Exemple #1
0
    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, ''
Exemple #2
0
    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('')
Exemple #3
0
   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
Exemple #4
0
   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, ''
Exemple #5
0
    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, ''
Exemple #6
0
    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
Exemple #7
0
    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)
Exemple #8
0
    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, ''
Exemple #9
0
   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)