atlases', '/usr/local/afni/atlases']:
if os.path.isfile('%s/%s.HEAD' % (ddir, atlas)):
glist.append(ddir)
if tryenv:
self.comments.append('consider setting %s to %s' %
(evar, ddir))
# fix to work with found after the fact
glist = UTIL.get_unique_sublist(glist)
if len(glist) == 0:
print 'atlas : did not find %s' % atlas
else:
for ddir in glist:
print 'atlas : found %-12s under %s' % (atlas, ddir)
if haveenv: print "\natlas var: %s = %s" % (evar, edir)
print
def find_data_root(self, ddir, hvar=1):
"""try to find ddir in common locations
if hvar, use $HOME for home directory
return status (0 = success) and path to (parent of) ddir
"""
# if we do not have a data root, check in a few places
if self.data_root != '':
hdir = self.data_root
plist = [self.data_root]
root_str = hdir
else:
hdir = self.home_dir
plist = [hdir, '%s/Desktop' % hdir, '%s/*data*' % hdir]
root_str = '$HOME'
dpath = self.find_data_dir(ddir=ddir, gdirs=plist)
if dpath != None:
if hvar: return 0, dpath.replace(self.home_dir, '$HOME')
else: return 0, dpath
# and check the current directory
dpath = self.find_data_dir(ddir=ddir, gdirs=['.'])
if dpath == None: return 1, ''
else:
dpath = os.path.realpath(dpath)
if hvar: return 0, dpath.replace(self.home_dir, '$HOME')
else: return 0, dpath
def find_data_dir(self, ddir, gdirs=[], depth=2):
"""search under a list of glob directories for the given ddir"""
if ddir == '' or len(gdirs) == 0: return None
dlist = []
for pdir in gdirs:
droot = pdir
for d in range(depth + 1):
dlist.extend(glob.glob('%s/%s' % (droot, ddir)))
droot += '/*'
if self.verb > 3: print '-- found %s dirs %s' % (ddir, dlist)
dlist = UTIL.get_unique_sublist(dlist)
if self.verb > 2: print '-- found trimmed %s dirs %s' % (ddir, dlist)
if len(dlist) == 0: return None
dlen = len(ddir) + 1
return dlist[0][0:-dlen]
def show_os_specific(self, header=1):
"""checks that are specific to one OS or another"""
if self.system not in ['Linux', 'Darwin']: return
if header: print UTIL.section_divider('OS specific', hchar='-')
if self.system == 'Linux': self.show_spec_linux()
elif self.system == 'Darwin': self.show_spec_mac()
print
def show_spec_linux(self):
"""linux specific checks
- is Ubuntu
- has Ubuntu AFNI installed
- atlas directory
"""
if self.os_dist.find('buntu') < 0: return
print 'have Ubuntu system: %s' % self.os_dist
if self.afni_ver.find('buntu') >= 0:
print 'have Ubuntu afni : %s' % self.afni_ver
def show_spec_mac(self):
"""look for fink, macports, homebrew"""
# if no pyqt4, check for brew and fink packages
if MT.test_import('PyQt4', verb=0):
glist = glob.glob('/usr/local/lib/python2*/site-packages/PyQt4')
if len(glist) == 0:
glist = glob.glob(
'/sw/lib/qt4*/lib/python2*/site-packages/PyQt4')
if len(glist) > 0:
gdir = glist[-1]
ghead = os.path.dirname(gdir)
print '++ found PyQt4 under %s' % ghead
print ' (consider adding %s to PYTHONPATH)' % ghead
def show_python_lib_info(self, plibs, header=1, verb=2):
if header: print UTIL.section_divider('python libs', hchar='-')
for lib in plibs:
MT.test_import(lib, verb=verb)
print
pdirs = glob.glob('/sw/bin/python*')
if len(pdirs) > 0:
pdirs = [dd for dd in pdirs if dd.find('config') < 0]
if len(pdirs) > 0:
print 'python binaries under /sw/bin:'
for pdir in pdirs:
if os.path.islink(pdir):
rstr = ' (sym link to %s)' % os.path.realpath(pdir)
else:
rstr = ''
print ' %-20s%s' % (pdir, rstr)
print
def show_path_vars(self, header=1):
print UTIL.section_divider('path vars', hchar='-')
for evar in [
'PATH', 'PYTHONPATH', 'LD_LIBRARY_PATH', 'DYLD_LIBRARY_PATH',
'DYLD_FALLBACK_LIBRARY_PATH'
]:
if os.environ.has_key(evar):
print "%s = %s\n" % (evar, os.environ[evar])
else:
print "%s = " % evar
print
def show_general_afni_info(self, header=1):
print UTIL.section_divider('AFNI and related program tests', hchar='-')
for prog in ['afni', 'python', 'R', 'tcsh']:
cmd = 'which %s' % prog
s, so, se = BASE.simple_shell_exec(cmd, capture=1)
if s: print '%-20s : %s' % (cmd, se)
else:
print '%-20s : %s' % (cmd, so.strip())
s, v = self.get_prog_version(prog)
if s:
print '%-20s : %s' % ('%s version' % prog, v)
if prog == 'afni': self.afni_ver = v # save result
print
# make generic but pretty
print "instances of various programs found in PATH:"
proglist = ['afni', 'R', 'python']
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' and len(files) > 1:
self.comments.append(
"consider only 1 version of AFNI in PATH")
print
print 'testing ability to start various programs...'
ind = '%8s' % ' '
indn = '\n%8s' % ' '
proglist = [
'afni', 'suma', '3dSkullStrip', 'uber_subject.py', '3dAllineate',
'3dRSFC', 'SurfMesh'
]
fcount = 0
for prog in proglist:
st, so, se = BASE.shell_exec2('%s -help' % prog, capture=1)
if st:
print ' %-20s : FAILURE' % prog
print ind + indn.join(se)
fcount += 1
else:
print ' %-20s : success' % prog
print
ascdir = UTIL.executable_dir()
if fcount == len(proglist) and self.get_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)
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
self.add_file_comment(None, '.afnirc',
'consider copying AFNI.afnirc to ~/.afnirc')
self.add_file_comment(
None, '.sumarc', 'consider running "suma -update_env" for .sumarc')
self.add_file_comment(
None, '.afni/help/all_progs.COMP',
'consider running "apsearch -update_all_afni_help"')
print
elif len(files) > 0: fstr = ' (%s)' % files[0]
else: fstr = ''
print ' %-*s : %d %s' % (ml, prog, len(files), fstr)
if prog == 'afni' and len(files) > 1:
self.comments.append("consider only 1 version of AFNI in PATH")
print
print 'testing ability to start various programs...'
ind = '%8s' % ' '
indn = '\n%8s' % ' '
proglist = ['afni', 'suma', '3dSkullStrip', 'uber_subject.py',
'3dAllineate', '3dRSFC', 'SurfMesh']
fcount = 0
for prog in proglist:
st, so, se = BASE.shell_exec2('%s -help'%prog, capture=1)
if st:
print ' %-20s : FAILURE' % prog
print ind + indn.join(se)
fcount += 1
else: print ' %-20s : success' % prog
print
ascdir = UTIL.executable_dir()
if fcount == len(proglist) and self.get_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
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_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']
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
# 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']
fcount = 0
for prog in proglist:
st, so, se = BASE.shell_exec2('%s -help'%prog, capture=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
# require every subsequent string to say verified
for estr in se:
if estr != '' and estr.find('has been verified') < 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
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 = 'running: cp %s/AFNI.afnirc ~/.afnirc' % self.afni_dir
else:
ccc = 'copying AFNI.afnirc to ~/.afnirc'
self.add_file_comment(None, '.afnirc', 'consider %s' % ccc)
self.add_file_comment(None, '.sumarc',
'consider running "suma -update_env" for .sumarc')
self.add_file_comment(None, '.afni/help/all_progs.COMP',
'consider running: apsearch -update_all_afni_help')
print