def get_prog_version(self, prog):
"""return a simple string with program version
each program might be handled a little differently
** but a common method might be PROG --version
return status and string
- status > 0 means to use, == 0 means not, < 0 means error
"""
if prog == 'afni':
cmd = 'afni -ver'
s, so, se = UTIL.limited_shell_exec(cmd, nlines=2)
if s:
if len(se) > 0: return 1, se[0]
else: return 1, ''
if len(so) > 1:
off1 = so[1].find('[[')
off2 = so[1].find(']]')
if off1 >= 0 and off2 >= 0: return 1, so[1][off1 + 2:off2]
else: return 1, so[1]
else:
off1 = so[0].find('(')
if off1 > 0:
vstr = so[0][0:off1]
off2 = so[0].find('AFNI_')
if off2 > off1:
ll = so[0][off2:]
self.afni_label = ll.split(')')[0]
else:
vstr = so[0]
return 1, vstr
elif prog == 'python':
return 1, platform.python_version()
elif prog == 'tcsh': # no version
return 0, ''
elif prog == 'port': # no dashes for version
cmd = '%s version' % prog
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: return 1, se[0]
else: return 1, so[0]
elif prog in ['dnf', 'yum', 'apt-get', 'brew', 'port', 'fink', 'R']:
cmd = '%s --version' % prog
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: return 1, se[0]
else: return 1, so[0]
else:
print('** no version method for prog : %s' % prog)
return -1, ''
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
rv = 0
rv += self.show_data_dir_info('AFNI_data6', 'history.txt')
rv += self.show_data_dir_info('AFNI_demos', 'history.txt')
rv += self.show_data_dir_info('suma_demo', 'README.archive_creation')
rv += self.show_data_dir_info('afni_handouts')
if rv: self.comments.append('insufficient data for AFNI bootcamp')
evar = 'AFNI_ATLAS_DIR'
tryenv = 0 # might suggest setting evar
haveenv = evar in os.environ
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
elif len(so) > 0: 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)
self.comments.append('possibly missing atlases')
else:
for ddir in glist:
print('atlas : found %-12s under %s' % (atlas, ddir))
if haveenv: print("\natlas var: %s = %s" % (evar, edir))
print('')
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
rv = 0
rv += self.show_data_dir_info('AFNI_data6', 'history.txt')
rv += self.show_data_dir_info('suma_demo', 'README.archive_creation')
rv += self.show_data_dir_info('FATCAT_DEMO', 'README.timestamp')
rv += self.show_data_dir_info('afni_handouts')
if rv: self.comments.append('insufficient data for AFNI bootcamp')
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
elif len(so) > 0: 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
self.comments.append('possibly missing atlases')
else:
for ddir in glist:
print 'atlas : found %-12s under %s' % (atlas, ddir)
if haveenv: print "\natlas var: %s = %s" % (evar, edir)
print
def get_prog_version(self, prog):
"""return a simple string with program version
each program might be handled a little differently
** but a common method might be PROG --version
return status and string
- status > 0 means to use, == 0 means not, < 0 means error
"""
if prog == 'afni':
cmd = 'afni -ver'
s, so, se = UTIL.limited_shell_exec(cmd, nlines=2)
if s:
if len(se) > 0: return 1, se[0]
else: return 1, ''
if len(so) > 1:
off1 = so[1].find('[[')
off2 = so[1].find(']]')
if off1 >= 0 and off2 >= 0: return 1, so[1][off1+2:off2]
else: return 1, so[1]
else:
off1 = so[0].find('(')
if off1 > 0: return 1, so[0][0:off1]
else: return 1, so[0]
elif prog == 'python':
return 1, platform.python_version()
elif prog == 'tcsh': # no version
return 0, ''
elif prog in ['dnf', 'yum', 'apt-get', 'brew', 'port', 'fink', 'R']:
cmd = '%s --version' % prog
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: return 1, se[0]
else: return 1, so[0]
else:
print '** no version method for prog : %s' % prog
return -1, ''
def get_prog_version(self, prog):
"""return a simple string with program version
each program might be handled a little differently
return status and string
- status > 0 means to use, == 0 means not, < 0 means error
"""
if prog == 'afni':
cmd = 'afni -ver'
s, so, se = UTIL.limited_shell_exec(cmd, nlines=2)
if s:
if len(se) > 0: return 1, se[0]
else: return 1, ''
if len(so) > 1:
off1 = so[1].find('[[')
off2 = so[1].find(']]')
if off1 >= 0 and off2 >= 0: return 1, so[1][off1 + 2:off2]
else: return 1, so[1]
else:
off1 = so[0].find('(')
if off1 > 0: return 1, so[0][0:off1]
else: return 1, so[0]
elif prog == 'python':
return 1, platform.python_version()
elif prog == 'R':
cmd = 'R --version'
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: return 1, se[0]
else: return 1, so[0]
elif prog == 'tcsh': # no version
return 0, ''
else:
print '** no version method for prog : %s' % prog
return -1, ''
def get_shell_value(self, shell, evar, verb=0):
"""really cheap way to grab a value from a new shell"""
cmd = "%s -ci 'echo $%s'" % (shell, evar)
s, so, se = UTIL.limited_shell_exec(cmd)
if len(so) > 0: so = so[-1]
else: so = ''
if verb:
print('++ status = %s for command: %s' % (s, cmd))
print(' stdout = %s' % so)
se = '\n'.join(se)
if se: print(' stderr = %s' % se)
return s, so
def set_shell_rc_file(self, slist):
"""and many any useful comments"""
cc = []
self.rc_file = 'NONE'
if 'sh' in slist:
# non-login shell ref: NONE
# login shell ref: .profile"
fname = '.profile'
self.rc_file = fname
if os.path.isfile('%s/%s' % (self.home_dir, fname)):
cc.append("shell sh : found login shell setup file %s" %
fname)
else:
cc.append("shell sh : MISSING login shell setup file %s" %
fname)
if 'bash' in slist:
# non-login shell ref: .bashrc
# login shell ref, first of: .bash_profile, .bash_login, .profile
f1name = '.bash_profile'
f2name = '.bashrc'
self.rc_file = f2name
f1found = 1
f2found = 1
if not self.home_file_exists(f1name):
f1name = '.bash_login'
if not self.home_file_exists(f1name):
f1name = '.profile'
if not self.home_file_exists(f1name):
f1name = '.bash_profile' # call this the default
cc.append("shell bash: MISSING login setup file, e.g. %s" %
f1name)
f1found = 0
if not self.home_file_exists(f2name):
cc.append("shell bash: MISSING non-login setup file %s" %
f2name)
f2found = 0
gfound = 0
if f1found and f2found:
# does f1name reference f2name?
st, so, se = UTIL.limited_shell_exec("\grep %s %s" %
(f2name, f1name))
if not st: gfound = 1
if not f1found or not f2found or not gfound:
ss="shell bash: consider sourcing (non-login) %s from (login) %s" \
% (f2name, f1name)
cc.append(ss)
# choose between tcsh and csh, if either is used
sname = ''
if 'tcsh' in slist: sname = 'tcsh'
if sname == '' and 'csh' in slist: sname = 'csh'
if sname != '':
f1name = '.tcshrc'
if not self.home_file_exists(f1name): f1name = '.cshrc'
self.rc_file = f1name
if not self.home_file_exists(f1name):
cc.append('shell %-4s: missing setup file %s' %
(sname, f1name))
self.comments.extend(cc)
def get_prog_version(self, prog):
"""return a simple string with program version
each program might be handled a little differently
** but a common method might be PROG --version
return status and string
- status > 0 means to use, == 0 means not, < 0 means error
"""
if prog == 'afni':
cmd = 'afni -ver'
s, so, se = UTIL.limited_shell_exec(cmd, nlines=2)
if s:
if len(se) > 0: return 1, se[0]
else: return 1, ''
if len(so) > 1:
off1 = so[1].find('[[')
off2 = so[1].find(']]')
if off1 >= 0 and off2 >= 0: return 1, so[1][off1 + 2:off2]
else: return 1, so[1]
else:
off1 = so[0].find('(')
if off1 > 0:
vstr = so[0][0:off1]
off2 = so[0].find('AFNI_')
if off2 > off1:
ll = so[0][off2:]
self.afni_label = ll.split(')')[0]
else:
vstr = so[0]
return 1, vstr
elif prog == 'python':
return 1, platform.python_version()
elif prog == 'tcsh': # no version
return 0, ''
elif prog == 'port': # no dashes for version
cmd = '%s version' % prog
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: return 1, se[0]
else: return 1, so[0]
elif prog in ['XQuartz', 'X11']:
droot = '/Applications/Utilities'
pname = '%s.app' % prog
app = '%s/%s' % (droot, pname)
dstr = ''
# get version string
vstr = self.get_kmdi_version(app)
# on failure, check the other app
if vstr == '':
if prog == 'XQuartz': pname = 'X11.app'
else: pname = 'XQuartz.app'
dstr = '(%s) ' % pname
app = '%s/%s' % (droot, pname)
vstr = self.get_kmdi_version(app)
# clear on failure
if vstr == '': dstr = ''
return 1, (dstr + vstr)
elif prog in ['dnf', 'yum', 'apt-get', 'brew', 'port', 'fink', 'R']:
cmd = '%s --version' % prog
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: return 1, se[0]
else: return 1, so[0]
else:
print('** no version method for prog : %s' % prog)
return -1, ''
def set_shell_rc_file(self, slist):
"""and many any useful comments"""
cc = []
self.rc_file = 'NONE'
if 'sh' in slist:
# non-login shell ref: NONE
# login shell ref: .profile"
fname = '.profile'
self.rc_file = fname
if os.path.isfile('%s/%s' % (self.home_dir,fname)):
cc.append("shell sh : found login shell setup file %s" % fname)
else:
cc.append("shell sh : MISSING login shell setup file %s" % fname)
if 'bash' in slist:
# non-login shell ref: .bashrc
# login shell ref, first of: .bash_profile, .bash_login, .profile
f1name = '.bash_profile'
f2name = '.bashrc'
self.rc_file = f2name
f1found = 1
f2found = 1
if not self.home_file_exists(f1name):
f1name = '.bash_login'
if not self.home_file_exists(f1name):
f1name = '.profile'
if not self.home_file_exists(f1name):
f1name = '.bash_profile' # call this the default
cc.append("shell bash: MISSING login setup file, e.g. %s" % f1name)
f1found = 0
if not self.home_file_exists(f2name):
cc.append("shell bash: MISSING non-login setup file %s" % f2name)
f2found = 0
gfound = 0
if f1found and f2found:
# does f1name reference f2name?
st, so, se = UTIL.limited_shell_exec("\grep %s %s"%(f2name,f1name))
if not st: gfound = 1
if not f1found or not f2found or not gfound:
ss="shell bash: consider sourcing (non-login) %s from (login) %s" \
% (f2name, f1name)
cc.append(ss)
# choose between tcsh and csh, if either is used
sname = ''
if 'tcsh' in slist: sname = 'tcsh'
if sname == '' and 'csh' in slist: sname = 'csh'
if sname != '':
f1name = '.tcshrc'
if not self.home_file_exists(f1name): f1name = '.cshrc'
self.rc_file = f1name
if not self.home_file_exists(f1name):
cc.append('shell %-4s: missing setup file %s' % (sname, f1name))
self.comments.extend(cc)
